From ea46f42ee640928b92947bfb204c41a482d80937 Mon Sep 17 00:00:00 2001 From: root Date: Tue, 8 May 2012 18:39:56 -0500 Subject: Add all the source codes into the github. --- web/dbdoc/UT_CEPH_RankInv0909.html | 291 +++++++++++++++++++++++++++++++++++++ 1 file changed, 291 insertions(+) create mode 100755 web/dbdoc/UT_CEPH_RankInv0909.html (limited to 'web/dbdoc/UT_CEPH_RankInv0909.html') diff --git a/web/dbdoc/UT_CEPH_RankInv0909.html b/web/dbdoc/UT_CEPH_RankInv0909.html new file mode 100755 index 00000000..7fb29231 --- /dev/null +++ b/web/dbdoc/UT_CEPH_RankInv0909.html @@ -0,0 +1,291 @@ + +UTHSC CEPH B-cells Illumina (Sep09) RankInv + + + + + + + + + + + + + + + + + + + + + + + + + +
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UTHSC CEPH B-cells Illumina (Sep09) RankInv (accession number: GN241) + modify this page

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The Illumina Human Whole Genome 6 v2.0 Rank Invariant data for CEPH lymphoblastoid cell lines obtained from the Coriell Institute for Medical Research. All cell lines were processed in Memphis in the UTHSC laboratory of Dr. Malak Kotb (2007-2009), by Dr. Rita G. Kasal, Nourtan Abdeltawab, and colleagues. +

Selection of CEPH families and members was done by Dr. Roel Ophoff (Utrecht and UCLA). +

Array data were generated at microarray core facility in laboratory of Dr. Weikuan Gu at VA medical center, Memphis, TN. +

Analysis by Mark Reimers, Stephanie Santorico, and Roel Ophoff + +

About the CEPH/UTAH families used to generate this data set:

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The CEPH/UTAH families used in this data set are part of CEPH repository linkage families of National Institute of General Medical Sciences (NIGMS) human genetic cell repository. These are immortalized human B-lymphocytes (EBV-transformed) from Caucasian donors of UTAH/Mormon ethnicity. The CEPH/UTAH families contain 48 families; the present data set includes 14 of these families with available DNA/genotypes for each member of these pedigrees. There are five families common with the published Monks et al (2004), namely families: 1346, 1362, 1418, 1421, and 1424.

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About the processing of cell lines:

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CEPH/UTAH families cell lines were purchased from Coriell repository of cell lines part of NIGMS. Upon arrival from the Coriell institute, we incubated the cell lines in 25ml flasks upright overnight at 37 ºC humidified incubator, with 5% carbon dioxide. We maintained the cells at a density of 5 X 105 cells/ml. The composition of the media used was RPMI-1640, 15% fetal bovine serum (FBS) and 2mM L-Glutamine; all FBS used was from the same lot. At 48 hours or when cell counts were ≥ 8 x 106 cells total, we harvested the cells and tested each cell line for mycoplasma contamination using e-Myco Mycoplasma PCR detection kit (iNtRON Biotechnology) according to manufacturer protocol. Cell lysates free of mycoplasma were used for RNA extraction as detailed below. We froze duplicates of each cell line at a concentration of ~2–6 x106 cells/ml according to standard procedures and stored in liquid nitrogen.

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About RNA processing:

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Two hundred and five cell lines were used for isolation of RNA. Ms. Sarah Rowe Hasty performed initial RNA isolation, purification and re-precipitation from 205 cell lines in Dr. Malak Kotb laboratory at VAMC. After initial RNA isolation, Ms. Nourtan Abdeltawab treated all samples for removal of contaminating DNA, along with further purification and re-precipitation of all samples. RNA samples that passed quality control were used to generate cRNA samples, those that didn't pass QC were re-extracted as we had duplicates of all cell lines lysates. RNA Extraction details: We used Qiagen RNeasy Mini purification of total RNA from tissues and cells spin protocol. RNA was isolated from 7.5 X 105 cells in duplicates. We froze cell lysates in RLT buffer and ß-mercaptoethanol at -80 ºC in 96 well plates until processed at a later time. We thawed samples, one 96 well plate at a time, and proceeded with RNA isolation steps and resuspended the pellets in RNase-free water. We then treated RNA to remove any DNA contamination using DNase digestion with RNase-free DNase kit (Qiagen) according to manufacturer protocol. RNA was finally purified by re-precipitation using ethanol precipitation using Purescript RNA purification kit (Gentra). Final purified RNA was resuspended in RNase-free water. RNA quality control: RNA samples were checked for RNA purity and integrity. RNA purity was evaluated using the 260/280 and 260/230 absorbance ratios. We used RNA samples with 260/280 ratio values ≥ 1.8 and 260/230 of ≥1.7. In cases were RNA samples did not meet these ratios, the RNA was purified by re-precipitation as above. RNA integrity was assessed using 1% RNA denaturing agrose gels. We required clear sharp bands of 18S and 28S rRNA for all samples compared to a control RNA sample to ensure intactness of rRNA.

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About arrays used to generate this data set:

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Array platform:

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Illumina HumanGW-6 v2.0 BeadChip: The Human-6 v2 beadchip simultaneously assays six samples, therefore, known as ‘array of arrays’. Each chip has ~1.8 million beads, beads have several hundred thousands copies of optimized 50-mer gene-specific probes. These probes cover more than 48,000 transcripts per sample, targeting genes and known alternative splice variants from the RefSeq database release 17 and UniGene build 188.

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Sample Processing:

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All RNA samples were processed by Yan Jiao at Dr. Weikuan Gu’s microarray core facility at VA medical center, Memphis, TN. We used only RNA samples that passed quality control as detailed above and of concentration ≥ 50ng/ul for cRNA synthesis using Illumina TotalPrep RNA amplification kit (Ambion) according to manufacturer protocol. The basic outline of the procedure involves reverse transcription of RNA to synthesize cDNA using oligo (dT) primer, followed by in vitro transcription of purified dsDNA to synthesize amplified biotinylated cRNA (aRNA). We evaluated purified labeled cRNA using same methods as mentioned above for RNA samples. cRNA samples of good quality (passing QC), were then used to hybridize to Illumina Human-6WG v2.0 according to Illumina standard protocols.

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Experimental Design and Batch Structure:

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This data set consists of arrays processed in seven groups. Groups consisted of 2, 3, 4, 4, 3, 6, and then 8 beadchips at a time, batch IDs are indicated in table 1. Samples from same family were scattered among array groups, with samples from six different families were run on one chip. This was done to ensure balance and to minimize batch effects and group-by-family statistical confounds in normalization. This was done with the exception of the first two chips, which were run with 3 generations of the same family on one chip. A single operator, Yan Jiao, processed all arrays using illumina protocol for hybridization, washing and scanning. All samples in a group were labeled on one day, hybridization station accommodates up to 24 samples, or 4 beadchips. Chips were scanned using BeadArray Reader in sets of three.

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About array data processing and analysis:

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RNA samples (n = 180) were processed using a total of 30 Illumina HumanWG-6 BeadChips, each beadchip analyses six samples covering 48,000 transcripts per sample. All chips passed quality control and error checking. This data set was extracted and processed using the Bead Studio 3. We applied Rank-invariant normalization to all the samples and the resulting expression values along with gene ID were exported in GeneSpring format. Dr. Rita Kansal performed the normalization steps.

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Financial support for this project was provided by Dr. Barrett Haik and the Hamilton Eye Institute, by NIH grant support to RWW and MK, and by the UT Center for Integrative and Translational Genomics.

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Data entered by Arthur Centeno, Sept 22, 2009. This file started Sept 22, 2009 by RWW.

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IndexRepository
Number
Case IDAge
(years)
GenderFamily IDFamily Member IDSentrix IDSentrix
Position
Batch ID
1GM07038133300141Male133314256249060A5
2GM06987133300239Female133324158260019B4
3GM07004133300319Male133334256249103A7
4GM07052133300417Male133344256249051A6
5GM06982133300516Male133354158260009F3
6GM07011133300614Female133364158260012C3
7GM07009133300712Male133374256249101F6
8GM07678133300812Male133384158260005B4
9GM0702613330096Male133394158260026C3
10GM0767913330106Male1333104158260030C3
11GM07049133301168Male1333114256249059A5
12GM07002133301263Female1333124158260001B4
13GM07017133301361Male1333134158260027B5
14GM07341133301461Female1333144256249042A6
15GM118201333015NAFemale1333154256249104E7
16GM07048134100143Male134114256249103B7
17GM06991134100242Female134124158260027A5
18GM07343134100322Female134134256249095C7
19GM07044134100420Female134144158260002C4
20GM07012134100518Female134154158260026D3
21GM07344134100617Female134164158260030B3
22GM07021134100714Male134174256249097B7
23GM07006134100810Female134184158260001C4
24GM0701013410098Female1341941582600011A2
25GM0702013410107Male1341104158260007A1
26GM07034134101171Male1341114158260007B1
27GM07055134101270Female1341124158260012E3
28GM06993134101374Male1341134256249059C5
29GM06985134101469Female1341144158260007C1
30GM10852134600248Female134624256249098D7
31GM12035134600327Male134634158260007D1
32GM12036134600425Male134644256249047A6
33GM12037134600524Male134654158260027E5
34GM12038134600621Male134664158260001E4
35GM12039134600721Male134674256249097C7
36GM12041134600913Female134694256249099B7
37GM12042134601010Female13461041582600011D2
38GM12043134601174Male1346114158260007E1
39GM12044134601270Female1346124256249096F7
40GM12046134601472Female1346144158260007F1
41GM10858134700142Male134714158260030A3
42GM10859134700241Female134724158260027C5
43GM11870134700321Female134734158260018C2
44GM11871134700419Male134744256249060B5
45GM11872134700518Male134754256249097A7
46GM11873134700616Male134764158260001A4
47GM11875134700813Female134784256249095E7
48GM11876134700911Male134794256249059E5
49GM1187713470108Male1347104158260021A2
50GM1187813470116Male1347114158260008A1
51GM11879134701266Male1347124158260019D4
52GM11880134701365Female1347134158260008B1
53GM11881134701462Male1347144256249101C6
54GM11882134701561Female1347154158260008C1
55GM1188313470166Male13471641582600011B2
56GM10860136200150Male136214256249097E7
57GM10861136200249Female136224158260027D5
58GM11982136200328Female136234158260019F4
59GM11983136200429Female136244158260030D3
60GM11984136200526Male136254158260008D1
61GM11985136200624Female136264158260002F4
62GM11986136200722Female136274256249060C5
63GM11987136200819Male136284158260005F4
64GM11988136200917Female136294256249042B6
65GM11989136201014Female1362104158260001F4
66GM1199013620119Male1362114256249094A6
67GM1199113620127Female1362124158260018E2
68GM11992136201386Male1362134256249059B5
69GM11993136201480Female1362144256249059F5
70GM11994136201580Male1362154158260008E1
71GM11995136201684Female1362164158260008F1
72GM11996136201721Male1362174158260021C2
73GM10835141600139Male141614256249060F5
74GM10834141600240Female141624158260018A2
75GM12240141600319Male141634158260019E4
76GM12241141600416Male141644256249059D5
77GM12243141600613Male141664256249096C7
78GM12244141600712Female141674256249047B6
79GM12245141600810Male1416841582600011E2
80GM1224614160098Female141694158260026E3
81GM1224714160105Female1416104158260021D2
82GM12248141601189Male1416114256249094B6
83GM12249141601277Female1416124256249041A6
84GM12250141601366Male1416134256249044F7
85GM12251141601463Female1416144158260005D4
86GM1225214160155Female1416154158260009E3
87GM1225314160166Female1416164158260027F5
88GM10836141800244Female141824158260018B2
89GM12328141800324Female141834256249047C6
90GM12266141800520Female1418541582600011F2
91GM12267141800618Male141864158260009D3
92GM1227014180099Female141894158260001D4
93GM1227114180106Female1418104158260012D3
94GM12272141801173Male1418114256249060E5
95GM12273141801271Female1418124158260002D4
96GM12274141801372Male1418134256249101A6
97GM12275141801469Female1418144158260005C4
98GM10841142100143Male142114158260030E3
99GM10840142100242Female142124256249098C7
100GM12276142100324Female142134158260012F3
101GM12278142100519Female142154256249042C6
102GM12280142100710Female142174256249041B6
103GM1228114210088Male142184256249047D6
104GM12282142100969Male142194158260026F3
105GM12283142101064Female1421104256249101B6
106GM12284142101121Male1421114256249094C6
107GM12285142101220Male1421124256249104B7
108GM12287142101469Female1421144256249051B6
109GM11910142300417Female142344256249103D7
110GM11911142300515Female142354256249096E7
111GM11912142300612Male142364158260009C3
112GM11913142300711Male142374256249044D7
113GM1191414230089Female142384256249098A7
114GM1191514230098Female1423941582600011C2
115GM1191614230105Male1423104158260018D2
116GM11917142301166Male1423114256249097F7
117GM11919142301367Male1423134256249104F7
118GM11920142301466Female1423144256249095D7
119GM1192114230157Female1423154256249099A7
120GM10845142400149Male142414256249104C7
121GM10844142400250Female142424256249103F7
122GM11922142400330Male142434256249044A7
123GM11923142400429Male142444256249097D7
124GM11924142400527Female142454256249096A7
125GM11925142400625Male142464158260021B2
126GM11926142400721Female142474256249051C6
127GM11927142400819Male142484256249042D6
128GM11928142400915Male142494256249098B7
129GM11929142401013Male1424104256249094D6
130GM119301424011NAMale1424114256249041C6
131GM11931142401278Female1424124158260002A4
132GM11932142401376Male1424134256249095A7
133GM11933142401474Female1424144158260005E4
134GM127521447001NAMale144714158260021E2
135GM127541447003NAFemale144734256249044E7
136GM127561447005NAMale144754256249098F7
137GM127581447007NAFemale144774256249099D7
138GM127591447008NAFemale144784158260002E4
139GM127601447009NAMale144794256249103E7
140GM127611447010NAFemale1447104158260009A3
141GM127621447011NAMale1447114158260018F2
142GM127631447012NAFemale1447124158260012A3
143GM127641447013NAMale1447134256249042E6
144GM127651447014NAMale1447144158260026A3
145GM127661451001NAMale145114158260009B3
146GM127671451002NAFemale145124158260012B3
147GM127681451003NAMale145134256249041D6
148GM127691451004NAFemale145144158260021F2
149GM127701451005NAFemale145154158260005A4
150GM127711451006NAMale145164256249047E6
151GM127721451007NAFemale145174158260019A4
152GM127731451008NAFemale145184158260002B4
153GM128481451009NAFemale145194256249051D6
154GM127741451010NAMale1451104158260030F3
155GM127761451012NAFemale1451124256249099E7
156GM127771451013NAMale1451134256249060D5
157GM128011454001NAMale145414256249103C7
158GM128031454003NAFemale145434158260019C4
159GM128041454004NAFemale145444256249101D6
160GM128051454005NAMale145454256249095F7
161GM128061454006NAMale145464256249098E7
162GM128081454008NAFemale145484256249099C7
163GM128091454009NAFemale145494256249051E6
164GM128101454010NAMale1454104256249104A7
165GM128111454011NAMale1454114256249044B7
166GM128121454012NAMale1454124256249042F6
167GM128131454013NAFemale1454134256249094E6
168GM128141454014NAMale1454144256249096D7
169GM128151454015NAFemale1454154256249041E6
170GM128161454016NAMale1454164256249047F6
171GM128171456001NAMale145614256249051F6
172GM128181456002NAFemale145624256249101E6
173GM128191456003NAMale145634256249095B7
174GM128211456005NAFemale145654256249044C7
175GM128221456006NAMale145664256249094F6
176GM128231456007NAMale145674256249096B7
177GM128241456008NAFemale145684256249104D7
178GM128251456009NAMale145694158260026B3
179GM128261456010NAFemale1456104256249041F6
180GM128281456012NAFemale1456124256249099F7
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