title: D3_MO_Butyrate_LPS

city: Badalona

first: LUCIA

last: LORENZI

state: Barcelona

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

country: Spain

institute: Josep Carreras Research Institute

data_processing:
Alignment to the human reference genome hg19 from UCSC was conducted by Hisat2 using standard settings.
The external gene names and Entrez gene IDs matching the original Ensembl gene IDs were obtained using The biomaRt package (v2.38.0)  and A DGEList object was created using the raw counts and gene annotation using the edgeR package (v3.24.0) (Robinson et al., 2009).
Since genes with very low counts are not useful, only genes that had at least 10 reads in a worthwhile number of samples determined by the design matrix were kept. In addition, each kept gene is required to have at least 15 reads across all the samples. Filtering was performed using the filterByExpr function
Normalisation was done by using TMM method (weighted, trimmed mean of M-values) with the application of edgeR calcNormFactors function
After data normalisation and with the edgeR package v3.24.0, estimateDisp was used to estimate common dispersion and tagwise dispersion and transform the data for linear modelling. Multidimensional scaling (MDS) plot visualising the relationship between the samples were displayed with the batch-corrected data according to all the donors
Assembly: hg19
Supplementary files format and content: Tab delimited file with raw gene counts for each sample. First column contains ENSEMBL gene_id and following columns contain each sample's counts

molecule: total RNA

organism: Homo sapiens

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 lysed in TRIZOL (Invitrogen) and total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA was eluted in RNase-free water.
Total RNA was converted into libraries of double-stranded cDNA molecules as a template for high-throughput sequencing using the Illumina TruSeq RNA Sample Preparation Kit v2.

treatment_protocol: GM-MDMs were treated NaCl (10 mM), SCFAs (acetate, propionate or butyrate; 10 mM) or TSA (0.5 μM) in the presence or absence of LPS (1 ng/ml) for 16 hours

value: GM-MDM

value: Butyrate+LPS


status: Public on Aug 19 2024

type: SRA

city: Amsterdam

first: Christina

last: Moene

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

description:
Sox2P_CDS-reporter -161 kb, population P6 pool2 rep1
E2555 Sox2P_CDS-reporter -161 kb, population P6 pool2 rep1 Rv
mapped_integrations_-161kb_Sox2P_CDS_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

organism: Mus musculus

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

tag: cell type

value: mESC

tag: genotype

value: WT

tag: launch pad_location

tag: insert

tag: sorted gate

tag: sample type

value: sorted pool


title: clone Sox2P-reporter 1-34_34 Rv

description:
clone Sox2P-reporter 1-34_34
E2221 clone Sox2P-reporter 1-34_34 Rv
mapped_integrations_Sox2P_clones.txt

value: deletion clone


title: D3_MO_Acetate_LPS

library_source: transcriptomic

tag: treatment

value: Acetate+LPS


description:
Sox2P_CDS-reporter -161 kb, population P6 pool1 rep1
E2555 Sox2P_CDS-reporter -161 kb, population P6 pool1 rep1 Rv
mapped_integrations_-161kb_Sox2P_CDS_pools.txt


title: clone Sox2P-reporter 1-45_34 Rv

description:
clone Sox2P-reporter 1-45_34
E2221 clone Sox2P-reporter 1-45_34 Rv
mapped_integrations_Sox2P_clones.txt


description:
Sox2P-reporter -161 kb Sox2::mCherry deleted, population P1 pool1 rep1
E2555 Sox2P-reporter -161 kb Sox2::mCherry deleted, population P1 pool1 rep1 Rv
mapped_integrations_-161kb_Sox2mCherrydel_Sox2P_pools.txt

value: Sox2::mCherry deleted


title: clone Sox2P-reporter 1-33_34 Rv

description:
clone Sox2P-reporter 1-33_34
E2221 clone Sox2P-reporter 1-33_34 Rv
mapped_integrations_Sox2P_clones.txt


title: D3_MO_Trichostatin_LPS

value: Trichostatin+LPS


title: clone Sox2P-reporter 1-32_34 Rv

description:
clone Sox2P-reporter 1-32_34
E2221 clone Sox2P-reporter 1-32_34 Rv
mapped_integrations_Sox2P_clones.txt

value: ambiguous clone


description:
Sox2P_CDS-reporter -161 kb, population P5 pool5 rep1
E2555 Sox2P_CDS-reporter -161 kb, population P5 pool5 rep1 Rv
mapped_integrations_-161kb_Sox2P_CDS_pools.txt


description:
Sox2P_CDS-reporter -161 kb, population P5 pool4 rep1
E2555 Sox2P_CDS-reporter -161 kb, population P5 pool4 rep1 Rv
mapped_integrations_-161kb_Sox2P_CDS_pools.txt


title: D3_MO_NaCL_LPS

value: NaCL+LPS


title: D3_MO_NaCL_wo_LPS

value: NaCL


title: D2_MO_Butyrate_LPS


title: clone Sox2P-reporter 1-30_34 Rv

description:
clone Sox2P-reporter 1-30_34
E2221 clone Sox2P-reporter 1-30_34 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-29_34 Rv

description:
clone Sox2P-reporter 1-29_34
E2221 clone Sox2P-reporter 1-29_34 Rv
mapped_integrations_Sox2P_clones.txt


description:
Sox2P_CDS-reporter -161 kb, population P5 pool2 rep1
E2555 Sox2P_CDS-reporter -161 kb, population P5 pool2 rep1 Rv
mapped_integrations_-161kb_Sox2P_CDS_pools.txt


title: D2_MO_Acetate_LPS


title: D2_MO_Propionate_LPS

value: Propionate+LPS


title: D2_MO_NaCL_wo_LPS


description:
Sox2P_CDS-reporter -161 kb, population P5 pool3 rep1
E2555 Sox2P_CDS-reporter -161 kb, population P5 pool3 rep1 Rv
mapped_integrations_-161kb_Sox2P_CDS_pools.txt


title: D2_MO_NaCL_LPS


description:
Sox2P_CDS-reporter -161 kb, population P5 pool1 rep1
E2555 Sox2P_CDS-reporter -161 kb, population P5 pool1 rep1 Rv
mapped_integrations_-161kb_Sox2P_CDS_pools.txt


description:
Sox2P-reporter -161 kb, population P6 pool1 rep1
E2555 Sox2P-reporter -161 kb, population P6 pool1 rep1 Fw
mapped_integrations_-161kb_Sox2P_pools.txt


title: D3_MO_Propionate_LPS


title: clone Sox2P-reporter 1-26_34 Rv

description:
clone Sox2P-reporter 1-26_34
E2221 clone Sox2P-reporter 1-26_34 Rv
mapped_integrations_Sox2P_clones.txt


title: D1_MO_Butyrate_LPS


title: clone Sox2P-reporter 1-23_34 Rv

description:
clone Sox2P-reporter 1-23_34
E2221 clone Sox2P-reporter 1-23_34 Rv
mapped_integrations_Sox2P_clones.txt


title: D1_MO_Propionate_LPS


description:
Sox2P_CDS-reporter -161 kb, population P4 pool2 rep1
E2555 Sox2P_CDS-reporter -161 kb, population P4 pool2 rep1 Rv
mapped_integrations_-161kb_Sox2P_CDS_pools.txt


title: D1_MO_Acetate_LPS


title: D1_MO_Trichostatin_LPS


title: clone Sox2P-reporter 2-61_34 Fw

description:
clone Sox2P-reporter 2-61_34
E2221 clone Sox2P-reporter 2-61_34 Fw
mapped_integrations_Sox2P_clones.txt


description:
Sox2P_CDS-reporter -161 kb, population P4 pool1 rep1
E2555 Sox2P_CDS-reporter -161 kb, population P4 pool1 rep1 Rv
mapped_integrations_-161kb_Sox2P_CDS_pools.txt


title: D1_MO_NaCL_LPS


title: clone Sox2P-reporter 1-22_34 Rv

description:
clone Sox2P-reporter 1-22_34
E2221 clone Sox2P-reporter 1-22_34 Rv
mapped_integrations_Sox2P_clones.txt


title: D1_MO_NaCL_wo_LPS


title: clone Sox2P-reporter 1-21_34 Rv

description:
clone Sox2P-reporter 1-21_34
E2221 clone Sox2P-reporter 1-21_34 Rv
mapped_integrations_Sox2P_clones.txt


description:
Sox2P-reporter -161 kb, population P5 pool5 rep1
E2555 Sox2P-reporter -161 kb, population P5 pool5 rep1 Fw
mapped_integrations_-161kb_Sox2P_pools.txt


title: D2_MO_Trichostatin_LPS


description:
Sox2P_CDS-reporter -161 kb, population P3 pool2 rep1
E2555 Sox2P_CDS-reporter -161 kb, population P3 pool2 rep1 Rv
mapped_integrations_-161kb_Sox2P_CDS_pools.txt


title: clone Sox2P-reporter 1-19_34 Rv

description:
clone Sox2P-reporter 1-19_34
E2221 clone Sox2P-reporter 1-19_34 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-20_34 Rv

description:
clone Sox2P-reporter 1-20_34
E2221 clone Sox2P-reporter 1-20_34 Rv
mapped_integrations_Sox2P_clones.txt


title: ERCC.NextSeq.b2.2

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

country: USA

institute: University of Pittsburgh

description: Illumina short-read RNA-seq

data_processing:
The raw RNA-seq data were pre-processed by FastQC and Trimmomatic for quality control and trimming.
Then the reads were aligned to ERCC reference genome by STAR aligner
Transcript counts were collected based on the alignment and the count per million (CPM) was calculated for transcript quantification.
BCFtools were applied on the aligned file to call the variant sites.
Assembly: ERCC
Supplementary files format and content: TAB files: transcript count file in TAB format
Supplementary files format and content: mpileup files: BCFtool variant calling file in TXT format

molecule: polyA RNA

organism: synthetic construct

source_name: External RNA Controls Consortium (ERCC)

extract_protocol:
1% dilution of ERCC RNA Spike-In Mix (4456740, ThermoFisher)
Sample was processed into a short read library using the TruSeq Stranded mRNA Sample Prep Kit from Illumina, Inc (Cat#: 20020594). The fragmented mRNA was reverse transcribed to cDNA using random primers. This was followed by second stranded cDNA synthesis. The library preparation processes of mono-adenylation, adapter ligation and amplification were performed following the manual provided by the manufacturer. The quantity and quality of the libraries were assessed in a manner similar to that described for whole genome DNA library preparation. The procedure of 150 cycle paired-end sequencing on the Illumina NextSeq550 followed per the manufacturer’s guidelines.

tag: tissue

value: ERCC


title: ERCC.NextSeq.b3.1

description: Illumina short-read RNA-seq


title: ERCC.NextSeq.b1.3

description: Illumina short-read RNA-seq


title: ERCC.NextSeq.b3.3

description: Illumina short-read RNA-seq


title: ERCC.NextSeq.b3.2

description: Illumina short-read RNA-seq


title: ERCC.NextSeq.b2.3

description: Illumina short-read RNA-seq


description:
Sox2P_CDS-reporter -161 kb, population P2 pool1 rep1
E2555 Sox2P_CDS-reporter -161 kb, population P2 pool1 rep1 Rv
mapped_integrations_-161kb_Sox2P_CDS_pools.txt


title: ERCC.NextSeq.b2.1

description: Illumina short-read RNA-seq


description:
Sox2P_CDS-reporter -161 kb, population P2 pool2 rep1
E2555 Sox2P_CDS-reporter -161 kb, population P2 pool2 rep1 Rv
mapped_integrations_-161kb_Sox2P_CDS_pools.txt


title: clone Sox2P-reporter 1-15_34 Rv

description:
clone Sox2P-reporter 1-15_34
E2221 clone Sox2P-reporter 1-15_34 Rv
mapped_integrations_Sox2P_clones.txt


title: ERCC.NextSeq.b1.1

description: Illumina short-read RNA-seq


title: HEPG2 ERCC spike-in

data_processing:
The raw RNA-seq data were pre-processed by FastQC and Trimmomatic for quality control and trimming.
Then the reads were aligned to ERCC reference genome by STAR aligner
Transcript counts were collected based on the alignment and the count per million (CPM) was calculated for transcript quantification.
BCFtools were applied on the aligned file to call the variant sites.
Assembly: ERCC
Supplementary files format and content: Illumina.HepG2_ERCC_S1.STAR.ReadsPerGene.out.tab: transcript count file in TAB format
Supplementary files format and content: Illumina.mpileup.txt: BCFtool variant calling file in TXT format

source_name: ERCC

extract_protocol:
1% dilution of ERCC RNA Spike-In Mix (4456740, ThermoFisher)
Sample was processed into a short read library using the TruSeq Stranded mRNA Sample Prep Kit from Illumina, Inc (Cat#: 20020594). The fragmented mRNA was reverse transcribed to cDNA using random primers. This was followed by second stranded cDNA synthesis. The library preparation processes of mono-adenylation, adapter ligation and amplification were performed following the manual provided by the manufacturer. The quantity and quality of the libraries were assessed in a manner similar to that described for whole genome DNA library preparation. The procedure of 150 cycle paired-end sequencing on the Illumina NextSeq550 followed per the manufacturer’s guidelines.
Illumina short-read RNA-seq


title: clone Sox2P-reporter 1-17_34 Rv

description:
clone Sox2P-reporter 1-17_34
E2221 clone Sox2P-reporter 1-17_34 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 1-12_34 Rv

description:
clone Sox2P-reporter 1-12_34
E2221 clone Sox2P-reporter 1-12_34 Rv
mapped_integrations_Sox2P_clones.txt


title: ERCC.NextSeq.b1.2

description: Illumina short-read RNA-seq


title: ERRgamma_rep2

city: Tokyo

first: Kaoru

last: Sato

address: 35-2 Sakae-cho, Itabashi-ku

country: Japan

institute: Tokyo Metropolitan Institute of Gerontology

data_processing:
Sequnce reads, which have been already trimmed for adaptor sequence in BGI, were then mapped to hg38. p13. whole genome using STAR version 2.7.10a with defalt parameters.
Overlapped peaks of ERRalpha and ERRgamma were calculated.
Assembly: hg38. p13.
Supplementary files format and content: ERRa_ERRg_peaks.chr.bed

growth_protocol: SH-SY5Y cells were grown with 5% CO2 at 37°C in culture medium prepared from Advanced DMEM/F-12 supplemented with 10% FBS, 1×GlutaMAX I, and 1×Penicillin-Streptomycin.

extract_protocol:
DNA fragments were extracted with phenol:chloroform.
ChIP libaries were constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645) and NEBNext Multiplex Oligos for Illumina (Index Primers Set 1) (NEB, E7335).

treatment_protocol: No treatment

value: Human neuroblastoma

tag: experimental condition

value: ERRgamma ChIP DNA (Replicate 2)

value: No treatment


title: ERRalpha_rep2

value: ERRalpha ChIP DNA (Replicate 2)


description:
Sox2P-reporter -161 kb, population P6 pool5 rep1
E2555 Sox2P-reporter -161 kb, population P6 pool5 rep1 Rv
mapped_integrations_-161kb_Sox2P_pools.txt

value: F1 hybrid 129/Sv:CAST/EiJ


description:
Sox2P-reporter -161 kb, population P6 pool4 rep1
E2555 Sox2P-reporter -161 kb, population P6 pool4 rep1 Rv
mapped_integrations_-161kb_Sox2P_pools.txt

value: mESC


title: ni_rep2

value: non-immune IgG (negative control) ChIP DNA (Replicate 2)


title: clone Sox2P-reporter 1-9_34 Rv

description:
clone Sox2P-reporter 1-9_34
E2221 clone Sox2P-reporter 1-9_34 Rv
mapped_integrations_Sox2P_clones.txt

value: WT


description:
Sox2P-reporter -161 kb, population P6 pool3 rep1
E2555 Sox2P-reporter -161 kb, population P6 pool3 rep1 Rv
mapped_integrations_-161kb_Sox2P_pools.txt

value: sorted pool


description:
Sox2P_CDS-reporter -161 kb, population P3 pool1 rep1
E2555 Sox2P_CDS-reporter -161 kb, population P3 pool1 rep1 Rv
mapped_integrations_-161kb_Sox2P_CDS_pools.txt


title: ERRgamma_rep1

value: ERRgamma ChIP DNA (Replicate 1)


description:
Sox2P-reporter -161 kb, population P6 pool2 rep1
E2555 Sox2P-reporter -161 kb, population P6 pool2 rep1 Rv
mapped_integrations_-161kb_Sox2P_pools.txt


title: clone Sox2P-reporter 1-8_34 Rv

description:
clone Sox2P-reporter 1-8_34
E2221 clone Sox2P-reporter 1-8_34 Rv
mapped_integrations_Sox2P_clones.txt

value: deletion clone


title: ERRalpha_rep1

value: ERRalpha ChIP DNA (Replicate 1)


title: ni_rep1

value: non-immune IgG (negative control) ChIP DNA (Replicate 1)


description:
Sox2P-reporter -161 kb, population P5 pool4 rep1
E2555 Sox2P-reporter -161 kb, population P5 pool4 rep1 Rv
mapped_integrations_-161kb_Sox2P_pools.txt


title: Control KD

data_processing:
Sequnce reads, which have been already trimmed for adaptor sequence in BGI, were then mapped to hg38. p13. whole genome using STAR version 2.7.10a with defalt parameters.
Transcripts Per Million (TPM) were calculated.
Assembly: hg38. p13.
Supplementary files format and content: TPMs of ERRa and ERRg double KD in SH-SY5Y.csv

extract_protocol:
For RNA-seq, total RNAs were isolated using ISOGEN II following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard DNBSEQ protocols.

treatment_protocol: SH-SY5Y cells were treated with siRNAs for 2-3 days.

value: Treated with control siRNA

value: Control knockdown


title: clone Sox2P-reporter 1-7_34 Rv

description:
clone Sox2P-reporter 1-7_34
E2221 clone Sox2P-reporter 1-7_34 Rv
mapped_integrations_Sox2P_clones.txt


title: ERRalpha and gamma dKD

value: Treated with siRNA against ERRalpha and ERRgamma

value: ERRalpha and ERRgamma knockdown


description:
Sox2P-reporter -161 kb, population P6 pool1 rep1
E2555 Sox2P-reporter -161 kb, population P6 pool1 rep1 Rv
mapped_integrations_-161kb_Sox2P_pools.txt


description:
Sox2P-reporter -161 kb, population P5 pool5 rep1
E2555 Sox2P-reporter -161 kb, population P5 pool5 rep1 Rv
mapped_integrations_-161kb_Sox2P_pools.txt


title: Input_rep2

value: Human neuroblastoma

value: Input DNA (Replicate 2)


title: Naïve_lung_CD45

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

library_source: transcriptomic single cell

data_processing:
Sequencing was performed on HiSeq 3000 platform in a 100+100 base paired-end mode.
Illumina RTA 2.7.7 software was used for base calling.
Generated reads were input into the  BD Rhapsody WTA Analysis Pipeline for UMI counting for each cell(index)-gene combination.
Assembly: GRCm38-PhiX-gencodevM19-20181206.tar.gz
Supplementary files format and content: comma-delimited text files including UMI count for each cell(index)-gene combination

source_name: Lung

extract_protocol:
Single-cell RNA-seq analysis was conducted using BD Rhapsody Single-Cell Analysis System (BD BioScience) following the manufacture’s protocol.
For library construction, we used BD Rhapsody Whole transcriptome analysis (WTA) Amplification Kit.

value: Lung

tag: strain

value: no treatment


title: SS5-siERRalpha [RNA-seq]

data_processing:
Sequnce reads, which have been already trimmed for adaptor sequence in BGI, were then mapped to hg38. p13. whole genome using STAR version 2.7.10a with defalt parameters.
Transcripts Per Million (TPM) were calculated.
Assembly: hg38. p13.
Supplementary files format and content: TPMs of ERRa and ERRg KD in SH-SY5Y.csv

extract_protocol:
Total RNAs were isolated using ISOGEN II following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard DNBSEQ protocols.


title: clone Sox2P-reporter 5-96_34 Rv

description:
clone Sox2P-reporter 5-96_34
E2221 clone Sox2P-reporter 5-96_34 Rv
mapped_integrations_Sox2P_clones.txt

value: F1 hybrid 129/Sv:CAST/EiJ

value: ambiguous clone


title: clone Sox2P-reporter 2-59_34 Fw

description:
clone Sox2P-reporter 2-59_34
E2221 clone Sox2P-reporter 2-59_34 Fw
mapped_integrations_Sox2P_clones.txt

value: mESC


description:
Sox2P-reporter -161 kb, population P5 pool4 rep1
E2555 Sox2P-reporter -161 kb, population P5 pool4 rep1 Fw
mapped_integrations_-161kb_Sox2P_pools.txt

value: WT


title: Bleomycin_lung_CD45

value: bleomycin


title: Input_rep1

value: Input DNA (Replicate 1)

value: No treatment


title: ERRalpha KD

value: Treated with siRNA against ERRalpha

value: ERRalpha knockdown


title: ChIPseq_CH12_WT_Med23_r2

city: bethesda

first: Seolkyoung

last: Jung

state: MD

address: 10 Center Dr

department: NIAMS

institute: NIH

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

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.

tag: chip antibody

value: Med23 (Bethyl A300-425A)

value: mouse lymphoma B cell


title: SS5-siCtrl [RNA-seq]


description:
Sox2P-reporter -161 kb, population P5 pool2 rep1
E2555 Sox2P-reporter -161 kb, population P5 pool2 rep1 Rv
mapped_integrations_-161kb_Sox2P_pools.txt

value: sorted pool


title: ERRgamma KD

value: Treated with siRNA against ERRgamma

value: ERRgamma knockdown


title: ChIPseq_CH12_WT_Med23_r1


title: clone Sox2P-reporter 5-95_34 Rv

description:
clone Sox2P-reporter 5-95_34
E2221 clone Sox2P-reporter 5-95_34 Rv
mapped_integrations_Sox2P_clones.txt

value: insertion clone


title: clone Sox2P-reporter 1-3_34 Rv

description:
clone Sox2P-reporter 1-3_34
E2221 clone Sox2P-reporter 1-3_34 Rv
mapped_integrations_Sox2P_clones.txt

value: deletion clone


title: ChiPseq_CH12_Med26mm_Med26

value: Med26 (Cell signaling 13641S)


description:
Sox2P-reporter -161 kb, population P5 pool1 rep1
E2555 Sox2P-reporter -161 kb, population P5 pool1 rep1 Rv
mapped_integrations_-161kb_Sox2P_pools.txt

value: F1 hybrid 129/Sv:CAST/EiJ


title: clone Sox2P-reporter 1-6_34 Rv

description:
clone Sox2P-reporter 1-6_34
E2221 clone Sox2P-reporter 1-6_34 Rv
mapped_integrations_Sox2P_clones.txt

value: ambiguous clone


title: SS5-siERRgamma [RNA-seq]


title: clone Sox2P-reporter 1-5_34 Rv

description:
clone Sox2P-reporter 1-5_34
E2221 clone Sox2P-reporter 1-5_34 Rv
mapped_integrations_Sox2P_clones.txt

value: mESC


title: clone Sox2P-reporter 2-95_34 Rv

description:
clone Sox2P-reporter 2-95_34
E2221 clone Sox2P-reporter 2-95_34 Rv
mapped_integrations_Sox2P_clones.txt

value: WT


description:
Sox2P-reporter -161 kb, population P5 pool3 rep1
E2555 Sox2P-reporter -161 kb, population P5 pool3 rep1 Rv
mapped_integrations_-161kb_Sox2P_pools.txt


title: G. soja- LVM 105-rep2

city: Knoxville

first: Tarek

last: Hewezi

address: 2621 Morgan Circle

institute: University of Tennessee, Knoxvile

description:
Sieb. & Zucc. PI 378683
Nodules were harvested at 25 days post inoculation (DPI)
GSCL2

data_processing:
The quality of raw reads was determined using FastQC.
Reads were then mapped against the soybean reference genome (Williams 82 genome assembly v4) using STAR.
The HTSeq tool was utilized to obtain the read count for all transcripts.
Assembly: Williams 82 genome assembly v4
Supplementary files format and content: Read count text files were generated using Htseq.

organism: Glycine soja

source_name: Root

extract_protocol:
Total RNA from 25 DPI soybean nodules were isolated using TRIzol® Reagent (Thermo Fisher Scientific, Waltham MA, USA). Contaminating genomic DNA was removed by treating total RNA with DNase I. RNA integrity was determined using Agilent 2100 (Agilent, Technologies, CA). mRNA was isolated and used for construction of non-stranded, nondirectional mRNA libraries.
Libraries were constructed using the Illumina RNA Library Prep Kit.

value: Root

value: Nodule

value: Whole nodule

value: G. soja

value: Roots of three-day old seedlings were inoculated with Bradyrhizobial strain LVM 105


title: clone Sox2P-reporter 2-91_34 Rv

description:
clone Sox2P-reporter 2-91_34
E2221 clone Sox2P-reporter 2-91_34 Rv
mapped_integrations_Sox2P_clones.txt


title: G. soja- LVM 105-rep3

description:
Sieb. & Zucc. PI 378683
Nodules were harvested at 25 days post inoculation (DPI)
GSCL3


title: G. soja- LVM 105-rep1

description:
Sieb. & Zucc. PI 378683
Nodules were harvested at 25 days post inoculation (DPI)
GSCL1


title: G. soja-USDA 110-rep3

description:
Sieb. & Zucc. PI 378683
Nodules were harvested at 25 days post inoculation (DPI)
GS1103

value: Roots of three-day old seedlings were inoculated with Bradyrhizobial strain USDA 110


title: clone Sox2P-reporter 2-90_34 Rv

description:
clone Sox2P-reporter 2-90_34
E2221 clone Sox2P-reporter 2-90_34 Rv
mapped_integrations_Sox2P_clones.txt


title: ChIPseq_CH12_WT_Med26

value: mouse lymphoma B cell


title: G. soja-USDA 110-rep1

description:
Sieb. & Zucc. PI 378683
Nodules were harvested at 25 days post inoculation (DPI)
GS1101


description:
Sox2P-reporter -161 kb, population P3 pool2 rep1
E2555 Sox2P-reporter -161 kb, population P3 pool2 rep1 Rv
mapped_integrations_-161kb_Sox2P_pools.txt

value: sorted pool


title: clone Sox2P-reporter 2-86_34 Rv

description:
clone Sox2P-reporter 2-86_34
E2221 clone Sox2P-reporter 2-86_34 Rv
mapped_integrations_Sox2P_clones.txt


title: G. soja-USDA 110-rep2

description:
Sieb. & Zucc. PI 378683
Nodules were harvested at 25 days post inoculation (DPI)
GS1102


title: RNA-seq of CD19-CAR T cells from healthy human donor 63, 14h post-stimulation

city: Stanford

first: Yiyun

last: Chen

state: California

address: 265 Campus Dr Room G2105

department: Stanford Cancer Institute

institute: Stanford University

description:
STIM_14H_CD19_DN63
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.count.csv
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.TPM.csv

data_processing:
The raw RNA sequencing data was mapped to human reference genome hg38 using the STAR aligner, and genes annotated in Gencode v36 was quantified using featurecounts in the subread package.
Assembly: hg38
Supplementary files format and content: Gene expression count and TPM matrices.

source_name: T cells

extract_protocol:
On days 14-16 control cells or GLUT1 overexpressing CAR-T cells were collected and total mRNA was isolated using Qiagen RNEasy Plus mini isolation kit.
Bulk RNAseq was performed by Novogene using the NovaSeq platform.

tag: subject status/id

value: healthy human donor 63

value: T cells

tag: cell subtype

value: CD19-CAR T cells

tag: treatment/time point

value: 14h post-stimulation


description:
Sox2P-reporter -161 kb, population P3 pool1 rep1
E2555 Sox2P-reporter -161 kb, population P3 pool1 rep1 Rv
mapped_integrations_-161kb_Sox2P_pools.txt


title: RNA-seq of GLUT1-OE HA-CAR T cells from healthy human donor 63, 14h post-stimulation

description:
STIM_14H_HA-GLUT1_DN63
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.count.csv
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.TPM.csv

value: GLUT1-OE HA-CAR T cells


title: RNA-seq of HA-CAR T cells from healthy human donor 63, 14h post-stimulation

description:
STIM_14H_HA_DN63
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.count.csv
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.TPM.csv

value: HA-CAR T cells


description:
Sox2P-reporter -161 kb, population P2 pool1 rep1
E2555 Sox2P-reporter -161 kb, population P2 pool1 rep1 Rv
mapped_integrations_-161kb_Sox2P_pools.txt

value: F1 hybrid 129/Sv:CAST/EiJ


title: RNA-seq of GLUT1-OE CD19-CAR T cells from healthy human donor 63, 14h post-stimulation

description:
STIM_14H_CD19-GLUT1_DN63
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.count.csv
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.TPM.csv

value: GLUT1-OE CD19-CAR T cells


title: RNA-seq of T cells from healthy human donor 63, 14h post-stimulation

description:
STIM_14H_MOCK_DN63
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.count.csv
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.TPM.csv


description:
Sox2P-reporter -161 kb, population P2 pool2 rep1
E2555 Sox2P-reporter -161 kb, population P2 pool2 rep1 Rv
mapped_integrations_-161kb_Sox2P_pools.txt

value: mESC

value: WT


title: RNA-seq of GLUT1-OE HA-CAR T cells from healthy human donor 62, 14h post-stimulation

description:
STIM_14H_HA-GLUT1_DN62
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.count.csv
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.TPM.csv

value: healthy human donor 62


title: clone Sox2P-reporter 2-58_34 Fw

description:
clone Sox2P-reporter 2-58_34
E2221 clone Sox2P-reporter 2-58_34 Fw
mapped_integrations_Sox2P_clones.txt

value: ambiguous clone


title: RNA-seq of HA-CAR T cells from healthy human donor 62, 14h post-stimulation

description:
STIM_14H_HA_DN62
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.count.csv
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.TPM.csv


title: clone Sox2P-reporter 2-79_34 Rv

description:
clone Sox2P-reporter 2-79_34
E2221 clone Sox2P-reporter 2-79_34 Rv
mapped_integrations_Sox2P_clones.txt


title: RNA-seq of GLUT1-OE CD19-CAR T cells from healthy human donor 62, 14h post-stimulation

description:
STIM_14H_CD19-GLUT1_DN62
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.count.csv
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.TPM.csv


title: clone Sox2P-reporter 2-85_34 Rv

description:
clone Sox2P-reporter 2-85_34
E2221 clone Sox2P-reporter 2-85_34 Rv
mapped_integrations_Sox2P_clones.txt

value: insertion clone


description:
Sox2P-reporter -161 kb, population P4 pool2 rep1
E2555 Sox2P-reporter -161 kb, population P4 pool2 rep1 Rv
mapped_integrations_-161kb_Sox2P_pools.txt


description:
Sox2P-reporter -161 kb, population P5 pool3 rep1
E2555 Sox2P-reporter -161 kb, population P5 pool3 rep1 Fw
mapped_integrations_-161kb_Sox2P_pools.txt


description:
Sox2P-reporter -161 kb, population P4 pool1 rep1
E2555 Sox2P-reporter -161 kb, population P4 pool1 rep1 Rv
mapped_integrations_-161kb_Sox2P_pools.txt


title: RNA-seq of CD19-CAR T cells from healthy human donor 62, 14h post-stimulation

description:
STIM_14H_CD19_DN62
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.count.csv
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.TPM.csv


title: clone Sox2P-reporter 2-77_34 Rv

description:
clone Sox2P-reporter 2-77_34
E2221 clone Sox2P-reporter 2-77_34 Rv
mapped_integrations_Sox2P_clones.txt


title: RNA-seq of T cells from healthy human donor 62, 14h post-stimulation

description:
STIM_14H_MOCK_DN62
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.count.csv
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.TPM.csv


title: RNA-seq of GLUT1-OE HA-CAR T cells from healthy human donor 61, 14h post-stimulation

description:
STIM_14H_HA-GLUT1_DN61
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.count.csv
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.TPM.csv

value: healthy human donor 61


description:
Sox2P-reporter -116 kb, population P3 pool4 rep3
E2285 Sox2P-reporter -116 kb, population P3 pool4 rep3 Fw
mapped_integrations_-116kb_Sox2P_pools.txt


title: clone Sox2P-reporter 2-89_34 Rv

description:
clone Sox2P-reporter 2-89_34
E2221 clone Sox2P-reporter 2-89_34 Rv
mapped_integrations_Sox2P_clones.txt


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


title: RNA-seq of HA-CAR T cells from healthy human donor 61, 14h post-stimulation

description:
STIM_14H_HA_DN61
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.count.csv
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.TPM.csv


title: clone Sox2P-reporter 2-76_34 Rv

description:
clone Sox2P-reporter 2-76_34
E2221 clone Sox2P-reporter 2-76_34 Rv
mapped_integrations_Sox2P_clones.txt


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


title: RNA-seq of CD19-CAR T cells from healthy human donor 61, 14h post-stimulation

description:
STIM_14H_CD19_DN61
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.count.csv
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.TPM.csv


title: RNA-seq of GLUT1-OE CD19-CAR T cells from healthy human donor 61, 14h post-stimulation

description:
STIM_14H_CD19-GLUT1_DN61
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.count.csv
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.TPM.csv


title: clone Sox2P-reporter 2-73_34 Rv

description:
clone Sox2P-reporter 2-73_34
E2221 clone Sox2P-reporter 2-73_34 Rv
mapped_integrations_Sox2P_clones.txt


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


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


title: clone Sox2P-reporter 2-69_34 Rv

description:
clone Sox2P-reporter 2-69_34
E2221 clone Sox2P-reporter 2-69_34 Rv
mapped_integrations_Sox2P_clones.txt


title: RNA-seq of GLUT1-OE HA-CAR T cells from healthy human donor 63, 4h post-stimulation

description:
STIM_4H_HA-GLUT1_DN63
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.count.csv
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.TPM.csv

value: 4h post-stimulation


title: RNA-seq of GLUT1-OE CD19-CAR T cells from healthy human donor 63, 4h post-stimulation

description:
STIM_4H_CD19-GLUT1_DN63
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.count.csv
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.TPM.csv


title: clone Sox2P-reporter 2-68_34 Rv

description:
clone Sox2P-reporter 2-68_34
E2221 clone Sox2P-reporter 2-68_34 Rv
mapped_integrations_Sox2P_clones.txt


title: RNA-seq of T cells from healthy human donor 63, 4h post-stimulation

description:
STIM_4H_MOCK_DN63
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.count.csv
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.TPM.csv


title: RNA-seq of HA-CAR T cells from healthy human donor 63, 4h post-stimulation

description:
STIM_4H_HA_DN63
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.count.csv
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.TPM.csv


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


title: RNA-seq of CD19-CAR T cells from healthy human donor 63, 4h post-stimulation

description:
STIM_4H_CD19_DN63
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.count.csv
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.TPM.csv


title: RNA-seq of GLUT1-OE HA-CAR T cells from healthy human donor 62, 4h post-stimulation

description:
STIM_4H_HA-GLUT1_DN62
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.count.csv
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.TPM.csv


title: RNA-seq of HA-CAR T cells from healthy human donor 62, 4h post-stimulation

description:
STIM_4H_HA_DN62
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.count.csv
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.TPM.csv


title: clone Sox2P-reporter 2-59_34 Rv

description:
clone Sox2P-reporter 2-59_34
E2221 clone Sox2P-reporter 2-59_34 Rv
mapped_integrations_Sox2P_clones.txt

value: deletion clone


description:
Sox2P-reporter -116 kb, unsorted control pool library9 rep3
E2285 Sox2P-reporter -116 kb, unsorted control pool library9 rep3 Fw
mapped_integrations_-116kb_Sox2P_pools.txt

value: control pool


title: RNA-seq of GLUT1-OE CD19-CAR T cells from healthy human donor 62, 4h post-stimulation

description:
STIM_4H_CD19-GLUT1_DN62
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.count.csv
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.TPM.csv


title: RNA-seq of CD19-CAR T cells from healthy human donor 62, 4h post-stimulation

description:
STIM_4H_CD19_DN62
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.count.csv
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.TPM.csv


title: clone Sox2P-reporter 2-58_34 Rv

description:
clone Sox2P-reporter 2-58_34
E2221 clone Sox2P-reporter 2-58_34 Rv
mapped_integrations_Sox2P_clones.txt


title: clone Sox2P-reporter 2-61_34 Rv

description:
clone Sox2P-reporter 2-61_34
E2221 clone Sox2P-reporter 2-61_34 Rv
mapped_integrations_Sox2P_clones.txt


title: RNA-seq of HA-CAR T cells from healthy human donor 61, 4h post-stimulation

description:
STIM_4H_HA_DN61
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.count.csv
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.TPM.csv


title: clone Sox2P-reporter 2-55_34 Fw

description:
clone Sox2P-reporter 2-55_34
E2221 clone Sox2P-reporter 2-55_34 Fw
mapped_integrations_Sox2P_clones.txt


description:
Sox2P-reporter -116 kb, unsorted control pool library7 rep3
E2285 Sox2P-reporter -116 kb, unsorted control pool library7 rep3 Fw
mapped_integrations_-116kb_Sox2P_pools.txt


title: RNA-seq of GLUT1-OE HA-CAR T cells from healthy human donor 61, 4h post-stimulation

description:
STIM_4H_HA-GLUT1_DN61
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.count.csv
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.TPM.csv


title: RNA-seq of GLUT1-OE CD19-CAR T cells from healthy human donor 61, 4h post-stimulation

description:
STIM_4H_CD19-GLUT1_DN61
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.count.csv
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.TPM.csv


title: RNA-seq of T cells from healthy human donor 61, 14h post-stimulation

description:
STIM_14H_MOCK_DN61
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.count.csv
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.TPM.csv


title: clone Sox2P-reporter 2-13_34 Fw

description:
clone Sox2P-reporter 2-13_34
E2221 clone Sox2P-reporter 2-13_34 Fw
mapped_integrations_Sox2P_clones.txt


description:
Sox2P-reporter -116 kb, unsorted control pool library6 rep3
E2285 Sox2P-reporter -116 kb, unsorted control pool library6 rep3 Fw
mapped_integrations_-116kb_Sox2P_pools.txt


title: clone Sox2P-reporter 23_C9_P7 Fw

description:
clone Sox2P-reporter 23_C9_P7
E2041 clone Sox2P-reporter 23_C9_P7 Fw
mapped_integrations_Sox2P_clones.txt


title: RNA-seq of CD19-CAR T cells from healthy human donor 61, 4h post-stimulation

description:
STIM_4H_CD19_DN61
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.count.csv
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.TPM.csv


description:
Sox2P-reporter -116 kb, unsorted control pool library5 rep3
E2285 Sox2P-reporter -116 kb, unsorted control pool library5 rep3 Fw
mapped_integrations_-116kb_Sox2P_pools.txt


title: RNA-seq of GLUT1-OE HA-CAR T cells from healthy human donor 86, unstimulated

description:
UNSTIM_HA-GLUT1_DN86
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_unstimulated.count.csv
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_unstimulated.TPM.csv

value: healthy human donor 86

value: unstimulated


title: RNA-seq of GLUT1-OE HA-CAR T cells from healthy human donor 90, unstimulated

description:
UNSTIM_HA-GLUT1_DN90
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_unstimulated.count.csv
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_unstimulated.TPM.csv

value: healthy human donor 90

value: T cells


title: RNA-seq of HA-CAR T cells from healthy human donor 90, unstimulated

description:
UNSTIM_HA_DN90
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_unstimulated.count.csv
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_unstimulated.TPM.csv


title: RNA-seq of GLUT1-OE HA-CAR T cells from healthy human donor 77, unstimulated

description:
UNSTIM_HA-GLUT1_DN77
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_unstimulated.count.csv
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_unstimulated.TPM.csv

value: healthy human donor 77

value: GLUT1-OE HA-CAR T cells


description:
Sox2P-reporter -116 kb, unsorted control pool library10 rep3
E2285 Sox2P-reporter -116 kb, unsorted control pool library10 rep3 Fw
mapped_integrations_-116kb_Sox2P_pools.txt

value: F1 hybrid 129/Sv:CAST/EiJ


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

value: sorted pool


title: RNA-seq of T cells from healthy human donor 62, 4h post-stimulation

description:
STIM_4H_MOCK_DN62
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.count.csv
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.TPM.csv


title: KGN-H3K27Ac-T-INPUT

city: HangZhou

first: JIAMIN

last: JIN

address: QingChun East Road

country: China

institute: ZheJiang University

data_processing:
The ChIP-seq reads were aligned to the human genome mm10 using Bowtie (Version 2.0) with default parameters.
For peak calling, MACS2.0 was employed with default parameters and a significance threshold (q value cutoff = 0.05), as described previously,
To visualize the ChIP-seq data, deepTools2 was utilized, BAM coverage was used to generate the bigwig files.
The genome tracks were visualized in the software program IGV.  in different samples.
Peak annotation was performed using R and the ChIPseeker package and bedtools were employed to analyze the overlapping regions
Assembly: hg38
Supplementary files format and content: excel, narrow peak

source_name: ovarian

growth_protocol: DMEM-F12 with 10% FBS

extract_protocol:
Cross-linked with a final concentration of 1.5% formaldehyde
TruSeq DNA LT/HT Sample Prep Kit (Illumina) and underwent quality control on the Bioanalyzer (Agilent 2200).

treatment_protocol: 10 um testosterone for 24 h

value: ovarian

value: KGN

value: immortalized human granulosa cell

value: 10 um testosterone for 24 h


title: RNA-seq of GLUT1-OE CD19-CAR T cells from healthy human donor 17, unstimulated

description:
UNSTIM_CD19-GLUT1_DN17
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_unstimulated.count.csv
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_unstimulated.TPM.csv

value: healthy human donor 17

value: GLUT1-OE CD19-CAR T cells


title: RNA-seq of HA-CAR T cells from healthy human donor 77, unstimulated

description:
UNSTIM_HA_DN77
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_unstimulated.count.csv
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_unstimulated.TPM.csv

value: HA-CAR T cells


description:
Sox2P-reporter -116 kb, unsorted control pool library3 rep3
E2285 Sox2P-reporter -116 kb, unsorted control pool library3 rep3 Fw
mapped_integrations_-116kb_Sox2P_pools.txt

value: mESC

value: WT


title: RNA-seq of HA-CAR T cells from healthy human donor 86, unstimulated

description:
UNSTIM_HA_DN86
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_unstimulated.count.csv
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_unstimulated.TPM.csv

value: healthy human donor 86


title: KGN-H3K27Ac-Ctrl-INPUT

value: control


description:
Sox2P-reporter -116 kb, unsorted control pool library8 rep3
E2285 Sox2P-reporter -116 kb, unsorted control pool library8 rep3 Fw
mapped_integrations_-116kb_Sox2P_pools.txt

value: control pool


title: RNA-seq of CD19-CAR T cells from healthy human donor 17, unstimulated

description:
UNSTIM_CD19_DN17
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_unstimulated.count.csv
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_unstimulated.TPM.csv

value: T cells

value: CD19-CAR T cells

value: unstimulated


description:
Sox2P-reporter -116 kb, unsorted control pool library4 rep3
E2285 Sox2P-reporter -116 kb, unsorted control pool library4 rep3 Fw
mapped_integrations_-116kb_Sox2P_pools.txt

value: F1 hybrid 129/Sv:CAST/EiJ


title: RNA-seq of GLUT1-OE CD19-CAR T cells from healthy human donor 16, unstimulated

description:
UNSTIM_CD19-GLUT1_DN16
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_unstimulated.count.csv
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_unstimulated.TPM.csv

value: healthy human donor 16


title: KGN-H3K27Ac-T-CHIP

value: ovarian


title: KGN-H3K27Ac-Ctrl-CHIP

value: KGN


description:
Sox2P-reporter -116 kb, unsorted control pool library1 rep3
E2285 Sox2P-reporter -116 kb, unsorted control pool library1 rep3 Fw
mapped_integrations_-116kb_Sox2P_pools.txt


title: RNA-seq of GLUT1-OE CD19-CAR T cells from healthy human donor 11, unstimulated

description:
UNSTIM_CD19-GLUT1_DN11
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_unstimulated.count.csv
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_unstimulated.TPM.csv

value: healthy human donor 11


description:
Sox2P-reporter -116 kb, unsorted control pool library2 rep3
E2285 Sox2P-reporter -116 kb, unsorted control pool library2 rep3 Fw
mapped_integrations_-116kb_Sox2P_pools.txt


title: RNA-seq of CD19-CAR T cells from healthy human donor 16, unstimulated

description:
UNSTIM_CD19_DN16
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_unstimulated.count.csv
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_unstimulated.TPM.csv


title: RNA-seq of CD19-CAR T cells from healthy human donor 11, unstimulated

description:
UNSTIM_CD19_DN11
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_unstimulated.count.csv
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_unstimulated.TPM.csv


title: B1 glucocorticoid receptor ChIP-Seq nodex 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)

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.


title: clone Sox2P-reporter 23_C9_P7 Rv

description:
clone Sox2P-reporter 23_C9_P7
E2041 clone Sox2P-reporter 23_C9_P7 Rv
mapped_integrations_Sox2P_clones.txt

value: insertion clone


title: RNA-seq of T cells from healthy human donor 61, 4h post-stimulation

description:
STIM_4H_MOCK_DN61
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.count.csv
RNAseq_CAR_T_cells_with_GLUT1_OE_and_control_stimulated.TPM.csv

value: healthy human donor 61

value: 4h post-stimulation


description:
Sox2P-reporter -116 kb, population P6 pool5 rep3
E2285 Sox2P-reporter -116 kb, population P6 pool5 rep3 Fw
mapped_integrations_-116kb_Sox2P_pools.txt

value: sorted pool


description:
Sox2P-reporter -116 kb, population P6 pool4 rep3
E2285 Sox2P-reporter -116 kb, population P6 pool4 rep3 Fw
mapped_integrations_-116kb_Sox2P_pools.txt

value: mESC


title: MPM167_LOW_SMRP

city: Houston

first: Sung Wook

last: Kang

state: TX

address: one plaza

department: Surgery

institute: Baylor college of medicine

data_processing:
The raw sequence reads were mapped to GRCh38 using STAR (V2.5.3a).
The alignmented bam file were performed using markduplicated.
The FPRM value extract were performed using cufflinks.
Assembly: CRCh38
Supplementary files format and content: tab-delimited text file FPKM counts for each samples
Supplementary files format and content: tab-delimited text file Cufflinks counts for each samples

source_name: Tumor

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1ug of total RNA was used for the construction of sequencing libraries.
The clean RNA samples were used for library preparation in the Genomic and RNA Profling Core, Baylor College of Medicine. Libraries were constructed using a Truseq library preparation kit (Illumina, USA) following the manufacturer’s instructions.

value: Tumor

tag: subject status

value: MPM patients receiving ICT

tag: smrp group

value: LOW SMRP

tag: smrp (nmol/l)

tag: age at_tx

tag: Sex

value: M

tag: race

value: White

tag: histology

value: Epithelioid

tag: asbestos hx

tag: pd-l1 ihc(%)

tag: ici abs

value: NIVOLUMAB


title: MPM106_LOW_SMRP

tag: tissue

value: F


title: SUP-B15 glucocorticoid receptor ChIP-Seq Exp3C nodex

tag: cell line

tag: treatment


title: B1 glucocorticoid receptor ChIP-Seq nodex Rep1

tag: chip antibody


title: MPM091_LOW_SMRP

value: African American


title: MPM094_LOW_SMRP


title: MPM081_LOW_SMRP

value: NIVOLUMAB+IPILIMUMAB


description:
Sox2P-reporter -116 kb, population P6 pool3 rep3
E2285 Sox2P-reporter -116 kb, population P6 pool3 rep3 Fw
mapped_integrations_-116kb_Sox2P_pools.txt

value: F1 hybrid 129/Sv:CAST/EiJ

tag: cell type

tag: genotype

value: WT

tag: launch pad_location

tag: insert

tag: sorted gate

tag: sample type


title: MPM038_LOW_SMRP

tag: subject status

tag: smrp group

tag: smrp (nmol/l)

tag: age at_tx


title: SUP-B15 glucocorticoid receptor ChIP-Seq Exp3A nodex


title: MPM059_LOW_SMRP

tag: Sex

tag: race

tag: histology

tag: asbestos hx


title: SUP-B15 glucocorticoid receptor ChIP-Seq Exp3B nodex

tag: cell line


title: MPM179_HIGH_SMRP

tag: tissue

value: HIGH SMRP

tag: pd-l1 ihc(%)

tag: ici abs


title: MPM015_LOW_SMRP


description:
Sox2P-reporter -116 kb, population P5 pool5 rep3
E2285 Sox2P-reporter -116 kb, population P5 pool5 rep3 Fw
mapped_integrations_-116kb_Sox2P_pools.txt

tag: cell type

tag: genotype


title: SUP-B15 glucocorticoid receptor ChIP-Seq Exp2B nodex

tag: treatment

tag: chip antibody


title: MPM057_HIGH_SMRP


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

tag: launch pad_location

tag: insert

tag: sorted gate

tag: sample type


title: MPM073_HIGH_SMRP

tag: subject status

tag: smrp group

tag: smrp (nmol/l)

tag: age at_tx


title: MPM054_HIGH_SMRP

tag: Sex

tag: race

tag: histology

tag: asbestos hx


title: MPM148_LOW_SMRP

tag: tissue

tag: pd-l1 ihc(%)

tag: ici abs


title: MPM047_HIGH_SMRP

value: PEMBROLIZUMAB


title: SUP-B15 glucocorticoid receptor ChIP-Seq Exp1B nodex

tag: cell line

tag: treatment


description:
Sox2P-reporter -116 kb, population P5 pool4 rep3
E2285 Sox2P-reporter -116 kb, population P5 pool4 rep3 Fw
mapped_integrations_-116kb_Sox2P_pools.txt

tag: cell type

tag: genotype

tag: launch pad_location


title: MPM030_HIGH_SMRP


title: MPM007_HIGH_SMRP


description:
Sox2P-reporter -116 kb, population P6 pool2 rep3
E2285 Sox2P-reporter -116 kb, population P6 pool2 rep3 Fw
mapped_integrations_-116kb_Sox2P_pools.txt

tag: insert

tag: sorted gate

tag: sample type


description:
Sox2P-reporter -116 kb, population P5 pool3 rep3
E2285 Sox2P-reporter -116 kb, population P5 pool3 rep3 Fw
mapped_integrations_-116kb_Sox2P_pools.txt


title: GD835_RPMI8226_DMSO_ctrl_rep3

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

data_processing:
Reads were aligned to human genome (hg38) with subread-align version 2.0.1 (PMID: 23558742)
Read counts were calculated with the featureCounts function from Rsubread version 2.0.1 (PMID: 24227677) against RefSeq gene annotation
Gene expression level from RNA-Seq is measured by rpkm (PMID: 18516045) with an in-house script.
Assembly: hg38
Supplementary files format and content: Txt file, from left to right represent entrz ID, gene symbol, and gene expression values in log2(RPKM+1) for each samples.

source_name: RPMI 8226

growth_protocol: MM cell lines MM.1S (ATCC, CRL-2974) and RPMI8226 (ATCC, CCL-155) were obtained from the American Type Culture Collection (Manassas, VA, USA). Cell lines tested for mycoplasma every six months. Cells were maintained in RPMI-1640 complete media as described previously (PMID: 35205675)

extract_protocol:
Total RNA was extracted using the Qiagen kit (RNeasy Plus Mini Kit, 74134)
RNA-Seq library were prepared by Admera Health (South Plainfield, NJ, USA) using NEBNext Ultra II RNA (Directional)

treatment_protocol: Cells were treated with CB-6644 (MedChemExpress, HY-114429) at concentrations (MM. 1S,120nM; RPMI 8226, 40nM) to assess its impact on cell viability over a 72-hour treatment period

value: RPMI 8226

value: DMSO


description:
Sox2P-reporter -116 kb, population P6 pool1 rep3
E2285 Sox2P-reporter -116 kb, population P6 pool1 rep3 Fw
mapped_integrations_-116kb_Sox2P_pools.txt

value: mESC

value: sorted pool


title: GD833_RPMI8226_DMSO_ctrl_rep1


description:
Sox2P-reporter -116 kb, unsorted control pool library9 rep3
E2285 Sox2P-reporter -116 kb, unsorted control pool library9 rep3 Rv
mapped_integrations_-116kb_Sox2P_pools.txt

value: control pool


title: MPM090_HIGH_SMRP

value: Tumor

tag: subject status

value: MPM patients receiving ICT

tag: smrp group

tag: smrp (nmol/l)


title: SUP-B15 glucocorticoid receptor ChIP-Seq Exp2C nodex

tag: chip antibody


title: GD832_RPMI8226_CB6644_rep3

value: CB-6644 treatment (40nM,72hrs)


description:
Sox2P-reporter -116 kb, unsorted control pool library10 rep3
E2285 Sox2P-reporter -116 kb, unsorted control pool library10 rep3 Rv
mapped_integrations_-116kb_Sox2P_pools.txt


title: GD830_RPMI8226_CB6644_rep1


title: B1 glucocorticoid receptor ChIP-Seq dex Rep1

value: 1 µM dexamethosone


title: GD831_RPMI8226_CB6644_rep2


description:
Sox2P-reporter -116 kb, unsorted control pool library8 rep3
E2285 Sox2P-reporter -116 kb, unsorted control pool library8 rep3 Rv
mapped_integrations_-116kb_Sox2P_pools.txt


title: SUP-B15 glucocorticoid receptor ChIP-Seq Exp1C nodex


title: GD182_MM1S_DMSO_rep3

data_processing:
Reads were aligned to mouse genome (hg38) with bowtie2 version 2.4.2 (PMID: 22388286),Reads mapped to multiple genomic positions were removed. For reads mapped to the same genomic coordinates, only one copy was kept.
Peaks were called using MACS v3.0 with the significance cut-off q-value <= 0.0001
Assembly: hg38
Supplementary files format and content: txt file; columns from left to right: chromosome, start, end, name, int(-10*log10qvalue), reserved column, fold-change at peak summit, -log10pvalue at peak summit, -log10qvalue at peak summit, relative summit position to peak start

growth_protocol: MM cell lines MM.1S (ATCC, CRL-2974) were obtained from the American Type Culture Collection (Manassas, VA, USA). Cell lines tested for mycoplasma every six months. Cells were maintained in RPMI-1640 complete media as described previously(PMID: 35205675)

extract_protocol:
DNA extract protocol follows previous description (PMID: 35205675).
Omni-ATAC libraries for chromatin accessibility were prepared using a Tagment DNA Enzyme and Buffer Large Kit (Illumina, San Diego, CA, USA, 20034198) and following procedures descried previously (PMID: 35205675)

treatment_protocol: Cells were treated with CB-6644 (MedChemExpress, HY-114429) at 120nM to assess its impact on cell viability over a 72-hour treatment period


title: SUP-B15 glucocorticoid receptor ChIP-Seq Exp3C dex


title: GD181_MM1S_DMSO_rep2


title: GD179_MM1S_CB6644_rep3

value: CB-6644 treatment (120nM,72hrs)


title: SUP-B15 glucocorticoid receptor ChIP-Seq Exp3B dex


title: GD180_MM1S_DMSO_rep1


description:
Sox2P-reporter -116 kb, unsorted control pool library7 rep3
E2285 Sox2P-reporter -116 kb, unsorted control pool library7 rep3 Rv
mapped_integrations_-116kb_Sox2P_pools.txt


description:
Sox2P-reporter -116 kb, unsorted control pool library6 rep3
E2285 Sox2P-reporter -116 kb, unsorted control pool library6 rep3 Rv
mapped_integrations_-116kb_Sox2P_pools.txt


title: GD178_MM1S_CB6644_rep2


title: SUP-B15 glucocorticoid receptor ChIP-Seq Exp3A dex


title: GD177_MM1S_CB6644_rep1


title: GD834_RPMI8226_DMSO_ctrl_rep2


description:
Sox2P-reporter -116 kb, unsorted control pool library5 rep3
E2285 Sox2P-reporter -116 kb, unsorted control pool library5 rep3 Rv
mapped_integrations_-116kb_Sox2P_pools.txt


title: SUP-B15 glucocorticoid receptor ChIP-Seq Exp1A nodex


title: B1 glucocorticoid receptor ChIP-Seq dex Rep2


title: SUP-B15 glucocorticoid receptor ChIP-Seq Exp2C dex


title: T109

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

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

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: No

tag: tumor size_(cm)

value: Synovial Sarcoma

tag: tumor type

tag: site

value: Peripheral


title: T85

description:
Sample_Counts.csv
Patient_Counts.csv

value: Yes

tag: tissue


title: T102

description:
Sample_Counts.csv
Patient_Counts.csv

value: visceral


title: T116

description:
Sample_Counts.csv
Patient_Counts.csv


title: SUP-B15 glucocorticoid receptor ChIP-Seq Exp2A dex

tag: cell line

tag: treatment


title: SUP-B15 glucocorticoid receptor ChIP-Seq Exp2B dex


description:
Sox2P-reporter -116 kb, population P5 pool2 rep3
E2285 Sox2P-reporter -116 kb, population P5 pool2 rep3 Fw
mapped_integrations_-116kb_Sox2P_pools.txt

value: F1 hybrid 129/Sv:CAST/EiJ

tag: cell type

tag: genotype

value: WT

tag: launch pad_location

tag: insert

tag: sorted gate

tag: sample type


description:
Sox2P-reporter -116 kb, unsorted control pool library3 rep3
E2285 Sox2P-reporter -116 kb, unsorted control pool library3 rep3 Rv
mapped_integrations_-116kb_Sox2P_pools.txt


title: T97

description:
Sample_Counts.csv
Patient_Counts.csv

tag: patient id

tag: fusion gene

tag: metastasis time_(days)

tag: metastasis


title: T87

description:
Sample_Counts.csv
Patient_Counts.csv

tag: overall survival_time_(days)

tag: overal survival

tag: histology

tag: poorly differentiated_histology


title: SUP-B15 glucocorticoid receptor ChIP-Seq Exp1C dex

tag: chip antibody


description:
Sox2P-reporter -116 kb, unsorted control pool library2 rep3
E2285 Sox2P-reporter -116 kb, unsorted control pool library2 rep3 Rv
mapped_integrations_-116kb_Sox2P_pools.txt

tag: cell line


description:
Sox2P-reporter -116 kb, unsorted control pool library4 rep3
E2285 Sox2P-reporter -116 kb, unsorted control pool library4 rep3 Rv
mapped_integrations_-116kb_Sox2P_pools.txt


title: SUP-B15 glucocorticoid receptor ChIP-Seq Exp1B dex

tag: treatment


title: T118

description:
Sample_Counts.csv
Patient_Counts.csv

tag: tumor size_(cm)

tag: tissue

tag: tumor type

tag: site


title: T14

description:
Sample_Counts.csv
Patient_Counts.csv


description:
Sox2P-reporter -116 kb, unsorted control pool library1 rep3
E2285 Sox2P-reporter -116 kb, unsorted control pool library1 rep3 Rv
mapped_integrations_-116kb_Sox2P_pools.txt

tag: cell type

tag: genotype

tag: launch pad_location

tag: insert

tag: sorted gate


title: T82

description:
Sample_Counts.csv
Patient_Counts.csv

tag: patient id

tag: fusion gene

tag: metastasis time_(days)

tag: metastasis


title: 1dpi

city: Toronto

first: Jeff

last: Wrana

state: Ontario

address: 600 University Avenue

country: Canada

institute: Lunenfeld-Tanenbaum Research Institute

description: 10x Genomics RNA

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm39
Supplementary files format and content: cluall_m5_dblt_filtd_nopeaksfilt_clu012_wnn_embedded_clusterd_idented_formatted_rna.Rdata: contains processed R object for all 3 samples.

source_name: Small intestine

extract_protocol:
Small intestines were flushed with ice-cold PBS, cut longitudinally into roughly 2-mm-long pieces, rinsed with ice-cold PBS, and incubated in 2mM EDTA at 4°C for 40min with continuous shaking. The whole-epithelial segments were isolated by vigorous shaking in ice-cold PBS, and enriched for crypts by passing dissociated epithelial segments through a 70µm mesh cell strainer.
10x Genomics Single Cell Gene Expression

value: Small intestine

value: 12Gy irradiation (24hr)


title: SUP-B15 glucocorticoid receptor ChIP-Seq Exp1A dex


title: T80

description:
Sample_Counts.csv
Patient_Counts.csv

tag: overall survival_time_(days)

tag: overal survival

tag: histology

tag: poorly differentiated_histology


title: T113

description:
Sample_Counts.csv
Patient_Counts.csv

tag: tumor size_(cm)

value: Central


title: LLC cells, low2

city: Jinan

first: guomeng

last: Sha

address: Beiyuan Street

institute: Second Hospital of Shandong University

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter-Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters-mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: LLC

extract_protocol:
After homogenization of tissue samples, total RNA was extracted by TRNzol Universal Reagent (TIANGEN, China).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: cell line

value: LLC

value: non-smal cell lung cancer cells

tag: stress

value: Low dose LPS

tag: treatment

value: treat with medicine


description:
Sox2P-reporter -116 kb, population P6 pool4 rep3
E2285 Sox2P-reporter -116 kb, population P6 pool4 rep3 Rv
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.

tag: cell type

value: mESC

tag: sample type

value: sorted pool


title: LLC cells, low3


title: LLC cells, low1


title: Bleomycin_spleen_Treg

data_processing:
Sequencing was performed on HiSeq 2500 platform in a 75-base single-end mode.
Illumina RTA 1.18.64 software was used for base calling.
Generated reads were mapped to the mouse (mm10) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: Spleen

extract_protocol:
Total RNA was extracted from cells with TRIzol reagent and a miRNeasy Micro kit (Qiagen) following the manufacturer’s instruction.
Full-length cDNA was prepared using a SMART-Seq HT Kit (Takara Bio, Japan). According to the SMART-Seq kit instructions, an Illumina library was then prepared using a NexteraXT DNA Library Preparation Kit (Illumina).

tag: tissue

value: Spleen

tag: genotype

value: bleomycin


title: LLC cells, high3

value: High dose LPS


description:
Sox2P-reporter -116 kb, population P6 pool3 rep3
E2285 Sox2P-reporter -116 kb, population P6 pool3 rep3 Rv
mapped_integrations_-116kb_Sox2P_pools.txt

tag: launch pad_location

tag: insert

tag: sorted gate


title: T115

description:
Sample_Counts.csv
Patient_Counts.csv

tag: patient id

tag: fusion gene

tag: metastasis time_(days)

value: Monophasic

value: No

value: Synovial Sarcoma

tag: tumor type

tag: site

value: Peripheral


title: Heart macrophages, WD, scRNAseq

city: Nanjing

first: Lai

last: Zhang

state: Jiangsu

address: Hushan Road, Jiangning District, Nanjing

institute: The Affiliated Jiangning Hospital of Nanjing Medical University

description: 10x Genomics

data_processing:
Celescope was used to base-calling, alignment, filtering and generation of normalized abundance measurements.
The highly variable features (genes) for this data were calculated with “find variable features” in Seurat which uses a mean variability plot. Here average expression and dispersion per feature is calculated and features are divided into bins to get z-scores for dispersion per bin.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Hearts

extract_protocol:
Freshly collected heart form diet mice were flushed with ice-cold HBSS (Mg2+/Ca2+ free, PH 7.2) to remove the blood. The heart was cut into small pieces and digested with collagenase II (HBSS without Mg2+/Ca2+ supplemented with 5mg/ml collagenase type II) for 30 minutes at 37℃. Cells were washed and re-suspended in PBS and stained with CD45, CD11b and F4/80 for 30 minutes at 4℃, washed and resuspended in PBS. After gating on CD45+F4/80+CD11b+ cells, doublets were excluded and live cells were analyzed using forward scatter (FSC) and side scatter (SSC) live-dead exclusion. Single cell analysis software (FlowJo) was used to analyze cell cytometric data. Cardiac macrophages were identified as CD45+CD11b+F4/80+ cells.
Single-cell suspensions were prepared as outlined by the 10x Genomics Single Cell 3′ v2 Reagent kit user guide. Briefly, samples were washed twice in PBS  plus 0.04% BSA . Each wash was performed with a 6 min centrifugation at 330g and resuspension in 1 ml PBS plus 0.04% BSA. Sample viability was assessed using trypan blue and a hemocytometer, and the appropriate volume for each sample was calculated. After droplet generation, samples were transferred onto a prechilled 96-well plate, plates were heat-sealed and reverse transcription was performed using a Veriti 96-well thermal cycler. After reverse transcription, cDNA was recovered using recovery agent provided by 10x Genomics followed by a Silane DynaBead cleanup as outlined by the user guide. Purified cDNA was amplified and cleaned up using SPRIselect beads. Samples were diluted at 4:1 (elution buffer (Qiagen)/cDNA) and run on a Bioanalyzer to determine cDNA concentration. cDNA libraries were prepared as outlined by the Single Cell 3′ Reagent kit v2 user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration (as recommended by 10x Genomics).

value: Hearts

value: Heart macrophages

value: Wild type

value: WD-induced mouse models

tag: age

value: 32-34weeks old


description:
Sox2P-reporter -116 kb, population P6 pool2 rep3
E2285 Sox2P-reporter -116 kb, population P6 pool2 rep3 Rv
mapped_integrations_-116kb_Sox2P_pools.txt

value: F1 hybrid 129/Sv:CAST/EiJ

value: WT


title: LLC cells, high2

value: LLC

value: non-smal cell lung cancer cells

value: treat with medicine


title: Heart macrophages, HFD, scRNAseq

description: 10x Genomics

value: HFD-induced mouse models


description:
Sox2P-reporter -116 kb, population P6 pool1 rep3
E2285 Sox2P-reporter -116 kb, population P6 pool1 rep3 Rv
mapped_integrations_-116kb_Sox2P_pools.txt

value: mESC

value: sorted pool


title: T89

description:
Sample_Counts.csv
Patient_Counts.csv

tag: metastasis

tag: overall survival_time_(days)

tag: overal survival

tag: histology

value: Monophasic

tag: poorly differentiated_histology

tag: tumor size_(cm)


title: LLC cells, high1

tag: cell line

tag: cell type

tag: stress

value: High dose LPS

tag: treatment


title: Heart macrophages, CD, scRNAseq

description: 10x Genomics

tag: tissue

tag: genotype

value: CD-induced mouse models


description:
Sox2P-reporter -116 kb, population P5 pool5 rep3
E2285 Sox2P-reporter -116 kb, population P5 pool5 rep3 Rv
mapped_integrations_-116kb_Sox2P_pools.txt

tag: launch pad_location

tag: insert

tag: sorted gate

tag: sample type


title: T79

description:
Sample_Counts.csv
Patient_Counts.csv

tag: patient id

tag: fusion gene

tag: metastasis time_(days)

value: Yes

value: Synovial Sarcoma

tag: tumor type

tag: site

value: Peripheral


description:
Sox2P-reporter -116 kb, population P6 pool5 rep3
E2285 Sox2P-reporter -116 kb, population P6 pool5 rep3 Rv
mapped_integrations_-116kb_Sox2P_pools.txt


title: LLC cells, control3

value: Control


title: T117

tag: histology

value: Biphasic

value: Central


title: LLC cells, control2


title: Bleomycin_lung_Treg

value: Lung

value: bleomycin


title: T100

description:
Sample_Counts.csv
Patient_Counts.csv

tag: metastasis

tag: overall survival_time_(days)

tag: overal survival

tag: poorly differentiated_histology

tag: tumor size_(cm)


title: Wildtype harvested following 5 hours of sleep deprivation and 2 hours of recovery sleep, replicate 4

city: Spokane

first: Lucia

last: Peixoto

state: WA

address: PO Box 1495

department: College of Medicine

institute: Washington State University, Spokane

data_processing:
HiSeq Control Software (v. 2.2.68) was used for base calling. Raw bcl files were converted to fastq files using bcl2fastq (v. 2.17.1.14). Adapters were trimmed from the fastq files during the conversion.
Raw sequencing reads from the fastq files were processed using the "mapping mode" in Salmon (v. 1.8), which consists of two steps, indexing and quantification. To improve the accuracy of quantification estimates from Salmon, an index was built that incorporated a set of genome targets as decoys. To prepare this index, the reference genome (GRCm39.primary_assembly.genome.fa.gz), reference transcriptome (gencode.vM28.transcripts.fa.gz), and GTF coordinates (gencode.vM28.annotation.gtf.gz) were obtained from GENCODE, release M28. Using the concatenated list of transcriptome targets along with the genome targets, the `salmon index` function was used to build the index with the flags `--gencode`, `--threads 4`, and  `-k 31`. `salmon quant` was used to perform quantification with the flags `--threads 6`, `--libType A`, and `--numBootstraps 30`.
Following quantification, the Tximeta package (v. 1.18) from the R/Bioconductor project was used to import transcript quantification data and summarize to the gene level.
The matrix of gene counts was filtered to remove genes with less than 10 reads across more than 5 samples. The matrix of expressed genes was then normalized with Upper Quartile (EDASeq, v. 2.34) followed by remove unwanted variation (RUVs) (RUVSeq, v. 1.34).
Assembly: GRCm39, GENCODE M28
Supplementary files format and content: text file, matrix of gene counts (summarized experiment object from Tximeta)

source_name: pre-frontal cortex

growth_protocol: Adult male (8-12 weeks old) wild-type C57BL/6J mice were individually housed in standard cages at 24 ± 1°C on a 12:12 hr light:dark cycle with food and water ad libitum.

extract_protocol:
RNA was extracted from thawed tissue using the Qiagen RNAeasy Microarray Tissue kit with RWT buffer. Tissue was lysed and homogenized using a TissueLyzer. 1ml of Qiazol was added to the pre-sterilized 2ml round bottom tubes with one 5mm steel bead inside and tissue was added. The TissueLyzer was operated for 3 min at 50Hz, allowed to come to a stop, and repeated. Tubes were spun down before opening. Lysate was transferred to a clean 2 ml tube. RNA was isolated through phase separation. 200 µl pf chloroform was added, following by vigorous shaking. Tubes were incubated at RT for 3 min and centrifuged at 12,000 g (max speed) at 4 °C for 15 min. The aqueous phase was transferred to a new tube and total RNA (binding and washing with the RNAeasy column) was purified. 600 µl (1 volume) of 100% EtOH was added. 600 µl was transferred to an RNAeasy mini spin column placed inside a 2ml collection tube and centrifuged 15 s at max speed at RT. This was repeated with the remaining 600 µl. 500 µl of Buffer RWT (bought separately from Qiagen) was added. The tube was centrifuged for 15 s at max speed at RT. The flow through was discarded and the collection tube was kept. 500 µl of buffer RPE was added. The tube was centrifuged for 15 s at max speed at RT. The flow through was discarded and the collection tube was kept. 500 µl of buffer RPE was added. The tube was centrifuged for 2 min at max speed at RT. The flow through was discarded and the collection tube was kept. The spin column was placed on a new collection tube and centrifuged at max speed for a minute to prevent EtOH carryover. RNA was then eluted, and the column was placed into a 1.5 ml Eppendorf tube. 30 µl of RNAse free water was added and the tube was centrifuged for 1 min at max speed at RT. The volume in the tube was pipetted back into the column and the previous step was repeated. 1 µl was used for quantification with the Nanodrop Spectrophotometer. Following quantification, RNA was frozen at -80 °C.
The integrity of total RNA was assessed using Fragment Analyzer (Advanced Analytical Technologies, Inc, Ankeny, IA) with the High Sensitivity RNA Analysis Kit (Advanced Analytical Technologies, Inc). RNA Quality Numbers (RQNs) from 1 to 10 were assigned to each sample to indicate its integrity or quality. ‘10’ stands for a perfect RNA sample without any degradation, whereas ‘1’ marks a completely degraded sample. All RNA samples had RQNs ranging from 8.8 to 10 and were used for RNA library preparation with the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA). Briefly, mRNA was isolated from 2.5 mg of total RNA using poly-T oligo attached to magnetic beads and then subjected to fragmentation, followed by cDNA synthesis, dA-tailing, adaptor ligation, and PCR enrichment. The sizes of RNA libraries were assessed by Fragment Analyzer with the High Sensitivity NGS Fragment Analysis Kit (Advanced Analytical Technologies, Inc). The concentrations of RNA libraries were measured by StepOnePlus Real-Time PCR System (ThermoFisher Scientific, San Jose, CA) with the KAPA Library Quantification Kit (Kapa Biosystems, Wilmington, MA). The libraries were diluted to 2 nM with Tris buffer (10 mM Tris-HCl, pH 8.5) and denatured with 0.1 M NaOH. Eighteen pM libraries were clustered in a high-output flow cell using HiSeq Cluster Kit v4 on a cBot (Illumina). After cluster generation, the flow cell was loaded onto HiSeq 2500 for sequencing using the HiSeq SBS kit v4 (Illumina). DNA was paired-end sequenced with a read length of 100 bp and an average sequencing depth of 52 million reads per sample.

treatment_protocol: Following acclimation and habituation, mice were divided into sleep deprivation, sleep deprivation with subsequent recovery sleep, or home cage control conditions. Beginning at light onset (zeitgeber time 0), sleep deprived mice were kept awake for 5 hours via gentle handling. Recovery sleep mice were then allowed to sleep for 2 hours. Home cage mice served as time-matched circadian controls and were allowed to sleep for either 5 or 7 hours, depending on the duration of the respective treatment.

tag: tissue

value: pre-frontal cortex

tag: cell type

value: brain cell

value: WT

tag: treatment

value: recovery sleep

tag: age

value: 8-12 weeks

tag: Sex

value: male


title: LLC cells, control1

tag: cell line

value: LLC

value: non-smal cell lung cancer cells

tag: stress


description:
Sox2P-reporter -116 kb, population P5 pool4 rep3
E2285 Sox2P-reporter -116 kb, population P5 pool4 rep3 Rv
mapped_integrations_-116kb_Sox2P_pools.txt

value: F1 hybrid 129/Sv:CAST/EiJ

value: mESC

tag: genotype

tag: launch pad_location

tag: insert

tag: sorted gate

tag: sample type

value: sorted pool


title: gastruloid t120 - R

city: Princeton

first: Harold

middle: Michael

last: McNamara

state: NJ

address: Carl Icahn Laboratory, South Drive

department: Lewis-Sigler Institute

institute: Princeton University

description: 10x Genomics

data_processing:
demultiplexing
conversion to counts tables (i.e., matrices of cell barcodes and gene expression reads) using CellRanger 6.0.1 platform (10x Genomics)
Assembly: Mm10_2020 build, modified to include additional synthetic genes (rtTA, iRFP, Cre, BFP, StoplightReporter) associated with signal reporters and recorders
Supplementary files format and content: all processed files are .h5 files comprising count matrices generated by CellRanger pipleine (10x Genomics)

source_name: gastruloid

extract_protocol:
Gastruloids were dissociated to single cells, and run on a flow cytometery (Sony SH800) to isolate signle cells. Cells were then captured using the Chromium microfluidics platform (10x genomics)
Libraries were prepared according to the 10x Genomics Single Cell 5' v2 Gene Expression workflow, with additional primer added for direct capture of a synthetic iRFP reporter

value: gastruloid

value: mouse embryonic stem cell

value: Engineered Wnt recording line

value: No Wnt activity recorded


city: Amsterdam

first: Christina

last: Moene

address: Plesmanlaan 121

institute: Netherlands Cancer Institute

description:
Sox2P-reporter -116 kb, population P5 pool3 rep3
E2285 Sox2P-reporter -116 kb, population P5 pool3 rep3 Rv
mapped_integrations_-116kb_Sox2P_pools.txt


title: Wildtype harvested following 5 hours of sleep deprivation and 2 hours of recovery sleep, replicate 3


title: Wildtype harvested following 5 hours of sleep deprivation and 2 hours of recovery sleep, replicate 2


title: T77

description:
Sample_Counts.csv
Patient_Counts.csv

tag: patient id

tag: fusion gene

tag: metastasis time_(days)

tag: metastasis

tag: histology

value: Monophasic

value: Yes

value: Synovial Sarcoma

tag: tumor type

tag: site

value: visceral


description:
Sox2P-reporter -116 kb, population P5 pool2 rep3
E2285 Sox2P-reporter -116 kb, population P5 pool2 rep3 Rv
mapped_integrations_-116kb_Sox2P_pools.txt

tag: cell type

value: WT


title: T92

value: Biphasic

tag: tissue

value: Central


title: gastruloid t120 - G

description: 10x Genomics

tag: treatment

value: Wnt recorded at 96 h


title: T8

value: Peripheral


description:
Sox2P-reporter -116 kb, population P5 pool1 rep3
E2285 Sox2P-reporter -116 kb, population P5 pool1 rep3 Rv
mapped_integrations_-116kb_Sox2P_pools.txt

tag: cell line


description:
Sox2P-reporter -116 kb, population P4 pool5 rep3
E2285 Sox2P-reporter -116 kb, population P4 pool5 rep3 Rv
mapped_integrations_-116kb_Sox2P_pools.txt


title: Wildtype homecage control harvested at ZT hour 7, replicate 4

value: pre-frontal cortex

value: brain cell

value: control

tag: age

value: 8-12 weeks

tag: Sex

value: male


description:
Sox2P-reporter -116 kb, population P5 pool1 rep3
E2285 Sox2P-reporter -116 kb, population P5 pool1 rep3 Fw
mapped_integrations_-116kb_Sox2P_pools.txt

value: F1 hybrid 129/Sv:CAST/EiJ

value: mESC

tag: genotype

tag: launch pad_location

value: sorted pool


title: Wildtype harvested following 5 hours of sleep deprivation and 2 hours of recovery sleep, replicate 5

value: recovery sleep


title: TGM treated mice Gene expression

city: Newark

first: Alexander

last: Lemenze

state: New Jersey

address: 185 South Orange Ave

institute: Rutgers

description: polyA RNA

data_processing:
Cellranger v7 count
Assembly: mm10
Supplementary files format and content: CellRanger h5 files per mouse

source_name: Skin (dermis & epidermis)

extract_protocol:
Immune cells were collected following skin tissue (dermis and epidermis) digestion  with collagenase type 1.  3 mice were used from each treatment.  Each single cell suspecion from the mice was stained with a CD45+ antibody and a unique Hastag #.  The cells were sorted for CD45+ cells and pooled by treatment before being submitted for the scRNAseq process.
10X scRNA gene expression and hashtagging.

value: Skin (dermis & epidermis)

value: TGM

tag: library type

value: mRNA


title: Wildtype homecage control harvested at ZT hour 7, replicate 5

value: WT


title: gastruloid t96

description: 10x Genomics

value: gastruloid

value: mouse embryonic stem cell

value: Engineered Wnt recording line


title: Wildtype homecage control harvested at ZT hour 7, replicate 3


title: TGM treated mice Hashtags

description: Hashtag-derived oligos (HTOs)

library_source: other

molecule: protein

value: HTO

tag: adt

value: TotalSeqA anti-mouse Hashtag 6, TotalSeqA anti-mouse Hashtag 9, TotalSeqA anti-mouse Hashtag 12


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

tag: insert

tag: sorted gate

tag: sample type


title: PBS treated mice Hashtags

description: Hashtag-derived oligos (HTOs)

value: PBS


title: Wildtype homecage control harvested at ZT hour 7, replicate 2

value: pre-frontal cortex

value: brain cell

value: control


title: T111

description:
Sample_Counts.csv
Patient_Counts.csv

tag: patient id

tag: fusion gene

tag: metastasis time_(days)

tag: metastasis

tag: overall survival_time_(days)

tag: overal survival

value: Biphasic

tag: poorly differentiated_histology

value: No

tag: tumor size_(cm)

value: Synovial Sarcoma

value: Peripheral


title: PBS treated mice Gene expression

description: polyA RNA

tag: tissue

value: Skin (dermis & epidermis)

tag: treatment


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

tag: cell line

value: F1 hybrid 129/Sv:CAST/EiJ

tag: cell type

value: mESC

tag: genotype

value: sorted pool


title: Wildtype homecage control harvested at ZT hour 7, replicate 1

value: WT

tag: age

value: 8-12 weeks

tag: Sex

value: male


title: T94

tag: histology

value: Monophasic

tag: tumor type

value: Metastasis

tag: site


title: T108

description:
Sample_Counts.csv
Patient_Counts.csv

tag: patient id

tag: fusion gene

value: Yes

value: visceral


title: T7

description:
Sample_Counts.csv
Patient_Counts.csv

tag: metastasis time_(days)

tag: metastasis


title: Wildtype harvested following 5 hours of sleep deprivation and 2 hours of recovery sleep, replicate 1

value: pre-frontal cortex

value: brain cell

value: recovery sleep


title: T112

description:
Sample_Counts.csv
Patient_Counts.csv

tag: overall survival_time_(days)

tag: overal survival


title: Dopaminergic neuron nuclei, Lrrk2 G2019S mutants, sample 2

city: Chicago

first: Rajeshwar

last: Awatramani

state: IL

address: 2344 W Charleston, APT 2

department: Neurology

institute: Northwestern University

description: 10x Genomics snRNA-Seq experiment

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

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.

value: Midbrain

tag: strain

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

value: Dopaminergic neurons

value: male and female

tag: developmental stage

value: adult


title: Dopaminergic neuron nuclei, Lrrk2 G2019S mutants, sample 1

description: 10x Genomics snRNA-Seq experiment

tag: tissue


title: Dopaminergic neuron nuclei, controls, sample 2

description: 10x Genomics snRNA-Seq experiment

value: Lrrk2 WT


description:
Sox2P-reporter -116 kb, population P4 pool5 rep3
E2285 Sox2P-reporter -116 kb, population P4 pool5 rep3 Fw
mapped_integrations_-116kb_Sox2P_pools.txt

source_name: F1 hybrid 129/Sv:CAST/EiJ

tag: cell line

value: F1 hybrid 129/Sv:CAST/EiJ

value: mESC

tag: launch pad_location

tag: insert

tag: sorted gate

tag: sample type

value: sorted pool


description:
Sox2P-reporter -116 kb, population P3 pool4 rep3
E2285 Sox2P-reporter -116 kb, population P3 pool4 rep3 Rv
mapped_integrations_-116kb_Sox2P_pools.txt

tag: cell type

tag: genotype

value: WT


title: T105

tag: histology

value: Monophasic

value: Synovial Sarcoma

tag: tumor type

tag: site


title: Tg1

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.

value: APP/PS1 mutant

value: Brain cortex

tag: disease state

value: Alzheimer's


title: Tg2


title: T104

tag: patient id

tag: fusion gene

value: Metastasis

value: visceral