title: ATAC-seq_HAP1_BCL7A_r1_2434_10

description:
ATAC-seq  on HAP1 cell line with BCL7A knockout, replicate 1
baf_complex.atacseq_peaks.raw_coverage.csv


title: ATAC-seq_HAP1_BCL11B_r2_2432_10

status: Public on Apr 30 2019

type: SRA

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

description:
ATAC-seq  on HAP1 cell line with BCL11B knockout, replicate 2
baf_complex.atacseq_peaks.raw_coverage.csv

library_source: genomic

data_processing:
Base calls provided by the Illumina Realtime Analysis software were converted into BAM format using Illumina2bam and demultiplexed using BamIndexDecoder (https://github.com/wtsi-npg/illumina2bam)
Sequenced reads were trimmed for adaptor sequences
Reads were mapped to hg19 whole genome using bowtie2 v2.2.4 with the –very-sensitive parameter
Duplicate reads were marked and removed with picard tools version 1.118
Peaks for ATAC-seq samples were called with MACS2 version 2.1.1.20160309 using the “–nomodel” and “–extsize 147” parameters
Genome_build: hg19
Supplementary_files_format_and_content: Each csv file contains read counts for each sample for each regulatory element

molecule: genomic DNA

organism: Homo sapiens

source_name: HAP1 cell line

growth_protocol: HAP1 WT and knock-out cells were cultured in Iscove’s Modified Dulbecco’s Medium (IMDM, Thermo Fisher Scientific, 21980-032) supplemented with 10% heat inactivated Fetal Bovine Serum (FBS, Thermo Fisher Scientific, 10500) and 1% Pen Strep (100 units/ml Penicillin, 100 µg/ml Streptomycin, Thermo Fisher Scientific, 15140-122). A549 cells were cultured in F-12K Nut Mix (Thermo Fisher Scientific, 21127-022) supplemented with 10% FBS and 1% Pen Strep.

extract_protocol: 50000 cells were resuspended in 25 µl transposase reaction mix (0.05% digitonin, 1x TD buffer, 0.08% TDE1 (Nextera DNA Library Preparation Kit, Illumina, FC-121-1031)) and incubated for 30 min, 37°C, 300 rpm. Then DNA was purified using MinElute kit (Qiagen, 28004) and eluted in 11 µl elution buffer. 1 µl was used to determine cycle number for PCR using a qPCR approach. The remaining 10 µl were complemented with 1x NEBnext High-Fidelity PCR master mix (New England BioLabs, M0541), 1.25 µM index primer 1 and 1.25 µM index primer containing a barcode. PCR was performed: 5 min 72°C, 30 sec 98°C, X cycles of 10 sec 98°C + 30 sec 63°C + 1 min 72°C, 1 min 72°C and then cleaned-up using Agencourt AMPure XP beads (Beckman Coulter, A63880).

tag: library

value: ATAC-seq

tag: cell line

tag: replicate

tag: clone

tag: knockout


title: ATAC-seq_HAP1_BCL7A_r2_2434_10

description:
ATAC-seq  on HAP1 cell line with BCL7A knockout, replicate 2
baf_complex.atacseq_peaks.raw_coverage.csv


title: 4C-seq_Fgf5_2i_4

city: Nijmegen

first: Hendrik

middle: G

last: Stunnenberg

address: Geert Grooteplein 30

country: Netherlands

institute: Radboud University

data_processing:
Library strategy: 4C-seq
4C-seq experiments were performed as described previously65 with minor modifications. Briefly, 10 million cells were cross-linked for 10 minutes with 2% paraformaldehyde in ES-culture medium, quenched with glycine and lysed in 30 ml lysis buffer (10mM Tris pH 7.5, 10mM NaCl, 0.2% NP-40, 1X protease inhibitors) for 30 minutes at 4 ̊ C . Nuclei were then incubated with 0.25% SDS for 30min in NEB buffer3 followed Triton X-100 treatment for 30 min both at 37 ̊ C. Nuclei were then digested with 700U DpnII enzyme (NEB) over night at 37 ̊C. Enzyme was inactivated at 65 ̊C for 15 min followed by  ‘in nuclei’ ligation at 16 ̊C with 2000U T4 ligase (NEB)66. Samples were then treated with protease K and RNAse A and DNA was purified by phenol–chloroform (Sigma: 77618-500ml). DNA was further digested with 50U BfaI enzyme, purified with QIAquick PCR Purification columns followed by second ligation at 16 ̊ C. 1000ng of 4C-seq library was amplified with bait-specific inverse primers using Expand Long template PCR sytem (Roche 11759060001) for 28 PCR cycles (Table S1). PCR products were then purified and 50ng DNA was used for library preparation using KAPA Hyperprep kit (Roche 07962363001) and 5 PCR cycles. Libraries were sequenced on the Illumina NextSeq500 to obtain paired-end sequenced of 50bp-long reads
Genome_build: mm9
Supplementary_files_format_and_content: BigWig tracks

organism: Mus musculus

source_name: Mouse Embryonic Stem Cells

growth_protocol: E14Tg2a ESCs were cultured in standard culture medium on gelatin coated-dishes without feeder cells. Serum supplemented medium contains Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 10% fetal calf serum, L-glutamine (2 nM), Na-Pyruvate (1 mM), non-essential amino acids (0.1 mM each), Penicillin Streptomycin, 2-mercaptoethanol (55 µM) and LIF (1000 U/ml, Milipore). For serum free culture, cells were maintained in NDiff 227 (StemCells, Inc.) supplemented with MEK inhibitor PD0325901 (1 μM) and GSK3 inhibitor CHIR99021 (3 μM) and LIF (1000 U/ml, Milipore). For EpiLSC-differentiation, 2i-ESCs were seeded in ~15,000 cells per cm2 density on Fibronectin (10 μg/ml) coated dishes and in NDiff 227 (StemCells, Inc.) supplemented with Penicillin Streptomycin (Gibco), 20 ng/ml ActivinA (R&D systems), 12 ng/ml bFGF (R&D systems) and 1% knock out serum replacement (Gibco) and cells were maintained for 72h in this culture.

extract_protocol:
Briefly, 10 million cells were cross-linked for 10 minutes with 2% paraformaldehyde in ES-culture medium, quenched with glycine and lysed in 30 ml lysis buffer (10mM Tris pH 7.5, 10mM NaCl, 0.2% NP-40, 1X protease inhibitors) for 30 minutes at 4°C  . Nuclei were then incubated with 0.25% SDS for 30 minutes in NEB buffer3 followed by Triton X-100 treatment for 30 minutes both at 37°C. Nuclei were then digested with 700 units DpnII enzyme (NEB) overnight at 37 ̊C. Enzyme was inactivated at 65 ̊C for 15 min followed by  ‘in nuclei’ ligation at 16 ̊C with 2,000 units T4 ligase (NEB)66. Samples were then treated with protease K and RNAseA and DNA was purified by phenol–chloroform (Sigma: 77618-500ml). DNA was further digested with 50 units BfaI, purified with QIAquick PCR purification columns followed by second ligation at 16°C. Next, 1000 ng of 4C-seq library was amplified with bait-specific inverse primers using Expand Long template PCR sytem (Roche 11759060001) for 28 PCR cycles.
PCR products were then purified and 50 ng DNA was used for library preparation using KAPA Hyperprep kit (Roche 07962363001) and 5 PCR cycles.  Illumina library preparation was done using the Kapa Hyper Prep Kit. For end repair and A-tailing double stranded DNA was incubated with end repair and A-tailing buffer and enzyme and incubated first for 30 minutes at 20°C and then for 30 minutes at 65°C.Subsequently adapters were  ligated  by adding 30µl ligation buffer, 10 Kapa l DNA  ligase, 5µl diluted adaptor  in a total volume of 110µl and incubated for 15 minutes at 15°C.Post-ligation cleanup was performed using Agencourt AMPure XP reagent and products were eluted in 20µl elution buffer. Libraries were amplified by adding 25µl 2x KAPA HiFi Hotstart ReadyMix and 5µl 10x Library Amplification Primer Mix and PCR, 10 cycles. Samples were purified using the QIAquick MinElute PCR purification kit and were size selected using bead purification protocol (200bp-1500bp).  Correct size selection was confirmed by BioAnalyzer analysis.   Sequencing was performed using Illumina Nextseq500  machines and generated 50bp pair end reads.

tag: cell type

value: Mouse Embryonic Stem Cells

tag: treatment


title: 4C-seq_Fgf5_Epi_1

value: EpiLSC


title: 4C-seq_Fgf5_ser_2

value: serum


title: ATAC-seq_HAP1_BCL11B_r1_2432_10

description:
ATAC-seq  on HAP1 cell line with BCL11B knockout, replicate 1
baf_complex.atacseq_peaks.raw_coverage.csv


title: 4C-seq_Fgf5_2i_3


title: ATAC-seq_HAP1_BCL11A_r1_2426_10

description:
ATAC-seq  on HAP1 cell line with BCL11A knockout, replicate 1
baf_complex.atacseq_peaks.raw_coverage.csv


title: ATAC-seq_HAP1_ARID2_r2_907_9

description:
ATAC-seq  on HAP1 cell line with ARID2 knockout, replicate 2
baf_complex.atacseq_peaks.raw_coverage.csv


title: 4C-seq_Bmi1_ser_4


title: 4C-seq_Fgf5_2i_1


title: 4C-seq_Fgf5_Epi_2


title: 4C-seq_Fgf5_Epi_3


title: ATAC-seq_HAP1_BCL11A_r2_2426_10

description:
ATAC-seq  on HAP1 cell line with BCL11A knockout, replicate 2
baf_complex.atacseq_peaks.raw_coverage.csv


title: 4C-seq_Bmi1_ser_3


title: 4C-seq_Fgf5_2i_2


title: 4C-seq_Bmi1_ser_2


title: ATAC-seq_HAP1_BRD7_r1_923_10

description:
ATAC-seq  on HAP1 cell line with BRD7 knockout, replicate 1
baf_complex.atacseq_peaks.raw_coverage.csv


title: ATAC-seq_HAP1_ARID1B_r2_582_7

description:
ATAC-seq  on HAP1 cell line with ARID1B knockout, replicate 2
baf_complex.atacseq_peaks.raw_coverage.csv


title: ATAC-seq_HAP1_ARID2_r1_907_9

description:
ATAC-seq  on HAP1 cell line with ARID2 knockout, replicate 1
baf_complex.atacseq_peaks.raw_coverage.csv


title: ATAC-seq_HAP1_ARID1B_r1_582_7

description:
ATAC-seq  on HAP1 cell line with ARID1B knockout, replicate 1
baf_complex.atacseq_peaks.raw_coverage.csv


title: ATAC-seq_HAP1_ARID1A_r2_618_3

description:
ATAC-seq  on HAP1 cell line with ARID1A knockout, replicate 2
baf_complex.atacseq_peaks.raw_coverage.csv


title: ATAC-seq_HAP1_ARID1A_r2_618_10


title: 4C-seq_Bmi1_ser_1


title: 4C-seq_Bmi1_Epi_2


title: ATAC-seq_HAP1_ARID1A_r1_618_3

description:
ATAC-seq  on HAP1 cell line with ARID1A knockout, replicate 1
baf_complex.atacseq_peaks.raw_coverage.csv


title: 4C-seq_Bmi1_Epi_1


title: 4C-seq_Bmi1_2i_4


title: ATAC-seq_HAP1_ACTB_r2_2471_10

description:
ATAC-seq  on HAP1 cell line with ACTB knockout, replicate 2
baf_complex.atacseq_peaks.raw_coverage.csv

value: ACTB


title: 4C-seq_Bmi1_2i_2


title: 4C-seq_Bmi1_2i_3


title: ATAC-seq_HAP1_ACTB_r1_2471_10

description:
ATAC-seq  on HAP1 cell line with ACTB knockout, replicate 1
baf_complex.atacseq_peaks.raw_coverage.csv


title: 4C-seq_Ablim2_ser_4


title: 4C-seq_Bmi1_2i_1


title: 4C-seq_Ablim2_Epi_4


title: 4C-seq_Ablim2_ser_1


title: 4C-seq_Ablim2_ser_3


title: ATAC-seq_HAP1_ARID1A_r1_618_10


title: 4C-seq_Ablim2_Epi_2


title: 4C-seq_Ablim2_Epi_1


title: 4C-seq_Ablim2_Epi_3


title: 4C-seq_Ablim2_2i_4


title: 4C-seq_Ablim2_2i_3


title: 4C-seq_Ablim2_2i_2


title: mouse_10_1

city: Seattle

first: Ting

last: Wang

state: WA

address: 1100 Fairview Ave. N.

department: Clinical Research

country: USA

institute: Fred Hutchinson Cancer Research Center

library_source: transcriptomic

data_processing:
Quality control for raw fastq files were performed with FastQC
Low quality reads and 3’ adapters were trimmed with Trim Galore! and Cutadapt.
The trimmed reads were aligned to mm10 with the RNA-seq aligner STAR v2.5.2a
Gene expressions of every sample were quantified by counting the number of unique fragments mapped to genes using featureCounts.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files including raw counts of genes for each sample.

molecule: total RNA

source_name: embryonic fibroblasts

extract_protocol:
Total RNA concentration and quality from each sample was assessed using Qubit 2.0 fluorometer (ThermoFisher Scientific) and Agilent TapeStation 2200 (Agilent, Santa Clara, CA)
Total RNA libraries were generated using Illumina TruSeq Stranded Total RNA Sample Preparation Guide Rev. E (Illumina, San Diego, CA). In brief, this process depletes nuclear ribosomal RNA (rRNA) and then fragments the remaining RNA, which was converted into first strand cDNA using reverse transcriptase and random primers. The second strand cDNA is generated using DNA polymerase I and RNase H. The cDNA fragments were further processed for adapter ligation, and then enriched with PCR to create the final cDNA library.

treatment_protocol: Mouse embryonic fibroblasts (MEFs), C2C12 myoblasts and HeLa cells were grown in DMEM medium supplemented with 25 mM glucose, 4 mM glutamine, 110 mg/ml pyruvate, 10% (v/v) FBS:FCS (1:1), 100 U/ml penicillin and 100 mg/ml streptomycin at 37°C under standard conditions (5% CO2; ambient O2; 95% relative humidity). HeLa cells were verified by SNP genotyping at the University of Pittsburgh HSCRF Genomics Research Core. Subconfluent wild type MEFs and HeLa cells were cultivated in media containing RHPS4 at indicated concentration (0, 1, 2, or 10 µM) and time (16 or 24h). Drug wash-out was performed by pre-warmed media replacement. EtBr treatment was conducted on subconfluent MEFs for 24 h in the presence of 25 or 250 ng/ml compound. Cells were collected by trypsinization, pelleted at 200 RCF for 5 min, washed with PBS, and flash freezed in liquid nitrogen for later DNA or RNA preparation.

tag: rhps4 treatment


title: mouse_10_2


title: 4C-seq_Ablim2_2i_1


title: mouse_2_3


title: metastasis sample from intestinal tumor reinjected specimen - T10 [2344 2016]

type: RNA

city: Sabadell

first: Antoni

last: Berenguer-LLergo

state: Barcelona

address: Parc del Taulí, 1

department: A8G2 Group - Rheumatology Service

country: Spain

institute: Parc Taulí Research and Innovation Institute (I3PT)

hyb_protocol: cDNA was hybridized to the microarray for 16 hours at 45ºC, washing and staining of microarrays was performed using a GeneChip Fluidics Station 450 (Affymetrix, Santa Clara, CA)

scan_protocol: Arrays were scanned with GeneChip scanner GSC3000 (Affymetrix, Santa Clara, CA)

data_processing: RMA normalization method as implemented in affy Bioconductor R package

label: biotin

organism: Drosophila melanogaster

label_protocol: 8 µg of cDNA was subsequently fragmented and labeled using GeneChip Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.

growth_protocol: Ttumours were grown and maintained by serial transplantation into adult hosts at 25ºC.

extract_protocol: RNA was isolated from tumor using magnetic beads. 25 ng of total RNA was amplified using the TransPlex® Complete Whole Transcriptome Amplification Kit (Sigma; reference WTA2). Amplification was performed for 17 cycles.

treatment_protocol: Allografts were dissected out of the adult host and splitted in several pieces. One was introduced in lysys buffer for RNA extraction and the rest were transplanted to new hosts.

tag: technical replicate

tag: tissue

tag: reinjection


title: mouse_2_2


title: 4C-seq_Ablim2_ser_2


title: mouse_0_1


title: mouse_0_2


title: mouse_2_1


title: mouse_0_3


title: metastasis sample from intestinal tumor reinjected specimen - T2 [2343 2016]


title: metastasis sample from intestinal tumor reinjected specimen - T1 [2342 2016]


title: metastasis sample from intestinal tumor reinjected specimen - T1 [2336 2016]


title: metastasis sample from intestinal tumor reinjected specimen - T10 [2341 2016]


title: metastasis sample from intestinal tumor reinjected specimen - T2 [2340 2016]


title: metastasis sample from intestinal tumor reinjected specimen - T2 [2337 2016]


title: MEL_4H8_ChIAPET_D0R1

city: Minneapolis

first: Marissa

last: Macchietto

address: 117 Pleasant Street SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota, Minneapolis

description:
ChIA-PET
processed_data_file: MEL_D0_3kb_edge_list.txt, MEL_D0_1kb_edge_list.txt, MEL_D0_3kb_vertices_with_connection_edge.bed, MEL_D0_1kb_vertices_with_connection_edge.bed

data_processing:
Half linker sequences were removed from reads and only the 20bp tags from each end were used for mapping. Tags were separated into two groups based on the half linker barcode information of the pair-end reads: the AA/BB group that should hold true interactions as well as some non-specific random ligations and the AB chimeric ligation group to estimate the extent of non-specific random ligations.
The tags were mapped to mm9 reference genomes with Bowtie, respectively using the parameters -S -q -v 2 -k 1 -m 1 --best –strata.
petNet pipeline was used to build Chromatin Interaction Graphs (Jansen el al, in preparation)
genome build: mm9
processed data files format and content: 3kb and 1kb vertices are generated from DNase-seq consolidated hotspots, together with the connection edges list and vertice list with edges based on both 3kb and 1kb vertices from day0 and day5 MEL ChIA-PET data

source_name: MEL

growth_protocol: Mouse erythroleukemia cells (MEL, ATCC, Manassas, VA) were grown in RPMI-1640 medium (Life Technologies, Carlsbad, CA) supplemented with penicillin/streptomycin (Life Technologies) and 10% FBS (VWR, Radnor, PA).  Trypan Blue (VWR) staining was performed before harvesting the cells for each assay in order to make sure that at least 90% of the cells were viable. All experiments were done with 2 biological replicates.

extract_protocol: Biological replicates of RNA Polymerase II ChIA-PET libraries for uninduced (MEL) and induced (MEL+DMSO) MEL were essentially constructed as previously described (Li et al. 2012) with additional changes to volume used in circularization (Heidari et al. 2014). The starting material was from 100-200 million cells and the ChIPs were performed using mouse anti-RNA polymerase II 4H8 antibody (catalog number sc-47701X, Santa Cruz Biotechnology, CA) and Dynabeads M-280 sheep anti-mouse beads (Life Technologies).

treatment_protocol: MELs grown to a density of 1 million/ml were differentiated using 2% DMSO (VWR) added to the medium and the cells were grown for another 5 days to induce the expression of hemoglobin genes. At least 80-90% of cells expressed hemoglobin based on their color and benzidine/hydrogen peroxide staining result.

value: MEL

tag: time


title: MEL_4H8_ChIAPET_D0R2


title: MEL_4H8_ChIAPET_D5R2

description:
ChIA-PET
processed_data_file: MEL_D5_3kb_edge_list.txt, MEL_D5_1kb_edge_list.txt, MEL_D5_3kb_vertices_with_connection_edge.bed, MEL_D5_1kb_vertices_with_connection_edge.bed


title: MEL_4H8_ChIAPET_D5R1


title: metastasis sample from intestinal tumor reinjected specimen - T1 [2339 2016]


title: MEL_DNase_D5R2

description:
DNAse-Seq
proessed_data_file: MEL_D5R2_DHS.bed, MEL_D5_R1R2_intersected_DHS.bed, MEL_D5_DNase_footprints_p_minus20.bed, MEL_D0D5_consolidated_DHS.bed, MEL_3kb_vertices.bed, MEL_1kb_vertices.bed

data_processing:
Reads were trimmed to 36bp and paired-end mapped to the mm9 reference genome using bowtie using parameters -S -q -v 2 -k 1 -m 1 -X 1000.
DNaseI hypersensitive sites were identified using the hotspot algorithm for each sample. DNaseI hotspot calls that passed the 1% FDR cutoff were used for further downstream analysis.
The intersection between hotspot calls of biological replicates is required to reciprocally overlap by 70% using Bedtools software
genome build: mm9
processed data files format and content: DNase-seq hotspot bed files from each individual samples, the intersected hotspot bed files from each differentiation stage and the consolidated hotspot bed file from both differentiation stages, together with Wellington footprint bed files with p-value lower than 10^(-20) from both undifferentiated and differentied MEL DNase-seq

extract_protocol: Biological replicates of DNase-seq libraries for uninduced and induced MELs were built as previously described except for the DNA purification below (Hesselberth et al. 2009). Briefly, 20 million nuclei were digested with 80U/ml DNaseI (Catalog number D4527, Sigma-Aldrich, St.Louis, MO) for 3 minutes at 37 degree Celsius. Following 1-hour digestion with proteinase K (Sigma-Aldrich), DNA samples were purified by phenol/chloroform (Fisher Scientific, Waltham, MA) and precipitated by isopropanol (Fisher Scientific) and sodium acetate, pH 5.5 (Life Technologies). DNA fragments between 25 and 100bp were purified by gel electrophoresis and constructed into sequencing libraries.


title: Day5_CPC_ATAC-seq-Rep1

city: Mannheim

first: Gergana

last: Dobreva

state: Baden Württemberg

address: Ludolf-Krehl-Str. 7-11

department: Cardiovascular Genomics and Epigenomics

country: Germany

institute: Medical Faculty Mannheim/University of Heidelberg

data_processing:
Library strategy: ATAC-Seq
Visualization of raw reads was done using FastQC
ATAC-Seq reads were mapped with bowtie2 to mm9 mouse genome. Samtools view (-F 1804 -f2) was used to remove unmapped, mate unmapped, not primary aligned reads. The MarkDuplicates.jar from Picard 1.136 was use to remove PCR artefacts. Peaks calling was performed with MACS14 60 (p1e5 --nomodel and --shiftsize 100), and peaks overlapping blacklist defined by ENCODE with the help of Bedtools v2.15 (intersect -wa)
BamCoverage function of deepTools2 62 (-b 20 -smooth 40 -e 150) was used to create normalized bigwig files (reads per genome coverage, RPGC)
Genome_build: mm9
Supplementary_files_format_and_content: Day5_CPC_Isl1_control_ATAC_Seq_merge.bw
Supplementary_files_format_and_content: Day5_CPC_control_ATAC_seq_peaks_annot.bed: Peaks file.

source_name: Cardiac progenitors

growth_protocol: E14 Tg(Nkx2–5-EmGFP) ES cells were maintained on mitomycin treated MEF in Knockout DMEM medium containing 4.5 mg/ml D-glucose, supplemented with 10% serum replacement, 2 mM L-Glutamine, 0.1 mM 2-mercaptoethanol, 1 mM sodium pyruvate, and 1,000 U/ml of leukemia inhibitory factor. For directed cardiomyocyte differentiation, ES cells were grown on gelatin in Neurobasal medium: DMEM/F12 (1:1) medium supplemented with 2,000 U/ml LIF and 10 ng/ml BMP4 for 2 days and differentiated by aggregation in low attachment bacterial dishes at a cell density of 75000 cells/ml in IMDM: F12 medium (3:1). After 48h aggregates were dissociated and re-aggregated in the presence of 5 ng/ml Activin A, 5ng/ml VEGF and 0.2ng/ml BMP4. 40h following the second aggregation, aggregates were dissociated and plated as a monolayer in Stempro-34 medium supplemented with Stempro34 nutrient supplement, L-Ascorbic Acid and 5ng/ml VEGF, 10ng/ml bFGF, and 25ng/ml FGF10 growth factors.

extract_protocol: ES cell derived cardiac progenitors were trypsinized and washed in PBS. 100,000 cells were resuspended in 50 uL cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal CA-630) and used for ATAC Library preparation using Tn5 Transposase from Nextera DNA Library Prep Kit (Illumina #15028211). After centrifugation (10 min, 500 g at 4 °C), cell pellet was resuspended in transposition reaction mix (25 µl TD-Buffer, 2.5 µl Tn5, 22.5 µl water) and incubated for 30 min at 37 °C with gentle mixing. Immediately following the transposition reaction, purification was carried out using MinElute PCR Purification Kit (Qiagen #28004).

value: ES cell derived cardiac progenitor cells

tag: passages

tag: strain


title: metastasis sample from intestinal tumor reinjected specimen - T10 [2338 2016]


title: MEL_DNase_D5R1

description:
DNAse-Seq
processed_data_file: MEL_D5R1_DHS.bed, MEL_D5_R1R2_intersected_DHS.bed, MEL_D5_DNase_footprints_p_minus20.bed, MEL_D0D5_consolidated_DHS.bed, MEL_3kb_vertices.bed, MEL_1kb_vertices.bed


title: MEL_DNase_D0R1

description:
DNAse-Seq
processed_data_file: MEL_D0R1_DHS.bed, MEL_D0_R1R2_intersected_DHS.bed, MEL_D0_DNase_footprints_p_minus20.bed, MEL_D0D5_consolidated_DHS.bed, MEL_3kb_vertices.bed, MEL_1kb_vertices.bed


title: MEL_RNA_D5R2

description: processed_data_file: MEL_RNA_seq_merged_fpkm.txt

data_processing:
Reads were trimmed to 50bp and mapped by Bowtie with mouse Gencode M1 transcriptome excluding all small RNAs as reference using the settings -aS --offrate 1 -v 3.
Transcription expression levels were determined by eXpress.
genome build: mm9, GENCODE M1 transcriptome
processed data files format and content: merged fpkm matrix file generated by eXpress

extract_protocol:
MEL total RNA was extract by RNeasy Kit (QIAGEN) and the quality was checked by RIN.
Biological replicates of stranded RNA-seq were built as previously described (Parkhomchuk et al. 2009). The cDNA was ligated to Nextflex DNA barcodes (Bioo Scientific, Austin, TX) compatible with Illumina Sequencing platform and the fraction of the ligation product between 300-350bp (corresponding to 175-225bp insert size) was selected by gel electrophoresis.


title: MEL_RNA_D0R2


title: MEL_RNA_D0R1


title: Day5_CPC_ATAC-seq-Rep2

data_processing:
Library strategy: ATAC-Seq
ATAC-Seq reads were mapped with bowtie2 to mm9 mouse genome. Samtools view (-F 1804 -f2) was used to remove unmapped, mate unmapped, not primary aligned reads. The MarkDuplicates.jar from Picard 1.136 was use to remove PCR artefacts. Peaks calling was performed with MACS14 60 (p1e5 --nomodel and --shiftsize 100), and peaks overlapping blacklist defined by ENCODE with the help of Bedtools v2.15 (intersect -wa)
Genome_build: mm9
Supplementary_files_format_and_content: Day5_CPC_Isl1_control_ATAC_Seq_merge.bw
Supplementary_files_format_and_content: Day5_CPC_control_ATAC_seq_peaks_annot.bed: Peaks file.


title: MEL_DNase_D0R2

description:
DNAse-Seq
processed_data_file: MEL_D0R2_DHS.bed, MEL_D0_R1R2_intersected_DHS.bed, MEL_D0_DNase_footprints_p_minus20.bed, MEL_D0D5_consolidated_DHS.bed, MEL_3kb_vertices.bed, MEL_1kb_vertices.bed


title: HEK sgMYOD cntrl BRD4

city: Bethesda

first: Javed

last: Khan

state: MD

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

description: DNA (ChIP-enriched)

data_processing:
ChIP enriched DNA reads were mapped to reference genome using BWA version 0.7.10.
The ChIP-seq and DNase-seq peaks were called by MACS2 version 2.1.0.
Enrichment of known and de novo motifs were found using HOMER version 4.8.2.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_peaks.narrowPeak.nobl.GREAT.bed: Peak files are tab-delimited text files for each sample.

growth_protocol: Cell lines were grown in high-glucose DMEM supplemented with 10% FBS serum, 10 mM HEPES, NEAA, Pen/Strep, and 55 μM 2-Mercaptoethanol.

extract_protocol:
DNA was extracted from ChIP-seq samples prepared following the Active Motif ChIP-IT High Sensitivity kit protocol.
Standard Illumina barcodes were introduced during library preparation.

treatment_protocol: (dCas9 & ms2-FKBPx2)-infected cells were grown to 70% confluence, transfected with sgRNA using a PEI protocol. Media was changed 16 hours later, and cells were treated with 50 nM of CEM87 for 48 hours. Samples were then harvested after 1% formaldehyde fixation for 10 minutes, sonicated, processed and ChIP-enriched via standard protocols (Active Motif ChIP-IT HS kit) with indicated antibodies.

value: 293 HEK

tag: antibody

tag: enrichment target

tag: target function

value: Acetylated Lysine Reader, Active Enhancers

value: 0nM CEM87, sgMYOD


title: HEK sgNT CEM87 BRD4

description: DNA (ChIP-enriched)

value: 50nM CEM87, sgNonTargeting


title: HEK sgMYOD CEM87 BRD4

description: DNA (ChIP-enriched)

value: 50nM CEM87, sgMYOD


title: MEL_RNA_D5R1


title: Ceben1OxBZ2

city: Calgary

first: John

middle: Stuart

last: Gilleard

state: Alberta

address: 3330, Hospital Dr, NW

department: Faculty Veterinary Medicine

country: Canada

institute: University of Calgary

data_processing:
Raw reads were aligned to the C. elegans genome (WS247) with subread 1.4.6 (default paramters).
Reads overlapping protein coding genes were counted with featureCounts (from subread 1.4.6, default paramters)
Genome_build: PRJNA13758 WS247
Supplementary_files_format_and_content: raw count data as generatecd by featureCounts, text file, WormBase gene ids in rows, samples in columns

organism: Caenorhabditis elegans

source_name: Mixed stages of larva

growth_protocol: C. elegans stock strains were maintained on NGM agar plates with OP50 E. coli as the food source using standard procedures.  Three biological replicates of approximately 20,000 L1 larvae C. elegans CB3474 ben-1(e1880)III were cultured in NGM liquid media with E. coli OP50 at 1% (w/vol) at 20°C for approximately 70 hours until the adult stage, concentrations were kept consistent with micro-array experiment performed previously.

extract_protocol:
RNA was extracted using TRIzol as described by the manufacturer protocol (Invitrogen # 15596-018); total RNA pellets were suspended in DEPC treated water. RNA was isolated and treated with DNaseI as per manufacturer protocol (Qiagen #74134). Only samples that had a minimum A260/A280 ratio of 1.7 and a RIN of greater than 8.0 were used.
Total RNA extracted and sent to Genome Quebec [http://gqinnovationcenter.com] for template preparation and RNA-Seq Next Generations Sequencing on the Illumina HiSeq platform with PE100 to read depth of >50,000,000 aligned reads.

treatment_protocol: Cultures were exposed to 1.13mM of either albendazole (Sigma Cat# A4673), mebendazole (Sigma Cat# M2523), thiabendazole (Sigma Cat#T8904), oxfendazole (Sigma Cat#34176), fenbendazole (Sigma Cat# F5396) dissolved in DMSO as well as a DMSO negative control solution of for 4 hours, care was taken to ensure that DMSO concentration were less than 1%. The worms were then harvested by centrifugation at 300xg for 3 minutes, no brake, and cleaned on a sucrose gradient, the supernatant was decanted and the pellet stored in TRIzol  (Invitrogen # 15596-018) and immediately frozen at -80°C until processing.

tag: drug

value: OxB


title: IL-4c-stimulated Bhlhe40WT LPM rep2

city: St. Louis

first: Brian

middle: T

last: Edelson

state: MO

address: 425 S. Euclid Ave.

department: Pathology and Immunology

institute: Washington University in St. Louis

hyb_protocol: hybridization performed by the Genome Technology Access Core (WUSTL)

data_processing: DNASTAR ArrayStar program using the RMA quantile method of normalization

source_name: peritoneal lavage

extract_protocol: RNA isolated with E.Z.N.A. MicroElute Total RNA kit (Omega Bio-Tek)

treatment_protocol: See above

tag: genotype

value: IL-4c injections

tag: tx conditions

value: Day 0, 2, sacrifice Day 4

value: LPM

tag: gender

value: male


title: naïve Bhlhe40WT LPM rep2

scan_protocol: performed by the Genome Technology Access Core (WUSTL)

value: untreated


title: Ceben1OxBZ3

value: OxBZ


title: IL-4c-stimulated Bhlhe40LysM LPM rep1

label_protocol: performed by the Genome Technology Access Core (WUSTL)


title: naïve Bhlhe40KO LPM rep2


title: IL-4c-stimulated Bhlhe40KO LPM rep1


title: IL-4c-stimulated Bhlhe40LysM LPM rep2


title: LNK overexpressing cells treated with interferon gamma

city: Singapore

first: SIQIN

last: ZHOU

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were quantile normalized followed by log2 transformed using beadarray Bioconductor package.

source_name: Human melanoma cell line M202

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: M202 cells were growth until 90% confluent, and then either treated with or without IFNG (2000 U/ml) for 24 hours.

extract_protocol: RNA was harvested using RNeasy Mini Kit.

tag: cell line


title: Ceben1OxBZ1


title: GFP overexpression control cells treated with interferon gamma

treatment_protocol: M202 cells were growth until 90% confluent, and then either treated with or without IFNG (2000 U/ml) for 24 hours.


title: naïve Bhlhe40WT AM rep1

source_name: lung digest

tag: cell type

value: AM


title: naïve Bhlhe40WT LPM rep3

tag: treatment


title: naïve Bhlhe40WT LPM rep1


title: IL-4c-stimulated Bhlhe40WT LPM rep1


title: naïve Bhlhe40WT AM rep2


title: naïve Bhlhe40KO AM rep1


title: naïve Bhlhe40KO LPM rep3


title: IL-4c-stimulated Bhlhe40KO LPM rep2


title: naïve Bhlhe40KO LPM rep1


title: naïve Bhlhe40KO AM rep2


title: GFP overexpression control cells


title: LNK overexpressing cells


title: Ceben1FBZ2

value: FBZ


title: Ceben1FBZ3


title: Ptet_2_plus_HR

city: Bronx

first: Kamini

last: Singh

state: NY

address: 1300 Morris Park Ave, Golding 203

department: Molecular Pharmacology

institute: Albert Einstein College of Medicine

description:
MycNeg_predicted_orfs_info.txt
RF_MycNeg_HarPos_Rep2.sorted.bam.MD.bam

data_processing:
Deep sequencing libraries were generated from these fragments and sequenced on the HiSeq 2000 platform. Genome annotation was from the Ensembl database release 75 (http:// www.ensembl.org/).
Ribosome footprint (RF) reads were aligned to reference genome GRCh37 using STAR . STAR clips the linker sequence (5’- CTGTAGGCACCATCAAT-3’), which is technically introduced during RF library construction, and trims the remaining sequence from the 3’ end while aligning the reads to reference sequence. Briefly, we set the parameters for PALMapper as follows: maximum number of mismatches: 2; minimum aligning length: 15; maximum intron length (splice alignment): 10000. We only use the uniquely aligned reads for further analysis.
To remove ribosome RNA, the footprint reads were also aligned to a ribosome sequence database using STAR with the same parameters except allowing splice alignment. We retrieved the human ribosome sequences from SILVA35 databases. The FASTA file was used as reference sequence to align against. The rRNA-aligned reads were filtered out from GRCh37-aligned reads.
After removing the rRNA, we still observed a portion of reads that were dominated by linker sequence and Illumina P7 adapter. These reads can also be trimmed during mapping and cause false alignment. Therefore, we searched a string of 1~8 nt from linker sequence around the trimming site (±2 bp) allowing 1 nt mismatch. We removed the read if there was no such linker sequence. Finally, we filtered out reads ≤ 24-bp and ≥ 36-bp, and the remaining reads with aligned length from 25- to 35-bp were used to analyse the translational effects of Myc.
Total mRNA sequencing reads were aligned to the GRCh37 reference using STAR. We performed the splice alignment and only use the uniquely aligned reads with maximum 3 mismatches. rRNA contaminating reads were also filtered out using the same strategy described before.
Genome_build: GRCh37
Supplementary_files_format_and_content: RiboDiff analysis of Ribosome footprint and total RNA libraries generated from human B-lymhoma cell line P493 in Myc On and Off samples is provided as a txt file.

source_name: P493 cell line

growth_protocol: Human P493 cells were grown in RPMI-1640 supplemented with 10% FBS and 1% Pen/Strep Cells were kept at 37 °C in humidified 5% CO2 in air.

extract_protocol:
Total RNA and ribosome protected fragments were isolated following published protocol ( Ingolia, et., al., Nature Protocols 2012).
RNA libraries were prepared for sequencing using standard Illumina protocols. Ribosome protected fragments were prepared for sequencing using  Ribosome footprinting protocole described in Ingolia, et., al., Nature Protocols 2012.

treatment_protocol: Human B-cell lymphoma P493 cells were treated with Tetracycline (0.1 uM) for 24 hrs followed by cycloheximide treatment for 10 minutes.


title: Ptet_1_plus_HR_RF

description:
Ribosome protected RNA
MycNeg_predicted_orfs_info.txt
RF_MycNeg_HarNeg_Rep1.sorted.bam.MD.bam

data_processing:
Library strategy: Ribo-seq
Deep sequencing libraries were generated from these fragments and sequenced on the HiSeq 2000 platform. Genome annotation was from the Ensembl database release 75 (http:// www.ensembl.org/).
Ribosome footprint (RF) reads were aligned to reference genome GRCh37 using STAR . STAR clips the linker sequence (5’- CTGTAGGCACCATCAAT-3’), which is technically introduced during RF library construction, and trims the remaining sequence from the 3’ end while aligning the reads to reference sequence. Briefly, we set the parameters for PALMapper as follows: maximum number of mismatches: 2; minimum aligning length: 15; maximum intron length (splice alignment): 10000. We only use the uniquely aligned reads for further analysis.
To remove ribosome RNA, the footprint reads were also aligned to a ribosome sequence database using STAR with the same parameters except allowing splice alignment. We retrieved the human ribosome sequences from SILVA35 databases. The FASTA file was used as reference sequence to align against. The rRNA-aligned reads were filtered out from GRCh37-aligned reads.
After removing the rRNA, we still observed a portion of reads that were dominated by linker sequence and Illumina P7 adapter. These reads can also be trimmed during mapping and cause false alignment. Therefore, we searched a string of 1~8 nt from linker sequence around the trimming site (±2 bp) allowing 1 nt mismatch. We removed the read if there was no such linker sequence. Finally, we filtered out reads ≤ 24-bp and ≥ 36-bp, and the remaining reads with aligned length from 25- to 35-bp were used to analyse the translational effects of Myc.
Total mRNA sequencing reads were aligned to the GRCh37 reference using STAR. We performed the splice alignment and only use the uniquely aligned reads with maximum 3 mismatches. rRNA contaminating reads were also filtered out using the same strategy described before.
Genome_build: GRCh37
Supplementary_files_format_and_content: RiboDiff analysis of Ribosome footprint and total RNA libraries generated from human B-lymhoma cell line P493 in Myc On and Off samples is provided as a txt file.


title: Ptet_1_plus_HR

description:
MycNeg_predicted_orfs_info.txt
RF_MycNeg_HarPos_Rep1.sorted.bam.MD.bam


title: Ptet_2_plus_HR_RF

description:
Ribosome protected RNA
MycNeg_predicted_orfs_info.txt
RF_MycNeg_HarNeg_Rep2.sorted.bam.MD.bam


title: Ptet_3_plus_HR_RF

description:
Ribosome protected RNA
MycNeg_predicted_orfs_info.txt
RF_MycNeg_HarNeg_Rep3.sorted.bam.MD.bam


title: P493_1_plus_HR_RF

description:
Ribosome protected RNA
MycPos_predicted_orfs_info.txt
RF_MycPos_HarPos_Rep1.sorted.bam.MD.bam


title: Ceben1FBZ1


title: P493_2_plus_HR_RF

description:
Ribosome protected RNA
MycPos_predicted_orfs_info.txt
RF_MycPos_HarPos_Rep2.sorted.bam.MD.bam


title: Ceben1TBZ4

value: TBZ


title: Ceben1MBZ2

value: MBZ


title: P493_2_plus_HR

description:
MycPos_predicted_orfs_info.txt
RF_MycPos_HarNeg_Rep3.sorted.bam.MD.bam


title: Ceben1MBZ3


title: Ceben1TBZ3


title: Ceben1MBZ1


title: P493_1_plus_HR

description:
MycPos_predicted_orfs_info.txt
RF_MycPos_HarNeg_Rep1.sorted.bam.MD.bam


title: Ceben1ABZ1

value: ABZ


title: Ceben1DMSO2

value: DMSO


title: Ceben1TBZ2


title: HAX-13 Activator-BCL6

city: Lisbon

first: Andreia

middle: Jesus

last: Amaral

state: Estremadura

address: Camp Grande

department: Gene Expression and Bioinformatics Unit

country: Portugal

institute: Center for Biosystems, Integrative and Functional Genomics

data_processing:
The raw reads obtained from each library were pre-processed using the HiSeq Control Software 1.5.15.1, RTA 1.13.48.0 and CASAVA-1.8.2.
Quality  control  and  filtering  were  performed  using  in-house  developed  PERL scripts for removal of reads with homopolymers, uncalled bases or an average Phred QS < 20. The  remaining  reads  were  mapped  into  the  GRch37.42  genome  using  Bowtie  0.12.7
The  identification  of  peaks  in  the  ChIP-Seq libraries  was  performed  within R  statistical  environment  (R  Development  Core  Team  (2008)) and Bioconductor (Gentleman et al. 2004). RSamtools package (Morgan et al. 2016) was used to import BAM files. GenomicRanges package (Lawrence et al. 2013) was used to identify naïve peaks and operations of intersection, union and subtraction between peaks of different libraries. Gene  ontology  and  enrichment  analyses were  performed  using  DAVID  v6.7 (Huang  et  al. 2009a,  2009b). MEME  suite (Bailey  et  al.  2009)  was  used  for de  novo  motif  discovery  and GeneMania (Warde-Farley  et  al.  2010)  to  construct  a  weighted  interaction  networks  from  hit gene lists.
Genome_build: GRch37.42  genome
Supplementary_files_format_and_content: correspnd to a tsv table with the genomic identification of peaks, width and number of reads in the relelvant libraries (the column is identified with the number of the library, e.g. ctrl2 corresponds to HAX2, and feature identification plus information of relative position of the peak to the feature.

source_name: colorectal adenocarcinoma cell line

growth_protocol: DLD-1 colorectal cells were maintained in DMEM medium and supplemented with 10% (v/v) foetal  bovine  serum  (FBS)  (all  from  Gibco),  regularly  checked  for  absence  of  mycoplasm infection. Cells were transfected  as previously described (15), using  a  1:4 proportion (g/l)  of DNA:Lipofectamine  2000  (Invitrogen).  Total  amounts  of  transfected  plasmid  DNA  for  ChIP assays were 15 g per  100-mm dish, for pull-down  assays were 5 g per 60-mm dish  and for transcript expression analysis were 2,5 g per 35-mm dish.

extract_protocol:
Beads were thoroughly washed and co-precipitated DNA was purified  with  the  IPure  Kit  (Diagenode), after  cross-link  reversion
Library  construction  for  ChIP  sequencing  was  performed  using  the TruSeq DNA sample prep kit from Illumina and following manufacturer's instruction.

treatment_protocol: DLD-1 cells were transfected with  empty  vector (basal/control)  or pEGFP-C1199Tiam1  and treated with vehicle (RAC1/PAK1 activation) or 20 microM EHT 1864 (RAC1/PAK1 inhibition) for 16 h.  ChIP  was  performed  20  h  after  transfection.

tag: passage

tag: disease state

value: Dukes' type C, colorectal adenocarcinoma

value: rabbit polyclonal anti-BCL6 (N-3) (sc-858 X)

value: transfected with pEGFP-C1199Tiam1 and treated with vehicle (RAC1/PAK1 activation)


title: HAX-11 Inhibitor-STAT5

value: rabbit polyclonal anti-STAT5 (C-17) (sc-835 X)

value: transfected with pEGFP-C1199Tiam1 and treated with 20 microM EHT 1864 (RAC1/PAK1 inhibition)


title: HAX-14 Inhibitor-BCL6

description: processed data file: Peak.Inib.HGNC.tsv


title: HAX-12 Inhibitor-BCL6

description: processed data file: Peak.Inib.BCL6.HGNC.tsv


title: HAX-8 Ctrl-BCL6

description: processed data file: Peak.Activ.HGNC.tsv

value: transfected with empty vector


title: HAX-9 Activator-STAT5

description: processed data file: Peak.Activ.STAT5.HGNC.tsv


title: Ceben1ABZ2


title: HAX-10 Activator-BCL6


title: Ceben1ABZ3


title: Ceben1DMSO3


title: P493_3_plus_HR_RF

description:
Ribosome protected RNA
MycPos_predicted_orfs_info.txt
RF_MycPos_HarPos_Rep3.sorted.bam.MD.bam


title: HAX-7 Ctrl-STAT5

description: processed data file: Peak.Inib.HGNC.tsv


title: HAX-6 Inhibitor-BCL6


title: HAX-4 Activator-BCL6


title: HAX-5 Inhibitor-STAT5


title: Ceben1DMSO1


title: HAX-3 Activator-STAT5


title: Spermatogonia_ChIP-seq16_H3K4me2

city: Ste Anne-de-Bellevue

first: Romain

last: Lambrot

state: QC

address: 21111 Lakeshore road

department: Animal Science

institute: McGill University

data_processing:
Basecalling was performed with RTA 1.18.64.
Sequenced reads were trimmed for adaptor sequence and were then aligned to the mm10 genome assembly using Bowtie2 (Version: 2.2.9). Aligned reads were then filterd to allow for a maximum of 3 mismatches.
Duplicates were marked using Picard tools.
Genomic regions enriched in H3K4me2 (peaks) were identified using the software MACS2 with the parameters --broad --broad-cutoff 0.05 --mfold 5 50 --nomodel over input files.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files were generated form the bedgraphs files generated by MACS2 using the bedGraphToBigWig utility (UCSC)

source_name: Testis of GOF/deltaPE-Oct4/GFP mice

extract_protocol:
Testes were removed and decapsulated. They were then digested with collagenase B (2mg/mL) for 10 minutes at 37°C. After rinsing in PBS, another digestion with 0.25% trypsin-EDTA for 5 minutes at 37°C was performed. The resulting cell suspension was washed twice, resuspended in sterile phosphate buffer solution (PBS) with DNase (50μg/mL) and filtered (40μm). Spermatogonia were isolated by fluorescence-activated cell sorting of Oct4-GFP positive germ cells with a FACSAria III laser sorter.
ChIP-seq libraries were prepared using the Kapa HTP Library Preparation Kit (Roche) as per the manufacturer's recommendations except that adapters and PCR primers were diluted 100-fold and the size selection step was done after the PCR step.

tag: tissue

value: testis

value: spermatogonia

tag: chip antibody

value: H3K4me2 (Millipore 07-030)


title: Spermatogonia_ChIP-seq15_H3K4me2


title: HAX-2 Ctrl-BCL6


title: HAX-1 Ctrl-STAT5

description: processed data file: Peak.Inib.HGNC.tsv


title: Sample_P493_1_RF

description: Ribosome protected RNA

data_processing:
Deep sequencing libraries were generated from these fragments and sequenced on the HiSeq 2000 platform. Genome annotation was from the Ensembl database release 75 (http:// www.ensembl.org/).
Ribosome footprint (RF) reads were aligned to reference genome GRCh37 using STARÊ. STAR clips the linker sequence (5Õ- CTGTAGGCACCATCAAT-3Õ), which is technically introduced during RF library construction, and trims the remaining sequence from the 3Õ end while aligning the reads to reference sequence. Briefly, we set the parameters for PALMapper as follows: maximum number of mismatches: 2; minimum aligning length: 15; maximum intron length (splice alignment): 10000. We only use the uniquely aligned reads for further analysis.
To remove ribosome RNA, the footprint reads were also aligned to a ribosome sequence database using STAR with the same parameters except allowing splice alignment. We retrieved the human ribosome sequences from SILVA35 databases. The FASTA file was used as reference sequence to align against. The rRNA-aligned reads were filtered out from GRCh37-aligned reads.
After removing the rRNA, we still observed a portion of reads that were dominated by linker sequence and Illumina P7 adapter. These reads can also be trimmed during mapping and cause false alignment. Therefore, we searched a string of 1~8 nt from linker sequence around the trimming site (±2 bp) allowing 1 nt mismatch. We removed the read if there was no such linker sequence. Finally, we filtered out reads ² 24-bp and ³ 36-bp, and the remaining reads with aligned length from 25- to 35-bp were used to analyse the translational effects of Myc.
Total mRNA sequencing reads were aligned to the GRCh37 reference using STAR. We performed the splice alignment and only use the uniquely aligned reads with maximum 3 mismatches. rRNA contaminating reads were also filtered out using the same strategy described before.
Genome_build: GRCh37
Supplementary_files_format_and_content: RiboDiff analysis of Ribosome footprint and total RNA libraries generated from human B-lymhoma cell line P493 in Myc On and Off samples is provided as a txt file.

growth_protocol: Human P493 cells were grown in RPMI-1640 supplemented with 10% FBS and 1% Pen/Strep Cells were kept at 37 ¡C in humidified 5% CO2 in air.

tag: molecule type

value: Ribosome protected RNA


title: Sample_P493tet_1_RF

description: Ribosome protected RNA

value: tetracycline (0.1 uM)


title: Sample_P493tet_3_RF

description: Ribosome protected RNA


title: Sample_P493_2_RF

description: Ribosome protected RNA


title: Sample_P493_3_RF

description: Ribosome protected RNA


title: Sample_P493tet_1_RNA

value: Total RNA


title: Sample_P493tet_2_RNA


title: Sample_P493_2_RNA


title: Sample_P493_1_RNA


title: ATACseq_serum_8h.Rep2

data_processing:
ATAC-seq reads were aligned to the mm9 genome assembly using Bowtie2 and reads with mapping quality less than 15 were discarded. PCR duplicates were removed from mapped BAM files and in case of pair-end sequencing, paired fragments were kept only when both reads were mapped uniquely to the same genomic region (unique and concordant alignments). Fragment size modeling was then applied on filtered BAM files (http://code.google.com/p/phantompeakqual-tools/) and peaks were called using MACS2  (http://github.com/taoliu/MACS/) and with default (narrow) settings.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig tracks, data are not normalized for sequencing depth.

growth_protocol: E14Tg2a ESCs were cultured in standard culture medium on gelatin coated-dishes without feeder cells. For serum culture, Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 10% fetal calf serum, L-glutamine (2 nM), Na-Pyruvate (1 mM), non-essential amino acids (0.1 mM each), Penicillin Streptomycin, 2-mercaptoethanol (55 µM) and LIF (1000 U/ml, Milipore) was used. For serum free culture, cells were transferred from serum-medium to NDiff 227 (StemCells, Inc.) supplemented with MEK inhibitor PD0325901 (1 μM) and GSK3 inhibitor CHIR99021 (3 μM) and LIF (1000 U/ml, Milipore) or maintained for long term (>4 weeks) in 2i medium (2i_LT).

extract_protocol:
Cells were fixed with 1% formaldehyde (Sigma) in ES-medium. Fixed cells were sonicated using a Diagenode Bioruptor UCD-300 for 4x1 minutes (30 seconds on; 30 seconds off). 50µl of chromatin (500,000 cells) were used with 0.5-1µg of H3K27ac antibody (Diagenode) and incubated overnight at 4ºC with rotation. For TF-ChiP-seq, 15-million cells were used per ChIP together with 15 μg anti-GFP antibody (ab290, Abcam) and 3 ChIP-samples were pooled to yield chromatin equal to 30-million cells per transcription factor. Antibody-chromatin complexes were incubated with protein-A/G magnetic beads, eluted, Supernatant was collected, 8µl 5M NaCl, 3µl proteinase K were added and samples were incubated for 4 hours at 65°C. Finally samples were purified using Qiagen; Qiaquick MinElute PCR purification Kit and eluted in 20µl EB. De-crosslinked DNA was used for library construction using KAPA Hifi kit according to manufacturer’s instruction.
Illumina library preparation was done using the Kapa Hyper Prep Kit. For end repair and A-tailing double stranded DNA was incubated with end repair and A-tailing buffer and enzyme and incubated first for 30 minutes at 20°C and then for 30 minutes at 65°C.Subsequently adapters were  ligated  by adding 30µl ligation buffer, 10 Kapa l DNA  ligase, 5µl diluted adaptor  in a total volume of 110µl and incubated for 15 minutes at 15°C.Post-ligation cleanup was performed using Agencourt AMPure XP reagent and products were eluted in 20µl elution buffer. Libraries were amplified by adding 25µl 2x KAPA HiFi Hotstart ReadyMix and 5µl 10x Library Amplification Primer Mix and PCR, 10 cycles. Samples were purified using the QIAquick MinElute PCR purification kit and 300bp fragments selected using E-gel. Correct size selection was confirmed by BioAnalyzer analysis.   Sequencing was performed using Illumina HiSeq 2000 machines and generated 43bp single end reads.

tag: background strain

value: Mouse Embryonic Stem Cells

value: serum


title: ATACseq_genomic


title: ATACseq_serum_Day1.Rep1


title: ATACseq_serum_Day3.Rep2


title: ATACseq_serum_8h.Rep1


title: ATACseq_2i_8h.Rep2


title: ATACseq_serum_Day3.Rep1


title: ATACseq_2i_Day1.Rep2


title: ATACseq_2i_8h.Rep1


title: ATACseq_2i_Day1.Rep1


title: Sample_P493tet_2_RF

description: Ribosome protected RNA


title: ATACseq_2iDay7.Rep1


title: U373MG_carnosic acid_24h

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

description: The drug administration was carried out in DMEM-3% FBS

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: ScanArray Express (PerkinElmer Japan Co., Ltd.) was used for scanning. Images were quantified using GenePix Pro version 6.0(Axon Instruments).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: U373MG cells

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: U373MG cells were continuously cultured in DMEM-10% FBS.

extract_protocol: Total RNA was extracted by using RNeasy Mini kit (QIAGEN).

treatment_protocol: U373MG cells were passaged into 10 cm diameter dishes. In the next day, the media was changed to DMEM-3% FBS. After 24 h incubation, the cells were administrated with DMSO (vehicle), or 1 mM edaravone, or 50 microM carnosic acid, or both 1 mM edaravone and 50 microM carnosic acid in DMEM-3% FBS for 24 h.

value: astrocytoma

value: 50 microM carnosic acid for 24 h


title: U373MG_edaravone/carnosic acid_24h

value: 1 mM edaravone and 50 microM carnosic acid for 24 h


title: ATACseq_2iDay3.Rep3


title: ATACseq_2iDay1.Rep3


title: U373MG_DMSO_24h

value: DMSO for 24 h


title: ATACseq_serum_Day1.Rep2


title: ATACseq_2i.Rep1


title: ATACseq_2i.Rep2


title: ATACseq_serum.Rep1


title: ATACseq_serum.Rep2


title: ATACseq_2i.Rep3


title: ATACseq_2i8h.Rep3


title: ATACseq_2i_Day3.Rep2


title: Klf4-C2-serum

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie2 and reads with mapping quality less than 15 were discarded. PCR duplicates were removed from mapped BAM files and in case of pair-end sequencing, paired fragments were kept only when both reads were mapped uniquely to the same genomic region (unique and concordant alignments). Fragment size modeling was then applied on filtered BAM files (http://code.google.com/p/phantompeakqual-tools/) and peaks were called using MACS2  (http://github.com/taoliu/MACS/) and with default (narrow) settings.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig tracks, data are not normalized for sequencing depth.

growth_protocol: E14Tg2a ESCs were cultured in standard culture medium without feeder and on gelatin coated-dishes. Serum supplemented medium contains Dulbecco's Modified Eagle's Medium (DMEM, Gibco) supplemented with 10% fetal calf serum (FCS, Gibco), L-glutamine (2 nM, Gibco), Na-Pyruvate (1 mM, Gibco), non-essential amino acids (0.1 mM each, Gibco), Penicillin Streptomycin (Gibco), 2-mercaptoethanol (55 µM, Gibco) and LIF (1000 U/ml, Milipore). For serum free culture, cells were maintained in NDiff 227 (StemCells, Inc.) supplemented with MEK inhibitor PD0325901 (1 μM) and GSK3 inhibitor CHIR99021 (3 μM) and LIF (1000 U/ml, Milipore). To test the genome wide binding of Esrrb, Nr5a2 and Klf4, we generated BAC lines expressing the GFP-tagged proteins as described previously by Poser et al (poser I et al Nat. Methods 5, 409–415 (2008). For Nr5a2-null ESCs, cre-recombination was induced by treating with 4-hydroxy tamoxifen (0.5 μM) for 2 days. Cells were confirmed for the correct deletion using PCR. All siRNA experiments were performed for 72h and by using 25pmol stealth siRNAs per well of 6-well plates.

value: GFP


title: Nr5a2-C2-serum


title: Nr5a2_C1_serum


title: Klf4_C1_serum


title: Nr5a2-C1-2iDay3


title: Klf4-C2-2iDay3


title: ATACseq_2i_Day3.Rep1


title: Nr5a2-C2-2iDay3


title: ATACseq_serum.Rep3


title: Esrrb-C2-2iDay3


title: Klf4-C1-2iDay3


title: Esrrb-C1_serum


title: Esrrb_C2_serum


title: H3K27ac_2i_Rep2

growth_protocol: E14Tg2a ESCs were cultured in standard culture medium on gelatin coated-dishes without feeder cells. For serum culture, Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 10% fetal calf serum, L-glutamine (2 nM), Na-Pyruvate (1 mM), non-essential amino acids (0.1 mM each), Penicillin Streptomycin, 2-mercaptoethanol (55 µM) and LIF (1000 U/ml, Milipore) was used. For serum free culture, cells were transferred from serum-medium to NDiff 227 (StemCells, Inc.) supplemented with MEK inhibitor PD0325901 (1 μM) and GSK3 inhibitor CHIR99021 (3 μM) and LIF (1000 U/ml, Milipore) or maintained for long term (>4 weeks) in 2i medium (2i_LT). For EpiLSC-differentiation, 2i-ESCs were seeded at ~15,000 cells per cm2 on Fibronectin (10 μg/ml) coated dishes and in NDiff 227 (StemCells, Inc.) supplemented with Penicillin Streptomycin (Gibco), 20 ng/ml Activin-A (R&D systems), 12 ng/ml bFGF (R&D systems) and 1% knock-out serum replacement (Gibco), and cells were maintained for 72h in this culture.


title: Esrrb-C1_2iDay3


title: H3K27ac_serum_Input


title: U373MG_edaravone_24h

value: 1 mM edaravone for 24 h


title: H3K27ac_2i8h_Rep2


title: H3K27ac_serum_Rep2


title: H3K27ac_2iDay3_Rep2


title: H3K27ac_2iDay1_Rep2


title: H3K27ac_2i_Rep1


title: H3K27ac_2iDay7_Rep1


title: H3K27ac_2i8h_Rep1


title: H3K27ac_2iDay1_Rep1


title: H3K27ac_2iDay7_Rep2


title: RNAseq_serum_Day3_Rep1

data_processing:
FASTQ files against mouse rRNA, tRNA, snRNA, snoRNA, mtRNA sequences using Bowtie (Ref) to deplete these small RNA contamination in sequenced libraries. We then mapped the cleaned files against mouse genome (mm9) using GSNAP (Ref) and by applying the following parameters:  -B 5 -t 15 -N 1 -E 100 -w 100000 -n 10 -s mm9refGene_splice.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig tracks, data are not normalized for sequencing depth.

extract_protocol:
RNA isolation was performed using 8 time points: Day1, Day3 and Day7 of serum-2i and 2i-serum transitions and both steady-states (serum and 2i) samples. RNA isolation was performed using Qiagen RNeasy protocol and 4 microgram RNA was employed for generating the RNA-seq libraries. Total RNA was subjected to rRNA depletion using the Ribo-ZeroTM Gold kit (Epicentre) according to manufacture instruction. rRNA-depleted samples were employed in first and second strand cDNA synthesis and by using dUTP for strand-specificity. Sequencing libraries were then prepared using Kapa-Hifi (KAPA Biosystems) according to manufactory’s instruction and the final libraries were sequenced on HiSeq 2000 Illumina sequencer.
Illumina library preparation was done using the Kapa Hyper Prep Kit. For end repair and A-tailing double stranded DNA was incubated with end repair and A-tailing buffer and enzyme and incubated first for 30 minutes at 20°C and then for 30 minutes at 65°C.Subsequently adapters were  ligated  by adding 30µl ligation buffer, 10 Kapa l DNA  ligase, 5µl diluted adaptor  in a total volume of 110µl and incubated for 15 minutes at 15°C.Post-ligation cleanup was performed using Agencourt AMPure XP reagent and products were eluted in 20µl elution buffer. Libraries were amplified by adding 25µl 2x KAPA HiFi Hotstart ReadyMix and 5µl 10x Library Amplification Primer Mix and PCR, 10 cycles. Samples were purified using the QIAquick MinElute PCR purification kit and 300bp fragments selected using E-gel. Correct size selection was confirmed by BioAnalyzer analysis.   Sequencing was performed using Illumina HiSeq 2000 machines and generated 43bp single end reads.


title: RNAseq_serum_Day7_Rep2


title: RNAseq_serum_Day7_Rep1


title: RNAseq_serum_Day3_Rep2


title: RNAseq_serum_Rep2


title: RNAseq_2i_Day7_Rep1


title: RNAseq_serum_Day1_Rep2


title: RNAseq_2i_Day7_Rep2


title: RNAseq_serum_Rep1


title: RNAseq_serum_Day1_Rep1


title: RNAseq_2i_Day3_Rep1


title: RNAseq_2i_Day1_Rep2


title: RNAseq_2i_Day1_Rep1


title: RNAseq_2i_Rep1


title: H3K27ac_2iDay3_Rep1


title: IL-4c-stimulated LPM Bhlhe40 ChIP

data_processing:
FASTQ quality control, FastQC (0.11.3)
Read mapping, Bowtie (1.1.1) (mm10 reference genome)
Peak calling, MACS v1.4 (relative to input controls)
Peaks from unmapped regions and/or with fold-enrichment <5 were excluded
Normalized track generation, Deeptools (2.5.3)
Genome_build: Peak annotation, R package ChIPseeker (1.14.1)
Supplementary_files_format_and_content: bed, peaks, bw

source_name: Peritoneal lavage

extract_protocol:
Bhlhe40 immunoprecipitation of bound, crosslinked DNA from LPMs
Genome Technology Access core (WUSTL)

tag: strain

value: IL-4c injections

value: Day 0, 2, sacrifice day 4

value: LPM

value: Novus Biologicals anti-Dec1 (Bhlhe40) NB100-1800, lot C1

value: male


title: IL-4c-stimulated LPM input DNA


title: H3K27ac_serum_Rep1


title: A2780_450a_2_PAR-CLIP

first: Markus

last: Hafner

address: 50 South Drive

department: NIAMS

institute: NIH

description:
RNA bound to AGO
replicate 2

data_processing:
Library strategy: PAR-CLIP
For RNA-Seq and small RNA-Seq, the sequence reads were aligned to the human genome h19 using TopHat.Differential expression was performed using Cuffdiff
For AGO 4SU-PAR-CLIP, the analyis was performed as described previously using PARalyzer (Corcoran et al., 2011a) built into the PARpipe (Corcoran et al., 2011b) pipeline
Genome_build: h19

source_name: ovarian cancer cell line

growth_protocol: A2780 and SKOV-3 were cultivated either in RPMI medium (Gibco, Catalog No. 31800–022) or in Dulbecco's Modified Eagle Medium (DMEM) (Gibco, Catalog No. 11995065), respectively, supplemented with 10% fetal bovine serum (FBS, GE Healthcare, Catalog No. SH30071.03) and 100 units of penicillin and 0,1 mg/ ml of streptomycin (Sigma-Aldrich Co., Catalog No. P4333). Cells were cultivated at 37°C and 5% CO2

extract_protocol:
Total RNA was extracted from three biological replicates from each cell line using TRIzol™ Reagent (Invitrogen, Catalog No. 15596026) second to recommendations from manufacturer. For small RNA cDNA library, we followed the protocol from Farazi et al (Farazi et al., 2012) after RNA extraction. AGO 4SU-PAR-CLIP method was performed as described previously (Benhalevy et al., 2016; Hafner et al., 2010)
All the samples were sequenced on an Illumina HiSeq 3000 machine using the 50 cycle single read protocol.

value: pri-miR-450a overexpression with lentivirus

value: ovarian cancer


title: naïve LPM Bhlhe40 ChIP

value: untreated


title: A2780_450a_1_PAR-CLIP

description:
RNA bound to AGO
replicate 1


title: RNAseq_2i_Day3_Rep2


title: MEL_PU.1_D5_inputcontrol

data_processing:
PU.1 ChIP-seq reads were aligned to the mouse genome (mm9) with bowtie version 1.0.0 (Langmead et al. 2009) using the following settings: -S, –k 10, -m 10, --best, and --strata.
Peaks were called from the alignments using MACS2 version 2.0.10 (options: -p1e-3, -f BAM), and reproducible peaks were determined between the replicates using the Irreproducible Discovery Rate (IDR)(Li et al. 2011)
Reproducible replicate peaks that had IDRs < 0.05 and that were not present within mouse genomic blacklisted regions were used for downstream analyses.
Genome_build: mm9
Supplementary_files_format_and_content: Provided are 1) the unfiltered MACS2 peaks for each MEL PU.1 ChIP-seq replicate at day 0 (undifferentiated) and day 5 (differentiated with DMSO) in bed format (macs2_MEL_PU.1_d0r1_peaks.encodePeak, macs2_MEL_PU.1_d0r2_peaks.encodePeak, macs2_MEL_PU.1_d5r1_peaks.encodePeak, macs2_MEL_PU.1_d5r2_peaks.encodePeak), and 2) the IDR reproducible peaks between replicate sets that are filtered of blacklisted regions (MEL.PU1.peaks.d0.idrmerged.NOBLKlist.bed, MEL.PU1.peaks.d5.idrmerged.NOBLKlist.bed)

growth_protocol: Mouse erythroleukemia cells (MEL, ATCC, Manassas, VA) were grown in RPMI-1640 medium (Life Technologies, Carlsbad, CA) supplemented with penicillin/streptomycin (Life Technologies) and 10% FBS (VWR, Radnor, PA). MELs grown to a density of 1 million/ml were differentiated using 2% DMSO (VWR) added to the medium and the cells were grown for another 5 days to induce the expression of hemoglobin genes. At least 80-90% of cells expressed hemoglobin based on their color and benzidine/hydrogen peroxide staining result. Trypan Blue (VWR) staining was performed before harvesting the cells for each assay in order to make sure that at least 90% of the cells were viable. All experiments were done with 2 biological replicates.

extract_protocol:
Samples were extracted accoding to the Myers Lab ChIP-seq protocol v042211 (http://myers.hudsonalpha.org/documents/Myers%20Lab%20ChIP-seq%20Protocol%20v042211.pdf)
MEL PU.1 ChIP-seq libraries was made based on Myers Lab protocol v042211 (http://myers.hudsonalpha.org/documents/Myers%20Lab%20ChIP-seq%20Protocol%20v042211.pdf) using a rabbit polyclonal IgG PU.1 antibody (Santa Cruz Technology, sc-352, Lot#B0513, 200μg/ml). The quality of ChIP was validated by qPCR through the use of primers flanking known PU.1 binding sites (ex. SPI1, FCGR28, NRIH3) and known negative control sites (ex. MYOD1, ACTA1). The best two undifferentiated and differentiated MEL PU.1 ChIP replicates were constructed into Illumina sequencing libraries.

value: MEL

value: input

tag: time


title: MEL_PU.1_D0_inputcontrol


title: RNAseq_2i_Rep2

value: Mouse Embryonic Stem Cells


title: MEL_PU.1_D5R2


title: MEL_PU.1_D0R2


title: MEL_PU.1_D5R1


title: MEL_PU.1_D0R1


title: naïve LPM input DNA


title: A2780_pLVX_2_PAR-CLIP

description:
RNA bound to AGO
replicate 2

value: empty lentivirus vector


title: A2780_pLVX_1_PAR-CLIP

description:
RNA bound to AGO
replicate 1


title: Day5_CPC_Baf60c_control_RNA_seq_Rep1

data_processing:
RNA-Seq reads were mapped to the mm9 reference genome using STAR (−alignIntronMin 20 −alignIntronMax 500000). Samples were quantified using analyzeRepeats.pl (mm9 –count exons –strand both –noadj). Differential expression (fold change >1.5; log2 fold change <−0.58, >0.58; p-value < 0.05) was quantified and normalized using DESEq2. Reads per kilobase per millions mapped (rpkm) was determined using rpkm.default from EdgeR. The KNIME 2.9.1 platform (Konstanz, Germany) was used to filter differentially regulated genes.
Genome_build: mm9
Supplementary_files_format_and_content: Day5_CPC_Baf60c_quanty_transcripts_diff_expr.xls

molecule: polyA RNA

source_name: Cardiac Progenitors

growth_protocol: Control E14 Tg(Nkx2-5–EmGFP) ES cells were maintained on mitomycin treated MEF in Knockout DMEM medium containing 4.5 mg/ml D-glucose, supplemented with 10% serum replacement, 2 mM L-Glutamine, 0.1 mM 2-mercaptoethanol, 1 mM sodium pyruvate, and 1,000 U/ml of leukemia inhibitory factor. For directed cardiomyocyte differentiation, ES cells were grown on gelatin in Neurobasal medium: DMEM/F12 (1:1) medium supplemented with 2,000 U/ml LIF and 10 ng/ml BMP4 for 2 days and differentiated by aggregation in low attachment bacterial dishes at a cell density of 75000 cells/ml in IMDM: F12 medium (3:1). After 48h aggregates were dissociated and re-aggregated in the presence of 5 ng/ml Activin A, 5ng/ml VEGF and 0.2ng/ml BMP4. 40h following the second aggregation, aggregates were dissociated and plated as a monolayer in Stempro-34 medium supplemented with Stempro34 nutrient supplement, L-Ascorbic Acid and 5ng/ml VEGF, 10ng/ml bFGF, and 25ng/ml FGF10 growth factors. Nkx2.5-GFP positive CPC cells were FACS sorted for RNA extraction.

extract_protocol: Control and Baf60c KD Nkx2.5-GFP ES cell lines were differentiated into cardiac progenitors. Nkx2.5-GFP positive cells from two different control and Baf60 KD ESCs pools were sorted and RNA was isolated using RNeasy microarray kit (Qiagen #73304). The integrity of RNA was assessed on Bioanalyzer 2100 (Agilent). For RNA-Seq of control and Baf60c KD CPCs, 1 µg RNA was used as input for Truseq Stranded mRNA library preparation (Illumina). Sequencing was performed on NextSeq500 (Illumina) using V2 chemistry.

value: Control E14 Tg(Nkx2-5-EmGFP) ES cells

value: Embryonic stem cells (ESC)

tag: sample description

value: RNA-Seq of Control ESC-derived cardiac progenitor cells


title: Ultrasonicated 4 weeks

city: Martonvásár

first: Norbert

middle: Tibor

last: Hidvégi

address: Brunszvik street 2.

department: Department of Biological Resources

country: Hungary

institute: HUN-REN Centre for Agricultural Research Agricultural Institute

data_processing:
Illumina Casava 1.7 software used for basecalling
Sequence reads were trimmed with TrimGalore v0.5.0 and aligned to the reference genome with HISAT2 v2.1.0.
From the aligned mRNA reads the differentially expressed genes were analyzed with SeqMonk v1.42.0. We calculated the quantitated values in reads per million reads of input and were log2 transformed. To filter the list of quantitated genes for significantly differentially expressed genes with the intensity difference filter in SeqMonk, which is based on the X2 probe.
Genome_build: HISAT2
Supplementary_files_format_and_content: SeqMonk data file in smk file format with intensity difference filter.

organism: Solanum tuberosum

source_name: In vitro explant

growth_protocol: Four-week-old in vitro potato plantlets (cv. Desirée) were used for the experiment. The culture conditions, medium and vessels used were the same as in our earlier study (Dobránszki et al., 2017). Dobránszki J, Asboth G, Homoki D, Bíró-Molnár P, Teixeira da Silva JA, Remenyik J (2017) Ultrasonication of in vitro potato single node explants: activation and recovery of antioxidant defence system and growth responses. Plant Physiology and Biochemistry 121: 153–160

extract_protocol:
Total RNA was purified from the 10 potato samples as a single replicate using the Direct-zolTM kit (Zymo Research, Irvine, CA, USA) with TRIzol reagent based on the manufacturer’s protocol.
mRNA from the 10 potato samples was enriched using oligo(dT) beads. For long non-coding libraries, rRNA was removed using the Plant Ribo-Zero rRNA removal kit (Illumina, San Diego, CA, USA) using the manufacturer’s protocol, resulting in mRNA (rRNA-depleted RNA-seq). Using the Illumina TruSeq Stranded mRNA kit, mRNA was first randomly fragmented by adding fragmentation buffer, then cDNA was synthesized with an mRNA template and a random hexamer primer, after which a custom second-strand synthesis buffer, dNTPs, RNase H and DNA polymerase I were added to initiate second-strand synthesis. The second step involved terminal repair, A ligation and sequencing adaptor ligation, after which the double-stranded cDNA library was completed through size selection and PCR enrichment.

treatment_protocol: Single-node segments with a single leaf were cut from 4-w-old in vitro potato plantlets (cv. Desirée) and used for the experiment. The culture conditions, medium and vessels used were the same as in our earlier study on the effects of ultrasonication on the antioxidant defence system and growth and development of in vitro potato (Dobránszki et al., 2017). Immediately after placing explants horizontally onto medium, they were ultrasonicated in an ultrasonication unit at 35 kHz (US) and at 70 W for 20 min, as described in Dobránszki et al. (2017). Ultrasonicated and non-ultrasonicated (treatment control) explants were placed on shoot regeneration medium (Murashige and Skoog (1962) medium without plant growth regulators) and subcultured for 4 w. Both control (unsonicated) and ultrasonicated plant material was sampled at 0 h, 24 h, 48 h, 1 w and 4 w after ultrasonication and establishment of the subculture (treatment controls).

value: Ultrasonicated 4 weeks

tag: cultivar

value: Desiree

value: leaf

value: wild type


title: Day5_CPC_Baf60c_KD_RNA_seq_Rep1

growth_protocol: Baf60c KD E14 Tg(Nkx2-5–EmGFP) ES cells were maintained on mitomycin treated MEF in Knockout DMEM medium containing 4.5 mg/ml D-glucose, supplemented with 10% serum replacement, 2 mM L-Glutamine, 0.1 mM 2-mercaptoethanol, 1 mM sodium pyruvate, and 1,000 U/ml of leukemia inhibitory factor. For directed cardiomyocyte differentiation, ES cells were grown on gelatin in Neurobasal medium: DMEM/F12 (1:1) medium supplemented with 2,000 U/ml LIF and 10 ng/ml BMP4 for 2 days and differentiated by aggregation in low attachment bacterial dishes at a cell density of 75000 cells/ml in IMDM: F12 medium (3:1). After 48h aggregates were dissociated and re-aggregated in the presence of 5 ng/ml Activin A, 5ng/ml VEGF and 0.2ng/ml BMP4. 40h following the second aggregation, aggregates were dissociated and plated as a monolayer in Stempro-34 medium supplemented with Stempro34 nutrient supplement, L-Ascorbic Acid and 5ng/ml VEGF, 10ng/ml bFGF, and 25ng/ml FGF10 growth factors. Nkx2.5-GFP positive CPC cells were FACS sorted for RNA extraction.

value: Baf60c KD E14 Tg(Nkx2-5-EmGFP) ES cells

value: RNA-Seq of Baf60c KD ESC-derived cardiac progenitor cells


title: Ultrasonicated 24 hours

value: Ultrasonicated 24 hours


title: Day5_CPC_Baf60c_KD_RNA_seq_Rep2


title: Control 4 weeks

value: Control 4 weeks


title: Day5_CPC_Baf60c_control_RNA_seq_Rep2


title: Ultrasonicated 1 week

value: Ultrasonicated 1 week


title: Control 48 hours

value: Control 48 hours


title: Ultrasonicated 0 hour

value: Ultrasonicated 0 hour


title: Control 24 hours

value: Control 24 hours


title: Lin28aCko TAC rep2

city: Chapel Hill

first: Jiandong

last: Liu

state: NC

address: 111 Mason Farm Road

department: Department of Pathology and Laboratory Medicine

institute: UNC at Chapel Hill

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and low-complexity or low-quality sequence until the average score of adjacent 4 bases is above 30, then mapped to mm10 whole genome using bowtie2 v2.2.6
Gene expression was counted with Htseq-count using the union mode. Gene expression was expressed as counts per million. DEG between samples were calculated with DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: comma-delimited text file

source_name: myocardium

extract_protocol:
Left ventricles were harvested, snap frozen on liquid nitrogen, homogenized and RNA was isolated using Trizol reagent. Illumina TruSeq Stranded mRNA Sample Prep Kit (Cat#RS-122-2101) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard illumina protocols

treatment_protocol: Mice were subjected to transverse aortic constriction (TAC). Hypertrophic hearts were harvested at Day 5 after TAC.

value: Heart, myocardium

value: TAC


title: Lin28aCko TAC rep1


title: Lin28aCko Sham rep2

value: Sham


title: Lin28aCko Sham rep1


title: axenic control

city: Urbana

first: Santiago

middle: Xavier

last: Mideros

state: Illinois

address: AW-101 Turner Hall / 1102 S. Goodwin Av.

department: Crop Sciences

institute: University of Illinois at Urbana Champaign

description: sample ID AX2331 from pure culture of a single spore F. graminearum strain isolated from a susceptible variety

data_processing:
The libraries were quantitated by qPCR and sequenced on one lane for 101 cycles from each end of the fragments on a HiSeq 4000 using a HiSeq 4000 sequencing kit version 1.
Fastq files were generated and demultiplexed with with the bcl2fastq v2.17.1.14 Conversion Software (Illumina), which trims off adaptors and removes sequences less than 35 nt
Each sample's fastq file was run through Trimmomatic 0.36 to first remove any remaining standard Illumina TruSeq SE v3 adapters, then trim bases from both ends with quality scores below 28, and finally to remove reads shorter than 30 bp (parameters ILLUMINACLIP:$EBROOTTRIMMOMATIC/adapters/TruSeq3-SE.fa:2:15:10 LEADING:28 TRAILING:28 MINLEN:30)
Alignment was done to EnsemblFungi's Fusarium graminearum PH-1 genome (Assembly: GCA_900044135.1) using STAR (version 2.5.3a) [30] using parameters --sjdbGTFfeatureExon exon, --sjdbGTFtagExonParentGene gene_id and --sjdbOverhang 99.
Gene counts were generated using featureCounts in the subread package (version 1.5.2) using only uniquely aligned reads.
Genome_build: EnsemblFungi Fusarium graminearum PH-1
Supplementary_files_format_and_content: tab-delimited text files of raw counts per gene per sample were used directly in edgeR 3.20.0 for statistical analysis and thus are the "normalized" data.

organism: Fusarium graminearum

source_name: pure culture from a single F. graminearum isolate

extract_protocol:
RNAs were extracted using a combination of TRIzol (ThermoFisher Scientific, Waltham, Massachusetts) and RNAeasy Min Elute Cleanup Kit (Qiagen, Hilden, Germany)
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina)

treatment_protocol: From one infected head for each variety, and at each location, the most diseased spikelet was placed in a 1.5mL micro-centrifuge tube containing 500µL of RNAlater (Sigma-Aldrich, St. Louis, Missouri) and kept at 4°C until arriving at the laboratory and then at -20°C until processing

tag: resistance level

value: control

tag: location


title: Ultrasonicated 48 hours

value: Ultrasonicated 48 hours

tag: genotype


title: Lin28afl/fl TAC rep1


title: Intermediate line from location 4

description: sample ID SMS229 collected in Savoy, IL

source_name: infected spikelet from soft red winter wheat head

value: intermediate


title: Control 1 week

value: Control 1 week

value: Desiree


title: Susceptible line from location 1

description: sample ID BHS050 collected in Brownstown, IL

value: susceptible


title: Lin28afl/fl Sham rep2


title: Susceptible line from location 4

description: sample ID SHS243 collected in Savoy, IL


title: Resistant line from location 3

description: sample ID JMR052 collected in St. Jacob, IL

value: resistant


title: Intermediate line from location 2

description: sample ID CMS120 collected in Carmi, IL


title: Susceptible line from location 3

description: sample ID JHS098 collected in St. Jacob, IL


title: Susceptible line from location 2

description: sample ID CHS141 collected in Carmi, IL


title: Resistant line from location 2

description: sample ID CMR105 collected in Carmi, IL


title: Intermediate line from location 3

description: sample ID JMS072 collected in St. Jacob, IL


title: Resistant line from location 1

description: sample ID BMR001 collected in Brownstown, IL


title: Resistant line from location 4

description: sample ID SMR201 collected in Savoy, IL


title: Intermediate line from location 1

description: sample ID BMS022 collected in Brownstown, IL


title: Lin28afl/fl Sham rep1


title: Control 0 hour

value: Control 0 hour

value: leaf

value: wild type


title: Lin28afl/fl TAC rep2


title: FB23-2-rep3

status: Public on Apr 29 2019

city: Monrovia

first: Jianjun

last: Chen

state: CA

department: Systems Biology

institute: Beckman Research Institute of City of Hope

data_processing:
sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
the RPKM were calculated using RSEM 1.2.31 with default parameters
Genome_build: GRCh38
Supplementary_files_format_and_content: RSEM output file containing the expression of genes

extract_protocol:
RNA was extracted by using TRIzol reagent (Invitrogen, Carlsbad, CA). NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, MA) was used for polyA RNA purification.
Library was prepared by or NEBNext Ultra Directional RNA Library Prep Kit (New England BioLabs, Ipswich, MA).

value: acute monocytic leukemia

value: FTO inhibition


title: FB23-2-rep1


title: FB23-rep3


title: 1hr_Ab_replicate3_QM9

city: Baltimore

first: Anne

middle: E.

last: Jedlicka

address: 615 N. Wolfe street

department: Molecular Microbiology and Immunology

institute: Johns Hopkins University, School of Public Health

description: Gene Expression Data

hyb_protocol: 600ng of Cy3-labelled cRNA was purified, fragmented and hybridized to Agilent SurePrint G3 Mouse v2 8x60K Gene Expression Arrays, according to the Agilent Low Input QuickAmp Labeling Kit protocol.   Post-hybridization washing of arrays was also performed according to these protocols.

scan_protocol: The arrays were scanned in an Agilent G2600D SureScan Microarray Scanner using scan protocol AgilentG3_GX_1color. Agilent’s Feature Extraction Software was used to assign grids, provide raw image files per array, and generate QC metric reports from the microarray scan data. The QC metric reports were used for quality assessment of all hybridizations and scans.

data_processing: Txt files from the Feature Extraction software were imported into the Partek Genomics Suite (v7.0; Partek) for detailed analyses of gene expression. Within Partek, the gProcessedSignal was imported and the intensity values were normalized to the 75th percentile, lower expressed genes were filtered out, and log transformation base 2.0 was performed.  The batch effect removal tool (analysis of variance [ANOVA]) was used to correct for effects of array (slide).

source_name: BMDM, Ab, 1hr

label_protocol: One hundred nanograms of total RNA was processed for hybridization to Agilent SurePrint G3 Mouse v2 8x60K Gene Expression Arrays according Agilent’s One Color Microarray-Based Analysis (Low Input QuickAmp Labeling) protocol, including cDNA synthesis, cRNA synthesis with Cy3 labeling and purification, fragmentation, hybridization, and post-hyb washing. Spike-In controls were utilized and processed according to Agilent’s One Color RNA Spike-In kit protocol.

extract_protocol: Total RNA was extracted using the PureLink RNA Mini kit (Ambion/Life Technologies) according to the manufacturer’s protocol, including on-column DNAse treatment. Following elution of purified RNA from the PureLink columns with Nuclease-free water, quantitation was performed using a NanoDrop spectrophotometer and quality assessment determined by RNA LabChip analysis on an Agilent BioAnalyzer 2100 or RNA Screen tape on an Agilent TapeStation 2200.

treatment_protocol: BMDMs were seeded in 6-well dishes at 1xE06 cells per well. Cells were activated overnight with IFNγ and LPS. Cells were then treated for 1 h with or without Fc receptor blocking antibody, or harvested before the incubation for a baseline. Cells were lifted from the dishes, pelleted, and resuspended in TRIzol reagent [ThermoFisher]. The supernatant was then flash frozen and stored at −80 °C.

value: Macrophages, bone marrow-derived, from female C57B/6 mice from Jackson Labs

tag: slide id (array batch)

value: Ab


title: DMSO-rep2

tag: cell line

value: Ctrl


title: DMSO-rep1

tag: cell type


title: FB23-rep2

tag: treatment


title: FB23-rep1


title: 1hr_NoAb_replicate2_QM5

description: Gene Expression Data

source_name: BMDM, NoAb, 1hr

value: NoAb


title: 1hr_Ab_replicate2_QM6

description: Gene Expression Data


title: 1hr_NoAb_replicate1_QM2

description: Gene Expression Data


title: 1hr_Ab_replicate1_QM3

description: Gene Expression Data


title: shFTO-rep2

tag: shRNA

value: shFTO


title: 0hr_NoAb_replicate2_QM4

description: Gene Expression Data

source_name: BMDM, NoAb, 0hr


title: 1hr_NoAb_replicate3_QM8

description: Gene Expression Data


title: shNS-rep1

value: shNS


title: 0hr_NoAb_replicate1_QM1

description: Gene Expression Data


title: m6A-seq_IP_FB23-2

data_processing:
Library strategy: m6A-seq
sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
m6A-seq reads were aligned to the hg38 genome assembly using Tophat 2.1.1
peaks were called using MACS2 and exomePeak.
the m6A peaks were annotated using an ad hoc perl script.
GSEA and DAVID tool were used to perform pathway enrichment analysis
Genome_build: GRCh38
Supplementary_files_format_and_content: bigwig files were generated by MACS2 and bedGraphToBigWig. BedWig files can be uploaded to UCSC Genome Browser for visualization

extract_protocol:
RNA was extracted by Trizol. Polyadenylated RNA was extracted using FastTrack MAC Maxi mRNA isolation kit (Invitrogen)
RNA fragmentation, m6A-Seq and library preparation were performed according to previous protocols (Dan et al., 2012)

value: peripheral blood

tag: antibody

value: m6A antibody


title: DMSO-rep3


title: shNS-rep2


title: input

tag: tissue

value: DMSO


title: m6A-seq_IP_DMSO


title: FB23-2-rep2


title: Positive Control - Pooled Samples – 252741410849

type: genomic

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

institute: Government of Canada

description: Positive Control

hyb_protocol: Hybridization was performed using the protocol recommended by the manufacturer.

scan_protocol: The hybridized slides were scanned using an Agilent C scanner and Feature Extraction v10.5 was used to extract the data.

data_processing:
Non-uniform features (outlier probes with signals influenced by array position) were removed from analysis. The algorithms previously used by Adewoye et al. were applied to detect autosomal CNVs as genomic segments with parent vs. offspring fluorescent signal log2 ratios above or below threshold values as described previously.
Following Feature Extraction, signal intensities (Cy3 and Cy5) were background subtracted and then normalized (Lowess normalization using Rank invariant probes). Log2 ratios of the Cy5/Cy3 were used for the analysis.

source_name: Mouse tissue

label_protocol: One µg of offspring DNA was labelled with Cy5 dye (5190-3400 SureTag DNA Labeling Kit). Five hundred ng of DNA from each respective parent were mixed together and labelled with Cy3 dye. As positive controls, and to identify existing strain differences, two additional arrays were used to compare MutaMouse with C57BL/6J DNA. DNA labelled with Cy3 and Cy5 were mixed together for hybridization onto the CGH array.

extract_protocol: DNA was extracted from the liver of each animal using the DNeasy Blood & Tissue Kit as per the manufacturer’s instructions.

treatment_protocol: Twelve MutaMouse males (BALB/C × DBA/2) approximately 15 weeks of age, were exposed daily to BaP (Sigma-Aldrich, Oakville, Ontario, Canada) dissolved in olive oil (Sigma-Aldrich; highly refined, low acidity) via oral gavage (approximately 150 µL) for 28 days (100 mg/kg body weight/day). Twelve concurrent males received olive oil and served as negative controls. Three days after the last treatment all males were mated with four C57Bl/6J females each over a two-week period to produce offspring

value: Positive Control

tag: Sex

value: Male

value: Liver

tag: mice sex

value: Female


title: 9FM2 - 252741410705

description: Control Exposure

value: Control Exposure

value: pooled male and female


title: 0hr_NoAb_replicate3_QM7

description: Gene Expression Data


title: 9FM1 - 252741410704

description: Control Exposure


title: 9FF4 - 252741411769

description: Control Exposure


title: shFTO-rep1

value: acute monocytic leukemia


title: 9FF3 - 252741411916

description: Control Exposure


title: 9FM3 - 252741411608

description: Control Exposure


title: 9FM4 - 252741411833

description: Control Exposure


title: 9FF2 - 252741410706

description: Control Exposure


title: 9FF1 - 252741410688

description: Control Exposure


title: 9CF3 - 252741412067

description: Control Exposure


title: 9CM1 - 252741411995

description: Control Exposure


title: 8HM4 - 252741411832

description: Control Exposure


title: 8HM1 - 252741410702

description: Control Exposure


title: 8HF3 - 252741411537

description: Control Exposure


title: 9CM2 - 252741412063

description: Control Exposure


title: 8HM3 - 252741410687

description: Control Exposure


title: 9CM3 - 252741412064

description: Control Exposure


title: 8HM2 - 252741410702

description: Control Exposure


title: 8HF1 - 252741410820

description: Control Exposure


title: 8HF2 - 252741410821

description: Control Exposure


title: 9CF2 - 252741412066

description: Control Exposure


title: 9CF4 - 252741412016

description: Control Exposure


title: 8HF4 - 252741411778

description: Control Exposure


title: TbetKO.Be2.d2.rep2

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

data_processing:
Raw sequencing reads were mapped to the mm9 version of the mouse genome using Bowtie-1.1.1
For each sample peaks of accessibility were identified and annotated using the HOMER package v4.8.2.
Bigwig files were created by normalizing all data to reads per peak per million (rppm) as previously described (Scharer et al. Scientific Reports. 2016).
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files normalized ot reads per peak per million (RPPM)

source_name: Ex vivo B cell

extract_protocol:
Bulk cultures on day 2 were used for ATAC-seq
Nuclei were extracted, incubated with Tn5 transposase (Illumina) for 30 minutes at 37°C and DNA samples were then purified with the MinElut Kit (Qiagen). Library amplification was performed using Nextera primers with NEBNext High-Fidelity 2X PCR Master Mix (New England Biolegends), followed by purification with the PCR Purification Kit.

treatment_protocol: Be1 cells were generated by co-culturing splenic B cells of the indicated genotype with mitomycin-treated Th1 or Th2 polarized OT-II cells in the presence of IL-2 (20units/ml), anti-IgM F(ab')2 (40gul/ml), and OT-II peptide (5uM)

value: Tbet-deficient

value: B cells

tag: cell subtype

tag: days in culture


title: TbetKO.Be2.d2.rep3


title: TbetKO.Be2.d2.rep1


title: 8AM1 - 252741411964

description: Control Exposure


title: TbetKO.Be1.d2.rep2


title: TbetKO.Be1.d2.rep3


title: 8AF3 - 252741412012

description: Control Exposure


title: 8AF2 - 252741411967

description: Control Exposure


title: 9CF1 - 252741411996

description: Control Exposure


title: TbetKO.Be1.d2.rep1


title: 9CM4 - 252741412065

description: Control Exposure


title: B6.Be2.d2.rep3

value: Wild type


title: B6.Be1.d2.rep3


title: 7GM1 - 252741411736

description: Control Exposure


title: B6.Be2.d2.rep1


title: 8AM4 - 252741412011

description: Control Exposure


title: 8AM2 - 252741411965

description: Control Exposure


title: 8AF1 - 252741411966

description: Control Exposure


title: 7FM1 - 252741410816

description: Control Exposure


title: B6.Be2.d2.rep2


title: 7FM2 - 252741411919

description: Control Exposure


title: 7FF6 - 252741411703

description: Control Exposure


title: 7FF3 - 252741411922

description: Control Exposure


title: 7FF5 - 252741411708

description: Control Exposure


title: 7FF2 - 252741411921

description: Control Exposure


title: 8AM3 - 252741412010

description: Control Exposure


title: 7FM3 - 252741411536

description: Control Exposure


title: 7BM4 - 252741411974

description: Control Exposure


title: 7FF4 - 252741411755

description: Control Exposure


title: B6.Be1.d2.rep2


title: 7BM3 - 252741411972

description: Control Exposure


title: 7FF1 - 252741411920

description: Control Exposure


title: B6.Be1.d2.rep1


title: 7BM1 - 252741411951

description: Control Exposure


title: 7BF3 - 252741411976

description: Control Exposure


title: 7BF4 - 252741411977

description: Control Exposure


title: 6FM2 - 252741410832

description: Control Exposure


title: 6FM3 - 252741410833

description: Control Exposure


title: 6FM1 - 252741410831

description: Control Exposure


title: 7BF2 - 252741411975

description: Control Exposure


title: 6FF2 - 252741410815

description: Control Exposure


title: 6FF1 - 252741410834

description: Control Exposure


title: 6CM3 - 252741411948

description: Control Exposure


title: 6FF3 - 252741411831

description: Control Exposure


title: 6CM1 - 252741411953

description: Control Exposure


title: 6CM4 - 252741411949

description: Control Exposure


title: 6CM2 - 252741411954

description: Control Exposure


title: 7BM2 - 252741411971

description: Control Exposure


title: 6CF4 - 252741411970

description: Control Exposure


title: 6CF1 - 252741411955

description: Control Exposure


title: 5GM2 - 252741411770

description: Control Exposure


title: 6FF4 - 252741411776

description: Control Exposure


title: 5GF1 - 252741411780

description: Control Exposure


title: 5EM3 - 252741411829

description: Control Exposure


title: 5GM1 - 252741411754

description: Control Exposure


title: 5EM2 - 252741411031

description: Control Exposure


title: 6CF2 - 252741411956

description: Control Exposure


title: 5EF5 - 252741411775

description: Control Exposure


title: 5EF4 - 252741411830

description: Control Exposure


title: 5EF3 - 252741411034

description: Control Exposure


title: 5EF2 - 252741411033

description: Control Exposure


title: 5EM1 - 252741411030

description: Control Exposure


title: 5EF1 - 252741411032

description: Control Exposure


title: 5CM2 - 252741411959

description: Control Exposure


title: 7BF1 - 252741411952

description: Control Exposure


title: 5CM1 - 252741412004

description: Control Exposure


title: 5CF5 - 252741411969

description: Control Exposure


title: 5CF4 - 252741411968

description: Control Exposure


title: 6FF5 - 252741411777

description: Control Exposure


title: 6CF3 - 252741411950

description: Control Exposure


title: 4HM3 - 252741410790

description: Control Exposure


title: 4HM4 - 252741411766

description: Control Exposure


title: 5CF3 - 252741411961

description: Control Exposure


title: 5CF1 - 252741412015

description: Control Exposure


title: 5CF2 - 252741411960

description: Control Exposure


title: 4HF4 - 252741411735

description: Control Exposure


title: 4HM1 - 252741410788

description: Control Exposure


title: 4HM2 - 252741410789

description: Control Exposure


title: 4CM1 - 252741412029

description: Control Exposure


title: 4CM4 - 252741411973

description: Control Exposure


title: 4HF2 - 252741411025

description: Control Exposure


title: 4HF3 - 252741411535

description: Control Exposure


title: 4CF2 - 252741412003

description: Control Exposure


title: 41FM1 - 252741411757

description: BaP Exposure

value: BaP Exposure


title: 4CF1 - 252741411957

description: Control Exposure


title: 41FM3 - 252741411705

description: BaP Exposure


title: 41FM2 - 252741411704

description: BaP Exposure


title: 41FF1 - 252741411774

description: BaP Exposure


title: 41EM4 - 252741411609

description: BaP Exposure


title: 4HF1 - 252741410805

description: Control Exposure


title: 41EM3 - 252741410824

description: BaP Exposure


title: 41EM2 - 252741410685

description: BaP Exposure


title: 41EM1 - 252741410822

description: BaP Exposure


title: 41EF4 - 252741411783

description: BaP Exposure


title: 41EF1 - 252741410825

description: BaP Exposure


title: 41EF2 - 252741410686

description: BaP Exposure


title: 41EF3 - 252741410673

description: BaP Exposure


title: 41CM1 - 252741411908

description: BaP Exposure


title: 4CF3 - 252741411962

description: Control Exposure


title: 41FM4 - 252741411706

description: BaP Exposure


title: 41CF1 - 252741411929

description: BaP Exposure


title: 41CF2 - 252741411928

description: BaP Exposure


title: 41BM5 - 252741411805

description: BaP Exposure


title: Be1.TbetNeg.rep1

data_processing:
Raw sequencing reads were mapped to the mm9 version of the mouse genome using Tophat2 and the mm9 reference genome and the mm9 UCSC known gene table as the reference transcriptome.
FPKM normalized read counts were generated using HOMER software.
Reads per million normalized Bigwig files for each sample were generated using Bioconductor/R.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM normlized read counts for all RefSeq genes for each sample

source_name: Be1 B cell culture

growth_protocol: Be1 cells were generated by co-culturing splenic B cells of the indicated genotype with mitomycin-treated Th1 polarized OT-II cells in the presence of IL-2 (20units/ml), anti-IgM F(ab')2 (40gul/ml), and OT-II peptide (5uM)

extract_protocol:
Total RNA was isolated by Trizol or the Qiagen RNeasy Mini kit with DNAse digestion.
500ng of total RNA was used as input for the Illumina TruSeq RNA-seq library kit and processed according to the manufacturers instructions

tag: strain

value: Tbx21 negative B cells


title: 41CF3 - 252741411891

description: BaP Exposure


title: Be1.TbetNeg.rep3


title: 41BM3 - 252741411872

description: BaP Exposure


title: 41BM4 - 252741411873

description: BaP Exposure


title: 41BM2 - 252741411871

description: BaP Exposure


title: 41BM1 - 252741411870

description: BaP Exposure


title: 41BF2 - 252741411807

description: BaP Exposure


title: Be1.B6.rep1

value: Wild type B cells


title: 3HM5 - 252741411741

description: BaP Exposure


title: 41BF1 - 252741411806

description: BaP Exposure


title: 41BF3 - 252741411808

description: BaP Exposure


title: 3HM6 - 252741411742

description: BaP Exposure


title: 3HM4 - 252741411746

description: BaP Exposure


title: Positive Control - MutaMouse vs C57Bl – 252741410850

description: Positive Control


title: Be1.B6.rep2


title: Be1.TbetNeg.rep2


title: Negative Control - Sample vs Self – 252741410851

description: Negative Control

value: Negative Control


title: 3HM1 - 252741410847

description: BaP Exposure


title: 3HM2 - 252741411611

description: BaP Exposure


title: 3HF3 - 252741411764

description: BaP Exposure


title: 3HM3 - 252741410792

description: BaP Exposure


title: 3HF2 - 252741410794

description: BaP Exposure


title: 41CF4 - 252741411892

description: BaP Exposure


title: 3DM3 - 252741411940

description: BaP Exposure


title: Be1.B6.rep3


title: 3HF1 - 252741411623

description: BaP Exposure


title: 3DM2 - 252741411939

description: BaP Exposure


title: 3DF2 - 252741412028

description: BaP Exposure


title: 3DF1 - 252741412027

description: BaP Exposure


title: 3DM1 - 252741411938

description: BaP Exposure


title: 39FM2 - 252741410807

description: BaP Exposure


title: 39FM1 - 252741410806

description: BaP Exposure


title: 39AM2 - 252741411852

description: BaP Exposure


title: 39FF1 - 252741410808

description: BaP Exposure


title: 39FF2 - 252741410823

description: BaP Exposure


title: 39AF4 - 252741411801

description: BaP Exposure


title: 39AM1 - 252741411869

description: BaP Exposure


title: 39AM3 - 252741411868

description: BaP Exposure


title: 39AF3 - 252741411800

description: BaP Exposure


title: 39FF3 - 252741410814

description: BaP Exposure


title: 38HF1 - 252741411049

description: BaP Exposure


title: 38HF4 - 252741411534

description: BaP Exposure


title: 38HF7 - 252741411858

description: BaP Exposure


title: 39AF2 - 252741411799

description: BaP Exposure


title: 38HM1 - 252741411850

description: BaP Exposure


title: 38GM4 - 252741411533

description: BaP Exposure


title: 38HF5 - 252741411883

description: BaP Exposure


title: 38HF6 - 252741411857

description: BaP Exposure


title: 38HF2 - 252741411037

description: BaP Exposure


title: 39AF1 - 252741411853

description: BaP Exposure


title: 38GM3 - 252741411036

description: BaP Exposure


title: 38GM2 - 252741411035

description: BaP Exposure


title: 38HF3 - 252741411038

description: BaP Exposure


title: 38GM1 - 252741411048

description: BaP Exposure


title: 38AM5 - 252741411866

description: BaP Exposure


title: 38AM6 - 252741411867

description: BaP Exposure


title: 38AM4 - 252741411865

description: BaP Exposure


title: 38AM3 - 252741411864

description: BaP Exposure


title: 38AM2 - 252741411851

description: BaP Exposure


title: 38AM1 - 252741411738

description: BaP Exposure


title: 38AF4 - 252741411758

description: BaP Exposure


title: 38AF3 - 252741411753

description: BaP Exposure


title: 38AF1 - 252741411738

description: BaP Exposure


title: 37HM6 - 252741411820

description: BaP Exposure


title: 37HM5 - 252741411819

description: BaP Exposure


title: 37HM3 - 252741410840

description: BaP Exposure


title: 37HM4 - 252741411064

description: BaP Exposure


title: 37HM2 - 252741410839

description: BaP Exposure


title: 37HF2 - 252741411068

description: BaP Exposure


title: 37HM1 - 252741410836

description: BaP Exposure


title: 37EF1 - 252741411882

description: BaP Exposure


title: 37BM4 - 252741411897

description: BaP Exposure


title: 37EF5 - 252741411856

description: BaP Exposure