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SRX027418: HLA Typing Dev on 454, HapMap 270
24 LS454 (454 GS FLX Titanium) runs: 11,106 spots, 5.6M bases, 13.4Mb 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: 454-3442
Instrument: 454 GS FLX Titanium
Strategy: OTHER
Source: GENOMIC
Selection: PCR
Layout: SINGLE
Spot descriptor:
          barcode
Group tagBasecalls
AmsterdamAGGTTGTC
BamakoTTGACAAC
BeirutAACACAAC
BratislavaACCGGAAGC
BridgetownCCTCTC
ColomboACCGTAATC
FongafaleCCAACCGGC
HanoiTCCTTCCAC
HavanaATACCAC
KathmanduTGTCGGAC
KievACCGAATAC
KishinevCGGTCTTC
LuxembourgAAGAGTTC
ManaguaTGGTGAAC
MaputoTGACCGTC
MaseruTTCTTGAC
MonacoAAGGCCTC
MonroviaTCCAAGTC
PragueATCTTAC
TripoliTTCGCGAC
VaduzCCGGTCGC
VallettaTCCAGAAC
VilniusACCTGAAC
WellingtonACGAGAAC
 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: 40757.1 40758.1 40759.1 40760.1 40761.1 40762.1 40763.1 40764.1 40765.1 40766.1 40767.1 40768.1 40769.1 40770.1 40771.1 40772.1 40773.1 40774.1 40775.1 40776.1 40777.1 40778.1 40779.1 40780.1
BI GSSR sample LSIDs: BROAD:SEQUENCING_SAMPLE:40757.1 BROAD:SEQUENCING_SAMPLE:40758.1 BROAD:SEQUENCING_SAMPLE:40759.1 BROAD:SEQUENCING_SAMPLE:40760.1 BROAD:SEQUENCING_SAMPLE:40761.1 BROAD:SEQUENCING_SAMPLE:40762.1 BROAD:SEQUENCING_SAMPLE:40763.1 BROAD:SEQUENCING_SAMPLE:40764.1 BROAD:SEQUENCING_SAMPLE:40765.1 BROAD:SEQUENCING_SAMPLE:40766.1 BROAD:SEQUENCING_SAMPLE:40767.1 BROAD:SEQUENCING_SAMPLE:40768.1 BROAD:SEQUENCING_SAMPLE:40769.1 BROAD:SEQUENCING_SAMPLE:40770.1 BROAD:SEQUENCING_SAMPLE:40771.1 BROAD:SEQUENCING_SAMPLE:40772.1 BROAD:SEQUENCING_SAMPLE:40773.1 BROAD:SEQUENCING_SAMPLE:40774.1 BROAD:SEQUENCING_SAMPLE:40775.1 BROAD:SEQUENCING_SAMPLE:40776.1 BROAD:SEQUENCING_SAMPLE:40777.1 BROAD:SEQUENCING_SAMPLE:40778.1 BROAD:SEQUENCING_SAMPLE:40779.1 BROAD:SEQUENCING_SAMPLE:40780.1
BI project name: G2399
BI work request ID: 20248
Pipeline: show...hide...
NameStepProgramVersion
base caller2009-11-23 15:53:31.0454BaseCaller2.0.01.12
Runs: 24 runs, 11,106 spots, 5.6M bases, 13.4Mb
Run# of Spots# of BasesSizePublished
SRR066885272137,358360,524b2010-10-01
SRR066902304150,345395,577b2010-10-01
SRR066903504253,258630,922b2010-10-01
SRR066927376181,193470,315b2010-10-01
SRR066936333165,067431,566b2010-10-01
SRR066983520262,317653,232b2010-10-01
SRR066990903448,8981Mb2010-10-01
SRR066997352178,162458,131b2010-10-01
SRR067001258128,481342,168b2010-10-01
SRR067021824422,2341,019,183b2010-10-01
SRR067023427213,895544,980b2010-10-01
SRR067029235119,222320,320b2010-10-01
SRR067032397202,338508,885b2010-10-01
SRR067033203100,983278,876b2010-10-01
SRR067035349175,846451,665b2010-10-01
There are 9 omitted runs. See all runs in Run Selector.

#Member# of Spots# of Bases
1SRS000078 : Colombo_ACCGTAATC732376,588
2SRS000079 : Kiev_ACCGAATAC903448,898
3SRS000080 : Bridgetown_CCTCTC895459,466
4SRS000082 : Prague_ATCTTAC504253,258
5SRS000083 : Fongafale_CCAACCGGC632321,314
6SRS000084 : Hanoi_TCCTTCCAC397202,338
7SRS000085 : Valletta_TCCAGAAC203100,983
8SRS000087 : Maputo_TGACCGTC352178,162
9SRS000088 : Kathmandu_TGTCGGAC375186,156
10SRS000089 : Amsterdam_AGGTTGTC376181,193
11SRS000090 : Managua_TGGTGAAC479243,713
12SRS000091 : Beirut_AACACAAC333165,067
13SRS000092 : Maseru_TTCTTGAC349175,846
14SRS000097 : Tripoli_TTCGCGAC236119,340
15SRS000098 : Vaduz_CCGGTCGC235119,222
16SRS000099 : Luxembourg_AAGAGTTC520262,317
17SRS000100 : Bamako_TTGACAAC258128,481
18SRS000604 : Wellington_ACGAGAAC427213,895
19SRS003552 : Bratislava_ACCGGAAGC402202,806
20SRS003553 : Havana_ATACCAC824422,234
21SRS003557 : Kishinev_CGGTCTTC511256,111
22SRS003558 : Monaco_AAGGCCTC304150,345
23SRS003563 : Monrovia_TCCAAGTC272137,358
24SRS003564 : Vilnius_ACCTGAAC587294,355
25 : defaultn/an/a

ID:
33279

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