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SRX027420: HLA Typing Dev on 454, HapMap 270
24 LS454 (454 GS FLX Titanium) runs: 30,041 spots, 14.4M bases, 32.9Mb 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
AmmanTAGGAATC
AmsterdamAGGTTGTC
BamakoTTGACAAC
BeirutAACACAAC
KathmanduTGTCGGAC
KingstonTGCCGAAC
KishinevCGGTCTTC
LuxembourgAAGAGTTC
ManaguaTGGTGAAC
MaputoTGACCGTC
MaseruTTCTTGAC
MonacoAAGGCCTC
MonroviaTCCAAGTC
NairobiCCGGCCAC
PyongyangTCTCCGTC
RigaTTCGTGGC
SeoulAACCTGGC
TarawaAATGGTAC
TokyoTATTCGTC
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: 40661.1 40662.1 40663.1 40664.1 40665.1 40666.1 40667.1 40668.1 40669.1 40670.1 40671.1 40672.1 40673.1 40674.1 40675.1 40676.1 40677.1 40678.1 40679.1 40680.1 40681.1 40682.1 40683.1 40684.1
BI GSSR sample LSIDs: BROAD:SEQUENCING_SAMPLE:40661.1 BROAD:SEQUENCING_SAMPLE:40662.1 BROAD:SEQUENCING_SAMPLE:40663.1 BROAD:SEQUENCING_SAMPLE:40664.1 BROAD:SEQUENCING_SAMPLE:40665.1 BROAD:SEQUENCING_SAMPLE:40666.1 BROAD:SEQUENCING_SAMPLE:40667.1 BROAD:SEQUENCING_SAMPLE:40668.1 BROAD:SEQUENCING_SAMPLE:40669.1 BROAD:SEQUENCING_SAMPLE:40670.1 BROAD:SEQUENCING_SAMPLE:40671.1 BROAD:SEQUENCING_SAMPLE:40672.1 BROAD:SEQUENCING_SAMPLE:40673.1 BROAD:SEQUENCING_SAMPLE:40674.1 BROAD:SEQUENCING_SAMPLE:40675.1 BROAD:SEQUENCING_SAMPLE:40676.1 BROAD:SEQUENCING_SAMPLE:40677.1 BROAD:SEQUENCING_SAMPLE:40678.1 BROAD:SEQUENCING_SAMPLE:40679.1 BROAD:SEQUENCING_SAMPLE:40680.1 BROAD:SEQUENCING_SAMPLE:40681.1 BROAD:SEQUENCING_SAMPLE:40682.1 BROAD:SEQUENCING_SAMPLE:40683.1 BROAD:SEQUENCING_SAMPLE:40684.1
BI project name: G2399
BI work request ID: 20163
Pipeline: show...hide...
NameStepProgramVersion
base caller2009-10-18 22:44:10.0454BaseCaller2.0.01.12
Runs: 24 runs, 30,041 spots, 14.4M bases, 32.9Mb
Run# of Spots# of BasesSizePublished
SRR0668871,092516,3501.2Mb2010-10-01
SRR0669241,450701,0971.6Mb2010-10-01
SRR0669291,019498,0541.1Mb2010-10-01
SRR0669341,044501,4301.2Mb2010-10-01
SRR0669351,469716,6651.6Mb2010-10-01
SRR0669401,217587,0481.3Mb2010-10-01
SRR0669551,610771,5101.7Mb2010-10-01
SRR0669931,344647,1671.5Mb2010-10-01
SRR067004835401,775969,948b2010-10-01
SRR0670191,321631,5971.4Mb2010-10-01
SRR0670241,074515,2191.2Mb2010-10-01
SRR067045986471,9901.1Mb2010-10-01
SRR0670471,311632,2851.4Mb2010-10-01
SRR067048946453,3651Mb2010-10-01
SRR0670661,232590,6001.3Mb2010-10-01
There are 9 omitted runs. See all runs in Run Selector.

#Member# of Spots# of Bases
1SRS000151 : Kingston_TGCCGAAC952459,923
2SRS000152 : Tokyo_TATTCGTC1,344647,167
3SRS000153 : Amman_TAGGAATC1,447686,841
4SRS000154 : Nairobi_CCGGCCAC1,232590,600
5SRS000155 : Tarawa_AATGGTAC835401,775
6SRS000156 : Pyongyang_TCTCCGTC1,044501,430
7SRS000157 : Seoul_AACCTGGC1,019498,054
8SRS000158 : Riga_TTCGTGGC1,074515,219
9SRS000159 : Beirut_AACACAAC1,311632,285
10SRS000160 : Maseru_TTCTTGAC1,092516,350
11SRS000161 : Monrovia_TCCAAGTC1,217587,048
12SRS000162 : Tripoli_TTCGCGAC1,610771,510
13SRS000163 : Vaduz_CCGGTCGC1,272628,277
14SRS000164 : Vilnius_ACCTGAAC1,141549,929
15SRS000165 : Luxembourg_AAGAGTTC1,321631,597
16SRS000166 : Bamako_TTGACAAC1,450701,097
17SRS000167 : Valletta_TCCAGAAC951458,581
18SRS000168 : Monaco_AAGGCCTC1,278605,163
19SRS000169 : Maputo_TGACCGTC946453,365
20SRS000170 : Kathmandu_TGTCGGAC1,469716,665
21SRS000171 : Amsterdam_AGGTTGTC1,493713,363
22SRS000172 : Wellington_ACGAGAAC1,815873,041
23SRS000173 : Managua_TGGTGAAC1,742837,720
24SRS000723 : Kishinev_CGGTCTTC986471,990
25 : defaultn/an/a

ID:
33281

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