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SRX027412: HLA Typing Dev on 454, HapMap 270
24 LS454 (454 GS FLX Titanium) runs: 25,158 spots, 12.5M bases, 28.8Mb 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: 454-3457
Instrument: 454 GS FLX Titanium
Strategy: OTHER
Source: GENOMIC
Selection: PCR
Layout: SINGLE
Spot descriptor:
          barcode
Group tagBasecalls
AmmanTAGGAATC
BamakoTTGACAAC
BeirutAACACAAC
BratislavaACCGGAAGC
BridgetownCCTCTC
ColomboACCGTAATC
FongafaleCCAACCGGC
HavanaATACCAC
KievACCGAATAC
KingstonTGCCGAAC
LuxembourgAAGAGTTC
ManaguaTGGTGAAC
MaseruTTCTTGAC
MonroviaTCCAAGTC
NairobiCCGGCCAC
PragueATCTTAC
PyongyangTCTCCGTC
RigaTTCGTGGC
SeoulAACCTGGC
TarawaAATGGTAC
TokyoTATTCGTC
TripoliTTCGCGAC
VaduzCCGGTCGC
VilniusACCTGAAC
 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: 40787.1 40788.1 40789.1 40790.1 40791.1 40792.1 40793.1 40794.1 40795.1 40796.1 40797.1 40798.1 40799.1 40800.1 40801.1 40802.1 40803.1 40804.1 40805.1 40806.1 40807.1 40808.1 40809.1 40810.1
BI GSSR sample LSIDs: BROAD:SEQUENCING_SAMPLE:40787.1 BROAD:SEQUENCING_SAMPLE:40788.1 BROAD:SEQUENCING_SAMPLE:40789.1 BROAD:SEQUENCING_SAMPLE:40790.1 BROAD:SEQUENCING_SAMPLE:40791.1 BROAD:SEQUENCING_SAMPLE:40792.1 BROAD:SEQUENCING_SAMPLE:40793.1 BROAD:SEQUENCING_SAMPLE:40794.1 BROAD:SEQUENCING_SAMPLE:40795.1 BROAD:SEQUENCING_SAMPLE:40796.1 BROAD:SEQUENCING_SAMPLE:40797.1 BROAD:SEQUENCING_SAMPLE:40798.1 BROAD:SEQUENCING_SAMPLE:40799.1 BROAD:SEQUENCING_SAMPLE:40800.1 BROAD:SEQUENCING_SAMPLE:40801.1 BROAD:SEQUENCING_SAMPLE:40802.1 BROAD:SEQUENCING_SAMPLE:40803.1 BROAD:SEQUENCING_SAMPLE:40804.1 BROAD:SEQUENCING_SAMPLE:40805.1 BROAD:SEQUENCING_SAMPLE:40806.1 BROAD:SEQUENCING_SAMPLE:40807.1 BROAD:SEQUENCING_SAMPLE:40808.1 BROAD:SEQUENCING_SAMPLE:40809.1 BROAD:SEQUENCING_SAMPLE:40810.1
BI project name: G2399
BI work request ID: 20280
Pipeline: show...hide...
NameStepProgramVersion
base caller2009-11-23 15:53:31.0454BaseCaller2.0.01.12
Runs: 24 runs, 25,158 spots, 12.5M bases, 28.8Mb
Run# of Spots# of BasesSizePublished
SRR0668651,432695,0911.6Mb2010-10-01
SRR0668831,611808,7211.8Mb2010-10-01
SRR0668981,151558,7171.3Mb2010-10-01
SRR0669381,033519,2601.2Mb2010-10-01
SRR066944447231,666567,982b2010-10-01
SRR066971977491,0991.1Mb2010-10-01
SRR0670001,357658,1891.5Mb2010-10-01
SRR067011677340,072826,276b2010-10-01
SRR0670421,619802,2841.8Mb2010-10-01
SRR067044973461,9861.1Mb2010-10-01
SRR0670571,015515,2801.2Mb2010-10-01
SRR067084760387,590934,183b2010-10-01
SRR0670851,107559,7581.3Mb2010-10-01
SRR067089350177,915450,979b2010-10-01
SRR0670901,082519,2751.2Mb2010-10-01
There are 9 omitted runs. See all runs in Run Selector.

#Member# of Spots# of Bases
1SRS000179 : Beirut_AACACAAC1,082519,275
2SRS000180 : Kingston_TGCCGAAC814399,869
3SRS000181 : Tarawa_AATGGTAC1,018513,542
4SRS000182 : Seoul_AACCTGGC1,270627,159
5SRS000183 : Riga_TTCGTGGC977491,099
6SRS000184 : Bridgetown_CCTCTC1,015515,280
7SRS000727 : Maseru_TTCTTGAC973461,986
8SRS000728 : Monrovia_TCCAAGTC1,151558,717
9SRS000729 : Tripoli_TTCGCGAC1,357658,189
10SRS000730 : Vaduz_CCGGTCGC1,107559,758
11SRS000732 : Vilnius_ACCTGAAC509252,912
12SRS000733 : Luxembourg_AAGAGTTC1,432695,091
13SRS000734 : Havana_ATACCAC350177,915
14SRS000735 : Prague_ATCTTAC561282,839
15SRS000736 : Managua_TGGTGAAC1,611808,721
16SRS000737 : Bamako_TTGACAAC1,619802,284
17SRS000740 : Fongafale_CCAACCGGC677340,072
18SRS000741 : Tokyo_TATTCGTC1,402690,511
19SRS000744 : Amman_TAGGAATC1,340659,292
20SRS000776 : Nairobi_CCGGCCAC1,033519,260
21SRS003588 : Pyongyang_TCTCCGTC2,0131M
22SRS003590 : Colombo_ACCGTAATC640323,567
23SRS003591 : Bratislava_ACCGGAAGC447231,666
24SRS003592 : Kiev_ACCGAATAC760387,590
25 : defaultn/an/a

ID:
33273

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