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SRX027413: HLA Typing Dev on 454, HapMap 270
24 LS454 (454 GS FLX Titanium) runs: 19,879 spots, 9.9M bases, 22.5Mb downloads

Design: 270 HapMap human genomic DNA samples of known HLA type were amplified by PCR with six different exon-specific primer pairs. The six amplicons for each individual were pooled, and underwent barcoded 454 library construction. A total of 96 unique barcodes were utilized, thus, sets of 96 individuals could be pooled prior to sequencing.
Submitted by: Broad Institute (BI)
Study: Homo sapiens
PRJNA50323 • SRP003652 • All experiments • All runs
show Abstracthide Abstract
The human leukocyte antigen system (HLA) is the name of the major histocompatibility complex (MHC) in humans. HLA variation plays a role in infectious and autoimmune disease.
Samples: pool of 24 samples • Homo sapiens
Library:
Name: 454-3416
Instrument: 454 GS FLX Titanium
Strategy: OTHER
Source: GENOMIC
Selection: PCR
Layout: SINGLE
Spot descriptor:
          barcode
Group tagBasecalls
AnkaraACACCGGTC
AshgabatTTGTCGAAC
BakuCGTGAC
BasseterreCGTTCCGGC
BrazzavilleACAAGGC
CaracasACGTGGAAC
DakarAACGAGGC
DohaATTCGTAC
DushanbeTCCGTCCGC
KhartoumACCTTGGTC
LondonAACTCGAAC
LusakaAATAACGAC
MbabaneCCGACGTTC
NassauACGCGC
NicosiaTCGCGGC
ParamariboACCAACCAC
PretoriaAACGGAGTC
RiyadhTTGAACTC
SingaporeTCGAGGAAC
SofiaAAGCCGC
StockholmTTAAGATTC
TashkentACCACCTTC
TiranaCGCAAC
WashingtonACCGCGGTC
 primer
Group tagBasecalls
HLA_A_exon2_30018486-30018849_ForwardCRGGTCTCAGCCACTSCTC
HLA_A_exon2_30018486-30018849_ReverseCTCGGACCCGGAGACTGT
HLA_A_exon3_30018988-30019360_ForwardCTYGGGGGACYGGGCTGAC
HLA_A_exon3_30018988-30019360_ReverseCCCAATTGTCTCCCCTCCTTG
HLA_B_exon2_31432401-31432811_ForwardGGATGGGGAGTCGTGACCT
HLA_B_exon2_31432401-31432811_ReverseGGSAGGGAAATGGCCTCT
HLA_B_exon3_31431877-31432282_ForwardCGGCGACCTATAGGAGATGG
HLA_B_exon3_31431877-31432282_ReverseGCGTTTACCCGGTTTCATT
HLA_C_exon2_31347190-31347707_ForwardTGAAACCGGGTAAAGGYGACT
HLA_C_exon2_31347190-31347707_ReverseCTCTGSGGAGAGGARCGAGG
HLA_C_exon3_31346739-31347191_ForwardAGYGCTGATCCCATTTTCCT
HLA_C_exon3_31346739-31347191_ReverseAGTCRCCTTTACCCGGTTTC
  forward

Experiment attributes: (show all 4 attributes...) (hide...)
4 BI attributes: (show...)(hide...)
BI GSSR sample IDs: 40613.1 40614.1 40615.1 40616.1 40617.1 40618.1 40619.1 40620.1 40621.1 40622.1 40623.1 40624.1 40625.1 40626.1 40627.1 40628.1 40629.1 40630.1 40631.1 40632.1 40633.1 40634.1 40635.1 40636.1
BI GSSR sample LSIDs: BROAD:SEQUENCING_SAMPLE:40613.1 BROAD:SEQUENCING_SAMPLE:40614.1 BROAD:SEQUENCING_SAMPLE:40615.1 BROAD:SEQUENCING_SAMPLE:40616.1 BROAD:SEQUENCING_SAMPLE:40617.1 BROAD:SEQUENCING_SAMPLE:40618.1 BROAD:SEQUENCING_SAMPLE:40619.1 BROAD:SEQUENCING_SAMPLE:40620.1 BROAD:SEQUENCING_SAMPLE:40621.1 BROAD:SEQUENCING_SAMPLE:40622.1 BROAD:SEQUENCING_SAMPLE:40623.1 BROAD:SEQUENCING_SAMPLE:40624.1 BROAD:SEQUENCING_SAMPLE:40625.1 BROAD:SEQUENCING_SAMPLE:40626.1 BROAD:SEQUENCING_SAMPLE:40627.1 BROAD:SEQUENCING_SAMPLE:40628.1 BROAD:SEQUENCING_SAMPLE:40629.1 BROAD:SEQUENCING_SAMPLE:40630.1 BROAD:SEQUENCING_SAMPLE:40631.1 BROAD:SEQUENCING_SAMPLE:40632.1 BROAD:SEQUENCING_SAMPLE:40633.1 BROAD:SEQUENCING_SAMPLE:40634.1 BROAD:SEQUENCING_SAMPLE:40635.1 BROAD:SEQUENCING_SAMPLE:40636.1
BI project name: G2399
BI work request ID: 20167
Pipeline: show...hide...
NameStepProgramVersion
base caller2009-10-18 22:44:10.0454BaseCaller2.0.01.12
Runs: 24 runs, 19,879 spots, 9.9M bases, 22.5Mb
Run# of Spots# of BasesSizePublished
SRR066866702351,733845,356b2010-10-01
SRR0668881,043521,4491.2Mb2010-10-01
SRR0668911,014507,5051.1Mb2010-10-01
SRR0669101,005503,4861.1Mb2010-10-01
SRR066914737367,147878,163b2010-10-01
SRR066933402195,081492,055b2010-10-01
SRR066943986486,9381.1Mb2010-10-01
SRR0669481,130559,7331.3Mb2010-10-01
SRR0669801,000496,9221.1Mb2010-10-01
SRR066986578284,987695,833b2010-10-01
SRR0669921,268638,9891.4Mb2010-10-01
SRR0669961,014510,5161.1Mb2010-10-01
SRR0670161,106550,7931.2Mb2010-10-01
SRR067027556272,982667,545b2010-10-01
SRR067051297148,717381,067b2010-10-01
There are 9 omitted runs. See all runs in Run Selector.

#Member# of Spots# of Bases
1SRS000123 : Nicosia_TCGCGGC737367,147
2SRS000124 : Tirana_CGCAAC750366,454
3SRS000125 : Singapore_TCGAGGAAC578284,987
4SRS000126 : Basseterre_CGTTCCGGC616303,025
5SRS000127 : Stockholm_TTAAGATTC1,014507,505
6SRS000128 : Ashgabat_TTGTCGAAC297148,717
7SRS000129 : Baku_CGTGAC942460,035
8SRS000130 : Riyadh_TTGAACTC402195,081
9SRS000131 : Dushanbe_TCCGTCCGC811405,360
10SRS000132 : Mbabane_CCGACGTTC1,014510,516
11SRS000133 : Doha_ATTCGTAC1,130559,733
12SRS000134 : Sofia_AAGCCGC1,005503,486
13SRS000135 : London_AACTCGAAC772386,916
14SRS000136 : Pretoria_AACGGAGTC441220,216
15SRS000137 : Lusaka_AATAACGAC556272,982
16SRS000138 : Ankara_ACACCGGTC949476,344
17SRS000139 : Brazzaville_ACAAGGC977478,564
18SRS000666 : Nassau_ACGCGC1,000496,922
19SRS000667 : Caracas_ACGTGGAAC1,106550,793
20SRS000674 : Khartoum_ACCTTGGTC986486,938
21SRS000675 : Tashkent_ACCACCTTC1,043521,449
22SRS000676 : Paramaribo_ACCAACCAC1,268638,989
23SRS000677 : Washington_ACCGCGGTC702351,733
24SRS003570 : Dakar_AACGAGGC783389,355
25 : defaultn/an/a

ID:
33274

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