title: E18_5_wholeThy_2

status: Public on Jun 05 2018

city: Worcester

first: Rene

last: Maehr

state: MA

address: 55 Lake Ave N

department: Program in Molecular Medicine

institute: UMass Medical School

description: Read 1 contains the barcode and Read 2 contains biological sequence

data_processing:
Base calling was performed using Illumina RTA version 2.4.11.
FASTQ's from resequenced runs were concatenated prior to processing.
Alignment and quantification were performed using the STAR aligner v2.4.2, Picard tools v1.96, Samtools v1.3, and Drop-seq tools v1.0.
Analysis step: Convert to SAM  Software package:  Picard tools   Command name:  FastqToSam.jar Parameters used:  --
Analysis step: Tag cell barcode  Software package:  DropSeq tools  Command name: TagBamWithReadSequenceExtended  Parameters used:  BASE_QUALITY=10, BARCODED_READ=1, NUM_BASES_BELOW_QUALITY=1,  DISCARD_READ=False
Analysis step: Tag molecular barcode  Software package:  DropSeq tools  Command name: TagBamWithReadSequenceExtended Parameters used:  BASE_QUALITY=10, BARCODED_READ=1, NUM_BASES_BELOW_QUALITY=1,  DISCARD_READ=True
Analysis step: Remove low-quality barcodes  Software package:  DropSeq tools  Command name:   FilterBAM  Parameters used:     --
Analysis step: Remove polyA tail  Software package:  DropSeq tools  Command name:   PolyATrimmer               Parameters used:  MISMATCHES=0, NUM_BASES=6
Analysis step: Convert to FASTQ  Software package:  Picard tools   Command name:   SamToFastq.jar             Parameters used:     --
Analysis step: Align reads to exome  Software package:  STAR  Command name:   --  Parameters used: --
Analysis step: Sort BAM to speed merging  Software package:  Picard tools  Command name:   SortSam.jar                 Parameters used:     --
Analysis step: Merge barcode and alignment info  Software package:  Picard tools  Command name:   MergeBamAlignment.jar       Parameters used:  INCLUDE_SECONDARY_ALIGNMENTS=False
Analysis step: Label read with exon  Software package:  DropSeq tools  Command name:   TagReadWithGeneExon        Parameters used:     --
Analysis step: Screen for bead errors  Software package:  DropSeq tools  Command name:  DetectBeadSynthesisErrors  Parameters used: NUM_BARCODES=2000
Analysis step: Form DGE matrix  Software package:  DropSeq tools  Command name:   DigitalExpression          Parameters used: MIN_NUM_GENES_PER_CELL=1000
The procedure was repeated with a  T-Cell receptor (TCR) contig added to the reference genome and the following two steps were used to generate improved TCR counts.
Analysis step: Subset reads aligning to TCR contig Software package: Samtools Command name: view Parameters used:  -bh
Analysis step: Form TCR-specific DGE matrix  Software package:  DropSeq tools  Command name:   DigitalExpression          Parameters used: MIN_NUM_GENES_PER_CELL=1 READ_MQ=1
Genome_build: For initial DGE calculations, mm10 was used. For TCR-specific DGE's, an artificial TCR contig was added.  The FASTA with the TCR sequence is available on the series record.
Supplementary_files_format_and_content: Processed files are digital gene expression matrices containing UMI counts. They are represented as dense matrices in (gzipped) tab-delimited text files. Each column is labeled with a cell barcode and each row is labeled with a gene.

growth_protocol: Thymic lobes were isolated from timed mouse embryos.

extract_protocol:
Thymic lobes were mechanically isolated, dissociated in trypsin, depleted of RBC's (only some samples), washed and stained with 7AAD cell viability dye, and 7AAD negative single cells were sorted on a BD FACSARIA.
Libraries were prepared according to the Drop-seq lab protocol version 3.1 (Macosko and Goldman, December 2015, McCarroll Lab).  Final libraries were sequenced on an Illumina NextSeq 500 using high-output 75-cycle kits.

tag: background strain

tag: genotype

value: wildtype

value: thymus

tag: developmental day

tag: rbc lysis buffer

value: eBioscience Cat# 00-4333-57

tag: treatment


title: P0_wholeThy_2

type: SRA

country: USA

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

tag: tissue


title: E18_5_wholeThy_1


title: Wild type Liver_rep3 [WL1137]

status: Public on Aug 09 2018

city: Pittsburgh

first: Edward

middle: V

last: Prochownik

state: PA

address: 4401 Penn Ave.

department: Division of Hematology/Oncology

institute: Children’s Hospital of Pittsburgh of UPMC

data_processing:
Raw sequencing reads were quality checked for potential sequencing issues and contaminants using FastQC (Babraham Bioinformatics, Inc, Cambridge, UK.). Adapter sequences, primers, Ns, and reads with quality score below 28 were trimmed using fastq-mcf of ea-utils and PRINSEQ (http://prinseq.sourceforge. net/manual.html). Reads with a remaining length of less than 20 bp after trimming were discarded. Paired end reads were mapped to the mouse genome (m10) using TopHat (http://ccb.jhu.edu/software/tophat/index.shtml) in a strand specific manner. Read coverage on forward and reverse strands for genome browser visualization was computed using SAMtools, BEDtools, and UCSC Genome Browser utilities. Pairwise differential expression was quantified using Cuffdiff and DESeq [4, 5]. Cufflinks was used to determine FPKM levels for each gene from the TopHat alignment and was used as input for Cuffdiff. Significant differentially expressed genes were determined by adjusted P-value with a threshold of 0.05. DESeq was utilized
for raw read counts, which were calculated by HTSeq based on the STAR alignment (http://www-huber.embl.de/users /anders/HTSeq/doc/count.html). Read counts were then normalized across all samples and significant differentially expressed genes were determined by adjusted P-value with a threshold of 0.05
Genome_build: mm10
Supplementary_files_format_and_content: cufflinks output including genes.fpkm_tracking and isoforms.fpkm_tracking values

molecule: total RNA

source_name: Wild type_liver

extract_protocol:
Total RNAs were extracted using Qiagen RNeasy columns (Valencia, CA). Each RNA sample was assessed for quality and quantity using a Qubit 2.0 fluorometer and Agilent Bioanalyzer TapeStation 2200. The Sample preparation was replicated using Illumina TruSeq Stranded mRNA kit (San Diego, CA). mRNA was used to generate poly-A+ libraries using oligo-dT beads following 2 rounds of poly-A selection.
mRNA was fragmented to an average length of 260 nt by magnesium-catalyzed hydrolysis at 940C and then converted into cDNA by random priming. cDNA 3’ ends were adenylated, followed by adaptor ligation and a 9-cycle PCR to enrich DNA fragments. cDNA libraries were then validated using KAPA Biosystems (Wilmington, MA) primer premix kit with Illumina-compatible DNA primers on the Qubit 2.0 fluorometer and Tapestation 2200 systems described above. Libraries were diluted in 0.1% Tween 20 to concentrations of 2 nM for stabilization. The cDNA libraries were then pooled to final concentrations of 2.5 pM.

tag: strain background

tag: genotype/variation

value: WT

value: liver


title: P0_wholeThy_1


title: Wild type Liver_rep2 [WL1132]


title: E17_5_wholeThy_2


title: E17_5_wholeThy_1


title: E15_5_wholeThy_1


title: E16_5_wholeThy_2


title: E14_5_wholeThy_2


title: E16_5_wholeThy_1


title: E14_5_wholeThy_1


title: E16_5_wholeThy_3


title: E13_5_wholeThy_3


title: E12_5_wholeThy_venus_3


title: Wild type Liver_rep5 [WL1153]


title: E13_5_wholeThy_1


title: E13_5_wholeThy_2


title: E12_5_wholeThy_venus_1


title: E15_5_wholeThy_2


title: E12_5_wholeThy_venus_2


title: Sample2460_BCellData

status: Public on Apr 18 2018

type: RNA

city: Newcastle upon Tyne

first: Arthur

last: Pratt

address: Framlington Place

department: Faculty of Medical Sciences

country: United Kingdom

institute: Newcastle University

description:
3999319005_J_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis

hyb_protocol: Illumina HT12 BeadChip

scan_protocol: Illumina iScan

data_processing: Normalisation via VST (Variance Stabilising Transformation and RSN (Robust Spline Normalisation)

label: biotin

organism: Homo sapiens

source_name: purified peripheral blood CD19+ B cells

label_protocol: cRNA generated from 250ng total RNA using Illumina TotalPrep RNA Amplification kit

growth_protocol: Peripheral blood mononuclear cells first isolated by density centrifugation on Lymphoprep (Axis-Shield Diagnostics, Dundee, UK) underwent positive selection using anti-CD19 magnetic microbeads (Miltenyi Biotec, Bergisch, Gladback, Germany); median cell purity was 96.4% by flow cytometry. Total B lymphocyte RNA was immediately extracted using the AllPrep DNA/RNA Mini kit (Qiagen GmbH, Germany), then quality controlled using an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, California, USA). The median RNA integrity number of samples used was 9.4

extract_protocol: AllPrep RNA extraction kit (Qiagen)

treatment_protocol: No ex vivo treatment

value: peripheral blood

tag: cell type

value: CD19+ B cells

value: Rheumatoid Arthritis

tag: Sex

value: F


title: Sample2361_BCellData

description:
9477874154_J_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Osteoarthritis

value: Osteoarthritis

value: M


title: Sample2745_BCellData

description:
3999350089_A_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample2360_BCellData

description:
3999350077_J_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Osteoarthritis


title: Sample2734_BCellData

description:
3999350063_J_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample2358_BCellData

description:
3999350077_H_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Non-Inflammatory

value: Non-Inflammatory


title: Sample2744_BCellData

description:
3999350063_L_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample2366_BCellData

description:
3999350077_L_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Other Inflammatory Arthritis

value: Other Inflammatory Arthritis


title: Sample2355_BCellData

description:
3999350077_D_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Non-Inflammatory


title: Sample2325_BCellData

description:
3999350077_A_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Osteoarthritis


title: Sample2770_BCellData

description:
3999350089_G_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample2321_BCellData

description:
3999350076_L_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Other Inflammatory Arthritis


title: Sample2492_BCellData

description:
3999350063_A_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample2299_BCellData

description:
3999350076_C_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Lupus/Other CTD-Associated

value: Lupus/Other CTD-Associated


title: Sample2347_BCellData

description:
3999350077_K_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Non-Inflammatory


title: Sample2310_BCellData

description:
3999350076_B_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample2370_BCellData

description:
3999319005_G_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Other Inflammatory Arthritis


title: Sample2468_BCellData

description:
3999319005_L_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample2290_BCellData

description:
3999350075_H_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Osteoarthritis


title: Sample2294_BCellData

description:
3999350075_J_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample2327_BCellData

description:
3999350077_C_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample2277_BCellData

description:
3999350075_K_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Other Inflammatory Arthritis


title: Sample2279_BCellData

description:
3999350075_B_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Non-Inflammatory


title: Sample2300_BCellData

description:
3999350076_E_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample2274_BCellData

description:
3999350075_I_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Non-Inflammatory


title: Sample2318_BCellData

description:
3999350076_H_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample2357_BCellData

description:
3999350077_F_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample2320_BCellData

description:
3999350076_J_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample2298_BCellData

description:
3999350076_A_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Osteoarthritis


title: Sample2269_BCellData

description:
3999350075_E_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Other Inflammatory Arthritis


title: Sample2265_BCellData

description:
3999350075_C_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Psoriatic Arthritis

value: Psoriatic Arthritis


title: Sample2335_BCellData

description:
3999350077_G_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Osteoarthritis


title: Sample2218_BCellData

description:
3999319015_C_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Ankylosing Spondylitis

value: Ankylosing Spondylitis


title: Sample2272_BCellData

description:
3999350075_G_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Non-Inflammatory


title: Sample2249_BCellData

description:
3999319015_F_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Other Inflammatory Arthritis


title: Sample2206_BCellData

description:
3999350115_H_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample2215_BCellData

description:
3999350115_L_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis

value: Undifferentiated Inflammatory Arthritis


title: Sample2188_BCellData

description:
3999350115_C_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Lupus/Other CTD-Associated


title: Sample2224_BCellData

description:
3999319015_G_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Other Inflammatory Arthritis


title: Sample2247_BCellData

description:
3999319015_D_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Osteoarthritis


title: Sample2255_BCellData

description:
3999319015_H_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample2216_BCellData

description:
3999319015_A_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Non-Inflammatory


title: Sample2234_BCellData

description:
3999319015_B_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Other Inflammatory Arthritis


title: Sample2219_BCellData

description:
3999319015_E_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Osteoarthritis


title: Sample2204_BCellData

description:
3999350115_F_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Psoriatic Arthritis


title: Sample2163_BCellData

description:
3999319008_D_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Osteoarthritis


title: Sample2171_BCellData

description:
3999319008_H_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Osteoarthritis


title: Sample2198_BCellData

description:
3999350115_I_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Psoriatic Arthritis


title: Sample2186_BCellData

description:
3999350115_A_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Non-Inflammatory


title: Sample2195_BCellData

description:
9477874154_B_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Osteoarthritis


title: Sample2172_BCellData

description:
3999319008_J_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Non-Inflammatory


title: Sample2169_BCellData

description:
3999319008_F_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Non-Inflammatory


title: Sample2140_BCellData

description:
3999319008_E_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample2138_BCellData

description:
3999319008_C_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample2127_BCellData

description:
3999350128_J_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Ankylosing Spondylitis


title: Sample2158_BCellData

description:
3999319008_K_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Non-Inflammatory


title: Sample2135_BCellData

description:
3999319008_A_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Non-Inflammatory


title: Sample2162_BCellData

description:
3999319008_B_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Osteoarthritis


title: Sample2110_BCellData

description:
3999350128_H_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample2317_BCellData

description:
3999350076_F_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Osteoarthritis


title: Sample2075_BCellData

description:
3999319019_J_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Reactive Arthritis

value: Reactive Arthritis


title: Sample2067_BCellData

description:
3999319019_F_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Unknown

value: Unknown


title: Sample2088_BCellData

description:
3999350128_E_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Non-Inflammatory


title: Sample2099_BCellData

description:
3999350128_K_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Non-Inflammatory


title: Sample2094_BCellData

description:
3999350128_G_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Osteoarthritis


title: Sample2021_BCellData

description:
3999319011_A_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Non-Inflammatory


title: Sample2033_BCellData

description:
3999319011_B_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Non-Inflammatory


title: Sample2096_BCellData

description:
3999350128_I_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Non-Inflammatory


title: Sample1097_BCellData

description:
3999319034_B_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample2101_BCellData

description:
3999350128_B_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Non-Inflammatory


title: Sample1096_BCellData

description:
3999319034_K_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Non-Inflammatory


title: Sample2063_BCellData

description:
3999319019_B_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Psoriatic Arthritis


title: Sample2014_BCellData

description:
3999319034_L_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Reactive Arthritis


title: Sample1084_BCellData

description:
3999319034_A_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Non-Inflammatory


title: Sample1086_BCellData

description:
3999350089_D_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample2053_BCellData

description:
3999319019_E_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Non-Inflammatory


title: Sample1059_BCellData

description:
3999319016_G_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Osteoarthritis


title: Sample1068_BCellData

description:
3999319016_I_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Osteoarthritis


title: Sample2042_BCellData

description:
3999319011_H_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample1071_BCellData

description:
3999319016_D_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Osteoarthritis


title: Sample1079_BCellData

description:
9477874154_G_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Osteoarthritis


title: Sample1050_BCellData

description:
3999319016_A_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Crystal Arthritis

value: Crystal Arthritis


title: Sample1069_BCellData

description:
3999319016_K_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Osteoarthritis


title: Sample1056_BCellData

description:
3999319016_E_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Osteoarthritis


title: Sample1045_BCellData

description:
3999319021_L_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Osteoarthritis


title: Sample1040_BCellData

description:
3999319036_D_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Psoriatic Arthritis


title: Sample1042_BCellData

description:
3999319021_G_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample1036_BCellData

description:
3999350082_G_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Osteoarthritis


title: Sample984_BCellData

description:
3999350082_H_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Non-Inflammatory


title: Sample997_BCellData

description:
3999350089_B_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample1018_BCellData

description:
3999319021_J_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Psoriatic Arthritis


title: Sample1014_BCellData

description:
3999319036_B_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Psoriatic Arthritis


title: Sample1015_BCellData

description:
3999319021_E_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Osteoarthritis


title: Sample2055_BCellData

description:
3999319019_I_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Psoriatic Arthritis


title: Sample1012_BCellData

description:
3999350082_J_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Osteoarthritis


title: Sample945_BCellData

description:
3999853061_A_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Unknown


title: Sample1033_BCellData

description:
3999319007_D_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Non-Inflammatory


title: Sample931_BCellData

description:
3999319036_G_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample907_BCellData

description:
3999319021_B_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample934_BCellData

description:
9477874155_C_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample906_BCellData

description:
3999319036_J_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Non-Inflammatory


title: Sample959_BCellData

description:
3999319036_I_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Non-Inflammatory


title: Sample2184_BCellData

description:
3999319008_L_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample913_BCellData

description:
9477874155_E_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Non-Inflammatory


title: Sample935_BCellData

description:
3999319021_D_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Psoriatic Arthritis


title: Sample2214_BCellData

description:
3999350115_J_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Non-Inflammatory


title: Sample2106_BCellData

description:
3999350128_F_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample1011_BCellData

description:
3999350082_E_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Osteoarthritis


title: Sample897_BCellData

description:
3999319007_E_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Non-Inflammatory


title: Sample968_BCellData

description:
9477874154_C_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample883_BCellData

description:
3999319021_K_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Osteoarthritis


title: Sample899_BCellData

description:
3999350082_B_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Osteoarthritis


title: Sample810_BCellData

description:
9477874155_G_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Rheumatoid Arthritis


title: Sample849_BCellData

description:
3999319021_I_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Non-Inflammatory


title: Sample873_BCellData

description:
3999319007_C_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Non-Inflammatory


title: Sample2025_BCellData

description:
3999319011_E_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Undifferentiated Spondylo-Arthropathy

value: Undifferentiated Spondylo-Arthropathy


title: EA2255_ACPApRA

status: Public on Apr 03 2018

hyb_protocol: cRNA was hybridized to the Illumina WG6 (version 4) BeadChip (Illumina, San Diego, following the manufacturer’s protocol.

scan_protocol: Illumina BeadArray Reader as per Illumina protocol.

data_processing: Normalisation of component dataset[s] (which, in some cases included raw data extracted from Pratt AG et al 2012; GEO accession GSE20098) was first carried out by robust spline normalisation (RSN) , and variance stability transformation (VST) (Du P et al 2008 Bioinformatics; Lin SM et al 2008 Nucleic Acids Res). Unique IDs for defined analyses are listed in relevant manuscript text. Where required data were merged using InSilicoMerging Bioconductor package (Taminau J et al 2012 BMC Bioinformatics), and batch correction was carried out by linear modelling Batch correction was carried out by linear modelling  (Ritchie ME et al 2015 Nucleic Acids Res).

source_name: ACPApRA_Blood CD4+ T Cells

label_protocol: 50ng RNA was reverse transcribed into cRNA, and biotin-UTP labeled, using the Illumina TotalPrep RNA Amplification Kit (Ambion, Texas).

extract_protocol: Monocytes were first depleted by immunorosetting (Rosettesep Human Monocyte depletion cocktail, Stemcell Technologies Inc., Vancouver, non-RA inflammatory arthritisanada), and remaining cells underwent positive selection using Easisep whole blood CD4+ positive selection kit reagents in conjunction with the Robosep automated cell separator (Stemcell). CD4+ T-cell purity was determined using standard flow cytometry techniques; FITC-conjugated anti-CD4 and PE-conjugated anti-CD14 antibodies were used (Beckton Dickinson, New Jersey, USA). RNA was immediately extracted from CD4+ T-cell isolates using RNeasy MINI kits (Qiagen GmbH, Germany), incorporating an “on-column” DNA digestion step.

treatment_protocol: Between 0900 and 1200hrs during the clinic appointment, 15ml peripheral whole blood was drawn into EDTA tubes (Greiner Bio-One, ACPA- RAustria) and stored at room temperature for a maximum of 4 hours before processing.

tag: gender

tag: age (yrs)

tag: diagnostic category

value: ACPA-pos RA

value: CD4+ T-cell


title: Sample881_BCellData

description:
3999319036_C_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Reactive Arthritis

value: peripheral blood

value: CD19+ B cells


title: EA2149_NRAIA

source_name: NRAIA_Blood CD4+ T Cells

value: Non-RA inflammatory arthritis (NRAIA) - includes Code A 4-11)


title: EA2154_ACPApRA

value: F


title: EA2014_NRAIA


title: EA1056_NiA

source_name: NiA_Blood CD4+ T Cells

value: Non-inflammatory arthritis/arthalgia - includes Code A 1 & 2


title: EA2234_NRAIA

value: M


title: EA1086_ACPApRA


title: EA1059_NiA


title: EA0830_NRAIA


title: EA2103_NiA


title: EA0850_NiA


title: EA2033_NiA


title: EA2124_NiA


title: EA2045_ACPApRA


title: EA2110_ACPApRA


title: EA2021_NiA


title: EA2101_NiA


title: EA0931_ACPApRA


title: EA2099_NiA


title: EA1028_NRAIA


title: EA2096_NiA


title: EA2063_NRAIA


title: EA2135_NiA


title: EA1079_NiA


title: EA1084_NiA


title: EA1029_ACPApRA


title: Sample2161_BCellData

description:
9477874154_K_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Osteoarthritis

value: Osteoarthritis


title: EA2094_NiA


title: EA1045_NiA


title: EA1033_NiA


title: EA1036_NiA


title: EA1040_NRAIA


title: EA1006_NiA


title: EA0997_ACPApRA


title: EA0968_ACPAnRA

source_name: ACPAnRA_Blood CD4+ T Cells

value: ACPA-neg RA


title: Sample842_BCellData

description:
3999350082_I_Grn.idat
Freshly isolated and purified peripheral blood CD19+ B cells - Enteropathic Arthritis

value: Enteropathic Arthritis


title: EA0950_NRAIA


title: EA2088_NiA


title: EA2128_NiA


title: EA2053_NiA


title: EA2055_NRAIA


title: EA1018_NRAIA


title: EA1015_NiA


title: EA1011_NiA


title: EA1012_NiA


title: EA2131_NiA


title: EA2022_NRAIA


title: EA0944_ACPAnRA


title: EA1014_NRAIA


title: EA2025_NRAIA


title: EA1096_NiA


title: EA0925_NiA


title: EA0914_NiA


title: EA1068_NiA


title: EA0890_NRAIA


title: EA0892_ACPApRA


title: EA0863_NiA


title: EA1069_NiA


title: EA0861_NRAIA


title: EA0873_NiA


title: EA1071_NiA


title: EA0857_NRAIA


title: EA0893_NRAIA


title: EA0860_NiA


title: EA0924_NRAIA


title: EA0884_NRAIA


title: EA0959_NiA


title: EA0957_ACPApRA


title: EA0913_NiA


title: EA0897_NiA


title: EA0828_NiA


title: EA0984_NiA


title: EA0899_NiA


title: H3K27ac-KO-6h

status: Public on Mar 24 2018

city: Beijing

first: Huiping

last: Lu

address: Tsinghua university

country: China

institute: Tsinghua university

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2 with the default parameters.Duplicate reads were removed after the alignment with samtools command-line tools.
peaks were called using SICER_V1.1 after filtering with input or IgG isotype control sequence with the following setting:Window size 200 and FDR 1e-5.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using SICER_V1.1 by a moving window of size 200bp and the tag count in the windown was further normalized by library size per million.

molecule: genomic DNA

source_name: Spleen and peripheral lymoh organs

growth_protocol: FACS Sorted CD4+ T cells were stimulated by plate-coated anti-CD3 plus anti-CD28 in the medium of RPMI 1640 with 10% FBS.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone or transcriptional factors-DNA complexes were isolated with antibody or isotype IgG.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Sample Prep Kit. Briefly, DNA was end-repaired  using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: FACS Sorted CD4+ T cells were stimulated by plate-coated anti-CD3 plus anti-CD28, or followed with retroviral infection.

value: CD4+ T cell

tag: strain

tag: activation

value: in vitro activation by TCR/Co-stimulation

tag: antibody

value: H3K27ac (ab4729, Abcam)


title: H3K27ac-WT-6h


title: EA0906_NiA


title: H3K27ac-WT-Naive


title: H3K27ac-KO-Naive


title: EA0883_NiA


title: H3K27ac-RV-vector


title: Batf-RV-Nr4a1

value: Batf (PAB4003, Brookwood biomedical)


title: C-Jun-WT-6h


title: H3K27ac-RV-Nr4a1


title: Batf-RV-vector


title: C-Jun-KO-6h

value: C-Jun (sc-45x, Santa Cruz)


title: EA0856_NiA


title: EA0811_NiA


title: EA0849_NiA


title: EA0812_NiA


title: EA0836_NiA


title: EA0881_NRAIA


title: inputK4K27_Ttol

data_processing:
Basecalls performed using CASAVA version 1.8.2.
ChIP-seq reads were aligned to the mm9 genome using bowtie2.
peaks were called using SICER version 1.1.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using SICER version 1.1

source_name: in vitro generated mouse Ttol cells

growth_protocol: Ttol cells, Naïve CD4+ OT-II T cells were primed with B7.1-/-B7.2-/- B7h-/- triple ko APCs in the presence of OT-II cells. Nr4a1-overexpressing T cells, preactivated CD4+ T cells were infected with Nr4a1-RV-GFP retrovirus.

extract_protocol:
Lysates were clarified from Mnase digested  nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit . Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: CD4+ T cells

tag: status

value: primed CD4+ T cells


title: inputNr4a1_Ttol

source_name: Nr4a1 overexpressed mouse CD4+ T cells


title: EA0832_NiA

value: CD4+ T-cell


title: EA0833_NiA

value: peripheral blood


title: EA0855_NRAIA


title: H3K4me3_Ttol

value: H3K4me3 ChIP-antibody (ab8580, Abcam)


title: EA0808_NiA


title: input


title: H3K27me3_Ttol

value: H3K27me3 ChIP-antibody (07-449, Millipore)


title: Cjun-RV-vector


title: HA-Nr4a1_1

value: HA (Cat3724, clone C29F4, Cell signaling technology)


title: IgG-conrtol

value: IgG


title: Nr4a1_Ttol

value: Nr4a1 ChIP-antibody (14-5964-82, clone 357, ebioscience)


title: colorectal cancer sample AUS2_340

status: Public on Jan 02 2018

city: Oslo

first: Anita

last: Sveen

address: P.O.Box 4953, Nydalen

department: Department of Molecular Oncology

country: Norway

institute: Institute for Cancer Research, Oslo University Hospital

description: SST RMA expression values at the gene-level derived using Expression Console software

hyb_protocol: Samples were hybridized onto Affymetrix Human Transcriptome 2.0 Arrays according to the manufacturer's protocol (Affymetrix).

scan_protocol: Array scanning was performed according to the manufacturer's protocol (Affymetrix).

data_processing: Gene-level expression signals were obtained from raw data CEL files by the SST RMA procedure implemented in the Affymetrix Expression Console software.

source_name: Colorectal cancer patient

label_protocol: RNA was amplified, fragmented and labelled according to the Affymetrix GeneChip HT WT User Guide.

extract_protocol: Total RNA was isolated from colorectal cancer tissue samples using the Qiagen Allprep DNA/RNA/miRNA Universal kit, according to the manufacturer's protocol (Qiagen).

value: colorectal cancer biopsy


title: colorectal cancer sample AUS2_328


title: colorectal cancer sample AUS2_376


title: colorectal cancer sample AUS2_325


title: colorectal cancer sample AUS2_412


title: colorectal cancer sample AUS2_301


title: colorectal cancer sample AUS2_420


title: colorectal cancer sample AUS2_317


title: colorectal cancer sample AUS2_330


title: colorectal cancer sample AUS2_348


title: colorectal cancer sample AUS2_320


title: colorectal cancer sample AUS2_307


title: colorectal cancer sample AUS2_319


title: colorectal cancer sample AUS2_308


title: colorectal cancer sample AUS2_529


title: colorectal cancer sample AUS2_283


title: colorectal cancer sample AUS2_313


title: colorectal cancer sample AUS2_288


title: colorectal cancer sample AUS2_286


title: colorectal cancer sample AUS2_310


title: colorectal cancer sample AUS2_561


title: colorectal cancer sample AUS2_562


title: colorectal cancer sample AUS2_565


title: colorectal cancer sample AUS2_296


title: EA0941_ACPAnRA

value: F

value: ACPA-neg RA


title: colorectal cancer sample AUS2_312


title: colorectal cancer sample AUS2_545


title: colorectal cancer sample AUS2_489


title: yw me2 (#07-452) input

status: Public on Dec 01 2017

city: Novosibirsk

first: Daniil

last: Maksimov

address: Lavrentjeva ave., 8/2

country: Russia

institute: MCB NSC RAS

description: yw_me2_div_input_profile_in_50000bp_bins_5000bp_shift_QN.txt.gz

data_processing:
The reads were mapped to BDGP R5/dm3 Drosophila genome assembly using MOSAIK software with following parameters: -m all -mmp 0.1 -act 20 -a single. Paired reads were combined.
For each genomic position, the RPM (reads per million) value was calculated for ChIP sample and input sample. Log2 of the ChIP to input ratio was used as a measure of local H3K27me3 enrichment.
To build the whole genome profile, the data were smoothed using a 50kb sliding window, step 5kb.
Genome_build: BDGP R5/dm3
Supplementary_files_format_and_content: wig files containing Log2 of the ChIP to input RPM ratio smoothed using a 50kb sliding window with 5kb step.

organism: Drosophila melanogaster

source_name: salivary glands

growth_protocol: Flies were raised at 23°C

extract_protocol:
20 pairs of 3rd instar larvae salivary glands were used as starting material. Cell Signaling Technology #9733 anti-H3K27me3  or Millipore #07-452 anti-H3K27me2 antibodies were used for chromatin immunoprecipitation. Chromatin was sheared using BioRuptor instrument (Diagenode).
DNA from precipitated material and input were used for library preparation using Illumina Nextera protocol.

value: yw

tag: chip antibody

value: 3rd instar larvae


title: yw me2 (#07-452) AB

tag: genotype

value: Millipore #07-452 anti-H3K27me2


title: SUUR me2 (#07-452) AB

description: SUUR_me2_div_input_profile_in_50000bp_bins_5000bp_shift_QN.txt.gz

value: SuUR mutant


title: SUUR me2 (#07-452) input


title: yw me3  (#9733) AB

description: yw_me3_div_input_profile_in_50000bp_bins_5000bp_shift_QN.txt.gz

value: Cell Signaling Technology #9733 anti-H3K27me3


title: yw me3  (#9733) input


title: SUUR me3 (#9733) AB

description: SUUR_me3_div_input_profile_in_50000bp_bins_5000bp_shift_QN.txt.gz


title: colorectal cancer sample AUS2_479


title: Ribo_noCHX_5_trm7D

status: Public on Sep 27 2017

first: Oliver

last: Rando

address: 364 Plantation Street

department: Biochemistry & Molecular Pharm

description:
Ribosome-protected footprint RNA
processed data file: Chou_Table_S6.txt

data_processing:
Library strategy: Ribosome profiling
Raw fastq reads were de-multiplexed and removed of adaptor sequence using homerTools function of HOMER package v4.6, with parameters "barcodes 5 -min 0.01" and "trim -5 2 -3 TGGAATTCTCGGGTGCCAAGG -mis 2 -minMatchLength 5", respectively.
De-multiplexed and adaptor-removed reads for RPF were mapped to S. cerevisiae rDNA and the mapping reads were discarded. The remaining RPF reads and RNA-seq reads were mapped to sacCer3 genome using TopHat v2.0.12 with parameters -p 4 -I 5000 --no-coverage-search
Uniquely mapping reads (filtered by samtools view function and parameter -q 10) in length of 27-34 nt (RPF) or >=27 nt (RNA-seq) were used for gene-level analysis, in which reads were quantified as raw counts or reads per kilobase of transcript per million mapped reads (RPKM) using HOMER package with open reading frame annotations downloaded from SGD.
Translational efficiency (TE) was calculated as relative ribosome footprint density (Ribo-rRPKM) divided by relative RNA abundance (RNA-rRPKM), with rRPKM calculated by normalizing RPKM in each mutant by the average of RPKM in WTs grown in the same batch.
Global codon occupancy analysis was calculated as described in (Nedialkova and Leidel, 2015), with minor modifications. The P-site offset was calculated by examining the cumulative distribution of 28-31 nt reads aligning at start codons. After applying the respective offset to reads of each size, only in-frame reads were used. The first 15 and the last 5 codons of each transcript were removed from the reference. The frequency of each codon in ribosomal A, P, and E sites was calculated for normalization, and divided by the average frequency of the same codon in the three downstream codons from the A site
Genome_build: sacCer3
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample (RPF or RNA-seq reads) and normalized codon frequencies per A/P/E site.

organism: Saccharomyces cerevisiae

source_name: Yeast

growth_protocol: 100 mL of yeast cultures were grown to mid-log phase (OD600=0.5-0.6) in YPD (1% Yeast extract, 2% Peptone, 2% Dextrose) at 30°C

extract_protocol:
For CHX-free samples, cells were harvested by rapid filtration system and lysed with frozen pellets of lysis buffer using CryoMill in liquid nitrogen, followed by RNase I treatment. Ribosomes were separated on 10-50% sucrose gradient and 80S monosome fractions were collected and RNA extracted. 27-34 nt ribosome footprints were isolated by denaturing PAGE.
RPF are constructed into deep-sequencing libraries as described in (Heyer et al., 2015). Briefly, RNA 3’ ends were dephosphorylated, ligated with a preadenylated adaptor, and reverse transcribed. cDNA was precipitated and size selected by denaturing PAGE. The purified cDNA was circularized and PCR amplified prior to sequencing. For RiboMeth-seq, total RNAs were end-repaired with T4 PNK, Antarctic phosphatase, or Shrimp alkaline phosphatase for 3’-end dephosphorylation and with T4 PNK and ATP for 5’-end phosphorylation, followed by library construction using NEB Next Small RNA Library Prep kit.
Amplified library was purified and subject to Illumina Nextseq 500 single-end sequencing with 75 cycles.

treatment_protocol: No treatment

tag: media

value: YPD

value: No


title: Ribo_noCHX_6_tyw4D


title: Ribo_noCHX_4_tan1D


title: Ribo_noCHX_3_mod5D


title: Ribo_noCHX_2_elp3D


title: Ribo_noCHX_1_BY4741


title: CC-FL-E105-Wt-Mm-Rep1 part2

status: Public on Feb 01 2017

city: Geneva

first: Guillaume

last: Andrey

address: Rue Michel-Servet 1

department: Department of Genetic Medicine and Development

country: Switzerland

institute: University of Geneva

description: Captured genomic DNA from 3C library

data_processing:
Frag profiles: Paired-end sequencing data from Capture-C experiments was mapped and cleaned from invalid di-tags and duplicates using the HiCUP pipeline v0.5.8 (Wingett et al. 2015) and Bowtie 2.2.6 (Langmead and Salzberg 2012). All sequencing data was mapped to mouse reference genome mm9. Viewpoint-specific contact profiles were generated from BAM files with custom Java code using htsjdk 1.139 (https://samtools.github.io/htsjdk/) for the processing of BAM files. A di-tag was considered only if one mate was located in an enriched viewpoint region while the other mapped to the non-enriched part of the genome. Contact profiles were generated for each viewpoint by counting the number reads per restriction fragment. Count data was binned into a regular grid of 1 kb intervals centered around the middle of the corresponding viewpoint region. The count value of each restriction fragment was assigned to the bin, which contains the fragment center.
Smoothed profiles: count data per fragments was combined from both replicates, binned, smoothed with a running window of 3 and 5 bins. To make contact profiles with different read densities comparable, each profile was scaled by the total contact count on the chromosome of the viewpoint (Sum of cis contacts/1000).
Peak calling: Scaled contact profiles were pooled across all samples and viewpoints to generate a simple, empirical background model, which incorporates the distance dependent decay of the contact frequency. The positioning of the grid around viewpoint center allows an overlay of all profiles by aligning their centers. Now, each 1 kb bin can be described by its offset relative to the viewpoint center and has the contact information from 6244 profiles (7 tissues/stages × 446 viewpoints × 2 replicates). The 99th and 95th percentile of the empirical distribution were used to derive an individual threshold for each bin. A spline function was used to smooth the resulting threshold line. To avoid the calling of spurious interactions due to a lower profile density at locations distant from the viewpoint, the threshold was set constant for all regions more than 0.5 Mb away from the viewpoint. A bin was selected as candidate region, when the contact value exceeds the threshold in both replicates. Within the candidate region the maximum value from the merged profile was used to determine the peak center. A region +-10 kb around the selected peak was excluded from the candidate region to suppress peaks nearby. The selection of maxima and exclusion of sub-peaks was repeated until no further candidates were left.
Enhancer calling: Putative enhancers were called based on the combination of three thresholds: the 95th percentile of the empirical background for the interaction strength, the 99th percentile for H3K27Ac and 95th percentile for H3K4me1. Percentiles of the histone modifications were computed based on genome wide distribution of mapped reads within 5 kb windows.
Genome_build: mm9
Supplementary_files_format_and_content: Bed and bedgraph files were generated in each sample for 446 different viewpoints and packed for each analysis into one archive.

source_name: Embryonic Limb Bud

growth_protocol: Limb bud sand midbrain were micro-dissected from mouse embryos

extract_protocol:
The 3C library was prepared according to (Hagege et al. 2007), i.e. crosslinking, cell lysis, DpnII digestion, ligation and de-crosslinking. Re-ligated products were then sheared using a covaris sonicator (Duty cycle: 10%, Intensity:5, Cycles per Burst: 200, Time: 6 cycles of 60 sec each, Set Mode: Frequency sweeping, Temperature: 4° to 7°C).
Adaptors were added to the sheared DNA and amplified. The adapted-ligated library was then hybridized to the custom-designed sure-select beads indexed for sequencing using an indexing PCR following Agilent instructions.

value: Forelimb

tag: age

value: wild type


title: SUUR me3  (#9733) input


title: LoVoSTTnocodazole0_CTCF_Goat

status: Public on Mar 20 2017

city: Stockholm

first: Martin

last: Enge

address: CCK, Z4

department: Dep of Oncology-Pathology

country: Sweden

institute: Karolinska Institute

description: ChIP-seq experiment on cells synchronized by thymidine block followed by M-phase block by nocodazole treatment

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: files generated using MACS 1.4

source_name: LoVo

growth_protocol: LoVo (ATCC CCL-229)  colon adenocarcinoma cells were cultured in DMEM supplemented with penicillin/streptomycin and 10% FBS under standard culture conditions.

extract_protocol: Cells were cross-linked by 1% formaldehyde, and DNA was sonicated to 200- 400 bp fragments. Antibodies (5 µg) were added and collected using protein G Sepharose (GE). Cross-links were reversed and proteins digested by incubation with proteinase K at 65 °C overnight. DNA was then purified using Qiagen PCR purification kit.

treatment_protocol: For S-phase synchronization, LoVo cells were arrested in early S phase by double thymidine block essentially as described in (Whitfield et al., 2002). Briefly, cells were cultured to 30 to 40% confluence and washed with PBS. Block medium (DMEM containing 10% FBS and 2 mM thymidine) was applied to cells for 12 h, followed by washing with PBS, and continued culture in culture medium for 8 h. The second thymidine block was applied by changing the medium to the block medium followed by another 12 h of culture before harvesting the cells. Genomic DNA was extracted from the synchronized cells and sequenced as described below. For M-phase synchronization, cells were cultured and incubated in block medium for 12 h as above. Then the block medium was replaced by culture medium (DMEM with 10% FBS) containing 200 ng/ml nocodazole (Sigma), in which cells were cultured for 8 h before harvest.

tag: cell line

value: LoVo

value: colon adenocarcinoma

tag: hgn

value: CTCF

value: Santa Cruz Biotechnology, Inc. :sc-15914 X

tag: control sample

tag: blocking protocol

value: Thymidine block + nocodazole

tag: number of peaks, < fdr 5%


title: CC-FL-E105-Wt-Mm-Rep1 part1

description: Captured genomic DNA from 3C library

tag: tissue


title: colorectal cancer sample AUS2_465

value: colorectal cancer biopsy


title: colorectal cancer sample AUS2_349


title: colorectal cancer sample AUS2_466


title: colorectal cancer sample AUS2_401


title: colorectal cancer sample AUS2_392


title: colorectal cancer sample AUS2_311


title: colorectal cancer sample AUS2_347


title: colorectal cancer sample AUS2_406


title: NHF1 CPD 24h XR-seq Rep2

status: Public on Mar 15 2016

city: Jerusalem

first: Sheera

last: Adar

state: Israel

address: Botnar Building Room 001, Faculty of Medicine, Hebrew University, Ein Kerem

department: Department of Microbiology and Molecular Genetics

country: Israel

institute: Hebrew University of Jerusalem

description:
Source of NHF1 cell line: W.K. Kaufmann, UNC, Chapel Hill (Heffernan et al. 2002).
Excised oligomer released in Nucleotide Excision Repair (XR-seq)

data_processing:
Library strategy: XR-seq
Base calling using Casava v1.8.2. Demultiplexing performed allowing 1 mismtach in the index
Flanking adapter sequences were removed from the reads using trimmomatic (Bolger et al. 2014).
Reads were aligned to the hg19 human genome using bowtie (Langmead et al. 2009) with the command options  -q --nomaqround --phred33-quals -m 4 -n 2 -e 70 -l 20 --best –S
Aligned readsfor each biological replicate were split into “PLUS” and “MINUS” strands, transformed to bed format, and sorted to remove duplicate reads.
Wiggle base counts files of 25bp fixed step windows were created for each of the replicates from the bed files. The count data was normalized for total sequencing depth on each chromosome. Wiggle files were d transferred to bigWig format for viewing on the UCSC browser.
Genome_build: hg19
Supplementary_files_format_and_content: For XR-seq performed for either CPD or (6-4)PP repair, in NHF1 and CS-B cells there are bigWig files of normalized 25bp fixedStep count data for both biological replicates, split into plus and minus strands

source_name: NHF1, CPD, 24h

growth_protocol: CS-B Mutant cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum at 37 °C in a 5% CO2 humidified chamber. The NHF1 cells were maintained under the same conditions with the addition of 2 mM glutamine.

extract_protocol:
Cell pellets from one 150mm tissue culture dish were resuspended in 400 µl of ice cold Buffer A (25 mM Hepes pH 7.9, 100 mM KCl, 12 mM MgCl2, 0.5 mM EDTA, 2 mM DTT, 12.5% glycerol, 0.5% NP-40) and incubated for 10 min on ice. Resuspended cells were transferred to an ice-cold Dounce homogenizer/tissue grinder and lysed on ice with 15 strokes using a tight plunger. The chromatin fraction was then pelleted by centrifugation for 30 min at 16, 873 x g at 4oC.
The supernatants were collected, 2 µg anti-p89 (XPB, Santa Cruz sc293 lot L1514), 1 µg anti-p62 (Santa Cruz sc292  lot F2113) and 200 µg RNaseA (Sigma R4642) were added. The reactions were rotated for 3-5 hrs at 4oC and then incubated overnight with 15 µL of recombinant protein A/G PLUS-agarose (Santa Cruz sc2003). After washing three times with 1 ml of buffer A and once with 1ml of buffer B (25 mM Hepes pH 7.9, 100 mM KCl, 12 mM MgCl2, 0.5 mM EDTA, 2 mM DTT, 12.5% glycerol, 1% NP-40), DNA was eluted from immunoprecipitates with 100 µl of buffer C (10 mM Tris-Cl pH 7.5, 1 mM EDTA, and 1% SDS) at 65oC for 15 min. The eluted DNA was then isolated by phenol/chloroform extraction followed by ethanol precipitation. DNA pellets were resuspended in 45 µl water, and then incubated with 5 µL of RNaseA/T1 mixture (Thermo EN0551) for 1 hr at 37oC. After phenol-chloroform extraction, purification through G50 filtration columns (GE Healthcare) and ethanol precipitation, the DNA was then used for ligation.  To add double-stranded adaptors to both ends, purified excised oligomers were incubated with 40 pmol 5′ adaptor and  100 pmol 3′ adaptor in 10 µL 2x Hybridization Buffer (20mM Tris-HCl pH7.5, 200mM NaCl, 0.2mM EDTA) at 60oC for 10min, then 16oC for 5min in a thermal cycler. To perform ligation, 4 µL 5x ligase buffer, 1 µL T4 DNA ligase HC (Life 15224-041), 1 µL 50% PEG8000 (NEB) and 4 µL H2O were added to each reaction. The reactions were incubated at 16oC overnight. After phenol-chloroform extraction and ethanol precipitation, ligation products were subjected to immunoprecipitation with anti-CPD (For the 16h sample - Cosmo NM-DND-001 lot TM-C-08, for all the rest, Kamiya cat MC-062, lot 11569062) or anti-(6-4)PP (Cosmo cat NM-DND-002, lot TM-P-04) antibodies.Purified DNA were repaired by (6-4)PP photolyase or CPD photolyase. DNA containing (6-4)PP or CPD were incubated with 1.25pmol E.coli (6-4)PP photolyase or 20pmol D.melanogaster CPD photolyase in 50 µL PLR buffer for 2hr on ice and irradiated with 18mW/cm2 of 366 nm light. 1% of unrepaired or repaired samples were used for quality check. After phenol-chloroform extraction and ethanol precipitation, repaired DNA were PCR amplified by Kapa Hifi HotStart ReadyMix with RP1 and RPIn (n means different index sequences, compatible with Illumina TrueSeq Small RNA Kit.) The PCR products were extracted with phenol-chloroform, precipitated with ethanol and subjected to electrophoresis in a 10% native polyacrylamide gel in 1xTBE. Gel slices corresponding to 130 to 155-nt fragments were excised. The DNA was eluted for 6 hrs in 0.3 M NaCl at room temperature, precipitated with ethanol and resuspended in buffer EB (10mM Tris-HCl pH8.5).

treatment_protocol: UV irradiation was performed as described previously (Gaddameedhi et al. 2010). Briefly, cells were grown to ~80% confluence before UV irradiation. Culture medium was removed, and then cells were placed under a GE germicidal lamp emitting primarily 254-nm UV light (1J/m2/s) connected with a digital timer for 10s or 20s (10 or 20J/m2 in total). Following irradiation, fresh culture medium was added to the cells, which were further incubated for the indicated time. Cells were washed with ice-cold PBS, harvested with a cell scraper in PBS and collected by centrifugation at 2500rpm for 4min.

tag: cell line source

value: normal newborn

tag: cell type

value: foreskin fibroblast

tag: uv exposure

tag: time after irradiation

tag: type of uv-induced dna damage

value: cyclobutane pyrimidine dimer (CPD)


title: NHF1 CPD 24h XR-seq Rep1


title: colorectal cancer sample AUS2_331


title: colorectal cancer sample AUS2_267

status: Public on Apr 12 2016

description: RMA expression values derived from Expression Console software; exon-core analysis

hyb_protocol: Samples were hybridized onto GeneChip Human Exon 1.0 ST Arrays (Affymetrix) according to the manufacturer's protocol.

data_processing: Exon-level expression signals were obtained from raw data by the RMA procedure implemented in the Affymetrix Expression Console software.

label_protocol: Single-stranded cDNA was generated from amplified cRNA using the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled using the WT Terminal Labeling Kit (Affymetrix).

extract_protocol: Total RNA was isolated from colorectal cancer biopsies using the AllPrep DNA/RNA Mini kit (Qiagen), according to the manufacturer's protocol.


title: NHF1 CPD 8h XR-seq Rep2

source_name: NHF1, CPD, 8h


title: NHF1 CPD 16h XR-seq Rep2

source_name: NHF1, CPD, 16h


title: colorectal cancer sample AUS2_225


title: colorectal cancer sample AUS2_245


title: NHF1 CPD 16h XR-seq Rep1


title: colorectal cancer sample AUS2_234


title: colorectal cancer sample AUS2_265


title: colorectal cancer sample AUS2_251


title: colorectal cancer sample AUS2_287


title: colorectal cancer sample AUS2_393


title: colorectal cancer sample AUS2_237


title: colorectal cancer sample AUS2_235


title: colorectal cancer sample AUS2_224


title: NHF1 CPD 8h XR-seq Rep1


title: colorectal cancer sample AUS2_208


title: colorectal cancer sample AUS2_220


title: colorectal cancer sample AUS2_210


title: colorectal cancer sample AUS2_263


title: colorectal cancer sample AUS2_056


title: colorectal cancer sample AUS2_230


title: colorectal cancer sample AUS2_231


title: colorectal cancer sample AUS2_222


title: colorectal cancer sample AUS2_205


title: colorectal cancer sample AUS2_218


title: colorectal cancer sample AUS2_203


title: colorectal cancer sample AUS2_259


title: N1461

status: Public on Jun 25 2015

city: Bethesda

first: Kendra

last: Williams

state: MD

address: 50 South Dr, Bldg 50

department: NHGRI

institute: NIH

description: TRAMPxNOD Metastasis

hyb_protocol: The hybridization cocktail containing the fragmented and labeled cDNAs were hybridized to The Affymetrix mouse GeneChip® 2.0 ST chips. The chips were washed and stained by the Affymetrix Fluidics Station using the standard format and protocols as described by Affymetrix.

scan_protocol: An Affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays.

data_processing: Data was processed using Partek

source_name: Tg+ F2 male

label_protocol: Labeling performed using GeneChip® Terminal Labeling kit according to manufacturer's protocol.

growth_protocol: Transgene-positive F2 male tumor growth and metastasis were quantified either at 30 weeks or when humane experimental endpoints were reached.

extract_protocol: Total RNA was isolated from tumor samples using QIAGEN Rneasy mini kit

treatment_protocol: Prostate tumor sample were collected and snap frozen in liquid nitrogen, then stored at -80 degrees until ready for RNA extraction

tag: gender

value: male

value: mouse prostate tumor


title: N1444

description: TRAMPxNOD Metastasis


title: colorectal cancer sample AUS2_262


title: N1340

description: TRAMPxNOD Metastasis


title: N1423

description: TRAMPxNOD Metastasis


title: colorectal cancer sample AUS2_216


title: colorectal cancer sample AUS2_257


title: N1500

description: TRAMPxNOD Metastasis


title: N1335

description: TRAMPxNOD Metastasis


title: colorectal cancer sample AUS2_212


title: N1425

description: TRAMPxNOD Metastasis


title: N1325

description: TRAMPxNOD Metastasis


title: N1234

description: TRAMPxNOD Metastasis


title: N1267

description: TRAMPxNOD Metastasis


title: N1331

description: TRAMPxNOD Metastasis


title: N1219

description: TRAMPxNOD Metastasis


title: N1165

description: TRAMPxNOD Metastasis


title: N1232

description: TRAMPxNOD Metastasis


title: N1212

description: TRAMPxNOD Metastasis


title: N1215

description: TRAMPxNOD Metastasis


title: N1205

description: TRAMPxNOD Metastasis


title: N1457

description: TRAMPxNOD Metastasis


title: N1207

description: TRAMPxNOD Metastasis


title: N1159

description: TRAMPxNOD Metastasis


title: N1223

description: TRAMPxNOD Metastasis


title: N1142

description: TRAMPxNOD Metastasis


title: N1134

description: TRAMPxNOD Metastasis


title: N1144

description: TRAMPxNOD Metastasis


title: N1139

description: TRAMPxNOD Metastasis


title: N1131

description: TRAMPxNOD Metastasis


title: N1220

description: TRAMPxNOD Metastasis


title: N950

description: TRAMPxNOD Metastasis


title: N1012

description: TRAMPxNOD Metastasis


title: N953

description: TRAMPxNOD Metastasis


title: N1086

description: TRAMPxNOD Metastasis


title: N951

description: TRAMPxNOD Metastasis


title: N1006

description: TRAMPxNOD Metastasis


title: N1087

description: TRAMPxNOD Metastasis


title: N963

description: TRAMPxNOD Metastasis


title: N934

description: TRAMPxNOD Metastasis


title: N947

description: TRAMPxNOD Metastasis


title: N945

description: TRAMPxNOD Metastasis


title: N889

description: TRAMPxNOD Metastasis


title: N891

description: TRAMPxNOD Metastasis


title: N894

description: TRAMPxNOD Metastasis


title: N826

description: TRAMPxNOD Metastasis


title: N887

description: TRAMPxNOD Metastasis


title: N818

description: TRAMPxNOD Metastasis


title: N940

description: TRAMPxNOD Metastasis


title: N924

description: TRAMPxNOD Metastasis


title: N929

description: TRAMPxNOD Metastasis


title: N927

description: TRAMPxNOD Metastasis


title: N921

description: TRAMPxNOD Metastasis


title: N898

description: TRAMPxNOD Metastasis


title: N926

description: TRAMPxNOD Metastasis


title: N817

description: TRAMPxNOD Metastasis


title: N820

description: TRAMPxNOD Metastasis


title: N637

description: TRAMPxNOD Metastasis


title: N918

description: TRAMPxNOD Metastasis


title: N821

description: TRAMPxNOD Metastasis


title: N812

description: TRAMPxNOD Metastasis


title: N649

description: TRAMPxNOD Metastasis


title: N662

description: TRAMPxNOD Metastasis


title: N858

description: TRAMPxNOD Metastasis


title: N663

description: TRAMPxNOD Metastasis


title: N655

description: TRAMPxNOD Metastasis


title: N803

description: TRAMPxNOD Metastasis


title: N816

description: TRAMPxNOD Metastasis


title: N619

description: TRAMPxNOD Metastasis


title: N1430

description: TRAMPxNOD Metastasis


title: N615

description: TRAMPxNOD Metastasis


title: N596

description: TRAMPxNOD Metastasis


title: N592

description: TRAMPxNOD Metastasis


title: N585

description: TRAMPxNOD Metastasis


title: N372

description: TRAMPxNOD Metastasis


title: N586

description: TRAMPxNOD Metastasis


title: N618

description: TRAMPxNOD Metastasis


title: N340

description: TRAMPxNOD Metastasis


title: N369

description: TRAMPxNOD Metastasis


title: N371

description: TRAMPxNOD Metastasis


title: N314

description: TRAMPxNOD Metastasis


title: N275

description: TRAMPxNOD Metastasis


title: N294

description: TRAMPxNOD Metastasis


title: N266

description: TRAMPxNOD Metastasis


title: N1442

description: TRAMPxNOD no metastasis


title: N1443

description: TRAMPxNOD no metastasis


title: N1227

description: TRAMPxNOD no metastasis


title: N197

description: TRAMPxNOD Metastasis


title: N1426

description: TRAMPxNOD no metastasis


title: N583

description: TRAMPxNOD Metastasis


title: N1357

description: TRAMPxNOD no metastasis


title: N1363

description: TRAMPxNOD no metastasis


title: N259

description: TRAMPxNOD Metastasis


title: N1263

description: TRAMPxNOD no metastasis


title: N185

description: TRAMPxNOD Metastasis


title: N1202

description: TRAMPxNOD no metastasis


title: N1407

description: TRAMPxNOD no metastasis


title: N1007

description: TRAMPxNOD no metastasis


title: N1130

description: TRAMPxNOD no metastasis


title: N329

description: TRAMPxNOD Metastasis


title: N961

description: TRAMPxNOD no metastasis


title: N1214

description: TRAMPxNOD no metastasis


title: N893

description: TRAMPxNOD no metastasis


title: N1216

description: TRAMPxNOD no metastasis


title: N343

description: TRAMPxNOD Metastasis


title: N1226

description: TRAMPxNOD no metastasis


title: N955

description: TRAMPxNOD no metastasis


title: N1229

description: TRAMPxNOD no metastasis


title: N919

description: TRAMPxNOD no metastasis


title: N1217

description: TRAMPxNOD no metastasis


title: N946

description: TRAMPxNOD no metastasis


title: N839

description: TRAMPxNOD no metastasis


title: N824

description: TRAMPxNOD no metastasis


title: N641

description: TRAMPxNOD no metastasis


title: N822

description: TRAMPxNOD no metastasis


title: singles-K562-rep3-well-191

status: Public on Jun 17 2015

city: Cambridge

first: Jason

middle: Daniel

last: Buenrostro

address: 415 Main Street

institute: Broad Institute

description: processed data file: single-K562.peaks.bed

data_processing:
library strategy: Single-cell ATAC-seq (scATAC-seq)
Adapter sequences were trimmed from FASTQs using custom python scripts to enable mapping fragments with sequences containing adapters. Paired-end reads were aligned to hg19 or mm10 using BOWTIE2 using the parameter –X2000 allowing fragments of up to 2 kb to align. Duplicates were removed using PICARD tools. Reads were subsequently filtered for alignment quality of >Q30 and were required to be properly paired. Reads mapping to the mitochondria, unmapped contigs and chromosome Y were removed and not considered.
We used MACS2 to call all reported ATAC-seq peaks. MACS2 was used with the following parameters (--nomodel --nolambda --keep-dup all --call-summits). Peaks were filtered using the consensus excludable ENCODE blacklist (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/) and a custom blacklist, designed to remove high-signal causing repeats and mitochondrial homologues. For all subsequent analysis we discarded peaks falling within these regions. Although we saw little effect on calculations of variability, in the case of K562 data, peaks were additionally filtered to exclude copy number amplifications. Using the filtered peak set, peak summits were extended +/-250 bps. The top 50,000 non-overlapping 500 bp summits are available here and were used for all downstream analysis.
Genome_build: hg19, mm10
Supplementary_files_format_and_content: Bam files across single-cells representing identical biological conditions have been merged. Reads pertaining to individual cells can be identified by their unique RGID tag corresponding to each assayed well. Bed files represent 500 bp peak summits as described above.

growth_protocol: K562 (ATCC) chronic myeloid leukemia cells were maintained in Iscove’s modified Dulbecco’s  medium (IMDM) containing 10% FBS (HyClone, Thermo Scientific) and 1% Penicillin Streptomycin (Pen/Strep).

extract_protocol:
Single cells were captured using the C1 Single-Cell Auto Prep IFC microfluidic chips. Cells were permeabilized and accessible fragments were captured using 20 µL of Tn5 transposition mix (1.5x TD buffer, 1.5 µL transposease (Nextera DNA Sample Prep Kit, Illumina), 1x C1 Loading Reagent with low salt (Fluidigm), and 0.15% NP40) at 30 minutes at 37°C.
In a 96-well plate, 10 µL of harvested libraries were amplified in 50 µL PCR for an additional 14 cycles (1.25 µM custom Nextera dual-index PCR primers (Supplementary Table 1) in 1x NEBnext High-Fidelity PCR Master Mix) using the following PCR conditions: 72°C for 5min; 98°C for 30 s; and thermocycling at 98°C for 10 s, 72°C for 30 s, and 72°C for 1 min. The PCR products were pooled creating a final volume of ~4.8 mL. The pooled library was purified on a single MinElute PCR purification column (Qiagen) yielding libraries at an approximate concentration of ~1 µM. Libraries were quantified using qPCR prior to sequencing.

value: chronic myeloid leukemia cells

tag: treated with

value: none (untreated)


title: singles-K562-rep3-well-189


title: singles-K562-rep3-well-190


title: N892

description: TRAMPxNOD no metastasis


title: singles-K562-rep3-well-186


title: singles-K562-rep3-well-185


title: N591

description: TRAMPxNOD no metastasis


title: N183

description: TRAMPxNOD no metastasis


title: singles-K562-rep3-well-181


title: N380

description: TRAMPxNOD no metastasis


title: N614

description: TRAMPxNOD no metastasis


title: N582

description: TRAMPxNOD no metastasis


title: N265

description: TRAMPxNOD no metastasis


title: N832

description: TRAMPxNOD no metastasis


title: N912

description: TRAMPxNOD no metastasis


title: singles-K562-rep3-well-182


title: singles-K562-rep3-well-180


title: singles-K562-rep3-well-187


title: N574

description: TRAMPxNOD no metastasis


title: singles-K562-rep3-well-179


title: singles-K562-rep3-well-178


title: N293

description: TRAMPxNOD no metastasis


title: N566

description: TRAMPxNOD no metastasis


title: singles-K562-rep3-well-175


title: singles-K562-rep3-well-177


title: N609

description: TRAMPxNOD no metastasis


title: N187

description: TRAMPxNOD no metastasis


title: singles-K562-rep3-well-172


title: singles-K562-rep3-well-173


title: singles-K562-rep3-well-174


title: singles-K562-rep3-well-171


title: singles-K562-rep3-well-169


title: singles-K562-rep3-well-168


title: singles-K562-rep3-well-164


title: singles-K562-rep3-well-167


title: singles-K562-rep3-well-166


title: singles-K562-rep3-well-170


title: singles-K562-rep3-well-161


title: singles-K562-rep3-well-160


title: singles-K562-rep3-well-163


title: singles-K562-rep3-well-162


title: singles-K562-rep3-well-158


title: singles-K562-rep3-well-157


title: singles-K562-rep3-well-155


title: singles-K562-rep3-well-156


title: singles-K562-rep3-well-153


title: singles-K562-rep3-well-154


title: singles-K562-rep3-well-152


title: singles-K562-rep3-well-151


title: singles-K562-rep3-well-147


title: singles-K562-rep3-well-165


title: singles-K562-rep3-well-146


title: singles-K562-rep3-well-159


title: singles-K562-rep3-well-144


title: singles-K562-rep3-well-142


title: singles-K562-rep3-well-143


title: singles-K562-rep3-well-139


title: singles-K562-rep3-well-141


title: singles-K562-rep3-well-137


title: singles-K562-rep3-well-138


title: singles-K562-rep3-well-135


title: singles-K562-rep3-well-136


title: singles-K562-rep3-well-134


title: singles-K562-rep3-well-133


title: singles-K562-rep3-well-149


title: singles-K562-rep3-well-145


title: singles-K562-rep3-well-132


title: singles-K562-rep3-well-150


title: singles-K562-rep3-well-131


title: singles-K562-rep3-well-129


title: singles-K562-rep3-well-148


title: singles-K562-rep3-well-128


title: singles-K562-rep3-well-127


title: singles-K562-rep3-well-140


title: singles-K562-rep3-well-125


title: singles-K562-rep3-well-124


title: singles-K562-rep3-well-130


title: singles-K562-rep3-well-123


title: singles-K562-rep3-well-122


title: N590

description: TRAMPxNOD Metastasis


title: singles-K562-rep3-well-119


title: singles-K562-rep3-well-121


title: singles-K562-rep3-well-118


title: singles-K562-rep3-well-115


title: singles-K562-rep3-well-116


title: singles-K562-rep3-well-117


title: singles-K562-rep3-well-114


title: singles-K562-rep3-well-111


title: singles-K562-rep3-well-109


title: singles-K562-rep3-well-113


title: singles-K562-rep3-well-120


title: singles-K562-rep3-well-112


title: singles-K562-rep3-well-126


title: singles-K562-rep3-well-107


title: singles-K562-rep3-well-108


title: singles-K562-rep3-well-106


title: singles-K562-rep3-well-105


title: singles-K562-rep3-well-110


title: singles-K562-rep3-well-104


title: singles-K562-rep3-well-103


title: singles-K562-rep3-well-102


title: singles-K562-rep3-well-101


title: singles-K562-rep3-well-99


title: singles-K562-rep2-well-95


title: singles-K562-rep3-well-97


title: singles-K562-rep2-well-96


title: singles-K562-rep3-well-98


title: singles-K562-rep2-well-94


title: singles-K562-rep3-well-100


title: singles-K562-rep2-well-93


title: singles-K562-rep2-well-92


title: singles-K562-rep2-well-91


title: singles-K562-rep2-well-89


title: singles-K562-rep2-well-88


title: singles-K562-rep2-well-87


title: singles-K562-rep2-well-84


title: singles-K562-rep2-well-83


title: singles-K562-rep2-well-79


title: singles-K562-rep2-well-77


title: singles-K562-rep2-well-85


title: singles-K562-rep2-well-76


title: singles-K562-rep2-well-78


title: singles-K562-rep2-well-86


title: singles-K562-rep2-well-80


title: singles-K562-rep2-well-73


title: singles-K562-rep2-well-81


title: singles-K562-rep2-well-71


title: singles-K562-rep2-well-72


title: singles-K562-rep2-well-75


title: singles-K562-rep2-well-70


title: singles-K562-rep2-well-90


title: singles-K562-rep2-well-68


title: singles-K562-rep2-well-67


title: singles-K562-rep2-well-74


title: singles-K562-rep2-well-66


title: singles-K562-rep2-well-65


title: singles-K562-rep2-well-69


title: singles-K562-rep2-well-64


title: singles-K562-rep2-well-63


title: singles-K562-rep2-well-62


title: singles-K562-rep2-well-61


title: singles-K562-rep2-well-60


title: singles-K562-rep2-well-82


title: singles-K562-rep2-well-59


title: singles-K562-rep2-well-57


title: singles-K562-rep2-well-55


title: singles-K562-rep2-well-56


title: singles-K562-rep2-well-58


title: singles-K562-rep2-well-52


title: singles-K562-rep2-well-54


title: singles-K562-rep2-well-49


title: singles-K562-rep2-well-53


title: singles-K562-rep2-well-51


title: singles-K562-rep2-well-50


title: singles-K562-rep3-well-188


title: singles-K562-rep2-well-45


title: singles-K562-rep2-well-48


title: singles-K562-rep3-well-184


title: singles-K562-rep2-well-44


title: singles-K562-rep2-well-46


title: singles-K562-rep2-well-40


title: singles-K562-rep2-well-41


title: singles-K562-rep2-well-43


title: singles-K562-rep2-well-38


title: singles-K562-rep2-well-37


title: singles-K562-rep2-well-47


title: singles-K562-rep3-well-192


title: singles-K562-rep3-well-183


title: singles-K562-rep2-well-36


title: singles-K562-rep2-well-39


title: singles-K562-rep2-well-31


title: singles-K562-rep2-well-34


title: singles-K562-rep2-well-32


title: singles-K562-rep2-well-27


title: singles-K562-rep2-well-26


title: singles-K562-rep2-well-33


title: singles-K562-rep2-well-42


title: singles-K562-rep2-well-28


title: singles-K562-rep2-well-25


title: singles-K562-rep2-well-35


title: singles-K562-rep2-well-24


title: singles-K562-rep2-well-22


title: singles-K562-rep2-well-23


title: singles-K562-rep2-well-30


title: singles-K562-rep2-well-17


title: singles-K562-rep2-well-16


title: singles-K562-rep2-well-21


title: singles-K562-rep2-well-19


title: singles-K562-rep2-well-18


title: singles-K562-rep2-well-20


title: singles-K562-rep2-well-15


title: singles-K562-rep3-well-176


title: singles-K562-rep2-well-13


title: singles-K562-rep2-well-11


title: singles-K562-rep2-well-10


title: singles-K562-rep2-well-14


title: singles-K562-rep2-well-12


title: singles-K562-rep2-well-9


title: singles-K562-rep2-well-8


title: singles-K562-rep2-well-6


title: singles-K562-rep2-well-7


title: singles-K562-rep2-well-4


title: singles-K562-rep2-well-3


title: singles-K562-rep2-well-2


title: singles-K562-rep2-well-5


title: singles-K562-rep1-well-190


title: singles-K562-rep1-well-192


title: singles-K562-rep1-well-186


title: singles-K562-rep1-well-185


title: singles-K562-rep2-well-1


title: singles-K562-rep1-well-187


title: singles-K562-rep1-well-183


title: singles-K562-rep1-well-184


title: singles-K562-rep1-well-182


title: singles-K562-rep1-well-189


title: singles-K562-rep1-well-180


title: singles-K562-rep1-well-177


title: singles-K562-rep1-well-176


title: singles-K562-rep1-well-174


title: singles-K562-rep1-well-178


title: singles-K562-rep1-well-173


title: singles-K562-rep1-well-172


title: singles-K562-rep1-well-171


title: singles-K562-rep1-well-191


title: singles-K562-rep1-well-170


title: singles-K562-rep2-well-29


title: singles-K562-rep1-well-169


title: singles-K562-rep1-well-167


title: singles-K562-rep1-well-166


title: singles-K562-rep1-well-188


title: singles-K562-rep1-well-164


title: singles-K562-rep1-well-168


title: singles-K562-rep1-well-181


title: singles-K562-rep1-well-163


title: singles-K562-rep1-well-162


title: singles-K562-rep1-well-156


title: singles-K562-rep1-well-159


title: singles-K562-rep1-well-155


title: singles-K562-rep1-well-160


title: singles-K562-rep1-well-161


title: singles-K562-rep1-well-154


title: singles-K562-rep1-well-175


title: singles-K562-rep1-well-158


title: singles-K562-rep1-well-152


title: singles-K562-rep1-well-150


title: singles-K562-rep1-well-153


title: singles-K562-rep1-well-148


title: singles-K562-rep1-well-151


title: singles-K562-rep1-well-149


title: singles-K562-rep1-well-147


title: singles-K562-rep1-well-165


title: singles-K562-rep1-well-145


title: singles-K562-rep1-well-144


title: singles-K562-rep1-well-146


title: singles-K562-rep1-well-141


title: singles-K562-rep1-well-140


title: singles-K562-rep1-well-143


title: singles-K562-rep1-well-139


title: singles-K562-rep1-well-157


title: singles-K562-rep1-well-132


title: singles-K562-rep1-well-134


title: singles-K562-rep1-well-133


title: singles-K562-rep1-well-135


title: singles-K562-rep1-well-131


title: singles-K562-rep1-well-126


title: singles-K562-rep1-well-130


title: singles-K562-rep1-well-136


title: singles-K562-rep1-well-124


title: singles-K562-rep1-well-125


title: singles-K562-rep1-well-123


title: singles-K562-rep1-well-128


title: singles-K562-rep1-well-121


title: singles-K562-rep1-well-137


title: singles-K562-rep1-well-122


title: singles-K562-rep1-well-119


title: singles-K562-rep1-well-138


title: singles-K562-rep1-well-116


title: singles-K562-rep1-well-117


title: singles-K562-rep1-well-142


title: singles-K562-rep1-well-115


title: singles-K562-rep1-well-113


title: singles-K562-rep1-well-112


title: singles-K562-rep1-well-129


title: singles-K562-rep1-well-111


title: singles-K562-rep1-well-127


title: singles-K562-rep1-well-114


title: singles-K562-rep1-well-108


title: singles-K562-rep1-well-106


title: singles-K562-rep1-well-107


title: singles-K562-rep1-well-104


title: singles-K562-rep1-well-103


title: singles-K562-rep1-well-100


title: singles-K562-rep1-well-101


title: singles-K562-rep1-well-99


title: singles-K562-rep1-well-120


title: singles-K562-rep1-well-97


title: singles-K562-rep1-well-98


title: CS-B CPD XR-seq, rep2

status: Public on Apr 19 2015

description:
Excised oligomer released in Nucleotide Excision Repair (XR-seq).
Processed data files:
CSBCPD_Merged_MINUS_UNIQUE_NORM_fixedStep_25.bw
CSBCPD_Merged_PLUS_UNIQUE_NORM_fixedStep_25.bw

data_processing:
Library strategy: XR-seq
Base calling using Casava v1.8.2. Demultiplexing performed allowing 1 mismatch in the index.
Flanking adapter sequences were removed from the reads using trimmomatic (Bolger et al. 2014).
Reads were aligned to the hg19 human genome using Bowtie (Langmead et al. 2009) with the command options -q --nomaqround --phred33-quals -m 4 -n 2 -e 70 -l 20 --best –S
Aligned reads for each biological replicate were split into "PLUS" and "MINUS" strands, transformed to bed format, and sorted to remove duplicate reads.
Aligned reads from both replicates were merged, wiggle base counts files of 25bp fixed step windows were created from the bed files. The count data was normalized for total sequencing depth on each chromosome. Wiggle files were transferred to bigWig format for viewing on the UCSC browser.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: For XR-seq performed for either CPD or (6-4)PP repair, in NHF1, XP-C and CS-B cells, there are bigWig files of normalized 25bp fixedStep count data for the merged data of both biological replicates, split into plus and minus strands.

source_name: CS-B, CPD

growth_protocol: XP-C and CS-B mutant cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum at 37 °C in a 5% CO2 humidified chamber. The NHF1 cells were maintained under the same conditions with the addition of 2 mM glutamine.

extract_protocol:
Cell pellets from one 150mm tissue culture dish were resuspended in 400 µl of ice cold Buffer A (25 mM Hepes pH 7.9, 100 mM KCl, 12 mM MgCl2, 0.5 mM EDTA, 2 mM DTT, 12.5% glycerol, 0.5% NP-40) and incubated for 10 min on ice. Resuspended cells were transferred to an ice-cold Dounce homogenizer/tissue grinder and lysed on ice with 15 strokes using a tight plunger. The chromatin fraction was then pelleted by centrifugation for 30 min at 16, 873 x g at 4oC.
The supernatants were collected, 2 µg anti-p89 (XPB, Santa Cruz, cat sc293, lot L1514), 1 µg anti-p62 (Santa Cruz, cat sc292, lot F2113) and 200 µg RNase A (Sigma R4642) were added. The reactions were rotated for 3-5 hrs at 4oC and then incubated overnight with 15 µL of recombinant protein A/G PLUS-agarose (Santa Cruz sc2003). After washing three times with 1 ml of buffer A and once with 1ml of buffer B (25 mM Hepes pH 7.9, 100 mM KCl, 12 mM MgCl2, 0.5 mM EDTA, 2 mM DTT, 12.5% glycerol, 1% NP-40), DNA was eluted from immunoprecipitates with 100 µl of buffer C (10 mM Tris-Cl pH 7.5, 1 mM EDTA, and 1% SDS) at 65oC for 15 min. The eluted DNA was then isolated by phenol/chloroform extraction followed by ethanol precipitation. DNA pellets were resuspended in 45 µl water, and then incubated with 5 µL of RNaseA/T1 mixture (Thermo EN0551) for 1 hr at 37oC. After phenol-chloroform extraction, purification through G50 filtration columns (GE Healthcare) and ethanol precipitation, the DNA was then used for ligation.
To add double-stranded adaptors to both ends, purified excised oligomers were incubated with 40 pmol 5' adaptor and 100 pmol 3' adaptor in 10 µL 2x Hybridization Buffer (20mM Tris-HCl pH7.5, 200mM NaCl, 0.2mM EDTA) at 60oC for 10min, then 16oC for 5min in a thermal cycler. To perform ligation, 4 µL 5x ligase buffer, 1 µL T4 DNA ligase HC (Life 15224-041), 1 µL 50% PEG8000 (NEB) and 4 µL H2O were added to each reaction. The reactions were incubated at 16oC overnight. After phenol-chloroform extraction and ethanol precipitation, ligation products were subjected to immunoprecipitation with anti-CPD (Kamiya, cat MC-062, lot 11569062) or anti-(6-4)PP (Cosmo, cat NM-DND-002, lot TM-P-03) antibodies. For NHF1 and CS-B samples, the ligation products were first immunoprecipitated with anti-CPD then the supernatant were subjected to immunoprecipitation with anti-(6-4)PP. For XP-C samples, the order was reversed: first IP with anti-(6-4)PP then the flowthrough IP with anti-CPD. Purified DNA were repaired by (6-4)PP photolyase or CPD photolyase. DNA containing (6-4)PP or CPD were incubated with 1.25pmol E.coli (6-4)PP photolyase or 20pmol D. melanogaster CPD photolyase in 50 µL PLR buffer for 2hr on ice and irradiated with 18mW/cm2 of 366 nm light. 1% of unrepaired or repaired samples were used for quality check. After phenol-chloroform extraction and ethanol precipitation, repaired DNA were PCR amplified by Kapa Hifi HotStart ReadyMix with RP1 and RPIn (n means different index sequences, compatible with Illumina TrueSeq Small RNA Kit.) The PCR products were extracted with phenol-chloroform, precipitated with ethanol and subjected to electrophoresis in a 10% native polyacrylamide gel in 1xTBE. Gel slices corresponding to 130- to 155-nt fragments were excised. The DNA was eluted for 6 hrs in 0.3 M NaCl at room temperature, precipitated with ethanol and resuspended in buffer EB (10mM Tris-HCl pH8.5).

treatment_protocol: UV irradiation was performed as described previously (Gaddameedhi et al. 2010). Briefly, cells were grown to ~80% confluence before UV irradiation. Culture medium was removed, and then cells were placed under a GE germicidal lamp emitting primarily 254-nm UV light (1J/m2/s) connected with a digital timer for 20s (20J/m2 in total). Following irradiation, fresh culture medium was added to the cells, which were further incubated for the indicated time. Cells were washed with ice-cold PBS, harvested with a cell scraper in PBS and collected by centrifugation at 2500rpm for 4min.

value: Coriell GM16095 (CS1ANps3g2)

value: Cockayne Syndrome patient (CS-B mutant)

value: skin fibroblast cell line

tag: time between uv exposure and harvesting


title: singles-K562-rep1-well-118


title: CS-B CPD XR-seq, rep1


title: singles-K562-rep1-well-110


title: singles-K562-rep1-well-109


title: Sample_8-F2

status: Public on Feb 23 2015

city: University Park

first: Hardik

last: Kundariya

address: 361 N. Frear

institute: The Pennsylvania State University

description: 4-weeks apical meristem, epiF3, biological replicate 2

data_processing:
adapter sequences and the barcodes were removed. FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to confirmsequencing quality.
Bowtie-2.1.0 (Langmead et al, 2009) and Tophat-2.0.10 (Kim D et al, 2013) (with the default parameter) were used to map the reads of tomato samples to gene models in the tomato reference genome ITAG 2.4
DESeq2 (Anders et al, 2010)was used to identify differentially expressed genes (DEGs)between each mutant and the wild-type control. Raw P-values were adjusted using theBenjamini-Hochberg procedure (Benjamini et al, 1995), and a cut-off value of adjusted p< 0.05 was used to identify significant DEGs. For cross comparison, BLAST was used to identify orthologs of tomato genes in Arabidopsis, with the match having the lowest E-value used in each case. After corresponding orthologs were identified, lists of differentially expressed genes in tomato msh1-RNAi and Arabidopsis msh1 (compared to their wild-type counterparts) were compared for overlap.
Genome_build: tomato reference genome ITAG 2.4  (ftp://ftp.solgenomics.net/tomato_genome/annotation/ITAG2.4_release/).
Supplementary_files_format_and_content: Tab delimited files containing FPKM gene-level values for each sample, as well as a cuffdiff generated and further annotated tab-delimited files containing fold-changes and q-values of AL versus AP and LL versus LP.
Supplementary_files_format_and_content: Annotation files are tab-delimited annotated cuffdiff file (log2 fold changes, q-value, gene annotation)

organism: Solanum lycopersicum

source_name: apical meristem

growth_protocol: Plants in the greenhouse were germinated on MetroMix 200 medium (SunGro,USA) and maintained at 26-28°C  with 15-h daylengthand at 20-22.8 °C  with 9-h dark periods.

extract_protocol:
At 4-weeks after sow , apical meristem tissues were quickly removed, frozen in liquid N2, and stored at –80°C. Total RNA was isolated from materials by using TRIzol Reagent (Invitrogen cat#: P/N 15596-018), followed by further purification by Qiagen RNeasy Mini Kit (P/N 74104). RNA qualities were assessed using an Agilent BioAnalyzer 2100 system (Agilent Technologies).
RNA libraries were constructed as described by TruSeq® RNA Sample Preparation v2 Guide. These libraries were sequenced at a final concentration of 5pM in a Hi-Seq 2500 rapid 100 bp single read runat theSequencing and Microarray Core Facilities of the University of Nebraska Medical Center.

treatment_protocol: regular growth condition

value: apical meristem

tag: cultivar

value: Rutgers

tag: genotype


title: Sample_9-F3

description: 4-weeks apical meristem, epiF3, biological replicate 3


title: Sample_15-H3

description: 4-weeks apical meristem, MSH1 mutant mild-dr, biological replicate 3

value: MSH1 mutant mild-dr


title: Sample_3-C3

description: 4-weeks apical meristem, MSH1 mutant Dwarf-dr, biological replicate 3

value: MSH1 mutant Dwarf-dr


title: Sample_13-H1

description: 4-weeks apical meristem, MSH1 mutant mild-dr, biological replicate 1


title: singles-K562-rep1-well-105


title: singles-K562-rep1-well-102


title: Sample_7-F1

description: 4-weeks apical meristem, epiF3, biological replicate 1


title: Sample_5-E2

description: 4-weeks apical meristem, Rutgers wild type, biological replicate 2

value: wild type


title: Sample_6-E3

description: 4-weeks apical meristem, Rutgers wild type, biological replicate 3


title: Sample_2-C2

description: 4-weeks apical meristem, MSH1 mutant Dwarf-dr, biological replicate 2


title: Sample_4-E1

description: 4-weeks apical meristem, Rutgers wild type, biological replicate 1


title: K562 GRO-seq

status: Public on Nov 10 2014

city: Ithaca

first: Leighton

middle: James

last: Core

state: NY

address: 417 Biotechnology Building

department: Moleular Biology and Genetics

institute: Cornell University

description: cDNA (from nascent RNA)

data_processing:
Library strategy: GRO-Seq
Pass Filter: Reads that pass filter were selected from fastq files.
Read Trimming: Reads were trimmed to 30 bases.
rDNA filter: Reads were first mapped to a copy of rRNA gene (GenBank accession #: U13369.1) including external and internal spacers, and only reads that were not mapped to the rDNA were kept.
Mapping to the genome: Bowtie was used to map 30mers with up to two mismatches to the genome.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Processed data files are bigWigs of each sample. Each entry represents the number of reads at each base.

source_name: K562 cells

growth_protocol: K562 cells were grown to a density of 5x10^6 cells/mL in RPMI 1640 supplemented with 10% fetal bovine serum, 100 units/mL penicillin and 100 μg/mL streptomycin, and 2 mmol/L L-glutamine. GM12878 were cultured as described previously (GSE39878).

extract_protocol:
Nuclei isolation: All steps performed and buffers kept at 4oC. 10 mls of cells were spun down at 700g in a swinging bucket rotor for 5 min. Cells were washed in 1X cold PBS. Cells were washed in 10ml of buffer W (10mM Tris-Cl, pH 7.5, 10mM KCl, 150mM sucrose, 5mM MgCl2, 0.5mM CaCl2, and 0.5 mM DTT). Cells were resuspended in 5mls of Buffer P (10mM Tris-Cl, pH 7.5, 10mM KCl, 250mM sucrose, 5mM MgCl2, 1mM EGTA, and 0.5 mM DTT, .05% tween-20 and/or .1% Igepal), and incubated 5 min. on ice. Permeabilized cells were washed twice in 5ml of buffer P, resuspended in 1ml of buffer P, and transferred to a 1.7ml eppendorf tube. Cells were pelleted at 1000 x g in a fixed angle rotor for 5min and then resuspended in 500 ml of buffer F (50 mM Tris-Cl pH 8.3, 40% glycerol, 5mM MgCl2, 0.1mM EDTA, 0.5mM DTT). Cells were pelleted at 100g for 5 min, resuspended in 100 ml of buffer F, and then flash frozen in liquid nitrogen.
GRO-seq libraries were prepared as in Core et al. (Core, Waterfall, and Lis, 2008), with the following modifications. Trizol (Invitrogen) was used to stop the reaction instead of DNase I and proteinase K treatment. The RNA was further extracted once with acid phenol:chloroform, and once with chloroform before precipitating with 2.5 volumes of -20oC ethanol. Bead binding buffers all contained 4units/ml of SUPERaseIN (Ambion) and the following buffers were slightly modified. Bead blocking buffer: 0.25X SSPE, 1mM EDTA, 0.05% Tween, 0.1% PVP, and 1mg/ml ultrapure BSA (Ambion); Binding buffer: 0.25XSSPE, 37.5mM NaCl, 1mM EDTA, 0.05% tween; Low-salt wash buffer: 0.2X SSPE, 1mM EDTA, 0.05% Tween. High-salt wash buffer: 0.25% SSPE, 137.5mM NaCl, 1mM EDTA, 0.05% Tween. The end repair steps were modified as follows. Pelleted RNA from the first bead binding was resuspended in 20ul, and heated to 70oC for 5min, followed by incubation on ice for 2min. 1.5ul tobacco acid pyrophosphatase (TAP) buffer, 4.5ul water, 1 ul SUPERaseIn, and 1.5ul TAP (Epicentre) were then added and the reaction incubated at 37oC for 1.5 hours. 1ul 300mM MgCl2 and 1ul T4 polynucleotide Kinase (PNK) were added to the reaction for an additional protocols l 30 min. for phosphorylating the 5'-ends, 20ul T4 PNK buffer, 2ul 100mM ATP, 145ul water, 1ul SUPERaseIn, and an additional 2ul of PNK were added for 30 min at 37oC. The reaction was then stopped by addition of 20mM EDTA followed by acid phenol extraction and precipitation.

treatment_protocol: No specific treatments performed for this study.

value: chronic myelogenous leukemic cell line

tag: rna source

value: nuclear run-on

tag: pull-down strategy

value: BrU

tag: antibody

value: anti-BrU (Santa Cruz Biotechnology, sc-32323-ac, lot# I2111)


title: Bone_marrow_2

status: Public on Oct 27 2014

city: Madison

first: Heidi

last: Dvinge

state: WI

address: 440 Henry Mall

department: Biomolecular Chemistry

institute: UW-Madison

data_processing:
Illumina CASAVA software was used for basecalling.
Reads were mapped to the UCSC hg19 (NCBI GRCh37) human genome assembly using Bowtie v1.0.0 and RSEM v1.2.4. RSEM was modified to call Bowtie  with the -v 2 mapping strategy. RSEM was then invoked with the arguments --bowtie-m 100 --bowtie-chunkmbs 500 --calc-ci --output-genome- bam on the gene annotation file.
Genome_build: hg19
Supplementary_files_format_and_content: Text files with RSEM-based expression estimates for coding and non-coding RNA transcripts.

source_name: Bone marrow

extract_protocol:
Bone marrow samples from healthy individuals were obtained from previously published samples (Stirewalt et al., Genes Chromosomes Cancer, 2008, PMID:17910043)
Libraries were prepared using the unstranded, polyA selected Illumina TruSeq protol.

value: Bone Marrow Mononuclear Cells


title: Bone_marrow_3


title: PBMC.cryo.48h.XX.01

description: gender: XX

data_processing:
Illumina CASAVA software was used for basecalling and sample de-multiplexing.
Reads were mapped to the UCSC hg19 (NCBI GRCh37) human genome assembly using Bowtie v1.0.0 and RSEM v1.2.4. RSEM was modified to call Bowtie  with the -v 2 mapping strategy. RSEM was then invoked with the arguments --bowtie-m 100 --bowtie-chunkmbs 500 --calc-ci --output-genome- bam on the gene annotation file.
Genome_build: hg19
Supplementary_files_format_and_content: Text files with RSEM-based expression estimates for coding and non-coding RNA transcripts.

source_name: Whole blood

extract_protocol:
Whole blood was extracted into purple-top BD Vacutainer vials with EDTA as anti-coagulent. PBMCs were isolated using a Ficoll gradient, and RNA was harvested using Trizol reagent and Qiagen RNA easy column.
The Illumina TruSeq RNA Sample Prep Kit was used with 2-4 ug of total RNA for the construction of sequencing libraries. The protocol was modified to select DNA fragments in the 100-400bp range using bead selection. Samples were multiplexed using Illumina barcodes to run four samples per sequencing lane.

value: PBMC

tag: treatment

value: cryopreserved

tag: donor

value: Female

tag: time


title: Bone_marrow_1


title: PBMC.cryo.24h.XY.02

description: gender: XY

value: Male


title: Sample_1-C1

description: 4-weeks apical meristem, MSH1 mutant Dwarf-dr, biological replicate 1

tag: tissue


title: Sample_14-H2

description: 4-weeks apical meristem, MSH1 mutant mild-dr, biological replicate 2


title: PBMC.cryo.1h.XY.02

description: gender: XY


title: Bone_marrow_4


title: PBMC.cryo.1h.XX.01

description: gender: XX


title: PBMC.cryo.24h.XX.01

description: gender: XX


title: PBMC.ice.48h.XX.03

description: gender: XX

value: stored on ice


title: PBMC.ice.48h.XY.04

description: gender: XY


title: PBMC.ice.24h.XY.04

description: gender: XY


title: PBMC.ice.0h.XY.04

description: gender: XY


title: PBMC.ice.24h.XX.03

description: gender: XX


title: PBMC.none.48h.XX.03

description: gender: XX

value: stored at room temperature


title: PBMC.none.0h.XX.01

description: gender: XX


title: PBMC.none.0h.XY.02

description: gender: XY


title: PBMC.none.24h.XY.04

description: gender: XY


title: PBMC.none.8h.XX.03

description: gender: XX


title: PBMC.none.24h.XX.03

description: gender: XX


title: PBMC.ice.0h.XX.03

description: gender: XX


title: PBMC.none.4h.XY.04

description: gender: XY


title: PBMC.cryo.48h.XY.02

description: gender: XY


title: PBMC.none.4h.XX.03

description: gender: XX


title: PBMC.none.8h.XY.04

description: gender: XY


title: PBMC.none.0h.XY.04

description: gender: XY


title: PBMC.none.0h.XX.03

description: gender: XX