title: PBMC_Cryo_408X_MSCB-182

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-183

status: Public on Feb 13 2017

type: SRA

city: Barcelona

first: Gustavo

last: Rodriguez-Esteban

state: Catalonia

address: C. Baldiri Reixac, 4; Barcelona Science Park

department: Development

country: Spain

institute: Centro Nacional de Análisis Genómico

description:
cryopreserved cells
PBMC_Cryo.tsv

library_source: transcriptomic

data_processing:
Illumina Real-Time Analysis (RTA) 1.18.66.3 software used for basecalling.
Sequenced reads were filtered for low-complexity or low-quality sequence.
Cells with less than 60% of reads mapping on the reference genome were discarded.
MARS-Seq libraries were mapped as single-end reads with the GEMTools 1.7.0 RNA pipeline on the genome reference  for human, mouse and canine cells. Smart-seq2 libraries were equally mapped as paired-end reads.
For MARS-seq samples, gene quantification was performed using UMI corrected transcript information to correct for amplification biases.
Genome_build: Human: Gencode release 24, assembly GRCh38.p5;  mouse: Gencode release M8, assembly GRCm38.p4; dog:  Ensembl v84, assembly CanFam3.1
Supplementary_files_format_and_content: Tab-separated values (.tsv) files containing gene expression values (rows) as raw read counts (Smart-seq2) or UMI counts (MARS-Seq) for each cell (columns) in condition.

molecule: polyA RNA

organism: Homo sapiens

source_name: blood

growth_protocol: Human cell lines HEK293 (human embryonic kidney cells) and K562 (human leukemia cells) were acquired from the German Collection of Microorganisms and Cell Cultures (DSMZ). NIH3T3 (mouse embryo fibroblasts) and MDCK (canine adult kidney cells) were kindly provided by Dr. Manel Esteller (IDIBELL, Spain). HEK293, NIH3T3 and MDCK were maintained in DMEM (10% Fetal Bovine Serum, FBS; 1% Penicillin/Streptomycin) at 37ºC (5% CO2). K562 suspension cells were cultured in RPMI (10% FBS; 1% Penicillin/Streptomycin) at 37ºC (5% CO2). For cryopreservation, cells were trypsinized, pelleted and resuspended in freezing solution I (10% DMSO; 10% heat-inactivated FBS; 80% DMEM) or solution II (10% DMSO; 90% non-inactivated FBS). Subsequently, cells were frozen with gradually decreasing temperatures (1ºC/min) to -80ºC (cryopreserved).

extract_protocol:
For single cell analysis, cryopreserved cells were rapidly thawed in a water bath in continuous agitation and placed into 25 ml of cold 1x HBSS. Fresh cells were trypsinized, pelleted and resuspended in 1x HBSS. Before sorting, cells from both conditions were filtered (70 µm nylon mesh) and propidium iodide staining identified dead/damaged cells.    Whole blood was collected from a healthy donor into EDTA tubes (Becton, Dickinson and Co). Separation of peripheral blood mononuclear cells (PBMC) was performed with Ficoll-Paque PREMIUM (GE Healthcare) according to manufacturer's instructions. Briefly, for density gradient separation, 4 ml of blood was added onto 3 ml of Ficoll-Paque PREMIUM. Centrifuged at 400 x g for 30 minutes at 18ºC without brake. PBMC layer was recuperated and washed twice with PBS at 400g for 15 minutes at 18ºC. PBMC were resuspended in freezing solution (10% DMSO, 90% non-inactivated FBS) and frozen with gradually decreasing temperatures (1ºC/min) to ‑80ºC (cryopreserved). After storage for one week at -80ºC, the cryopreserved sample was rapidly thawed in a water bath in continuous agitation and placed into 25 ml of cold 1x HBSS. Cells were washed once in ice cold 1x HBSS and resuspended in DMEM before sorting. To avoid batch effects, fresh PBMC were sorted in parallel with the cryopreserved material and distributed over the same sequencing pools. Therefore, blood from the same donor was isolated as described above and directly resuspended in DMEM. Dead and damaged cells were identified by propidium iodide staining.    Primary mouse colon was dissected from an athymic nu/nu mouse and placed on ice. The sample was divided and half of the colon was immediately prepared for single cell separation, while the other half was minced on ice, placed into freezing solution II (10% DMSO, 90% non-inactivated FBS) and frozen with gradually decreasing temperatures (1ºC/min) to ‑80ºC (cryopreserved). After storage for one week at -80ºC, the sample was rapidly thawed in a water bath in continuous agitation and placed into 25 ml of cold 1x HBSS. For single cell separation the fresh and conserved samples were minced on ice and enzymatically digested in 5 ml 1x HBSS and 83 µl collagenase IV (10,000 U/ml) for 10 min at 37ºC. Single cells were separated by passing the sample through a 0.9 mm needle and filtration (70 µm nylon mesh). Cells were washed once in ice cold 1x HBSS and resuspended in DMEM before sorting. Dead and damaged cells were identified by propidium iodide staining.    We generated ovarian and lung orthotopic tumor models, referred as Orthoxenograft® or patient derived orthotopic xenograft (PDOX). For single cell separation the fresh and conserved samples were minced on ice and enzymatically digested in 5 ml 1x HBSS and 83 µl collagenase IV (10,000 U/ml) for 15 min at 37ºC. Single cells were separated by passing the sample through a 0.9 mm needle and filtration (70 µm nylon mesh). Cells were washed once in ice cold 1x HBSS and resuspended in DMEM before sorting. In order to enrich human cells during the sorting procedure, tumor cells were stained for 1 hour at 4ºC with α-EpCam (CD326, eBioscience, 1:100). Propidium iodide staining identified dead/damaged cells.
To construct single cell libraries from polyA-tailed RNA, we applied massively parallel single-cell RNA sequencing (MARS-Seq; Jaitin et al., Science 2014).  This methodology generates paired-end reads where read 1 contains the transcript sequence and read 2 the cell and UMI barcodes. Briefly, single cells were FACS-sorted into 384-well plates, containing lysis buffer and reverse-transcription (RT) primers. The RT primers contained the single cell barcodes and unique molecular identifiers (UMIs) for subsequent de-multiplexing and correction for amplification biases, respectively.    Full-length RNA sequencing libraries were prepared using the SMARTseq2 protocol (Picelli et al., Nat Methods 2013) with minor modifications. Briefly, freshly harvested or cryopreserved (1 week at -80ºC) single cells were sorted into 96-well plates containing the lysis buffer. Reverse transcription was performed using SuperScrpit II (Invitrogen) in the presence of oligo-dT30VN, template-switching oligonucleotides and betaine. The cDNA was amplified using the KAPA Hifi Hotstart ReadyMix (Kappa Biosystems), ISPCR primer and 20 cycles of amplification. Following purification with Agencourt Ampure XP beads (Beckmann Coulter), product size distribution and quantity were assessed on a Bioanalyzer using a High Sensitvity DNA Kit (Agilent). 200 ng of the amplified cDNA was fragmented using Nextera® XT (Illumina) and amplified with indexed Nextera® PCR primers. Products were purified twice with Agencourt Ampure XP beads and quantified again using a Bioanalyzer High Sensitvity DNA Kit.

treatment_protocol: For single cell analysis, cryopreserved cells were rapidly thawed in a water bath in continuous agitation and placed into 25 ml of cold 1x HBSS. Fresh cells were trypsinized, pelleted and resuspended in 1x HBSS. Before sorting, cells from both conditions were filtered (70 µm nylon mesh) and propidium iodide staining identified dead/damaged cells. Whole blood was collected from a healthy donor into EDTA tubes (Becton, Dickinson and Co). Separation of peripheral blood mononuclear cells (PBMC) was performed with Ficoll-Paque PREMIUM (GE Healthcare) according to manufacturer's instructions. Briefly, for density gradient separation, 4 ml of blood was added onto 3 ml of Ficoll-Paque PREMIUM. Centrifuged at 400 x g for 30 minutes at 18ºC without brake. PBMC layer was recuperated and washed twice with PBS at 400g for 15 minutes at 18ºC. PBMC were resuspended in freezing solution (10% DMSO, 90% non-inactivated FBS) and frozen with gradually decreasing temperatures (1ºC/min) to -80ºC (cryopreserved). After storage for one week at -80ºC, the cryopreserved sample was rapidly thawed in a water bath in continuous agitation and placed into 25 ml of cold 1x HBSS. Cells were washed once in ice cold 1x HBSS and resuspended in DMEM before sorting. To avoid batch effects, fresh PBMC were sorted in parallel with the cryopreserved material and distributed over the same sequencing pools. Therefore, blood from the same donor was isolated as described above and directly resuspended in DMEM. Dead and damaged cells were identified by propidium iodide staining. Primary mouse colon was dissected from an athymic nu/nu mouse and placed on ice. The sample was divided and half of the colon was immediately prepared for single cell separation, while the other half was minced on ice, placed into freezing solution II (10% DMSO, 90% non-inactivated FBS) and frozen with gradually decreasing temperatures (1ºC/min) to -80ºC (cryopreserved). After storage for one week at -80ºC, the sample was rapidly thawed in a water bath in continuous agitation and placed into 25 ml of cold 1x HBSS. For single cell separation the fresh and conserved samples were minced on ice and enzymatically digested in 5 ml 1x HBSS and 83 µl collagenase IV (10,000 U/ml) for 10 min at 37ºC. Single cells were separated by passing the sample through a 0.9 mm needle and filtration (70 µm nylon mesh). Cells were washed once in ice cold 1x HBSS and resuspended in DMEM before sorting. Dead and damaged cells were identified by propidium iodide staining. We generated an ovarian orthotopic tumor model, referred as Orthoxenograft® or patient derived orthotopic xenograft (PDOX). For single cell separation the fresh and conserved samples were minced on ice and enzymatically digested in 5 ml 1x HBSS and 83 µl collagenase IV (10,000 U/ml) for 15 min at 37ºC. Single cells were separated by passing the sample through a 0.9 mm needle and filtration (70 µm nylon mesh). Cells were washed once in ice cold 1x HBSS and resuspended in DMEM before sorting. In order to enrich human cells during the sorting procedure, tumor cells were stained for 1 hour at 4ºC with a-EpCam (CD326, eBioscience, 1:100). Propidium iodide staining identified dead/damaged cells.

tag: cell type

value: peripheral blood mononuclear cells


title: Colon_Cryo_089V_MSCB-096

description:
cryopreserved cells
Colon_Cryo.tsv

organism: Mus musculus

source_name: colon cells

value: primary mouse colon cells


title: PBMC_Fresh_407X_MSCB-007

description:
fresh cells
PBMC_Fresh.tsv


title: Colon_Cryo_089V_MSCB-095

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_089V_MSCB-094

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-180

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-184

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-181

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_089V_MSCB-088

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-178

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-176

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_089V_MSCB-087

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_089V_MSCB-086

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_089V_MSCB-085

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-175

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-174

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_089V_MSCB-077

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-173

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_089V_MSCB-093

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-179

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_089V_MSCB-072

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_089V_MSCB-071

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-172

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_089V_MSCB-064

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_089V_MSCB-070

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_089V_MSCB-069

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_089V_MSCB-063

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_089V_MSCB-062

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_089V_MSCB-061

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_089V_MSCB-056

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-171

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-185

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-166

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-167

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_089V_MSCB-055

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-168

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_089V_MSCB-080

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_089V_MSCB-054

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_089V_MSCB-053

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-170

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-162

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-165

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-163

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-160

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-161

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-169

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_089V_MSCB-048

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_089V_MSCB-046

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_089V_MSCB-047

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-157

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_089V_MSCB-040

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-164

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_089V_MSCB-045

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-158

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-156

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-154

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-155

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_089V_MSCB-030

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_089V_MSCB-039

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-153

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_089V_MSCB-029

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_089V_MSCB-023

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-152

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-149

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_089V_MSCB-021

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_089V_MSCB-022

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_089V_MSCB-016

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-148

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-146

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-147

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-145

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_089V_MSCB-015

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_089V_MSCB-013

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_089V_MSCB-031

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_089V_MSCB-014

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-144

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-151

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-143

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-141

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-140

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-150

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_089V_MSCB-008

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-136

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-142

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_089V_MSCB-006

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_089V_MSCB-007

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_089V_MSCB-005

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_088V_MSCB-191

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_088V_MSCB-190

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_088V_MSCB-184

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_089V_MSCB-038

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-133

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-176

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_088V_MSCB-181

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_088V_MSCB-192

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_088V_MSCB-182

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_088V_MSCB-175

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-131

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-130

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-127

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-128

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-174

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-132

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-173

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-126

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-167

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-139

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-168

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-125

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-165

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-138

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-123

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-135

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-134

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-183

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_088V_MSCB-159

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_088V_MSCB-158

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_088V_MSCB-157

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-121

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-152

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-120

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-151

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-122

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-119

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-124

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-160

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_088V_MSCB-150

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-116

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-114

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-149

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-118

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-144

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-109

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-111

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-112

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-143

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_088V_MSCB-142

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-108

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-141

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_088V_MSCB-136

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-106

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-135

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-105

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-134

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-104

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-115

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-113

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-103

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-133

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-102

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-101

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-128

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_088V_MSCB-127

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_088V_MSCB-126

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-100

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-120

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-099

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-125

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_088V_MSCB-119

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_088V_MSCB-117

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_088V_MSCB-112

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_088V_MSCB-118

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-192

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-110

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-191

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-190

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-109

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-097

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-104

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-187

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-189

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-188

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-103

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-098

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-102

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-185

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-101

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-184

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-183

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-111

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_088V_MSCB-095

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-181

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-094

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-180

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-093

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-179

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-088

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_088V_MSCB-087

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_088V_MSCB-086

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_088V_MSCB-085

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-186

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-177

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-080

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_088V_MSCB-079

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-172

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-173

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-174

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-176

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-078

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-171

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-077

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_088V_MSCB-096

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_088V_MSCB-072

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-182

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-170

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-071

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-178

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-069

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-168

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-166

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-167

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-070

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_088V_MSCB-064

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-165

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-164

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-063

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_088V_MSCB-061

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-162

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-161

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-163

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-054

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-159

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-160

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-158

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-062

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-157

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-048

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_088V_MSCB-053

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-155

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-056

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_088V_MSCB-055

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_088V_MSCB-047

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-156

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-046

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-154

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-152

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-040

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_088V_MSCB-045

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_088V_MSCB-039

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-149

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-038

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-150

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-037

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_088V_MSCB-032

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-148

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-153

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-146

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-147

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-145

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-143

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-030

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_088V_MSCB-029

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_088V_MSCB-021

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-144

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-024

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-141

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-016

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-140

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-023

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-142

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-138

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-015

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-137

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-014

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-139

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-136

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-031

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_088V_MSCB-008

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_088V_MSCB-013

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_088V_MSCB-007

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-135

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Colon_Cryo_088V_MSCB-006

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_088V_MSCB-005

description:
cryopreserved cells
Colon_Cryo.tsv


title: Colon_Cryo_088V_MSCB-022

description:
cryopreserved cells
Colon_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-133

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-131

description:
cryopreserved cells
PBMC_Cryo.tsv


title: BCR-ABL1_rep2_RNAseq

city: London

first: Niklas

last: Feldhahn

address: The Commonwealth Building, Hammersmith Hospital, Du Cane Road

department: Department of Medicine

country: United Kingdom

institute: Imperial College London

data_processing:
Reads were aligned to the mouse genome (GRCm38/mm10) using STAR v2.5.0. STAR indexes were supplemented with UCSC known gene reference transcript assemblies. Alignment was performed with the following settings: --outFilterType BySJout, --outFilterMultimanNmax 20, --alignSJoverhangMin 8, --alignSJDBoverhangMin 1, --outFilterMismatchNmax 999, --outFilterMismatchNoverLmax 0.04, --alignIntronMin 20, --alignIntronMax 1000000.
Raw counts were obtained from STAR output and FPKM values were calculated with StringTie v1.3.0
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited file of raw read counts per gene
Supplementary_files_format_and_content: Tab delimited file of FPKM values per gene

source_name: BCR-ABL1 expressing primary B cell precursors (D7-9 post transduction)

growth_protocol: Primary B-cell precursors were maintained by ex vivo culture in Iscove's Modified Dulbecco's Medium (IMDM) containing 20% fetal calf serum (FCS) (Invitrogen), 1% Penicillin/Streptomycin (Gibco), 1% L-Glutamine (Gibco) and 50Î¼M 2-mercaptoethanol (Sigma) at 37°C in a humidified incubator with 5% CO2 in presence of 10 ng/ml of recombinant mouse IL-7 (Peprotech).

extract_protocol: RNA was extracted from 5 million cells using the RNeasy mini kit (Qiagen) and poly-A enriched using the NEBNext Poly(A) mRNA magnetic isolation module (NEB). cDNA libraries were generated from pre-enriched mRNA using the NEBNext® mRNA Library Prep Reagent Set for Illumina (NEB).

treatment_protocol: Transduction with MIGRI vectors was performed by spinoculation on day 2 and 3 after start of cell culture.

tag: genotype

tag: vector transduced

value: BCR-ABL1p210 MIGR1


title: PBMC_Cryo_407X_MSCB-130

description:
cryopreserved cells
PBMC_Cryo.tsv


title: C-MYC_rep2_RNAseq

source_name: C-MYC expressing primary B cell precursors (D7-9 post transduction)

value: C-MYC MIGR1


title: BCR-ABL1_rep1_RNAseq


title: PBMC_Cryo_407X_MSCB-129

description:
cryopreserved cells
PBMC_Cryo.tsv


title: EV_rep1_RNAseq

source_name: Empty vector (EV) transformed primary B cell precursors (D7-9 post transduction)


title: PBMC_Cryo_407X_MSCB-128

description:
cryopreserved cells
PBMC_Cryo.tsv


title: EV_rep2_RNAseq


title: PBMC_Cryo_407X_MSCB-126

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-132

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-125

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Mut_6

city: New York

first: Igor

last: Dolgalev

state: New York

address: 550 1st Ave

country: USA

institute: NYU Grossman School of Medicine

description:
Processed data file: counts.raw.txt
Processed data file: counts.norm.txt

data_processing:
Base calling and demultiplexing were performed using Illumina bcl2fastq software.
The sequencing reads were aligned to the mouse genome (UCSC build mm10) using the TopHat aligner.
HTSeq was utilized to generate counts for each gene based on how many aligned reads overlap its exons.
Counts were normalized and tested for differential expression with the DESeq2 R package.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: counts.raw.txt: Tab-delimited text file contains raw counts for all genes and samples.
Supplementary_files_format_and_content: counts.norm.txt: Tab-delimited text file contains normalized counts for all genes and samples.

molecule: total RNA

source_name: ES cells, KBP(KK/RR)

extract_protocol:
Total RNA was extracted using RNeasy Qiagen extraction kit according to the manufacturer's instructions.
Libraries were prepared using the mammalian RiboZero magnetic rRNA depletion kit (Epicenter, Madison, WI) following the manufacturer’s protocol. Five nanograms of RiboZero-treated RNA were used to construct a library using Epicenter’s ScriptSeq v2 RNASeq Library Preparation Kit.

treatment_protocol: Mouse ES cells were stably transduced with a lentivirus expressing either wild-type KBP or the stable mutant KBP(KK/RR) and maintained in self-renewing growth conditions.

value: embryonic stem (ES) cells

tag: lentivirus

value: KBP(KK/RR)


title: PBMC_Cryo_407X_MSCB-127

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Mut_5


title: WT_3

source_name: ES cells, wild-type KBP

value: wild-type KBP


title: PBMC_Cryo_407X_MSCB-134

description:
cryopreserved cells
PBMC_Cryo.tsv


title: WT_2


title: PBMC_Cryo_407X_MSCB-123

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-122

description:
cryopreserved cells
PBMC_Cryo.tsv


title: CEBPA-DOX_input_ChIPseq

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were aligned to the mm10 genome assembly using BWA-MEM version 3.2 with default parameters
Reads were filtered to remove non-uniquely aligned and duplicate reads using SAMtools v0.1.19 and Picard tools  v2.0.1
Peaks were called using SICER v1.1 (parameters: window size 100, fragment size 300, effective genome fraction 0.9, gap size 300, FDR 0.00001), a custom script was used to merge peaks within 10kb and remove peaks <1.5 RPKM, <5kb wide or with <1.1 fold change vs. isotyp control.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph files were generated using deepTools bamCoverage, scores represent RPKM read coverage

molecule: genomic DNA

source_name: Untreated BCR-ABL1-transformed primary B cell precursors that carry a DOX-inducible CEBPA vector. Cells are succesfully transformed cells.

growth_protocol: DOX-inducible CEBPA and control cells (reported in Chen et al., 2015) were maintained by ex vivo culture in Iscove's Modified Dulbecco's Medium (IMDM) containing 20% fetal calf serum (FCS) (Invitrogen), 1% Penicillin/Streptomycin (Gibco), 1% L-Glutamine (Gibco) and 50μM 2-mercaptoethanol (Sigma) but without addition of IL7 at 37°C in a humidified incubator with 5% CO2.

extract_protocol: Cells were enriched for CD11B and dead cells removed using MACS, cells formaldehyde treated and pellets snap frozen. Pellets were resuspended in sonication buffer, sonicated and lysed in RIPA buffer before performing ChIP with the appropriate antibody. ChIP-seq libraries were prepared using NEBNext ChIP-Seq Library Prep Master Mix Set and NEBNEXT Multiplex Oligos for Illumina.

treatment_protocol: Selection of expression cassettes was maintained using 2μg/mL Puromycin (Sigma) and 500μg/mL Geneticin/G418 (Sigma).

value: MSCV BCR-ABL1-p210; pRetroX-TRE3G-Cebpa; pRetroX-Tet3G

tag: antibody

tag: treatment


title: EV+DOX_gH2AX_ChIPseq

source_name: Doxycycline-treated BCR-ABL1-transformed primary B cell precursors that carry the empty vector (EV) respective to the DOX-inducible CEBPA vector used in the other experimens.  Cells are succesfully transformed cells.

growth_protocol: DOX-inducible CEBPA and control cells (reported in Chen et al., 2015) were maintained by ex vivo culture in Iscove's Modified Dulbecco's Medium (IMDM) containing 20% fetal calf serum (FCS) (Invitrogen), 1% Penicillin/Streptomycin (Gibco), 1% L-Glutamine (Gibco) and 50μM 2-mercaptoethanol (Sigma) but without addition of IL7 at 37°C in a humidified incubator with 5% CO2

treatment_protocol: Selection of expression cassettes was maintained using 2μg/mL Puromycin (Sigma) and 500μg/mL Geneticin/G418 (Sigma). Mock CEBPA-mediated reprogramming was induced by addition of 1μg/mL Doxycycline (DOX) (Sigma) for 7 days.

value: MSCV BCR-ABL1-p210; pRetroX-TRE3G; pRetroX-Tet3G

value: Anti-gamma H2A.X (phospho S139) (ab2893, Abcam)

value: Doxycycline treated


title: PBMC_Cryo_407X_MSCB-124

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-119

description:
cryopreserved cells
PBMC_Cryo.tsv


title: WT_1


title: Mut_4


title: PBMC_Cryo_407X_MSCB-117

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-120

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-118

description:
cryopreserved cells
PBMC_Cryo.tsv


title: CEBPA-DOX_gH2AX_ChIPseq


title: CEBPA+DOX_input_ChIPseq

source_name: Doxycycline (DOX) treated BCR-ABL1-transformed primary B cell precursors that carry a DOX-inducible CEBPA vector. Cells were enriched for CD11B+ myeloid phenotype by MACS. Cells are succesfully transformed cells.

treatment_protocol: Selection of expression cassettes was maintained using 2μg/mL Puromycin (Sigma) and 500μg/mL Geneticin/G418 (Sigma). CEBPA-mediated reprogramming was induced by addition of 1μg/mL Doxycycline (DOX) (Sigma) for 7 days.


title: C-MYC_rep1_RNAseq


title: CEBPA+DOX_gH2AX_ChIPseq


title: PBMC_Cryo_407X_MSCB-115

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-116

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-114

description:
cryopreserved cells
PBMC_Cryo.tsv


title: C-MYC_input_ChIPseq

growth_protocol: Primary B-cell precursors were maintained by ex vivo culture in Iscove's Modified Dulbecco's Medium (IMDM) containing 20% fetal calf serum (FCS) (Invitrogen), 1% Penicillin/Streptomycin (Gibco), 1% L-Glutamine (Gibco) and 50μM 2-mercaptoethanol (Sigma) at 37°C in a humidified incubator with 5% CO2 in presence of 10 ng/ml of recombinant mouse IL-7 (Peprotech).

extract_protocol: Dead cells were removed, cells formaldehyde treated and pellets snap frozen. Pellets were resuspended in sonication buffer, sonicated and lysed in RIPA buffer before performing ChIP with the appropriate antibody. Cells from ChIP-seq libraries were prepared using NEBNext ChIP-Seq Library Prep Master Mix Set and NEBNEXT Multiplex Oligos for Illumina.


title: BCR-ABL1_input_ChIPseq

extract_protocol: Dead cells were removed, cells formaldehyde treated and pellets snap frozen. Pellets were resuspended in sonication buffer, sonicated and lysed in RIPA buffer before performing ChIP with the appropriate antibody. ChIP-seq libraries were prepared using NEBNext ChIP-Seq Library Prep Master Mix Set and NEBNEXT Multiplex Oligos for Illumina.


title: BCR-ABL1_H3K27ac_ChIPseq

value: Anti-Histone H3 (acetyl K27) (ab4729, Abcam)


title: PBMC_Cryo_407X_MSCB-113

description:
cryopreserved cells
PBMC_Cryo.tsv


title: C-MYC_H3K27ac_ChIPseq


title: PBMC_Cryo_407X_MSCB-112

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-111

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-110

description:
cryopreserved cells
PBMC_Cryo.tsv


title: C-MYC_gH2AX_rep2_ChIPseq


title: BCR-ABL1_>D50_gH2AX_ChIPseq

source_name: BCR-ABL1 expressing primary B cell precursors that were cultured for >50 days (>D50) in cell culture with IL7 post transduction. Cells were also treated with 10mM hydroxyurea (HU) for 2 hours before harvest.

treatment_protocol: Transduction with MIGRI vectors was performed by spinoculation on day 2 and 3 after start of cell culture. Cells were also treated with 10mM hydroxyurea (HU) for 2 hours before harvest.

value: Hydroxyurea treated


title: BCR-ABL1_gH2AX_rep2_ChIPseq

growth_protocol: Bone marrow was isolated and B-cell precursors maintained in IMDM +20% FCS and 10ng/ml murine IL7


title: PBMC_Cryo_407X_MSCB-109

description:
cryopreserved cells
PBMC_Cryo.tsv


title: BCR-ABL1_iso_ChIPseq

value: polyclonal rabbit IgG (sc2027, Santa Cruz Biotechnologies)


title: PBMC_Cryo_407X_MSCB-108

description:
cryopreserved cells
PBMC_Cryo.tsv


title: C-MYC_gH2AX_rep1_ChIPseq


title: PBMC_Cryo_407X_MSCB-107

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Pale_2

city: Boston

first: Ann

last: Hochschild

state: MA

address: 4 Blackfan Circle

department: Microbiology and Immunobiology

institute: Harvard Medical School

description:
Total RNA isolated from cells descended from a pale (Rho prion-lacking) colony.
Pale_2.fastq (see "Data processing" Supplementary_files_format_and_content)

data_processing:
All data analysis was performed using Rockhopper (McClure et al., 2013) and Escherichia coli str. K-12 substr. MG1655 as the reference genome.
Specifically, data were treated as two experiments constituting either two ("blue" cell transcriptomes) or three ("pale" cell transcriptomes) biological replicates.
Data were visualized in the Rockhopper IGV genome browser (McClure et al., 2013) and TreeView 3.0 (Saldana et al., 2004).
Genome_build: ASM584v2
Supplementary_files_format_and_content: Tab-delimited text file includes Rockhopper (McClure et al., 2013) normalized transcript abundance measurements (Expression), transcript abundance ratios (Expression Ratio), and qValues (qValue) for raw data that were treated as two experiments constituting either two ("blue" cell transcriptomes; Blue_1.fastq, Blue_2.fastq) or three ("pale" cell transcriptomes; Pale_1.fastq, Pale_2.fastq, Pale_3.fastq) biological replicates.  Gene annotation, gene product description, and strand information is also included.

organism: Escherichia coli

source_name: Total RNA extracted from Rho prion-lacking cells

growth_protocol: Log-phase cultures (LB broth, Miller formulation) inoculated with either blue or pale colonies were grown for 5 hr at 37 degrees celsius.  Cells were pelleted by centrifugation and flash frozen on dry ice.

extract_protocol:
Total RNA was extracted from cell pellets with TRI Reagent (MRC).  RNA was precipitated, resuspended in DNase Reaction Buffer (Invitrogen) for 30 min at room temperature.  DNase-treated samples were subsequently purified with an Rneasy Plus Mini Kit (Qiagen).
Purified total RNA was depleted of rRNA using a Ribo-Zero (Bacteria) rRNA Removal Kit (Illumina).  cDNA libraries were constructed and sequenced on an Illumina NextSeq 500 sequencer at the Harvard Biopolymers Facility.

tag: growth protocol

value: Log-phase culture (LB broth, Miller formulation) inoculated with one pale colony and grown for 5 hr at 37 degrees celsius

tag: phenotype

value: Pale colony-color (prion-lacking)

tag: parent strain


title: PBMC_Cryo_407X_MSCB-105

description:
cryopreserved cells
PBMC_Cryo.tsv


title: Pale_3

description:
Total RNA isolated from cells descended from a pale (Rho prion-lacking) colony.
Pale_3.fastq (see "Data processing" Supplementary_files_format_and_content)


title: PBMC_Cryo_407X_MSCB-104

description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_407X_MSCB-103

description:
cryopreserved cells
PBMC_Cryo.tsv


title: REST KO-2

city: Bronx

first: Deyou

last: Zheng

state: NY

address: 1301 Morris Park Ave

institute: Albert Einstein College of Medicine

data_processing:
RNA-seq reads were mapped to the mouse reference genome (mm10) using TopHat v2.0.13. Based on GENCODE database (vM6), the number of RNA-seq fragments mapped to each gene was determined by HTSeq. Unnormalized count numbers are provided as processed data files.
Genome_build: mm10
Supplementary_files_format_and_content: unnormalized count numbers

source_name: REST KO_E12.5_venticular

growth_protocol: Mice of wildtype (n=12) and REST gene knockout (n=12) at embryonic 12.5 daies were isolated form anaesthetized littles.

extract_protocol:
Total RNA isolated according TRIZOL Reagent (ambion, lot:123906) protocol. Detail steps could be find at the link of: https://tools.thermofisher.com/content/sfs/manuals/trizol_reagent.pdf
RNA libraries were prepared for sequencing using standard Illumina strand-specific protocols. Detail steps could be find at the link of: http://wasp.einstein.yu.edu/index.php/Protocol:directional_WholeTranscript_seq

treatment_protocol: Ventricular hearts were isolated from mice body at ice bed and collected in 1ml of Trizol. 4 pooled hearts as one biological repeat.

tag: strain background

tag: age

value: Embryonic 12.5 day

tag: genotype/variation

value: Rest gene knockout at cardiomyocyte by Troponin-T Cre

tag: tissue

value: heart; venticular


title: Blue_2

description:
Total RNA isolated from cells descended from a blue (Rho prion-containing) colony.
Blue_2.fastq (see "Data processing" Supplementary_files_format_and_content)

source_name: Total RNA extracted from Rho prion-containing cells

value: Log-phase culture (LB broth, Miller formulation) inoculated with one blue colony and grown for 5 hr at 37 degrees celsius

value: Blue colony-color (prion-containing)


title: REST KO-3


title: PBMC_Cryo_407X_MSCB-102

description:
cryopreserved cells
PBMC_Cryo.tsv

value: peripheral blood mononuclear cells


title: REST KO-1


title: PBMC_Cryo_407X_MSCB-101

description:
cryopreserved cells
PBMC_Cryo.tsv


title: MDCK_Fresh_401U_MSCB-089

description:
fresh cells
MDCK_Fresh.tsv

organism: Canis lupus familiaris

source_name: kidney cells

value: cell line derived from canine adult kidney cells

tag: cell line

value: MDCK


title: WT-3

value: wild type


title: MDCK_Fresh_401U_MSCB-087

description:
fresh cells
MDCK_Fresh.tsv


title: PBMC_Cryo_407X_MSCB-099

description:
cryopreserved cells
PBMC_Cryo.tsv


title: MDCK_Fresh_401U_MSCB-090

description:
fresh cells
MDCK_Fresh.tsv


title: PBMC_Cryo_407X_MSCB-106

description:
cryopreserved cells
PBMC_Cryo.tsv


title: MDCK_Fresh_401U_MSCB-077

description:
fresh cells
MDCK_Fresh.tsv


title: BCR-ABL1_gH2AX_rep1_ChIPseq

data_processing:
Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were aligned to the mm10 genome assembly using BWA-MEM version 3.2 with default parameters
Reads were filtered to remove non-uniquely aligned and duplicate reads using SAMtools v0.1.19 and Picard tools  v2.0.1
Peaks were called using SICER v1.1 (parameters: window size 100, fragment size 300, effective genome fraction 0.9, gap size 300, FDR 0.00001), a custom script was used to merge peaks within 10kb and remove peaks <1.5 RPKM, <5kb wide or with <1.1 fold change vs. isotype control.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph files were generated using deepTools bamCoverage, scores represent RPKM read coverage

value: BCR-ABL1p210 MIGR1


title: PBMC_Cryo_407X_MSCB-098

description:
cryopreserved cells
PBMC_Cryo.tsv


title: WT-1


title: MDCK_Fresh_401U_MSCB-075

description:
fresh cells
MDCK_Fresh.tsv


title: MDCK_Fresh_401U_MSCB-066

description:
fresh cells
MDCK_Fresh.tsv


title: PBMC_Cryo_407X_MSCB-097

description:
cryopreserved cells
PBMC_Cryo.tsv


title: MDCK_Fresh_401U_MSCB-065

description:
fresh cells
MDCK_Fresh.tsv


title: WT-2


title: VEGF_minus_48h_H3K27me3_Rep2

city: Tokyo

first: Yasuharu

last: Kanki

address: 4-6-1 Komaba, Meguro-ku

country: Japan

institute: The University of Tokyo

data_processing:
Illumina CASAVA1.8.2 software used for basecalling and demultiplexing.
ChIP-seq reads were aligned to the NCBI Build #37 (UCSC mm9) reference mouse genome, using ELAND (Illumina mapping program)
The mapped sequence reads were extended to 500 bp and converted to the continuous signal data in wig format.  Wig files were converted to bigwig files using UCSC wigToBigWig program.
Genome_build: NCBI Build #37 (UCSC mm9)
Supplementary_files_format_and_content: bigWig

growth_protocol: Mouse ES cells were maintained as previously described. Induction of differentiation was performed using differentiation medium (DM; alpha minimal essential medium [MEM; Gibco, Carlsbad, CA, USA] supplemented with 10% fetal calf serum [Japan Bioserum Co Ltd, Hiroshima, Japan] and 5*10^-5 M 2-mercaptoethanol [Gibco]) as previously described. In brief, undifferentiated ES cells were cultured without leukemia inhibitory factor on collagen-coated dishes (Becton Dickson) at a cell density of 0.75 to 1*10^3 cells/cm^2 for 96 h. Cells were harvested and purified by magnetic cell sorting (MACS) with an anti-Flk-1 antibody. Purified Flk-1-positive cells were seeded onto collagen-coated dishes at a density of 0.75 to 1*10^4 cells/cm^2 in DM.

extract_protocol:
For ChIP-seq, sonicated nuclear fraction was incubated with each antibody and histone-DNA were isolated.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: Cells were treated for 6 h or 48 h with presense or absense VEGF

tag: culture condition

value: without VEGF

tag: time

value: 48 hours after without VEGF

tag: chip antibody

value: H3K27me3 (#07-449, Millipore, Billerica, MA, USA)


title: Pale_1

description:
Total RNA isolated from cells descended from a pale (Rho prion-lacking) colony.
Pale_1.fastq (see "Data processing" Supplementary_files_format_and_content)


title: Blue_1

description:
Total RNA isolated from cells descended from a blue (Rho prion-containing) colony.
Blue_1.fastq (see "Data processing" Supplementary_files_format_and_content)


title: MDCK_Fresh_401U_MSCB-053

description:
fresh cells
MDCK_Fresh.tsv

tag: cell type


title: HEK293_Nitrogen_Exp_2_406X_MSCB-192

description:
cryopreserved cells
HEK293_Nitrogen_Exp_2.tsv

value: cell line derived from human embryonic kidney cells


title: MDCK_Fresh_401U_MSCB-062

description:
fresh cells
MDCK_Fresh.tsv


title: VEGF_minus_48h_H3K27me3_Rep1


title: MDCK_Fresh_401U_MSCB-063

description:
fresh cells
MDCK_Fresh.tsv


title: HEK293_Nitrogen_Exp_2_406X_MSCB-191


title: MDCK_Fresh_401U_MSCB-052

description:
fresh cells
MDCK_Fresh.tsv


title: MDCK_Fresh_401U_MSCB-086

description:
fresh cells
MDCK_Fresh.tsv


title: VEGF_minus_48h_H3K4me3_Rep1

value: H3K4me3 (non-commercial, gifted by Dr. Hiroshi Kimura, Tokyo Institute Technology, Japan)


title: MDCK_Fresh_401U_MSCB-041

description:
fresh cells
MDCK_Fresh.tsv


title: MDCK_Fresh_401U_MSCB-039

description:
fresh cells
MDCK_Fresh.tsv


title: MDCK_Fresh_401U_MSCB-038

description:
fresh cells
MDCK_Fresh.tsv


title: VEGF_plus_48h_H3K27me3_Rep2

value: with VEGF

value: 48 hours after VEGF stimulation


title: HEK293_Nitrogen_Exp_2_406X_MSCB-190


title: HEK293_Nitrogen_Exp_2_406X_MSCB-189


title: MDCK_Fresh_401U_MSCB-029

description:
fresh cells
MDCK_Fresh.tsv


title: HEK293_Nitrogen_Exp_2_406X_MSCB-187


title: MDCK_Fresh_401U_MSCB-028

description:
fresh cells
MDCK_Fresh.tsv


title: VEGF_plus_48h_H3K27me3_Rep1


title: MDCK_Fresh_401U_MSCB-018

description:
fresh cells
MDCK_Fresh.tsv


title: HEK293_Nitrogen_Exp_2_406X_MSCB-184


title: MDCK_Fresh_401U_MSCB-017

description:
fresh cells
MDCK_Fresh.tsv


title: VEGF_minus_48h_H3K4me3_Rep2


title: MDCK_Fresh_401U_MSCB-042

description:
fresh cells
MDCK_Fresh.tsv


title: HEK293_Nitrogen_Exp_2_406X_MSCB-183


title: MDCK_Fresh_401U_MSCB-015

description:
fresh cells
MDCK_Fresh.tsv


title: MDCK_Fresh_401U_MSCB-014

description:
fresh cells
MDCK_Fresh.tsv


title: VEGF_minus_6h_H3K27me3_Rep2

value: 6 hours after without VEGF


title: MDCK_Fresh_401U_MSCB-003

description:
fresh cells
MDCK_Fresh.tsv


title: MDCK_Fresh_400U_MSCB-091

description:
fresh cells
MDCK_Fresh.tsv


title: HEK293_Nitrogen_Exp_2_406X_MSCB-182


title: VEGF_plus_48h_H3K4me3_Rep1


title: MDCK_Fresh_401U_MSCB-005

description:
fresh cells
MDCK_Fresh.tsv


title: VEGF_minus_6h_H3K27me3_Rep1


title: MDCK_Fresh_400U_MSCB-090

description:
fresh cells
MDCK_Fresh.tsv


title: HEK293_Nitrogen_Exp_2_406X_MSCB-180


title: VEGF_minus_6h_H3K4me3_Rep2


title: VEGF_minus_6h_H3K4me3_Rep1


title: MDCK_Fresh_400U_MSCB-087

description:
fresh cells
MDCK_Fresh.tsv


title: MDCK_Fresh_400U_MSCB-089

description:
fresh cells
MDCK_Fresh.tsv


title: MDCK_Fresh_400U_MSCB-077

description:
fresh cells
MDCK_Fresh.tsv


title: MDCK_Fresh_401U_MSCB-027

description:
fresh cells
MDCK_Fresh.tsv


title: HEK293_Nitrogen_Exp_2_406X_MSCB-179


title: HEK293_Nitrogen_Exp_2_406X_MSCB-177


title: VEGF_plus_48h_H3K4me3_Rep2


title: MDCK_Fresh_400U_MSCB-076

description:
fresh cells
MDCK_Fresh.tsv


title: MDCK_Fresh_400U_MSCB-067

description:
fresh cells
MDCK_Fresh.tsv


title: HEK293_Nitrogen_Exp_2_406X_MSCB-175


title: VEGF_plus_6h_H3K27me3_Rep2

value: 6 hours after VEGF stimulation


title: MDCK_Fresh_400U_MSCB-066

description:
fresh cells
MDCK_Fresh.tsv


title: HEK293_Nitrogen_Exp_2_406X_MSCB-174


title: VEGF_plus_6h_H3K27me3_Rep1


title: MDCK_Fresh_400U_MSCB-065

description:
fresh cells
MDCK_Fresh.tsv


title: MDCK_Fresh_400U_MSCB-064

description:
fresh cells
MDCK_Fresh.tsv


title: VEGF_plus_6h_H3K4me3_Rep2


title: HEK293_Nitrogen_Exp_2_406X_MSCB-172


title: MDCK_Fresh_400U_MSCB-063

description:
fresh cells
MDCK_Fresh.tsv


title: MDCK_Fresh_400U_MSCB-062

description:
fresh cells
MDCK_Fresh.tsv


title: MDCK_Fresh_400U_MSCB-053

description:
fresh cells
MDCK_Fresh.tsv


title: HEK293_Nitrogen_Exp_2_406X_MSCB-168


title: Flk_H3K27me3_Rep2

value: Flk-sorted


title: MDCK_Fresh_400U_MSCB-086

description:
fresh cells
MDCK_Fresh.tsv


title: MDCK_Fresh_400U_MSCB-043

description:
fresh cells
MDCK_Fresh.tsv


title: MDCK_Fresh_400U_MSCB-041

description:
fresh cells
MDCK_Fresh.tsv


title: MDCK_Fresh_400U_MSCB-040

description:
fresh cells
MDCK_Fresh.tsv


title: HEK293_Nitrogen_Exp_2_406X_MSCB-165


title: Flk_H3K4me3_Rep2


title: MDCK_Fresh_400U_MSCB-039

description:
fresh cells
MDCK_Fresh.tsv


title: MDCK_Fresh_400U_MSCB-038

description:
fresh cells
MDCK_Fresh.tsv


title: HEK293_Nitrogen_Exp_2_406X_MSCB-162


title: HEK293_Nitrogen_Exp_2_406X_MSCB-161


title: MDCK_Fresh_400U_MSCB-019

description:
fresh cells
MDCK_Fresh.tsv


title: Flk_H3K4me3_Rep1


title: HEK293_Nitrogen_Exp_2_406X_MSCB-164


title: MDCK_Fresh_400U_MSCB-029

description:
fresh cells
MDCK_Fresh.tsv


title: VEGF_plus_6h_H3K4me3_Rep1


title: MDCK_Fresh_400U_MSCB-017

description:
fresh cells
MDCK_Fresh.tsv


title: MDCK_Fresh_400U_MSCB-052

description:
fresh cells
MDCK_Fresh.tsv


title: HEK293_Nitrogen_Exp_2_406X_MSCB-159


title: MDCK_Fresh_400U_MSCB-016

description:
fresh cells
MDCK_Fresh.tsv


title: HEK293_Nitrogen_Exp_2_406X_MSCB-157


title: MDCK_Fresh_400U_MSCB-015

description:
fresh cells
MDCK_Fresh.tsv


title: MDCK_Fresh_400U_MSCB-005

description:
fresh cells
MDCK_Fresh.tsv


title: HEK293_Nitrogen_Exp_2_406X_MSCB-170


title: MDCK_Cryo_401U_MSCB-183

description:
cryopreserved cells
MDCK_Cryo.tsv


title: HEK293_Nitrogen_Exp_2_406X_MSCB-156


title: Flk_H3K27me3_Rep1


title: MDCK_Fresh_400U_MSCB-042

description:
fresh cells
MDCK_Fresh.tsv


title: HEK293_Nitrogen_Exp_2_406X_MSCB-167


title: MDCK_Cryo_401U_MSCB-182

description:
cryopreserved cells
MDCK_Cryo.tsv


title: MDCK_Cryo_401U_MSCB-172

description:
cryopreserved cells
MDCK_Cryo.tsv


title: MDCK_Cryo_401U_MSCB-171

description:
cryopreserved cells
MDCK_Cryo.tsv


title: MDCK_Cryo_401U_MSCB-162

description:
cryopreserved cells
MDCK_Cryo.tsv


title: MDCK_Fresh_400U_MSCB-028

description:
fresh cells
MDCK_Fresh.tsv


title: MDCK_Cryo_401U_MSCB-161

description:
cryopreserved cells
MDCK_Cryo.tsv


title: MDCK_Cryo_401U_MSCB-159

description:
cryopreserved cells
MDCK_Cryo.tsv


title: HEK293_Nitrogen_Exp_2_406X_MSCB-151


title: MDCK_Cryo_401U_MSCB-158

description:
cryopreserved cells
MDCK_Cryo.tsv


title: MDCK_Cryo_401U_MSCB-138

description:
cryopreserved cells
MDCK_Cryo.tsv


title: MDCK_Cryo_401U_MSCB-147

description:
cryopreserved cells
MDCK_Cryo.tsv


title: MDCK_Fresh_400U_MSCB-014

description:
fresh cells
MDCK_Fresh.tsv


title: HEK293_Nitrogen_Exp_2_406X_MSCB-148


title: MDCK_Cryo_401U_MSCB-125

description:
cryopreserved cells
MDCK_Cryo.tsv


title: HEK293_Nitrogen_Exp_2_406X_MSCB-147


title: MDCK_Cryo_401U_MSCB-148

description:
cryopreserved cells
MDCK_Cryo.tsv


title: HEK293_Nitrogen_Exp_2_406X_MSCB-146


title: MDCK_Cryo_401U_MSCB-134

description:
cryopreserved cells
MDCK_Cryo.tsv


title: MDCK_Cryo_401U_MSCB-114

description:
cryopreserved cells
MDCK_Cryo.tsv


title: HEK293_Nitrogen_Exp_2_406X_MSCB-144


title: MDCK_Cryo_401U_MSCB-111

description:
cryopreserved cells
MDCK_Cryo.tsv


title: MDCK_Cryo_401U_MSCB-110

description:
cryopreserved cells
MDCK_Cryo.tsv


title: HEK293_Nitrogen_Exp_2_406X_MSCB-154


title: MDCK_Cryo_401U_MSCB-113

description:
cryopreserved cells
MDCK_Cryo.tsv


title: HEK293_Nitrogen_Exp_2_406X_MSCB-143


title: MDCK_Cryo_401U_MSCB-100

description:
cryopreserved cells
MDCK_Cryo.tsv


title: HEK293_Nitrogen_Exp_2_406X_MSCB-140


title: MDCK_Cryo_401U_MSCB-124

description:
cryopreserved cells
MDCK_Cryo.tsv


title: HEK293_Nitrogen_Exp_2_406X_MSCB-139


title: MDCK_Cryo_401U_MSCB-099

description:
cryopreserved cells
MDCK_Cryo.tsv


title: HEK293_Nitrogen_Exp_2_406X_MSCB-152


title: MDCK_Cryo_400U_MSCB-183

description:
cryopreserved cells
MDCK_Cryo.tsv


title: MDCK_Cryo_401U_MSCB-101

description:
cryopreserved cells
MDCK_Cryo.tsv


title: HEK293_Nitrogen_Exp_2_406X_MSCB-138


title: MDCK_Cryo_400U_MSCB-173

description:
cryopreserved cells
MDCK_Cryo.tsv


title: MDCK_Cryo_400U_MSCB-182

description:
cryopreserved cells
MDCK_Cryo.tsv


title: MDCK_Cryo_400U_MSCB-172

description:
cryopreserved cells
MDCK_Cryo.tsv


title: MDCK_Cryo_400U_MSCB-161

description:
cryopreserved cells
MDCK_Cryo.tsv


title: MDCK_Cryo_400U_MSCB-159

description:
cryopreserved cells
MDCK_Cryo.tsv


title: MDCK_Cryo_400U_MSCB-158

description:
cryopreserved cells
MDCK_Cryo.tsv


title: MDCK_Cryo_400U_MSCB-163

description:
cryopreserved cells
MDCK_Cryo.tsv


title: HEK293_Nitrogen_Exp_2_406X_MSCB-134


title: HEK293_Nitrogen_Exp_2_406X_MSCB-135


title: MDCK_Cryo_400U_MSCB-160

description:
cryopreserved cells
MDCK_Cryo.tsv


title: K562_Fresh_Exp_2_K562_H7

description:
fresh cells
K562_Fresh_Exp_2.tsv

source_name: leukemia cells

value: cell line derived from human leukemia cells


title: HEK293_Nitrogen_Exp_2_406X_MSCB-131


title: MDCK_Cryo_400U_MSCB-149

description:
cryopreserved cells
MDCK_Cryo.tsv


title: K562_Fresh_Exp_2_K562_H5

description:
fresh cells
K562_Fresh_Exp_2.tsv


title: HEK293_Nitrogen_Exp_2_406X_MSCB-130


title: MDCK_Cryo_400U_MSCB-139

description:
cryopreserved cells
MDCK_Cryo.tsv


title: MDCK_Cryo_400U_MSCB-148

description:
cryopreserved cells
MDCK_Cryo.tsv


title: MDCK_Cryo_400U_MSCB-138

description:
cryopreserved cells
MDCK_Cryo.tsv


title: K562_Fresh_Exp_2_K562_H1

description:
fresh cells
K562_Fresh_Exp_2.tsv


title: MDCK_Cryo_400U_MSCB-134

description:
cryopreserved cells
MDCK_Cryo.tsv


title: MDCK_Cryo_400U_MSCB-125

description:
cryopreserved cells
MDCK_Cryo.tsv


title: K562_Fresh_Exp_2_K562_G5

description:
fresh cells
K562_Fresh_Exp_2.tsv


title: MDCK_Cryo_400U_MSCB-124

description:
cryopreserved cells
MDCK_Cryo.tsv


title: K562_Fresh_Exp_2_K562_F9

description:
fresh cells
K562_Fresh_Exp_2.tsv


title: MDCK_Cryo_400U_MSCB-135

description:
cryopreserved cells
MDCK_Cryo.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-064

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: MDCK_Cryo_400U_MSCB-115

description:
cryopreserved cells
MDCK_Cryo.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-063

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-062

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: HEK293_Nitrogen_Exp_2_406X_MSCB-137


title: HEK293_Fresh_Exp_2_406X_MSCB-059

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: MDCK_Cryo_400U_MSCB-113

description:
cryopreserved cells
MDCK_Cryo.tsv


title: MDCK_Cryo_400U_MSCB-114

description:
cryopreserved cells
MDCK_Cryo.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-058

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: K562_Fresh_Exp_2_K562_E5

description:
fresh cells
K562_Fresh_Exp_2.tsv


title: K562_Fresh_Exp_2_K562_E3

description:
fresh cells
K562_Fresh_Exp_2.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-057

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: MDCK_Cryo_400U_MSCB-112

description:
cryopreserved cells
MDCK_Cryo.tsv


title: MDCK_Cryo_400U_MSCB-136

description:
cryopreserved cells
MDCK_Cryo.tsv


title: K562_Fresh_Exp_2_K562_D7

description:
fresh cells
K562_Fresh_Exp_2.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-056

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: K562_Fresh_Exp_2_K562_D5

description:
fresh cells
K562_Fresh_Exp_2.tsv


title: MDCK_Cryo_400U_MSCB-101

description:
cryopreserved cells
MDCK_Cryo.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-055

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: K562_Fresh_Exp_2_K562_D3

description:
fresh cells
K562_Fresh_Exp_2.tsv


title: K562_Fresh_Exp_2_K562_F3

description:
fresh cells
K562_Fresh_Exp_2.tsv


title: K562_Fresh_Exp_2_K562_D1

description:
fresh cells
K562_Fresh_Exp_2.tsv


title: K562_Fresh_Exp_2_K562_D11

description:
fresh cells
K562_Fresh_Exp_2.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-052

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-054

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-051

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: K562_Fresh_Exp_2_K562_C7

description:
fresh cells
K562_Fresh_Exp_2.tsv


title: K562_Fresh_Exp_2_K562_F11

description:
fresh cells
K562_Fresh_Exp_2.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-050

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: K562_Fresh_Exp_2_K562_C1

description:
fresh cells
K562_Fresh_Exp_2.tsv


title: K562_Fresh_Exp_2_K562_C5

description:
fresh cells
K562_Fresh_Exp_2.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-048

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: MDCK_Cryo_400U_MSCB-111

description:
cryopreserved cells
MDCK_Cryo.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-045

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-047

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: K562_Fresh_Exp_2_K562_B9

description:
fresh cells
K562_Fresh_Exp_2.tsv


title: K562_Fresh_Exp_2_K562_C11

description:
fresh cells
K562_Fresh_Exp_2.tsv


title: K562_Fresh_Exp_2_K562_B7

description:
fresh cells
K562_Fresh_Exp_2.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-044

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-043

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-053

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-041

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: K562_Fresh_Exp_2_K562_A3

description:
fresh cells
K562_Fresh_Exp_2.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-042

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: K562_Fresh_Exp_2_K562_A7

description:
fresh cells
K562_Fresh_Exp_2.tsv


title: K562_Fresh_Exp_2_K562_B11

description:
fresh cells
K562_Fresh_Exp_2.tsv


title: K562_Fresh_Exp_2_K562_B3

description:
fresh cells
K562_Fresh_Exp_2.tsv


title: K562_Cryo_Exp_2_K562_H8

description:
cryopreserved cells
K562_Cryo_Exp_2.tsv


title: K562_Cryo_Exp_2_K562_H4

description:
cryopreserved cells
K562_Cryo_Exp_2.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-040

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-038

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-037

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-039

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: K562_Cryo_Exp_2_K562_H2

description:
cryopreserved cells
K562_Cryo_Exp_2.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-036

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: K562_Cryo_Exp_2_K562_G8

description:
cryopreserved cells
K562_Cryo_Exp_2.tsv


title: K562_Cryo_Exp_2_K562_G10

description:
cryopreserved cells
K562_Cryo_Exp_2.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-035

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: K562_Cryo_Exp_2_K562_E6

description:
cryopreserved cells
K562_Cryo_Exp_2.tsv


title: K562_Cryo_Exp_2_K562_E4

description:
cryopreserved cells
K562_Cryo_Exp_2.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-033

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-034

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: K562_Cryo_Exp_2_K562_E10

description:
cryopreserved cells
K562_Cryo_Exp_2.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-032

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-030

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-029

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: K562_Cryo_Exp_2_K562_D2

description:
cryopreserved cells
K562_Cryo_Exp_2.tsv


title: K562_Cryo_Exp_2_K562_D4

description:
cryopreserved cells
K562_Cryo_Exp_2.tsv


title: K562_Cryo_Exp_2_K562_D12

description:
cryopreserved cells
K562_Cryo_Exp_2.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-031

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-026

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: K562_Cryo_Exp_2_K562_C12

description:
cryopreserved cells
K562_Cryo_Exp_2.tsv


title: K562_Cryo_Exp_2_K562_C6

description:
cryopreserved cells
K562_Cryo_Exp_2.tsv


title: K562_Cryo_Exp_2_K562_D10

description:
cryopreserved cells
K562_Cryo_Exp_2.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-027

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-025

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-024

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


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description:
cryopreserved cells
K562_Cryo_Exp_2.tsv


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description:
cryopreserved cells
K562_Cryo_Exp_2.tsv


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description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-021

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: K562_Cryo_Exp_2_K562_B4

description:
cryopreserved cells
K562_Cryo_Exp_2.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-023

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-018

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: K562_Cryo_Exp_2_K562_D6

description:
cryopreserved cells
K562_Cryo_Exp_2.tsv


title: K562_Cryo_Exp_2_K562_B12

description:
cryopreserved cells
K562_Cryo_Exp_2.tsv


title: K562_Cryo_Exp_2_K562_A2

description:
cryopreserved cells
K562_Cryo_Exp_2.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-019

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-017

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-022

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: K562_Cryo_Exp_2_K562_A10

description:
cryopreserved cells
K562_Cryo_Exp_2.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-015

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: K562_Cryo_Exp_2_K562_B10

description:
cryopreserved cells
K562_Cryo_Exp_2.tsv


title: HEK293_Fresh_Exp_3_HEK293_F7

description:
fresh cells
HEK293_Fresh_Exp_3.tsv


title: HEK293_Fresh_Exp_3_HEK293_G7

description:
fresh cells
HEK293_Fresh_Exp_3.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-013

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-014

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: HEK293_Fresh_Exp_3_HEK293_F5

description:
fresh cells
HEK293_Fresh_Exp_3.tsv


title: K562_Cryo_Exp_2_K562_B6

description:
cryopreserved cells
K562_Cryo_Exp_2.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-011

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-016

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-009

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: HEK293_Fresh_Exp_3_HEK293_F3

description:
fresh cells
HEK293_Fresh_Exp_3.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-010

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: HEK293_Fresh_Exp_3_HEK293_E9

description:
fresh cells
HEK293_Fresh_Exp_3.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-007

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: HEK293_Fresh_Exp_3_HEK293_E7

description:
fresh cells
HEK293_Fresh_Exp_3.tsv


title: HEK293_Fresh_Exp_3_HEK293_E5

description:
fresh cells
HEK293_Fresh_Exp_3.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-006

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: HEK293_Fresh_Exp_3_HEK293_E3

description:
fresh cells
HEK293_Fresh_Exp_3.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-005

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: HEK293_Fresh_Exp_3_HEK293_D3

description:
fresh cells
HEK293_Fresh_Exp_3.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-004

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-003

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: HEK293_Fresh_Exp_3_HEK293_D1

description:
fresh cells
HEK293_Fresh_Exp_3.tsv


title: HEK293_Fresh_Exp_3_HEK293_D5

description:
fresh cells
HEK293_Fresh_Exp_3.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-002

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-001

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: HEK293_Fresh_Exp_3_HEK293_C5

description:
fresh cells
HEK293_Fresh_Exp_3.tsv


title: HEK293_Fresh_Exp_3_HEK293_F11

description:
fresh cells
HEK293_Fresh_Exp_3.tsv


title: HEK293_Fresh_Exp_2_406X_MSCB-012

description:
fresh cells
HEK293_Fresh_Exp_2.tsv


title: HEK293_Cryo_Exp_2_406X_MSCB-124

description:
cryopreserved cells
HEK293_Cryo_Exp_2.tsv


title: HEK293_Fresh_Exp_3_HEK293_B9

description:
fresh cells
HEK293_Fresh_Exp_3.tsv


title: HEK293_Cryo_Exp_2_406X_MSCB-128


title: HEK293_Fresh_Exp_3_HEK293_B7

description:
fresh cells
HEK293_Fresh_Exp_3.tsv


title: HEK293_Fresh_Exp_3_HEK293_A9

description:
fresh cells
HEK293_Fresh_Exp_3.tsv


title: HEK293_Cryo_Exp_2_406X_MSCB-120


title: HEK293_Fresh_Exp_3_HEK293_D11

description:
fresh cells
HEK293_Fresh_Exp_3.tsv


title: HEK293_Fresh_Exp_3_HEK293_B1

description:
fresh cells
HEK293_Fresh_Exp_3.tsv


title: HEK293_Fresh_Exp_3_HEK293_C3

description:
fresh cells
HEK293_Fresh_Exp_3.tsv


title: HEK293_Cryo_Exp_2_406X_MSCB-119


title: HEK293_Cryo_Exp_2_406X_MSCB-122


title: jmjd-5_25C_6G_A06

city: Copenhagen

first: Anna Elisabetta

last: Salcini

address: Ole Maaloes vej 5

department: BRIC

country: Denmark

institute: University of Copenhagen

data_processing:
Data basecalled by BGI
Raw fastq data was aligned to the ce10 genome assembly using the STAR alignment tool (v2.3.0) with default parameters except: outFilterMismatchNoverLmax=0.1, outFilterMatchNmin=16
Uniquely mapped reads were assigned RefSeq genes using htseq-count (parameters: -a 30 -s no -m intersection-nonempty)
The RefSeq gene database was downloaded from UCSC (data stamped March 17 2013), ambigiously mapped genes removed and then filtered to keep only the longest transcript variant of a given gene
Genome_build: ce10
Supplementary_files_format_and_content: .counts files contain the raw output from htseq-count

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: N2 and jmjd-5(tm3735) animals were gronw in OP50 plates using stardard conditions

extract_protocol:
Total RNA was extracted from all samples using Trizol and Chlorophorm, purified using RNeasy Mini Kit from Qiagen and eluted in RNase-free water.
BGI protocol

treatment_protocol: N2 and jmjd-5(tm3735) animals were grown at the indicated temperatures

tag: temperature

tag: generation


title: HEK293_Cryo_Exp_2_406X_MSCB-121


title: jmjd-5_25C_6G_A12


title: jmjd-5_25C_1G_A10


title: HEK293_Fresh_Exp_3_HEK293_A3

description:
fresh cells
HEK293_Fresh_Exp_3.tsv


title: HEK293_Cryo_Exp_2_406X_MSCB-127


title: HEK293_Fresh_Exp_3_HEK293_A5

description:
fresh cells
HEK293_Fresh_Exp_3.tsv


title: HEK293_Fresh_Exp_3_HEK293_A1

description:
fresh cells
HEK293_Fresh_Exp_3.tsv


title: HEK293_Fresh_Exp_3_HEK293_B3

description:
fresh cells
HEK293_Fresh_Exp_3.tsv


title: HEK293_Cryo_Exp_2_406X_MSCB-117


title: HEK293_Cryo_Exp_2_406X_MSCB-118


title: jmjd-5_25C_1G_A04


title: jmjd-5_20C_A08


title: HEK293_Cryo_Exp_2_406X_MSCB-116


title: HEK293_Cryo_Exp_3_HEK293_H6

description:
cryopreserved cells
HEK293_Cryo_Exp_3.tsv


title: HEK293_Cryo_Exp_2_406X_MSCB-112


title: HEK293_Cryo_Exp_2_406X_MSCB-111


title: N2_25C_6G_A11

value: N2(wild type)


title: HEK293_Cryo_Exp_2_406X_MSCB-110


title: N2_25C_6G_A05


title: HEK293_Cryo_Exp_3_HEK293_H2


title: HEK293_Cryo_Exp_2_406X_MSCB-108


title: HEK293_Cryo_Exp_3_HEK293_H10


title: N2_25C_1G_A03


title: N2_25C_1G_A09


title: HEK293_Cryo_Exp_2_406X_MSCB-107


title: HEK293_Cryo_Exp_2_406X_MSCB-106


title: HEK293_Cryo_Exp_3_HEK293_G8


title: N2_20C_A01


title: HEK293_Cryo_Exp_3_HEK293_G10


title: HEK293_Cryo_Exp_3_HEK293_G4


title: HEK293_Fresh_Exp_3_HEK293_A11

description:
fresh cells
HEK293_Fresh_Exp_3.tsv


title: WTbiorep_16535_S

city: Seattle

first: Eric

middle: Jan

last: Foss

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

description:
single end Illumina sequence
WTbiorep_16535_S

data_processing:
bedtools genomeCoverageBed
Genome_build: sacCer3
Supplementary_files_format_and_content: genomeCoverageBed chromosome, position, read count, tab-delimited

organism: Saccharomyces cerevisiae

growth_protocol: 30 degrees log phase YEPD

extract_protocol:
DNA extraction
Illumina

treatment_protocol: flow sorting

tag: Stage

value: S

value: WT


title: HEK293_Cryo_Exp_2_406X_MSCB-102


title: jmjd-5_20C_A02


title: YAC_16528_lateG2

description:
single end Illumina sequence
YAC_16528_lateG2

value: YAC


title: HEK293_Cryo_Exp_2_406X_MSCB-098


title: HEK293_Cryo_Exp_2_406X_MSCB-105


title: HEK293_Cryo_Exp_3_HEK293_F8


title: HEK293_Cryo_Exp_3_HEK293_F2


title: HEK293_Cryo_Exp_3_HEK293_F10


title: HEK293_Cryo_Exp_3_HEK293_H4


title: HEK293_Cryo_Exp_2_406X_MSCB-097


title: YAC_16528_earlyG2

description:
single end Illumina sequence
YAC_16528_earlyG2


title: N2_20C_A07


title: HEK293_Cryo_Exp_2_406X_MSCB-109


title: HEK293_Cryo_Exp_3_HEK293_E8


title: HEK293_Cryo_Exp_2_406X_MSCB-095


title: WTbiorep_16535_G1

description:
single end Illumina sequence
WTbiorep_16535_G1


title: YAC_16528_S

description:
single end Illumina sequence
YAC_16528_S


title: HEK293_Cryo_Exp_2_406X_MSCB-093


title: YAC_16528_G1

description:
single end Illumina sequence
YAC_16528_G1


title: weakrARSsir2_16663_S

description:
single end Illumina sequence
weakrARSsir2_16663_S


title: HEK293_Cryo_Exp_2_406X_MSCB-091


title: HEK293_Cryo_Exp_3_HEK293_C2


title: HEK293_Cryo_Exp_3_HEK293_D4


title: HEK293_Cryo_Exp_2_406X_MSCB-087


title: weakrARSsir2_16663_earlyG2

description:
single end Illumina sequence
weakrARSsir2_16663_earlyG2


title: weakrARSsir2_16663_G1

description:
single end Illumina sequence
weakrARSsir2_16663_G1


title: weakrARS_15985_lateG2

description:
single end Illumina sequence
weakrARS_15985_lateG2

value: weakrARS


title: HEK293_Cryo_Exp_3_HEK293_B8


title: HEK293_Cryo_Exp_3_HEK293_C10


title: HEK293_Cryo_Exp_2_406X_MSCB-086


title: weakrARSsir2_16663_lateG2

description:
single end Illumina sequence
weakrARSsir2_16663_lateG2


title: HEK293_Cryo_Exp_3_HEK293_B6


title: HEK293_Cryo_Exp_3_HEK293_B4


title: HEK293_Cryo_Exp_2_406X_MSCB-080


title: weakrARS_15985_G1

description:
single end Illumina sequence
weakrARS_15985_G1


title: HEK293_Cryo_Exp_2_406X_MSCB-082


title: HEK293_Cryo_Exp_2_406X_MSCB-078


title: HEK293_Cryo_Exp_2_406X_MSCB-085


title: weakrARS_15985_earlyG2

description:
single end Illumina sequence
weakrARS_15985_earlyG2


title: HEK293_Cryo_Exp_2_406X_MSCB-084


title: HEK293_Cryo_Exp_3_HEK293_B2


title: HEK293_Cryo_Exp_3_HEK293_A6


title: HEK293_Cryo_Exp_2_406X_MSCB-094


title: HEK293_Cryo_Exp_3_HEK293_E4


title: sir2_15984_lateG2

description:
single end Illumina sequence
sir2_15984_lateG2


title: weakrARS_15985_S

description:
single end Illumina sequence
weakrARS_15985_S


title: HEK293_Cryo_Exp_3_HEK293_C6


title: HEK293_Cryo_Exp_3_HEK293_A4


title: sir2_15984_earlyG2

description:
single end Illumina sequence
sir2_15984_earlyG2


title: HEK293_Cryo_Exp_3_HEK293_A12

description:
cryopreserved cells
HEK293_Cryo_Exp_3.tsv


title: sir2_15984_S

description:
single end Illumina sequence
sir2_15984_S


title: HEK293_Cryo_Exp_2_406X_MSCB-076

description:
cryopreserved cells
HEK293_Cryo_Exp_2.tsv


title: HEK293_Cryo_Exp_2_406X_MSCB-075


title: HEK293_Cryo_Exp_3_HEK293_A10


title: sir2_15984_G1

description:
single end Illumina sequence
sir2_15984_G1


title: HEK293_Cryo_Exp_2_406X_MSCB-072


title: Luciferase knockdown in DU145 cells using shRNA replicate 3 re-analyzed

city: North Chicago

first: Josh

last: Plotnik

state: IL

address: 1 North Waukegan Rd, AP10/210A

institute: AbbVie Inc.

data_processing:
Illumina Casava1.8.2 software used for basecalling
Reads were aligned to the Homo sapien genome (UCSC hg19) using TopHat2 (v2.0.7) running BowTie2 (v2.0.6) and Samtools (v.0.1.18) using a modified protocol from Trapnell et al., Nature Protocols,  2012. The parameters used were -G -p 8
Differential expression of aligned reads was produced using Cufflinks (v2.1.1) using a modified protocol from Trapnell et al., Nature Protocols,  2012. The three replicates for each shRNA DU145 cell line were combined for the differential expression analysis. The parameters used were -b -p 8 -u -L
Genome_build: UCSC hg19
Supplementary_files_format_and_content: tab-delimited text files include for each combination of replicates: RPKM values, locus, status, log2(fold_change), test_stat, p-value, q-value, and significance

source_name: brain mets prostate adenocarcinoma

growth_protocol: DU145 cells were maintained in DMEM media (Mediatech-Cellgro) with 10% FBS, 100 U/ml Penicillin/Streptomycin, and 5microgram/ml puromycin (if selected)

extract_protocol:
Total RNA was isolated from DU145 cells transduced with shRNA knockdown vector using the Rneasy mini kit (Qiagen) according to manufacturer's instruction
Sequencing libraries were generated using a modified Illumina Truseq sample preparation protocol.Total RNA was DNAase treated with TURBO DNase (Invitrogen) The DNase treated RNA was polyA selected with oligo(dT) beads (Invitrogen). A Superscript III Reverse Transcriptase First-Strand Synthesis (Invitrogen) system was used to generate cDNA from the polyA selected RNA with random hexamer primers (Invitrogen). After first strand synthesis a second strand was generated using E. coli DNA ligase (New England BioLabs) and E. coli DNA polymerase I (New England BioLabs). The double stranded cDNAs were sheared to ~150 nucleotides using a Diagenode BioRuptor and the size was confirmed by DNA gel electrophoresis. DNA end repair of the cDNA was performed using Klenow DNA polymerase (New England BioLabs), T4 DNA polymerase (New England BioLabs), and T4 DNA ligase (New England BioLabs) before the sample was subjected to QIAquick PCR purification (Qiagen). Adapters were ligated to DNA fragments using the T4 DNA ligase (New England BioLabs). The product was run on a 2% agarose gel and size selected between 200 and 300 nucleotides to then be purified by a Gel Extraction kit (Qiagen). Universal and indexing adapters were taken from the TruSeq sample preparation kit (Illumina).

value: prostate adenocarcinoma metastaticized to brain

tag: cancer type

value: Pca


title: WT_15213_lateG2

description:
single end Illumina sequence
WT_15213_lateG2


title: Luciferase knockdown in DU145 cells using shRNA replicate 2 re-analyzed


title: HEK293_Cryo_Exp_2_406X_MSCB-071


title: HEK293_Cryo_Exp_2_406X_MSCB-073


title: WT_15213_earlyG2

description:
single end Illumina sequence
WT_15213_earlyG2


title: HEK293_Cryo_Exp_2_406X_MSCB-070


title: HEK293_Cryo_Exp_2_406X_MSCB-069


title: WT_15213_G1

description:
single end Illumina sequence
WT_15213_G1


title: Luciferase knockdown in DU145 cells using shRNA replicate 1 re-analyzed


title: WT_15213_S

description:
single end Illumina sequence
WT_15213_S


title: UCSD_Ccr_rep3

city: Cambridge

first: Gabriela

last: Alexe

address: 415 Main St.

department: Computational Biology and Bioinformatics

institute: Broad Institute

data_processing:
Total RNA was extracted and profiled by RNA sequencing (HiSeq, Illumina) at BioMicroCenter from Massachusetts Institute of Technology (Cambridge, MA, USA). Quality control tests for the unmapped reads were performed using the FASTQC software avaialble from the Babraham Lab http://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
The reads were aligned to the GRCh37 (hg19) annotated human reference genome by using tophat2 (Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013 Apr 25;14(4):R36).
The count reads and the FPKM scores for genes were computed based on the RSEM R software package (Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome.BMC Bioinformatics. 2011 Aug 4;12:323). Expression data was evaluated as log2 (FPKM). The significance of the differential expression between the control and cyclocreatine treatment phenotypes was estimated using the EBSeq method implemented in R (Bioconductor v.3.3, Leng N, Dawson JA, Thomson JA, Ruotti V, Rissman AI, Smits BM, Haag JD, Gould MN, Stewart RM, Kendziorski C.  EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments. Bioinformatics. 2013 Apr 15;29(8):1035-43), based on the significance cutoff 0.05 for the posterior probability.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text files include gene level read counts values for each sample. The genes are annotated based on the RefSeq hg19 database.

source_name: Human bone marrow

extract_protocol:
RNA was extracted from cells with an RNeasy Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cyclocreatine was purchased from Sigma-Aldrich (Sigma). TF-1, UT-7 and UCSD-AML1 cells were treated in quadruplicate with either vehicle or 3 mM cyclocreatine for 24 hours.

value: Human blood

tag: disease

value: Acute Myeloid Leukemia

tag: treatment

value: Cyclocreatine (3mM)

value: 24 hours


title: UCSD_Ccr_rep2


title: UCSD_Ccr_rep4


title: UCSD_ctl_rep4

value: Vehicle


title: UCSD_Ccr_rep1


title: HEK293_Cryo_Exp_2_406X_MSCB-077

value: cell line derived from human embryonic kidney cells


title: UCSD_ctl_rep3


title: HEK293_Cryo_Exp_2_406X_MSCB-067


title: HEK293_Cryo_Exp_2_406X_MSCB-066


title: HEK293_Cryo_Exp_2_406X_MSCB-065


title: UCSD_ctl_rep1


title: HEK293_Cryo_Exp_2_406X_MSCB-068


title: Vehicle_Input

city: Irvine

first: Tallie

middle: Z.

last: Baram

state: California

address: Medical Sciences I, ZOT 4475

institute: University of California-Irvine

data_processing:
reads were aligned using Bowtie2 v.2.2.3 with default parameters to the genome assembly rat rn5.
NRSF-bound regions (or peaks) were detected using MACS2 v.2.0.10 with default parameters except ‘-p 0.001’
Peaks were considered reproducible when they were identified in both replicates.
Genome_build: rn5
Supplementary_files_format_and_content: bed files with peak coordinates

organism: Rattus norvegicus

source_name: PVN

growth_protocol: 350uM organotypic PVN explants were obtained from P7 rat pups

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared using NextFlex Rapid DNA seq kit (Bioo Scientific) according to the manufacturer’s protocol.

treatment_protocol: On DIV6 organotypic cultures were treated with either vehicle or CNQX/MK-801 (50 uM) for 52 h.  Treatment was refreshed every 12 h.

tag: strain

value: Sprague-Dawley

value: hypothalamus

tag: tissue compartment

value: paraventricular nucleus (PVN)

tag: antibody

value: NRSF (Santa Cruz, sc25398x)


title: CNQX/MK801_input

tag: age


title: UT7_Ccr_rep1


title: UT7_Ccr_rep2


title: UT7_ctl_rep3


title: Vehicle_IP


title: UT7_ctl_rep2


title: HUVEC 5 Empty OE Flag_ChIP

city: Leuven

first: Bernard

last: Thienpont

address: herestraat 42

country: Belgium

institute: KULeuven

description:
Sample 28
processed data file: Prox1 peak raw reads.txt

data_processing:
FastQ files were mapped to the human genome (build GRCh37/hg19) using bowtie (version 0.12.8; settings -v 2 -m 1 -p --best -S).
Peaks were called in Prox1-FLAG ChIP-seq data by model-based analysis of ChIP-sequencing (MACS), using libraries of FLAG-ChIP on cells transfected with the empty overexpression plasmid as background data set. For calling H3K9ac peaks, MACS was applied on pooled H3K9ac data using the input as background set.
Read counts at H3K9ac peak areas were quantified in each sample using SeqMonk, and background-normalized to enable enrichment assessment.
Differential acetylation at H3K9ac peaks between two groups was assessed in R (version 3.1.0) with EdgeR (version 3.6.8), computing exact tests for differences in the means of negative-binomially distributed counts. We called peak areas as differentially acetylated when the corresponding FDR-adjusted P-value was below 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: Raw read files contain read numbers overlapping H3K9ac and Prox1 peaks. Differential acetylation at H3K9ac peaks was called using EdgeR, comparing GFP-overexpression and Prox1-overexpression HUVECs, and short-hairpin-mediated knockdown of Cpt1a in Prox1-overexpression HUVECs.

source_name: human umbilical vein endothelial cells

growth_protocol:
HUVECs between passages 1 and 5 were initially cultured in M199 medium (1 mg/mL D-glucose) supplemented with 20% fetal bovine serum (FBS; Biochrom GmBH, Germany), 2 mM L-glutamine, 30 µg L-1 endothelail cell growth factor supplements (ECGS), 10 units mL-1 heparin, 50 IU mL-1 penicillin and 50 µg mL-1 streptomycin, and switched to growth in endothelial cell growth medium 2 (ECGM2, Promocell, Heidelberg, Germany) for experiment.
Overexpression protocol: Lentiviral expression vector constructs for prospero homeobox protein 1 (Prox1) and GFP control virus were obtained from GeneCopoeia (Rockville, USA) and cloned in the pRRLsinPPT.CMV.MCS.MM W prevector 56. FLAG-tagged Prox1 was also generated and cloned into the pRRL prevector, and an empty vector pRRL virus was used as control.  For Prox1 overexpression experiments, cells were used at least 6 days after transduction to allow stable induction of the lymphatic phenotype.
Knockdown protocol: To generate shRNA vectors against CPT1a, oligonucleotides were cloned into the pLKO.1 vector (Sigma). A nonsense scrambled shRNA sequence was used as negative control. Production of lentiviruses was performed in 293T cells. For transductions, a multiplicity of infection of 20 was used. Cells were transduced overnight in the presence of 0.5 µg/mL polybrene, then rinsed with PBS and refreshed with new media the next day. For shRNA experiments, cells were used 2-4 days post-transduction.

extract_protocol:
Cultured cells were fixed by adding 1% Formaldehyde (16% Formaldehyde (w/v), Methanol-free, Thermo Scientific) directly to the medium and incubating for 8 minutes. Glycine (150 µM) was added for 5 min to quench the formaldehyde. Cells were washed twice with ice-cold PBS 0.5% Triton-X100, scraped and collected by centrifugation (1000 × G for 5 min at 4 °C). The pellet was resuspended in 1400 µL of RIPA buffer (50 mM Tris-HCl pH 8, 150 mM NaCl, 2 mM EDTA pH 8, 1% Triton-X100, 0.5% Sodium deoxycholate, 1% SDS, 1% protease inhibitors) and transferred in a new eppendorf tube. The lysate was homogenized by passing through an insulin syringe, and incubated on ice for 10 min. The chromatin was sonicated for 3 min by using a 250 Digital Sonifier (Branson) with 0.7 s 'On' and 1.3 s 'Off' pulses at 40% power amplitude, yielding a DNA fragment size of 100 to 500 bp. The sample was kept ice-cold at all times during the sonication. The samples were centrifuged (10 min at 16000 × G at 4 °C) and supernatants transferred to a new eppendorf tube. 50 µL of sheared chromatin was set apart as “input”, and 5 µg of either rabbit anti-FLAG (Pierce), rabbit anti-Prox1 (ProteinTech), rabbit anti-p300 antibody (Santa Cruz) or rabbit anti-H3K9ac (Cell Signaling) antibody was added to the remainder of the chromatin. Samples were incubated overnight at 4 °C on a rotator. 20 µL Pierce Protein A/G Magnetic Beads (Life Technologies) were added to the samples and incubated at 4 °C for at least 5 hours. A/G Magnetic Beads were collected and washed 5 times with washing buffer (50 mM Tris-HCl, 200 mM LiCl, 2 mM EDTA, pH 8, 1% Triton, 0.5% Sodium deoxycholate, 0.1% SDS, 1% protease inhibitors), and twice with TE buffer. The A/G magnetic beads were resuspended in 50 µL of TE buffer, and 1.5 µL of RNase A (200 units, NEB, Ipswich, MA, USA) were added to the A/G beads samples and to the input, incubated for 10 minutes at 37 °C. After addition of 1.5 µL of proteinase K (NEB, 200 units) and overnight incubation at 65°C, the DNA was purified using 1.8 × volume of Agencourt AMPure XP (Beckman Coulter) according to the manufacturer’s specifications, and then eluted in 30 µL of TE buffer.
Input and immunoprecipitated DNA was transformed into libraries using the NEBNext Ultra DNA library prep kit for Illumina (NEB), and amplified using KAPA HiFi HotStart ReadyMix for 14 cycles.

value: human umbilical vein endothelial cells

tag: overexpression

value: empty

tag: knockdown

value: rabbit anti-FLAG (Pierce)


title: UT7_ctl_rep4

tag: cell line

tag: tissue


title: TF1_Ccr_rep4

tag: time


title: TF1_Ccr_rep3


title: rgh3 roots replicate 3

city: Gainesville

first: A.

middle: Mark

last: Settles

state: FL

address: 1301 Fifield Hall

department: Horticultural Sciences

institute: University of Florida

description: Sample 11

data_processing:
The FASTQ/A trimmer from the FASTX toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) trimmed off bases that had a quality score of less than 20. The FASTX quality filter discarded reads if less than 80% of the bases in the read had a quality score of at least 20.
To remove any contaminating reads derived from rRNA, Bowtie software version 0.12.7 (Langmead et al, 2009) aligned reads from all libraries in a non-unique manner to sequences of repetitive elements in the MIPS database (Nussbaumer et al., 2013). The reads that did not align to repetitive elements were kept for downstream analyses.
The six wild-type libraries were uniquely mapped to the Zea mays B73 genome (RefGen_v2) using indel-tolerant Mosaik 2 software version 2.1.33 (https://code.google.com/p/mosaik-aligner/). Mosaik 2 was run with a maximum of 100 hash positions per seed, a hash size of 14, and 2% allowed mismatch between the read and genome.
Duplicate reads were removed using Picard software version 1.54 (http://picard.sourceforge.net).
Freebayes software version 0.9.5 identified W22 variant alleles from the merged wild-type alignments given the parameter of 2% pairwise differences assumed between W22 and B73. The Freebayes parameters used in this study required variant alleles to have more than 10 mapped reads, more than 40% of the reads within each library supporting the variant, at least one read to have a base quality of at least 20 at the site of variation, and a 99% probability that the variant existed.
GSNAP software version 2012-5-24 (Wu and Nacu, 2010), which uniquely aligned wild-type and rgh3 reads to B73 RefGen_v2. During the alignment process, 2% of the read length was permitted to mismatch with the genome, and mate pairs were allowed to deviate 800 bp from the expected paired-end length of 200 bp as a consequence of the large variation in fragment sizes within the dataset. GSNAP was guided by the ZmB73 5b Filtered Gene Set annotations but was permitted to discover novel splicing events.
Transcript isoforms were then assembled from the GSNAP read alignment files. Cufflinks software version 1.3.0 (Trapnell et al., 2010) assembled transcript fragments within each library individually using a minimum intron size of 10 bp and an overlap radius of 10 bp. Cufflinks was restricted to using the ZmB73 5b Filtered Gene Set annotations to estimate isoform expression with the ‘-G’ option. The reference annotation file was merged with the transcript assemblies from all twelve RNA-seq libraries using Cuffmerge. Cuffdiff tested for differential splicing between wild-type and rgh3 roots separately from wild-type and rgh3 shoots. Cuffdiff was run using bias detection and correction algorithm and upper-quartile normalization.
Genome_build: B73 RefGen_v2
Supplementary_files_format_and_content: .gtf files report Cufflinks abundance measurements

organism: Zea mays

source_name: seedling roots

growth_protocol: seedlings grown to 2 inches tall

extract_protocol:
Tissues were separately ground in liquid nitrogen. Total mRNA was extracted using the TRIzol Reagent (Life Technologies) protocol, during which RNAse-free glycogen (Fermentas) was used as a carrier for RNA. The TruSeqTM RNA Sample Preparation Kit (Illumina) was used to build cDNA libraries from 2 ug of input total RNA. The Illumina fragmentation protocol for producing inserts with a median length of 200 bp was used. The KAPA Library Quantification Kit for Illumina Genome Analyzer platform (KAPABIOSYSTEMS) facilitated the accurate pooling of twelve libraries at nearly equal concentrations. The multiplexed pool was sequenced on one lane of the HiSeq 2000 platform to produce 2x100 bp reads.
Illumina TruSeq RNA sample preparation kit

tag: developmental stage

value: seedling

value: roots

tag: genotype/variation

value: rough endosperm3


title: Norm roots replicate 3

description: Sample 9

value: wild-type


title: Norm shoots replicate 3

description: Sample 10

source_name: seedling shoot

value: shoot


title: HUVEC 8 ProxOE_shScramble p300_ChIP

description:
Sample 25
processed data file: Prox1 peak raw reads.txt

tag: cell type

value: rabbit anti-p300 antibody (Santa Cruz)


title: HUVEC 5 Prox1OE Prox1_ChIP

description:
Sample 26
processed data file: Prox1 peak raw reads.txt

value: rabbit anti-Prox1 (ProteinTech)


title: HUVEC 7 ProxOE_shScramble p300_ChIP

description:
Sample 24
processed data file: Prox1 peak raw reads.txt


title: UCSD_ctl_rep2

value: Human blood

value: Acute Myeloid Leukemia

value: 24 hours


title: UT7_Ccr_rep4

value: Cyclocreatine (3mM)


title: rgh3 shoots replicate 2

description: Sample 8


title: UT7_Ccr_rep3


title: TF1_Ccr_rep2


title: HUVEC 5 Flag-Prox1OE Prox1 ChIP Input

description:
Sample 30
processed data file: Prox1 peak raw reads.txt


title: CNQX/MK801_IP

value: Sprague-Dawley

value: hypothalamus


title: Norm shoots replicate 2

description: Sample 6


title: TF1_Ccr_rep1