title: AM+K rep2

tag: host genotype

value: roots


title: 3_29C_zt15

status: Public on Feb 13 2017

type: SRA

city: Berkeley

first: Shaked

last: Afik

state: CA

address: Stanley Hall

department: Computational Biology Graduate Group

country: USA

institute: UC Berkeley

description: processed data file: 3_false.merged.tdf, 3_true.merged.tdf

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to dm3 whole genome and transcriptome using tophat2
peaks were called using our a stand alone java program build to analyze our novel sequencing method
Genome_build: dm3
Supplementary_files_format_and_content: All 3’ without RNaseH treatment data was divided to true and false based on whether or not the 3 last bases of the first read were adenines or not (in order to separate internal poly(A) tracts and poly(A) tails). TDF files were created by IGVtools with the parameters igvtools -count -w 5. Wig files were created using a customized python scripts, where for each genomic position we counted the number of read that started on this position (i.e. the first base of the read was aligned to this position). For every sequencing method (ExoCAGE, 3’-sequencing and RNaseH sequencing) the data from different temperatures and time points were merged together to create the processesed files.

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: 3’ RNA-Seq (without RNase H treatment)

growth_protocol: Drosophila Canton S (CS) wild type flies were reared at 25 °C on a standard diet (yeast: 38gr/L, Yellow corn mill: 91gr/L, agar: 10gr/L, molassas: 8.7% v/v, propanoic acid (BioLab): 0.9% v/v, Tegasept solution (Sigma-Aldrich; 300g/L in EtOH (BioLab)): 0.8% v/v)). Flies were kept in 12-h light:12-h dark cycles at 25 °C.

extract_protocol:
For RNA extraction, new-born flies were entrained for three days in 12:12 light:dark conditions at one of the different temperatures tested (18C, 25C or 29C) and collected at one of the time points (ZT3,ZT7,ZT9,ZT11,ZT15,ZT19,ZT21 or ZT23). RNA was extracted using Trizol (Invitrogen).
ExoCAGE: 50ng-1ug of total RNA was polyA selected using Oligo-dT beads (Invitrogen) and then fragmented using Ambion Fragmentation buffer using incubation time of 1 min 50sec at 70C. Fragmented RNA was then cleaned-up using 2.5X volume on SPRI beads (Agencourt), PNK treated (T4 PNK, NEB) and incubated with Terminator Exonuclease (Epicentre) for 70 minutes. Reaction mixture was dephosphorylated with FastAP (Fermentas), cleaned (2.5X SPRI) and then lygated to a linker1 (5Phos/AXXXXXXXXAGATCGGAAGAGCGTCGTGTAG/3ddC/, XXXXXXXX is an internal barcode specific for each sample,) using T4 RNA ligase I (NEB). Ligated RNA was cleaned-up by Silane beads (Dynabeads MyOne, Life Technologies) and pooled into a single tube. RT was then performed for the pooled sample, with a specific primer (5´-CCTACACGACGCTCTTCC-3´) using AffinityScript Multiple Temperature cDNA Synthesis Kit (Agilent Technologies). Then, RNA-DNA hybrids were degraded by incubating the RT mixture with 10% 1M NaOH (e.g. 2ul to 20ul of RT mixture) at 70C for 12 minutes. pH was then normalized by addition of corresponding amount of 0.5M AcOH (e.g. 4ul for 22 ul of NaOH+RT mixture). The reaction mixture was cleaned up using Silane beads and second lygation was performed, where 3’end of cDNA was lygated to linker2 (5Phos/AGATCGGAAGAGCACACGTCTG/3ddC/) using T4 RNA ligase I. The sequences of linker1 and linker2 are partially complementary to the standard Illumina read1 and read2/barcode adapters, respectively. Reaction Mixture was cleaned up (Silane beads) and PCR enrichment was set up using enrichment primers 1 and 2 (5’- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’, 5’-CAAGCAGAAGACGGCATACGAGATXXXXXXXXGTGACTGGAGTTCAGAC  GTGTGCTCTTCCGATCT-3’, where XXXXXXX is barcode sequence) and Phusion HF MasterMix (NEB). 10-12 cycles of enrichment were performed depending on the initial input amount of RNA. After clean-up with 0.8X volume of SPRI beads library was ready for characterization by Bioanalyzer.
3’ RNase H-sequencing: 50ng-1ug of total RNA was fragmented using NEBNext magnesium RNA fragmentation module (NEB) with incubation time of 2 minutes at 94C. Fragmented RNA was cleaned-up using 2.5X volume on SPRI beads (Agencourt), and then subjected to PolyA selection using Oligo-dT beads (Invitrogen). PolyA+ RNA was incubated with oligoDT primer (Fermentas) and polyA tails were digested by RNAseH (NEB) treatment for 1 hour at 37C. RNA was then cleaned (Silane beads), dephosphorylated with FastAP (Fermentas), cleaned (Silane beads) and lygated to a linker1 using T4 RNA ligase I (NEB). Ligated RNA was cleaned-up by Silane beads (Dynabeads MyOne, Life Technologies) and pooled into a single tube. Library preparation was then processed in the same way as in ExoCAGE protocol starting with RT step and so on.
3’ RNA-Seq without RNase H treatment: 50ng-1ug of total RNA was fragmented using NEBNext magnesium RNA fragmentation module (NEB) with incubation time of 5 minutes at 94C. Fragmented RNA was cleaned-up using 2.5X volume on SPRI beads (Agencourt), dephosphorylated with FastAP (Fermentas), cleaned (2.5X SPRI) and then ligated to a linker1 using T4 RNA ligase I (NEB). Ligated RNA was cleaned-up by Silane beads (Dynabeads MyOne, Life Technologies) and pooled into a single tube. The pooled sample was then subjected to poly(A) selection using Oligo(dT) beads (Invitrogen). Library preparation was then processed in the same way as in the ExoCAGE protocol starting with RT step and so on.

tag: strain

value: Canton S

tag: tissue

value: head

tag: temperature tested

tag: time point


title: ExoCAGE_29C_zt23

description: processed data file: ExoCAGE.merged.wig

source_name: 5’ sequenced using ExoCAGe


title: ExoCAGE_29C_zt9

description: processed data file: ExoCAGE.merged.wig


title: 3_29C_zt7


title: 3_29C_zt3


title: 3_29C_zt11


title: 3_25C_zt11


title: 3_25C_zt15


title: 3_25C_zt19


title: ExoCAGE_18C_zt15

description: processed data file: ExoCAGE.merged.wig


title: 3_25C_zt7


title: 3_25C_zt3


title: 3_18C_zt23


title: 3_18C_zt3


title: 3_18C_zt7


title: 3_25C_zt23


title: 3_18C_zt15


title: PDOX_Fresh_Exp_1_403U_MSCB-184

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:
fresh cells
PDOX_Fresh_Exp_1.tsv

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.

organism: Homo sapiens

source_name: ovarian carcinoma

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.

tag: cell type

value: ovarian orthotopic tumor cells


title: PDOX_Fresh_Exp_1_403U_MSCB-183

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-179

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-182

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-165

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-167

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-178

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-166

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-181

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-162

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-163

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-151

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-161

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-147

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-149

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-150

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: 3_18C_zt11


title: PDOX_Fresh_Exp_1_403U_MSCB-136

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-146

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: 3_18C_zt19


title: PDOX_Fresh_Exp_1_403U_MSCB-145

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-135

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-134

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-132

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-116

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-120

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-117

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-115

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-164

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-114

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-104

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-103

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-102

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-101

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-087

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-085

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-086

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-084

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-099

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-083

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-100

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-082

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-098

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-081

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-071

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-069

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-067

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-065

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-066

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-056

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-055

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-053

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-052

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-049

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-038

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-088

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-034

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-024

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-072

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-023

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-021

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-007

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-070

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_402U_MSCB-183

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-004

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-001

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_402U_MSCB-184

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-054

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-019

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-006

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-050

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_402U_MSCB-177

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_402U_MSCB-178

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_402U_MSCB-162

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_402U_MSCB-164

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-002

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_402U_MSCB-163

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_402U_MSCB-151

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_402U_MSCB-161

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_402U_MSCB-180

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_402U_MSCB-136

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_402U_MSCB-135

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_402U_MSCB-152

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_402U_MSCB-147

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_402U_MSCB-145

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_403U_MSCB-003

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_402U_MSCB-166

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_402U_MSCB-133

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_402U_MSCB-132

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_402U_MSCB-131

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_402U_MSCB-130

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_402U_MSCB-129

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_402U_MSCB-119

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_402U_MSCB-115

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_402U_MSCB-116

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_402U_MSCB-117

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_402U_MSCB-104

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_402U_MSCB-118

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_402U_MSCB-098

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_402U_MSCB-103

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_402U_MSCB-099

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_402U_MSCB-100

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_402U_MSCB-113

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_402U_MSCB-088

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_402U_MSCB-102

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_402U_MSCB-086

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_402U_MSCB-087

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_402U_MSCB-085

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_402U_MSCB-082

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_402U_MSCB-081

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_402U_MSCB-070

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_402U_MSCB-069

description:
fresh cells
PDOX_Fresh_Exp_1.tsv


title: PDOX_Fresh_Exp_1_402U_MSCB-067

description:
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fresh cells
K562_Fresh_Exp_1.tsv


title: K562_Fresh_Exp_1_044U_MSCB-097

description:
fresh cells
K562_Fresh_Exp_1.tsv


title: PDOX_Cryo_Exp_1_402U_MSCB-027

description:
cryopreserved cells
PDOX_Cryo_Exp_1.tsv


title: PDOX_Cryo_Exp_1_402U_MSCB-032

description:
cryopreserved cells
PDOX_Cryo_Exp_1.tsv


title: K562_Fresh_Exp_1_044U_MSCB-081

description:
fresh cells
K562_Fresh_Exp_1.tsv


title: K562_Fresh_Exp_1_044U_MSCB-065

description:
fresh cells
K562_Fresh_Exp_1.tsv


title: PDOX_Cryo_Exp_1_402U_MSCB-012

description:
cryopreserved cells
PDOX_Cryo_Exp_1.tsv


title: K562_Fresh_Exp_1_044U_MSCB-017

description:
fresh cells
K562_Fresh_Exp_1.tsv


title: K562_Fresh_Exp_1_044U_MSCB-049

description:
fresh cells
K562_Fresh_Exp_1.tsv


title: K562_Fresh_Exp_1_044U_MSCB-025

description:
fresh cells
K562_Fresh_Exp_1.tsv


title: K562_Cryo_Exp_1_044U_MSCB-162

description:
cryopreserved cells
K562_Cryo_Exp_1.tsv


title: K562_Cryo_Exp_1_044U_MSCB-178

description:
cryopreserved cells
K562_Cryo_Exp_1.tsv


title: K562_Cryo_Exp_1_044U_MSCB-154

description:
cryopreserved cells
K562_Cryo_Exp_1.tsv


title: K562_Fresh_Exp_1_044U_MSCB-161

description:
fresh cells
K562_Fresh_Exp_1.tsv


title: K562_Cryo_Exp_1_044U_MSCB-130

description:
cryopreserved cells
K562_Cryo_Exp_1.tsv


title: K562_Cryo_Exp_1_044U_MSCB-138

description:
cryopreserved cells
K562_Cryo_Exp_1.tsv


title: PDOX_Cryo_Exp_1_402U_MSCB-026

description:
cryopreserved cells
PDOX_Cryo_Exp_1.tsv


title: K562_Cryo_Exp_1_044U_MSCB-122

description:
cryopreserved cells
K562_Cryo_Exp_1.tsv


title: TK2-Q125*.M132T-KOH HincII

city: Göteborg

first: Anders R.

last: Clausen

address: Box 440

country: Sweden

institute: University of Gothenburg

library_source: genomic

data_processing:
Library strategy: HydEn-seq
All reads were trimmed for quality and adaptor sequence with cutadapt 1.2.1 (-m 15 -q 10–match-read-wildcards)50. Pairs with one or both reads shorter than 15 nt were discarded. Mate 1 of the remaining pairs was aligned to an index containing the sequence of all oligos used in the preparation of these libraries with bowtie 0.12.8 (-m1 -v2), and all pairs with successful alignments were discarded. Pairs passing this filter were subsequently aligned to the hg38 H. sapiens reference genome6 (-m1 -v2 -X10000–best). Single-end alignments were then performed with mate 1 of all unaligned pairs (-m1 -v2). To calculate the base identity of ribonucleotides in mtDNA, the count of 5′-ends of all multiple paired-end and single-end alignments were determined for all samples and shifted one base upstream to the location of the free 5′-end or hydrolyzed ribonucleotide. The counts were visualized using Circos software.
Genome_build: Human NCBI genome build GRCh38
Supplementary_files_format_and_content: bed: tab-separated bedgraph file format. Column one holds the chromosome name, column two and three hold the nucleotide position, column four holds the read count.

molecule: genomic DNA

source_name: Patient-derived fibroblast cells

growth_protocol: Primary skin fibroblast cultures were obtained from healthy age-matched controls and patients with confirmed pathogenic variants in one of three genes implicated in disorders of mtDNA maintenance, TK2, DGUOK and MPV17, leading to mtDNA depletion myopathy (patients with TK2 variants) or hepatocerebral mtDNA depletion (patients with DGUOK and MPV17 variants).

extract_protocol:
Cells were grown in 70 ml of DMEM GlutaMAX medium (Gibco), 10% fetal bovine serum (Gibco) in 250 ml Spinner flasks (Bellco Glass Inc.). A total of 5x106 cells were collected by centrifugation for 5 min at 200 ´ g and washed once with PBS. Pellets were resuspended in 2 ml of lysis buffer (75 mM NaCl, 50 mM EDTA, 1% SDS, 20 mM HEPES pH 8.0, 200 µg/ml Proteinase K) and incubated at 42 °C for 30 min. One volume of phenol-chloroform was added to the samples, then mixed and centrifuged at 15000 ´ g for 5 min (4 °C). The water phase was then transferred to a new tube for precipitation with 100 mM NaCl and 1 v of isopropanol. Samples were incubated at -20 °C at least for 1 h. After precipitation, the samples were centrifuged (15000 ´ g, 20 min, 4 °C) and washed with 70% EtOH..Pellets were dissolved in 100 µl of TE buffer. DNA concentrations for library preparations, was measured with a Qubit fluorometric instrument (ThermoFisher Scientific). Patient and control fibroblast cells were grown in DMEM GlutaMAX medium, supplemented with 10% FBS, PEST and 50 µg/ml uridine. Between 4 and 11 ´ 106 cells were collected and total DNA was isolated using the Gentra Puregene Cell Kit (Qiagen) according to the manufacturer´s protocol.
Free 5´-ends in mtDNA of HeLa and primary fibroblast cells were mapped by 5´-End-seq by treating 1 µg DNA with 0.3 M KCl for 2 h at 55 °C. RNA residues in mtDNA of HeLa and primary fibroblast cells were mapped by HydEn-seq by hydrolyzing 1 µg DNA with 0.3 M KOH for 2 h at 55 °C. To calculate the number of ribonucleotides per mtDNA molecule, we treated 1 µg DNA with 10 U of HincII and the digests were purified with HighPrep PCR beads (MagBio), before the KCl or KOH treatment. After ethanol precipitation, the DNA fragments were treated for 3 min at 85 °C, phosphorylated with 10 U of 3′-phosphatase-minus T4 polynucleotide kinase (New England BioLabs) for 30 min at 37 °C, heat inactivated for 20 min at 65 °C and purified with HighPrep PCR beads (MagBio). Phosphorylated products were treated for 3 min at 85 °C, ligated to oligo ARC140 overnight at room temperature with 10 U of T4 RNA ligase, 25% PEG 8000 and 1 mM CoCl3(NH3)6, and purified with HighPrep PCR beads (MagBio). Ligated products were treated for 3 min at 85 °C. The ARC76–ARC77 adaptor was annealed to the second strand for 5 min at room temperature. The second strand was synthesized with 4 U of T7 DNA polymerase (New England BioLabs) and purified with HighPrep PCR beads (MagBio). Libraries were purified, quantified with a Qubit fluorometric instrument (ThermoFisher Scientific) and 50-base paired-end sequenced on an Illumina NextSeq500 instrument, to identify the location of the free 5´-ends.

tag: genotype

tag: restriction digest

value: HincII


title: K562_Fresh_Exp_1_044U_MSCB-057

description:
fresh cells
K562_Fresh_Exp_1.tsv


title: TK2-M1V-KOH HincII

value: TK2 p.M1V (homozygous)


title: K562_Cryo_Exp_1_044U_MSCB-114

description:
cryopreserved cells
K562_Cryo_Exp_1.tsv


title: K562_Fresh_Exp_1_044U_MSCB-041

description:
fresh cells
K562_Fresh_Exp_1.tsv


title: TK2-M1V-KCl HincII


title: TK2-Q125*.M132T-KCl HincII


title: K562_Cryo_Exp_1_044U_MSCB-106

description:
cryopreserved cells
K562_Cryo_Exp_1.tsv


title: K562_Cryo_Exp_1_044U_MSCB-098

description:
cryopreserved cells
K562_Cryo_Exp_1.tsv


title: K562_Cryo_Exp_1_044U_MSCB-090

description:
cryopreserved cells
K562_Cryo_Exp_1.tsv


title: DGUOK-F256*-KOH HincII

value: DGUOK p.F256* (homozygous)


title: DGUOK-N46S.delGC-KCl HincII

value: DGUOK p.N46S;c.13_14delGC


title: K562_Cryo_Exp_1_044U_MSCB-082

description:
cryopreserved cells
K562_Cryo_Exp_1.tsv


title: DGUOK-N46S.delGC-KOH HincII


title: K562_Cryo_Exp_1_044U_MSCB-058

description:
cryopreserved cells
K562_Cryo_Exp_1.tsv


title: K562_Cryo_Exp_1_044U_MSCB-042

description:
cryopreserved cells
K562_Cryo_Exp_1.tsv


title: K562_Cryo_Exp_1_044U_MSCB-034

description:
cryopreserved cells
K562_Cryo_Exp_1.tsv


title: MPV17-A23P.E45D-KOH HincII

value: MPV17 p.A23P;p.E45DfsX8


title: K562_Cryo_Exp_1_044U_MSCB-010

description:
cryopreserved cells
K562_Cryo_Exp_1.tsv


title: TK2-Q87*.N100S-KOH HincII


title: K562_Cryo_Exp_1_044U_MSCB-018

description:
cryopreserved cells
K562_Cryo_Exp_1.tsv


title: MPV17-Q93P-KOH HincII

value: MPV17 p.G93P (homozygous)


title: TK2-Q87*.N100S-KCl HincII


title: K562_Cryo_Exp_1_044U_MSCB-002

description:
cryopreserved cells
K562_Cryo_Exp_1.tsv


title: DGUOK-F256*-KCl HincII


title: HEK293_Fresh_Exp_1_401U_MSCB-085

description:
fresh cells
HEK293_Fresh_Exp_1.tsv

source_name: kidney cells

value: cell line derived from human embryonic kidney cells


title: HEK293_Fresh_Exp_1_401U_MSCB-094

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: FB1-KOH HincII

source_name: Fibroblast cell culture

value: wild type


title: FB1-KCl HincII


title: HEK293_Fresh_Exp_1_401U_MSCB-083

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: HEK293_Fresh_Exp_1_401U_MSCB-084

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: TK2-M1V-KOH

value: No


title: TK2-Q125*.M132T-KOH


title: TK2-M1V-KCl


title: HEK293_Fresh_Exp_1_401U_MSCB-073

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: DGUOK-N46S.delGC-KOH


title: HEK293_Fresh_Exp_1_401U_MSCB-074

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: PDOX_Cryo_Exp_1_402U_MSCB-123

description:
cryopreserved cells
PDOX_Cryo_Exp_1.tsv


title: MPV17-A23P.E45D-KCl HincII


title: HEK293_Fresh_Exp_1_401U_MSCB-071

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: DGUOK-N46S.delGC-KCl


title: HEK293_Fresh_Exp_1_401U_MSCB-095

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: DGUOK-F256*-KOH


title: HEK293_Fresh_Exp_1_401U_MSCB-070

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: MPV17-Q93P-KCl HincII


title: DGUOK-F256*-KCl


title: HEK293_Fresh_Exp_1_401U_MSCB-061

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: HEK293_Fresh_Exp_1_401U_MSCB-060

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: MPV17-A23P.E45D-KOH


title: K562_Cryo_Exp_1_044U_MSCB-050

description:
cryopreserved cells
K562_Cryo_Exp_1.tsv


title: MPV17-A23P.E45D-KCl


title: TK2-Q87*.N100S-KOH


title: TK2-Q87*.N100S-KCl


title: MPV17-Q93P-KOH


title: MPV17-Q93P-KCl


title: HeLa C KOH HincII

source_name: HeLa cell culture

value: HeLa


title: FB1-KCl


title: HeLa B KOH HincII


title: HeLa B KCl HincII


title: HEK293_Fresh_Exp_1_401U_MSCB-012

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: HeLa A KOH HincII


title: HEK293_Fresh_Exp_1_401U_MSCB-011

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: FB1-KOH


title: HEK293_Fresh_Exp_1_401U_MSCB-022

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: HEK293_Fresh_Exp_1_401U_MSCB-025

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: HEK293_Fresh_Exp_1_401U_MSCB-023

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: HEK293_Fresh_Exp_1_401U_MSCB-013

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: HEK293_Fresh_Exp_1_401U_MSCB-037

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: HEK293_Fresh_Exp_1_401U_MSCB-047

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: HEK293_Fresh_Exp_1_401U_MSCB-050

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: HEK293_Fresh_Exp_1_401U_MSCB-059

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: HEK293_Fresh_Exp_1_401U_MSCB-046

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: HEK293_Fresh_Exp_1_401U_MSCB-026

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: HEK293_Fresh_Exp_1_401U_MSCB-049

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: HEK293_Fresh_Exp_1_401U_MSCB-035

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: HEK293_Fresh_Exp_1_401U_MSCB-001

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: HEK293_Fresh_Exp_1_401U_MSCB-002

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: HeLa C KCl HincII


title: HeLa C KCl


title: HEK293_Fresh_Exp_1_400U_MSCB-096

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: HeLa B KOH


title: HeLa A KCl HincII


title: HeLa B KCl


title: HeLa A KOH


title: HEK293_Fresh_Exp_1_400U_MSCB-095

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: HEK293_Fresh_Exp_1_400U_MSCB-085

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: HEK293_Fresh_Exp_1_400U_MSCB-084

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: HeLa C KOH


title: HeLa A KCl


title: HEK293_Fresh_Exp_1_400U_MSCB-094

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: TK2-Q125*.M132T-KCl


title: HEK293_Fresh_Exp_1_400U_MSCB-061

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: ETS2 knockdown in DU145 cells using shRNA replicate 2

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

molecule: total RNA

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: ETS2 ChIP DU145 w/ ETS1 KO

data_processing:
Illumina Casava1.8.2 software used for basecalling
Reads were aligned to the Homo sapien genome (UCSC hg19) using Bowtie2 (v2.0.6)
Peak calling was accomplished using the Useq platform (v8.0.1).
Genome_build: UCSC hg19
Supplementary_files_format_and_content: tab-delimited text files include bound regions for each stated sample: chromosome, start, stop

extract_protocol:
ChIP DNA was isolated as described in Hollenhorst et. al., Genes and Development, 2011
Sequencing libraries were created as described in Plotnik et.al. Nucleic Acids Research. 2014.

tag: chip target


title: HEK293_Fresh_Exp_1_400U_MSCB-075

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: ETS2 knockdown in DU145 cells using shRNA replicate 3


title: HEK293_Fresh_Exp_1_400U_MSCB-073

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: HEK293_Fresh_Exp_1_400U_MSCB-074

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: BS69 ChIP DU145 w/ ETS1 KO


title: HEK293_Fresh_Exp_1_400U_MSCB-070

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: HEK293_Fresh_Exp_1_400U_MSCB-072

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: ETS2 knockdown in DU145 cells using shRNA replicate 1


title: BM_DN3_aBcl11b-ChIP-rep2

city: Isehara

first: Hiroyuki

last: Hosokawa

state: Kanagawa

address: 143 Shimokasuya

department: Department of Immunology

country: Japan

institute: Tokai University School of Medicine

data_processing:
ChIP-Sequencing and data analysis: ChIP sequences were mapped to the mouse genome build NCBI37/mm9 using Bowtie (v1.1.1; http://bowtie-bio.sourceforge.net/index.shtml) with “-v 3 -k 11 -m 10 -t --best –strata” settings and HOMER tagdirectories were created with makeTagDirectory {Heinz, 2010 #67} for further downstream analysis. In addition, read alignments from the Scid.adh.2c2-PU.1ert2 experiment were filtered against PCR duplicates using Samtools as well as genomic repeats and Broad blacklisted regions using Bedtools (full script provided upon request) prior to tag directory generation. Transcription factor peaks were identified with findPeaks.pl against a matched control sample using the settings “-P .1 -LP .1 -poisson .1 -style factor”. Transcription factor peak reproducibility was determined by a HOMER adaptation of the IDR (Irreproducibility Discovery Rate) package according to ENCODE guidelines (https://sites.google.com/site/anshulkundaje/projects/idr). Only reproducible high quality peaks, with a normalized peak score >= 15, were considered for further analysis.  Regions enriched for histone modifications were identified with findPeaks.pl with the option –style histone against a matched input control. Only regions consistently called in two independent experiments were used for downstream analyses.  Motif enrichment analysis was performed with the findMotifsGenome.pl command in the HOMER package using a 200bp window or a window size defined by the width of each identified peak. Overlapping peaks between samples were derived using mergePeaks.pl (default parameters). Annotation of peaks to genes and genomic regions (e.g. promoters, CG-rich regions, repeat regions) were performed with annotatePeaks.pl (default settings). Tag density plots and heat maps were created with annotatePeaks.pl ( –hist or –hist & -ghist respectively), normalizing data to 10 million mapped reads per experiment.
Genome_build: mm9
Supplementary_files_format_and_content: HOMER peak file;  All genomic coordinates are relative to mm9 mouse assembly.

organism: Mus musculus

growth_protocol: Lin- BM isolation/culture protocol: Bone marrow (BM) was removed from the femur and tibia of 2-3 month-old Cas9 mice. Suspensions of BM cells were prepared and stained for lineage markers using biotin-conjugated lineage antibodies (CD11b, CD11c, Gr1, TER-119, NK1.1, CD19, CD3ε, B220), then incubated with streptavidin-coated magnetic beads, and passed through a magnetic column. Lin− cells were eluted and cultured on OP9-DL1 monolayers using OP9 medium supplemented with 10 ng/ml of IL-7 and 10 ng/ml of Flt3L. On day 7, cultured cells were disaggregated, filtered through 40-μm nylon mesh, transferred onto RetroNectin-coated virus bound plates, and cultured with OP9 medium supplemented with 10 ng/ml of IL-7, 10 ng/ml of Flt3L and 10 ng/ml of SCF. Infected cells were cultured for an additional 7 days on OP9-DL1 and subjected to further analysis. For sorting, cells were stained with CD45, CD25, and a biotin-conjugated lineage cocktail (CD8α, CD11b, CD11c, Gr1, TER-119, NK1.1, CD19, TCRβ, TCRγδ), and were sorted for CD25+ infected cells (Lin-CD45+CD25+CFP+).

extract_protocol: Ten million of BM-derived DN3 cells were fixed with 1 mg/ml DSG (Thermo Scientific) in PBS for 30 min at RT followed by additional 10 min with addition of formaldehyde up to 1%. The reaction was quenched by addition of 1/10 volume of 0.125M glycine and the cells were washed with HBSS (Gibco). Pelleted nucleus were dissolved in lysis buffer (0.5% SDS, 10 mM EDTA, 0.5 mM EGTA, 50 mM Tris-HCl (pH 8) and PIC) and sonicated on a Bioruptor (Diagenode) for 18 cycles of 30sec sonication followed by 30sec rest, with max power. Six μg per 10^7 cells of anti-Bcl11b Abs (a mixture of A300-383A (Bethyl), A300-385A (Bethyl), ab18465 (Abcam) and 12120 (CST)) were hybridized to Dynabeads Protein A/G (Invitrogen) and added to the diluted chromatin complex. They were incubated over night at 4°C, then washed and eluted for 6hr at 65°C in ChIP elution buffer (20 mM Tris-HCl, pH 7.5, 5 mM EDTA 50 mM NaCl, 1% SDS, and 50 μg proteinase K). Precipitated chromatin fragments were cleaned up using Zymo ChIP DNA Clean & Concentrator. ChIP-seq libraries were constructed using NEBNext ChIP-Seq Library Preparation Kit (NEB #E6240) following manufacturer’s instructions. Libraries were sequenced on Illumina HiSeq2500 in single read mode with the read length of 50 nt following manufacturer's instructions. Base calls were performed with RTA 1.13.48.0 followed by conversion to FASTQ with bcl2fastq 1.8.4 and produced approximately 30 million reads per sample.

tag: strain background

value: Lin- BM derived DN3 cells

tag: cultured on

tag: chip antibody

value: anti-Bcl11b Abs, a mixture of A300-383A (Bethyl), A300-385A (Bethyl), ab18465 (Abcam) and 12120 (CST)


title: BS69 ChIP DU145 WT


title: BM_DN3_1%_input-rep1


title: HEK293_Fresh_Exp_1_400U_MSCB-050

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: HEK293_Fresh_Exp_1_400U_MSCB-049

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: HEK293_Fresh_Exp_1_400U_MSCB-071

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: HEK293_Fresh_Exp_1_400U_MSCB-060

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: NIH3T3_Fresh_401U_MSCB-093

description:
fresh cells
NIH3T3_Fresh.tsv

source_name: fibroblasts

value: cell line derived from mouse embryo fibroblasts


title: HEK293_Fresh_Exp_1_400U_MSCB-047

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: NIH3T3_Fresh_401U_MSCB-091

description:
fresh cells
NIH3T3_Fresh.tsv


title: BM_DN3_aBcl11b-ChIP-rep1


title: NIH3T3_Fresh_401U_MSCB-082

description:
fresh cells
NIH3T3_Fresh.tsv


title: NIH3T3_Fresh_401U_MSCB-092

description:
fresh cells
NIH3T3_Fresh.tsv


title: BM_DN3_1%_input-rep2


title: NIH3T3_Fresh_401U_MSCB-079

description:
fresh cells
NIH3T3_Fresh.tsv


title: HEK293_Fresh_Exp_1_400U_MSCB-036

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: HEK293_Fresh_Exp_1_400U_MSCB-037

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: NIH3T3_Fresh_401U_MSCB-078

description:
fresh cells
NIH3T3_Fresh.tsv


title: NIH3T3_Fresh_401U_MSCB-069

description:
fresh cells
NIH3T3_Fresh.tsv


title: NIH3T3_Fresh_401U_MSCB-067

description:
fresh cells
NIH3T3_Fresh.tsv


title: NIH3T3_Fresh_401U_MSCB-058

description:
fresh cells
NIH3T3_Fresh.tsv


title: HEK293_Fresh_Exp_1_400U_MSCB-026

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: HEK293_Fresh_Exp_1_400U_MSCB-027

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: NIH3T3_Fresh_401U_MSCB-055

description:
fresh cells
NIH3T3_Fresh.tsv


title: NIH3T3_Fresh_401U_MSCB-057

description:
fresh cells
NIH3T3_Fresh.tsv


title: NIH3T3_Fresh_401U_MSCB-045

description:
fresh cells
NIH3T3_Fresh.tsv


title: HEK293_Fresh_Exp_1_400U_MSCB-022

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: HEK293_Fresh_Exp_1_400U_MSCB-025

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: HEK293_Fresh_Exp_1_400U_MSCB-048

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: NIH3T3_Fresh_401U_MSCB-044

description:
fresh cells
NIH3T3_Fresh.tsv


title: HEK293_Fresh_Exp_1_400U_MSCB-023

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: HEK293_Fresh_Exp_1_400U_MSCB-013

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: HEK293_Fresh_Exp_1_400U_MSCB-003

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: HEK293_Fresh_Exp_1_400U_MSCB-012

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: NIH3T3_Fresh_401U_MSCB-043

description:
fresh cells
NIH3T3_Fresh.tsv


title: HEK293_Cryo_Exp_1_401U_MSCB-179

description:
cryopreserved cells
HEK293_Cryo_Exp_1.tsv


title: NIH3T3_Fresh_401U_MSCB-068

description:
fresh cells
NIH3T3_Fresh.tsv


title: HEK293_Fresh_Exp_1_400U_MSCB-001

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: HEK293_Fresh_Exp_1_400U_MSCB-024

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: HEK293_Cryo_Exp_1_401U_MSCB-180


title: NIH3T3_Fresh_401U_MSCB-033

description:
fresh cells
NIH3T3_Fresh.tsv


title: NIH3T3_Fresh_401U_MSCB-034

description:
fresh cells
NIH3T3_Fresh.tsv


title: NIH3T3_Fresh_401U_MSCB-030

description:
fresh cells
NIH3T3_Fresh.tsv


title: NIH3T3_Fresh_401U_MSCB-031

description:
fresh cells
NIH3T3_Fresh.tsv


title: HEK293_Cryo_Exp_1_401U_MSCB-169


title: NIH3T3_Fresh_401U_MSCB-020

description:
fresh cells
NIH3T3_Fresh.tsv


title: NIH3T3_Fresh_401U_MSCB-019

description:
fresh cells
NIH3T3_Fresh.tsv


title: NIH3T3_Fresh_401U_MSCB-009

description:
fresh cells
NIH3T3_Fresh.tsv


title: HEK293_Cryo_Exp_1_401U_MSCB-166


title: HEK293_Cryo_Exp_1_401U_MSCB-181


title: HEK293_Cryo_Exp_1_401U_MSCB-170


title: HEK293_Cryo_Exp_1_401U_MSCB-167


title: NIH3T3_Fresh_401U_MSCB-010

description:
fresh cells
NIH3T3_Fresh.tsv


title: HEK293_Fresh_Exp_1_400U_MSCB-002

description:
fresh cells
HEK293_Fresh_Exp_1.tsv


title: HEK293_Cryo_Exp_1_401U_MSCB-157


title: NIH3T3_Fresh_401U_MSCB-007

description:
fresh cells
NIH3T3_Fresh.tsv


title: HEK293_Cryo_Exp_1_401U_MSCB-156


title: HEK293_Cryo_Exp_1_401U_MSCB-146


title: HEK293_Cryo_Exp_1_401U_MSCB-155


title: NIH3T3_Fresh_400U_MSCB-093

description:
fresh cells
NIH3T3_Fresh.tsv


title: NIH3T3_Fresh_400U_MSCB-092

description:
fresh cells
NIH3T3_Fresh.tsv


title: NIH3T3_Fresh_401U_MSCB-006

description:
fresh cells
NIH3T3_Fresh.tsv


title: HEK293_Cryo_Exp_1_401U_MSCB-145


title: NIH3T3_Fresh_400U_MSCB-083

description:
fresh cells
NIH3T3_Fresh.tsv


title: NIH3T3_Fresh_400U_MSCB-082

description:
fresh cells
NIH3T3_Fresh.tsv


title: NIH3T3_Fresh_400U_MSCB-081

description:
fresh cells
NIH3T3_Fresh.tsv


title: HEK293_Cryo_Exp_1_401U_MSCB-143


title: HEK293_Cryo_Exp_1_401U_MSCB-142


title: NIH3T3_Fresh_400U_MSCB-080

description:
fresh cells
NIH3T3_Fresh.tsv


title: HEK293_Cryo_Exp_1_401U_MSCB-133


title: HEK293_Cryo_Exp_1_401U_MSCB-131


title: NIH3T3_Fresh_400U_MSCB-078

description:
fresh cells
NIH3T3_Fresh.tsv


title: NIH3T3_Fresh_400U_MSCB-069

description:
fresh cells
NIH3T3_Fresh.tsv


title: HEK293_Cryo_Exp_1_401U_MSCB-121


title: HEK293_Cryo_Exp_1_401U_MSCB-122


title: HEK293_Cryo_Exp_1_401U_MSCB-119


title: NIH3T3_Fresh_400U_MSCB-058

description:
fresh cells
NIH3T3_Fresh.tsv


title: NIH3T3_Fresh_400U_MSCB-079

description:
fresh cells
NIH3T3_Fresh.tsv


title: NIH3T3_Fresh_400U_MSCB-068

description:
fresh cells
NIH3T3_Fresh.tsv


title: HEK293_Cryo_Exp_1_401U_MSCB-132


title: HEK293_Cryo_Exp_1_401U_MSCB-108


title: NIH3T3_Fresh_400U_MSCB-057

description:
fresh cells
NIH3T3_Fresh.tsv


title: HEK293_Cryo_Exp_1_401U_MSCB-109


title: NIH3T3_Fresh_400U_MSCB-054

description:
fresh cells
NIH3T3_Fresh.tsv


title: HEK293_Cryo_Exp_1_401U_MSCB-118


title: HEK293_Cryo_Exp_1_401U_MSCB-107


title: NIH3T3_Fresh_400U_MSCB-045

description:
fresh cells
NIH3T3_Fresh.tsv


title: HEK293_Cryo_Exp_1_401U_MSCB-097


title: NIH3T3_Fresh_400U_MSCB-044

description:
fresh cells
NIH3T3_Fresh.tsv


title: NIH3T3_Fresh_400U_MSCB-059

description:
fresh cells
NIH3T3_Fresh.tsv


title: NIH3T3_Fresh_400U_MSCB-035

description:
fresh cells
NIH3T3_Fresh.tsv


title: NIH3T3_Fresh_400U_MSCB-034

description:
fresh cells
NIH3T3_Fresh.tsv


title: HEK293_Cryo_Exp_1_401U_MSCB-098


title: HEK293_Cryo_Exp_1_400U_MSCB-170


title: HEK293_Cryo_Exp_1_400U_MSCB-171


title: NIH3T3_Fresh_400U_MSCB-032

description:
fresh cells
NIH3T3_Fresh.tsv


title: NIH3T3_Fresh_400U_MSCB-031

description:
fresh cells
NIH3T3_Fresh.tsv


title: HEK293_Cryo_Exp_1_400U_MSCB-168


title: HEK293_Cryo_Exp_1_400U_MSCB-169


title: NIH3T3_Fresh_400U_MSCB-030

description:
fresh cells
NIH3T3_Fresh.tsv


title: NIH3T3_Fresh_400U_MSCB-033

description:
fresh cells
NIH3T3_Fresh.tsv


title: NIH3T3_Fresh_400U_MSCB-020

description:
fresh cells
NIH3T3_Fresh.tsv


title: HEK293_Cryo_Exp_1_400U_MSCB-166


title: NIH3T3_Fresh_400U_MSCB-055

description:
fresh cells
NIH3T3_Fresh.tsv


title: HEK293_Cryo_Exp_1_400U_MSCB-157


title: NIH3T3_Fresh_400U_MSCB-011

description:
fresh cells
NIH3T3_Fresh.tsv


title: HEK293_Cryo_Exp_1_400U_MSCB-156


title: HEK293_Cryo_Exp_1_400U_MSCB-147


title: NIH3T3_Fresh_400U_MSCB-010

description:
fresh cells
NIH3T3_Fresh.tsv


title: HEK293_Cryo_Exp_1_400U_MSCB-146


title: HEK293_Cryo_Exp_1_400U_MSCB-167


title: HEK293_Cryo_Exp_1_400U_MSCB-144


title: HEK293_Cryo_Exp_1_400U_MSCB-181


title: NIH3T3_Fresh_400U_MSCB-009

description:
fresh cells
NIH3T3_Fresh.tsv


title: NIH3T3_Fresh_400U_MSCB-008

description:
fresh cells
NIH3T3_Fresh.tsv


title: HEK293_Cryo_Exp_1_400U_MSCB-180


title: NIH3T3_Fresh_400U_MSCB-006

description:
fresh cells
NIH3T3_Fresh.tsv


title: HEK293_Cryo_Exp_1_400U_MSCB-143


title: NIH3T3_Cryo_401U_MSCB-178

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: HEK293_Cryo_Exp_1_400U_MSCB-123


title: NIH3T3_Cryo_401U_MSCB-177

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: HEK293_Cryo_Exp_1_400U_MSCB-132


title: HEK293_Cryo_Exp_1_400U_MSCB-122


title: NIH3T3_Fresh_400U_MSCB-021

description:
fresh cells
NIH3T3_Fresh.tsv


title: NIH3T3_Cryo_401U_MSCB-175

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: NIH3T3_Cryo_401U_MSCB-165

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: HEK293_Cryo_Exp_1_400U_MSCB-121


title: HEK293_Cryo_Exp_1_400U_MSCB-120


title: HEK293_Cryo_Exp_1_400U_MSCB-119


title: NIH3T3_Fresh_400U_MSCB-007

description:
fresh cells
NIH3T3_Fresh.tsv


title: NIH3T3_Cryo_401U_MSCB-164

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: HEK293_Cryo_Exp_1_400U_MSCB-145


title: HEK293_Cryo_Exp_1_400U_MSCB-109


title: HEK293_Cryo_Exp_1_400U_MSCB-118


title: NIH3T3_Cryo_401U_MSCB-153

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: HEK293_Cryo_Exp_1_400U_MSCB-108


title: NIH3T3_Cryo_401U_MSCB-154

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: NIH3T3_Cryo_401U_MSCB-163

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: HEK293_Cryo_Exp_1_400U_MSCB-098


title: HEK293_Cryo_Exp_1_400U_MSCB-099


title: NIH3T3_Cryo_401U_MSCB-151

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: HEK293_Cryo_Exp_1_400U_MSCB-097


title: NIH3T3_Cryo_401U_MSCB-139

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: NIH3T3_Cryo_401U_MSCB-130

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: NIH3T3_Cryo_401U_MSCB-174

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: PBMC_Fresh_408X_MSCB-096

description:
fresh cells
PBMC_Fresh.tsv

source_name: blood

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.

value: peripheral blood mononuclear cells


title: NIH3T3_Cryo_401U_MSCB-150

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: NIH3T3_Cryo_401U_MSCB-140

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: PBMC_Fresh_408X_MSCB-093

description:
fresh cells
PBMC_Fresh.tsv


title: PBMC_Fresh_408X_MSCB-092

description:
fresh cells
PBMC_Fresh.tsv


title: NIH3T3_Cryo_401U_MSCB-129

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: NIH3T3_Cryo_401U_MSCB-116

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: NIH3T3_Cryo_401U_MSCB-127

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: PBMC_Fresh_408X_MSCB-091

description:
fresh cells
PBMC_Fresh.tsv


title: PBMC_Fresh_408X_MSCB-090

description:
fresh cells
PBMC_Fresh.tsv


title: NIH3T3_Cryo_401U_MSCB-126

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: NIH3T3_Cryo_401U_MSCB-105

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: PBMC_Fresh_408X_MSCB-087

description:
fresh cells
PBMC_Fresh.tsv


title: NIH3T3_Cryo_401U_MSCB-106

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: PBMC_Fresh_408X_MSCB-088

description:
fresh cells
PBMC_Fresh.tsv


title: PBMC_Fresh_408X_MSCB-086

description:
fresh cells
PBMC_Fresh.tsv


title: NIH3T3_Cryo_401U_MSCB-141

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: NIH3T3_Cryo_400U_MSCB-179

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: NIH3T3_Cryo_401U_MSCB-115

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: NIH3T3_Cryo_400U_MSCB-178

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: NIH3T3_Cryo_401U_MSCB-103

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: PBMC_Fresh_408X_MSCB-082

description:
fresh cells
PBMC_Fresh.tsv


title: NIH3T3_Cryo_401U_MSCB-102

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: NIH3T3_Cryo_400U_MSCB-177

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: PBMC_Fresh_408X_MSCB-094

description:
fresh cells
PBMC_Fresh.tsv


title: PBMC_Fresh_408X_MSCB-085

description:
fresh cells
PBMC_Fresh.tsv


title: PBMC_Fresh_408X_MSCB-089

description:
fresh cells
PBMC_Fresh.tsv


title: PBMC_Fresh_408X_MSCB-080

description:
fresh cells
PBMC_Fresh.tsv


title: NIH3T3_Cryo_400U_MSCB-175

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: NIH3T3_Cryo_400U_MSCB-176

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: PBMC_Fresh_408X_MSCB-077

description:
fresh cells
PBMC_Fresh.tsv


title: PBMC_Fresh_408X_MSCB-078

description:
fresh cells
PBMC_Fresh.tsv


title: NIH3T3_Cryo_400U_MSCB-174

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: NIH3T3_Cryo_400U_MSCB-165

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: NIH3T3_Cryo_400U_MSCB-164

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: PBMC_Fresh_408X_MSCB-076

description:
fresh cells
PBMC_Fresh.tsv


title: PBMC_Fresh_408X_MSCB-074

description:
fresh cells
PBMC_Fresh.tsv


title: PBMC_Fresh_408X_MSCB-079

description:
fresh cells
PBMC_Fresh.tsv


title: PBMC_Fresh_408X_MSCB-075

description:
fresh cells
PBMC_Fresh.tsv


title: PBMC_Fresh_408X_MSCB-081

description:
fresh cells
PBMC_Fresh.tsv


title: NIH3T3_Cryo_400U_MSCB-152

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: NIH3T3_Cryo_400U_MSCB-150

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: NIH3T3_Cryo_400U_MSCB-154

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: PBMC_Fresh_408X_MSCB-070

description:
fresh cells
PBMC_Fresh.tsv


title: NIH3T3_Cryo_400U_MSCB-141

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: PBMC_Fresh_408X_MSCB-072

description:
fresh cells
PBMC_Fresh.tsv


title: NIH3T3_Cryo_400U_MSCB-140

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: PBMC_Fresh_408X_MSCB-067

description:
fresh cells
PBMC_Fresh.tsv


title: PBMC_Fresh_408X_MSCB-069

description:
fresh cells
PBMC_Fresh.tsv


title: NIH3T3_Cryo_400U_MSCB-128

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: NIH3T3_Cryo_400U_MSCB-127

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: PBMC_Fresh_408X_MSCB-066

description:
fresh cells
PBMC_Fresh.tsv


title: PBMC_Fresh_408X_MSCB-063

description:
fresh cells
PBMC_Fresh.tsv


title: NIH3T3_Cryo_400U_MSCB-126

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: PBMC_Fresh_408X_MSCB-064

description:
fresh cells
PBMC_Fresh.tsv


title: NIH3T3_Cryo_400U_MSCB-131

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: NIH3T3_Cryo_400U_MSCB-155

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: NIH3T3_Cryo_400U_MSCB-117

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: NIH3T3_Cryo_400U_MSCB-116

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: PBMC_Fresh_408X_MSCB-059

description:
fresh cells
PBMC_Fresh.tsv


title: PBMC_Fresh_408X_MSCB-058

description:
fresh cells
PBMC_Fresh.tsv


title: PBMC_Fresh_408X_MSCB-060

description:
fresh cells
PBMC_Fresh.tsv


title: NIH3T3_Cryo_400U_MSCB-153

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: PBMC_Fresh_408X_MSCB-071

description:
fresh cells
PBMC_Fresh.tsv


title: NIH3T3_Cryo_400U_MSCB-107

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: PBMC_Fresh_408X_MSCB-061

description:
fresh cells
PBMC_Fresh.tsv


title: PBMC_Fresh_408X_MSCB-073

description:
fresh cells
PBMC_Fresh.tsv


title: NIH3T3_Cryo_400U_MSCB-106

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: PBMC_Fresh_408X_MSCB-056

description:
fresh cells
PBMC_Fresh.tsv


title: NIH3T3_Cryo_400U_MSCB-104

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: PBMC_Fresh_408X_MSCB-057

description:
fresh cells
PBMC_Fresh.tsv


title: PBMC_Fresh_408X_MSCB-055

description:
fresh cells
PBMC_Fresh.tsv


title: NIH3T3_Cryo_400U_MSCB-103

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: NIH3T3_Cryo_400U_MSCB-102

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: NIH3T3_Cryo_400U_MSCB-130

description:
cryopreserved cells
NIH3T3_Cryo.tsv


title: PBMC_Fresh_408X_MSCB-051

description:
fresh cells
PBMC_Fresh.tsv


title: PBMC_Fresh_408X_MSCB-052

description:
fresh cells
PBMC_Fresh.tsv


title: Colon_Fresh_087V_MSCB-192

description:
fresh cells
Colon_Fresh.tsv

source_name: colon cells

value: primary mouse colon cells


title: Colon_Fresh_087V_MSCB-190

description:
fresh cells
Colon_Fresh.tsv


title: PBMC_Fresh_408X_MSCB-048

description:
fresh cells
PBMC_Fresh.tsv


title: Colon_Fresh_087V_MSCB-189

description:
fresh cells
Colon_Fresh.tsv


title: PBMC_Fresh_408X_MSCB-050

description:
fresh cells
PBMC_Fresh.tsv


title: PBMC_Fresh_408X_MSCB-047

description:
fresh cells
PBMC_Fresh.tsv


title: Colon_Fresh_087V_MSCB-184

description:
fresh cells
Colon_Fresh.tsv


title: PBMC_Fresh_408X_MSCB-046

description:
fresh cells
PBMC_Fresh.tsv


title: PBMC_Fresh_408X_MSCB-044

description:
fresh cells
PBMC_Fresh.tsv


title: PBMC_Fresh_408X_MSCB-045

description:
fresh cells
PBMC_Fresh.tsv


title: PBMC_Fresh_408X_MSCB-043

description:
fresh cells
PBMC_Fresh.tsv


title: Colon_Fresh_087V_MSCB-176

description:
fresh cells
Colon_Fresh.tsv


title: Colon_Fresh_087V_MSCB-181

description:
fresh cells
Colon_Fresh.tsv


title: Colon_Fresh_087V_MSCB-174

description:
fresh cells
Colon_Fresh.tsv


title: Colon_Fresh_087V_MSCB-175

description:
fresh cells
Colon_Fresh.tsv


title: Colon_Fresh_087V_MSCB-182

description:
fresh cells
Colon_Fresh.tsv


title: PBMC_Fresh_408X_MSCB-053

description:
fresh cells
PBMC_Fresh.tsv


title: Colon_Fresh_087V_MSCB-173

description:
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description:
cryopreserved cells
PBMC_Cryo.tsv


title: PBMC_Cryo_408X_MSCB-186

description:
cryopreserved cells
PBMC_Cryo.tsv