title: IgG

city: bethesda

first: Seolkyoung

last: Jung

address: 10 Center Dr

institute: NIH

data_processing:
CUT&RUN sequencing reads were trimmed using Cutadapt: Illumina adapter sequences were removed and reads trimmed to 140 bp. Reads less than 35 bp were discarded. Trimmed reads were aligned to the mm10 version of the mouse genome using bowtie2. Aligned reads were then processed from sam to bed files using Samtools and Bedtools and reads containing the same chromosome start and end coordinates (duplicate) were discarded from subsequent analysis.
Assembly: mm10
Supplementary files format and content: Unique reads were filtered for fragments in the range of 140 and 400 bp and used to generate bigwig files.
Library strategy: CUT&RUN

growth_protocol: CH12 B cells were cultured in RPMI-1640 media (Gibco) supplemented with 10% Fetal Bovine Serum (Gibco), 1% Penicillin-Streptomycin (Gibco) and 50 μM β- mercaptoethanol (Gibco) as described previously14. Briefly, CH12 B cells were expanded in 2.8L baffled Fernbach flasks (PYREXTM) at 37°C with 5% CO2. Cells were counted, pelleted, and washed with cold PBS buffer. For CUT&RUN experiments, MED25FLAG/FLAG and MED26-/- CH12 B cells were cultured as described above, pelleted at 1500 rpm for 5 minutes at room temperature, resuspended in growth media supplemented with 10% charcoal stripped Fetal Bovine Serum (Gibco), and expanded at 37°C with 5% CO2 overnight. Prior to running all CUT&RUN experiments cells were counted and assessed for viability.

extract_protocol:
For CUT&RUN experiments, five hundred thousand cells were harvested per condition and washed twice in wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine and 1x protease inhibitor cocktail). Cells were bound to magnetic Concanavalin A beads for 10 min, at RT, followed by overnight incubation with primary antibody (MED6 (Proteintech, cat # 15338-1-AP) or IgG (Proteintech, cat # 15338-1-AP), 0.5 ug/sample) in antibody buffer (2 mM EDTA in Digitonin 150 buffer), at +4°C. Cells were washed twice in Digitonin buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 1x protease inhibitor cocktail and 0.01% digitonin), incubated with pAG-MNase (Epicypher Inc., 1:20) in Digitonin buffer for 10 min, at RT, and washed once in Digitonin buffer. Samples were resuspended in cold Digitonin buffer containing 100mM CaCl2 and incubated for 2 hours, at +4°C, for pAG-MNase activation and chromatin digestion. Digestion was stopped by adding stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 50 ug/ml RNase A, 50 ug/ml Glycogen) to the samples, followed by 10 min incubation at 37°C. Samples placed in magnetic rack and the supernatant containing the released chromatin fragments was collected in new tubes. SDS was added to the samples to a final concentration of 0.1% and samples were treated with 0.2 ug/ul of Proteinase K for 10 min, at 70°C. Samples were next submitted to two rounds of phenol:chloroform:isoamyl alcohol extraction (1:1) and one round of chloroform extraction (1:1). The aqueous phase was collected in new tubes and the extracted DNA was purified by binding to AMPure XP beads using a 2X ratio.
CUT&RUN libraries were then prepared using the SRSLY PicoPlus kit (ClaretBio) according to the manufacturer’s instructions, and two biological replicates from each condition were subjected to PE150 sequencing on NovaSeq 6000 (Illumina).

treatment_protocol: For experiments involving D3-dependent activation, D3 (Sigma, prepared as 1M stock in 200 proof ethanol) was added to cells at 1 nM final concentration (ethanol only was added to controls), cells were incubated at 37°C with 5% CO2 for 1 hour, and then harvested for CUT&RUN analysis.

value: mouse lymphoma B cell

tag: treatment

value: Vehicle control (ethanol)


title: Dopaminergic neuron nuclei, controls, sample 1

status: Public on Aug 19 2024

type: SRA

city: Chicago

first: Rajeshwar

last: Awatramani

state: IL

address: 2344 W Charleston, APT 2

department: Neurology

country: USA

institute: Northwestern University

description: 10x Genomics snRNA-Seq experiment

library_source: transcriptomic single cell

data_processing:
Data was demultiplexed and counted using Cell Ranger version 7.0.1
Downstream analysis was performed in Seurat v5.0.1.
Assembly: mm10-2020-A
Supplementary files format and content: 10x Cell Ranger output files corresponding to barcodes, features, and matrix of counts.

molecule: nuclear RNA

organism: Mus musculus

source_name: Midbrain

extract_protocol:
A 2mm thick block of ventral midbrain tissue was dissected out from each mouse and collected for isolation. Tissue was dounce homogenized in a nuclear extraction buffer (10mM Tris, 146mM NaCl, 1mM CaCl2, 21mM MgCl2, 0.1% NP-40, 40u/mL Protector RNAse inhibitor (Roche 3335399001). Dounce homogenizer was washed with 4mL of a washing buffer (10mM Tris, 146mM NaCl, 1mM CaCl2, 21mM MgCl2, 0.01% BSA, 40U/mL Protector RNAse inhibitor) and filtered through a 30uM cell strainer. After three rounds of washing by centrifugation at 500g for 5 minutes, nuclei pellets were resuspended resuspension buffer (10mM Tris, 146mM NaCl, 1mM CaCl2, 21mM MgCl2, 2% BSA, 0.02% Tween-20) and filtered through a 20uM strainer. This nuclei suspension was loaded onto a MACSQuant Tyto HS chip and diluted with 1x PBS. Nuclei were sorted using gates set for isolation of GFP+ singlet nuclei.
The cDNA and library were generated using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10X Genomics, PN-1000286) and Dual Index Kit TT Set A (10X Genomics, PN-1000215) according to the manufacturer’s manual with following modification: PCR cycle used for cDNA generation was 16 and the resulting PCR products was size-selected using 0.8X SPRI beads instead of 0.6X SPRI beads as stated in protocol.

tag: tissue

value: Midbrain

tag: strain

value: Dat-IRES-Cre, CAG-Sun1/sfGFP, Lrrk2 G2019S

tag: cell type

value: Dopaminergic neurons

tag: genotype

value: Lrrk2 WT

tag: Sex

value: male and female

tag: developmental stage

value: adult


city: Amsterdam

first: Christina

last: Moene

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

description:
Sox2P-reporter -116 kb, population P3 pool3 rep3
E2285 Sox2P-reporter -116 kb, population P3 pool3 rep3 Rv
mapped_integrations_-116kb_Sox2P_pools.txt

library_source: genomic

data_processing:
The full protocol is described in the corresponding manuscript. In short, reads overlapping the SB-genome junction were selected, SB-sequences were trimmed off (using an adapted version of cutadapt) and reads were mapped to the genome (mm10 or an in silico version of mm10 including the hopping launch pad at -116 kb), filtering for mapq >=10. All putative integrations are lifted over to mm10.
Assembly: mm10
Supplementary files format and content: The processed data file reports all putative integrations mapped in a pool or clone (supported by at least one mapping read, filtering in the manuscript can be more strict). Columns: chr = chromosome; start, end = integration location; seq = dinucleotide at integration site (expected for SB: TA); strand = strand of integration (orientation); read_count = total read count, mapq = total mapping quality (of all reads); read_count_1/mapq_1 = forward mapping reads (3' ITR); read_count_2/mapq_2 = reverse mapping reads (5' ITR); all other columns specify and annotate the sequenced sample. There is one processed data file per founder cell line (pool-based experiments) and one for the isolated clones.

molecule: genomic DNA

source_name: F1 hybrid 129/Sv:CAST/EiJ

growth_protocol: F121/9 (CAST/EiJ x S129/Sv) Sox2 mCherry+/eGFP+ were cultured in Serum+Lif+2i condition. Briefly, cells were cultured on gelatin-coated (0.1%) culture plates in Glasgow minimum essential medium (Sigma-Aldrich, G5154) supplemented with 15% fetal bovine serum (Thermo Fisher Scientific, 10270-106), 1% L-glutamine (Thermo Fisher Scientific, 25030024), 1% sodium pyruvate (Thermo Fisher Scientific, 11360-70), 1% MEM non-essential amino acids (Thermo Fisher Scientific, 11140-50), 1% penicillin-streptomycin (Thermo Fisher Scientific, 15070063), 100 µM ß-mercaptoethanol, 10 x 4 U leukemia inhibitory factor (LIF; esg1107, Millipore), 1 μM MEK inhibitor PD0325901 (Mirdametinib, MedChemExpress), 3 μM GSK-3β inhibitor CHIR99021 (Laduviglusib, MedChemExpress) in 5% CO2 at 37°C. Cells were passaged every 2 days.

extract_protocol:
Sorted pools and clones were expanded and crude lysates were obtained from a full 96 well plate by lysing with 50 µL DirectPCR Lysis Reagent (102-T, Viagen Biotec) supplemented with 100 µg/mL proteinase K, and incubating 2.5 h at 55 °C and 45 min at 85 °C. For unsorted control cell pools, gDNA was extracted after expansion using the ISOLATE II Genomic DNA Kit (BIO-52067, Bioline).
SBt integrations were mapped by amplifying and sequencing the ITR-genome junction using a tagmentation-based approach. The procedure was similar to {Schep, 2021, 33848455}, but using the following SB-ITR specific primers: MEP009 (5′ ITR, reverse) or LD027 (3′ ITR, forward) for the linear enrichment and MEP011 (5′ ITR, reverse) or MEP034 (3′ ITR, forward) for PCR.Input for one tagmentation reaction was either 100ng gDNA or 3 µL crude lysate. The 72 °C extension times of all PCRs were increased to 1 min. In addition, the composition of the linear enrichment PCR was changed to 10 μL of tagmented DNA, 2 μL of 1 μM primer, 4 μL dNTPs (10mM), 8 μL 5x Phusion® HF Buffer (NEB), 0.5 μL Phusion® HS Flex polymerase (2 U/μL - NEB), in a final volume of 40 μL. For all clones and some experiments with sorted pools (proof-of-principle experiment, third replicate of the reporter hopping) we halved this reaction to a final volume of 20 µL. For the unsorted control pools, 10 separate tagmentation reactions and library preparations were performed, usually using one set of sequencing indices. Libraries were sequenced with 150 bp paired-end reads using either an Illumina MiSeq system (reagent kit v2) or  Illumina NextSeq 550 system (mid-output kit) including 10% of PhiX spike-in.  Primers are described in the corresponding manuscript.

treatment_protocol: SB hopping was induced by transfecting 2.5 to 5 million cells with the bicistronic plasmid (pME07) encoding SB transposase SB100x and the human nerve growth factor receptor (LNGFR), using Lipofectamine 2000 (Invitrogen, 11668019) and 5 µg of plasmid per million cells. After 30 hours, transfected cells were enriched using MACS MS columns (130-042-201, Miltenyi Biotec) and LNGFR MicroBeads (130-091-330, Miltenyi Biotec) according to the manufacturer’s protocol. One week after transfection, 0.2 million SB-transposase-transfected cells were set apart as an unsorted pool and the remaining cells were FACS sorted into pools (of up to 1000 cells) based on reporter expression. Clones were obtained by sorting single cells from previously obtained pools, or sorted directly from the full pool of SB-transposase-transfected cells.

tag: cell line

value: F1 hybrid 129/Sv:CAST/EiJ

value: mESC

value: WT

tag: launch pad_location

tag: insert

tag: sorted gate

tag: sample type

value: sorted pool


title: T96

city: Solna

first: Felix

last: Haglund de Flon

state: Stockholm

address: Solnavägen 1

department: Oncology-Pathology

country: Sweden

institute: Karolinska Institute

description:
Sample_Counts.csv
Patient_Counts.csv

library_source: transcriptomic

data_processing:
RNA library preparation was done using the Illumina TruSeq Stranded Total RNA and the Illumina RiboZero.  Clustering was done by 'cBot,' and samples were sequenced on NovaSeq6000 (NovaSeq Control Software 1.6.0/RTA v3.4.4) with a 2x151 setup using 'NovaSeqStandard’ workflow in ‘SP’ mode flowcell. The Bcl to FastQ conversion was performed using bcl2fastq_v2.19.1.403 from the CASAVA software suite. The quality scale used was Sanger / phred33 / Illumina 1.8. The average sequence depth was 37.5 M reads (min 16.4 – max 82.3 M reads).
Assembly: Hg19/GRCh37
Supplementary files format and content: Comma delimited text file includes raw counts for each sample
Supplementary files format and content: Comma delimited text file includes raw counts for each patient

molecule: total RNA

organism: Homo sapiens

growth_protocol: Not applicable

extract_protocol:
Total RNA was extracted from FFPE using QIAamp DNA FFPE Tissue Kit
Illumina TruSeq Stranded Total RNA and the Illumina RiboZero

treatment_protocol: Not applicable

tag: patient id

tag: fusion gene

tag: metastasis time_(days)

tag: metastasis

tag: overall survival_time_(days)

tag: overal survival

tag: histology

value: Monophasic

tag: poorly differentiated_histology

value: Yes

tag: tumor size_(cm)

value: Synovial Sarcoma

tag: tumor type

value: Metastasis

tag: site

value: Peripheral


title: WT1

city: Delhi

first: Chen

last: Chongtham

state: Delhi

address: Aruna Asaf Ali Road

country: India

institute: National Institute of Immunology

data_processing:
FastQC
Alignment using Bowtie2
Counting using HT-Seq
Differential expression using DEseq2
Assembly: GRCm38.p6
Supplementary files format and content: Tabular files with raw read counts as calculated by Htseq-count

source_name: Primary cortical neurons

growth_protocol: Embryonic E16.5 mouse cortex tissue was dissected and trypsinised to obtain  single cell suspension of cells, which were maintained in serum free differentiating media for five days in vitro.

extract_protocol:
Isolation of total RNA was performed using TRIzol reagent (Ambion). Small RNA library preparation (with TrueSeq sRNA library kit) and sequencing (miRNA Sequencing using Illumina HiSeq2500 Rapid Mode 50bp PE with 10-15Mn reads) was outsourced from Novogene through Bencos Research Solution.
Library for Small RNA (TruSeq sRNA Library Kit) was outsourced from Novogene through Bencos Research Solutions.

tag: genotype

tag: tissue

value: Brain cortex

tag: disease state

value: Normal


title: T2

description:
Sample_Counts.csv
Patient_Counts.csv

value: No


description:
Sox2P-reporter -116 kb, population P3 pool2 rep3
E2285 Sox2P-reporter -116 kb, population P3 pool2 rep3 Rv
mapped_integrations_-116kb_Sox2P_pools.txt

tag: cell line

tag: cell type

tag: launch pad_location

tag: insert


title: Med26 KO +D3 rep2

state: MD

department: NIAMS

value: mouse lymphoma B cell

tag: treatment

value: 1 nM D3


title: T71

description:
Sample_Counts.csv
Patient_Counts.csv

tag: patient id

tag: fusion gene

tag: metastasis time_(days)

value: visceral


description:
Sox2P-reporter -116 kb, population P3 pool5 rep3
E2285 Sox2P-reporter -116 kb, population P3 pool5 rep3 Rv
mapped_integrations_-116kb_Sox2P_pools.txt

tag: sorted gate

tag: sample type


title: MDA-MB-231-derived BCSCs, RA treatment 3, 48h

city: Fuzhou

first: Wei

last: Wang

address: 福州市闽侯荆溪关口366号

country: China

institute: Fujian medical university

data_processing:
After total RNA samples were analyzed by agarose electrophoresis and nanodrop inspection and quantification, libraries were constructed, library quality was determined by Agilent 2100 Bioanalyzer, libraries of different samples were sequenced, single-stranded DNA was denatured in 0.1M NaOH and sequenced on Illumina sequencer according to the sequencing instructions.
Preparation of miRNA sequencing libraries using total RNA from each sample, Including the following steps: 1) 3'joint connection; 2) 5'connector connection; 3) cDNA synthesis; 4) PCR amplification; 5) Select the PCR amplified fragments of 135 ~ 155 bp (corresponding to 15 ~ 35 nt small RNAs); Denaturing the library into single-stranded DNA molecules, Captured on the Illumina flow cell, In situ amplification into a cluster (cluster), And, according to the sequencing instructions, Sequencing was performed on a Illumina sequencer.
The sequencing data generated by the Illumina sequencer is the raw sequencing data, raw sequencing data After sequencing quality control (Quality Control) to evaluate whether the sequencing data can be used for subsequent data analysis; after QC, the trimmed data alignment generated by pre-processing filtering step (removing joint sequence and short fragments in Read) is applied to the reference genome; the statistical analysis of the comparison results can be used for subsequent data analysis
Assembly: hg19
Supplementary files format and content: excel files include tag count and RPM values for each Sample

source_name: breast

growth_protocol: BCSCs were seeded in RPMI-1640 medium (HyClone; cat. #SH30809.01) and 100 ng/mL cholera toxin. All the mediums were supplemented with 10% fetal calf serum (PAN Biotech, Aidenbach, German) in the presence of streptomycin and penicillin. BCSCs were enzymatically lysed in 0.05% trypsin/0.025% EDTA solution and cell suspensions were cultured in bottles with low surface attachment (Corning) in serum-free RPMI-1640 medium containing 10 ng/mL basic fibroblast growth factor (Peprotech, Rocky Hill, NJ; cat. #AF-100-15), 20 ng/mL EGF (Peprotech, Rocky Hill, NJ; cat. #100-18B) and 2% B‑27 Supplement (Gibco, New York, US; cat. #17504-044). Such culture conditions help the cell suspensions convert to sphere-forming cells. All these cells were incubated in a humidified 5% CO2 incubator at 37°C

extract_protocol:
After deeply anesthetized and saline perfused at days 21, brain tissue surrounding the hemorrhagic region (the right globus pallidus) was harvested for following detections. Total RNAs were extracted according to the manufacturer’s instruction (Qiagen, USA). The purity and concentration of total RNA samples were determined with NanoDrop ND-1000. Then we did the following treatments to remove some RNA modifications which might interfere with small RNA-sequencing library construction: 3’-aminoacyl (charged) deacylation to 3’-OH (hydroxyl group) for 3’ adaptor ligation, 3’-cP (2’,3’-cyclic phosphate) removal to 3’-OH for 3’ adaptor ligation, 5’-OH phosphorylation to 5’-P for 5’-adaptor ligation, N1-methyladenosine and N3-methylcytidine demethylation for efficient reverse transcription. All procedures were performed using rtStar tRF&tiRNA Pretreatment Kit (Arraystar) protocols.
Total RNA samples were sequentially ligated to 3’ and 5’ small RNA adapters using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, USA). cDNA was then synthesized and amplified using Illumina’s proprietary reverse transcription primers and amplification primers. Subsequently, 135-170 bp PCR amplified fragments (corresponding to 15-50 nt small RNA size range) were extracted and purified from the PAGE gel. The completed libraries were quantified by Agilent 2100 Bioanalyzer. Libraries were mixed in equal amounts according to the quantification results and used for sequencing on the instrument. And then, the DNA fragments in well-mixed libraries were denatured to generate single-stranded DNA molecules and loaded onto the reagent cartridge. Finally, the sequencing run was performed on Illumina NextSeq 500 system using NextSeq 500/550 V2 kit (Illumina) according to the manufacturer’s instructions. Sequencing was carried out by running 50 cycles.

treatment_protocol: Cells were washed twice with PBS and replaced with 10% serum medium (PAN Biotech, Aidenbach, German) containing various concentrations of 0 and 200 μg/mL of Rosmarinic acid （ extracted from S. glabra）at 0 and 48 h (3 wells per group)。

value: breast

value: MDA-MB-231 Human Breast Carcinoma Cell

value: MDA-MB-231-derived breast cancer stem-like cells

value: Rosmarinic acid, 200ug/ml, 48 h

tag: time


title: Med26 KO +D3 rep1


description:
Sox2P-reporter -116 kb, population P3 pool1 rep3
E2285 Sox2P-reporter -116 kb, population P3 pool1 rep3 Rv
mapped_integrations_-116kb_Sox2P_pools.txt

value: F1 hybrid 129/Sv:CAST/EiJ

value: mESC

value: WT


title: WT2


title: T68

description:
Sample_Counts.csv
Patient_Counts.csv

tag: metastasis

tag: overall survival_time_(days)

tag: overal survival

tag: histology

value: Biphasic

tag: poorly differentiated_histology

tag: tumor size_(cm)


title: Med26 KO -D3 rep2

tag: cell line

tag: genotype

value: Vehicle control (ethanol)


description:
Sox2P-reporter -116 kb, population P2 pool4 rep3
E2285 Sox2P-reporter -116 kb, population P2 pool4 rep3 Rv
mapped_integrations_-116kb_Sox2P_pools.txt

tag: cell type

tag: launch pad_location

value: sorted pool


title: T114

value: Monophasic

tag: tissue

value: Synovial Sarcoma

tag: tumor type

value: Metastasis

tag: site

value: Peripheral


description:
Sox2P-reporter -116 kb, population P2 pool3 rep3
E2285 Sox2P-reporter -116 kb, population P2 pool3 rep3 Rv
mapped_integrations_-116kb_Sox2P_pools.txt

tag: insert


title: T88

tag: patient id

tag: fusion gene


title: MDA-MB-231-derived BCSCs, RA treatment 1, 48h

address: 福州市闽侯荆溪关口366号

tag: treatment

tag: time


title: WT +D3 rep2

value: mouse lymphoma B cell


title: Med26 KO -D3 rep1


description:
Sox2P-reporter -116 kb, population P2 pool2 rep3
E2285 Sox2P-reporter -116 kb, population P2 pool2 rep3 Rv
mapped_integrations_-116kb_Sox2P_pools.txt

tag: sorted gate

tag: sample type


title: MDA-MB-231-derived BCSCs, Control 3,48h

address: 福州市闽侯荆溪关口366号

value: Control


title: T72

description:
Sample_Counts.csv
Patient_Counts.csv

tag: metastasis time_(days)

tag: metastasis

tag: overall survival_time_(days)

tag: overal survival

tag: histology

value: No


description:
Sox2P-reporter -116 kb, population P1 pool1 rep3
E2285 Sox2P-reporter -116 kb, population P1 pool1 rep3 Rv
mapped_integrations_-116kb_Sox2P_pools.txt

tag: cell line

tag: cell type

tag: genotype


title: MDA-MB-231-derived BCSCs, Control 2,48h

address: 福州市闽侯荆溪关口366号

tag: tissue

value: breast


title: MDA-MB-231-derived BCSCs, Control 1,48h

address: 福州市闽侯荆溪关口366号

value: MDA-MB-231 Human Breast Carcinoma Cell


description:
Sox2P-reporter -116 kb, population P2 pool1 rep3
E2285 Sox2P-reporter -116 kb, population P2 pool1 rep3 Rv
mapped_integrations_-116kb_Sox2P_pools.txt

tag: launch pad_location


title: T61

description:
Sample_Counts.csv
Patient_Counts.csv

tag: poorly differentiated_histology

value: Yes

tag: tumor size_(cm)

tag: tumor type

tag: site


title: WT -D3 rep2

tag: treatment


title: T64

description:
Sample_Counts.csv
Patient_Counts.csv

tag: patient id

tag: fusion gene


title: MDA-MB-231-derived BCSCs, RA treatment 2, 48h

address: 福州市闽侯荆溪关口366号

value: MDA-MB-231-derived breast cancer stem-like cells

value: Rosmarinic acid, 200ug/ml, 48 h

tag: time


description:
Sox2P-reporter -116 kb, population P4 pool4 rep3
E2285 Sox2P-reporter -116 kb, population P4 pool4 rep3 Fw
mapped_integrations_-116kb_Sox2P_pools.txt

value: F1 hybrid 129/Sv:CAST/EiJ

value: mESC

tag: insert

tag: sorted gate

tag: sample type


title: WT -D3 rep1

value: WT


title: H1 cells, PSC to definitive endoderm (click-tag)

city: Worcester

first: Rene

last: Maehr

state: MA

address: 55 Lake Ave N

department: Program in Molecular Medicine

institute: UMass Medical School

description:
10x Genomics
This library consists of molecules derived from the same sample, but including UMI, cell barcode, and click-tag sequence instead of primarily genomic sequence.

library_source: other

data_processing:
Data were quantified using CellRanger 2.1.0 with reference transcriptome hg19-1.2.0.
ClickTags were counted using CITE-seq_count v1.3.1.
Assembly: hg19
Supplementary files format and content: Gzipped output of cellranger count
Supplementary files format and content: Gzipped whitespace separated table of ClickTag counts.

molecule: other

growth_protocol: Cell culture and endoderm induction followed Genga et al. 2019 (Genga, R. M., Kernfeld, E. M., Parsi, K. M., Parsons, T. J., Ziller, M. J., & Maehr, R. (2019). Single-cell RNA-sequencing-based CRISPRi screening resolves molecular drivers of early human endoderm development.Cell reports,27(3), 708-718.)

extract_protocol: Fixation, tagging, and library construction follow Gehring et al. 2018 (Gehring, J., Park, J. H., Chen, S., Thomson, M., & Pachter, L. (2018). Highly multiplexed single-cell RNA-seq for defining cell population and transcriptional spaces. BioRxiv, 315333.). The same chemistry, 10X 3’ v2, was used.

treatment_protocol: There was no treatment beyond endoderm induction (no genetic perturbation).

value: PSC to definitive endoderm


title: T76

tag: histology

value: Central


title: T60

description:
Sample_Counts.csv
Patient_Counts.csv

tag: metastasis time_(days)

tag: metastasis

tag: overall survival_time_(days)

tag: overal survival

value: Monophasic


description:
Sox2P-reporter -116 kb, population P4 pool3 rep3
E2285 Sox2P-reporter -116 kb, population P4 pool3 rep3 Fw
mapped_integrations_-116kb_Sox2P_pools.txt

tag: cell line

tag: cell type

tag: genotype

tag: launch pad_location

value: sorted pool


title: T70

tag: tissue

value: Synovial Sarcoma

tag: tumor type

value: Metastasis

tag: site


title: Day6_Sox1+FoxA2+_Rep3

city: Basel

first: Markus

last: Auler

address: Schanzenstrasse 44

department: Department of Biosystems Science and Engineering ETH

country: Switzerland

institute: ETH Zürich

data_processing:
RNA-Seq STAR mapping pipeline (Version 2.5.3a).
The obtained reads were aligned to the M 21 release mouse genome using STAR.
Subsequently, sorted .bam files were generated using SAMtools.
Counts were then extracted using featureCounts.
Assembly: M21      ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M21
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

growth_protocol: Cells were maintained in standard SerumLIF prior to start of experiment with 5% CO2 and 37 C.

extract_protocol:
Equal numbers of cells were sorted into low-binding 96-well plates filled with 1xPBS using fluorescence-activated cell sorting and promptly stored at -80°C until use.
The RNA extraction involved isolation and fragmentation, and the synthesis of the double-stranded cDNA library were performed according to the SMART-Seq Stranded Kit protocol from Takara (Catalog # 634444).

treatment_protocol: Cells were switched to Retinoic Acid (1 uM) differentiation media at start of experiment for indicated time prior to RNA extraction.

value: Mouse Embryonic Stem Cell

tag: treatment

value: Retinoic Acid Differentiation

value: Day 6

tag: facs sorted_cell_population


title: WT +D3 rep1

value: mouse lymphoma B cell

value: 1 nM D3


title: T62

description:
Sample_Counts.csv
Patient_Counts.csv

tag: patient id

tag: fusion gene

tag: poorly differentiated_histology

value: Yes

tag: tumor size_(cm)

value: Peripheral


description:
Sox2P-reporter -116 kb, population P4 pool2 rep3
E2285 Sox2P-reporter -116 kb, population P4 pool2 rep3 Fw
mapped_integrations_-116kb_Sox2P_pools.txt

tag: insert

tag: sorted gate

tag: sample type


title: Jurkat-Input

city: Rome

first: daniele

last: santoni

address: via dei taurini 19

country: Italy

institute: IASI - CNR

data_processing:
The 75-nt single-end (SE75) sequence reads generated by Illumina sequencing were mapped to the genome using the BWA algorithm ("bwa aln/samse" with default settings).
The tags were extended in silico (using Active Motif software) at their 3´-ends to a length of 200 bp, which corresponds to the average fragment length in the size-selected library.
Active Motif's two main peak callers are MACS/MACS2 and SICER.
To compare peak metrics between 2 or more samples, overlapping intervals were grouped into Merged Regions, defined by the start coordinate of the most upstream interval and the end coordinate of the most downstream interval. After defining the Intervals and Merged Regions, their genomic locations, along with their proximities to gene annotations and other genomic features, were determined, and average and peak fragment densities within Intervals and Merged Regions were compiled.
MACS 2.1.0 algorithm was used for peak calling. Threshold to identify statistically significant regions modulated : -0.5 ≤ shrunken LogFC ≤ 0.5 and p adjusted-value ≤ 0.05.
Assembly: mm10 and hg38
Supplementary files format and content: bigWig, chr-start-end-value, peak files

source_name: Jurkat, Clone E6-1 (ATCC TIB-152)

growth_protocol: DMEM(B16F10) and RPMI1640 (Jurkat) supplemented with 10% Foetal Bovine Serum, 1% L-Glutamine and 1% Penicillin-Streptomycin. Cells were cultured at 37°, 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde solution and quenched with 120 mM Glycine. Samples were then treated with 0.5% Igepal supplemented with 1 mM PMSF, pelleted, snap frozen, and sent to Active Motif (Carlsbad, CA, USA) for H3K27Ac-ChIP-seq analysis. Lysates were sonicated, and the DNA sheared to an average length of 300–500 bp with an EpiShear probe sonicator (Active Motif, cat# 53051).
Illumina sequencing libraries were prepared from ChIPs and Input DNAs at Active Motif  on an automated system (Apollo 342, Wafergen Biosystems/Takara). After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on the Illumina NextSeq 500 platform.

treatment_protocol: WT vs KO_HDAC6 by CRISPR/Cas9 and Vehicle (DMSO) vs HDAC6i (ITF3756, 1uM, 16h) (n=3 biological replicates per group).

value: Jurkat, Clone E6-1 (ATCC TIB-152)

value: T-lymphocyte, Acute leukemia

value: pool

tag: chip antibody


title: Jurkat-H4, H3K27Ac, ChIP-seq

tag: cell line

value: HDAC6 inhibitor (ITF3756, 1uM, 16h)

value: H3K27Ac Active Motif #39133


title: Day6_Sox1+FoxA2-_Rep3

tag: cell type

tag: time


title: Jurkat-J4, H3K27Ac, ChIP-seq

value: Vehicle (DMSO)


title: Jurkat-H2, H3K27Ac, ChIP-seq


title: Day6_Sox1-FoxA2-_Rep3


title: T59

description:
Sample_Counts.csv
Patient_Counts.csv

tag: metastasis time_(days)

tag: metastasis

tag: overall survival_time_(days)

tag: overal survival

tag: histology

value: Biphasic

value: No


description:
Sox2P-reporter -116 kb, population P3 pool5 rep3
E2285 Sox2P-reporter -116 kb, population P3 pool5 rep3 Fw
mapped_integrations_-116kb_Sox2P_pools.txt

value: F1 hybrid 129/Sv:CAST/EiJ

value: mESC

tag: genotype

value: WT

tag: launch pad_location

value: sorted pool


title: T56

description:
Sample_Counts.csv
Patient_Counts.csv

tag: patient id

tag: fusion gene

tag: tissue

value: Synovial Sarcoma

tag: tumor type

tag: site


title: Jurkat-J2, H3K27Ac, ChIP-seq

tag: treatment


title: H1 cells, PSC to definitive endoderm (scRNA-seq)

description:
10x Genomics
All samples were multiplexed

molecule: polyA RNA

value: PSC to definitive endoderm

value: endoderm induction (no genetic perturbation)


title: Day4_Sox1-FoxA2+_Rep3

value: Mouse Embryonic Stem Cell

value: Retinoic Acid Differentiation

value: Day 4

tag: facs sorted_cell_population


title: Jurkat-H1, H3K27Ac, ChIP-seq

tag: cell line

value: Jurkat, Clone E6-1 (ATCC TIB-152)

value: T-lymphocyte, Acute leukemia

tag: chip antibody


title: T58

description:
Sample_Counts.csv
Patient_Counts.csv

value: Monophasic

tag: poorly differentiated_histology

value: Yes

tag: tumor size_(cm)

value: Peripheral


description:
Sox2P-reporter -116 kb, population P5 pool4 rep2
E2282 Sox2P-reporter -116 kb, population P5 pool4 rep2 Rv
mapped_integrations_-116kb_Sox2P_pools.txt

tag: cell type

tag: insert

tag: sorted gate

tag: sample type


title: Day4_Sox1+FoxA2-_Rep3

tag: time


description:
Sox2P-reporter -116 kb, population P5 pool3 rep2
E2282 Sox2P-reporter -116 kb, population P5 pool3 rep2 Rv
mapped_integrations_-116kb_Sox2P_pools.txt

tag: genotype

tag: launch pad_location


title: Day6_Sox1-FoxA2+_Rep3

value: Day 6


title: T103

tag: patient id

tag: fusion gene

tag: histology

value: Metastasis


title: Jurkat-J1, H3K27Ac, ChIP-seq

value: Vehicle (DMSO)

value: H3K27Ac Active Motif #39133


description:
Sox2P-reporter -116 kb, population P4 pool1 rep3
E2285 Sox2P-reporter -116 kb, population P4 pool1 rep3 Fw
mapped_integrations_-116kb_Sox2P_pools.txt

value: F1 hybrid 129/Sv:CAST/EiJ

value: mESC

value: WT


title: Day4_Sox1-FoxA2-_Rep3


title: T110

tag: tissue

value: Synovial Sarcoma

tag: tumor type

tag: site


title: Day4_Sox1+FoxA2+_Rep3

tag: cell line

tag: treatment

tag: facs sorted_cell_population


title: Day2_Sox1+FoxA2+_Rep3

value: Day 2


title: T54

description:
Sample_Counts.csv
Patient_Counts.csv

tag: metastasis time_(days)

tag: metastasis

tag: overall survival_time_(days)

tag: overal survival

tag: poorly differentiated_histology

value: No

tag: tumor size_(cm)


title: Jurkat-F15, ATAC-seq

data_processing:
The paired-end 42 bp sequencing reads (PE42) generated by Illumina sequencing were mapped to the genome using the BWA algorithm with default settings ("bwa mem").
Genomic regions with high transposition/tagging events were determined using the MACS3 peak calling algorithm (Zhang et al., Genome Biology 2008, 9: R137). The chromosome number and a start and end coordinate defined the genomic regions identified by MACS3 (Intervals).
To compare peak metrics between 2 or more samples, overlapping intervals were grouped into Merged Regions, defined by the start coordinate of the most upstream interval and the end coordinate of the most downstream interval (= union of overlapping intervals; "merged peaks"). This interval defines the Merged Region in locations where only one sample has an Interval. Merged Regions are necessary because the locations and lengths of Intervals are rarely the same when comparing different samples.
MACS 3.0.0 algorithm was used for peak calling. Threshold to identify statistically significant regions modulated : -0.5 ≤ shrunken LogFC ≤ 0.5 and p adjusted-value ≤ 0.05.
Assembly: mm10 and hg38
Supplementary files format and content: bigWig,chr-start-end-value, tag density files

extract_protocol:
Cell pellets were resuspended in lysis buffer, pelleted, and tagmented using the enzyme and buffer provided in the Nextera Library Prep Kit (Illumina). Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter).
Samples were quantified using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems) and sequenced with PE42 sequencing on the NextSeq 500 sequencer (Illumina).

treatment_protocol: WT vs KO_HDAC6 by CRISPR/Cas9 and Vehicle (DMSO) vs HDAC6i (ITF3756, 1uM, 16h) (n=3 biological replicates per group). Cells were cultured for 16h, then treated for 30 min at 37°C with 1X DNase buffer (200 units/mL in HBSS, 2.5 mM MgCl2, 0.5 mM CaCl2). Cells were countend and cryopreserved in 50% FBS, 40% growth media, 10% DMSO, frozen, and sent to Active Motif (Carlsbad, CA, USA) for analysis.

tag: cell type

value: HDAC6 inhibitor (ITF3756, 1uM, 16h)


description:
Sox2P-reporter -116 kb, population P5 pool1 rep2
E2282 Sox2P-reporter -116 kb, population P5 pool1 rep2 Rv
mapped_integrations_-116kb_Sox2P_pools.txt

tag: genotype

tag: launch pad_location

tag: insert

tag: sorted gate

tag: sample type

value: sorted pool


title: T67

tag: patient id

tag: fusion gene

tag: histology

tag: tissue

tag: tumor type


description:
Sox2P-reporter -116 kb, population P4 pool5 rep2
E2282 Sox2P-reporter -116 kb, population P4 pool5 rep2 Rv
mapped_integrations_-116kb_Sox2P_pools.txt

tag: cell line


description:
Sox2P-reporter -116 kb, population P1 pool1 rep3
E2285 Sox2P-reporter -116 kb, population P1 pool1 rep3 Fw
mapped_integrations_-116kb_Sox2P_pools.txt


title: Day2_Sox1-FoxA2+_Rep3

value: Mouse Embryonic Stem Cell

tag: treatment

value: Retinoic Acid Differentiation

tag: time

tag: facs sorted_cell_population


title: Jurkat-S15, ATAC-seq

value: Jurkat, Clone E6-1 (ATCC TIB-152)

value: T-lymphocyte, Acute leukemia


title: Jurkat-F14, ATAC-seq


title: Day2_Sox1-FoxA2-_Rep3


description:
Sox2P-reporter -116 kb, population P4 pool4 rep2
E2282 Sox2P-reporter -116 kb, population P4 pool4 rep2 Rv
mapped_integrations_-116kb_Sox2P_pools.txt


title: Day2_Sox1+FoxA2-_Rep3


title: Jurkat-S14, ATAC-seq


title: T66

value: Monophasic

tag: site

value: Peripheral


description:
Sox2P-reporter -116 kb, population P4 pool3 rep2
E2282 Sox2P-reporter -116 kb, population P4 pool3 rep2 Rv
mapped_integrations_-116kb_Sox2P_pools.txt


title: T53

value: Metastasis


title: Day0_Sox1-FoxA2-_Rep3

value: Day 0


description:
Sox2P-reporter -116 kb, population P5 pool2 rep2
E2282 Sox2P-reporter -116 kb, population P5 pool2 rep2 Rv
mapped_integrations_-116kb_Sox2P_pools.txt


title: Progeny_Day6_Sox1+FoxA2+_Rep3

value: Day 6


title: Jurkat-S13, ATAC-seq

value: Vehicle (DMSO)


description:
Sox2P-reporter -116 kb, population P4 pool3 rep3
E2285 Sox2P-reporter -116 kb, population P4 pool3 rep3 Rv
mapped_integrations_-116kb_Sox2P_pools.txt

value: F1 hybrid 129/Sv:CAST/EiJ

value: mESC


description:
Sox2P-reporter -116 kb, population P4 pool2 rep2
E2282 Sox2P-reporter -116 kb, population P4 pool2 rep2 Rv
mapped_integrations_-116kb_Sox2P_pools.txt

value: WT


title: T55

value: Synovial Sarcoma


title: T75


description:
Sox2P-reporter -116 kb, population P4 pool1 rep2
E2282 Sox2P-reporter -116 kb, population P4 pool1 rep2 Rv
mapped_integrations_-116kb_Sox2P_pools.txt


description:
Sox2P-reporter -116 kb, population P3 pool3 rep2
E2282 Sox2P-reporter -116 kb, population P3 pool3 rep2 Fw
mapped_integrations_-116kb_Sox2P_pools.txt


title: T74


title: Progeny_Day6_Sox1-FoxA2+_Rep3


title: Skeletal Muscle, Ischemic

city: Sydney

first: Mary

last: Kavurma

state: New South Whales

address: 7 Eliza Street, Newtown

country: Australia

institute: Heart Research Insitute

description: 10X Chromium

data_processing:
Demultiplexing, barcode processing, gene counting and agregation were performed by Cell Rnager software v7.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separate values files and matrix files

source_name: Skeletal muscle; Flexus hallucis longus

extract_protocol:
Skeletal muscle tissue was collected during surgery and prepared as described in Skelet Muscle. 2020;10:19. doi: 10.1186/s13395-020-00236-3
The library was performed according to manufacturer's instructions (single cell 3' v3 protocol, 10x Genomics). Briefly, cells were checked for viability before the cells were resuspended in the master mix and loaded with partitioning oil and gel beads to generate the gel-bead-in-emulsion (GEM). Poly-A RNA from cell lysates in each GEM were retrotranscipted to cDNA containg a unique molecular identifier (UMI), 10x barcode and Ilumina R1 primer sequences. cDNA was pooled and cleaned with Dynabeads, amplified by PCR and fragments of the appropriate size were selected by addition of SPRIreagent. Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequnces and a sample index were additionally added during library construction.

tag: Sex

value: Male

value: Skeletal muscle; Flexus hallucis longus

value: mononucelar cells

tag: disease state

value: Ischemic; diabetic


title: T48

description:
Sample_Counts.csv
Patient_Counts.csv

tag: metastasis time_(days)

tag: metastasis

tag: overall survival_time_(days)

tag: overal survival

tag: poorly differentiated_histology

value: Yes

tag: tumor size_(cm)


description:
Sox2P-reporter -116 kb, population P3 pool5 rep2
E2282 Sox2P-reporter -116 kb, population P3 pool5 rep2 Rv
mapped_integrations_-116kb_Sox2P_pools.txt

tag: cell type

tag: genotype

tag: launch pad_location

tag: insert

tag: sorted gate

tag: sample type

value: sorted pool


title: Skeletal Muscle, Non-ischemic

description: 10X Chromium

source_name: Skeletal muscle; Tibialis anterior

tag: tissue

value: Skeletal muscle; Tibialis anterior

value: mononuclear cells

value: Non-ischemic; diabetic


description:
Sox2P-reporter -116 kb, population P3 pool4 rep2
E2282 Sox2P-reporter -116 kb, population P3 pool4 rep2 Rv
mapped_integrations_-116kb_Sox2P_pools.txt

tag: cell line


description:
Sox2P-reporter -116 kb, population P3 pool2 rep2
E2282 Sox2P-reporter -116 kb, population P3 pool2 rep2 Rv
mapped_integrations_-116kb_Sox2P_pools.txt


title: Progeny_Day4_Sox1+FoxA2-_Rep3

value: Mouse Embryonic Stem Cell

tag: treatment

value: Retinoic Acid Differentiation

tag: time

value: Day 4

tag: facs sorted_cell_population


title: T65

tag: patient id

tag: fusion gene

tag: histology

value: Monophasic

tag: tumor type

value: Metastasis

tag: site

value: Peripheral


title: Progeny_Day4_Sox1+FoxA2+_Rep3


title: Progeny_Day6_Sox1+FoxA2-_Rep3

value: Day 6


title: Progeny_Day4_Sox1-FoxA2+_Rep3


title: Jurkat-F13, ATAC-seq

value: Jurkat, Clone E6-1 (ATCC TIB-152)

value: T-lymphocyte, Acute leukemia

value: HDAC6 inhibitor (ITF3756, 1uM, 16h)


description:
Sox2P-reporter -116 kb, population P3 pool3 rep2
E2282 Sox2P-reporter -116 kb, population P3 pool3 rep2 Rv
mapped_integrations_-116kb_Sox2P_pools.txt

value: F1 hybrid 129/Sv:CAST/EiJ

value: mESC

value: WT


description:
Sox2P-reporter -116 kb, population P2 pool5 rep2
E2282 Sox2P-reporter -116 kb, population P2 pool5 rep2 Rv
mapped_integrations_-116kb_Sox2P_pools.txt

value: sorted pool


title: T42

value: Synovial Sarcoma


title: T49

description:
Sample_Counts.csv
Patient_Counts.csv

tag: metastasis time_(days)

tag: metastasis

tag: overall survival_time_(days)

tag: overal survival

tag: poorly differentiated_histology

value: Yes

tag: tumor size_(cm)


title: T63

description:
Sample_Counts.csv
Patient_Counts.csv


title: T40

description:
Sample_Counts.csv
Patient_Counts.csv

value: No


description:
Sox2P-reporter -116 kb, population P2 pool4 rep2
E2282 Sox2P-reporter -116 kb, population P2 pool4 rep2 Rv
mapped_integrations_-116kb_Sox2P_pools.txt

tag: cell type

tag: genotype

tag: launch pad_location

tag: insert

tag: sorted gate

tag: sample type


description:
Sox2P-reporter -116 kb, population P3 pool1 rep2
E2282 Sox2P-reporter -116 kb, population P3 pool1 rep2 Rv
mapped_integrations_-116kb_Sox2P_pools.txt

tag: cell line


title: T46

description:
Sample_Counts.csv
Patient_Counts.csv

tag: patient id

tag: fusion gene

tag: tissue

value: visceral


title: T44

description:
Sample_Counts.csv
Patient_Counts.csv

tag: histology

tag: tumor type

tag: site


title: Progeny_Day6_Sox1+FoxA2+_Rep2

value: Mouse Embryonic Stem Cell

tag: treatment

value: Retinoic Acid Differentiation

tag: time

tag: facs sorted_cell_population


title: T43

description:
Sample_Counts.csv
Patient_Counts.csv

tag: metastasis time_(days)

tag: metastasis

tag: overall survival_time_(days)

tag: overal survival

value: Monophasic

tag: poorly differentiated_histology

tag: tumor size_(cm)


description:
Sox2P-reporter -116 kb, population P2 pool3 rep2
E2282 Sox2P-reporter -116 kb, population P2 pool3 rep2 Rv
mapped_integrations_-116kb_Sox2P_pools.txt

tag: cell type

tag: genotype

tag: launch pad_location

tag: insert

tag: sorted gate

tag: sample type


title: Progeny_Day4_Sox1-FoxA2+_Rep2

tag: cell line

value: Day 4


title: T57

tag: patient id

tag: fusion gene

tag: histology

value: Biphasic

tag: tissue

tag: tumor type

value: Metastasis

tag: site

value: Peripheral


title: Progeny_Day4_Sox1+FoxA2-_Rep2

tag: treatment

tag: time

tag: facs sorted_cell_population


title: Progeny_Day6_Sox1+FoxA2-_Rep2

value: Day 6


title: Progeny_Day6_Sox1-FoxA2+_Rep2


title: Progeny_Day4_Sox1+FoxA2+_Rep2


title: T73


description:
Sox2P-reporter -116 kb, population P2 pool2 rep2
E2282 Sox2P-reporter -116 kb, population P2 pool2 rep2 Rv
mapped_integrations_-116kb_Sox2P_pools.txt


title: GROseq_CH12_WT

data_processing:
library strategy: GRO-seq
base calling: illumina CASAVA 1.8.2
ChIP-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50
ChIP-Seq_density: filtering (uniquely aligned reads): samtools-0.1.19-1.2/samtools view -S -b -F4
ChIP-Seq_density: normalized tag density: custom script, maximum 2 reads with the same start position allowed
mRNA-Seq_density:alignment: gsnap --use-sarray=0 --novelsplicing=0 --use-splicing refseq.splices.iit --format=sam -B 4
mRNA-Seq_density: filtering: samtools-1.2/samtools view -S -b -F132 -q 20
mRNA-Seq density: normalized tag density: bedtools-2.25/genomeCoverageBed -ibam -bg -split -scale normalization_factor, ucsc-314/bedGraphToBigWig
Gro-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50 --trim5 2
Gro-Seq_density: filtering (uniquely aligned reads): samtools-1.2/samtools view -S -b -F4
Gro-Seq_density: normalized tag density: bedtools-2.25/genomeCoverageBed -ibam -bg -split -scale normalization_factor -strand, ucsc-314/bedGraphToBigWig
Assembly: mm9
Supplementary files format and content: bigwig

growth_protocol: CH12B cells were cultured in RPMI-1640 media (Gibco) supplemented with 10% Fetal Bovine Serum (Gibco), 1% Penicillin-Streptomycin (Gibco) and 50 µM β-mercaptoethanol (Gibco). CH12B cells were expanded in 2.8L baffled Fernbach flasks (PYREX™) at 37°C with 5% CO2.

extract_protocol:
Gro-seq:  Nuclei was extracted from 8-12 million cells grown on 10 cm plates and after run-on reaction the  RNA was extracted with Trizol LS Reagent (Invitrogen, Carlsbad, CA, USA). RNA was treated. ChIP-Seq: Cultured cells were fixed with 1% formaldehyde (Sigma) for 10’ at 37°C. Fixation was quenched by addition of glycine (Sigma) at a final concentration of 125mM. Twenty million fixed cells were washed with PBS and resuspended in 1ml of RIPA buffer (10mM Tris [pH 7.6], 1mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, 1× Complete Mini EDTA free proteinase inhibitor (Roche)) or stored at−80°C until further processing. Sonication was performed using Covaris S2 sonicator at duty cycle 20%, intensity 5, cycle/burst 200 for 30min or Branson sonifier at amplitude 35%, 12 cycles of 20” sonication and 30” of pause.   with TURBO DNase (Ambion), fragmented using RNA Fragmentation Reagents (Ambion) and  purified by running through P-30 column (Bio-Rad, Hercules, CA, USA). Fragmented RNA was  dephosphorylated with PNK (New England Biolabs, Ipswich, MA, USA) followed by heatinactivation.  Dephosphorylation reactions were purified using anti-BrdU beads (SantaCruz  Biotech, Santa Cruz, CA, USA) and precipitated overnight. Poly(A)-tailing and cDNA synthesis  was performed the next day as described in (Wang et al., 2011). However, for reverse  transcription oligos with custom barcodes (underlined) were used : 5’-Phos CA/TG/AC/GT  GATCGTCGGACTGTAGAACTCT /idSp/CAAGCAGAAGACGGCATACGA  TTTTTTTTTTTTTTTTTTTTVN-3'. After cDNA synthesis, Exonuclease I (New England  Biolabs; 30 min) was used to catalyze the removal of excess oligo. Enzyme was inactivated and  RNA hydrolyzed by alkaline treatment (100 mM NaOH) and heat (25 min, 95°C). The cDNA  fragments of were purified on a denaturing Novex 10% polyacrylamide TBE-urea gel  (Invitrogen). The recovered cDNA was circularized, linearized, amplified for 10-14 cycles. The  final product was ran on Novex 10%TBE gel, gel purified and cleaned-up using ChIP DNA  clean & Concentrator Kit (Zymo Research Corporation, Irvine, CA, USA).   mRNA-seq: Total  RNA  from  CH12  cells  was  isolated  by  Trizol  extraction. mRNA   was   then   isolated . ERCC-spike-in was added on some samples for quantative comparison between two conditions.
ChIP-Seq :  Library was prepared in Ovation SP Ultralow library system (Nugen). 50 cycles of sequencing data were acquired on the HiSeq 3000 or Novaseq 6000 (Illumina).   mRNA-seq: standard RNA-Seq   library   preparation   was performed following Illuminaǯs RNA-Seq protocol v2. 50 cycles of sequencing data were acquired on Novaseq 6000 (Illumina).  Gro-seq: 50 cycles of sequencing data were acquired on the HiSeq 2500 (Illumina).

treatment_protocol: biotag Chipseq: Med25 was PCR amplified with gene specific primers and Q5 High Fidelity polymerase (NEB) from cDNA of CH12 or primary activated B cells using Superscript III reverse transcription (Invitrogen). Biotag was cloned at the N-terminus of Med25 combined with P2A-mOrange or P2AGFP by stitch PCR. Stitch PCR products were cloned into the retroviral vector pMy using restriction digestion and ligation. Retroviral particles were produced in Platinum-A retroviral packaging cell line by transfecting the clones pMy vector in presence of Lipofectamine LTX and Plus reagent (Life Technologies). Infectious retrovirus was harvested 48 h post transfection. CH12 B cells were transduced with Vector1 (pMy-biotag-MED25-T2A-mOrange) and Vector2 (pMy-BirA-T2A-EGFP) by centrifugation for 90 min at 2,500 rpm, at 32oC in the presence of 6 mg/ml polybrene. After 6 h, cells were diluted to 0.2 million cells per ml using reconstituted RPMI medium. A second infection was performed in a similar manner. 48 hours after the second infection, B cells were harvested and GFP + mOrange double positive cells were sorted using a BD FACSAria III cell sorter (Becton Dickinson). Sorted cells (10-20 million) were activated, (1 M retinoic acid for 4 h) crosslinked for 10 min at 37oC with 1% (v/v) formaldehyde and quenched with 0.125 M glycine.

value: mouse lymphoma B cell


description:
Sox2P-reporter -116 kb, population P2 pool1 rep2
E2282 Sox2P-reporter -116 kb, population P2 pool1 rep2 Rv
mapped_integrations_-116kb_Sox2P_pools.txt

value: F1 hybrid 129/Sv:CAST/EiJ


title: B16-F10-W4, H3K27Ac, ChIP-seq

value: Skin melanoma, epithelial

value: Wild Type

tag: chip antibody

value: H3K27Ac Active Motif #39133


description:
Sox2P-reporter -116 kb, population P3 pool2 rep2
E2282 Sox2P-reporter -116 kb, population P3 pool2 rep2 Fw
mapped_integrations_-116kb_Sox2P_pools.txt

tag: cell type

value: mESC

value: WT

value: sorted pool


description:
Sox2P-reporter -116 kb, population P4 pool1 rep3
E2285 Sox2P-reporter -116 kb, population P4 pool1 rep3 Rv
mapped_integrations_-116kb_Sox2P_pools.txt

tag: genotype


title: B16-F10-Input

value: pool


title: B16-F10-K3, H3K27Ac, ChIP-seq


title: Progeny_Day6_Sox1+FoxA2+_Rep1

value: Mouse Embryonic Stem Cell


title: T39

description:
Sample_Counts.csv
Patient_Counts.csv

tag: metastasis time_(days)

tag: metastasis

tag: overall survival_time_(days)

tag: overal survival

tag: poorly differentiated_histology

value: No

tag: tumor size_(cm)

value: Synovial Sarcoma


title: Progeny_Day4_Sox1+FoxA2+_Rep1

tag: cell line

value: Retinoic Acid Differentiation

value: Day 4


description:
Sox2P-reporter -116 kb, unsorted control pool rep2
E2282 Sox2P-reporter -116 kb, unsorted control pool rep2 Fw
mapped_integrations_-116kb_Sox2P_pools.txt

tag: launch pad_location

tag: insert

tag: sorted gate

tag: sample type

value: control pool


description:
Sox2P-reporter -116 kb, population P1 pool1 rep2
E2282 Sox2P-reporter -116 kb, population P1 pool1 rep2 Rv
mapped_integrations_-116kb_Sox2P_pools.txt


title: Progeny_Day6_Sox1-FoxA2+_Rep1

tag: treatment


title: T45

description:
Sample_Counts.csv
Patient_Counts.csv

tag: patient id

tag: fusion gene

tag: histology

value: Monophasic

value: Yes

tag: tissue

tag: tumor type

tag: site

value: Peripheral


description:
Sox2P-reporter -116 kb, population P2 pool5 rep2
E2282 Sox2P-reporter -116 kb, population P2 pool5 rep2 Fw
mapped_integrations_-116kb_Sox2P_pools.txt

value: F1 hybrid 129/Sv:CAST/EiJ

tag: cell type

tag: genotype


title: Progeny_Day6_Sox1+FoxA2-_Rep1

tag: time

value: Day 6

tag: facs sorted_cell_population


description:
Sox2P-reporter -116 kb, population P2 pool4 rep2
E2282 Sox2P-reporter -116 kb, population P2 pool4 rep2 Fw
mapped_integrations_-116kb_Sox2P_pools.txt


title: Progeny_Day4_Sox1+FoxA2-_Rep1


title: B16-F10-K2, H3K27Ac, ChIP-seq

value: Skin melanoma, epithelial

tag: chip antibody


title: B16-F10-K4, ATAC-seq

tag: cell line


description:
Sox2P-reporter -116 kb, population P3 pool1 rep2
E2282 Sox2P-reporter -116 kb, population P3 pool1 rep2 Fw
mapped_integrations_-116kb_Sox2P_pools.txt

tag: launch pad_location


title: B16-F10-W3, H3K27Ac, ChIP-seq

value: Wild Type

value: H3K27Ac Active Motif #39133


title: T38

description:
Sample_Counts.csv
Patient_Counts.csv

tag: metastasis time_(days)

tag: metastasis

tag: overall survival_time_(days)

tag: overal survival

tag: poorly differentiated_histology

tag: tumor size_(cm)

value: Metastasis


title: Day4_Sox1+FoxA2+_Rep2

tag: treatment


title: Day4_Sox1-FoxA2+_Rep2


description:
Sox2P-reporter -116 kb, population P2 pool3 rep2
E2282 Sox2P-reporter -116 kb, population P2 pool3 rep2 Fw
mapped_integrations_-116kb_Sox2P_pools.txt

value: mESC

value: WT

tag: insert

tag: sorted gate

tag: sample type

value: sorted pool


title: T37

description:
Sample_Counts.csv
Patient_Counts.csv

tag: patient id

tag: fusion gene

tag: histology

value: No

tag: tissue

tag: tumor type

tag: site


title: T36

value: Biphasic

value: Synovial Sarcoma


title: T34

description:
Sample_Counts.csv
Patient_Counts.csv


description:
Sox2P-reporter -116 kb, population P2 pool2 rep2
E2282 Sox2P-reporter -116 kb, population P2 pool2 rep2 Fw
mapped_integrations_-116kb_Sox2P_pools.txt

tag: cell line

tag: cell type

tag: genotype

tag: launch pad_location


title: Progeny_Day4_Sox1-FoxA2+_Rep1

value: Mouse Embryonic Stem Cell

value: Retinoic Acid Differentiation

tag: time

value: Day 4

tag: facs sorted_cell_population


description:
Sox2P-reporter -116 kb, population P6 pool5 rep2
E2282 Sox2P-reporter -116 kb, population P6 pool5 rep2 Fw
mapped_integrations_-116kb_Sox2P_pools.txt


title: Day4_Sox1-FoxA2-_Rep2


title: B16-F10-K3, ATAC-seq


title: B16-F10-W3, ATAC-seq


title: T35


description:
Sox2P-reporter -116 kb, population P6 pool4 rep2
E2282 Sox2P-reporter -116 kb, population P6 pool4 rep2 Fw
mapped_integrations_-116kb_Sox2P_pools.txt


title: Day4_Sox1+FoxA2-_Rep2


title: B16-F10-W4, ATAC-seq


title: Day6_Sox1+FoxA2+_Rep2


description:
Sox2P-reporter -116 kb, population P6 pool3 rep2
E2282 Sox2P-reporter -116 kb, population P6 pool3 rep2 Fw
mapped_integrations_-116kb_Sox2P_pools.txt


title: T52

value: Monophasic


title: T23

description:
Sample_Counts.csv
Patient_Counts.csv

tag: metastasis time_(days)

tag: metastasis

tag: overall survival_time_(days)

tag: overal survival

tag: poorly differentiated_histology

tag: tumor size_(cm)

value: Peripheral


description:
Sox2P-reporter -116 kb, population P6 pool2 rep2
E2282 Sox2P-reporter -116 kb, population P6 pool2 rep2 Fw
mapped_integrations_-116kb_Sox2P_pools.txt

value: F1 hybrid 129/Sv:CAST/EiJ

tag: insert

tag: sorted gate

tag: sample type


title: B16-F10-W2, H3K27Ac, ChIP-seq

tag: treatment

tag: chip antibody


title: Wildtype TrailEC-/- Ischemic

description:
EC_TKO_HLI
10X Chromium

data_processing:
Demultiplexing, barcode processing, gene counting and agregation were performed by Cell Rnager software v7.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
The 20,000 cells with the highest UMI counts were used for analysis in the EC_TKO_HLI as a result of cell viability
Assembly: mm10-2020-A
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: gastrocnemius muscle collected 14 d after hindlimb ischemia surgery

extract_protocol:
gastrocnemius were colleceted and prepared as described in Skelet Muscle. 2020;10:19. doi: 10.1186/s13395-020-00236-3
The library was performed according to manufacturer's instructions (single cell 3' v3 protocol, 10x Genomics). Briefly, cells were checked for viability before the cells were resuspended in the master mix and loaded with partitioning oil and gel beads to generate the gel-bead-in-emulsion (GEM). Poly-A RNA from cell lysates in each GEM were retrotranscipted to cDNA containg a unique molecular identifier (UMI), 10x barcode and Ilumina R1 primer sequences. cDNA was pooled and cleaned with Dynabeads, amplified by PCR and fragments of the appropriate size were selected by addition of SPRIreagent. Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequnces and a sample index were additionally added during library construction.

treatment_protocol: Hindlimb ischemia surgery in adult mice. Mice euthanised 14 days later; Gatrocnemius isolated; single cell suspension and cryopresereved prior to 10X chromium

tag: tissue

value: mononuclear cells

value: Trail-/-, VECre/+ 2/genotype/sex (total n=4 pooled)

tag: strain


title: B16-F10-K2, ATAC-seq

tag: cell line

tag: cell type

value: Skin melanoma, epithelial


title: Day6_Sox1-FoxA2+_Rep2

tag: time

value: Day 6


title: T17

description:
Sample_Counts.csv
Patient_Counts.csv

tag: patient id

tag: fusion gene

tag: histology

tag: tumor type

tag: site


description:
Sox2P-reporter -116 kb, population P6 pool1 rep2
E2282 Sox2P-reporter -116 kb, population P6 pool1 rep2 Fw
mapped_integrations_-116kb_Sox2P_pools.txt

tag: genotype

tag: launch pad_location


title: Day6_Sox1+FoxA2-_Rep2

tag: facs sorted_cell_population


title: T28

value: Metastasis


title: T25

description:
Sample_Counts.csv
Patient_Counts.csv

tag: metastasis time_(days)

tag: metastasis

tag: overall survival_time_(days)

tag: overal survival

tag: poorly differentiated_histology

tag: tumor size_(cm)


description:
Sox2P-reporter -116 kb, population P5 pool5 rep2
E2282 Sox2P-reporter -116 kb, population P5 pool5 rep2 Fw
mapped_integrations_-116kb_Sox2P_pools.txt

tag: cell line

value: mESC

tag: insert

tag: sorted gate

tag: sample type


title: T16

description:
Sample_Counts.csv
Patient_Counts.csv

tag: patient id

tag: fusion gene

value: Yes

tag: tissue


description:
Sox2P-reporter -116 kb, population P5 pool4 rep2
E2282 Sox2P-reporter -116 kb, population P5 pool4 rep2 Fw
mapped_integrations_-116kb_Sox2P_pools.txt

tag: cell type

value: WT

value: sorted pool


title: Day0_Sox1-FoxA2-_Rep2

tag: treatment

tag: time

value: Day 0


title: T26

tag: histology

value: Synovial Sarcoma

tag: tumor type

tag: site


title: Day2_Sox1+FoxA2+_Rep2

value: Mouse Embryonic Stem Cell

value: Day 2

tag: facs sorted_cell_population


description:
Sox2P-reporter -116 kb, population P2 pool1 rep2
E2282 Sox2P-reporter -116 kb, population P2 pool1 rep2 Fw
mapped_integrations_-116kb_Sox2P_pools.txt

tag: genotype

tag: launch pad_location


title: Wildtype TrailEC+/+ Ischemic

description:
EC_WT_HLI
10X Chromium

value: gastrocnemius muscle collected 14 d after hindlimb ischemia surgery

value: Trail+/+, VECre/+ n=2/genotype/sex (total n=4 pooled)

tag: strain


title: T83

description:
Sample_Counts.csv
Patient_Counts.csv

tag: metastasis time_(days)

tag: metastasis

tag: overall survival_time_(days)

tag: overal survival

value: Monophasic

tag: poorly differentiated_histology

tag: tumor size_(cm)

value: Peripheral


title: B16-F10-W2, ATAC-seq

tag: cell line

value: Wild Type


title: 33_3700wt_Nissle_epithelial_cells

city: Gent

first: Lars

last: Vereecke

address: Technologiepark-Zwijnaarde 927

department: IRC

country: Belgium

institute: VIB

data_processing:
Sequence reads were extracted from UMI’s and deduplicated using UMI-Tools v1.14 (BCPattern:"(?P<umi_1>.{6})(?P<discard_1>.{4}).*") as recommended by the Library Prep Kit
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v0.39 (Leading:20 , Trailing:20, SlidingWindow:4:20, MinLen:37,-phred33, IlluminaClip:Trimmomatic-0.39/adapters/TruSeq3-SE.fa:2:30:10)
Trimmed reads were mapped to GRCm39 using STAR v2.7.10b (--alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --outFilterMultimapNmax 20 --outFilterType BySJout --outFilterMismatchNoverLmax 0.1 --clip3pAdapterSeq AAAAAAAA) as recommended by the Library Prep Kit
Read count extraction was done using FeatureCounts v2.0.6
Assembly: GRCm39 (Ensembl release 109)
Supplementary files format and content: comma-seperated file includes raw deduplicated counts for each Sample

source_name: colon

growth_protocol: Mice were housed in individually ventilated cages at the VIB Center of Inflammation Research in a specific pathogen-free animal facility.

extract_protocol:
RNA was extracted by Trizol (Invitrogen) and 12 ng input RNA was used for library preparation.
RNA libraries for RNA-seq were prepared using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD by NXTGNT following manufacturer’s protocols

treatment_protocol: 6 week old mice were administered 20 mg streptomycin by oral gavage 24h before infection. Mice were orally challenged with 10^8 CFU of Nisse or 11G5 and followed up for 28 days. Colon was dissected and flushed with 1x PBS and tumors were dissociated using a mouse tumor dissociation kit (Miltenyi) according to the manufacturer's instructions. Total viable cells were sorted using anti-CD326 and anti-CD45 antibodies.

tag: tissue

value: colon

tag: cell type

value: epithelial cells

tag: condition

value: Nissle 1917


description:
Sox2P-reporter -116 kb, population P5 pool3 rep2
E2282 Sox2P-reporter -116 kb, population P5 pool3 rep2 Fw
mapped_integrations_-116kb_Sox2P_pools.txt

value: F1 hybrid 129/Sv:CAST/EiJ

tag: insert

tag: sorted gate

tag: sample type


title: T24

tag: patient id

tag: fusion gene

tag: histology

tag: tumor type

value: Metastasis

tag: site


title: 31_3699wt_Nissle_epithelial_cells

tag: genotype


title: Day2_Sox1+FoxA2-_Rep2

tag: treatment

value: Retinoic Acid Differentiation

tag: time

tag: facs sorted_cell_population


title: T30


title: Day2_Sox1-FoxA2-_Rep2


description:
Sox2P-reporter -116 kb, population P5 pool1 rep2
E2282 Sox2P-reporter -116 kb, population P5 pool1 rep2 Fw
mapped_integrations_-116kb_Sox2P_pools.txt

value: mESC

value: WT

tag: launch pad_location


description:
Sox2P-reporter -116 kb, population P5 pool2 rep2
E2282 Sox2P-reporter -116 kb, population P5 pool2 rep2 Fw
mapped_integrations_-116kb_Sox2P_pools.txt

tag: cell line

value: sorted pool


title: 29_3792wt_Nissle_epithelial_cells

tag: tissue


title: Wildtype TrailEC-/- Control

description:
EC_TKO_Ctrl
10X Chromium

tag: cell type

value: mononuclear cells

value: Trail-/-, VECre/+ 2/genotype/sex (total n=4 pooled)

tag: strain


title: T29

value: Synovial Sarcoma


title: Day6_Sox1-FoxA2-_Rep2

value: Mouse Embryonic Stem Cell

value: Day 6


title: Day2_Sox1+FoxA2+_Rep1

value: Day 2


description:
Sox2P-reporter -116 kb, population P4 pool5 rep2
E2282 Sox2P-reporter -116 kb, population P4 pool5 rep2 Fw
mapped_integrations_-116kb_Sox2P_pools.txt

tag: insert


title: T15

description:
Sample_Counts.csv
Patient_Counts.csv

tag: metastasis time_(days)

tag: metastasis

tag: overall survival_time_(days)

tag: overal survival

value: Monophasic

tag: poorly differentiated_histology

value: No

tag: tumor size_(cm)

value: Peripheral


title: Wildtype TrailEC+/+ Control

description:
EC_WT_Ctrl
10X Chromium

value: gastrocnemius muscle collected 14 d after hindlimb ischemia surgery

value: Trail+/+, VECre/+ n=2/genotype/sex (total n=4 pooled)


title: 28_5089wt_CCR20_CD45_cells

value: colon

value: immune cells

tag: condition


description:
Sox2P-reporter -116 kb, unsorted control pool rep2
E2282 Sox2P-reporter -116 kb, unsorted control pool rep2 Rv
mapped_integrations_-116kb_Sox2P_pools.txt

value: F1 hybrid 129/Sv:CAST/EiJ

tag: genotype

tag: sorted gate

tag: sample type

value: control pool


title: T11

tag: patient id

tag: fusion gene

tag: histology

tag: tumor type

tag: site


title: Day2_Sox1-FoxA2+_Rep2

tag: cell line

tag: cell type

tag: treatment

value: Retinoic Acid Differentiation

tag: time

tag: facs sorted_cell_population


title: T22

description:
Sample_Counts.csv
Patient_Counts.csv

tag: metastasis time_(days)

tag: metastasis

tag: overall survival_time_(days)

tag: overal survival

value: Yes

tag: tissue


title: Day2_Sox1+FoxA2-_Rep1


title: 23_3695wt_CCR20_epithelial_cells

value: epithelial cells

tag: genotype

value: WT

tag: condition


title: Day2_Sox1-FoxA2-_Rep1


title: 30_32_34_Nissle_CD45_cells

value: Nissle 1917


title: 27_5089wt_CCR20_epithelial_cells


title: T31

tag: patient id

value: Synovial Sarcoma

value: Metastasis


description:
Sox2P-reporter -116 kb, population P4 pool3 rep2
E2282 Sox2P-reporter -116 kb, population P4 pool3 rep2 Fw
mapped_integrations_-116kb_Sox2P_pools.txt

value: mESC

tag: launch pad_location

tag: insert

tag: sorted gate

tag: sample type

value: sorted pool


title: T10

description:
Sample_Counts.csv
Patient_Counts.csv

tag: fusion gene

tag: histology

value: Monophasic

tag: poorly differentiated_histology

tag: tumor size_(cm)

tag: tumor type

tag: site


title: 22_3794tg_Nissle_CD45_cells

tag: cell type

value: TG (Zeb2IEC-tg/+)


title: T21

description:
Sample_Counts.csv
Patient_Counts.csv

tag: metastasis time_(days)

tag: metastasis

tag: overall survival_time_(days)

value: No

value: Peripheral


title: 24_3695wt_CCR20_CD45_cells

tag: tissue

value: colon

tag: genotype


description:
Sox2P-reporter -116 kb, population P4 pool2 rep2
E2282 Sox2P-reporter -116 kb, population P4 pool2 rep2 Fw
mapped_integrations_-116kb_Sox2P_pools.txt

tag: cell line


title: Day4_Sox1-FoxA2+_Rep1

value: Mouse Embryonic Stem Cell

tag: treatment

tag: time

value: Day 4

tag: facs sorted_cell_population


title: T6

tag: patient id


title: Day4_Sox1+FoxA2+_Rep1


title: 21_3794tg_Nissle_epithelial_cells

tag: condition


description:
Sox2P-reporter -116 kb, population P4 pool4 rep2
E2282 Sox2P-reporter -116 kb, population P4 pool4 rep2 Fw
mapped_integrations_-116kb_Sox2P_pools.txt

value: F1 hybrid 129/Sv:CAST/EiJ

tag: launch pad_location

tag: insert

tag: sorted gate

tag: sample type


title: Day2_Sox1-FoxA2+_Rep1

value: Retinoic Acid Differentiation

value: Day 2


description:
Sox2P-reporter -116 kb, population P4 pool1 rep2
E2282 Sox2P-reporter -116 kb, population P4 pool1 rep2 Fw
mapped_integrations_-116kb_Sox2P_pools.txt


title: T18

tag: fusion gene

tag: histology

tag: tumor type

tag: site


title: 19_3793tg_Nissle_epithelial_cells

tag: cell type

value: epithelial cells


title: Day6_Sox1+FoxA2+_Rep1

value: Day 6


title: Day4_Sox1+FoxA2-_Rep1


title: 20_3793tg_Nissle_CD45_cells

tag: tissue

value: immune cells

value: Nissle 1917


description:
Sox2P-reporter -116 kb, population P6 pool4 rep2
E2282 Sox2P-reporter -116 kb, population P6 pool4 rep2 Rv
mapped_integrations_-116kb_Sox2P_pools.txt

tag: genotype

value: WT


title: Day4_Sox1-FoxA2-_Rep1

tag: cell line


title: T5

value: Synovial Sarcoma

value: Metastasis


title: T3

value: Monophasic


title: 18_5092tg_Nissle_CD45_cells

value: TG (Zeb2IEC-tg/+)


description:
Sox2P-reporter -116 kb, population P6 pool5 rep2
E2282 Sox2P-reporter -116 kb, population P6 pool5 rep2 Rv
mapped_integrations_-116kb_Sox2P_pools.txt

value: mESC

value: sorted pool


description:
Sox2P-reporter -116 kb, population P6 pool3 rep2
E2282 Sox2P-reporter -116 kb, population P6 pool3 rep2 Rv
mapped_integrations_-116kb_Sox2P_pools.txt


title: T1

description:
Sample_Counts.csv
Patient_Counts.csv

tag: metastasis time_(days)

tag: metastasis

tag: overall survival_time_(days)

tag: overal survival

tag: poorly differentiated_histology

value: Yes

tag: tumor size_(cm)

value: Peripheral


title: Day6_Sox1-FoxA2+_Rep1

value: Mouse Embryonic Stem Cell

tag: treatment

tag: time

tag: facs sorted_cell_population


title: Day6_Sox1+FoxA2-_Rep1


description:
Sox2P-reporter -116 kb, population P6 pool2 rep2
E2282 Sox2P-reporter -116 kb, population P6 pool2 rep2 Rv
mapped_integrations_-116kb_Sox2P_pools.txt

value: F1 hybrid 129/Sv:CAST/EiJ

tag: launch pad_location

tag: insert

tag: sorted gate

tag: sample type


title: 17_5092tg_Nissle_epithelial_cells

value: colon

tag: cell type

tag: condition


title: 16_5091tg_Nissle_CD45_cells

tag: tissue

tag: genotype


title: HeLa crosslinked MED1 DFF-ChIP Rep2

city: Iowa City

first: David

last: Price

state: Iowa

address: 500 Newton Road, 260 EMRB

institute: University of Iowa

data_processing:
Adapter trimming using trim_galore 0.6.
Alignment of trimmed reads to hg38 using bowtie 1.2.2.
Deduplication of fragments based on their unique molecular index tags using awk and bash.
Conversion of deduped bed files into bedGraph and bigwig using bedtools genomecov and kentUtils bedGraphToBigWig programs.
Assembly: hg38, mm39
Supplementary files format and content: bigwig files containing pileup of DFF ChIP-Seq fragments across whole genomes. Supplementary files are combined replicate bigwigs and bedfiles indicating regions found in analyses (CC, motifs found in CCs, peaks, motifs found near peaks)

source_name: HeLa

growth_protocol: SUP-B15 cells were grown in RPMI 1640 media supplemented with 10% FBS. 4T1 cells and HeLa cells were grown in DMEM (Gibco 11965-092) supplemented with 10% FBS.

extract_protocol:
Rapid nuclei isolation steps were performed on wet ice using ice-cold buffers as previously described (Nilson et al. 2017; Ball et al. 2019). Prior to digestion, spike-in 4T1 nuclei were mixed with SUP-B15 nuclei for DFF-ChIP. Following DFF digestion, nuclei were lightly sonicated for 20s and the soluble material was immunoprecipitated with 2.5 - 5 µg of antibodies.
Library construction is detailed in the manuscript.

tag: cell line

value: HeLa

tag: chip antibody

value: MED1:A300-793A Bethyl Labs


title: Day6_Sox1-FoxA2-_Rep1

value: Retinoic Acid Differentiation

value: Day 6


description:
Sox2P-reporter -116 kb, population P6 pool1 rep2
E2282 Sox2P-reporter -116 kb, population P6 pool1 rep2 Rv
mapped_integrations_-116kb_Sox2P_pools.txt


title: HeLa crosslinked MED1 DFF-ChIP Rep1


description:
Sox2P-reporter -116 kb, population P5 pool5 rep2
E2282 Sox2P-reporter -116 kb, population P5 pool5 rep2 Rv
mapped_integrations_-116kb_Sox2P_pools.txt


title: 15_5091tg_Nissle_epithelial_cells

value: epithelial cells

value: Nissle 1917


title: Day0_Sox1-FoxA2-_Rep1

value: Day 0


title: 14_5090tg_Nissle_CD45_cells

value: immune cells


description:
Sox2P-reporter -116 kb, population P3 pool5 rep2
E2282 Sox2P-reporter -116 kb, population P3 pool5 rep2 Fw
mapped_integrations_-116kb_Sox2P_pools.txt

value: WT


title: I/R 3day3

city: New haven

first: Yilin

last: Yang

state: CONNECTICUT

address: 300 Cedar street, S220

institute: yale university

data_processing:
Reads were trimmed using Trim Galore (v0.5.0) and mapped to the mouse reference genome (mm10) using HISAT2 (v2.1.0).  Gene expression levels were quantified using StringTie (v1.3.3b) with gene models (v27) from the GENCODE project.Differentially expressed genes (DEGs) were identified using DESeq2 (v1.22.1)
Assembly: mm10
Supplementary files format and content: xls file of normalized count

source_name: liver lymphatic endothelial cell

extract_protocol:
For RNA-seq analysis, 2 to 5×104 LyECs were sorted directly into 500 µl of TRIzol reagent and total RNA was extracted.
rRNA depletion library

value: liver lymphatic endothelial cell

value: I/R


title: HeLa native MED1 DFF-ChIP Rep2


description:
Sox2P-reporter -116 kb, population P3 pool4 rep2
E2282 Sox2P-reporter -116 kb, population P3 pool4 rep2 Fw
mapped_integrations_-116kb_Sox2P_pools.txt

value: mESC

value: sorted pool


description:
Sox2P-reporter -116 kb, population P1 pool1 rep2
E2282 Sox2P-reporter -116 kb, population P1 pool1 rep2 Fw
mapped_integrations_-116kb_Sox2P_pools.txt


title: 13_5090tg_Nissle_epithelial_cells

value: TG (Zeb2IEC-tg/+)


title: HeLa crosslinked DSIF DFF-ChIP Rep2


title: I/R 3day1


title: 12_3698tg_CCR20_CD45_cells


description:
Sox2P-reporter -116 kb, population P5 pool2 rep1
E2138 Sox2P-reporter -116 kb, population P5 pool2 rep1 Rv
mapped_integrations_-116kb_Sox2P_pools.txt


title: Sham3

value: Sham


title: HeLa crosslinked DSIF DFF-ChIP Rep1


title: 11_3698tg_CCR20_epithelial_cells


title: 10_5087wt_CCR20_CD45_cells


title: Sham2


description:
Sox2P-reporter -116 kb, population P5 pool1 rep1
E2138 Sox2P-reporter -116 kb, population P5 pool1 rep1 Rv
mapped_integrations_-116kb_Sox2P_pools.txt

value: F1 hybrid 129/Sv:CAST/EiJ


title: HeLa native DSIF DFF-ChIP Rep1


description:
Sox2P-reporter -116 kb, population P4 pool4 rep1
E2138 Sox2P-reporter -116 kb, population P4 pool4 rep1 Rv
mapped_integrations_-116kb_Sox2P_pools.txt


description:
Sox2P-reporter -116 kb, population P4 pool3 rep1
E2138 Sox2P-reporter -116 kb, population P4 pool3 rep1 Rv
mapped_integrations_-116kb_Sox2P_pools.txt


title: HeLa crosslinked NELF DFF-ChIP Rep2


title: 8_5086tg_CCR20_CD45_cells

value: colon


title: HeLa crosslinked NELF DFF-ChIP Rep1

value: HeLa


description:
Sox2P-reporter -116 kb, population P4 pool1 rep1
E2138 Sox2P-reporter -116 kb, population P4 pool1 rep1 Rv
mapped_integrations_-116kb_Sox2P_pools.txt


title: replicate_9_AP1067_COT

city: Houston

first: Lanlan

last: Shen

state: Texas

address: 1100 Bates Ave

department: Pediatrics

institute: Baylor College of Medicine

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Supplementary files format and content: mm10
Supplementary files format and content: matrix files

source_name: Colon tumor

extract_protocol:
Adjacent mucosa were dissociated by 9mM EDTA for 1h, and then followed by TrypLE™ Express Enzyme (1X) (ThermoFisher Scientific) incubation (37°C, 5min) to dissociate intosingle cells. Colon tumor cells were dissociated using the Miltenyi Biotec MACS Tumor Dissociation Kit (Miltenyi Biotec) according to manufacturer instructions. Colon tumors and adjacent mucosa tissues were collected and processed on the same day for scRNA-seq.
Single cell Gene Expression Library was prepared according to Chromium Single Cell Gene Expression 3v3.1 kit (10x Genomics). In Brief, single cells, reverse transcription (RT) reagents, Gel Beads containing barcoded oligonucleotides, and oil were loaded on a Chromium controller (10x Genomics) to generate single cell GEMS (Gel Beads-In-Emulsions) where full length cDNA was synthesized and barcoded for each single cell. Subsequently the GEMS are broken and cDNA from each single cell are pooled. Following cleanup using Dynabeads MyOne Silane Beads, cDNA is amplified by PCR.  The amplified product is fragmented to optimal size before end-repair, A-tailing, and adaptor ligation. Final library was generated by amplification.

value: Colon tumor

tag: strain

value: ApcMin/+; p16cis/cis

tag: Sex

value: Female

tag: age

value: 23 wks

value: supplemented diet


title: HeLa native NELF DFF-ChIP Rep2


description:
Sox2P-reporter -116 kb, population P4 pool2 rep1
E2138 Sox2P-reporter -116 kb, population P4 pool2 rep1 Rv
mapped_integrations_-116kb_Sox2P_pools.txt


title: replicate_8_AP1044_COT

description: 10x Genomics

value: 24 wks


title: HeLa native DSIF DFF-ChIP Rep2


title: 5_5085wt_CCR20_epithelial_cells

value: epithelial cells


title: 4_3697tg_CCR20_CD45_cells

value: immune cells


title: I/R 3day2

value: liver lymphatic endothelial cell


title: replicate_10_AP1067_COT

description: 10x Genomics


description:
Sox2P-reporter -116 kb, population P3 pool3 rep1
E2138 Sox2P-reporter -116 kb, population P3 pool3 rep1 Rv
mapped_integrations_-116kb_Sox2P_pools.txt

value: WT


title: replicate_7_AP1044_COT

description: 10x Genomics

value: Male


title: replicate_6_AP1044_COT

description: 10x Genomics


title: HeLa crosslinked CTCF DFF-ChIP Rep2


title: HeLa crosslinked CTCF DFF-ChIP Rep1


description:
Sox2P-reporter -116 kb, population P3 pool2 rep1
E2138 Sox2P-reporter -116 kb, population P3 pool2 rep1 Rv
mapped_integrations_-116kb_Sox2P_pools.txt

value: mESC

value: sorted pool


title: 3_3697tg_CCR20_epithelial_cells

value: TG (Zeb2IEC-tg/+)


title: HeLa native CTCF DFF-ChIP Rep2


title: replicate_5_AP1044_COT

description: 10x Genomics


description:
Sox2P-reporter -116 kb, population P3 pool1 rep1
E2138 Sox2P-reporter -116 kb, population P3 pool1 rep1 Rv
mapped_integrations_-116kb_Sox2P_pools.txt

value: F1 hybrid 129/Sv:CAST/EiJ


description:
Sox2P-reporter -116 kb, population P3 pool4 rep1
E2138 Sox2P-reporter -116 kb, population P3 pool4 rep1 Rv
mapped_integrations_-116kb_Sox2P_pools.txt


title: replicate_4_AP1086_COT

description: 10x Genomics

value: 20 wks


title: 7_5086tg_CCR20_epithelial_cells

value: colon


title: Sham1

value: Sham


title: 1_3694tg_CCR20_epithelial_cells


title: replicate_3_AP1086_COT

description: 10x Genomics

value: Colon tumor

value: ApcMin/+; p16cis/cis


description:
Sox2P-reporter -116 kb, population P3 pool4 rep1
E2138 Sox2P-reporter -116 kb, population P3 pool4 rep1 Fw
mapped_integrations_-116kb_Sox2P_pools.txt


description:
Sox2P-reporter -116 kb, population P2 pool3 rep1
E2138 Sox2P-reporter -116 kb, population P2 pool3 rep1 Rv
mapped_integrations_-116kb_Sox2P_pools.txt


title: SUP-B15 crosslinked glucocorticoid receptor DFF-ChIP Rep2

value: 1 µM dexamethosone


title: SUP-B15 crosslinked glucocorticoid receptor DFF-ChIP Rep1


title: replicate_2_AP1086_COT

description: 10x Genomics

value: Female

value: supplemented diet


title: HeLa native NELF DFF-ChIP Rep1

value: HeLa


title: 9_5087wt_CCR20_epithelial_cells

value: epithelial cells


title: EEC, corticosterone, D9, 5

city: Aurora

first: Nickole

last: Moon

state: CO

address: 12700 East 19th Avenue, RC2, Rm 9480

institute: University of Colorado

data_processing:
FASTQ files were processed for pseudoalignment and abundance quantification of reads to the Mus musculus reference transcriptome (version 38) using Kallisto.
Our DC2 RNA sequencing pipeline was designed using the DIY Transcriptomics framework.
Genes included in the analysis had >1 counts per million in at least 4 samples.
Gene expression distributions were normalized using Bioconductor package edgeR (version 3.40.1).
The limma Bioconductor package (version 3.54.0) function voom was used for normalization.
Assembly: mm10
Supplementary files format and content: The processed file includes the log2 counts per million of the normalized expression data.
Supplementary files format and content: There is no second processed data file.

growth_protocol: Cells were seeded in on plates coated collagen type 1, rat tail (Millipore, C3867). Cells were grown in Iscove’s Modified Dulbecco’s Medium (IMDM) (Gibco, 12440061) supplemented with 10% fetal bovine serum (Gibco, 26140079) and 1% penicillin-streptomycin (Gibco, 15070063).

extract_protocol:
Total RNA extraction from DC2 cell pellets was done using the TRIzol reagent (Thermo Fisher, 15596026) according to manufacturer’s protocol.
Libraries for RNA-seq were made using a TruSeq Stranded mRNA Sample Preparation Kit (Illumina) with 500 ng RNA. All library sizes and concentrations were confirmed on a TapeStation 4200 (Agilent) and Qubit 3.0 Fluorometer (Thermo Fisher).

treatment_protocol: At monolayer confluency, the media was replaced, and cells were either treated with 1:1000 vehicle (ethanol; resulting in 0.1% ethanol) or 1:1000 corticosterone in ethanol (Cayman Chemical, 16063; 1.4mM, resulting in 500 ng/ml of corticosterone). The media was replaced 72 hours (day 3) and 144 h (day 6) following the treatment. Depending on the experiment, cells were collected at media changes prior to treatment, immediately following treatment on day 3, after 3 days of recovery on day 6, or after 6 days of recovery on day 9.

value: epididymal epithelial cell

tag: day

value: corticosterone


title: replicate_1_AP1086_COT

description: 10x Genomics

value: Male

tag: treatment


title: SUP-B15 native glucocorticoid receptor DFF-ChIP Rep2


description:
Sox2P-reporter -116 kb, population P2 pool4 rep1
E2138 Sox2P-reporter -116 kb, population P2 pool4 rep1 Rv
mapped_integrations_-116kb_Sox2P_pools.txt

value: mESC

value: WT


title: EEC, corticosterone, D9, 4


title: HeLa native MED1 DFF-ChIP Rep1

value: MED1:A300-793A Bethyl Labs


title: EEC, corticosterone, D9, 6


title: 2_3694tg_CCR20_CD45_cells

value: immune cells

value: TG (Zeb2IEC-tg/+)


title: SUP-B15 native glucocorticoid receptor DFF-ChIP Rep1


title: replicate_3_AP1067_Adj

description: 10x Genomics

source_name: Adjacent mucosa

value: Adjacent mucosa

value: 23 wks


description:
Sox2P-reporter -116 kb, population P2 pool2 rep1
E2138 Sox2P-reporter -116 kb, population P2 pool2 rep1 Rv
mapped_integrations_-116kb_Sox2P_pools.txt

value: F1 hybrid 129/Sv:CAST/EiJ

value: sorted pool


description:
Sox2P-reporter -116 kb, population P2 pool1 rep1
E2138 Sox2P-reporter -116 kb, population P2 pool1 rep1 Rv
mapped_integrations_-116kb_Sox2P_pools.txt


title: EEC, corticosterone, D9, 3


title: EEC, corticosterone, D6, 6


title: HeLa native CTCF DFF-ChIP Rep1


title: replicate_2_AP1044_Adj

description: 10x Genomics

value: ApcMin/+; p16cis/cis

value: 24 wks


title: replicate_1_AP1086_Adj

description: 10x Genomics

value: Female

value: 20 wks

value: supplemented diet


title: Polysome fractions – G5OV treatment – Rep4

city: Madrid

first: Encarnacion

last: Martinez-Salas

state: Madrid

address: Nicolás Cabrera 1

country: Spain

institute: Centro de Biologia Molecular Severo Ochoa, CSIC-UAM

description: RNA isolated from polysome fractions of HEK-293 cells transfected with the plasmid pcDNA3Xpress-Gemin5 – Rep4

data_processing:
Sequences were aligned against the human reference genome GRCh38 downloaded from Ensembl release 108 using STAR aligner (version 2.7.10a)
Reads aligning in the reversely stranded sense (2) for each gene of GRCh38 GFF file downloaded from Ensembl release 108 were quantified with the function featureCounts (ignoreDup=TRUE, primaryOnly=TRUE, requireBothEndsMapped=TRUE) of Bioconductor package Rsubread.
Splicing event inclusion levels obtained with vast-tools (version 2.5.1) out using the annotations of Homo sapiens (hg38) available in VastDB (23/06/2020) and the default parameters.
Assembly: GRCh38
Supplementary files format and content: Tab delimited file with raw gene counts for all genes and samples.
Supplementary files format and content: Tab delimited file of alternative splicing inclusion table for all samples.

growth_protocol: HEK293 cells and Gemin5 overexpression cells grown in DMEM medium

extract_protocol:
1 P100 cells per gradient were incubated with 0.1 mg/mL cycloheximide for 10 min on ice to block ribosomes in the elongation step. Then, cells were washed twice with 0.1 mg/mL cycloheximide in cold PBS ad lysed in buffer A (15 mM Tris-HCl pH 7.4, 80 mM KCl, 5 mM MgCl2, 0.1 mg/ml cycloheximide) supplemented with 1% (v/v) Triton X-100, 40 U/ml RNase OUT (Thermo Fisher Scientific), and protease inhibitors (Complete mini, Roche). The lysates were centrifuged 10 min at 14000 g, 4ºC and the clear supernatants were loaded into a linear 10-50% (w/v) sucrose gradient prepared previously in buffer A, and the loaded sucrose gradients were centrifuged at 39000 rpm using a SW40 Ti rotor during 2 h 15 min at 4ºC. The sucrose gradients were fractionated using a fractionation system (ISCO UA-5 UV monitor) measuring the absorbance at A260 to record the polysome profile. Twelve fractions (1 ml) were collected from each gradient. RNA from cytoplasmic lysates and polysomal fractions (8-12) was extracted using phenol-chloroform, isopropanol precipitated, and resuspended in RNase-free H2O. RNA samples were cleaned with the RNeasy kit (Qiagen). RNA quality and concentration was determined using Agilent 2100 Bioanalyzer (Agilent Technologies).
cDNA libraries were prepared with 1 µg of RNA using the Illumina TruSeq Stranded mRNA (Macrogen).

treatment_protocol: HEK293 monolayers grown to 80% confluency were transfected with the plasmid pcDNA3Xpress-Gemin5 using Lipofectamine LTX (Thermo Fisher Scientific). Cells expressing elevated levels of Gemin5 were harvested 24 h post-transfection.

tag: fraction

value: polysomal

value: GEMIN5 Overexpression (plasmid)


description:
Sox2P-reporter -116 kb, population P3 pool3 rep1
E2138 Sox2P-reporter -116 kb, population P3 pool3 rep1 Fw
mapped_integrations_-116kb_Sox2P_pools.txt

data_processing:
The full protocol is described in the corresponding manuscript. In short, reads overlapping the SB-genome junction were selected, SB-sequences were trimmed off (using an adapted version of cutadapt) and reads were mapped to the genome (mm10 or an in silico version of mm10 including the hopping launch pad at -116 kb), filtering for mapq >=10. All putative integrations are lifted over to mm10.
Assembly: mm10
Supplementary files format and content: The processed data file reports all putative integrations mapped in a pool or clone (supported by at least one mapping read, filtering in the manuscript can be more strict). Columns: chr = chromosome; start, end = integration location; seq = dinucleotide at integration site (expected for SB: TA); strand = strand of integration (orientation); read_count = total read count, mapq = total mapping quality (of all reads); read_count_1/mapq_1 = forward mapping reads (3' ITR); read_count_2/mapq_2 = reverse mapping reads (5' ITR); all other columns specify and annotate the sequenced sample. There is one processed data file per founder cell line (pool-based experiments) and one for the isolated clones.

extract_protocol:
Sorted pools and clones were expanded and crude lysates were obtained from a full 96 well plate by lysing with 50 µL DirectPCR Lysis Reagent (102-T, Viagen Biotec) supplemented with 100 µg/mL proteinase K, and incubating 2.5 h at 55 °C and 45 min at 85 °C. For unsorted control cell pools, gDNA was extracted after expansion using the ISOLATE II Genomic DNA Kit (BIO-52067, Bioline).
SBt integrations were mapped by amplifying and sequencing the ITR-genome junction using a tagmentation-based approach. The procedure was similar to {Schep, 2021, 33848455}, but using the following SB-ITR specific primers: MEP009 (5′ ITR, reverse) or LD027 (3′ ITR, forward) for the linear enrichment and MEP011 (5′ ITR, reverse) or MEP034 (3′ ITR, forward) for PCR.Input for one tagmentation reaction was either 100ng gDNA or 3 µL crude lysate. The 72 °C extension times of all PCRs were increased to 1 min. In addition, the composition of the linear enrichment PCR was changed to 10 μL of tagmented DNA, 2 μL of 1 μM primer, 4 μL dNTPs (10mM), 8 μL 5x Phusion® HF Buffer (NEB), 0.5 μL Phusion® HS Flex polymerase (2 U/μL - NEB), in a final volume of 40 μL. For all clones and some experiments with sorted pools (proof-of-principle experiment, third replicate of the reporter hopping) we halved this reaction to a final volume of 20 µL. For the unsorted control pools, 10 separate tagmentation reactions and library preparations were performed, usually using one set of sequencing indices. Libraries were sequenced with 150 bp paired-end reads using either an Illumina MiSeq system (reagent kit v2) or  Illumina NextSeq 550 system (mid-output kit) including 10% of PhiX spike-in.  Primers are described in the corresponding manuscript.


title: ChIPseq_CH12_Med25mm_biotMed25_RA_biot_r2

data_processing:
base calling: illumina CASAVA 1.8.2
ChIP-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50
ChIP-Seq_density: filtering (uniquely aligned reads): samtools-0.1.19-1.2/samtools view -S -b -F4
ChIP-Seq_density: normalized tag density: custom script, maximum 2 reads with the same start position allowed
mRNA-Seq_density:alignment: gsnap --use-sarray=0 --novelsplicing=0 --use-splicing refseq.splices.iit --format=sam -B 4
mRNA-Seq_density: filtering: samtools-1.2/samtools view -S -b -F132 -q 20
mRNA-Seq density: normalized tag density: bedtools-2.25/genomeCoverageBed -ibam -bg -split -scale normalization_factor, ucsc-314/bedGraphToBigWig
Gro-Seq_density: alignment: bowtie-1.1.1/bowtie -S -m 1 -p 20 -a --best --strata -n 2 -l 50 --trim5 2
Gro-Seq_density: filtering (uniquely aligned reads): samtools-1.2/samtools view -S -b -F4
Gro-Seq_density: normalized tag density: bedtools-2.25/genomeCoverageBed -ibam -bg -split -scale normalization_factor -strand, ucsc-314/bedGraphToBigWig
Assembly: mm9
Supplementary files format and content: bigwig

value: biotag (Dynabeads M-280 Streptavidin)

value: mouse lymphoma B cell

value: biot_Med25 overexpression with retinoic acid


description:
Sox2P-reporter -116 kb, unsorted control pool rep1
E2138 Sox2P-reporter -116 kb, unsorted control pool rep1 Fw
mapped_integrations_-116kb_Sox2P_pools.txt

value: mESC

value: WT

value: control pool


title: EEC, corticosterone, D6, 5

value: epididymal epithelial cell

value: corticosterone


title: Polysome fractions – G5OV treatment – Rep2

description: RNA isolated from polysome fractions of HEK-293 cells transfected with the plasmid pcDNA3Xpress-Gemin5 – Rep2


title: Polysome fractions – G5OV treatment – Rep1

description: RNA isolated from polysome fractions of HEK-293 cells transfected with the plasmid pcDNA3Xpress-Gemin5 - Rep1


title: EEC, corticosterone, D6, 3


title: EEC, corticosterone, D6, 1


description:
Sox2P-reporter -116 kb, population P1 pool1 rep1
E2138 Sox2P-reporter -116 kb, population P1 pool1 rep1 Rv
mapped_integrations_-116kb_Sox2P_pools.txt

value: F1 hybrid 129/Sv:CAST/EiJ


title: ChIPseq_CH12_H3K27ac_r2

value: H3K27ac (Abcam ab4729)


description:
Sox2P-reporter -116 kb, population P2 pool4 rep1
E2138 Sox2P-reporter -116 kb, population P2 pool4 rep1 Fw
mapped_integrations_-116kb_Sox2P_pools.txt

value: sorted pool


title: ChIPseq_CH12_H3K27ac_r1


title: EEC, corticosterone, D3, 6


title: Polysome fractions – Untreated Control – Rep3

description: RNA isolated from polysome fractions of untreated HEK-293 cells – Rep3

value: Untreated


title: Polysome fractions – Untreated Control – Rep4

description: RNA isolated from polysome fractions of untreated HEK-293 cells – Rep4


title: EEC, corticosterone, D3, 5


description:
Sox2P-reporter -116 kb, population P3 pool2 rep1
E2138 Sox2P-reporter -116 kb, population P3 pool2 rep1 Fw
mapped_integrations_-116kb_Sox2P_pools.txt


title: EEC, corticosterone, D3, 4


description:
Sox2P-reporter -116 kb, population P2 pool3 rep1
E2138 Sox2P-reporter -116 kb, population P2 pool3 rep1 Fw
mapped_integrations_-116kb_Sox2P_pools.txt


title: ChIPseq_CH12_WT_PolII_r2

value: PolII (Abcam ab817)


title: Polysome fractions – Untreated Control – Rep1

description: RNA isolated from polysome fractions of untreated HEK-293 cells – Rep1


description:
Sox2P-reporter -116 kb, population P2 pool2 rep1
E2138 Sox2P-reporter -116 kb, population P2 pool2 rep1 Fw
mapped_integrations_-116kb_Sox2P_pools.txt


title: Polysome fractions – Untreated Control – Rep2

description: RNA isolated from polysome fractions of untreated HEK-293 cells – Rep2


title: EEC, corticosterone, D3, 1


title: ChIPseq_CH12_WT_PolII_r1


description:
Sox2P-reporter -116 kb, population P3 pool1 rep1
E2138 Sox2P-reporter -116 kb, population P3 pool1 rep1 Fw
mapped_integrations_-116kb_Sox2P_pools.txt


title: ChIPseq_CH12_WT_input_r3


title: Polysome fractions – G5OV treatment – Rep3

description: RNA isolated from polysome fractions of HEK-293 cells transfected with the plasmid pcDNA3Xpress-Gemin5 – Rep3


description:
Sox2P-reporter -116 kb, population P6 pool3 rep1
E2138 Sox2P-reporter -116 kb, population P6 pool3 rep1 Fw
mapped_integrations_-116kb_Sox2P_pools.txt


title: ChIPseq_CH12_WT_input_r2


description:
Sox2P-reporter -116 kb, population P2 pool1 rep1
E2138 Sox2P-reporter -116 kb, population P2 pool1 rep1 Fw
mapped_integrations_-116kb_Sox2P_pools.txt


title: Cytoplasmic Input RNA – G5OV treatment – Rep2

description: Total RNA from cytoplasmic lysates of HEK-293 cells transfected with the plasmid pcDNA3Xpress-Gemin5 – Rep2

value: cytoplasmic


title: EEC, vehicle, D9, 5

value: vehicle


title: EEC, vehicle, D9, 4


title: ChIPseq_CH12_WT_input_r1


description:
Sox2P-reporter -116 kb, population P6 pool2 rep1
E2138 Sox2P-reporter -116 kb, population P6 pool2 rep1 Fw
mapped_integrations_-116kb_Sox2P_pools.txt


title: EEC, vehicle, D9, 6


title: ChIPseq_CH12_WT_PolII_r3


title: Cytoplasmic Input RNA – Control – Rep4

description: Total RNA from cytoplasmic lysates of untreated HEK-293 cells – Rep4


title: Cytoplasmic Input RNA – Control – Rep3

description: Total RNA from cytoplasmic lysates of untreated HEK-293 cells – Rep3


title: EEC, vehicle, D6, 6


title: ChIPseq_CH12_Med26mm_PolII_r2


description:
Sox2P-reporter -116 kb, population P6 pool4 rep1
E2138 Sox2P-reporter -116 kb, population P6 pool4 rep1 Fw
mapped_integrations_-116kb_Sox2P_pools.txt


title: ChIPseq_CH12_Med26mm_PolII_r3


title: EEC, vehicle, D6, 5


title: Cytoplasmic Input RNA – Control – Rep2

description: Total RNA from cytoplasmic lysates of untreated HEK-293 cells – Rep2


description:
Sox2P-reporter -116 kb, population P5 pool4 rep1
E2138 Sox2P-reporter -116 kb, population P5 pool4 rep1 Fw
mapped_integrations_-116kb_Sox2P_pools.txt


title: Cytoplasmic Input RNA – G5OV treatment – Rep3

description: Total RNA from cytoplasmic lysates of HEK-293 cells transfected with the plasmid pcDNA3Xpress-Gemin5 – Rep3


title: ChIPseq_CH12_Med26mm_PolII_r1


title: EEC, vehicle, D6, 4


description:
Sox2P-reporter -116 kb, unsorted control pool rep1
E2138 Sox2P-reporter -116 kb, unsorted control pool rep1 Rv
mapped_integrations_-116kb_Sox2P_pools.txt


title: Cytoplasmic Input RNA – G5OV treatment – Rep1

description: Total RNA from cytoplasmic lysates of HEK-293 cells transfected with the plasmid pcDNA3Xpress-Gemin5 - Rep1


title: ChIPseq_CH12_Med26mm_input_r3


description:
Sox2P-reporter -116 kb, population P5 pool1 rep1
E2138 Sox2P-reporter -116 kb, population P5 pool1 rep1 Fw
mapped_integrations_-116kb_Sox2P_pools.txt


title: EEC, vehicle, D6, 3


title: EEC, vehicle, D9, 3


description:
Sox2P-reporter -116 kb, population P6 pool1 rep1
E2138 Sox2P-reporter -116 kb, population P6 pool1 rep1 Fw
mapped_integrations_-116kb_Sox2P_pools.txt


title: INP D2 LPS

city: Badalona

first: LUCIA

last: LORENZI

state: Barcelona

address: Ctra de Can Ruti, Camí de les Escoles s/n

institute: Josep Carreras Research Institute

data_processing:
Reads were aligned to human genome hg38 and to fruit fly genome fruit dm6 using Bowtie2 version 2.4.4 with ‘--very-sensitive’ flag set and a minimum fragment length (-X flag) of 1000bp, all other parameters set to default.
Duplicate reads were identified using Picard MarkDuplicates and excluded from the downstream analysis
Genome wide coverage tracks in bigwig format were generated using DeepTools bamCoverage (v. 3.3.1).
ChIP-Seq Peaks were identified by MACS2 (v. 2.2.5) using input libraries as control.
Assembly: hg38
Supplementary files format and content: tab-delimited narrowPeak files contain macs2 called peaks for each sample (except for input files)

source_name: GM-MDM

growth_protocol: Primary human macrophages were generated through differentiation of CD14+ monocytes with 500 U/mL of recombinant human GM-CSF  in RPMI 1640 medium  containing 10% FBS , 1% penicillin/streptomycin, 1x GlutaMAX, and 1x sodium pyruvate  for 3 days.

extract_protocol:
Cells were cross-linked with 1% formaldehyde, lysed and sonicated in 1% Triton, 0.1% sodium deoxycholate, 0.5% SDS, 0.2M NaCl, 10mM Tris, pH 7.5, 10mM EDTA, and 1X protease inhibitor cocktail.
Libraries were prepared using the NEBNext Ultra DNA Library Prep kit (E7645, New England Biolabs).

treatment_protocol: GM-MDMs were treated with LPS (1 ng/ml) in the presence or absence of butyrate (10 mM) for 16 hours

value: GM-MDM

value: input

value: LPS


title: INP D2 L_B

value: LPS But


description:
Sox2P-reporter -116 kb, population P5 pool2 rep1
E2138 Sox2P-reporter -116 kb, population P5 pool2 rep1 Fw
mapped_integrations_-116kb_Sox2P_pools.txt


title: EEC, vehicle, D3, 6


title: EEC, vehicle, D3, 5


title: EEC, vehicle, D3, 4


title: mRNA_CH12_WT_r3

city: bethesda

first: Seolkyoung

last: Jung

institute: NIH

value: mouse lymphoma B cell


title: INP D2 UT

value: UT


title: INP D1 LPS


title: ChIPseq_CH12_Med26mm_input_r1


title: ChIPseq_CH12_Med25mm_biotMed25_RA_biot_r1

value: biotag (Dynabeads M-280 Streptavidin)

value: biot_Med25 overexpression with retinoic acid


description:
Sox2P-reporter -116 kb, population P4 pool4 rep1
E2138 Sox2P-reporter -116 kb, population P4 pool4 rep1 Fw
mapped_integrations_-116kb_Sox2P_pools.txt

value: mESC

value: WT


title: mRNA_CH12_WT_r1


title: Cytoplasmic Input RNA – Control – Rep1

description: Total RNA from cytoplasmic lysates of untreated HEK-293 cells - Rep1


description:
Sox2P-reporter -116 kb, population P5 pool3 rep1
E2138 Sox2P-reporter -116 kb, population P5 pool3 rep1 Fw
mapped_integrations_-116kb_Sox2P_pools.txt

value: F1 hybrid 129/Sv:CAST/EiJ


title: EEC, vehicle, D0, 6

value: epididymal epithelial cell


title: INP D1 UT


title: mRNA_CH12_WT_r2


title: ChIPseq_CH12_Med26mm_input_r2


description:
Sox2P-reporter -116 kb, population P4 pool3 rep1
E2138 Sox2P-reporter -116 kb, population P4 pool3 rep1 Fw
mapped_integrations_-116kb_Sox2P_pools.txt

value: sorted pool


description:
Sox2P-reporter -116 kb, population P4 pool2 rep1
E2138 Sox2P-reporter -116 kb, population P4 pool2 rep1 Fw
mapped_integrations_-116kb_Sox2P_pools.txt


title: mRNA_CH12_Med26mm_r3


description:
Sox2P-reporter -116 kb, population P6 pool4 rep1
E2138 Sox2P-reporter -116 kb, population P6 pool4 rep1 Rv
mapped_integrations_-116kb_Sox2P_pools.txt


title: D2 L_B

value: H3K27ac antibody (Abcam ab4729)


description:
Sox2P-reporter -116 kb, population P6 pool3 rep1
E2138 Sox2P-reporter -116 kb, population P6 pool3 rep1 Rv
mapped_integrations_-116kb_Sox2P_pools.txt


title: EEC, vehicle, D0, 5


title: mRNA_CH12_Med26mm_r1


title: INP D1 L_B


description:
Sox2P-reporter -116 kb, population P6 pool2 rep1
E2138 Sox2P-reporter -116 kb, population P6 pool2 rep1 Rv
mapped_integrations_-116kb_Sox2P_pools.txt


title: D2 LPS


title: mRNA_CH12_Med26mm_r2


title: EEC, vehicle, D3, 3


title: EEC, vehicle, D0, 3


title: D1 L_B


title: EEC, vehicle, D0, 4