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RNA-Seq polyA+ T Cells CD4 Memory
RNA-Seq polyA+ T Cells
Project News:
2011/1/27:
EXPERIMENT XML file 'experiment.REMC_20110120_mRNA_Seq.xml' uploaded
expected_number_runs: 2
center_name: BCCAGSC
alias: A01027-1
STUDY_REF: UCSF_UBC_HREMP
SAMPLE_DESCRIPTOR: CD4 Memory TC014
LIBRARY
LIBRARY_NAME: A01027
LIBRARY_STRATEGY: mRNA-Seq
LIBRARY_SOURCE: TRANSCRIPTOMIC
LIBRARY_SELECTION: cDNA
LIBRARY_LAYOUT: PAIRED
POOLING_STRATEGY: none
LIBRARY_CONSTRUCTION_PROTOCOL: PolyA+ RNA was purified using the MACS mRNA isolation kit (Miltenyi Biotec, Bergisch Gladbach, Germany), from 2-10ug of DNaseI-treated total RNA as per the manufacturer?s instructions. Double-stranded cDNA was synthesized from the purified polyA+ RNA using the Superscript Double-Stranded cDNA Synthesis kit (Invitrogen, Carlsbad, CA, USA) and random hexamer primers (Invitrogen) at a concentration of 5µM. The cDNA was fragmented by sonication and a paired-end sequencing library prepared following the BCCAGSC Indexed plate based library construction standard operating procedure for the Illumina GA platform.
SPOT
NUMBER_OF_READS_PER_SPOT: 2
READ_INDEX: 0
READ_CLASS: Application Read
READ_TYPE: Forward
BASE_COORD: 1
READ_INDEX: 1
READ_CLASS: Application Read
READ_TYPE: Reverse
BASE_COORD: 77
PLATFORM
ILLUMINA
INSTRUMENT_MODEL: Illumina Genome Analyzer II
SEQUENCE_LENGTH: 152
BASE CALLS
Illumina 1.8.0 RTA 1.8.70.0
QUALITY SCORES
Illumina 1.8.0 RTA 1.8.70.0
ATTRIBUTES
EXPERIMENT_TYPE: mRNA-Seq
EXTRACTION_PROTOCOL: Costello Lab Protocol
EXTRACTION_PROTOCOL_MRNA_ENRICHMENT: Miltenyi-Biotec MACS mRNA purification
RNA_PREPARATION_INITIAL_RNA_QLTY: RIN 8.8
RNA_PREPARATION_INITIAL_RNA_QNTY: 2 ug
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: NNNNNN
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: Invitrogen Superscript II RT
LIBRARY_GENERATION_PCR_TEMPLATE: cDNA
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 94-315bp
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 15
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
center_name: BCCAGSC
alias: A01027-1
STUDY_REF: UCSF_UBC_HREMP
SAMPLE_DESCRIPTOR: CD4 Memory TC014
LIBRARY
LIBRARY_NAME: A01027
LIBRARY_STRATEGY: mRNA-Seq
LIBRARY_SOURCE: TRANSCRIPTOMIC
LIBRARY_SELECTION: cDNA
LIBRARY_LAYOUT: PAIRED
POOLING_STRATEGY: none
LIBRARY_CONSTRUCTION_PROTOCOL: PolyA+ RNA was purified using the MACS mRNA isolation kit (Miltenyi Biotec, Bergisch Gladbach, Germany), from 2-10ug of DNaseI-treated total RNA as per the manufacturer?s instructions. Double-stranded cDNA was synthesized from the purified polyA+ RNA using the Superscript Double-Stranded cDNA Synthesis kit (Invitrogen, Carlsbad, CA, USA) and random hexamer primers (Invitrogen) at a concentration of 5µM. The cDNA was fragmented by sonication and a paired-end sequencing library prepared following the BCCAGSC Indexed plate based library construction standard operating procedure for the Illumina GA platform.
SPOT
NUMBER_OF_READS_PER_SPOT: 2
READ_INDEX: 0
READ_CLASS: Application Read
READ_TYPE: Forward
BASE_COORD: 1
READ_INDEX: 1
READ_CLASS: Application Read
READ_TYPE: Reverse
BASE_COORD: 77
PLATFORM
ILLUMINA
INSTRUMENT_MODEL: Illumina Genome Analyzer II
SEQUENCE_LENGTH: 152
BASE CALLS
Illumina 1.8.0 RTA 1.8.70.0
QUALITY SCORES
Illumina 1.8.0 RTA 1.8.70.0
ATTRIBUTES
EXPERIMENT_TYPE: mRNA-Seq
EXTRACTION_PROTOCOL: Costello Lab Protocol
EXTRACTION_PROTOCOL_MRNA_ENRICHMENT: Miltenyi-Biotec MACS mRNA purification
RNA_PREPARATION_INITIAL_RNA_QLTY: RIN 8.8
RNA_PREPARATION_INITIAL_RNA_QNTY: 2 ug
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: NNNNNN
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: Invitrogen Superscript II RT
LIBRARY_GENERATION_PCR_TEMPLATE: cDNA
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 94-315bp
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 15
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
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