title: RTG3-myc_gcn4d_INPUT_3

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
gcn4del RTG3-myc tag INPUT for IP3


title: RTG3-myc_gcn4d_INPUT_2

status: Public on Aug 11 2014

type: SRA

city: St. Louis

first: Aaron

last: Spivak

state: MO

address: 4444 Forest Park Avenue

country: USA

institute: Washington University in St. Louis

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
gcn4del RTG3-myc tag INPUT for IP2

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the S288C genome assembly using novoalign-2.07.0
If a sequenced fragment did not uniquely align to the genome, it was discarded
peaks were called using MACS-1.4.0rc2 with the following options "-g 12156677 --diag  --call-subpeaks -w"
Genome_build: S288C R64-1-1
Supplementary_files_format_and_content: peaks.bed files were generated by MACS

molecule: genomic DNA

organism: Saccharomyces cerevisiae

growth_protocol: NRG1-myc, SUT1-myc, and SWI4-myc strains were grown at 30° C in YPD rich media to exponential mid-log phase (OD600 ~ 0.8).  GCN4-myc and RTG3-myc strains were grown in YPD rich media to OD600 ~ 0.7, after which rapamycin was added to the media to a final concentration of 100 nM and the cultures were harvested after 20 minutes

extract_protocol:
Cells were lysed in a beadbeater and then sonicated.  The supernatant was collected and used for immunoprecipitation.  A sample was removed and labeled as the INPUT sample. Immunoprecipitations were performed using anti-c-myc resin. Samples were incubated overnight at 70°C to reverse cross-links.  Samples were RNAse treated and DNA was isolated by Phenol:Chlorofom extraction.
ChIP DNA was blunt ended, had addition of “A” base to 3’ end, and had sequencing adapters ligated to the ends. The fragments were size selected to 200-600 base pairs, and underwent amplification for 15 cycles. The resulting libraries were sequenced using the Illumina HiSeq-2000 as single reads extending 42 bases.

treatment_protocol: cross-linked in a final concentration of 1% formaldehyde for 15 minutes.  The reaction was quenched with 150 ml 2.5M glycine (50 mL for the 330mL cultures) and incubated at room temperature for 10 minutes.

tag: strain

value: W303 yeast strain Z1256

tag: chip antibody


title: RTG3-myc_gcn4d_IP3

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
gcn4del RTG3-myc tag IP3

value: anti-Myc EZiew affinity gel; Sigma E6779


title: RTG3-myc_gcn4d_IP1

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
gcn4del RTG3-myc tag IP1


title: RTG3-myc_gcn4d_INPUT_1

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
gcn4del RTG3-myc tag INPUT for IP1


title: NRG1-myc_sut1d_IP_2

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
sut1del NRG1-myc tag IP2


title: RTG3-myc_gcn4d_IP2

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
gcn4del RTG3-myc tag IP2


title: scRNA_control_untreated_replicate1

city: Goettingen

first: Anna

last: Sawicka

address: Am Fassberg 11

department: Dep. of Molecular Biology

country: Germany

institute: Max Planck Institure for Biophysical Chemistry

description: Short-capped RNA after 72h starvation in the medium containing 0.2% FCS (replicate1)

library_source: transcriptomic

data_processing:
Base callling was performed using RTA version 1.8.70.0 (samples scRNA_0h_1 and scRNA_1hA_1) and RTA version 1.13.48.0 (samples scRNA_0h_2 and scRNA_1hA_2).
Following adapter removal, reads derived from scRNA-seq were first trimmed to 25bp and then mapped to the mouse genome (mm9) using TopHat version 1.4.1 allowing for one mismatchin a n 18bp segment.  Only uniquely mapped reads were retained.
Duplicated reads were removed a bedgraph file (normalized to the total library size) using genomeCoverageBed -bga from BedTools was generated. Chromosome size information was downloaded from UCSC. BigWig files were generated from bedgraph files using bedGraphToBigWig.
Genome_build: mm9
Supplementary_files_format_and_content: read desity at genomic positions (bigWig format)

molecule: total RNA

organism: Mus musculus

source_name: Serum-starved (72h)  Swiss 3T3 fibroblasts, replicate 1

growth_protocol: Swiss 3T3 fibroblasts were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% (vol/vol) fetal calf serum (FCS) in the presence of Penicillin and Streptomycin. The cells were serum-deprived for 72 h using DMEM containing 0.2% FCS (vol/vol).

extract_protocol:
The cells growing onto 15-cm Petri dishes were washed twice with 10 ml of ice cold PBS, harvested in 5 ml of ice cold PBS and centrifuged for 5 min 500 x g, 4oC. The cell pellet was resuspended in 10 ml of Solution I (150 mM KCl, 4 mM MgOAc, 10 mM Tris-HCl pH 7.4) and spun down for 5 min at 500 x g, 4oC. The supernatant was removed; the cells were reuspended in 10 ml of Solution II (Solution I + 0.5% NP40) and incubated on ice for 10 min. The nuclei were pelleted through a 4 ml cushion of 0.6 M sucrose at 900 x g for 10 min, 4oC. All but 200 l of supernatant was removed and 2 ml of Solution I was added. The pellet was resuspended and spun down at 900 x g for 5 min, 4oC.  Following the removal of the supernatant, 1 ml of Trizol® reagent (Invitrogen) was added and RNA was further isolated according to the manufacturer's protocol.
scRNA-seq was performed as described (Nechaev et al., Science 2010), with modifications.The following adapters and primers were used: 3’adaptor_PE: 5‘-/5Phos/rArGrATCGGAAGAGCGGTTCAGC/3ddC/ -3‘; 5’adaptor_PE: 5‘rArCrArCrUrCrUrUrUrCrCrCrUrArCrArCrGrArCrGrCrUrCrUrUrCrCrGrArUrCrU-3‘; RT_Primer_PE (primer for reverse transcription):5‘- TCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT -3‘; Library amplification primers: 5‘-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’ and 5‘-CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT-3’. Briefly, 10 μg of nuclear RNA was size selected on a 15% TBE-urea gel (Bio-Rad) and RNA molecules sized between 25 nt and 120 nt were extracted and subjected to RNA 5’Polyphosphatase treatment (1 u/μl, Epibio) for 30 min at 37oC and subsequently with Terminator 5’phosphate-Dependent Exonuclease (0.05 u/μl, Epibio) for 60 min at 30oC, what was followed by ligation of 30 pmol of 3’adapter in the presence of 0.1 u/μl of T4 ssRNA Ligase I ( NEB) and 1 mM of ATP at 20oC for 6 hours.  Then RNA was size selected on 15% TBE-urea gel (Bio-Rad), RNA molecules between 50 nt and 150 nt were excised and treated with 1 μl  of APexTM Heat-Labile Alkaline Phosphatase (Epibio) for 10 min at 37oC  followed by the treatment with 2.5 u of Tobacco Acid Pyrophosphatase (Epibio) for 1 hour at 37oC.  Subsequently, 50 pmol of 5’adapter was ligated in the presence of 0.1 u/μl of T4 ssRNA Ligase I (NEB) and 1mM of ATP at 20oC for 6 hours. Following size selection on 10% TBE-urea gel (Bio-Rad), RNA was subjected to reverse transcription using Superscript III Reverse Transcriptase kit (Invitrogen). cDNA was amplified using PhusionTM DNA Polymerase (Finnzymes), 15 cycles of amplification were performed. The library was size selected on 6% TBE gel (Rio-Rad).

treatment_protocol: Serum-straved (72 h) mouse 3T3 fibroblasts we treated with 188.5 nM of anisomycin (Sigma) for 1 h.

tag: cell line

value: Swiss 3T3

tag: cell type

value: fibroblasts


title: scRNA_1hA_replicate1

description: Short-capped RNA after 72h starvation in the medium containing 0.2% FCS followed by 1h treatment with anisomycin (188.5 nM) (replicate1)

source_name: Serum-starved (72h)  Swiss 3T3 fibroblasts, 1h anisomycin treated (188.5 nM), replicate 1


title: SUT1-myc_nrg1d_IP_3

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
nrg1del SUT1-myc tag IP3


title: RNAPIIS2ph_1hA_replicate2

description: RNAPIIS2ph ChIP in serum-starved (72h)  Swiss 3T3 fibroblasts, 1h anisomycin treated (188.5 nM), replicate 2

data_processing:
Basecalling with Bustard version 1.8.0 (samples H3S28ph_0h_rep1, H3S28ph_1hA_rep1,  RNAPIIS2ph_0h_rep2, H3K9ac_0h_rep1, H3K9ac_1hA_rep1) or Bustard version 1.9.4 (samples H3K9ac_0h_rep2, H3K9ac_1hA_rep2) or RTA version 1.8.70.0 (samples RNAPIIS5ph_0h_rep1, RNAPIIS5ph_1hA_rep1, RNAPIIS2ph_0h_rep1, RNAPIIS2ph_1hA_rep1, RNAPIIS5ph_0h_rep2, RNAPIIS5ph_1hA_rep2, RNAPIIS2ph_1hA_rep2, H3K4me3_0h_rep1, H3K4me3_1hA_rep1, H3S28ph_0h_rep2, H3S28ph_1hA_rep2) or RTA version 1.13.48.0 (samples input_0h, input_1hA, H3K4me3_0h_rep2, H3K4me3_1hA_rep2).
ChIP-seq reads were mapped to the mouse genome (mm9) using Bowtie version 12.5. Up to two mismatches were allowed. Reads that map to only one genomic location were retained. Reads derived from the input samples were trimmed to 36bp prior to the mapping.
Duplicated reads were removed and unique reads were extended to the length of 200 bp (average DNA fragment size of after chromatin sanitation). Then a bedgraph file (normalized to the total library size) using genomeCoverageBed -bga from BedTools was generated. Chromosome size information was downloaded from UCSC. BigWig files were generated from bedgraph files using bedGraphToBigWig.
Genome_build: mm9
Supplementary_files_format_and_content: read desity at genomic positions (bigWig format)

source_name: RNAPIIS2ph, Serum-starved (72h)  Swiss 3T3 fibroblasts, 1h anisomycin treated (188.5 nM), replicate 2

extract_protocol:
Chromatin immunorecipitation was performed as described (Hauser et al., Molecular and Cellular Biology, 2002) with the following modifications: chromatin-antibody complexes were pulled down using Dynabeads® protein A or G beads (Invitrogen). The following antibodies were used in the study: H3S28ph (Sigma, cat number H9908), H3K9ac (Millipore, cat number 06-942), H3K4me3 (Millipore, cat number 07-473), RNAPIIS5ph (Bethyl, cat number A300-655A), RNAPIIS2ph (Bethyl, cat number  A300-654A).
Immunoprecipitated DNA as well as input samples were subjected to library preparation protocol using NEBNext® Library Prep Reagent Set for Illumina (NEB). The following TrueSeq barcodes were used for the input samples: sample input_0h TTAGGC, sample input_1hA  TGACCA.

tag: antibody


title: GCN4-myc_rtg3d_IP1

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
rtg3del GCN4-myc tag IP1


title: RNAPIIS2ph_1hA_replicate1

description: RNAPIIS2ph ChIP in serum-starved (72h)  Swiss 3T3 fibroblasts, 1h anisomycin treated (188.5 nM), replicate 1

source_name: RNAPIIS2ph, Serum-starved (72h)  Swiss 3T3 fibroblasts, 1h anisomycin treated (188.5 nM), replicate 1

value: RNAPIIS2ph (Bethyl, cat number  A300-654A)


title: GCN4-myc_rtg3d_IP2

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
rtg3del GCN4-myc tag IP2


title: RNAPIIS2ph_control_untreated_replicate1

description: RNAPIIS2ph ChIP in serum-starved (72h)  Swiss 3T3 fibroblasts, replicate 1

source_name: RNAPIIS2ph, Serum-starved (72h)  Swiss 3T3 fibroblasts, replicate 1


title: GCN4-myc_rtg3d_INPUT_2

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
rtg3del GCN4-myc tag INPUT for IP2


title: GCN4-myc_rtg3d_INPUT_3

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
rtg3del GCN4-myc tag INPUT for IP3


title: RNAPIIS5ph_1hA_replicate1

description: RNAPIIS5ph ChIP in serum-starved (72h)  Swiss 3T3 fibroblasts, 1h anisomycin treated (188.5 nM), replicate 1

source_name: RNAPIIS5ph, Serum-starved (72h)  Swiss 3T3 fibroblasts, 1h anisomycin treated (188.5 nM), replicate 1

value: RNAPIIS5ph (Bethyl, cat number A300-655A)


title: RNAPIIS5ph_control_untreated_replicate2

description: RNAPIIS5ph ChIP in serum-starved (72h)  Swiss 3T3 fibroblasts, replicate 2

source_name: RNAPIIS5ph, Serum-starved (72h)  Swiss 3T3 fibroblasts, replicate 2


title: NRG1-myc_sut1d_IP_1

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
sut1del NRG1-myc tag IP1


title: RTG3-myc_INPUT3

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
wild-type RTG3-myc tag INPUT for IP3


title: RTG3-myc_IP3

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
wild-type RTG3-myc tag IP3


title: RNAPIIS5ph_control_untreated_replicate1

description: RNAPIIS5ph ChIP in serum-starved (72h)  Swiss 3T3 fibroblasts, replicate 1

source_name: RNAPIIS5ph, Serum-starved (72h)  Swiss 3T3 fibroblasts, replicate 1


title: RTG3-myc_IP2

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
wild-type RTG3-myc tag IP2


title: H3K4me3_1hA_replicate1

description: H3K4me3 ChIP in serum-starved (72h)  Swiss 3T3 fibroblasts, 1h anisomycin treated (188.5 nM), replicate 1

source_name: H3K4me3, Serum-starved (72h)  Swiss 3T3 fibroblasts, 1h anisomycin treated (188.5 nM), replicate 1

value: H3K4me3 (Millipore, cat number 07-473)


title: H3K4me3_1hA_replicate2

description: H3K4me3 ChIP in serum-starved (72h)  Swiss 3T3 fibroblasts, 1h anisomycin treated (188.5 nM), replicate 2

source_name: H3K4me3, Serum-starved (72h)  Swiss 3T3 fibroblasts, 1h anisomycin treated (188.5 nM), replicate 2


title: H3K4me3_control_untreated_replicate2

description: H3K4me3 ChIP in serum-starved (72h)  Swiss 3T3 fibroblasts, replicate 2

source_name: H3K4me3, Serum-starved (72h)  Swiss 3T3 fibroblasts, replicate 2


title: RTG3-myc_INPUT2

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
wild-type RTG3-myc tag INPUT for IP2


title: RTG3-myc_IP1

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
wild-type RTG3-myc tag IP1


title: GCN4-myc_rtg3d_IP3

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
rtg3del GCN4-myc tag IP3


title: H3K4me3_control_untreated_replicate1

description: H3K4me3 ChIP in serum-starved (72h)  Swiss 3T3 fibroblasts, replicate 1

source_name: H3K4me3, Serum-starved (72h)  Swiss 3T3 fibroblasts, replicate 1


title: GCN4-myc_IP3

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
wild-type GCN4-myc tag IP3


title: RTG3-myc_INPUT1

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
wild-type RTG3-myc tag INPUT for IP1


title: H3K9ac_control_untreated_replicate2

description: H3K9ac ChIP in serum-starved (72h)  Swiss 3T3 fibroblasts, replicate 2

source_name: H3K9ac, Serum-starved (72h)  Swiss 3T3 fibroblasts, replicate 2

value: H3K9ac (Millipore, cat number 06-942)


title: H3K9ac_1hA_replicate2

description: H3K9ac ChIP in serum-starved (72h)  Swiss 3T3 fibroblasts, 1h anisomycin treated (188.5 nM), replicate 2

source_name: H3K9ac, Serum-starved (72h)  Swiss 3T3 fibroblasts, 1h anisomycin treated (188.5 nM), replicate 2


title: GCN4-myc_IP2

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
wild-type GCN4-myc tag IP2


title: GCN4-myc_rtg3d_INPUT_1

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
rtg3del GCN4-myc tag INPUT for IP1


title: H3K9ac_1hA_replicate1

description: H3K9ac ChIP in serum-starved (72h)  Swiss 3T3 fibroblasts, 1h anisomycin treated (188.5 nM), replicate 1

source_name: H3K9ac, Serum-starved (72h)  Swiss 3T3 fibroblasts, 1h anisomycin treated (188.5 nM), replicate 1


title: H3K9ac_control_untreated_replicate1

description: H3K9ac ChIP in serum-starved (72h)  Swiss 3T3 fibroblasts, replicate 1

source_name: H3K9ac, Serum-starved (72h)  Swiss 3T3 fibroblasts, replicate 1


title: GCN4-myc_INPUT2

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
wild-type GCN4-myc tag INPUT for IP2


title: GCN4-myc_IP1

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
wild-type GCN4-myc tag IP1


title: GCN4-myc_INPUT1

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
wild-type GCN4-myc tag INPUT for IP1


title: H3S28ph_1hA_replicate1

description: H3S28ph ChIP in serum-starved (72h)  Swiss 3T3 fibroblasts, 1h anisomycin treated (188.5 nM), replicate 1

source_name: H3S28ph, Serum-starved (72h)  Swiss 3T3 fibroblasts, 1h anisomycin treated (188.5 nM), replicate 1

value: H3S28ph (Sigma, cat number H9908)


title: Muscle_rep2

city: Liverpool

first: Peter

last: Davidsen

state: Merseyside

address: Crown Street

country: United Kingdom

institute: University of Liverpool

description: Sample 4

data_processing:
Illumina Casava1.8 software was used for basecalling.
Paired end reads were mapped to the G. Pig assembly (Cavia_porcellus.cavPor3.64.dna) using TopHat v1.3.3 and transcripts were assembled using Cufflinks v1.1.0. and Cuffdiff v2.1.1 for FPKM generation
Cufflinks v2.1.1 (via Cuffdiff) used to generate FPKM values. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnol. 2010
Genome_build: Cavpor3.0
Supplementary_files_format_and_content: Tab-delimited .txt file includes FPKM values derived by Cufflinks Cuffdiff

organism: Cavia porcellus

source_name: skeletal muscle

extract_protocol:
Tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Poly-A selection was used to select/sequence mRNAs
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Hartley

tag: gender

value: male

tag: tissue

value: skeletal muscle


title: H3S28ph_1hA_replicate2

description: H3S28ph ChIP in serum-starved (72h)  Swiss 3T3 fibroblasts, 1h anisomycin treated (188.5 nM), replicate 2

source_name: H3S28ph, Serum-starved (72h)  Swiss 3T3 fibroblasts, 1h anisomycin treated (188.5 nM), replicate 2


title: Muscle_rep1

description: Sample 3


title: H3S28ph_control_untreated_replicate1

description: H3S28ph ChIP in serum-starved (72h)  Swiss 3T3 fibroblasts, replicate 1

source_name: H3S28ph, Serum-starved (72h)  Swiss 3T3 fibroblasts, replicate 1


title: Lung_rep2

description: Sample 2

source_name: whole lung

value: whole lung


title: Lung_rep1

description: Sample 1


title: MNase-seq_ISWI_RNAi

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

institute: Justus-Liebig-University Giessen

description: MNase-seq after ISWI-specific RNAi

data_processing:
Quality control of FASTQ files was done using FastQC.
Removal of low quality reads was done using fastx_toolkit-0.06
Reads were aligned to a pre-compiled index of the mouse hg19 genome using Bowtie (options: -k 1 -m 1) 0.12.5.
Duplicate reads were removed with Samtools' rmdup function.
Samtools was used to convert aligned reads to BAM format.
For Browser visualization wiggle tracks were generated using MACS 1.4 at 10 bp resolution
In order to determine the effect of RNAi treatments on MNase accessibility the dm3 genome was binned into 100 bp bins. For each condition the total number of overlapping reads was determined. Next we used DESeq in order to correct for differential library sizes and to calculate fold enrichment/depletion per bin between two conditions (e.g. ISWI RNAi versus luciferase RNAi).
Genome_build: dm3
Supplementary_files_format_and_content: Wiggle (WIG) files were produced using Macs 1.4 at 10 bp resolution

organism: Drosophila melanogaster

source_name: S2 cells

growth_protocol: S2 cells were grown in Drosophila's Schneider Medium (GIBCO) supplemented with 10% FCS and 1% Penicillin/Streptomycin at 25°C.

extract_protocol:
4x10^7 S2 cells were fixed with 0.3% formaldehyde for 3 min at 18°C with shaking and the reaction terminated by addition of 125 mM glycine. The cell pellet is washed first with PBS and second with 1 ml Nuclei Buffer (10 mM Tris (pH 7.4), 10 mM KCl, 1.5 mM MgCl2, 1 mM DTT, protease inhibitors) and centrifuged after every step at 720 g for 5 min at 4°C. The pellet is resuspended in 1 ml Nuclei Buffer, incubated for 10 min at 4°C and cells disrupted with 20 strokes of a loose pestle. Nuclei were collected by centrifugation as described above and resuspended in 1 ml MNase Buffer (15 mM Tris (pH 7.4), 60 mM KCl, 15 mM NaCl, 1 mM CaCl2, 250 mM sucrose, 0.5 mM DTT,). 200 µl aliquots were treated with 250 U MNase (Thermo Scientific #EN0181) for 40 min at 18°C and afterwards the reaction is stopped with 12.5 mM EDTA and 0.5% SDS. Proteins and RNA were degraded, the resulting DNA purified and electrophoresed on an agarose gel. Mononucleosome bands were excised from gel and processed for sequencing.
Sequencing libraries were prepared from 10 ng of immunoprecipitated DNA with the Illumina ChIPSeq DNA Sample Prep Kit according to Illuminas instructions. Cluster generation was performed using the Illumina cluster station, sequencing on the Genome Analyzer IIx followed a standard protocol. The fluorescent images were processed to sequences using the Genome Analyzer Pipeline Analysis software 1.8 (Illumina).

treatment_protocol: 2x10^6 S2 cells were treated with 32µg dsRNA according to the DRSC protocol (http://flyrnai.org/DRSC-PRR.html).

tag: RNAi treatment

value: ISWI RNAi


title: MNase-seq_CTCF_CP190_RNAi

description: MNase-seq after CTCF/CP190-specific RNAi

value: DKD (CTCF/CP190 RNAi)


title: MNase-seq_luciferase_RNAi

description: MNase-seq after control RNAi

value: luciferase RNAi


title: GCN4-myc_INPUT3

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
wild-type GCN4-myc tag INPUT for IP3


title: H3_ChIPseq_ISWI_RNAi

description: H3 ChIP-seq after ISWI-specific RNAi

data_processing:
Quality control of FASTQ files was done using FastQC.
Removal of low quality reads was done using fastx_toolkit-0.06
Reads were aligned to a pre-compiled index of the mouse hg19 genome using Bowtie (options: -k 1 -m 1) 0.12.5.
Duplicate reads were removed with Samtools' rmdup function.
Samtools was used to convert aligned reads to BAM format.
For Browser visualization wiggle tracks were generated using MACS 1.4 at 10 bp resolution
In order to determine the effect of RNAi treatments on H3 density the dm3 genome was binned into 100 bp bins. For each condition the total number of overlapping reads was determined. Next we used DESeq in order to correct for differential library sizes and to calculate fold enrichment/depletion per bin between two conditions (e.g. ISWI RNAi versus luciferase RNAi).
Genome_build: dm3
Supplementary_files_format_and_content: Wiggle (WIG) files were produced using Macs 1.4 at 10 bp resolution

extract_protocol:
S2 cells were fixed in 1% formaldehyde for 15 min at 18°C. The reaction was stopped by adding glycine to a final concentration of 125 mM. After washing, cells were resuspended in SDS Lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl (pH 8.1), protease inhibitors) and incubated 10 min on ice. Chromatin was prepared by shearing with Bioruptor (Diagenode) at setting “high” for 20 cycles with 30 sec “On” and 30 sec “Off” to yield chromatin with a size ranging from 200-800 bp. The sonicated chromatin was diluted 10 fold in dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl (pH 8.1), 167 mM NaCl, protease inhibitors). Chromatin was immunoprecipitated by incubating with the appropriate antibodies overnight at 4°C. To collect the antibody/chromatin complexes the solution is incubated for 1 h at 4°C with 30 µl Protein G Plus/Protein A Agarose Suspension (Millipore). After washing  one time with Low Salt Buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1), 150 mM NaCl), one time with High Salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1), 500 mM NaCl), one time with LiCl Buffer (0.25 M LiCl, 1% NP40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl (pH 8.1)) and two times with TE Buffer (10 mM Tris-HCl, 1 mM EDTA (pH 8.0)) the crosslinks were reversed and DNA is recovered by illustra GFX columns (GE Healthcare)
Sequencing libraries were prepared from 10 ng of immunoprecipitated DNA with the Illumina ChIPSeq DNA Sample Prep Kit according to Illuminas instructions. Cluster generation was performed using the Illumina cluster station, sequencing on the Genome Analyzer IIx followed a standard protocol. The fluorescent images were processed to sequences using the Genome Analyzer Pipeline Analysis software 1.8 (Illumina).

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #


title: H3_ChIPseq_luciferase_RNAi

description: H3 ChIP-seq after control RNAi


title: H3_ChIPseq_CTCF_CP190_RNAi

description: H3 ChIP-seq after CTCF/CP190-specific RNAi


title: H3S28ph_control_untreated_replicate2

description: H3S28ph ChIP in serum-starved (72h)  Swiss 3T3 fibroblasts, replicate 2

source_name: H3S28ph, Serum-starved (72h)  Swiss 3T3 fibroblasts, replicate 2


title: Del Baf60c rep3 D5.3

status: Public on Aug 10 2014

city: San Francisco

first: Gladstone

last: Bioinformatics

state: CA

address: 1650 Owens St

department: Data Science and Biotechnology

institute: Gladstone Institutes

data_processing: Per-gene counts and FPKM values provided by "DefinedRegionDifferentialSeq" version 8.6.4, part of the USeq software package (http://useq.sourceforge.net/). Gene annotation used was ENSEMBL version 65.

source_name: Differentiated embryonic stem cells (129 SvEv background), at cardiac precursor (d5.3) stage

growth_protocol: Es cells were grown in DMEM media supplemented with fetal bovine serum and LIF. ES cells were differentiated to Cardiac precursor  and Cardiomyocyte by following a directed differentiation protocol (Kattman et al,  2011). Briefly ES cells were cultured in suspension / low attachement dishes to form embryoid bodies (EBs). EBs were induced in presence of VEGF, BMP4 and Activin A and cultured in monolayers in presence of VEGF, FGF-b and FGF-10 to form cardiac precursors and cardiac myocytes.

extract_protocol:
Total RNA was isolated from the samples using miRNeasy micro kit (Qiagen, cat no. 217084) following manufacture protocol with on-column DNase I digestion. Total RNA was qunatified using nanodrop and quality checked using bioanalyser.
RNA-seq libraries were prepared with ovation RNA-seq system v2 kit (NuGEN). The double-stranded DNA was then amplified using single primer isothermal amplification (SPIA). Random hexamers were used to amplify the second-strand cDNA linearly.  Finally, libraries from the SPIA amplified cDNA were made using the Ultralow DR library kit (NuGEN).
The RNA-seq libraries were analyzed by Bioanalyzer and quantified by qPCR (KAPA). All 12 indexed samples were sequenced in each of three lanes on an Illumina HiSeq 2500.

treatment_protocol: Both WT (Brg1) and Baf60c KO cardiac precurosor and cardiomyocytes were harvested by treating with TrpLE (cell dissociation reagent, life technologies, cat no. 12604-013). The cells were washed 2x with cold PBS, flash frozen in liquid nitrogen ans stored at -80C before total RNA isolation.

tag: barcode

value: TGTTGC

tag: timepoint

value: day 5.3

tag: genetic background

value: Baf60c null (homozygous Knockout)

tag: replicate number

value: Replicate 3

value: 129 SvEv


title: Del Baf60c rep2 D5.3

value: CACCTC

value: Replicate 2


title: Del Baf60c rep2 D10

source_name: Differentiated embryonic stem cells (129 SvEv background), at cardiomyocyte (d10) stage.

value: ACAAAC

value: day 10


title: Del Baf60c rep1 D10

value: GTGTTA

value: Replicate 1


title: Brg1 rep3 D5.3

value: CACACA

value: WT (Wildtype)


title: Brg1 rep1 D5.3

value: CCTCGG


title: Del Baf60c rep3 D10

value: GTGGCC


title: input_pKC27.vg.fwd'/daGAL4

city: Vienna

first: Leonie

last: Ringrose

address: Dr. Bohr Gasse 3

country: Austria

institute: IMBA

data_processing:
sequencing: HiSeq Control Software DS:Controlling software on instrument VN:2.0.12.0
basecalling: RTA PP:SCS DS:Basecalling Package VN:1.17.21.3
demultiplexing: Illumina2bam PP:basecalling DS:Convert Illumina BCL to BAM or SAM file VN:1.03
BamIndexDecoder PP:Illumina2bam DS:A command-line tool to decode multiplexed bam file VN:V1.13-3-g8bb9b0b
alignment: with bowtie 0.12.5 to dm3 genome
bin/align/bowtie/bowtie-0.12.5/bowtie -S -p 6 --trim5 0 --trim3 0 -v 2 --best --strata --tryhard -m 1 --phred33-quals --chunkmbs 256
Genome_build: dm3, BDGP Release 5
Supplementary_files_format_and_content: Aligned files (.bed) are given. Analysis was done by comparing the binding profiles on defined loci (transgenic and genomic).

source_name: 0-16h embryos

growth_protocol: Homozygous transgenic lines were crossed to homozygous daughterless GAL4 flies, and embryos resulting from this cross were collected for 16 hours.

extract_protocol:
Crosslinked lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody, as described in Orlando, et al., Embo J (1998)
Sequencing libraries were prepared with the KAPA Library Preparation Kit Illumina series (KK8201) according to the manufacturer's instructions.

value: 0-16h embryos


title: Brg1 rep2 D5.3

value: TTCGCT


title: Brg1 rep3 D10

value: ACACGA


title: Del Baf60c rep1 D5.3

value: TGTGAA

value: day 5.3


title: input_pKC27.vg.rev'/daGAL4


title: H3K27me3_pKC27.vg.rev'/daGAL4

value: anti-H3K27me3, CS200603 (Milipore)


title: H3K27me3_pKC27.vg.fwd'/daGAL4


title: Brg1 rep2 D10

value: GGATGT

value: 129 SvEv


title: E(Z)_pKC27.vg.rev'/daGAL4

value: anti-E(Z), Carrington & Jones, Development (1996).


title: MEF HA 6 hrs

status: Public on Aug 08 2014

city: Hsin-Chu

first: Jui-Hung

last: Hung

address: 75 Bo-Ai Street

country: Taiwan

institute: National Chiao Tung University

description: Chromatin IP against HA-macroH2A2

data_processing:
Alignment by bowtie v1.0
Transform bowtie outputs into BED format by in-house scripts that extend the alignment downstream 150 or 400 bp depending on the size of the expected bound DNA fragments
Genome_build: mm9
Supplementary_files_format_and_content: bed, alignment

source_name: embryonic fibroblasts

growth_protocol: ES cells were grown in standard ES medium: KO DMEM + 10% FBS, glutamine, LIF, non-essential amino acids, beta-mercaptoethanol, with mitotically inactivated feeder MEFs on gelatin coated plates until approximately 80% confluence

extract_protocol:
Eluted ChIP materials were PCI (Phenol-Chloroform-Isoamylalcohol) extracted
ChIP material was gel purified (100 to 800bp in size) from a 2% TAE agarose gel using  MiniElute columns QiaQuick (Qiagen). Gel purified DNA fragments were blunt ended and phosphorylated with an EPICENTRE End-it-Repair kit (1X buffer, 0.25mM dNTPs,1mM ATP, 1ul/50ul reaction of Enzyme mix) for 1hr at RT and cleaned up with Qiagen MiniElute spin columns. Adenosine nucleotide overhangs were added using EPICENTRE exo- Klenow for 45min at RT (with 0.2mM dATP). Illumina genome sequencing adaptors were then ligated using the EPICENTRE Fast-Link ligation kit: 11.5µl A tailed DNA eluted from a MinElute column was mixed with 1.5µl 10X ligation buffer, 0.75µl 10mMATP, 0.5µl Illumina DNA adaptors and 1µl ligase. The reaction was incubated for 1hr at RT and subsequently supplemented with 7.5 µl water, 1µl 10X buffer, 0.5µl 10mM ATP and 1µl ligase, and incubated overnight at 16οC. The ligation reaction was cleaned up with MiniElute columns (with an additional wash step to eliminate all the excess adaptors) and the adaptor ligated fragments were amplified by PCR as follows:0.75 µl of each Illumina genomic DNA sequencing primers, 6µl 10xPfx buffer 1.8µl 10mM dNTPs, 1.2µl 50mM MgSO4 and 1µl Pfx DNA polymerase (Invitrogen) were added to 30µl DNA template in a 100ul reaction.  The cycling parameters were: 1. 94οC 2’; 2. 94οC 15’’; 3. 65οC 1’; 4. 68οC 30’’; 5. repeat from step 2 16 times; 6. 68οC 5’. The PCR product (250 to 450bp in size) was gel purified from a 2% TAE agarose gel using the QiaQuick columns (Qiagen). Gel purified fragments were finally precipitated with Sodium acetate and ethanol and pellets were resuspended (25nM final concentration) in TE buffer.

treatment_protocol: At the day of induction, ES cells were pre-plated on gelatin and incubated for 45 min to deplete feeder MEFs. ES cells were then split onto three gelatinized plates each of which was induced at different time points by the addition of final 2 μg/mL doxycycline hyclate (Sigma). A similar procedure was used for induction of MEFs at passage 2.

tag: time point

value: 6 hr

tag: treatment

value: Dox

value: HA-MacroH2A2 inducible MEF cells isolated from HA-MacroH2A2 embryos

value: HA antibody, Abcam ab9110


title: Brg1 rep1 D10

value: AAGACG

value: day 10

value: Replicate 1


title: trf4 deletion

status: Public on Aug 09 2014

city: Babraham

first: Jonathan

last: Houseley

state: Cambridgeshire

address: Babraham Institute

department: Epigenetics Programme

institute: Babraham Institute

description: processed data file: ORF analysis log quant for GEO.txt, 100bp quant for GEO.txt

data_processing:
Quality and adapter trimming using Trim Galore (v0.3.5; default options; http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)
Aligned to the yeast genome (build SGD1.01) using Bowtie (Langmead et al., 2009)  (v0.12.7; default settings)
Genome_build: SGD1.01 (December 2006 build; http://may2009.archive.ensembl.org/Saccharomyces_cerevisiae/Info/Index)
Supplementary_files_format_and_content: ORF analysis log quant for GEO.txt - log2 transformed readcounts for wildtype and trf4 for each ORF. Chromosome and start and end positions are given for each entry.
Supplementary_files_format_and_content: 100bp quant for GEO.txt -The genome was divided into 100bp tiles and log2 transformed readcounts for wildtype and trf4 are given for each. Chromosome and start and end positions are given for each entry, along with any overalpping feature. This is the data used for CUT analysis in the associated publication.

source_name: Cbc2-associated RNA from meiotic cells

growth_protocol: For synchronised sporulation, cells from 15% glycerol stocks were plated onto YPGly (YP+2% glycerol) plates and grown over night. Cells were transferred to YP4D (YP+4% glucose) plates and grown for 4-6 hours before inoculating 25ml YPD cultures. Cultures were grown over night at 30deg, and diluted the following afternoon into YPA (YP+2% KOAc) at 2.6x10^6 cells/ml or 5x106 cells/ml for wt and trf4Δ cells respectively. Cells were grown for ~18 hours at 30deg  with shaking at 200 rpm, then washed and re-suspended in SPO medium (3g/L KOAc, 5mg/L uracil, 5mg/L histidine, 25mg/L leucine, 12.5mg/L tryptophan, 200mg/L raffinose) at 4x10^7 cells/ml and incubated at 25deg with shaking at 250rpm.

extract_protocol:
1.6x10^10 sporulating cells were harvested and washed with PBS. The cells were resuspended in one pellet volume of lysis buffer (50mM HEPES pH7.5, 50mM KCl, 5mM MgCl2, 1mM DTT, cOmplete Mini EDTA-free Protease Inhibitors) and frozen drop-wise on liquid nitrogen. Cells were ground to a fine powder in a pestle and mortar under liquid nitrogen and thawed in a 50 ml tube on ice. The lysate was centrifuged for 5 min at 4500 rpm and the supernatant clarified by centrifugation for 20 min at 30,000g. Cleared lysate was transferred to a 15 ml tube and incubated with 100µl of IgG sepharose beads (G.E. Healthcare) for 2 hours at 4degC with gentle agitation. Beads were washed five times for 10 minutes at 4degC with IP Buffer (10mM Tris pH7.5, 120mM NaCl, 5mM MgCl2, 0.1% NP-40, 1mM DTT). Beads were incubated for 2 hours at 16degC with 100µl IP buffer and 1µl AcTEV protease (Invitrogen). Beads were removed by centrifuging through a Micro Bio-Spin column (Bio-rad), and the flow-through was diluted with 500µl IP buffer + 2mM CaCl2 and incubated for 50min at 4degC with 100µl calmodulin sepharose beads (G.E. Healthcare). Beads were washed three times for five minutes with IP buffer + 2mM CaCl2 and protein was eluted in 100µl calmodulin elution buffer (10mM Tris pH7.5, 120mM NaCl, 5mM EGTA). Beads were removed by centrifuging through a Micro Bio-Spin Column, and RNA was extracted by phenol:chloroform extraction and ethanol precipitation.
RNA was fragmented in 200mM Tris acetate pH 8.2, 500mM KOAc, 150mM MgOAc2 for 3 min at 94deg, ethanol precipitated and reverse transcribed from random hexamers using Superscript II (Life Technologies) according to manufacturer’s instructions. Tris pH7.8 and MgCl2 were added to 50mM and 5mM respectively, and second strand synthesis was performed with 2U RNase H (NEB) and 50U DNA polymerase I (NEB) at 16deg for 2.5 hours. Ends were repaired using 15U T4 DNA polymerase (NEB), 5U Klenow DNA polymerase (NEB) and 50U T4 PNK (NEB) in T4 DNA ligase buffer (Life Technologies) at 20deg for 30 min. cDNA was tailed with dATP using 15U Klenow (3’-5’ exo-) (NEB) in NEBuffer 2 at 37deg for 30 min, and 1:10 diluted Illumina adapters were ligated using a Ligafast kit (Promega) followed by gel purification of ~200bp species. Libraries were amplified for 15 cycles using Phusion polymerase (NEB) and Illumina PCR primers 1.0 and 2.0.

tag: strain background

tag: genotype/variation

value: trf4 deletion

tag: Stage

value: meiosis

tag: time

value: 6 hours

tag: molecule subtype

value: Cbc2-associated RNA


title: E(Z)_pKC27.vg.fwd'/daGAL4

tag: antibody

value: 0-16h embryos


title: ES HA 6 hrs

description: Chromatin IP against HA-macroH2A2

source_name: Embryonic Stem Cells

tag: strain

tag: cell type

value: HA-MacroH2A2 inducible mouseES (KH2) cells

tag: chip antibody


title: MEF HA 3 hrs

description: Chromatin IP against HA-macroH2A2

value: 3 hr


title: ES HA 12 hrs

description: Chromatin IP against HA-macroH2A2


title: MEF HA 12 hrs

description: Chromatin IP against HA-macroH2A2


title: Anti Macro MEF 2Reps

description: Chromatin IP against macroH2A2

value: no treatment

value: Wild type MEF cells

value: MacroH2A2 antibody, Abcam ab4173


title: ES HA No Dox

description: Chromatin IP against HA-macroH2A2


title: ES HA 3 hrs

description: Chromatin IP against HA-macroH2A2


title: H3.3 6 hrs

description: Chromatin IP against HA-H3.3

value: 6 hr

value: HA-H3.3 inducible mouseES (KH2) cells


title: H3.3 3 hrs

description: Chromatin IP against HA-H3.3

value: Dox


title: Anti-Macro ES 2Reps

description: Chromatin IP against macroH2A2

value: Parental mouse ES(KH2) cells


title: SEQC_ILM_NYG_F_2_L08_GTTTCG_AC132FACXX

city: Shanghai

first: Leming

last: Shi

address: 2005 Songhu Road

department: School of Life Sciences

country: China

institute: Fudan University

data_processing:
Illumina Casava1.8 software used for Illumina basecalling
Reads were aligned with bowtie against hg19 genome
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts for the samples

organism: Homo sapiens

source_name: Mix of A and B (1:3)

extract_protocol: libraries were prepared using standard Illumina mRNA-Seq protocol

tag: seqc sample

value: F

tag: platform

value: Illumina HiSeq 2000

tag: site

value: NYG

tag: library id

tag: lane

value: GTTTCG

tag: flowcell


title: SEQC_ILM_NYG_F_2_L07_GTTTCG_AC132FACXX

tag: barcode


title: SEQC_ILM_NYG_F_2_L06_GTTTCG_AC132FACXX


title: SEQC_ILM_NYG_F_2_L02_GTTTCG_AC132FACXX


title: SEQC_ILM_NYG_F_2_L04_GTTTCG_AC132FACXX


title: SEQC_ILM_NYG_F_2_L05_GTTTCG_AC132FACXX


title: Wild type

value: Wild type

value: meiosis


title: SEQC_ILM_NYG_F_2_L03_GTTTCG_AC132FACXX


title: SEQC_ILM_NYG_F_1_L06_GTGAAA_AC132FACXX

value: GTGAAA


title: SEQC_ILM_NYG_F_1_L07_GTGAAA_AC132FACXX


title: SEQC_ILM_NYG_F_1_L04_GTGAAA_AC132FACXX


title: SEQC_ILM_NYG_F_1_L03_GTGAAA_AC132FACXX


title: SEQC_ILM_NYG_F_1_L05_GTGAAA_AC132FACXX


title: SEQC_ILM_NYG_F_1_L02_GTGAAA_AC132FACXX


title: SEQC_ILM_NYG_E_2_L08_GTGGCC_AC132FACXX

value: E

value: GTGGCC


title: SEQC_ILM_NYG_E_2_L05_GTGGCC_AC132FACXX


title: SEQC_ILM_NYG_E_2_L07_GTGGCC_AC132FACXX


title: SEQC_ILM_NYG_E_2_L03_GTGGCC_AC132FACXX


title: SEQC_ILM_NYG_E_2_L04_GTGGCC_AC132FACXX


title: SEQC_ILM_NYG_E_1_L08_GTCCGC_AC132FACXX

value: GTCCGC


title: SEQC_ILM_NYG_D_4_L08_CTTGTA_AC132FACXX

value: D

value: CTTGTA


title: SEQC_ILM_NYG_F_1_L08_GTGAAA_AC132FACXX


title: SEQC_ILM_NYG_E_2_L02_GTGGCC_AC132FACXX


title: SEQC_ILM_NYG_E_1_L04_GTCCGC_AC132FACXX


title: SEQC_ILM_NYG_D_4_L07_CTTGTA_AC132FACXX


title: SEQC_ILM_NYG_E_1_L05_GTCCGC_AC132FACXX


title: SEQC_ILM_NYG_D_4_L06_CTTGTA_AC132FACXX


title: SEQC_ILM_NYG_D_4_L02_CTTGTA_AC132FACXX


title: SEQC_ILM_NYG_D_4_L03_CTTGTA_AC132FACXX


title: SEQC_ILM_NYG_D_4_L04_CTTGTA_AC132FACXX


title: SEQC_ILM_NYG_D_3_L08_ACTTGA_AC132FACXX

value: ACTTGA


title: SEQC_ILM_NYG_D_3_L05_ACTTGA_AC132FACXX


title: SEQC_ILM_NYG_E_1_L02_GTCCGC_AC132FACXX


title: SEQC_ILM_NYG_E_1_L03_GTCCGC_AC132FACXX


title: SEQC_ILM_NYG_D_3_L07_ACTTGA_AC132FACXX


title: SEQC_ILM_NYG_E_2_L06_GTGGCC_AC132FACXX


title: SEQC_ILM_NYG_D_3_L03_ACTTGA_AC132FACXX


title: SEQC_ILM_NYG_E_1_L07_GTCCGC_AC132FACXX


title: SEQC_ILM_NYG_D_3_L06_ACTTGA_AC132FACXX


title: SEQC_ILM_NYG_D_3_L04_ACTTGA_AC132FACXX


title: SEQC_ILM_NYG_D_2_L06_CCGTCC_AC132FACXX

value: CCGTCC


title: SEQC_ILM_NYG_D_2_L05_CCGTCC_AC132FACXX


title: SEQC_ILM_NYG_D_2_L04_CCGTCC_AC132FACXX


title: SEQC_ILM_NYG_D_2_L02_CCGTCC_AC132FACXX


title: SEQC_ILM_NYG_D_3_L02_ACTTGA_AC132FACXX


title: SEQC_ILM_NYG_D_2_L03_CCGTCC_AC132FACXX


title: SEQC_ILM_NYG_D_2_L08_CCGTCC_AC132FACXX


title: SEQC_ILM_NYG_D_2_L07_CCGTCC_AC132FACXX


title: SEQC_ILM_NYG_E_1_L06_GTCCGC_AC132FACXX


title: SEQC_ILM_NYG_D_1_L06_TGACCA_AC132FACXX

value: TGACCA


title: SEQC_ILM_NYG_D_1_L03_TGACCA_AC132FACXX


title: SEQC_ILM_NYG_D_1_L05_TGACCA_AC132FACXX


title: SEQC_ILM_NYG_D_4_L05_CTTGTA_AC132FACXX


title: SEQC_ILM_NYG_D_1_L07_TGACCA_AC132FACXX


title: SEQC_ILM_NYG_D_1_L02_TGACCA_AC132FACXX


title: SEQC_ILM_NYG_D_1_L04_TGACCA_AC132FACXX


title: SEQC_ILM_NYG_C_4_L02_GGCTAC_AC132FACXX

source_name: Mix of A and B (3:1)

value: C

value: GGCTAC


title: SEQC_ILM_NYG_C_3_L07_ATGTCA_AC132FACXX

value: ATGTCA


title: SEQC_ILM_NYG_C_3_L04_ATGTCA_AC132FACXX

value: Illumina HiSeq 2000


title: SEQC_ILM_NYG_C_4_L04_GGCTAC_AC132FACXX

value: NYG


title: SEQC_ILM_NYG_C_3_L08_ATGTCA_AC132FACXX


title: SEQC_ILM_NYG_C_4_L05_GGCTAC_AC132FACXX


title: SEQC_ILM_NYG_C_4_L03_GGCTAC_AC132FACXX


title: SEQC_ILM_NYG_C_4_L06_GGCTAC_AC132FACXX


title: SEQC_ILM_NYG_C_2_L08_CAGATC_AC132FACXX

value: CAGATC


title: SEQC_ILM_NYG_C_3_L06_ATGTCA_AC132FACXX


title: SEQC_ILM_NYG_C_2_L07_CAGATC_AC132FACXX


title: SEQC_ILM_NYG_C_3_L05_ATGTCA_AC132FACXX


title: SEQC_ILM_NYG_C_3_L03_ATGTCA_AC132FACXX


title: SEQC_ILM_NYG_C_2_L06_CAGATC_AC132FACXX


title: SEQC_ILM_NYG_D_1_L08_TGACCA_AC132FACXX


title: SEQC_ILM_NYG_C_2_L05_CAGATC_AC132FACXX


title: SEQC_ILM_NYG_C_1_L08_TTAGGC_AC132FACXX

value: TTAGGC


title: SEQC_ILM_NYG_C_2_L03_CAGATC_AC132FACXX


title: SEQC_ILM_NYG_C_1_L07_TTAGGC_AC132FACXX


title: SEQC_ILM_NYG_C_2_L04_CAGATC_AC132FACXX


title: SEQC_ILM_NYG_C_4_L08_GGCTAC_AC132FACXX


title: SEQC_ILM_NYG_C_4_L07_GGCTAC_AC132FACXX


title: SEQC_ILM_NYG_C_1_L06_TTAGGC_AC132FACXX


title: SEQC_ILM_NYG_B_4_L08_TAGCTT_AC132FACXX

source_name: Human Brain Reference RNA (HBRR) from Ambion

value: B

value: TAGCTT


title: SEQC_ILM_NYG_B_4_L07_TAGCTT_AC132FACXX


title: SEQC_ILM_NYG_C_1_L04_TTAGGC_AC132FACXX


title: SEQC_ILM_NYG_C_1_L05_TTAGGC_AC132FACXX


title: SEQC_ILM_NYG_C_3_L02_ATGTCA_AC132FACXX


title: SEQC_ILM_NYG_B_4_L05_TAGCTT_AC132FACXX


title: SEQC_ILM_NYG_B_4_L06_TAGCTT_AC132FACXX


title: SEQC_ILM_NYG_C_1_L03_TTAGGC_AC132FACXX


title: SEQC_ILM_NYG_B_4_L02_TAGCTT_AC132FACXX


title: SEQC_ILM_NYG_B_4_L03_TAGCTT_AC132FACXX


title: SEQC_ILM_NYG_B_3_L06_AGTTCC_AC132FACXX

value: AGTTCC


title: SEQC_ILM_NYG_B_3_L03_AGTTCC_AC132FACXX


title: SEQC_ILM_NYG_B_3_L05_AGTTCC_AC132FACXX


title: SEQC_ILM_NYG_C_2_L02_CAGATC_AC132FACXX


title: SEQC_ILM_NYG_B_3_L07_AGTTCC_AC132FACXX


title: SEQC_ILM_NYG_B_2_L08_GCCAAT_AC132FACXX

value: GCCAAT


title: SEQC_ILM_NYG_B_3_L04_AGTTCC_AC132FACXX


title: SEQC_ILM_NYG_B_2_L07_GCCAAT_AC132FACXX


title: SEQC_ILM_NYG_B_2_L04_GCCAAT_AC132FACXX


title: SEQC_ILM_NYG_B_2_L06_GCCAAT_AC132FACXX


title: SEQC_ILM_NYG_B_2_L03_GCCAAT_AC132FACXX


title: SEQC_ILM_NYG_B_3_L02_AGTTCC_AC132FACXX


title: SEQC_ILM_NYG_C_1_L02_TTAGGC_AC132FACXX


title: SEQC_ILM_NYG_B_2_L02_GCCAAT_AC132FACXX


title: SEQC_ILM_NYG_B_2_L05_GCCAAT_AC132FACXX


title: SEQC_ILM_NYG_B_1_L08_CGATGT_AC132FACXX

value: CGATGT


title: SEQC_ILM_NYG_B_1_L05_CGATGT_AC132FACXX


title: SEQC_ILM_NYG_B_1_L07_CGATGT_AC132FACXX


title: SEQC_ILM_NYG_B_1_L06_CGATGT_AC132FACXX


title: SEQC_ILM_NYG_B_1_L03_CGATGT_AC132FACXX


title: SEQC_ILM_NYG_B_1_L04_CGATGT_AC132FACXX


title: SEQC_ILM_NYG_B_1_L02_CGATGT_AC132FACXX


title: SEQC_ILM_NYG_A_4_L07_GATCAG_AC132FACXX

source_name: Universal Human Reference RNA (UHRR) from Stratagene

value: A

value: GATCAG


title: SEQC_ILM_NYG_A_4_L06_GATCAG_AC132FACXX


title: SEQC_ILM_NYG_A_4_L05_GATCAG_AC132FACXX


title: SEQC_ILM_NYG_A_4_L08_GATCAG_AC132FACXX


title: SEQC_ILM_NYG_B_4_L04_TAGCTT_AC132FACXX


title: SEQC_ILM_NYG_A_4_L03_GATCAG_AC132FACXX


title: SEQC_ILM_NYG_B_3_L08_AGTTCC_AC132FACXX


title: SEQC_ILM_NYG_A_4_L04_GATCAG_AC132FACXX


title: SEQC_ILM_NYG_A_3_L08_AGTCAA_AC132FACXX

value: AGTCAA


title: SEQC_ILM_NYG_A_3_L05_AGTCAA_AC132FACXX


title: SEQC_ILM_NYG_A_3_L06_AGTCAA_AC132FACXX


title: SEQC_ILM_NYG_A_3_L04_AGTCAA_AC132FACXX


title: SEQC_ILM_NYG_A_3_L02_AGTCAA_AC132FACXX


title: SEQC_ILM_NYG_A_2_L08_ACAGTG_AC132FACXX

value: ACAGTG


title: SEQC_ILM_NYG_A_2_L06_ACAGTG_AC132FACXX


title: SEQC_ILM_NYG_A_2_L04_ACAGTG_AC132FACXX


title: SEQC_ILM_NYG_A_2_L07_ACAGTG_AC132FACXX


title: SEQC_ILM_NYG_A_2_L05_ACAGTG_AC132FACXX


title: SEQC_ILM_NYG_A_1_L08_ATCACG_AC132FACXX

value: ATCACG


title: SEQC_ILM_NYG_A_2_L02_ACAGTG_AC132FACXX


title: SEQC_ILM_NYG_A_2_L03_ACAGTG_AC132FACXX


title: SEQC_ILM_NYG_A_1_L05_ATCACG_AC132FACXX


title: SEQC_ILM_NYG_A_1_L06_ATCACG_AC132FACXX


title: SEQC_ILM_NYG_A_1_L04_ATCACG_AC132FACXX


title: SEQC_ILM_NYG_A_4_L02_GATCAG_AC132FACXX


title: SEQC_ILM_NYG_A_1_L02_ATCACG_AC132FACXX


title: SEQC_ILM_NYG_A_1_L03_ATCACG_AC132FACXX


title: SEQC_ILM_NYG_A_3_L07_AGTCAA_AC132FACXX


title: SEQC_ILM_AGR_D_4_L07_CCGTCC_AC0C1TACXX

data_processing:
Illumina Casava1.8 software used for Illumina basecalling. SOLiD 5500 and 454 reads were generated with SOLiD and Roche squencers respectively.
Reads were aligned with Magic, Tophat2, SubRead, Cstar, Novoalign and NovoalignCS
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts for the samples from one sequencing site

source_name: Mix of Sample A (UHRR) and Sample B (HBRR) (1:3)

extract_protocol: Illumina, SOLiD, and 454 libraries were prepared using standard Illumina, SOLiD, and 454 RNA-Seq protocols respectively.

value: D

value: AGR

value: CCGTCC


title: SEQC_ILM_AGR_D_4_L08_CCGTCC_BD0J2JACXX

value: Illumina HiSeq 2000


title: SEQC_ILM_AGR_D_4_L06_CCGTCC_AC0C1TACXX


title: SEQC_ILM_AGR_D_4_L05_CCGTCC_AC0C1TACXX


title: SEQC_ILM_AGR_D_4_L05_CCGTCC_BD0J2JACXX


title: SEQC_ILM_AGR_D_4_L08_CCGTCC_AC0C1TACXX


title: SEQC_ILM_AGR_D_4_L06_CCGTCC_BD0J2JACXX


title: SEQC_ILM_AGR_D_4_L07_CCGTCC_BD0J2JACXX


title: SEQC_ILM_AGR_D_4_L04_CCGTCC_AC0C1TACXX


title: SEQC_ILM_AGR_D_4_L03_CCGTCC_AC0C1TACXX


title: SEQC_ILM_AGR_D_4_L03_CCGTCC_BD0J2JACXX


title: SEQC_ILM_AGR_D_4_L04_CCGTCC_BD0J2JACXX


title: SEQC_ILM_NYG_A_3_L03_AGTCAA_AC132FACXX

value: NYG


title: SEQC_ILM_AGR_D_4_L02_CCGTCC_BD0J2JACXX


title: SEQC_ILM_AGR_D_4_L02_CCGTCC_AC0C1TACXX


title: SEQC_ILM_NYG_A_1_L07_ATCACG_AC132FACXX


title: SEQC_ILM_AGR_D_4_L01_CCGTCC_BD0J2JACXX


title: SEQC_ILM_AGR_D_3_L08_CTTGTA_BD0J2JACXX

value: CTTGTA


title: SEQC_ILM_AGR_D_4_L01_CCGTCC_AC0C1TACXX


title: SEQC_ILM_AGR_D_3_L08_CTTGTA_AC0C1TACXX


title: SEQC_ILM_AGR_D_3_L07_CTTGTA_AC0C1TACXX


title: SEQC_ILM_AGR_D_3_L06_CTTGTA_AC0C1TACXX


title: SEQC_ILM_AGR_D_3_L07_CTTGTA_BD0J2JACXX


title: SEQC_ILM_AGR_D_3_L04_CTTGTA_BD0J2JACXX


title: SEQC_ILM_AGR_D_3_L03_CTTGTA_AC0C1TACXX


title: SEQC_ILM_AGR_D_3_L05_CTTGTA_AC0C1TACXX


title: SEQC_ILM_AGR_D_3_L03_CTTGTA_BD0J2JACXX


title: SEQC_ILM_AGR_D_3_L04_CTTGTA_AC0C1TACXX


title: SEQC_ILM_AGR_D_3_L02_CTTGTA_BD0J2JACXX


title: SEQC_ILM_AGR_D_2_L08_ACTTGA_AC0C1TACXX

value: ACTTGA


title: SEQC_ILM_AGR_D_3_L02_CTTGTA_AC0C1TACXX


title: SEQC_ILM_AGR_D_2_L08_ACTTGA_BD0J2JACXX


title: SEQC_ILM_AGR_D_3_L01_CTTGTA_AC0C1TACXX


title: SEQC_ILM_AGR_D_2_L03_ACTTGA_BD0J2JACXX


title: SEQC_ILM_AGR_D_2_L05_ACTTGA_BD0J2JACXX


title: SEQC_ILM_AGR_D_2_L06_ACTTGA_BD0J2JACXX


title: SEQC_ILM_AGR_D_2_L04_ACTTGA_AC0C1TACXX


title: SEQC_ILM_AGR_D_2_L07_ACTTGA_BD0J2JACXX


title: SEQC_ILM_AGR_D_2_L04_ACTTGA_BD0J2JACXX


title: SEQC_ILM_AGR_D_2_L07_ACTTGA_AC0C1TACXX


title: SEQC_ILM_AGR_D_2_L01_ACTTGA_BD0J2JACXX


title: SEQC_ILM_AGR_D_2_L01_ACTTGA_AC0C1TACXX


title: SEQC_ILM_AGR_D_2_L02_ACTTGA_BD0J2JACXX


title: SEQC_ILM_AGR_D_2_L03_ACTTGA_AC0C1TACXX


title: SEQC_ILM_AGR_D_3_L06_CTTGTA_BD0J2JACXX


title: SEQC_ILM_AGR_D_2_L02_ACTTGA_AC0C1TACXX


title: SEQC_ILM_AGR_D_1_L08_TGACCA_BD0J2JACXX

value: TGACCA


title: SEQC_ILM_AGR_D_1_L07_TGACCA_BD0J2JACXX


title: SEQC_ILM_AGR_D_1_L06_TGACCA_BD0J2JACXX


title: SEQC_ILM_AGR_D_1_L05_TGACCA_BD0J2JACXX


title: SEQC_ILM_AGR_D_1_L07_TGACCA_AC0C1TACXX


title: SEQC_ILM_AGR_D_1_L05_TGACCA_AC0C1TACXX


title: SEQC_ILM_AGR_D_1_L06_TGACCA_AC0C1TACXX


title: SEQC_ILM_AGR_D_3_L01_CTTGTA_BD0J2JACXX


title: SEQC_ILM_AGR_D_3_L05_CTTGTA_BD0J2JACXX


title: SEQC_ILM_AGR_D_2_L06_ACTTGA_AC0C1TACXX


title: SEQC_ILM_AGR_D_1_L04_TGACCA_BD0J2JACXX


title: SEQC_ILM_AGR_D_1_L04_TGACCA_AC0C1TACXX


title: SEQC_ILM_AGR_D_1_L03_TGACCA_AC0C1TACXX


title: SEQC_ILM_AGR_D_1_L03_TGACCA_BD0J2JACXX


title: SEQC_ILM_AGR_D_1_L01_TGACCA_AC0C1TACXX


title: SEQC_ILM_AGR_C_4_L08_ATGTCA_BD0J2JACXX

source_name: Mix of Sample A (UHRR) and Sample B (HBRR) (3:1)

value: C

value: ATGTCA


title: SEQC_ILM_AGR_C_4_L07_ATGTCA_BD0J2JACXX


title: SEQC_ILM_AGR_C_4_L08_ATGTCA_AC0C1TACXX


title: SEQC_ILM_AGR_C_4_L07_ATGTCA_AC0C1TACXX


title: SEQC_ILM_AGR_C_4_L06_ATGTCA_AC0C1TACXX


title: SEQC_ILM_AGR_C_4_L05_ATGTCA_AC0C1TACXX


title: SEQC_ILM_AGR_D_1_L01_TGACCA_BD0J2JACXX


title: SEQC_ILM_AGR_C_4_L06_ATGTCA_BD0J2JACXX


title: SEQC_ILM_AGR_C_4_L04_ATGTCA_BD0J2JACXX


title: SEQC_ILM_AGR_C_4_L03_ATGTCA_BD0J2JACXX


title: SEQC_ILM_AGR_C_4_L05_ATGTCA_BD0J2JACXX


title: SEQC_ILM_AGR_C_4_L03_ATGTCA_AC0C1TACXX


title: SEQC_ILM_AGR_D_1_L08_TGACCA_AC0C1TACXX


title: SEQC_ILM_AGR_D_2_L05_ACTTGA_AC0C1TACXX


title: SEQC_ILM_AGR_D_1_L02_TGACCA_BD0J2JACXX


title: SEQC_ILM_AGR_C_4_L02_ATGTCA_AC0C1TACXX


title: SEQC_ILM_AGR_C_4_L02_ATGTCA_BD0J2JACXX


title: SEQC_ILM_AGR_C_3_L08_GGCTAC_AC0C1TACXX

value: GGCTAC


title: SEQC_ILM_AGR_C_3_L07_GGCTAC_AC0C1TACXX


title: SEQC_ILM_AGR_C_4_L01_ATGTCA_BD0J2JACXX


title: SEQC_ILM_AGR_C_3_L08_GGCTAC_BD0J2JACXX


title: SEQC_ILM_AGR_C_3_L07_GGCTAC_BD0J2JACXX


title: SEQC_ILM_AGR_C_3_L05_GGCTAC_BD0J2JACXX


title: SEQC_ILM_AGR_D_1_L02_TGACCA_AC0C1TACXX


title: SEQC_ILM_AGR_C_4_L01_ATGTCA_AC0C1TACXX


title: SEQC_ILM_AGR_C_3_L06_GGCTAC_BD0J2JACXX


title: SEQC_ILM_AGR_C_3_L05_GGCTAC_AC0C1TACXX


title: SEQC_ILM_AGR_C_3_L06_GGCTAC_AC0C1TACXX


title: SEQC_ILM_AGR_C_3_L01_GGCTAC_AC0C1TACXX


title: SEQC_ILM_AGR_C_3_L04_GGCTAC_BD0J2JACXX


title: SEQC_ILM_AGR_C_2_L08_CAGATC_BD0J2JACXX

value: CAGATC


title: SEQC_ILM_AGR_C_3_L03_GGCTAC_BD0J2JACXX


title: SEQC_ILM_AGR_C_2_L07_CAGATC_BD0J2JACXX


title: SEQC_ILM_AGR_C_3_L03_GGCTAC_AC0C1TACXX


title: SEQC_ILM_AGR_C_3_L04_GGCTAC_AC0C1TACXX


title: SEQC_ILM_AGR_C_3_L01_GGCTAC_BD0J2JACXX


title: SEQC_ILM_AGR_C_3_L02_GGCTAC_BD0J2JACXX


title: SEQC_ILM_AGR_C_2_L08_CAGATC_AC0C1TACXX


title: SEQC_ILM_AGR_C_2_L06_CAGATC_BD0J2JACXX


title: SEQC_ILM_AGR_C_2_L06_CAGATC_AC0C1TACXX


title: SEQC_ILM_AGR_C_4_L04_ATGTCA_AC0C1TACXX


title: SEQC_ILM_AGR_C_2_L05_CAGATC_BD0J2JACXX


title: SEQC_ILM_AGR_C_2_L04_CAGATC_BD0J2JACXX


title: SEQC_ILM_AGR_C_2_L01_CAGATC_BD0J2JACXX


title: SEQC_ILM_AGR_C_2_L04_CAGATC_AC0C1TACXX


title: SEQC_ILM_AGR_C_2_L03_CAGATC_BD0J2JACXX


title: SEQC_ILM_AGR_C_2_L03_CAGATC_AC0C1TACXX


title: SEQC_ILM_AGR_C_1_L08_TTAGGC_AC0C1TACXX

value: TTAGGC


title: SEQC_ILM_AGR_C_1_L07_TTAGGC_BD0J2JACXX


title: SEQC_ILM_AGR_C_2_L05_CAGATC_AC0C1TACXX


title: SEQC_ILM_AGR_C_2_L07_CAGATC_AC0C1TACXX


title: SEQC_ILM_AGR_C_2_L02_CAGATC_BD0J2JACXX


title: SEQC_ILM_AGR_C_2_L01_CAGATC_AC0C1TACXX


title: SEQC_ILM_AGR_C_2_L02_CAGATC_AC0C1TACXX


title: SEQC_ILM_AGR_C_1_L04_TTAGGC_BD0J2JACXX


title: SEQC_ILM_AGR_C_3_L02_GGCTAC_AC0C1TACXX


title: SEQC_ILM_AGR_C_1_L03_TTAGGC_AC0C1TACXX


title: SEQC_ILM_AGR_C_1_L04_TTAGGC_AC0C1TACXX


title: SEQC_ILM_AGR_C_1_L06_TTAGGC_AC0C1TACXX


title: SEQC_ILM_AGR_C_1_L06_TTAGGC_BD0J2JACXX


title: SEQC_ILM_AGR_C_1_L03_TTAGGC_BD0J2JACXX


title: SEQC_ILM_AGR_C_1_L05_TTAGGC_AC0C1TACXX


title: SEQC_ILM_AGR_C_1_L08_TTAGGC_BD0J2JACXX


title: SEQC_ILM_AGR_C_1_L02_TTAGGC_AC0C1TACXX


title: SEQC_ILM_AGR_C_1_L02_TTAGGC_BD0J2JACXX


title: SEQC_ILM_AGR_C_1_L01_TTAGGC_BD0J2JACXX


title: SEQC_ILM_AGR_C_1_L01_TTAGGC_AC0C1TACXX


title: SEQC_ILM_AGR_B_4_L08_AGTTCC_AC0C1TACXX

value: B

value: AGTTCC


title: SEQC_ILM_AGR_B_4_L05_AGTTCC_BD0J2JACXX


title: SEQC_ILM_AGR_B_4_L05_AGTTCC_AC0C1TACXX


title: SEQC_ILM_AGR_C_1_L07_TTAGGC_AC0C1TACXX


title: SEQC_ILM_AGR_B_4_L06_AGTTCC_AC0C1TACXX


title: SEQC_ILM_AGR_B_4_L04_AGTTCC_AC0C1TACXX


title: SEQC_ILM_AGR_B_4_L07_AGTTCC_BD0J2JACXX


title: SEQC_ILM_AGR_B_4_L06_AGTTCC_BD0J2JACXX


title: SEQC_ILM_AGR_B_4_L03_AGTTCC_BD0J2JACXX


title: SEQC_ILM_AGR_B_4_L03_AGTTCC_AC0C1TACXX


title: SEQC_ILM_AGR_C_1_L05_TTAGGC_BD0J2JACXX


title: SEQC_ILM_AGR_B_4_L02_AGTTCC_BD0J2JACXX


title: SEQC_ILM_AGR_B_4_L02_AGTTCC_AC0C1TACXX


title: SEQC_ILM_AGR_B_4_L08_AGTTCC_BD0J2JACXX


title: SEQC_ILM_AGR_B_3_L08_TAGCTT_BD0J2JACXX

value: TAGCTT


title: SEQC_ILM_AGR_B_3_L08_TAGCTT_AC0C1TACXX


title: SEQC_ILM_AGR_B_4_L01_AGTTCC_AC0C1TACXX


title: SEQC_ILM_AGR_B_3_L07_TAGCTT_BD0J2JACXX


title: SEQC_ILM_AGR_B_3_L06_TAGCTT_BD0J2JACXX


title: SEQC_ILM_AGR_B_3_L05_TAGCTT_BD0J2JACXX


title: SEQC_ILM_AGR_B_3_L07_TAGCTT_AC0C1TACXX


title: SEQC_ILM_AGR_B_3_L03_TAGCTT_BD0J2JACXX


title: SEQC_ILM_AGR_B_3_L04_TAGCTT_BD0J2JACXX


title: SEQC_ILM_AGR_B_4_L01_AGTTCC_BD0J2JACXX


title: SEQC_ILM_AGR_B_3_L04_TAGCTT_AC0C1TACXX


title: SEQC_ILM_AGR_B_3_L05_TAGCTT_AC0C1TACXX


title: SEQC_ILM_AGR_B_4_L07_AGTTCC_AC0C1TACXX


title: SEQC_ILM_AGR_B_3_L06_TAGCTT_AC0C1TACXX


title: SEQC_ILM_AGR_B_3_L03_TAGCTT_AC0C1TACXX


title: SEQC_ILM_AGR_B_3_L02_TAGCTT_BD0J2JACXX


title: SEQC_ILM_AGR_B_4_L04_AGTTCC_BD0J2JACXX


title: SEQC_ILM_AGR_B_3_L01_TAGCTT_AC0C1TACXX


title: SEQC_ILM_AGR_B_3_L01_TAGCTT_BD0J2JACXX


title: SEQC_ILM_AGR_B_2_L08_GCCAAT_AC0C1TACXX

value: GCCAAT


title: SEQC_ILM_AGR_B_3_L02_TAGCTT_AC0C1TACXX


title: SEQC_ILM_AGR_B_2_L08_GCCAAT_BD0J2JACXX


title: SEQC_ILM_AGR_B_2_L06_GCCAAT_BD0J2JACXX


title: SEQC_ILM_AGR_B_2_L07_GCCAAT_BD0J2JACXX


title: SEQC_ILM_AGR_B_2_L07_GCCAAT_AC0C1TACXX


title: SEQC_ILM_AGR_B_2_L06_GCCAAT_AC0C1TACXX


title: SEQC_ILM_AGR_B_2_L05_GCCAAT_AC0C1TACXX


title: SEQC_ILM_AGR_B_2_L05_GCCAAT_BD0J2JACXX


title: SEQC_ILM_AGR_B_2_L04_GCCAAT_BD0J2JACXX


title: SEQC_ILM_AGR_B_2_L02_GCCAAT_BD0J2JACXX


title: SEQC_ILM_AGR_B_2_L03_GCCAAT_AC0C1TACXX


title: SEQC_ILM_AGR_B_2_L01_GCCAAT_AC0C1TACXX


title: SEQC_ILM_AGR_B_2_L04_GCCAAT_AC0C1TACXX


title: SEQC_ILM_AGR_B_2_L02_GCCAAT_AC0C1TACXX


title: SEQC_ILM_AGR_B_2_L03_GCCAAT_BD0J2JACXX


title: SEQC_ILM_AGR_B_2_L01_GCCAAT_BD0J2JACXX


title: SEQC_ILM_AGR_B_1_L08_CGATGT_AC0C1TACXX

value: CGATGT


title: SEQC_ILM_AGR_B_1_L08_CGATGT_BD0J2JACXX

value: AGR


title: SEQC_ILM_AGR_B_1_L07_CGATGT_AC0C1TACXX


title: SEQC_ILM_AGR_B_1_L06_CGATGT_AC0C1TACXX


title: SEQC_ILM_AGR_B_1_L05_CGATGT_BD0J2JACXX


title: SEQC_ILM_AGR_B_1_L07_CGATGT_BD0J2JACXX


title: SEQC_ILM_AGR_B_1_L04_CGATGT_BD0J2JACXX


title: SEQC_ILM_AGR_B_1_L05_CGATGT_AC0C1TACXX


title: SEQC_ILM_AGR_B_1_L06_CGATGT_BD0J2JACXX


title: SEQC_ILM_AGR_B_1_L04_CGATGT_AC0C1TACXX


title: SEQC_ILM_AGR_B_1_L03_CGATGT_BD0J2JACXX


title: SEQC_ILM_AGR_B_1_L02_CGATGT_BD0J2JACXX


title: SEQC_ILM_AGR_B_1_L01_CGATGT_BD0J2JACXX


title: SEQC_ILM_AGR_A_4_L08_AGTCAA_AC0C1TACXX

value: A

value: AGTCAA


title: SEQC_ILM_AGR_B_1_L03_CGATGT_AC0C1TACXX

value: Illumina HiSeq 2000


title: SEQC_ILM_AGR_A_4_L06_AGTCAA_BD0J2JACXX


title: SEQC_ILM_AGR_A_4_L07_AGTCAA_AC0C1TACXX


title: SEQC_ILM_AGR_A_4_L07_AGTCAA_BD0J2JACXX


title: SEQC_ILM_AGR_B_1_L01_CGATGT_AC0C1TACXX


title: SEQC_ILM_AGR_B_1_L02_CGATGT_AC0C1TACXX


title: SEQC_ILM_AGR_A_4_L06_AGTCAA_AC0C1TACXX


title: SEQC_ILM_AGR_A_4_L04_AGTCAA_BD0J2JACXX


title: SEQC_ILM_AGR_A_4_L04_AGTCAA_AC0C1TACXX


title: SEQC_ILM_AGR_A_4_L05_AGTCAA_AC0C1TACXX


title: SEQC_ILM_AGR_A_4_L05_AGTCAA_BD0J2JACXX


title: SEQC_ILM_AGR_A_4_L01_AGTCAA_BD0J2JACXX


title: SEQC_ILM_AGR_A_4_L02_AGTCAA_BD0J2JACXX


title: SEQC_ILM_AGR_A_3_L08_GATCAG_AC0C1TACXX

value: GATCAG


title: SEQC_ILM_AGR_A_3_L07_GATCAG_BD0J2JACXX


title: SEQC_ILM_AGR_A_3_L08_GATCAG_BD0J2JACXX


title: SEQC_ILM_AGR_A_4_L03_AGTCAA_BD0J2JACXX


title: SEQC_ILM_AGR_A_3_L06_GATCAG_BD0J2JACXX


title: SEQC_ILM_AGR_A_4_L01_AGTCAA_AC0C1TACXX


title: SEQC_ILM_AGR_A_3_L06_GATCAG_AC0C1TACXX


title: SEQC_ILM_AGR_A_3_L05_GATCAG_BD0J2JACXX


title: SEQC_ILM_AGR_A_3_L04_GATCAG_BD0J2JACXX


title: SEQC_ILM_AGR_A_4_L08_AGTCAA_BD0J2JACXX


title: SEQC_ILM_AGR_A_3_L05_GATCAG_AC0C1TACXX


title: SEQC_ILM_AGR_A_3_L04_GATCAG_AC0C1TACXX


title: SEQC_ILM_AGR_A_3_L02_GATCAG_BD0J2JACXX


title: SEQC_ILM_AGR_A_2_L08_ACAGTG_BD0J2JACXX

value: ACAGTG


title: SEQC_ILM_AGR_A_3_L03_GATCAG_AC0C1TACXX


title: SEQC_ILM_AGR_A_4_L03_AGTCAA_AC0C1TACXX


title: SEQC_ILM_AGR_A_3_L03_GATCAG_BD0J2JACXX


title: SEQC_ILM_AGR_A_3_L01_GATCAG_BD0J2JACXX


title: SEQC_ILM_AGR_A_3_L01_GATCAG_AC0C1TACXX


title: SEQC_ILM_AGR_A_4_L02_AGTCAA_AC0C1TACXX


title: SEQC_ILM_AGR_A_2_L08_ACAGTG_AC0C1TACXX


title: SEQC_ILM_AGR_A_3_L02_GATCAG_AC0C1TACXX


title: SEQC_ILM_AGR_A_2_L07_ACAGTG_BD0J2JACXX


title: SEQC_ILM_AGR_A_3_L07_GATCAG_AC0C1TACXX


title: SEQC_ILM_AGR_A_2_L05_ACAGTG_BD0J2JACXX


title: SEQC_ILM_AGR_A_2_L06_ACAGTG_BD0J2JACXX


title: SEQC_ILM_AGR_A_2_L05_ACAGTG_AC0C1TACXX


title: SEQC_ILM_AGR_A_2_L04_ACAGTG_BD0J2JACXX


title: SEQC_ILM_AGR_A_2_L04_ACAGTG_AC0C1TACXX


title: SEQC_ILM_AGR_A_2_L06_ACAGTG_AC0C1TACXX


title: SEQC_ILM_AGR_A_2_L03_ACAGTG_BD0J2JACXX


title: SEQC_ILM_AGR_A_2_L01_ACAGTG_BD0J2JACXX


title: SEQC_ILM_AGR_A_1_L08_ATCACG_BD0J2JACXX

value: ATCACG


title: SEQC_ILM_AGR_A_2_L01_ACAGTG_AC0C1TACXX


title: SEQC_ILM_AGR_A_2_L02_ACAGTG_BD0J2JACXX


title: SEQC_ILM_AGR_A_1_L08_ATCACG_AC0C1TACXX


title: SEQC_ILM_AGR_A_1_L07_ATCACG_AC0C1TACXX


title: SEQC_ILM_AGR_A_1_L07_ATCACG_BD0J2JACXX


title: SEQC_ILM_AGR_A_2_L07_ACAGTG_AC0C1TACXX


title: SEQC_ILM_AGR_A_1_L06_ATCACG_BD0J2JACXX


title: SEQC_ILM_AGR_A_1_L05_ATCACG_BD0J2JACXX


title: SEQC_ILM_AGR_A_1_L06_ATCACG_AC0C1TACXX


title: SEQC_ILM_AGR_A_1_L04_ATCACG_BD0J2JACXX


title: SEQC_ILM_AGR_A_1_L05_ATCACG_AC0C1TACXX


title: SEQC_ILM_AGR_A_1_L03_ATCACG_AC0C1TACXX


title: SEQC_ILM_AGR_A_1_L04_ATCACG_AC0C1TACXX


title: SEQC_ILM_AGR_A_1_L03_ATCACG_BD0J2JACXX


title: SEQC_ILM_AGR_A_1_L02_ATCACG_BD0J2JACXX


title: SEQC_ILM_AGR_A_1_L01_ATCACG_BD0J2JACXX


title: SEQC_ILM_AGR_A_2_L03_ACAGTG_AC0C1TACXX


title: SEQC_ILM_AGR_A_2_L02_ACAGTG_AC0C1TACXX


title: SEQC_ILM_COH_D_4_L04_CCGTCC_AC03KTACXX

value: D

value: COH

value: CCGTCC


title: SEQC_ILM_AGR_A_1_L01_ATCACG_AC0C1TACXX


title: SEQC_ILM_COH_D_4_L03_CCGTCC_AC03KTACXX


title: SEQC_ILM_COH_D_4_L08_CCGTCC_AC03KTACXX


title: SEQC_ILM_COH_D_4_L07_CCGTCC_AC03KTACXX


title: SEQC_ILM_COH_D_4_L05_CCGTCC_AC03KTACXX


title: SEQC_ILM_COH_D_3_L06_CTTGTA_AC03KTACXX

value: CTTGTA


title: SEQC_ILM_COH_D_4_L01_CCGTCC_AC03KTACXX


title: SEQC_ILM_COH_D_3_L05_CTTGTA_AC03KTACXX


title: SEQC_ILM_COH_D_4_L02_CCGTCC_AC03KTACXX


title: SEQC_ILM_COH_D_3_L04_CTTGTA_AC03KTACXX


title: SEQC_ILM_COH_D_3_L07_CTTGTA_AC03KTACXX


title: SEQC_ILM_COH_D_3_L02_CTTGTA_AC03KTACXX


title: SEQC_ILM_COH_D_3_L03_CTTGTA_AC03KTACXX


title: SEQC_ILM_COH_D_3_L01_CTTGTA_AC03KTACXX


title: SEQC_ILM_AGR_A_1_L02_ATCACG_AC0C1TACXX


title: SEQC_ILM_COH_D_2_L05_ACTTGA_AC03KTACXX

value: ACTTGA


title: SEQC_ILM_COH_D_4_L06_CCGTCC_AC03KTACXX


title: SEQC_ILM_COH_D_2_L04_ACTTGA_AC03KTACXX


title: SEQC_ILM_COH_D_1_L07_TGACCA_AC03KTACXX

value: TGACCA


title: SEQC_ILM_COH_D_2_L07_ACTTGA_AC03KTACXX


title: SEQC_ILM_COH_D_1_L08_TGACCA_AC03KTACXX


title: SEQC_ILM_COH_D_2_L08_ACTTGA_AC03KTACXX


title: SEQC_ILM_COH_D_2_L06_ACTTGA_AC03KTACXX


title: SEQC_ILM_COH_D_2_L02_ACTTGA_AC03KTACXX


title: SEQC_ILM_COH_D_2_L01_ACTTGA_AC03KTACXX


title: SEQC_ILM_COH_D_3_L08_CTTGTA_AC03KTACXX


title: SEQC_ILM_COH_D_1_L06_TGACCA_AC03KTACXX


title: SEQC_ILM_COH_D_1_L04_TGACCA_AC03KTACXX


title: SEQC_ILM_COH_D_1_L02_TGACCA_AC03KTACXX


title: SEQC_ILM_COH_D_1_L05_TGACCA_AC03KTACXX


title: SEQC_ILM_COH_D_1_L03_TGACCA_AC03KTACXX


title: SEQC_ILM_COH_C_4_L05_ATGTCA_AC03KTACXX

value: C

value: ATGTCA


title: SEQC_ILM_COH_C_4_L07_ATGTCA_AC03KTACXX


title: SEQC_ILM_COH_C_4_L03_ATGTCA_AC03KTACXX


title: SEQC_ILM_COH_C_4_L04_ATGTCA_AC03KTACXX


title: SEQC_ILM_COH_D_1_L01_TGACCA_AC03KTACXX


title: SEQC_ILM_COH_C_4_L02_ATGTCA_AC03KTACXX


title: SEQC_ILM_COH_D_2_L03_ACTTGA_AC03KTACXX


title: SEQC_ILM_COH_C_3_L08_GGCTAC_AC03KTACXX

value: GGCTAC


title: SEQC_ILM_COH_C_3_L06_GGCTAC_AC03KTACXX


title: SEQC_ILM_COH_C_3_L05_GGCTAC_AC03KTACXX


title: SEQC_ILM_COH_C_3_L07_GGCTAC_AC03KTACXX


title: SEQC_ILM_COH_C_4_L01_ATGTCA_AC03KTACXX


title: SEQC_ILM_COH_C_3_L04_GGCTAC_AC03KTACXX


title: SEQC_ILM_COH_C_3_L02_GGCTAC_AC03KTACXX


title: SEQC_ILM_COH_C_3_L03_GGCTAC_AC03KTACXX


title: SEQC_ILM_COH_C_2_L05_CAGATC_AC03KTACXX

value: CAGATC


title: SEQC_ILM_COH_C_2_L04_CAGATC_AC03KTACXX


title: SEQC_ILM_COH_C_4_L08_ATGTCA_AC03KTACXX


title: SEQC_ILM_COH_C_2_L07_CAGATC_AC03KTACXX


title: SEQC_ILM_COH_C_2_L06_CAGATC_AC03KTACXX


title: SEQC_ILM_COH_C_4_L06_ATGTCA_AC03KTACXX


title: SEQC_ILM_COH_C_2_L03_CAGATC_AC03KTACXX


title: SEQC_ILM_COH_C_2_L02_CAGATC_AC03KTACXX


title: SEQC_ILM_COH_C_1_L08_TTAGGC_AC03KTACXX

value: TTAGGC


title: SEQC_ILM_COH_C_1_L07_TTAGGC_AC03KTACXX


title: SEQC_ILM_COH_C_1_L06_TTAGGC_AC03KTACXX


title: SEQC_ILM_COH_C_1_L05_TTAGGC_AC03KTACXX


title: SEQC_ILM_COH_C_2_L01_CAGATC_AC03KTACXX


title: SEQC_ILM_COH_C_1_L04_TTAGGC_AC03KTACXX


title: SEQC_ILM_COH_B_4_L08_AGTTCC_AC03KTACXX

value: B

value: AGTTCC


title: SEQC_ILM_COH_B_4_L07_AGTTCC_AC03KTACXX

value: Illumina HiSeq 2000


title: SEQC_ILM_COH_C_1_L03_TTAGGC_AC03KTACXX


title: SEQC_ILM_COH_C_1_L01_TTAGGC_AC03KTACXX


title: SEQC_ILM_COH_C_3_L01_GGCTAC_AC03KTACXX


title: SEQC_ILM_COH_B_4_L04_AGTTCC_AC03KTACXX


title: SEQC_ILM_COH_B_4_L03_AGTTCC_AC03KTACXX


title: SEQC_ILM_COH_B_4_L06_AGTTCC_AC03KTACXX


title: SEQC_ILM_COH_B_4_L05_AGTTCC_AC03KTACXX


title: SEQC_ILM_COH_C_2_L08_CAGATC_AC03KTACXX


title: SEQC_ILM_COH_B_3_L08_TAGCTT_AC03KTACXX

value: TAGCTT


title: SEQC_ILM_COH_B_4_L02_AGTTCC_AC03KTACXX


title: SEQC_ILM_COH_B_3_L06_TAGCTT_AC03KTACXX


title: SEQC_ILM_COH_B_3_L04_TAGCTT_AC03KTACXX


title: SEQC_ILM_COH_B_3_L05_TAGCTT_AC03KTACXX


title: SEQC_ILM_COH_B_3_L03_TAGCTT_AC03KTACXX


title: SEQC_ILM_COH_B_3_L07_TAGCTT_AC03KTACXX


title: SEQC_ILM_COH_B_3_L01_TAGCTT_AC03KTACXX


title: SEQC_ILM_COH_B_2_L05_GCCAAT_AC03KTACXX

value: GCCAAT


title: SEQC_ILM_COH_B_2_L02_GCCAAT_AC03KTACXX


title: SEQC_ILM_COH_B_2_L01_GCCAAT_AC03KTACXX


title: SEQC_ILM_COH_B_2_L07_GCCAAT_AC03KTACXX


title: SEQC_ILM_COH_B_2_L08_GCCAAT_AC03KTACXX


title: SEQC_ILM_COH_B_1_L07_CGATGT_AC03KTACXX

value: CGATGT


title: SEQC_ILM_COH_B_1_L08_CGATGT_AC03KTACXX


title: SEQC_ILM_COH_B_1_L06_CGATGT_AC03KTACXX


title: SEQC_ILM_COH_C_1_L02_TTAGGC_AC03KTACXX


title: SEQC_ILM_COH_B_2_L04_GCCAAT_AC03KTACXX


title: SEQC_ILM_COH_B_2_L06_GCCAAT_AC03KTACXX


title: SEQC_ILM_COH_B_2_L03_GCCAAT_AC03KTACXX


title: SEQC_ILM_COH_B_4_L01_AGTTCC_AC03KTACXX


title: SEQC_ILM_COH_B_3_L02_TAGCTT_AC03KTACXX


title: SEQC_ILM_COH_B_1_L03_CGATGT_AC03KTACXX


title: SEQC_ILM_COH_A_4_L08_AGTCAA_AC03KTACXX

value: A

value: AGTCAA


title: SEQC_ILM_COH_B_1_L01_CGATGT_AC03KTACXX

value: COH


title: SEQC_ILM_COH_A_4_L07_AGTCAA_AC03KTACXX


title: SEQC_ILM_COH_A_4_L05_AGTCAA_AC03KTACXX


title: SEQC_ILM_COH_B_1_L04_CGATGT_AC03KTACXX


title: SEQC_ILM_COH_B_1_L02_CGATGT_AC03KTACXX


title: SEQC_ILM_COH_A_4_L06_AGTCAA_AC03KTACXX


title: SEQC_ILM_COH_A_4_L03_AGTCAA_AC03KTACXX


title: SEQC_ILM_COH_A_4_L04_AGTCAA_AC03KTACXX


title: SEQC_ILM_COH_A_4_L01_AGTCAA_AC03KTACXX


title: SEQC_ILM_COH_A_3_L07_GATCAG_AC03KTACXX

value: GATCAG


title: SEQC_ILM_COH_A_3_L08_GATCAG_AC03KTACXX


title: SEQC_ILM_COH_B_1_L05_CGATGT_AC03KTACXX


title: SEQC_ILM_COH_A_3_L04_GATCAG_AC03KTACXX


title: SEQC_ILM_COH_A_3_L03_GATCAG_AC03KTACXX


title: SEQC_ILM_COH_A_3_L01_GATCAG_AC03KTACXX


title: SEQC_ILM_COH_A_3_L05_GATCAG_AC03KTACXX


title: SEQC_ILM_COH_A_2_L06_ACAGTG_AC03KTACXX

value: ACAGTG


title: SEQC_ILM_COH_A_2_L07_ACAGTG_AC03KTACXX


title: SEQC_ILM_COH_A_3_L02_GATCAG_AC03KTACXX


title: SEQC_ILM_COH_A_2_L08_ACAGTG_AC03KTACXX


title: SEQC_ILM_COH_A_2_L05_ACAGTG_AC03KTACXX


title: SEQC_ILM_COH_A_4_L02_AGTCAA_AC03KTACXX


title: SEQC_ILM_COH_A_2_L02_ACAGTG_AC03KTACXX


title: SEQC_ILM_COH_A_2_L01_ACAGTG_AC03KTACXX


title: SEQC_ILM_COH_A_1_L05_ATCACG_AC03KTACXX

value: ATCACG


title: SEQC_ILM_COH_A_2_L03_ACAGTG_AC03KTACXX


title: SEQC_ILM_COH_A_1_L08_ATCACG_AC03KTACXX


title: SEQC_ILM_COH_A_1_L06_ATCACG_AC03KTACXX


title: SEQC_ILM_COH_A_1_L04_ATCACG_AC03KTACXX


title: SEQC_ILM_COH_A_1_L03_ATCACG_AC03KTACXX


title: SEQC_ILM_COH_A_1_L01_ATCACG_AC03KTACXX


title: SEQC_ILM_COH_A_2_L04_ACAGTG_AC03KTACXX


title: SEQC_ILM_COH_A_1_L07_ATCACG_AC03KTACXX


title: SEQC_ILM_COH_A_3_L06_GATCAG_AC03KTACXX


title: SEQC_ILM_COH_A_1_L02_ATCACG_AC03KTACXX


title: SEQC_ILM_NVS_D_4_L08_CCGTCC_AD0902ACXX

value: D

value: NVS

value: CCGTCC


title: SEQC_ILM_NVS_D_4_L07_CCGTCC_BD08PVACXX


title: SEQC_ILM_NVS_D_4_L08_CCGTCC_BD08PVACXX


title: SEQC_ILM_NVS_D_4_L05_CCGTCC_AD0902ACXX


title: SEQC_ILM_NVS_D_4_L04_CCGTCC_AD0902ACXX


title: SEQC_ILM_NVS_D_4_L06_CCGTCC_AD0902ACXX


title: SEQC_ILM_NVS_D_4_L07_CCGTCC_AD0902ACXX


title: SEQC_ILM_NVS_D_4_L05_CCGTCC_BD08PVACXX


title: SEQC_ILM_NVS_D_4_L03_CCGTCC_BD08PVACXX


title: SEQC_ILM_NVS_D_4_L04_CCGTCC_BD08PVACXX


title: SEQC_ILM_NVS_D_4_L02_CCGTCC_BD08PVACXX


title: SEQC_ILM_NVS_D_4_L02_CCGTCC_AD0902ACXX


title: SEQC_ILM_NVS_D_4_L03_CCGTCC_AD0902ACXX


title: SEQC_ILM_NVS_D_4_L01_CCGTCC_BD08PVACXX


title: SEQC_ILM_NVS_D_4_L01_CCGTCC_AD0902ACXX


title: SEQC_ILM_NVS_D_3_L07_CTTGTA_AD0902ACXX

value: CTTGTA


title: SEQC_ILM_NVS_D_3_L06_CTTGTA_AD0902ACXX


title: SEQC_ILM_NVS_D_3_L08_CTTGTA_AD0902ACXX


title: SEQC_ILM_NVS_D_3_L04_CTTGTA_BD08PVACXX


title: SEQC_ILM_NVS_D_3_L05_CTTGTA_AD0902ACXX


title: SEQC_ILM_NVS_D_3_L06_CTTGTA_BD08PVACXX


title: SEQC_ILM_NVS_D_3_L05_CTTGTA_BD08PVACXX


title: SEQC_ILM_NVS_D_3_L07_CTTGTA_BD08PVACXX


title: SEQC_ILM_NVS_D_3_L03_CTTGTA_AD0902ACXX


title: SEQC_ILM_NVS_D_4_L06_CCGTCC_BD08PVACXX


title: SEQC_ILM_NVS_D_3_L08_CTTGTA_BD08PVACXX


title: SEQC_ILM_NVS_D_3_L04_CTTGTA_AD0902ACXX


title: SEQC_ILM_NVS_D_2_L08_ACTTGA_AD0902ACXX

value: ACTTGA


title: SEQC_ILM_NVS_D_3_L01_CTTGTA_BD08PVACXX


title: SEQC_ILM_NVS_D_3_L02_CTTGTA_BD08PVACXX


title: SEQC_ILM_NVS_D_2_L07_ACTTGA_BD08PVACXX


title: SEQC_ILM_NVS_D_2_L08_ACTTGA_BD08PVACXX


title: SEQC_ILM_NVS_D_2_L06_ACTTGA_AD0902ACXX


title: SEQC_ILM_NVS_D_2_L07_ACTTGA_AD0902ACXX


title: SEQC_ILM_NVS_D_2_L06_ACTTGA_BD08PVACXX


title: SEQC_ILM_NVS_D_2_L03_ACTTGA_AD0902ACXX


title: SEQC_ILM_NVS_D_2_L05_ACTTGA_AD0902ACXX


title: SEQC_ILM_NVS_D_2_L04_ACTTGA_BD08PVACXX


title: SEQC_ILM_NVS_D_2_L03_ACTTGA_BD08PVACXX


title: SEQC_ILM_NVS_D_2_L02_ACTTGA_BD08PVACXX


title: SEQC_ILM_NVS_D_3_L03_CTTGTA_BD08PVACXX


title: SEQC_ILM_NVS_D_2_L02_ACTTGA_AD0902ACXX


title: SEQC_ILM_NVS_D_2_L01_ACTTGA_BD08PVACXX


title: SEQC_ILM_NVS_D_3_L02_CTTGTA_AD0902ACXX


title: SEQC_ILM_NVS_D_1_L08_TGACCA_BD08PVACXX

value: TGACCA


title: SEQC_ILM_NVS_D_2_L01_ACTTGA_AD0902ACXX


title: SEQC_ILM_NVS_D_3_L01_CTTGTA_AD0902ACXX


title: SEQC_ILM_NVS_D_1_L06_TGACCA_AD0902ACXX


title: SEQC_ILM_NVS_D_1_L07_TGACCA_BD08PVACXX


title: SEQC_ILM_NVS_D_1_L05_TGACCA_AD0902ACXX


title: SEQC_ILM_NVS_D_1_L04_TGACCA_BD08PVACXX


title: SEQC_ILM_NVS_D_2_L05_ACTTGA_BD08PVACXX


title: SEQC_ILM_NVS_D_1_L06_TGACCA_BD08PVACXX


title: SEQC_ILM_NVS_D_2_L04_ACTTGA_AD0902ACXX


title: SEQC_ILM_NVS_D_1_L08_TGACCA_AD0902ACXX


title: SEQC_ILM_NVS_D_1_L07_TGACCA_AD0902ACXX


title: SEQC_ILM_NVS_D_1_L05_TGACCA_BD08PVACXX


title: SEQC_ILM_NVS_D_1_L03_TGACCA_AD0902ACXX


title: SEQC_ILM_NVS_D_1_L02_TGACCA_BD08PVACXX


title: SEQC_ILM_NVS_D_1_L02_TGACCA_AD0902ACXX


title: SEQC_ILM_NVS_D_1_L03_TGACCA_BD08PVACXX


title: SEQC_ILM_NVS_C_4_L07_ATGTCA_BD08PVACXX

value: C

value: ATGTCA


title: SEQC_ILM_NVS_D_1_L01_TGACCA_BD08PVACXX

value: Illumina HiSeq 2000


title: SEQC_ILM_NVS_C_4_L06_ATGTCA_AD0902ACXX


title: SEQC_ILM_NVS_D_1_L01_TGACCA_AD0902ACXX


title: SEQC_ILM_NVS_C_4_L08_ATGTCA_AD0902ACXX


title: SEQC_ILM_NVS_C_4_L05_ATGTCA_BD08PVACXX


title: SEQC_ILM_NVS_C_4_L04_ATGTCA_AD0902ACXX


title: SEQC_ILM_NVS_C_4_L05_ATGTCA_AD0902ACXX


title: SEQC_ILM_NVS_C_4_L04_ATGTCA_BD08PVACXX


title: SEQC_ILM_NVS_C_4_L03_ATGTCA_BD08PVACXX


title: SEQC_ILM_NVS_C_4_L03_ATGTCA_AD0902ACXX


title: SEQC_ILM_NVS_D_1_L04_TGACCA_AD0902ACXX


title: SEQC_ILM_NVS_C_4_L08_ATGTCA_BD08PVACXX


title: SEQC_ILM_NVS_C_4_L02_ATGTCA_AD0902ACXX


title: SEQC_ILM_NVS_C_4_L01_ATGTCA_AD0902ACXX


title: SEQC_ILM_NVS_C_3_L08_GGCTAC_BD08PVACXX

value: GGCTAC


title: SEQC_ILM_NVS_C_4_L01_ATGTCA_BD08PVACXX


title: SEQC_ILM_NVS_C_3_L07_GGCTAC_BD08PVACXX


title: SEQC_ILM_NVS_C_3_L06_GGCTAC_BD08PVACXX


title: SEQC_ILM_NVS_C_4_L06_ATGTCA_BD08PVACXX


title: SEQC_ILM_NVS_C_3_L07_GGCTAC_AD0902ACXX


title: SEQC_ILM_NVS_C_3_L06_GGCTAC_AD0902ACXX


title: SEQC_ILM_NVS_C_4_L02_ATGTCA_BD08PVACXX


title: SEQC_ILM_NVS_C_3_L05_GGCTAC_BD08PVACXX


title: SEQC_ILM_NVS_C_3_L08_GGCTAC_AD0902ACXX


title: SEQC_ILM_NVS_C_3_L04_GGCTAC_BD08PVACXX


title: SEQC_ILM_NVS_C_4_L07_ATGTCA_AD0902ACXX


title: SEQC_ILM_NVS_C_3_L05_GGCTAC_AD0902ACXX


title: SEQC_ILM_NVS_C_3_L04_GGCTAC_AD0902ACXX


title: SEQC_ILM_NVS_C_3_L02_GGCTAC_AD0902ACXX


title: SEQC_ILM_NVS_C_3_L03_GGCTAC_AD0902ACXX


title: SEQC_ILM_NVS_C_3_L02_GGCTAC_BD08PVACXX


title: SEQC_ILM_NVS_C_3_L03_GGCTAC_BD08PVACXX


title: SEQC_ILM_NVS_C_3_L01_GGCTAC_AD0902ACXX


title: SEQC_ILM_NVS_C_3_L01_GGCTAC_BD08PVACXX


title: SEQC_ILM_NVS_C_2_L08_CAGATC_BD08PVACXX

value: CAGATC


title: SEQC_ILM_NVS_C_2_L08_CAGATC_AD0902ACXX


title: SEQC_ILM_NVS_C_2_L07_CAGATC_AD0902ACXX


title: SEQC_ILM_NVS_C_2_L06_CAGATC_BD08PVACXX


title: SEQC_ILM_NVS_C_2_L07_CAGATC_BD08PVACXX


title: SEQC_ILM_NVS_C_2_L06_CAGATC_AD0902ACXX


title: SEQC_ILM_NVS_C_2_L05_CAGATC_BD08PVACXX


title: SEQC_ILM_NVS_C_2_L05_CAGATC_AD0902ACXX


title: SEQC_ILM_NVS_C_2_L03_CAGATC_BD08PVACXX


title: SEQC_ILM_NVS_C_2_L01_CAGATC_BD08PVACXX


title: SEQC_ILM_NVS_C_2_L04_CAGATC_BD08PVACXX


title: SEQC_ILM_NVS_C_2_L03_CAGATC_AD0902ACXX


title: SEQC_ILM_NVS_C_2_L04_CAGATC_AD0902ACXX


title: SEQC_ILM_NVS_C_1_L07_TTAGGC_AD0902ACXX

value: TTAGGC


title: SEQC_ILM_NVS_C_1_L08_TTAGGC_BD08PVACXX


title: SEQC_ILM_NVS_C_2_L01_CAGATC_AD0902ACXX


title: SEQC_ILM_NVS_C_2_L02_CAGATC_AD0902ACXX


title: SEQC_ILM_NVS_C_1_L08_TTAGGC_AD0902ACXX


title: SEQC_ILM_NVS_C_1_L06_TTAGGC_BD08PVACXX


title: SEQC_ILM_NVS_C_1_L07_TTAGGC_BD08PVACXX


title: SEQC_ILM_NVS_C_1_L02_TTAGGC_BD08PVACXX


title: SEQC_ILM_NVS_C_1_L06_TTAGGC_AD0902ACXX


title: SEQC_ILM_NVS_C_1_L03_TTAGGC_AD0902ACXX


title: SEQC_ILM_NVS_C_1_L02_TTAGGC_AD0902ACXX


title: SEQC_ILM_NVS_C_1_L04_TTAGGC_BD08PVACXX


title: SEQC_ILM_NVS_C_1_L05_TTAGGC_AD0902ACXX


title: SEQC_ILM_NVS_C_1_L04_TTAGGC_AD0902ACXX


title: SEQC_ILM_NVS_C_1_L01_TTAGGC_BD08PVACXX


title: SEQC_ILM_NVS_C_1_L05_TTAGGC_BD08PVACXX


title: SEQC_ILM_NVS_C_1_L01_TTAGGC_AD0902ACXX


title: SEQC_ILM_NVS_B_4_L08_AGTTCC_BD08PVACXX

value: B

value: AGTTCC


title: SEQC_ILM_NVS_B_4_L06_AGTTCC_BD08PVACXX


title: SEQC_ILM_NVS_B_4_L07_AGTTCC_AD0902ACXX


title: SEQC_ILM_NVS_B_4_L07_AGTTCC_BD08PVACXX


title: SEQC_ILM_NVS_B_4_L06_AGTTCC_AD0902ACXX


title: SEQC_ILM_NVS_B_4_L05_AGTTCC_AD0902ACXX


title: SEQC_ILM_NVS_C_1_L03_TTAGGC_BD08PVACXX


title: SEQC_ILM_NVS_B_4_L05_AGTTCC_BD08PVACXX


title: SEQC_ILM_NVS_B_4_L04_AGTTCC_BD08PVACXX


title: SEQC_ILM_NVS_B_4_L04_AGTTCC_AD0902ACXX


title: SEQC_ILM_NVS_B_4_L03_AGTTCC_BD08PVACXX


title: SEQC_ILM_NVS_B_4_L02_AGTTCC_AD0902ACXX


title: SEQC_ILM_NVS_B_4_L01_AGTTCC_AD0902ACXX


title: SEQC_ILM_NVS_B_4_L03_AGTTCC_AD0902ACXX


title: SEQC_ILM_NVS_B_4_L08_AGTTCC_AD0902ACXX


title: SEQC_ILM_NVS_B_3_L05_TAGCTT_AD0902ACXX

value: TAGCTT


title: SEQC_ILM_NVS_B_3_L07_TAGCTT_AD0902ACXX


title: SEQC_ILM_NVS_B_3_L06_TAGCTT_BD08PVACXX


title: SEQC_ILM_NVS_B_3_L08_TAGCTT_BD08PVACXX


title: SEQC_ILM_NVS_B_3_L05_TAGCTT_BD08PVACXX


title: SEQC_ILM_NVS_B_4_L02_AGTTCC_BD08PVACXX


title: SEQC_ILM_NVS_B_3_L06_TAGCTT_AD0902ACXX


title: SEQC_ILM_NVS_B_3_L04_TAGCTT_AD0902ACXX


title: SEQC_ILM_NVS_B_3_L08_TAGCTT_AD0902ACXX


title: SEQC_ILM_NVS_B_3_L03_TAGCTT_BD08PVACXX


title: SEQC_ILM_NVS_B_3_L02_TAGCTT_AD0902ACXX


title: SEQC_ILM_NVS_B_3_L03_TAGCTT_AD0902ACXX


title: SEQC_ILM_NVS_B_3_L04_TAGCTT_BD08PVACXX


title: SEQC_ILM_NVS_B_3_L01_TAGCTT_BD08PVACXX


title: SEQC_ILM_NVS_B_4_L01_AGTTCC_BD08PVACXX


title: SEQC_ILM_NVS_B_3_L01_TAGCTT_AD0902ACXX


title: SEQC_ILM_NVS_B_2_L08_GCCAAT_BD08PVACXX

value: GCCAAT


title: SEQC_ILM_NVS_B_2_L08_GCCAAT_AD0902ACXX


title: SEQC_ILM_NVS_B_3_L07_TAGCTT_BD08PVACXX


title: SEQC_ILM_NVS_B_2_L06_GCCAAT_AD0902ACXX


title: SEQC_ILM_NVS_B_3_L02_TAGCTT_BD08PVACXX


title: EryB

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description:
Sample 16
3' RNA-seq for digital gene expression quantitation

data_processing:
single end protocol ( some samples used read2 to read molecule barcodes only)
Illumina Casava1.8 software used for basecalling.
alignment: bowtie2 with deafult parameters
create tag directory using makeTagDirectory from HOMER tools (http://homer.salk.edu/homer/ngs/)
Quantifying RNA expression in genes: analyzeRNA.pl rna mm9 -d <tag directory> -norm 1e7 (HOMER)
Genome_build: mm9
Supplementary_files_format_and_content: 1256271tableS2.txt is a tab-delimited expression matrix that includes mRNA molecule count values for each Sample

molecule: polyA RNA

source_name: Erythrocytes B (Ery B)

growth_protocol: 12 to 15 weeks-old mice housed at the Weizmann Institute animal facility

extract_protocol:
Each mouse was euthanized and either leg bones or spleen, or both,  removed, homogenized to single cell suspension, red cells removed by selective lysis.
3' end mRNA libraries were prepared for sequencing using a method developed at Dr. Ido Amit's lab, Weizmann Institute of Science

treatment_protocol: Samples were extracted from unrteated, C57BL/6 female wild-type mice.

tag: organ

value: Spleen

tag: selection marker

tag: treatment

value: Erythrocytes B (Ery B)


title: SEQC_ILM_NVS_B_2_L05_GCCAAT_BD08PVACXX

value: NVS


title: SEQC_ILM_NVS_B_2_L06_GCCAAT_BD08PVACXX


title: SEQC_ILM_NVS_B_1_L08_CGATGT_AD0902ACXX

value: CGATGT


title: SEQC_ILM_NVS_B_1_L08_CGATGT_BD08PVACXX


title: SEQC_ILM_NVS_B_2_L02_GCCAAT_AD0902ACXX


title: SEQC_ILM_NVS_B_2_L01_GCCAAT_BD08PVACXX


title: SEQC_ILM_NVS_B_2_L04_GCCAAT_AD0902ACXX


title: SEQC_ILM_NVS_B_2_L04_GCCAAT_BD08PVACXX


title: SEQC_ILM_NVS_B_2_L01_GCCAAT_AD0902ACXX


title: SEQC_ILM_NVS_B_1_L07_CGATGT_BD08PVACXX


title: SEQC_ILM_NVS_B_2_L03_GCCAAT_AD0902ACXX


title: SEQC_ILM_NVS_B_2_L07_GCCAAT_BD08PVACXX


title: SEQC_ILM_NVS_B_2_L05_GCCAAT_AD0902ACXX


title: SEQC_ILM_NVS_B_1_L07_CGATGT_AD0902ACXX


title: SEQC_ILM_NVS_B_1_L05_CGATGT_BD08PVACXX


title: SEQC_ILM_NVS_B_1_L05_CGATGT_AD0902ACXX


title: SEQC_ILM_NVS_B_2_L03_GCCAAT_BD08PVACXX


title: SEQC_ILM_NVS_B_2_L02_GCCAAT_BD08PVACXX


title: SEQC_ILM_NVS_B_1_L06_CGATGT_BD08PVACXX


title: CD8

description:
Sample 12
3' RNA-seq for digital gene expression quantitation

source_name: T CD8+ cells

value: T CD8+ cells


title: SEQC_ILM_NVS_B_2_L07_GCCAAT_AD0902ACXX


title: EryA

description:
Sample 15
3' RNA-seq for digital gene expression quantitation

source_name: Erythrocytes A (Ery A)

value: Erythrocytes A (Ery A)


title: SEQC_ILM_NVS_B_1_L06_CGATGT_AD0902ACXX


title: SEQC_ILM_NVS_B_1_L04_CGATGT_BD08PVACXX


title: MEP

description:
Sample 14
3' RNA-seq for digital gene expression quantitation

source_name: Megakaryocitic erythroyd progenitor (MEP)

value: Bone Marrow

value: Lin-, ckit+, Sca1-, Flk2-, CD34-


title: SEQC_ILM_NVS_B_1_L04_CGATGT_AD0902ACXX


title: SEQC_ILM_NVS_B_1_L03_CGATGT_BD08PVACXX


title: NK

description:
Sample 13
3' RNA-seq for digital gene expression quantitation

source_name: NK Cells

value: NK Cells


title: B

description:
Sample 10
3' RNA-seq for digital gene expression quantitation

source_name: B cells

value: B cells


title: CD4

description:
Sample 11
3' RNA-seq for digital gene expression quantitation

source_name: T CD4+ cells

value: T CD4+ cells


title: Mono

description:
Sample 9
3' RNA-seq for digital gene expression quantitation

source_name: Monocytes

value: Monocytes


title: MF

description:
Sample 7
3' RNA-seq for digital gene expression quantitation

source_name: Bone Marrow Macrophages

value: Bone Marrow Macrophages


title: Granulocyte

description:
Sample 8
3' RNA-seq for digital gene expression quantitation

source_name: Granulocytes

value: Granulocytes


title: SEQC_ILM_NVS_B_1_L02_CGATGT_AD0902ACXX

value: B

value: Illumina HiSeq 2000


title: CMP

description:
Sample 5
3' RNA-seq for digital gene expression quantitation

source_name: Common Myeloid Progenitor (CMP)

value: Lin-, ckit+, Sca1-, CD34+, FcgRIII int

value: Common Myeloid Progenitor (CMP)


title: SEQC_ILM_NVS_B_1_L01_CGATGT_AD0902ACXX


title: SEQC_ILM_NVS_B_1_L01_CGATGT_BD08PVACXX


title: SEQC_ILM_NVS_B_1_L03_CGATGT_AD0902ACXX


title: CLP

description:
Sample 4
3' RNA-seq for digital gene expression quantitation

source_name: Common Lymphoid Progenitor (CLP)

value: Lin-, ckit+, Flk2+, Il7R+

value: Common Lymphoid Progenitor (CLP)


title: GMP

description:
Sample 6
3' RNA-seq for digital gene expression quantitation

source_name: Granulocyte Monocyte Progenitor (GMP)

value: Lin-, ckit+, Sca1-, CD34+, FcgRIII high

value: Granulocyte Monocyte Progenitor (GMP)


title: MPP

description:
Sample 3
3' RNA-seq for digital gene expression quantitation

source_name: Multipotent Progenitor (MPP)

value: Lin-, ckit+, Sca1+, Flk2+, CD34+

value: Multipotent Progenitor (MPP)


title: SEQC_ILM_NVS_A_4_L08_AGTCAA_AD0902ACXX

source_name: Universal Human Reference RNA (UHRR) from Stratagene

value: A

value: NVS

value: AGTCAA


title: SEQC_ILM_NVS_A_4_L08_AGTCAA_BD08PVACXX


title: SEQC_ILM_NVS_A_4_L07_AGTCAA_BD08PVACXX


title: HSC

description:
Sample 2
3' RNA-seq for digital gene expression quantitation

source_name: Hematopoietic Stem Cell (HSC)

value: Bone Marrow

value: Lin-, ckit+, Sca1+, Flk2-, CD34+

value: Hematopoietic Stem Cell (HSC)


title: SEQC_ILM_NVS_A_4_L07_AGTCAA_AD0902ACXX


title: LT-HSC

description:
Sample 1
3' RNA-seq for digital gene expression quantitation

source_name: Long Term Hematopoietic Stem Cell (LT-HSC)

value: Lin-, ckit+, Sca1+, Flk2-, CD34-


title: MEP ATAC_seq

description: ATAC-seq

data_processing:
Basecalls performed using CASAVA version 1.4
bowtie2 using default parameters
Using uniquely maped tag only
Genome_build: mm9

growth_protocol: Cells were sorted by FACS according to stablished markers

extract_protocol:
pelleted by centrifugation
two sets of 9 cycles of PCR using indexing primers from Nextera kit

value: Megakaryocitic erythroyd progenitor (MEP)

tag: passages

value: In vivo FACS purified cells


title: SEQC_ILM_NVS_A_4_L06_AGTCAA_BD08PVACXX

value: Illumina HiSeq 2000


title: CMP ATAC_seq

description: ATAC-seq

value: Common Myeloid Progenitor (CMP)


title: SEQC_ILM_NVS_B_1_L02_CGATGT_BD08PVACXX

source_name: Human Brain Reference RNA (HBRR) from Ambion

value: B

value: CGATGT


title: SEQC_ILM_NVS_A_4_L06_AGTCAA_AD0902ACXX


title: Lsk ATAC_seq

description: ATAC-seq

source_name: Lin-Sca1+Kit- bone marrow cells

value: Lin-Sca1+Kit- bone marrow cells


title: SEQC_ILM_NVS_A_4_L04_AGTCAA_BD08PVACXX


title: SEQC_ILM_NVS_A_4_L05_AGTCAA_AD0902ACXX


title: NK ATAC_seq

description: ATAC-seq

value: NK Cells


title: CD8 ATAC_seq

description: ATAC-seq

source_name: T CD8+ cells

value: T CD8+ cells


title: SEQC_ILM_NVS_A_4_L04_AGTCAA_AD0902ACXX


title: SEQC_ILM_NVS_A_4_L03_AGTCAA_AD0902ACXX


title: Monocytes ATAC_seq

description: ATAC-seq

value: Monocytes


title: SEQC_ILM_NVS_A_4_L02_AGTCAA_AD0902ACXX

value: A


title: SEQC_ILM_NVS_A_4_L01_AGTCAA_BD08PVACXX

value: NVS


title: H3K4me3_CLP.ucsc

data_processing:
Basecalls performed using CASAVA version 1.4
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using …; Scores represent …

growth_protocol: Cells were fixated and FACS sorted according to stablished markers

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
A new protocol (iChIP) was designed to perform iCHIP from small cell numbers

value: Common Lymphoid Progenitor (CLP)


title: SEQC_ILM_NVS_A_4_L05_AGTCAA_BD08PVACXX

value: AGTCAA


title: GMP ATAC_seq

description: ATAC-seq

value: Granulocyte Monocyte Progenitor (GMP)


title: SEQC_ILM_NVS_A_4_L02_AGTCAA_BD08PVACXX


title: H3K4me3_NK.ucsc


title: H3K4me3_CD8.ucsc


title: SEQC_ILM_NVS_A_4_L01_AGTCAA_AD0902ACXX


title: SEQC_ILM_NVS_A_3_L08_GATCAG_AD0902ACXX

value: GATCAG


title: SEQC_ILM_NVS_A_3_L07_GATCAG_BD08PVACXX


title: SEQC_ILM_NVS_A_3_L08_GATCAG_BD08PVACXX


title: H3K4me3_CD4.ucsc

value: T CD4+ cells


title: H3K4me3_MF.ucsc

value: Bone Marrow Macrophages


title: H3K4me3_B.ucsc

value: B cells

value: In vivo FACS purified cells


title: SEQC_ILM_NVS_A_3_L07_GATCAG_AD0902ACXX

value: Illumina HiSeq 2000


title: Granulocytes ATAC_seq

description: ATAC-seq

value: Granulocytes


title: H3K4me3_Mono.ucsc


title: SEQC_ILM_NVS_A_4_L03_AGTCAA_BD08PVACXX


title: SEQC_ILM_NVS_A_3_L06_GATCAG_BD08PVACXX


title: CD4 ATAC_seq

description: ATAC-seq


title: SEQC_ILM_NVS_A_3_L06_GATCAG_AD0902ACXX


title: H3K4me3_GN.ucsc


title: H3K4me3_EryB.ucsc

source_name: Erythrocytes B (Ery B)

value: Erythrocytes B (Ery B)


title: B ATAC_seq

description: ATAC-seq


title: SEQC_ILM_NVS_A_3_L05_GATCAG_BD08PVACXX


title: SEQC_ILM_NVS_A_3_L05_GATCAG_AD0902ACXX


title: H3K4me3_GMP.ucsc


title: SEQC_ILM_NVS_A_3_L04_GATCAG_BD08PVACXX


title: H3K4me3_MEP.ucsc

source_name: Megakaryocitic erythroyd progenitor (MEP)


title: H3K4me3_CMP.ucsc

value: Common Myeloid Progenitor (CMP)


title: SEQC_ILM_NVS_A_3_L04_GATCAG_AD0902ACXX


title: SEQC_ILM_NVS_A_3_L03_GATCAG_AD0902ACXX


title: H3K4me3_LT_HSC.ucsc

value: Long Term Hematopoietic Stem Cell (LT-HSC)


title: SEQC_ILM_NVS_A_3_L02_GATCAG_AD0902ACXX


title: H3K4me3_ST_HSC.ucsc

source_name: Short Term Hematopoietic Stem Cell (ST-HSC)


title: SEQC_ILM_NVS_A_3_L02_GATCAG_BD08PVACXX


title: H3K4me2_CLP.ucsc


title: H3K4me2_CD8.ucsc

value: T CD8+ cells


title: SEQC_ILM_NVS_A_3_L01_GATCAG_BD08PVACXX


title: H3K4me2_CD4.ucsc

source_name: T CD4+ cells


title: SEQC_ILM_NVS_A_2_L08_ACAGTG_BD08PVACXX

value: ACAGTG


title: SEQC_ILM_NVS_A_3_L01_GATCAG_AD0902ACXX

value: A


title: H3K4me3_EryA.ucsc

source_name: Erythrocytes A (Ery A)

value: Erythrocytes A (Ery A)


title: H3K4me2_NK.ucsc

source_name: NK Cells

value: NK Cells


title: SEQC_ILM_NVS_A_2_L08_ACAGTG_AD0902ACXX

value: NVS


title: H3K4me2_Mono.ucsc

source_name: Monocytes

value: Monocytes


title: H3K4me2_B.ucsc

source_name: B cells


title: SEQC_ILM_NVS_A_2_L07_ACAGTG_AD0902ACXX


title: SEQC_ILM_NVS_A_2_L07_ACAGTG_BD08PVACXX


title: H3K4me2_GN.ucsc

source_name: Granulocytes


title: SEQC_ILM_NVS_A_2_L06_ACAGTG_BD08PVACXX


title: H3K4me2_EryB.ucsc


title: H3K4me2_MF.ucsc

source_name: Bone Marrow Macrophages


title: SEQC_ILM_NVS_A_3_L03_GATCAG_BD08PVACXX

value: GATCAG


title: SEQC_ILM_NVS_A_2_L05_ACAGTG_BD08PVACXX


title: SEQC_ILM_NVS_A_2_L04_ACAGTG_BD08PVACXX


title: SEQC_ILM_NVS_A_2_L06_ACAGTG_AD0902ACXX


title: H3K4me3_MPP.ucsc

source_name: Multipotent Progenitor (MPP)

value: Multipotent Progenitor (MPP)


title: H3K4me2_EryA.ucsc


title: SEQC_ILM_NVS_A_2_L05_ACAGTG_AD0902ACXX

source_name: Universal Human Reference RNA (UHRR) from Stratagene


title: H3K4me2_GMP.ucsc

source_name: Granulocyte Monocyte Progenitor (GMP)

value: Granulocyte Monocyte Progenitor (GMP)


title: SEQC_ILM_NVS_A_2_L04_ACAGTG_AD0902ACXX


title: SEQC_ILM_NVS_A_2_L03_ACAGTG_BD08PVACXX


title: H3K4me2_MEP.ucsc

value: Megakaryocitic erythroyd progenitor (MEP)


title: H3K4me2_MPP.ucsc

value: In vivo FACS purified cells


title: SEQC_ILM_NVS_A_2_L03_ACAGTG_AD0902ACXX

value: Illumina HiSeq 2000


title: H3K4me2_CMP.ucsc

source_name: Common Myeloid Progenitor (CMP)


title: H3K4me2_ST_HSC.ucsc

value: Short Term Hematopoietic Stem Cell (ST-HSC)


title: H3K4me2_LT_HSC.ucsc

source_name: Long Term Hematopoietic Stem Cell (LT-HSC)


title: SEQC_ILM_NVS_A_2_L02_ACAGTG_BD08PVACXX


title: H3K4me1_CLP.ucsc

source_name: Common Lymphoid Progenitor (CLP)

value: Common Lymphoid Progenitor (CLP)


title: H3K4me1_NK.ucsc


title: SEQC_ILM_NVS_A_2_L01_ACAGTG_BD08PVACXX


title: SEQC_ILM_NVS_A_2_L01_ACAGTG_AD0902ACXX


title: H3K4me1_CD8.ucsc

source_name: T CD8+ cells


title: SEQC_ILM_NVS_A_2_L02_ACAGTG_AD0902ACXX


title: H3K4me1_CD4.ucsc

value: T CD4+ cells


title: SEQC_ILM_NVS_A_1_L08_ATCACG_AD0902ACXX

value: ATCACG


title: SEQC_ILM_NVS_A_1_L07_ATCACG_AD0902ACXX


title: H3K4me1_B.ucsc

value: B cells


title: H3K4me1_GN.ucsc

value: Granulocytes


title: SEQC_ILM_NVS_A_1_L06_ATCACG_BD08PVACXX

value: A


title: H3K4me1_Mono.ucsc


title: SEQC_ILM_NVS_A_1_L07_ATCACG_BD08PVACXX


title: H3K4me1_EryB.ucsc

source_name: Erythrocytes B (Ery B)

value: Erythrocytes B (Ery B)


title: SEQC_ILM_NVS_A_1_L06_ATCACG_AD0902ACXX


title: SEQC_ILM_NVS_A_1_L05_ATCACG_AD0902ACXX


title: H3K4me1_EryA.ucsc

value: Erythrocytes A (Ery A)


title: SEQC_ILM_NVS_A_1_L05_ATCACG_BD08PVACXX

value: NVS


title: H3K4me1_MEP.ucsc

source_name: Megakaryocitic erythroyd progenitor (MEP)


title: H3K4me1_GMP.ucsc


title: H3K4me1_CMP.ucsc

value: Common Myeloid Progenitor (CMP)


title: SEQC_ILM_NVS_A_1_L03_ATCACG_BD08PVACXX


title: SEQC_ILM_NVS_A_1_L04_ATCACG_AD0902ACXX


title: SEQC_ILM_NVS_A_1_L04_ATCACG_BD08PVACXX


title: SEQC_ILM_NVS_A_1_L08_ATCACG_BD08PVACXX


title: H3K4me1_MPP.ucsc


title: SEQC_ILM_NVS_A_1_L03_ATCACG_AD0902ACXX


title: SEQC_ILM_NVS_A_1_L02_ATCACG_BD08PVACXX


title: SEQC_ILM_NVS_A_1_L02_ATCACG_AD0902ACXX


title: H3K4me1_LT_HSC.ucsc

value: Long Term Hematopoietic Stem Cell (LT-HSC)


title: H3K27Ac_CLP.ucsc


title: H3K4me1_MF.ucsc

value: Bone Marrow Macrophages


title: H3K4me1_ST_HSC.ucsc

source_name: Short Term Hematopoietic Stem Cell (ST-HSC)


title: SEQC_ILM_NVS_A_1_L01_ATCACG_BD08PVACXX


title: SEQC_ILM_MAY_D_5_L08_ATTCCT_BD0E99ACXX

source_name: Mix of Sample A (UHRR) and Sample B (HBRR) (1:3)

value: D

value: MAY

value: ATTCCT


title: SEQC_ILM_NVS_A_1_L01_ATCACG_AD0902ACXX

value: Illumina HiSeq 2000


title: H3K27Ac_MF.ucsc

value: In vivo FACS purified cells


title: H3K27Ac_NK.ucsc

value: NK Cells


title: SEQC_ILM_MAY_D_5_L08_ATTCCT_AD0E8UACXX


title: SEQC_ILM_MAY_D_5_L07_ATTCCT_AD0E8UACXX


title: H3K27Ac_CD8.ucsc

value: T CD8+ cells


title: SEQC_ILM_MAY_D_5_L06_ATTCCT_BD0E99ACXX


title: H3K27Ac_B.ucsc


title: H3K27Ac_Mono.ucsc

value: Monocytes


title: H3K27Ac_GN.ucsc


title: SEQC_ILM_MAY_D_5_L06_ATTCCT_AD0E8UACXX


title: H3K27Ac_EryB.ucsc


title: SEQC_ILM_MAY_D_5_L05_ATTCCT_BD0E99ACXX


title: H3K27Ac_EryA.ucsc

source_name: Erythrocytes A (Ery A)


title: H3K27Ac_MEP.ucsc

value: Megakaryocitic erythroyd progenitor (MEP)


title: SEQC_ILM_MAY_D_5_L04_ATTCCT_BD0E99ACXX


title: H3K27Ac_GMP.ucsc

value: Granulocyte Monocyte Progenitor (GMP)


title: H3K27Ac_CMP.ucsc


title: SEQC_ILM_MAY_D_5_L03_ATTCCT_AD0E8UACXX


title: SEQC_ILM_MAY_D_5_L03_ATTCCT_BD0E99ACXX


title: H3K27Ac_MPP.ucsc

value: Multipotent Progenitor (MPP)


title: H3K27Ac_CD4.ucsc

source_name: T CD4+ cells

value: T CD4+ cells


title: SEQC_ILM_MAY_D_5_L02_ATTCCT_BD0E99ACXX


title: H3K27Ac_LT_HSC.ucsc


title: SEQC_ILM_MAY_D_5_L07_ATTCCT_BD0E99ACXX


title: H3K27Ac_ST_HSC.ucsc

value: Short Term Hematopoietic Stem Cell (ST-HSC)


title: SEQC_ILM_MAY_D_5_L01_ATTCCT_BD0E99ACXX


title: SEQC_ILM_MAY_D_4_L08_CCGTCC_AD0E8UACXX

value: CCGTCC


title: SEQC_ILM_MAY_D_5_L02_ATTCCT_AD0E8UACXX


title: SEQC_ILM_MAY_D_4_L08_CCGTCC_BD0E99ACXX


title: transcriptome_0

city: Beijing

first: wang

middle: xiu

address: NO.1 Beichen West Road, Chaoyang District, Beijing

institute: Institute of Microbiology, Chinese Academy of Sciences

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Pestalotiopsi ficiW106-1 whole genome using tophat
Fragments Per Kilobase of exon per Million mapped reads (FPKM) were calculated using cufflink
Genome_build: PFICI
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Pestalotiopsis fici W106-1

source_name: Hyphal cells and spores

extract_protocol:
sample were collected after 20 days,the total RNA was extracted with TriZol®.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: SEQC_ILM_MAY_D_4_L07_CCGTCC_BD0E99ACXX


title: SEQC_ILM_MAY_D_4_L07_CCGTCC_AD0E8UACXX


title: SEQC_ILM_MAY_D_4_L06_CCGTCC_AD0E8UACXX


title: SEQC_ILM_MAY_D_4_L06_CCGTCC_BD0E99ACXX


title: SEQC_ILM_MAY_D_4_L05_CCGTCC_BD0E99ACXX


title: SEQC_ILM_MAY_D_4_L05_CCGTCC_AD0E8UACXX


title: SEQC_ILM_MAY_D_5_L04_ATTCCT_AD0E8UACXX


title: SEQC_ILM_MAY_D_4_L04_CCGTCC_AD0E8UACXX


title: cid14Δ

city: Zürich

first: Claus

middle: M

last: Azzalin

address: Otto-Stern-Weg 3

department: Institute of Biochemistry

country: Switzerland

institute: ETH Zürich

description:
GQY30
PCR product corresponding to U6 snRNA was sequenced.

data_processing:
Basecalls performed using CASAVA version 1.8.2
Adapter sequences were removed using cutadapt
Reads were aligned to the indicated reference sequence using BLAT version 35x1. If applicable, read pairs where any of the reads matches the intron were removed.
Read pairs corresponding to full-length species were retained, and the terminal nucleotide sequence was extracted. The frequency of each terminal nucleotide sequence in the sample was computed.
Supplementary_files_format_and_content: txt files containing the frequency of each terminal nucleotide sequence

organism: Schizosaccharomyces pombe

source_name: fission yeast

growth_protocol: Logarithmically growing yeast cells  in liquid YES media at 30°C, shaking at 150 rpm

extract_protocol:
Hot phenol RNA dextraction protocol (Schmitt ME, Brown TA & Trumpower BL (1990) A rapid and simple method for preparation of RNA from Saccharomyces cerevisiae. Nucleic Acids Res. 18: 3091–3092)
PNK treated total RNA was purified with the RNA clean and concentrator kit (Zymo Research). 120 pmol of 5’ phosphorylated 3’ RACE adapter oligonucleotide (cctatagtgagtcgtattaattctgtgctcgc(tdd)) were mixed with 3 µg of purified RNA and ligated with T4 RNA ligase as above. 1 µg of ligated RNA was reverse-transcribed with Superscript III (Invitrogen) using adapter-specific oligonucleotide (GCGAGCACAGAATTAATACGACT). cDNA was PCR-amplified with the Phusion High-Fidelity PCR kit (Thermo Scientific) and PCR products were sequenced. Primers to amlify U6 snRNA (acactctttccctacacgacgctcttccgatctgatcttcggatcactttggt + ctcggcattcctgctgaaccgctcttccgatctcgcggatccgaattaatacgactcactatagg); Primers to amplify tagged U6 (acactctttccctacacgacgctcttccgatctgatcttcggatcactttgatcttcg + ctcggcattcctgctgaaccgctcttccgatctcgcggatccgaattaatacgactcactatagg)

tag: genotype/variation


title: mpn1Δ

description:
GQY27
PCR product corresponding to U6 snRNA was sequenced.


title: SEQC_ILM_MAY_D_4_L03_CCGTCC_AD0E8UACXX


title: SEQC_ILM_MAY_D_4_L03_CCGTCC_BD0E99ACXX


title: rrp6Δ (NO PNK)

description:
GQY32
PCR product corresponding to U6 snRNA was sequenced. PNK treatment was omited

value: rrp6Δ (NO PNK)


title: SEQC_ILM_MAY_D_4_L02_CCGTCC_BD0E99ACXX


title: SEQC_ILM_MAY_D_4_L01_CCGTCC_BD0E99ACXX


title: rrp6Δ

description:
GQY28
PCR product corresponding to U6 snRNA was sequenced.


title: SEQC_ROC_SQW_B_1_R02_HJ3EX7N02

source_name: Human Brain Reference RNA (HBRR) from Ambion

value: B

value: 454 GS FLX Titanium

value: SQW


title: SEQC_ILM_MAY_D_3_L08_CTTGTA_BD0E99ACXX

value: D

value: MAY

value: CTTGTA


title: SEQC_ILM_MAY_D_4_L01_CCGTCC_AD0E8UACXX

value: Illumina HiSeq 2000


title: wt

description:
GQY26
PCR product corresponding to U6 snRNA was sequenced.

value: wt


title: SEQC_ILM_MAY_D_5_L01_ATTCCT_AD0E8UACXX

value: ATTCCT


title: SEQC_ROC_SQW_B_1_R01_HJ3EX7N01


title: SEQC_ROC_SQW_A_1_R01_HJV2COY01

value: A


title: SEQC_ILM_MAY_D_3_L07_CTTGTA_BD0E99ACXX


title: cid14Δmpn1Δ

description:
GQY31
PCR product corresponding to U6 snRNA was sequenced.


title: SEQC_ILM_MAY_D_3_L08_CTTGTA_AD0E8UACXX


title: SEQC_ROC_NYU_A_1_R02_HK7QKYM02

value: NYU


title: SEQC_ROC_SQW_A_1_R02_HJV2COY02


title: mpn1Δrrp6Δ

description:
GQY29
PCR product corresponding to U6 snRNA was sequenced.


title: SEQC_ILM_MAY_D_3_L07_CTTGTA_AD0E8UACXX


title: SEQC_ILM_MAY_D_3_L06_CTTGTA_BD0E99ACXX


title: SEQC_ROC_NYU_B_1_R01_HLIUF4W01


title: SEQC_ILM_MAY_D_4_L04_CCGTCC_BD0E99ACXX


title: SEQC_ROC_MGP_B_1_R02_HKJMKOB02

value: MGP


title: SEQC_ILM_MAY_D_3_L06_CTTGTA_AD0E8UACXX


title: SEQC_ILM_MAY_D_3_L05_CTTGTA_BD0E99ACXX


title: SEQC_ROC_MGP_B_1_R01_HKJMKOB01


title: SEQC_ROC_MGP_A_1_R02_HKGG12G02


title: SEQC_ILM_MAY_D_3_L05_CTTGTA_AD0E8UACXX


title: SEQC_ILM_MAY_D_4_L02_CCGTCC_AD0E8UACXX


title: SEQC_ILM_MAY_D_3_L04_CTTGTA_BD0E99ACXX


title: SEQC_ROC_MGP_A_1_R01_HKGG12G01


title: SEQC_ROC_NYU_B_1_R02_HLIUF4W02


title: SEQC_ROC_NYU_A_1_R01_HK7QKYM01


title: SEQC_ILM_MAY_D_3_L03_CTTGTA_BD0E99ACXX


title: SEQC_ILM_MAY_D_3_L03_CTTGTA_AD0E8UACXX


title: SEQC_ILM_MAY_D_3_L04_CTTGTA_AD0E8UACXX


title: SEQC_ILM_MAY_D_3_L02_CTTGTA_BD0E99ACXX


title: SEQC_ILM_MAY_D_3_L02_CTTGTA_AD0E8UACXX


title: SEQC_ILM_MAY_D_3_L01_CTTGTA_AD0E8UACXX


title: SEQC_ILM_MAY_D_5_L05_ATTCCT_AD0E8UACXX


title: SEQC_ILM_MAY_D_2_L08_ACTTGA_BD0E99ACXX

value: ACTTGA


title: SEQC_ILM_MAY_D_3_L01_CTTGTA_BD0E99ACXX


title: SEQC_ILM_MAY_D_2_L08_ACTTGA_AD0E8UACXX


title: SEQC_ILM_MAY_D_2_L07_ACTTGA_BD0E99ACXX


title: SEQC_ILM_MAY_D_2_L07_ACTTGA_AD0E8UACXX


title: SEQC_ILM_MAY_D_2_L04_ACTTGA_BD0E99ACXX


title: SEQC_ILM_MAY_D_2_L06_ACTTGA_AD0E8UACXX


title: SEQC_ILM_MAY_D_2_L06_ACTTGA_BD0E99ACXX


title: SEQC_ILM_MAY_D_2_L05_ACTTGA_BD0E99ACXX


title: SEQC_ILM_MAY_D_2_L04_ACTTGA_AD0E8UACXX


title: SEQC_ILM_MAY_D_2_L05_ACTTGA_AD0E8UACXX


title: SEQC_ILM_MAY_D_2_L02_ACTTGA_AD0E8UACXX


title: SEQC_ILM_MAY_D_2_L02_ACTTGA_BD0E99ACXX


title: SEQC_ILM_MAY_D_2_L03_ACTTGA_BD0E99ACXX


title: SEQC_ILM_MAY_D_2_L03_ACTTGA_AD0E8UACXX


title: SEQC_ILM_MAY_D_2_L01_ACTTGA_AD0E8UACXX


title: SEQC_ILM_MAY_D_2_L01_ACTTGA_BD0E99ACXX


title: SEQC_ILM_MAY_D_1_L08_TGACCA_BD0E99ACXX

value: TGACCA


title: SEQC_ILM_MAY_D_1_L07_TGACCA_BD0E99ACXX


title: SEQC_ILM_MAY_D_1_L06_TGACCA_BD0E99ACXX


title: SEQC_ILM_MAY_D_1_L05_TGACCA_AD0E8UACXX


title: SEQC_ILM_MAY_D_1_L08_TGACCA_AD0E8UACXX


title: SEQC_ILM_MAY_D_1_L04_TGACCA_BD0E99ACXX


title: SEQC_ILM_MAY_D_1_L05_TGACCA_BD0E99ACXX


title: SEQC_ILM_MAY_D_1_L01_TGACCA_BD0E99ACXX


title: SEQC_ILM_MAY_D_1_L04_TGACCA_AD0E8UACXX


title: SEQC_ILM_MAY_D_1_L07_TGACCA_AD0E8UACXX


title: SEQC_ILM_MAY_D_1_L02_TGACCA_BD0E99ACXX


title: SEQC_ILM_MAY_D_1_L02_TGACCA_AD0E8UACXX


title: SEQC_ILM_MAY_C_5_L08_ACTGAT_BD0E99ACXX

source_name: Mix of Sample A (UHRR) and Sample B (HBRR) (3:1)

value: C

value: ACTGAT


title: SEQC_ILM_MAY_D_1_L01_TGACCA_AD0E8UACXX


title: SEQC_ILM_MAY_C_5_L07_ACTGAT_AD0E8UACXX


title: SEQC_ILM_MAY_D_1_L03_TGACCA_BD0E99ACXX


title: SEQC_ILM_MAY_C_5_L05_ACTGAT_BD0E99ACXX


title: SEQC_ILM_MAY_C_5_L04_ACTGAT_BD0E99ACXX


title: SEQC_ILM_MAY_C_5_L05_ACTGAT_AD0E8UACXX


title: SEQC_ILM_MAY_C_5_L07_ACTGAT_BD0E99ACXX


title: SEQC_ILM_MAY_C_5_L06_ACTGAT_AD0E8UACXX


title: SEQC_ILM_MAY_C_5_L06_ACTGAT_BD0E99ACXX


title: SEQC_ILM_MAY_C_5_L04_ACTGAT_AD0E8UACXX


title: SEQC_ILM_MAY_C_5_L02_ACTGAT_BD0E99ACXX


title: SEQC_ILM_MAY_D_1_L06_TGACCA_AD0E8UACXX


title: SEQC_ILM_MAY_D_1_L03_TGACCA_AD0E8UACXX


title: SEQC_ILM_MAY_C_5_L02_ACTGAT_AD0E8UACXX


title: SEQC_ILM_MAY_C_5_L01_ACTGAT_BD0E99ACXX


title: SEQC_ILM_MAY_C_5_L01_ACTGAT_AD0E8UACXX


title: SEQC_ILM_MAY_C_4_L08_ATGTCA_BD0E99ACXX

value: ATGTCA


title: SEQC_ILM_MAY_C_4_L07_ATGTCA_BD0E99ACXX


title: SEQC_ILM_MAY_C_4_L07_ATGTCA_AD0E8UACXX


title: SEQC_ILM_MAY_C_5_L08_ACTGAT_AD0E8UACXX


title: SEQC_ILM_MAY_C_4_L08_ATGTCA_AD0E8UACXX


title: SEQC_ILM_MAY_C_4_L04_ATGTCA_AD0E8UACXX


title: SEQC_ILM_MAY_C_4_L05_ATGTCA_BD0E99ACXX


title: SEQC_ILM_MAY_C_4_L06_ATGTCA_AD0E8UACXX


title: SEQC_ILM_MAY_C_4_L06_ATGTCA_BD0E99ACXX


title: SEQC_ILM_MAY_C_4_L03_ATGTCA_BD0E99ACXX


title: SEQC_ILM_MAY_C_4_L02_ATGTCA_AD0E8UACXX


title: SEQC_ILM_MAY_C_4_L02_ATGTCA_BD0E99ACXX


title: SEQC_ILM_MAY_C_4_L03_ATGTCA_AD0E8UACXX


title: SEQC_ILM_MAY_C_4_L01_ATGTCA_AD0E8UACXX


title: SEQC_ILM_MAY_C_5_L03_ACTGAT_BD0E99ACXX


title: SEQC_ILM_MAY_C_3_L07_GGCTAC_BD0E99ACXX

value: GGCTAC


title: SEQC_ILM_MAY_C_3_L08_GGCTAC_BD0E99ACXX