title: HEK293_HiC_Rep2

description: in situ Hi-C library

data_processing:
The raw Hi-C data were quality-controlled using FastQC (v0.11.7).
The sequence reads were mapped to human genome (hg19) by using bwa (v0.7.8) mem were called by juicer. Only the uniquely mapped reads were kept for the subsequent analyses.
PCR duplicates were removed by picard MarkDuplicates (v1.131).
The contact domains were called by arrowhead a command of juicer tools (v1.8.9).
The contact loops were called by hiccups a command of juicer tools (v1.8.9).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include contact domain (HEK293_HiC_contact_domains_5k_results.txt), loops (HEK293_HiC_hiccups_loops_5k_10k_merged_loops.txt) and compartment (HEK293_HiC_Norm_1Mb_compartment_results.txt) calling results.

source_name: HEK293T cells

growth_protocol: HEK293T cells were cultured in DMEM (Invitrogen, Life Technologies) supplemented with 10% FBS, Pen/Strep antibiotics, in 5% CO2 at 37 degrees Celsius.

extract_protocol:
Cells were washed with ice-cold PBS and collected into a 1.5 mL Eppendorf tube. Lysis buffer (10mM Tris-HCl pH 8.0, 10mM NaCl, 0.2% Igepal CA630 (Sigma)) was applied to the cell pellets followed by 15 min incubation on ice. Centrifugation (2,500 x g) was performed to remove to supernatant and remaining nuclei were suspended in 0.5% SDS (Sigma) and incubated at 62 °C for 5-10min. After heating, the nuclei were treated with 10% TritonX-100 and incubated at 37 °C for 15min. Chromatin was digested with 100U MboI in NEB buffer 2 overnight at 37 °C. After inactivation of MboI by 62 °C for 20 min, the chromatin was tagged with biotin-dA in an end-filling step with Klenow (NEB) at 37 °C for 90 min. To re-ligate the free ends, T4 DNA Ligase (NEB, M0202) was used and the reverse crosslinking reaction was performed with Proteinase K (NEB, P8102) and 1% SDS (Sigma) at 55 °C for 30 min followed by 68 °C overnight. DNA was purified with Phenol-Chloroform extraction and ethanol precipitation, followed by Sonication into ~500 bp fragments by Covaris M220 ultrasonicator. Biotinylated DNA was size selected (300-500 bp) followed by enrichment with Dynabeads My One T1 Strepvavidin-coated beads (Invitrogen).
The DNA fragments were processed with blunt end filling, dT-addition and illumina Truseq adaptor ligation and PCR amplification.

treatment_protocol: crosslinking was performed with 1% formaldehyde for 10 min at room temperature and the reaction was quenched with 0.125mM glycine for 5 min at room temperature

value: human embryonic kidney (HEK) 293T cells

value: crosslinked with 1% formaldehyde


title: Stag2_Spleen_Fwd_rep1

status: Public on May 02 2026

type: SRA

city: Oxford

first: Felice

middle: Hoching

last: Tsang

state: Oxfordshire

address: John Radcliffe Hospital/Headley Way

department: Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description:
Library name: Sample 13
Genome-wide library of Immunoprecipitated fragments

library_source: genomic

data_processing:
Trimming: trimgalore --stringency 2
Mapping : bowtie2
samtools view chr11
Removing duplicates : samtools rmdup
Generating bigwig tracks: deeptools -bs 20 --normalizeUsingRPKM
Assembly: mm9 or mm9 based custom genome
Supplementary files format and content: bigWig : (deeptools) bamCoverage converison of filtered fragments (duplicate-filtered fragments) from bam to bigwig,  (--binSize 20 --normalizeUsingRPKM)

molecule: genomic DNA

organism: Mus musculus

source_name: mouse spleen cells

growth_protocol: EB: Proliferating ES cells were cultured in IMDM-ES media (Iscove’s Modified Dulbecco Medium (IMDM) (Gibco) supplemented with 15% FBS, 100 U/ml penicillin/streptomycin, 1000 U/ml LIF, and 1.5 x 10-4 M monothioglycerol (MTG; Sigma-Aldrich: M6145)) for 24 to 48 hours prior to primary plating. Subsequently, cells were plated in 10 ml differentiation media on bacterial petri dishes (15000-50000 cells/plate) and cultured for 7 days. Differentiation medium consisted of IMDM media supplemented with 15% heat-inactivated FBS (1 hour at 56 °C), 2 mM L-Glutamine, 0.3 mg/ml transferrin (Roche), 0.05 mg/ml ascorbic acid, MTG and 5% Protein-Free Hybridoma Media II (Gibco). At day 7, EBs were disaggregated and selected for CD71 surface marker. FL: E12.5 mouse fetal liver were dissected and cultured in StemPro medium (Invitrogen) supplemented with Epo (1 U/mL; Janssen, PL 00242/029), SCF (50 ng/mL; Peprotech, 250-03), dexamethasone (1 μM; Hameln, DEXA3.3) and 1× L-Glutamine (Invitrogen) for 6–7d to expand the erythroid progenitor population. If necessary cells were frozen at day 4 and after thawing expanded for a further 2-4 days. Cells were selected for Ter119.

extract_protocol:
DNA was purified by phenol-chloroform extraction and ethanol precipitation with NaOAc, and 1 µl GlycoBlue (Invitrogen). ChIP enrichment was determined by RT-qPCR.
NEBNext Ultra II DNA Library Prep kit for Illumina (New England Biolabs).

treatment_protocol: For ChIP-seq, chromatin was crosslinked with 1 % formaldehyde (Sigma) at room temperature for 10 minutes. Crosslinking was quenched with 130 mM glycine, and cells were washed with cold PBS before snap freezing pelleted cells. Fixed material was stored at -80 ºC. Chromatin immunoprecipitation was performed using Agarose ChIP Assay Kit (Merck Millipore). Briefly, 5-107 cells were lysed by incubation on ice in lysis buffer for 10 minutes. Chromatin was sonicated using the Bioruptor or Bioruptor pico to generate 200-400 bp fragments. Insoluble material was removed by centrifugation (15,000 rcf, 10 min, 4 ºC) and soluble material was diluted to 2 ml with dilution buffer. Immunoprecipitation was performed by incubation of diluted chromatin with antibodies for CTCF (10 µl 07-729; Millipore); RAD21 (5 µg ab154769; Abcam); STAG2 (5 µg A302-580A; Bethyl) overnight. Chromatin incubation with Protein A/agarose slurry, washes and elution were performed according to the manufacturer’s instructions.

tag: cell line

value: mouse spleen cells

tag: cell type

value: Erythroid


city: Hong Kong

first: Jian

last: Yan

state: Hong Kong Special Administrative Region

address: 83 Tat Chee Avenue, Kowloon

department: Department of Biomedical Sciences

country: China

institute: City University of Hong Kong

description: PCR products from CTCF-DBD_oligoLib3_Methyl-SELEX_cycle3_rep1

library_source: other

data_processing:
Quality control of the raw sequencing data using FastQC version v0.11.7 with default parameters.
Sequences from the 41-nt target region without bases annotated as N were extracted using custom script.
Then the CG dinucleotide frequencies at each position on target region of oligos were generated using custom script.
Assembly: NA
Supplementary files format and content: tab-delimited text file include the statistical results of CG dinucleotide frequencies at each position on oligos for each sample.
Library strategy: SELEX

molecule: other

organism: Escherichia coli

source_name: Rosetta (DE3)

growth_protocol: The E. coli strains for protein purification were grown at 37 ℃ in LB (Luria-Bertani) broth with shaking at 220 rpm or on LB agar plates until OD600=0.6.

extract_protocol:
The pellet was suspended in 10 ml buffer A (0.5 mg/ml Lysozyme, 50 mM tris-HCl pH 7.5, 300 mM NaCl, 10 mM Imidazole, 1 mM DTT, 1 mM PMSF) and lysed by sonication at ten seconds interval for 10 minutes and then centrifuged at 4 °C (12000 rpm, 30 min) to collect protein supernatant. The supernatant was filtered with a 0.45 μm filter and the filtrate was added into a Ni-NTA column (Bio-Rad) which had been equilibrated with buffer A before using. The Ni-NTA beads was set at 4 ℃ for 30min before being eluted with Buffer A containing 300 mM imidazole
The HT-SELEX experiments were carried out using a previously established protocol12. Briefly, selection ligands consisted of 41 bp (with a 19 bp core CTCF motif sequence flanked by 11 bp random sequences on each side) adapted to Illumina HiSeq Xten sequencing system with multiplexing indices. Ligand libraries were then generated by PCR amplification using primers in Extended Data Table 6 and 41-bp SELEX ligands as templates. The input library was amplified for 16 cycles using Q5® High-Fidelity DNA Polymerase (NEB). All PCR reactions were performed according to the manufacturer's manual. Libraries were sequenced using an Illumina HiSeq Xten sequencer to analyze the identity of each base (A, T, C, G). Then, 150 ng protein and 5 μL of selection ligand were added to Promega binding buffer (10 mM Tris, pH 7.5, 50 mM NaCl, 1 mM DTT, 1 mM MgCl2, 4% glycerol, 0.5 mM EDTA, 5 μg/ml poly -dIdC (Sigma P4929)) until the total volume reaches 25 μL. After a 30-minute incubation at room temperature, 150-µL Promega buffer (without poly-dIdC) containing 10-µL Nickel Sepharose 6 Fast Flow resin (GE) equilibrated in binding buffer was added to the mixture, followed by incubation for 60 minutes with gentle shaking. After binding, the Nickel Sepharose beads were washed for 12 consecutive times with 200 μl Promega Binding Buffer (without poly-dIdC) with gentle shaking. Each wash took 5 min. Subsequently, the residual water was carefully removed from the beads by centrifugation at 500×g for 30 seconds. Then, beads with bound DNA were resuspended in 200 μL of mili-Q water. Finally, approximately 20 μL of beads was PCR amplified for 18 cycles using Phusion DNA polymerase (NEB), and the resulting PCR product was used as the selection ligand for the next cycle of SELEX. This process was repeated four times. After each cycle, purified PCR products were pooled and sequenced using an Illumina HiSeq Xten sequencer.The methylation sensitive-SELEX experiments were carried out using a previously established protocol13. CpG methylation is modified by the CpG-specific methyltransferase M.SssI. The methylation protocol was adapted from13 as follows: 2.5 μL (10U, for initial library) or 1.25 μL (5U, for cycles 1 to 3) CpG methyltransferase M.SssI (NEB; twofold excess units in input and SELEX cycle beyond), with 0.4 μL (for initial library) or 0.2 μL (for cycles 1 to 3) S-adenosylmethionine (SAM), 3.4 μL of 50 mM MgCl2, and 0.2 μL of 100 mM DTT to DNA ligand in a total volume of 20 μL. The mixture was incubated at 37°C for 3 hours to methylate CpG dinucleotides in double-stranded DNA ligands, then at 65°C for 20 minutes to inactivate the M.SssI enzyme before each selection cycle. The methylation status of the ligands was examined by the methylation-specific restriction enzyme BstBI digestion (Extended Data Fig. 5a). CpG methylated DNA ligands and unmethylated DNA ligands SELEX assays were performed in parallel for each protein in separate tubes, and the selection process was repeated for up to 4 cycles to enrich for binding sequences. After each cycle, purified PCR products from each cycle of methyl-SELEX and HT-SELEX were pooled separately and sequenced using an Illumina HiSeq Xten sequencer.

treatment_protocol: 1 mM IPTG (Isopropyl β-D-1-Thiogalactopyranoside) was added into the bacterial culture to induce protein expression at 16 °C for 16 h.

value: Rosetta (DE3)

tag: genotype

value: WT

tag: treatment

value: no treatment


title: mESC_SKO_IP_CTCF_rep2

description:
mESC_SKO_IP_CTCF_rep123_treat_pileup.bigwig
mESC_SKO_IP_CTCF_rep123_TvsC_peaks.narrowPeak.gz

data_processing:
The raw ChIP-Seq data were quality-controlled using FastQC (v0.11.7) with default parameters.
ChIP-seq reads were aligned to mouse genome (mm10) using bowtie2 (v2.3.4) with default parameters and only the uniquely mapped reads were kept for the subsequent analyses.
Sam files were converted to bam files by using samtools (v1.9) with default parameters.
Binding peaks for each sample were identified by using MACS2 software (v2.1.2) with default parameters.
Peaks were annotated by using bedtools (v2.25.0).
The ChIP signal enrichment heat map of the flank of a specific point collection (such as CTCF binding sites) was calculated using deeptools (v3.5.0).
All peaks and reads distribution were visualized by using IGV software (v2.4.14).
Assembly: mm10
Supplementary files format and content: bigwig
Supplementary files format and content: narrowPeak (except for input sample)  were generated by MACS2 (v2.1.2) which include the detail informations for all binding peaks;

source_name: mESC

growth_protocol: Mouse embryonic stem (mES) cells were cultured in mouse ES cell medium containing KnockOut Serum Replacement: DMEM 85%, 15% KnockOut Serum Replacement (Gibco), penicillin–streptomycin (Gibco), 1× non-essential amino acids (Gibco), 1× GlutaMax (Gibco), 1000 U ml–1 LIF (Millipore), 0.4 mM β-mercaptoethanol (Gibco). The cells were typically grown  on 0.1% gelatin-coated plates with irradiated mouse embryonic fibroblasts (MEFs) (Thermo Fisher).

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody (CTCF (abcam, Cat. #ab128873).
Sequencing libraries were made following the protocol of NEB Next ChIP-Seq DNA Sample Prep Kit with minor modifications. To perform end repair of DNA fragments, 12 μL mixture (5µL NEB T4 DNA ligase buffer with 10mM ATP, 2µL dNTPs mix 10mM each, 2µL T4 DNA polymerase 3u/µL, 1µL Klenow DNA polymerase 5u/µL, 2µL T4 PNK 10u/µL) was added to 38 μL of IP DNA and input DNA (20 ng in 38 μL) and incubated for 30 min at 20 °C. The DNA was then purified using VAHTS® DNA Clean Beads (N411-01, Vazyme) and eluted in 41 μL H2O, following the manufacturer’s instructions. To prepare the DNA fragments for ligation to adapters by adding an “A” base to the 3' end, 9 μL mix (5µL NEB Buffer 2, 1µL dATP 100mM, 3µL Klenow 3'-5' exo minus 5u/µL) was added to 41 μL DNA from previous step and incubated for 30 min at 37 °C. After “A” base addition, the DNA was then purified using VAHTS® DNA Clean Beads (N411-01, Vazyme) and eluted in 42 μL H2O. To ligate adapters to DNA fragments, 8 µL reaction mixture (1µL adapter mix (1uM) (1000005282, MGI), 5µL NEB T4 DNA ligase buffer, 2µL NEB T4 DNA ligase) was added to 42 μL DNA from the previous step and incubated at 16 °C overnight. Size selection (200–500 bp) was achieved using a 1.5% agarose gel and NEB Monarch DNA Gel Extraction Kit (T1020S), and the DNA was eluted in 20 μL H2O. Finally, the libraries were amplified by 18 PCR cycles using Phusion High-Fidelity DNA Polymerases (M0530L, NEB) with the DNA from size selection and purified as size selection.

value: mESC

value: mouse embryonic stem cells (mESC)

value: SKO (Dnmt1/3a/3b and Tet1/2/3 sextuple knockout)

tag: chip antibody

value: Anti-CTCF


title: mESC_SKO_IP_CTCF_rep1


title: CTCF-DBD_oligoLib3_HT-SELEX_cycle3_rep1

description: PCR products from CTCF-DBD_oligoLib3_HT-SELEX_cycle3_rep1


title: mESC_SKO_INPUT_rep3

description: mESC_SKO_INPUT_rep123_control_lambda.bigwig

value: INPUT


title: osteoclast, ctrl3, day3

city: Hangzhou

first: Yani

last: Chen

state: Zhejiang

address: No. 268, Kaixuan Rd.

institute: Zhejiang University

description: Library name: BLANK3

library_source: transcriptomic

data_processing:
Raw reads were quality-filtered using KneadData (v0.7.2) and host DNA (GRCh37/C57BL) and rRNA (SILVA v128) were removed with Bowtie2 (v2.4.4). Trimmed reads were assembled with MEGAHIT (v1.2.9), and coding sequences were predicted with Prodigal (v2.6.3). A non-redundant gene catalog was generated using CD-HIT (v4.8.1; 95% identity, 90% coverage).
Assembly: GRCm39.112
Supplementary files format and content: csv files include FPKM values for each Sample

molecule: total RNA

source_name: osteoclast

extract_protocol:
RNA was harvested using a total RNA extraction kit (Tiangen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Total RNA was extracted using the appropriate kit based on sample type (Tiangen DP411, Tiangen DP762-T1C, Aidlab RN40 with CLB or CTAB, or TRIzol, etc.). RNA quality and integrity were assessed using a NanoDrop2000 and an Agilent 2100 Bioanalyzer / LabChip GX, with the following criteria: total amount ≥ 2 μg, concentration ≥ 40 ng/μl, OD260/280 1.7-2.5, OD260/230 0.5-2.5, RIN ≥ 7 (non-plant) or ≥ 6.5 (plant) (or RIN 6.0-6.4 with 28S/18S ≥ 1 and no baseline elevation). mRNA Capture Beads were equilibrated for 30 min on a four-dimensional rotator. mRNA was enriched by two rounds of binding: total RNA was mixed with the beads, denatured at 65°C, held at room temperature for 5 min, and magnetically separated; after washing, mRNA was eluted in Tris Buffer at 80°C. For the second binding, Beads Binding Buffer was added, incubated for 5 min at room temperature, washed, and then Frag/Prime Buffer was added. mRNA fragmentation was performed in a thermal cycler according to sample quality. First-strand cDNA was synthesized using reverse transcriptase in a thermal cycler, and second-strand cDNA synthesis was carried out in a metal bath, followed by purification with 1.8X VAHTS™ DNA Clean Beads and elution in Nuclease-free Water. After end repair and A-tailing, adapters containing index sequences were ligated. The ligation products were purified and size-selected by sequential bead-based steps: 0.9X beads, then 0.6X beads (supernatant retained), and finally 0.1X beads (beads retained), with 80% ethanol washes. PCR amplification was performed, and the PCR products were purified using beads. Library quality was checked on a Qsep-400 system, and only libraries rated A (or B with negligible effect) were used. Libraries were constructed with the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme, NR604-02) and purified with VAHTS™ DNA Clean Beads (Vazyme, N411-03). The qualified libraries were sequenced on an Illumina NovaSeq X Plus platform using paired-end 150 bp reads.

tag: strain

value: osteoclast

value: wildtype


title: CTCF-DBD_oligoLib2_HT-SELEX_cycle3_rep1

description: PCR products from CTCF-DBD_oligoLib2_HT-SELEX_cycle3_rep1


title: CTCF-DBD_oligoLib2_input_cycle0_rep1

description: PCR products from CTCF-DBD_oligoLib2_input_cycle0_rep1


description: PCR products from CTCF-DBD_oligoLib2_Methyl-SELEX_cycle4_rep1


title: osteoclast, ctrl1, day3

description: Library name: BLANK1


description: PCR products from CTCF-DBD_oligoLib2_Methyl-SELEX_cycle3_rep1


title: Rad21_Spleen_Fwd_rep2

description:
Library name: Sample 8
Genome-wide library of Immunoprecipitated fragments


title: mESC_WT_IP_CTCF_rep3

description:
mESC_WT_IP_CTCF_rep123_treat_pileup.bigwig
mESC_WT_IP_CTCF_rep123_TvsC_peaks.narrowPeak.gz


title: Rad21_EB_Rev_F2G6_rep3

description:
Library name: Sample 6
Genome-wide library of Immunoprecipitated fragments

source_name: EB day 7

value: EB day 7


title: CTCF-DBD_oligoLib2_HT-SELEX_cycle4_rep1

description: PCR products from CTCF-DBD_oligoLib2_HT-SELEX_cycle4_rep1


title: mESC_WT_IP_CTCF_rep1


title: Rad21_Spleen_Fwd_rep1

description:
Library name: Sample 7
Genome-wide library of Immunoprecipitated fragments


title: mESC_WT_IP_CTCF_rep2


title: 293T_ERT_CTCF_48h_pd_rep2

data_processing:
The raw bisulfite-sequencing (BS-Seq) data were quality-controlled using FastQC (v0.11.7) and sequencing adapter were removed by cutadapt (v2.7).
The preprocessed sequence data were mapped to human genome (hg19) by using Bismark (v0.22.3). Only the uniquely mapped reads were kept for the subsequent analyses.
PCR duplicates were removed by 'deduplicate_bismark' (a command in the Bismark software package).
Genome-wide m5C sites information was extracted using 'bismark_methylation_extractor' (key parameters: --no_header --comprehensive  --cytosine_report --CX --zero_based).
The classification results of genome-wide CpG and GpC m5C methylation were extracted based on the 'bismark_methylation_extractor' results by using custom script.
CpG and GpC m5C methylation information of every reads were analysed based on the methylation call string from bismark results by using custom script.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files (bed6 plus 4 column with additional important values) include CpG/GpC methylation results.

organism: Homo sapiens

growth_protocol: The HEK293T (ATCC, CRL-3216) and its derived edited cells were cultured with DMEM (Invitrogen) supplemented with 10% FBS and antibiotics (penicillin and streptomycin), under the regular tissue culture condition, i.e. 5% CO2 at 37°C.

extract_protocol:
The genomic DNA was extracted with Blood & Cell Culture DNA Kits (Thermo Fisher, Cat. #13323). Concentration of the DNA was measured with NanoDrop 2000 Spectrophotometers (Thermo Fisher).
To prepare the bisulfite-seq sample, 5 μg of genomic DNA was sonicated into 250-550bp fragments with Covaris M220 ultrasonicator with the manufacturer’s instructed setting. The fragmented DNA was directly applied for illumina Tru-seq library preparation. The library was quantified with Qubit and sequenced with illumina Hiseq 4000 sequencer with at least 20% Spike-in PhiX.

treatment_protocol: Before transfection, the cells were cultured in fresh culture medium for at least 1 hour. For plasmid transfection into HEK293T cells, 2 μg of plasmids were mixed with 5 μL of Fugene HD transfection reagents (Promega) in serum-free Opti-MEM (Invitrogen) by vortexing and incubation at Room Temperature (RT) for 5 min to allow formation of stable transfection complex. The mixture was evenly applied to ~300,000 cells cultured in a single well of a 6-well plate.

value: tag the endogenous CTCF protein with Suntag system


title: HEK293_HiC_Rep1

description: in situ Hi-C library


title: Rad21_EB_Rev_D3H2_rep2

description:
Library name: Sample 5
Genome-wide library of Immunoprecipitated fragments


title: 293T_ERT_CTCF_48h_pd_rep1


title: mESC_WT_INPUT_rep2

description: mESC_WT_INPUT_rep123_control_lambda.bigwig


description: PCR products from CTCF-DBD_oligoLib1_Methyl-SELEX_cycle3_rep1


title: Rad21_EB_Fwd_F2D3_rep3

description:
Library name: Sample 3
Genome-wide library of Immunoprecipitated fragments


title: Rad21_EB_Rev_D2D6_rep1

description:
Library name: Sample 4
Genome-wide library of Immunoprecipitated fragments


title: mESC_WT_INPUT_rep3


description: PCR products from CTCF-DBD_oligoLib1_Methyl-SELEX_cycle4_rep1


status: Public on May 01 2026

city: Rochester

first: Haidong

last: Dong

state: MN

address: 200 First Street SW

country: USA

institute: Mayo Clinic

description:
Library name: JR18_6605_E2 | JR18_6605_E2_010 | NKG7+ CD8+
GeoMx DSP WTA

data_processing:
Data analysis was conducted using the GeoMx NGS Pipeline software for spatial alignment, normalization, and quantification of transcript counts. Further analyses, including ROI-specific differential gene expression and pathway enrichment, were performed using the GeoMx DSP Analysis Suite. The uploaded data contains regions of interests selected for NKG7+ and NKG7- CD8+ T cells.
Assembly: GRCh38
Supplementary files format and content: tab-delimited normalized count value files
Library strategy: Spatial Transcriptomics

source_name: Human Bladder cancer

extract_protocol:
Mouse splenic and thymic CD8+ T cells were isolated using CD8a+ T cell isolation kit (Miltenyi Biotec, Cat#130-104-075). Mouse splenic naïve CD8+ T cells were isolated using Naive CD8a+ T Cell Isolation Kit, mouse (Miltenyi Biotec, Cat#130-096-543). For isolating CD8+ tumor infiltrating lymphocytes (TILs), tumors were first cut into small pieces of 2-4mm and digested using tumor dissociation kit at 37°C for 45 minutes with gentle agitation (Miltenyi Biotec, Cat#130-096-730). Dead cells were further removed using Dead cell Removal kit (Miltenyi Biotec, Cat# 130-090-101). CD8+ TILs were then isolated using CD8 (TIL) microbeads, mouse (Miltenyi Biotec, Cat#130-116-478).
ROIs were selected based on fluorescence imaging using the GeoMx instrument. The selected ROIs were then hybridized with barcoded RNA detection probes (GeoMx DSP RNA assays). Following hybridization, ultraviolet (UV) light was used to release ROI-specific oligonucleotide barcodes. Released barcodes were collected, amplified by PCR. Library quality and quantity were assessed using an Agilent 2100 Bioanalyzer and qPCR. Sequencing was performed on an Illumina NovaSeq S4 platform, generating paired end reads.

tag: tissue

value: Human Bladder cancer

value: CD8+ T cells

tag: patient

tag: roi


description:
Library name: JR18_6605_E2 | JR18_6605_E2_009 | NKG7- CD8+
GeoMx DSP WTA


title: 293T_ERT_CTCF_24h_pd_rep2

value: human embryonic kidney (HEK) 293T cells


title: mESC_WT_INPUT_rep1


title: 293T_ERT_CTCF_24h_pd_rep1


title: 293T_ERT_WT_48h_pd


title: CTCF-DBD_oligoLib1_HT-SELEX_cycle4_rep1

description: PCR products from CTCF-DBD_oligoLib1_HT-SELEX_cycle4_rep1


description:
Library name: JR18_6605_E2 | JR18_6605_E2_009 | NKG7+ CD8+
GeoMx DSP WTA


description:
Library name: JR18_6605_E2 | JR18_6605_E2_008 | NKG7+ CD8+
GeoMx DSP WTA


title: Rad21_EB_Fwd_D3F3_rep2

description:
Library name: Sample 2
Genome-wide library of Immunoprecipitated fragments


description:
Library name: JR18_6605_E2 | JR18_6605_E2_007 | NKG7+ CD8+
GeoMx DSP WTA


title: CTCF-DBD_oligoLib1_HT-SELEX_cycle3_rep1

description: PCR products from CTCF-DBD_oligoLib1_HT-SELEX_cycle3_rep1


description:
Library name: JR18_6605_E2 | JR18_6605_E2_006 | NKG7+ CD8+
GeoMx DSP WTA


description:
Library name: JR18_6605_E2 | JR18_6605_E2_006 | NKG7- CD8+
GeoMx DSP WTA


title: mESC_BPK25_HiC_rep2

data_processing:
The raw Hi-C data were quality-controlled using FastQC (v0.11.7).
The sequence reads were mapped to mouse genome (mm10) by using bwa (v0.7.17) mem were called by juicer. Only the uniquely mapped reads were kept for the subsequent analyses.
PCR duplicates were removed by picard MarkDuplicates (v1.131).
The contact domains were called by arrowhead a command of juicer tools (v1.22.01).
The contact loops were called by hiccups a command of juicer tools (v1.22.01).
The Aggregate Peak Analysis (APA) were done by apa a command in juicer tools (v1.22.01).
Assembly: mm10
Supplementary files format and content: mESC_BPK25.inter_30.hic is a highly compressed binary file that stores the reads contact matrix.
Supplementary files format and content: mESC_BPK25.hiccups_merged_loops.bedpe is the result file of the chromatin loops generated by hiccups.

growth_protocol: Mouse embryonic stem (mES) cells were cultured in mouse ES cell medium containing KnockOut Serum Replacement: DMEM 85%, 15% KnockOut Serum Replacement (Gibco),  penicillin–streptomycin (Gibco), 1× non-essential amino acids (Gibco), 1× GlutaMax (Gibco), 1000 U ml–1 LIF (Millipore), 0.4 mM β-mercaptoethanol (Gibco). The cells were typically grown  on 0.1% gelatin-coated plates with irradiated mouse embryonic fibroblasts (MEFs) (Thermo Fisher).

extract_protocol:
Genomic DNA were extracted.
Four to five million cells were fixed for 5 min with 2 % formaldehyde in PBS and then the reaction was quenched for another 5 min in 0.125 M glycine. Nuclei were then extracted by incubating cells on ice for 30 min (inverting every 10 min) in 10 mM Tris pH 8.0, 10 mM NaCl, 0.2 % NP-40 (IGEPAL CA-630) and protease inhibitor cocktail (Roche).Hi-C libraries were prepared using an adaptor ligation method. Briefly, biotinylated junctions were captured on streptavidin M-280 dynabeads and digested with DpNII enzyme to generate blunt ends. The blunt ends were A-tailed with Klenow (3'→5' exo-) before ligation with adaptor sequences containing unique barcode. After adaptor ligation DNA was PCR amplified with Illumina primers for 25 cycles and library fragments of ~300-1000 bp (insert plus adaptor and PCR primer sequences) were isolated using AMPure beads (Beckman). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Hiseq 4000 following the manufacturer's protocols.

treatment_protocol: DMSO, BPK25


title: mESC_BPK25_HiC_rep1


title: Rad21_EB_Fwd_D2H3_rep1

description:
Library name: Sample 1
Genome-wide library of Immunoprecipitated fragments


title: 293T_ERT_WT_24h_pd


description:
Library name: JR18_6605_E2 | JR18_6605_E2_005 | NKG7+ CD8+
GeoMx DSP WTA


title: Citeseq, T-cells, ADT, HTO

city: Kgs. Lyngby

first: Kamilla Kjærgaard

last: Munk

address: Henrik Dams Allé, 204

department: Department of Health Technology

country: Denmark

institute: Technical University of Denmark

description:
Library name: Scaffold_ADT_and_HTO
Antibody-derived oligonucleotide (ADT) and Hashing-derived oligonucleotide (HTO)

data_processing:
transcriptome (RNA), surfaceprotein (containing barcodes for ADT, HTO) and TCR (VDJ) files where processed together using the Cellranger multi pipeline, resulting in the output files described in the 'processed data files format and content' field below. The supplementary file 'feature.csv' was used as a reference file for processing the barcodes (ADT and HTO) in the surfaceprotein files.
Assembly: hg38
Supplementary files format and content: Cellranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, filtered_contig_annotations.csv
Library strategy: CITE-seq

molecule: protein

source_name: PBMCs in culture

extract_protocol:
Cells were washed three times through sedimentation at 390 g and resuspended in PBS+0.5% BSA before sorting single, live, CD8+ and tetramer positive cells on a BD FACS Melody cell sorter. Tetramer-positive T-cells from each sample were sorted into a common tube and centrifuged on 390 g for 10 min at 4°C. The supernatant was removed, and cells were loaded into a Chromium Controller and prepared for sequencing as described in the Chromium Next GEM Single Cell 5’ v2 protocol (CG000330).
Library was constructed according to the manufacturer's instructions as described in the Chromium Next GEM Single Cell 5’ v2 protocol (CG000330). The supernatant was removed, and cells were loaded onto Chromium according to the manufacturer’s instructions. Downstream processing was performed according to manufacturer’s instructions (Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index), with the Feature Barcode technology for Cell Surface Protein & Immune Receptor Mapping) (10x Genomics, USA). Gene expression (RNA), antibody-derived-tag (ADT), and hashtag-oligonucleotide (HTO) libraries were sequenced at Novogene using NovaSeq 150 paired-end.

treatment_protocol: Specific T cells with pre-defined viral responses were expanded from PBMCs over a 10 to 14-day period. Briefly, PBMCs were cultured in VIVO 15 media (Lonza, BE02-060Q) supplemented with 5% human serum (Sigma Aldrich Heat Inactivated H3667) supplemented with Ag-scaffolds (0.16 nM prefiltration) or specific peptide (5 µM), soluble IL-2 (40 U/mL, Peprotech 200–02) and soluble IL-21 (25 ng/mL, Peprotech 200–21). Ag-scaffold or free components were supplemented to the culture at initiation and twice weekly until harvest.

value: PBMCs in culture

value: No

value: Ag-scaffold expanded

tag: library type

value: ADT

tag: adt

value: TotalSeq-C Human Universal Cocktail V1.0 (BioLegend, 399905)

tag: hto

value: TotalSeq-C anti-Human Hashtag antibodies


title: TCR-seq, T-cells, VDJ

description:
Library name: Scaffold_TCR
Single-cell transcriptomic profiling of CD8+ T cells. Includes clonotype assignments and TCR alpha/beta chain sequences.

data_processing:
transcriptome (RNA), surfaceprotein (containing barcodes for ADT, HTO) and TCR (VDJ) files where processed together using the Cellranger multi pipeline, resulting in the output files described in the 'processed data files format and content' field below. The supplementary file 'feature.csv' was used as a reference file for processing the barcodes (ADT and HTO) in the surfaceprotein files.
Assembly: hg38
Supplementary files format and content: Cellranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, filtered_contig_annotations.csv

molecule: polyA RNA

value: VDJ


title: Multiome, T-cells, GEX

description:
Library name: Scaffold_RNA
polyA RNA

library_source: transcriptomic single cell

value: RNA


description:
Library name: JR18_6605_E2 | JR18_6605_E2_007 | NKG7- CD8+
GeoMx DSP WTA


description:
Library name: JR19_2987_E4 | JR19_2987_E4_008 | NKG7+ CD8+
GeoMx DSP WTA


description:
Library name: JR19_2987_E4 | JR19_2987_E4_008 | NKG7- CD8+
GeoMx DSP WTA


title: CTCF-DBD_oligoLib1_input_cycle0_rep1

description: PCR products from CTCF-DBD_oligoLib1_input_cycle0_rep1

value: Rosetta (DE3)

value: WT

value: no treatment


description:
Library name: JR19_2987_E4 | JR19_2987_E4_007 | NKG7+ CD8+
GeoMx DSP WTA


description:
Library name: JR19_2987_E4 | JR19_2987_E4_004 | NKG7- CD8+
GeoMx DSP WTA


description:
Library name: JR19_2987_E4 | JR19_2987_E4_006 | NKG7- CD8+
GeoMx DSP WTA


description:
Library name: JR19_2987_E4 | JR19_2987_E4_005 | NKG7- CD8+
GeoMx DSP WTA


description:
Library name: JR19_2987_E4 | JR19_2987_E4_005 | NKG7+ CD8+
GeoMx DSP WTA


description:
Library name: JR19_2987_E4 | JR19_2987_E4_004 | NKG7+ CD8+
GeoMx DSP WTA


description:
Library name: JR19_2987_E4 | JR19_2987_E4_002 | NKG7+ CD8+
GeoMx DSP WTA


description:
Library name: JR19_2987_E4 | JR19_2987_E4_001 | NKG7+ CD8+
GeoMx DSP WTA


description:
Library name: JR18_6605_E2 | JR18_6605_E2_004 | NKG7- CD8+
GeoMx DSP WTA


description:
Library name: JR19_1207_D12 | JR191207_D12_007 | NKG7+ CD8+
GeoMx DSP WTA


description:
Library name: JR19_1207_D12 | JR191207_D12_008 | NKG7+ CD8+
GeoMx DSP WTA


description:
Library name: JR18_6605_E2 | JR18_6605_E2_004 | NKG7+ CD8+
GeoMx DSP WTA


description:
Library name: JR18_6605_E2 | JR18_6605_E2_003 | NKG7+ CD8+
GeoMx DSP WTA


description:
Library name: JR18_6605_E2 | JR18_6605_E2_002 | NKG7+ CD8+
GeoMx DSP WTA


description:
Library name: JR19_1207_D12 | JR191207_D12_005 | NKG7- CD8+
GeoMx DSP WTA


description:
Library name: JR18_6605_E2 | JR18_6605_E2_001 | NKG7+ CD8+
GeoMx DSP WTA


description:
Library name: JR18_6605_E2 | JR18_6605_E2_001 | NKG7- CD8+
GeoMx DSP WTA


description:
Library name: JR19_1207_D12 | JR191207_D12_005 | NKG7+ CD8+
GeoMx DSP WTA


description:
Library name: JR19_1207_D12 | JR191207_D12_004 | NKG7- CD8+
GeoMx DSP WTA


description:
Library name: JR19_1207_D12 | JR191207_D12_002 | NKG7+ CD8+
GeoMx DSP WTA


description:
Library name: JR19_2987_E4 | JR19_2987_E4_007 | NKG7- CD8+
GeoMx DSP WTA


description:
Library name: JR-6989_E5 | JR_6989_E5_006 | NKG7+ CD8+
GeoMx DSP WTA


description:
Library name: JR19_2987_E4 | JR19_2987_E4_006 | NKG7+ CD8+
GeoMx DSP WTA


description:
Library name: JR-6989_E5 | JR_6989_E5_005 | NKG7+ CD8+
GeoMx DSP WTA


description:
Library name: JR-6989_E5 | JR_6989_E5_007 | NKG7+ CD8+
GeoMx DSP WTA


description:
Library name: JR-6989_E5 | JR_6989_E5_004 | NKG7+ CD8+
GeoMx DSP WTA


description:
Library name: JR19_2987_E4 | JR19_2987_E4_003 | NKG7- CD8+
GeoMx DSP WTA


description:
Library name: JR-6989_E5 | JR_6989_E5_003 | NKG7+ CD8+
GeoMx DSP WTA


description:
Library name: JR-6989_E5 | JR_6989_E5_001 | NKG7- CD8+
GeoMx DSP WTA


description:
Library name: JR-6989_E5 | JR_6989_E5_002 | NKG7+ CD8+
GeoMx DSP WTA


description:
Library name: JR-6989_E5 | JR_6989_E5_004 | NKG7- CD8+
GeoMx DSP WTA


description:
Library name: JR-6989_E5 | JR_6989_E5_008 | NKG7+ CD8+
GeoMx DSP WTA


description:
Library name: JR19_2987_E4 | JR19_2987_E4_003 | NKG7+ CD8+
GeoMx DSP WTA


description:
Library name: JR19_2987_E4 | JR19_2987_E4_002 | NKG7- CD8+
GeoMx DSP WTA


description:
Library name: JR19_2987_E4 | JR19_2987_E4_001 | NKG7- CD8+
GeoMx DSP WTA


title: T196_B_BAL_TB

city: London

first: Probir

last: Chakravarty

address: 1 Midland Road

institute: Francis Crick Institute

description: Library name: T196_B

data_processing:
nf-core/rnaseq pipeline v3.16.1; default parameters
Assembly: GRCh38, Homo sapiens
Supplementary files format and content: csv of DESeq2 normalised expression values

source_name: Bronchoalveolar lavage

extract_protocol:
Cell suspensions containing 0.5 x 106 live cells were pelleted by centrifuging at 400 x G for 5 minutes at 4oC and pellets suspended in TRI reagent (Sigma-Aldrich). Samples were vortexed at high speed for around 20 seconds before storage at -80oC until RNA extraction. RNA extraction was performed using the DirectZol RNA Microprep kit (Zymo Technologies), as per manufacturer’s instructions, including on-column DNase I digestion.
Extracted RNA from whole BAL cell pellets was subjected to Agilent TapeStation quality control analysis and RNA integrity (RIN) values determine to be ≥7.4 and ≤9.9, except for one sample (T219_1, from active TB patient #219), which had a RIN value of 4.1. 200 ng of total RNA was used for library preparation using the RNA library prep kit with Polaris ribosomal RNA depletion (Watchmaker Genomics). Approximately 2.5 x107 100 base pair paired end reads were obtained per sample using an Illumina NovaSeq X sequencer.

value: Bronchoalveolar lavage

tag: sample status

value: TB


title: T218_B_BAL_TB

description: Library name: T218_B


title: T185_B_BAL_TB

description: Library name: T185_B


title: T166_B_BAL_TB

description: Library name: T166_B


title: T146_B_BAL_TB

description: Library name: T146_B


title: T147_B_BAL_TB

description: Library name: T147_B


description:
Library name: JR19_1207_D12 | JR191207_D12_008 | NKG7- CD8+
GeoMx DSP WTA


title: T173_B_BAL_TB

description: Library name: T173_B


description:
Library name: JR19_1207_D12 | JR191207_D12_009 | NKG7+ CD8+
GeoMx DSP WTA


description:
Library name: JR19_1207_D12 | JR191207_D12_007 | NKG7- CD8+
GeoMx DSP WTA


title: T117_B_BAL_TB

description: Library name: T117_B


title: T096_B_BAL_TB

description: Library name: T096_B


title: T082_B_BAL_TB

description: Library name: T082_B


description:
Library name: JR19_1207_D12 | JR191207_D12_006 | NKG7+ CD8+
GeoMx DSP WTA


title: T044_B_BAL_TB

description: Library name: T044_B


title: T043_B_BAL_TB

description: Library name: T043_B


description:
Library name: JR19_1207_D12 | JR191207_D12_004 | NKG7+ CD8+
GeoMx DSP WTA


description:
Library name: JR19_1207_D12 | JR191207_D12_002 | NKG7- CD8+
GeoMx DSP WTA


description:
Library name: JR19_1207_D12 | JR191207_D12_003 | NKG7+ CD8+
GeoMx DSP WTA


description:
Library name: JR19_1207_D12 | JR191207_D12_001 | NKG7+ CD8+
GeoMx DSP WTA


description:
Library name: JR-6989_E5 | JR_6989_E5_008 | NKG7- CD8+
GeoMx DSP WTA


description:
Library name: JR19_1207_D12 | JR191207_D12_001 | NKG7- CD8+
GeoMx DSP WTA


description:
Library name: JR-6989_E5 | JR_6989_E5_007 | NKG7- CD8+
GeoMx DSP WTA


description:
Library name: JR-6989_E5 | JR_6989_E5_006 | NKG7- CD8+
GeoMx DSP WTA


title: P122_P_BAL_Progressor

description: Library name: P122_P

value: Progressor


description:
Library name: JR-6989_E5 | JR_6989_E5_002 | NKG7- CD8+
GeoMx DSP WTA

value: Human Bladder cancer


description:
Library name: JR-6989_E5 | JR_6989_E5_001 | NKG7+ CD8+
GeoMx DSP WTA

value: CD8+ T cells


title: C239_B_BAL_IGRApos_PETpos

description: Library name: C239_B


title: T202_B_BAL_TB

description: Library name: T202_B


title: T219_B_BAL_TB

description: Library name: T219_B


title: P013_P_BAL_Progressor

description: Library name: P013_P


title: T158_B_BAL_TB

description: Library name: T158_B


title: T156_B_BAL_TB

description: Library name: T156_B


title: T132_B_BAL_TB

description: Library name: T132_B


title: T137_B_BAL_TB

description: Library name: T137_B


title: T123_B_BAL_TB

description: Library name: T123_B


title: T111_B_BAL_TB

description: Library name: T111_B


title: C224_B_BAL_IGRAneg_PETpos

description: Library name: C224_B


title: T127_B_BAL_TB

description: Library name: T127_B


title: C223_B_BAL_IGRApos_PETneg

description: Library name: C223_B


title: T105_B_BAL_TB

description: Library name: T105_B


title: T095_B_BAL_TB

description: Library name: T095_B


title: T048_B_BAL_IGRApos_PETpos

description: Library name: T048_B


title: T094_B_BAL_TB

description: Library name: T094_B


title: C222_B_BAL_Progressor

description: Library name: C222_B


title: T067_B_BAL_TB

description: Library name: T067_B


title: T083_B_BAL_TB

description: Library name: T083_B


title: C220_B_BAL_IGRAneg

description: Library name: C220_B

value: IGRAneg


title: T017_B_BAL_TB

description: Library name: T017_B


title: T020_B_BAL_TB

description: Library name: T020_B


title: C211_B_BAL_IGRApos_PETpos

description: Library name: C211_B


title: C155_F_BAL_IGRApos_PETneg

description: Library name: C155_F


title: T004_B_BAL_TB

description: Library name: T004_B


title: C141_F_BAL_IGRApos_PETpos

description: Library name: C141_F


title: C140_B_BAL_IGRApos_PETpos

description: Library name: C140_B


title: T001_B_BAL_TB

description: Library name: T001_B


title: C141_B_BAL_IGRAneg_PETpos

description: Library name: C141_B


title: P164_T_BAL_Post-treatment

description: Library name: P164_T

value: Post-treatment


title: P077_P_BAL_Progressor

description: Library name: P077_P


title: P103_P_BAL_Progressor

description: Library name: P103_P


title: C136_B_BAL_IGRAneg

description: Library name: C136_B


title: C134_B_BAL_IGRAneg

description: Library name: C134_B


title: P026_P_BAL_Progressor

description: Library name: P026_P


title: C128_B_BAL_IGRAneg

description: Library name: C128_B


title: C233_B_BAL_IGRApos_PETpos

description: Library name: C233_B


title: C122_B_BAL_IGRAneg_PETpos

description: Library name: C122_B


title: C118_B_BAL_IGRAneg

description: Library name: C118_B


title: C107_F_BAL_IGRApos_PETneg

description: Library name: C107_F


title: P074_P_BAL_Progressor

description: Library name: P074_P


title: C231_B_BAL_IGRAneg

description: Library name: C231_B


title: C106_F_BAL_IGRApos_PETpos

description: Library name: C106_F


title: C225_F_BAL_Progressor

description: Library name: C225_F


title: C224_F_BAL_IGRAneg_PETpos

description: Library name: C224_F


title: C103_F_BAL_IGRApos_PETpos

description: Library name: C103_F


title: C097_B_BAL_IGRAneg

description: Library name: C097_B


title: C189_B_BAL_IGRAneg_PETpos

description: Library name: C189_B


title: C089_B_BAL_IGRAneg

description: Library name: C089_B


title: C079_F_BAL_IGRApos_PETpos

description: Library name: C079_F


title: C078_P_BAL_Progressor

description: Library name: C078_P


title: C211_F_BAL_IGRApos_PETpos

description: Library name: C211_F


title: C091_F_BAL_IGRAneg

description: Library name: C091_F


title: C164_P_BAL_Progressor

description: Library name: C164_P


title: T212_B_BAL_TB

description: Library name: T212_B


title: C075_P_BAL_Progressor

description: Library name: C075_P


title: C182_B_BAL_IGRApos_PETpos

description: Library name: C182_B


title: C157_F_BAL_IGRApos_PETneg

description: Library name: C157_F


title: C157_B_BAL_IGRAneg

description: Library name: C157_B


title: C155_B_BAL_IGRApos_PETneg

description: Library name: C155_B


title: C142_B_BAL_IGRAneg

description: Library name: C142_B


title: C154_B_BAL_IGRAneg

description: Library name: C154_B


title: C135_F_BAL_IGRAneg

description: Library name: C135_F


title: C075_F_BAL_Progressor

description: Library name: C075_F


title: C074_F_BAL_Progressor

description: Library name: C074_F


title: C131_B_BAL_IGRAneg

description: Library name: C131_B


title: C115_B_BAL_IGRAneg

description: Library name: C115_B


title: C110_B_BAL_IGRAneg

description: Library name: C110_B


title: C140_F_BAL_IGRApos_PETpos

description: Library name: C140_F


title: C058_F_BAL_IGRApos_PETpos

description: Library name: C058_F


title: C107_B_BAL_IGRApos_PETneg

description: Library name: C107_B


title: C058_B_BAL_IGRApos_PETneg

description: Library name: C058_B


title: C052_B_BAL_IGRApos_PETneg

description: Library name: C052_B


title: C103_B_BAL_IGRAneg_PETpos

description: Library name: C103_B


title: C106_B_BAL_IGRApos_PETpos

description: Library name: C106_B


title: C071_B_BAL_IGRAneg

description: Library name: C071_B


title: C098_B_BAL_IGRAneg

description: Library name: C098_B


title: C042_B_BAL_IGRAneg

description: Library name: C042_B


title: C038_B_BAL_IGRAneg

description: Library name: C038_B


title: C040_B_BAL_IGRApos_PETneg

description: Library name: C040_B


title: C093_F_BAL_IGRAneg

description: Library name: C093_F


title: C037_B_BAL_IGRAneg

description: Library name: C037_B


title: C039_F_BAL_IGRApos_PETpos

description: Library name: C039_F


title: C090_F_BAL_IGRApos_PETneg

description: Library name: C090_F


title: C090_B_BAL_IGRApos_PETneg

description: Library name: C090_B


title: C034_F_BAL_IGRAneg

description: Library name: C034_F


title: C079_B_BAL_IGRAneg_PETpos

description: Library name: C079_B


title: C077_F_BAL_IGRApos_PETpos

description: Library name: C077_F


title: C077_B_BAL_IGRApos_PETpos

description: Library name: C077_B


title: C013_B_BAL_IGRApos_PETpos

description: Library name: C013_B


title: C073_B_BAL_IGRAneg

description: Library name: C073_B


title: C074_B_BAL_IGRApos_PETpos

description: Library name: C074_B


title: Liver_mCRPC

city: San Francisco

first: Hanbing

last: Song

state: CA

address: 513 Parnassus Ave, HSE

department: Department of Medicine

institute: UCSF

description: Library name: Liver_mCRPC

data_processing:
Demultiplexed pair-end FASTQ files were aligned to hg38 whole genome using dropseq_workflow (Seqwell samples) pipeline on Terra and cellranger (Liver and Sphenoid mCRPC samples).
Assembly: hg38
Supplementary files format and content: txt format matrix table with raw gene counts for every gene and every cell barcode

source_name: Liver

extract_protocol:
Tumor and adjacent normal liver tissues were dissociated by mincing tissue in 1-2mm squares, followed by incubation in Liver Perfusion Medium (ThermoFisher Scientific) for 15 min at 37°C in a rotating oven. After being washed in PBS (ThermoFisher Scientific), tissues were incubated with Liver Digest Medium (ThermoFisher Scientific) supplemented with HEPES and collagenase type IV (Worthington Biochemical, Lakewood, NJ) (600 to 800 U/ml) for 30 min at 37°C with rotation. Further dissociation was achieved by pipetting 10 times through a 25 mL serological pipette. Single cells were then separated from clumps using a 70 µm strainer (Fisher Scientific, Hampton, NH). After lysis of red blood cells with ACK RBC Lysis Buffer (Fisher Scientific), single cells were counted using a LUNA™ Automated Cell Counter (Logos biosystems, South Korea) and processed for scRNA-seq analysis. Patient derived spheroids embedded in Matrigel were washed with PBS, then digested in TrypLE 1X (ThermoFisher Scientific) for 30 to 45 min at 37°C with rotation to obtain a single cell suspension. Cells were washed, then, filtered through a 70-µm strainer, counted using a LUNA™ Automated Cell Counter, and processed for scRNA-seq analysis.
Libraries were prepared for each pool, using 800-1000 pg of DNA and the Nextera XT DNA Library Preparation Kit. They were dual-indexed with N700 and N500 oligonucleotides. Library products were purified using SPRI beads, first at 0.6x and then at a 1x volumetric ratio. Libraries were then run on an HSD1000 tape (Agilent, Cat: 50675584) to determine the concentration between 100-1000 bp. For each library, 3 nM dilutions were prepared. These dilutions were pooled for sequencing on a NovaSeq S4 flow cell.
36 localized prostate cancer patients and 2 metastatic prostate cancer patients (one liver metastatic and one sphenoid metastatic) enrolled in this study. cDNA library preparation was performed using the Seq-Well platform as previously described. Briefly, 10,000-20,000 cells were loaded onto a Seq-Well array containing 110,000 barcoded mRNA capture beads (ChemGenes, Ct: MACOSKO-2011-10(V+)). Arrays were sealed using a polycarbonate membrane (Sterlitech, Cat: PCT00162X22100) at 37 °C for 40 minutes. Cells were then lysed in lysis buffer (5 M guanidine thiocyanate, 1 mM EDTA, 0.5% sarkosyl, 1% BME) for 20 minutes at room temperature. Hybridization of mRNA to the beads was performed in hybridization buffer (2 M NaCL, 4% PEG8000) for 40 minutes. The beads were then collected and washed with 2 M NaCl, 3 mM MgCl2, 20 mM Tris-HCl pH 8.0, 4% PEG8000. Reverse transcription was then performed using Maxima H Minus Reverse Transcriptase (ThermoFisher, Cat: EP0753) in Maxima RT buffer, PEG8000, template switch Oligo dNTPs (NEB, Cat: No447L), and RNase inhibitor (Life Technologies, Cat: AM2696) at room temperature for 15 minutes and then 52 °C overnight. Second strand synthesis was performed using Klenow Exo- (NEB, Cat: M0212L) in Maxima RT buffer, PEG8000, dNTPs, and dN-SMRT oligo for 1 hr at 37 °C.  Whole transcriptome amplification was performed with KAPA HiFi Hotstart Readymix PCR kit (Kapa Biosystems, Cat: KK2602) and SMART PCR Primer. The reactions were purified using SPRI beads (Beckman Coulter) at 0.6X and then 0.8X volumetric ratio. Libraries were prepared using 800-1000 pg of DNA and the Nextera DNA Library Preparation Kit. Dual-indexing was performed using N700 and N500 oligonucleotides. Library products were purified using SPRI beads at 0.6X and then 1X volumetric ratio. A final 3 nM dilution was prepared for each library and sequenced on an Illumina NovaSeq S4 flow cell.

value: Liver

tag: disease state

value: metastatic prostate cancer


title: Patient_PCa6_Tumor_Replica3

description: Library name: PCa6T_3

source_name: Prostate

value: Prostate

value: localized prostate cancer


title: C070_B_BAL_IGRAneg_PETpos

description: Library name: C070_B


title: Patient_PCa6_Normal_ReplicaC

description: Library name: PCa_6N_C


title: Patient_PCa6_Tumor_Replica4

description: Library name: PCa6T_4_


title: C075_B_BAL_IGRApos_PETpos

description: Library name: C075_B


title: C070_F_BAL_IGRAneg_PETpos

description: Library name: C070_F


title: Patient_PCa6_Normal_ReplicaB

description: Library name: PCa_6N_B


title: C069_B_BAL_IGRApos_PETpos

description: Library name: C069_B


title: Patient_PCa6_Tumor_Replica1

description: Library name: PCa6T_1


title: Patient_PCa6_Normal_ReplicaA

description: Library name: PCa_6N_A


title: C068_B_BAL_IGRAneg

description: Library name: C068_B


title: Patient_PCa3_Tumor_Replica1

description: Library name: PCa3_T_1


title: Patient_VAPROS1-1_replicaD2

description: Library name: PA_VAPROS1-1_D2


title: Patient_PCa3_Tumor_Replica4

description: Library name: PCa3_T_4


title: Patient_PCa3_Tumor_Replica3

description: Library name: PCa3_T_3


title: C052_F_BAL_IGRApos_PETneg

description: Library name: C052_F


title: Patient_VAPROS1-1_replicaB2

description: Library name: PA_VAPROS1-1_B2


title: C046_B_BAL_IGRAneg

description: Library name: C046_B


title: C056_F_BAL_IGRApos_PETpos

description: Library name: C056_F


title: C047_B_BAL_IGRAneg

description: Library name: C047_B


title: Patient_VAPROS1-1_replicaC1

description: Library name: PA_VAPROS1-1_C1


title: Patient_VAPROS1-1_replicaA2

description: Library name: PA_VAPROS1-1_A2


title: C039_B_BAL_IGRAneg_PETpos

description: Library name: C039_B


title: Patient_PROS505-3_replicaD2

description: Library name: PA_PROS505-3_D2


title: C036_B_BAL_IGRAneg_PETpos

description: Library name: C036_B


title: C026_B_BAL_IGRApos_PETpos

description: Library name: C026_B


title: C031_B_BAL_IGRAneg

description: Library name: C031_B


title: C030_B_BAL_IGRAneg

description: Library name: C030_B


title: Patient_PROS505-3_replicaD1

description: Library name: PA_PROS505-3_D1


title: C018_F_BAL_IGRApos_PETpos

description: Library name: C018_F


title: C018_B_BAL_IGRApos_PETpos

description: Library name: C018_B


title: Patient_PROS505-3_replicaC1

description: Library name: PA_PROS505-3_C1


title: Patient_PROS505-3_replicaA1

description: Library name: PA_PROS505-3_A1


title: Patient_PCA2_replicaA

description: Library name: PA_PCA2_A


title: Patient_PROS505-3_replicaB1

description: Library name: PA_PROS505-3_B1


title: Patient_PCA2_replicaB

description: Library name: PA_PCA2_B


title: Patient_PR5316_T_apex_V2

description: Library name: HNW_PR5316_T_apex_V2


title: Patient_PROS505-3_replicaB2

description: Library name: PA_PROS505-3_B2


title: C011_F_BAL_IGRApos_PETneg

description: Library name: C011_F


title: Patient_PR5316_T_apex_V1

description: Library name: HNW_PR5316_T_apex_V1


title: C011_B_BAL_IGRApos_PETneg

description: Library name: C011_B


title: Sphenoid_mCRPC

description: Library name: Sphenoid_mCRPC

source_name: Sphenoid

value: Sphenoid


title: Patient_PR5316_N_base_V1

description: Library name: HNW_PR5316_N_base_V1


title: C012_B_BAL_IGRApos_PETneg

description: Library name: C012_B


title: Patient_PR5316_N_apex_V2

description: Library name: HNW_PR5316_N_apex_V2


title: Patient_PCa6_Tumor_Replica2

description: Library name: PCa6T_2


title: HCASMC, shSUV39H1, Replicate 1

city: New Haven

first: Kathleen

last: Martin

state: CT

address: 300 George Street

institute: Yale School of Medicine

description: Library name: Sample 5

data_processing:
Paired-end reads were trimmed of adaptors with Trim Galore (v0.6.7) and mapped to the reference genome hg38 using Bowtie2 (v2.5.1) with parameters --very-sensitive -X 2000. Mapped reads were converted to BAM file and then sorted with SAMtools (v1.21). Reads were further processed: 1) PCR duplicates were filtered with Picard (v2.25.6); 2) chrM reads were removed with SAMtools (v1.21); 3) blacklist reads (hg38-blacklist.v2.bed) were removed with BEDTools (v2.30.0). To obtain the Tn5 cutsite, forward and reverse strand reads were shifted +5 bp and −4 bp with deepTools (v3.5.5), respectively. Shifted reads in each group were merged and then converted to bigWig file using deepTools (v3.5.5) with parameter --normalizeUsing CPM. The bigWig files for each replicate and each group were visualized with IGV (v2.18.2). For transcription start site (TSS) enrichment analysis, bigWig files for each group were analyzed using compute Matrix in deepTools (v3.5.5). Peaks were called for each replicate using MACS3 (v3.0.1) with parameters --no model -q 0.01 --bdg. All peaks were merged to generate a consensus ATAC-seq peak set for downstream analyses. For differential accessibility analysis, reads in the consensus peak set were counted for each replicate and analyzed with DESeq2 (v1.44.0) using total library sizes as the size factors. Significant upregulated peaks (adjusted P < 0.05, log2FoldChange > 1.0) were analyzed with findMotifsGenome.pl program in Homer (v5.1) to identify gained motifs. Differential peak annotation was performed with ChIPseeker and plotted with clusterProfiler.
Assembly: hg38
Supplementary files format and content: bw (reads coverage files for visualization)
Supplementary files format and content: narrowPeak (peak files for downstream analysis)

source_name: Smooth muscle

extract_protocol:
ATAC-Seq Kit (Active Motif, cat# 53150) was used to acquire the open chromatin.
ATAC-Seq Kit (Active Motif, cat# 53150) was used to prepare the ATAC-Seq sequencing library.

value: Smooth muscle

value: Human Coronary Artery Smooth Muscle Cells (HCASMC)

value: Smooth muscle cells

value: SUV39H1 knockdown


title: HCASMC, shSUV39H1, Replicate 3

description: Library name: Sample 7


title: HCASMC, shSUV39H1, Replicate 2

description: Library name: Sample 6


title: HCASMC, shCtrl, Replicate 1

description: Library name: Sample 1

value: WT


title: HCASMC, shCtrl, Replicate 2

description: Library name: Sample 2


title: Differentiated human bronchial epithelial cells from Donor 4, smoldering red oak, chronic exposure

city: Chapel Hill

first: Julia

last: Rager

state: NC

address: 135 Dauer Drive, CB 7431

institute: UNC

description:
Library name: D4_RO_Ch
Column name in raw_counts_HBEC_RO.txt: D4_RO_Ch

data_processing:
Software: BioSpyder TempO-Seq R
Base-calling: BCL to Fastq (bcl2fastq v2.20.0.422) was used for the base-calling with the use-base mask parameter (Y51,i9,i9 1)
FASTQ read alignment: STAR aligner (version 2.5.3a) with the end-to-end option, allowing up to two mismatches
Count table generation: featureCounts (version v1.5.3) with default parameters
Assembly: GRCh38/h38
Supplementary files format and content: Tab-delimited text file includes raw, non-normalized counts for each Sample.

source_name: Primary differentiated human bronchial epithlial cells from healthy donor

growth_protocol: Human lung basal cells acquired from the Marsico Lung Institute (UNC Chapel Hill) were expanded in collage I-coated T25 flasks with PneumaCult-Ex Plus media until 70-90% confluent. Cells were then seeded on collagen-IV coated Transwell inserts and expanded in submerged culture until confluent in PneumaCult-Ex Plus media. Apical media was removed, and basolateral media was replaced with PneumaCult-ALI media. Cells were maintained in PneumaCult-ALI media for a minimum of four weeks to allow for differentiation prior to exposure. For all steps, cells were maintained in a humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested and extracted using the RNeasy Micro Kit (Qiagen) following manufacturer’s protocols.
RNA libraries for RNA-seq were prepared using the TempO-Seq Assay Kit following manufacturer’s protocols.

treatment_protocol: Condensate generated from combusting red oak at 500C (smoldering) was diluted in PneumaCult-ALI media and applied to cells apically (250 uL per well in a 12-well Transwell) for a final dose of 22 ug/cm^2. Exposure paradigms were acute (4 hours treatment, with collection immediately following) or chronic (4 hours treatment, 3 days per week for two week, with collection immediately following the last treatment). PBS diluted in media was used as a vehicle control.

tag: Sex

value: Male

tag: donor id

tag: age of_donor

tag: race of_donor

value: White

value: Smoldering red oak condensate diluted in media

tag: exposure paradigm

value: Apical exposure, 4 hours, 3 times per week, 2 weeks


title: Differentiated human bronchial epithelial cells from Donor 4, control, chronic exposure

description:
Library name: D4_CT_Ch
Column name in raw_counts_HBEC_RO.txt: D4_CT_Ch

tag: cell type

value: Primary differentiated human bronchial epithlial cells from healthy donor

value: PBS diluted in media


title: Differentiated human bronchial epithelial cells from Donor 3, smoldering red oak, chronic exposure

description:
Library name: D3_RO_Ch
Column name in raw_counts_HBEC_RO.txt: D3_RO_Ch

value: Female

tag: treatment


title: Differentiated human bronchial epithelial cells from Donor 4, control, acute exposure

description:
Library name: D4_CT_Ac
Column name in raw_counts_HBEC_RO.txt: D4_CT_Ac

value: Apical exposure, 4 hours


title: Differentiated human bronchial epithelial cells from Donor 2, smoldering red oak, acute exposure

description:
Library name: D2_RO_Ac
Column name in raw_counts_HBEC_RO.txt: D2_RO_Ac

value: Black


title: Patient_PCa3_Tumor_Replica2

description: Library name: PCa3_T_2

value: Prostate


title: Differentiated human bronchial epithelial cells from Donor 2, control, acute exposure

description:
Library name: D2_CT_Ac
Column name in raw_counts_HBEC_RO.txt: D2_CT_Ac


title: Differentiated human bronchial epithelial cells from Donor 1, smoldering red oak, acute exposure

description:
Library name: D1_RO_Ac
Column name in raw_counts_HBEC_RO.txt: D1_RO_Ac


title: Differentiated human bronchial epithelial cells from Donor 1, smoldering red oak, chronic exposure

description:
Library name: D1_RO_Ch
Column name in raw_counts_HBEC_RO.txt: D1_RO_Ch


title: Differentiated human bronchial epithelial cells from Donor 1, control, acute exposure

description:
Library name: D1_CT_Ac
Column name in raw_counts_HBEC_RO.txt: D1_CT_Ac


title: phoP::Tn MG-treated biol rep 2

city: New York

first: Alejandro

last: Pironti

state: NY

address: 430 E29th Street

department: Microbiology

institute: NYU Grossman School of Medicine

description:
Library name: phoP::Tn MG-treated biol rep 2
36-8D_MG_2-1_S69_L005

data_processing:
Sequence reads were mapped to the M. tuberculosis H37Rv genome sequence (RefSeq identifier GCF_000195955.2) using Bowtie2 v2.4.1. An average of 97.36% of reads were mapped to the reference genome, indicating high quality of samples. Using the alignment files generated for each sample, the featureCounts command in Subread v2.0.1 was used to count the reads mapping to each gene in the reference.
Assembly: GCF_000195955.2
Supplementary files format and content: tab delimited text file contains raw counts for each sample.

organism: Mycobacterium tuberculosis

source_name: Mycobacterium tuberculosis

extract_protocol:
R. A. Festa et al., A novel copper-responsive regulon in Mycobacterium tuberculosis. Mol Microbiol 79, 133-148 (2011)
RiboZero Gold

value: Mycobacterium tuberculosis

tag: genotype

value: 1.6 mM methylglyoxal


title: Patient_VAPROS1-1_replicaD1

description: Library name: PA_VAPROS1-1_D1

value: localized prostate cancer


title: phoP::Tn untreated biol rep 3

description:
Library name: phoP::Tn untreated biol rep 3
36-8D_3-1_S66_L005

tag: strain


title: H37Rv MG-treated biol rep 4

description:
Library name: H37Rv MG-treated biol rep 4
WT_MG_4-1_S63_L005

value: Wild-type


title: Patient_VAPROS1-1_replicaC2

description: Library name: PA_VAPROS1-1_C2

tag: tissue


title: H37Rv MG-treated biol rep 2

description:
Library name: H37Rv MG-treated biol rep 2
WT_MG_2-1_S61_L005


title: Patient_VAPROS1-1_replicaB1

description: Library name: PA_VAPROS1-1_B1


title: H37Rv MG-treated biol rep 3

description:
Library name: H37Rv MG-treated biol rep 3
WT_MG_3-1_S62_L005


title: Patient_VAPROS1-1_replicaA1

description: Library name: PA_VAPROS1-1_A1


title: H37Rv untreated biol rep 2

description:
Library name: H37Rv untreated biol rep 2
WT_2-2_S57_L005


title: Patient_PROS505-3_replicaC2

description: Library name: PA_PROS505-3_C2


title: Patient_PR5316_T_base_V1

description: Library name: HNW_PR5316_T_base_V1


title: Patient_PR5316_N_apex_V1

description: Library name: HNW_PR5316_N_apex_V1


title: Patient_PR5316_N_base_V2

description: Library name: HNW_PR5316_N_base_V2


title: Patient_PROS505-3_replicaA2

description: Library name: PA_PROS505-3_A2


title: HCASMC, shSUV39H1, Replicate 4

description: Library name: Sample 8

value: Smooth muscle

tag: cell line

value: Human Coronary Artery Smooth Muscle Cells (HCASMC)

value: Smooth muscle cells


title: HCASMC, shCtrl, Replicate 3

description: Library name: Sample 3

value: WT


title: HCASMC, shCtrl, Replicate 4

description: Library name: Sample 4


title: Differentiated human bronchial epithelial cells from Donor 4, smoldering red oak, acute exposure

description:
Library name: D4_RO_Ac
Column name in raw_counts_HBEC_RO.txt: D4_RO_Ac

value: Male

value: White


title: Differentiated human bronchial epithelial cells from Donor 3, control, acute exposure

description:
Library name: D3_CT_Ac
Column name in raw_counts_HBEC_RO.txt: D3_CT_Ac


title: Differentiated human bronchial epithelial cells from Donor 3, smoldering red oak, acute exposure

description:
Library name: D3_RO_Ac
Column name in raw_counts_HBEC_RO.txt: D3_RO_Ac

value: Smoldering red oak condensate diluted in media


title: Differentiated human bronchial epithelial cells from Donor 3, control, chronic exposure

description:
Library name: D3_CT_Ch
Column name in raw_counts_HBEC_RO.txt: D3_CT_Ch

value: Primary differentiated human bronchial epithlial cells from healthy donor

value: Apical exposure, 4 hours, 3 times per week, 2 weeks


title: Differentiated human bronchial epithelial cells from Donor 2, smoldering red oak, chronic exposure

description:
Library name: D2_RO_Ch
Column name in raw_counts_HBEC_RO.txt: D2_RO_Ch


title: MUSCLE  LBW 5

city: Frederiksberg C

first: Andrew

last: Williams

address: Dyrlægevej 100

institute: University of Copenhagen

description: Library name: L5

data_processing:
Adaptor sequences and low quality reads removed
Mapped to S. scrofa genome (Sscrofa11.1)
DEG determined using DESeq2
Assembly: Sscrofa11.1
Supplementary files format and content: excel file with count data and gene symbol for each sample

organism: Sus scrofa

source_name: semitendinosus muscle

extract_protocol:
RNA was extracted using RNeasy kit (Qiagen) following instructions provided by the manufacturer
standard Illumina

value: semitendinosus muscle


title: Differentiated human bronchial epithelial cells from Donor 2, control, chronic exposure

description:
Library name: D2_CT_Ch
Column name in raw_counts_HBEC_RO.txt: D2_CT_Ch

value: PBS diluted in media


title: Differentiated human bronchial epithelial cells from Donor 1, control, chronic exposure

description:
Library name: D1_CT_Ch
Column name in raw_counts_HBEC_RO.txt: D1_CT_Ch

value: Female

value: Black


title: phoP::Tn MG-treated biol rep 4

description:
Library name: phoP::Tn MG-treated biol rep 4
36-8D_MG_4-2_S71_L005

value: Mycobacterium tuberculosis


title: phoP::Tn MG-treated biol rep 3

description:
Library name: phoP::Tn MG-treated biol rep 3
36-8D_MG_3-1_S70_L005

value: 1.6 mM methylglyoxal


title: phoP::Tn untreated biol rep 4

description:
Library name: phoP::Tn untreated biol rep 4
36-8D_4-1_S67_L005


title: phoP::Tn untreated biol rep 2

description:
Library name: phoP::Tn untreated biol rep 2
36-8D_2-2_S65_L005


title: phoP::Tn untreated biol rep 1

description:
Library name: phoP::Tn untreated biol rep 1
36-8D_1-2_S64_L005


title: phoP::Tn MG-treated biol rep 1

description:
Library name: phoP::Tn MG-treated biol rep 1
36-8D_MG_1-2_S68_L005


title: MUSCLE  LBW 3

description: Library name: L3


title: MUSCLE  LBW 1

description: Library name: L1


title: H37Rv untreated biol rep 4

description:
Library name: H37Rv untreated biol rep 4
WT_4-2_S59_L005


title: MUSCLE  LBW HFHP 5

description: Library name: K5


title: H37Rv MG-treated biol rep 1

description:
Library name: H37Rv MG-treated biol rep 1
WT_MG_1-2_S60_L005


title: MUSCLE  LBW HFHP 1

description: Library name: K1


title: MUSCLE  LBW HFHP 3

description: Library name: K3


title: H37Rv untreated biol rep 3

description:
Library name: H37Rv untreated biol rep 3
WT_3-2_S58_L005


title: MUSCLE  LBW 7

description: Library name: L7


title: H37Rv untreated biol rep 1

description:
Library name: H37Rv untreated biol rep 1
WT_1-2_S56_L005


title: MUSCLE  NBW 5

description: Library name: J5


title: MUSCLE  NBW 4

description: Library name: J4


title: MUSCLE  NBW 2

description: Library name: J2


title: MUSCLE  LBW 6

description: Library name: L6


title: MUSCLE  NBW 3

description: Library name: J3


title: MUSCLE  NBW HFHP 6

description: Library name: I6


title: MUSCLE  NBW 1

description: Library name: J1


title: MUSCLE  NBW HFHP 5

description: Library name: I5


title: MUSCLE  LBW 4

description: Library name: L4


title: MUSCLE  LBW 2

description: Library name: L2


title: MUSCLE  NBW HFHP 1

description: Library name: I1


title: MUSCLE  LBW HFHP 4

description: Library name: K4


title: LIVER LBW 4

description: Library name: H4

value: Liver


title: LIVER LBW 2

description: Library name: H2


title: MUSCLE  LBW HFHP 2

description: Library name: K2


title: LIVER LBW HFHP 2

description: Library name: G2


title: LIVER NBW 5

description: Library name: F5


title: LIVER NBW 4

description: Library name: F4


title: MUSCLE  NBW 6

description: Library name: J6


title: LIVER NBW HFHP 5

description: Library name: E5


title: LIVER NBW HFHP 4

description: Library name: E4


title: LIVER NBW HFHP 3

description: Library name: E3


title: SI LBW 6

description: Library name: D6

source_name: Small Inestine

value: Small Inestine


title: SI LBW 5

description: Library name: D5


title: SI LBW 2

description: Library name: D2


title: SI LBW HFHP 2

description: Library name: C2


title: MUSCLE  NBW HFHP 4

description: Library name: I4


title: SI LBW HFHP 1

description: Library name: C1


title: MUSCLE  NBW HFHP 3

description: Library name: I3


title: SI NBW 7

description: Library name: B7


title: MUSCLE  NBW HFHP 2

description: Library name: I2


title: LIVER LBW 6

description: Library name: H6


title: LIVER LBW 5

description: Library name: H5


title: SI NBW 4

description: Library name: B4


title: SI NBW 3

description: Library name: B3


title: LIVER LBW 1

description: Library name: H1


title: LIVER LBW HFHP 5

description: Library name: G5


title: LIVER LBW HFHP 4

description: Library name: G4


title: LIVER LBW HFHP 3

description: Library name: G3


title: LIVER LBW HFHP 1

description: Library name: G1


title: LIVER LBW 3

description: Library name: H3


title: LIVER NBW 3

description: Library name: F3


title: SI NBW HFHP 7

description: Library name: A7


title: LIVER NBW 1

description: Library name: F1


title: SI NBW HFHP 8

description: Library name: A8


title: LIVER NBW HFHP 6

description: Library name: E6


title: LIVER NBW 2

description: Library name: F2


title: SI NBW HFHP 6

description: Library name: A6


title: SI NBW HFHP 4

description: Library name: A4


title: SI NBW HFHP 2

description: Library name: A2


title: LIVER NBW HFHP 2

description: Library name: E2


title: LIVER NBW HFHP 1

description: Library name: E1


title: SI NBW HFHP 1

description: Library name: A1


title: SI LBW 7

description: Library name: D7


title: SI LBW 4

description: Library name: D4


title: SI LBW 3

description: Library name: D3


title: SI LBW 1

description: Library name: D1


title: SCC-2

city: Lanzhou City

first: zhengjie

last: suo

state: Gansu

address: 营门村1号

institute: Gansu Agricultural University

description:
Library name: Sample 29
SCC-vs-SCT1.all.annot.txt

data_processing:
Reads obtained from the sequencing machines included raw reads containing adapters or low quality bases which would affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered according to the following rules: 1) Removing reads containing adapters; 2) Removing reads consisting of all A bases; 3) Removing reads containing more than 10% of unknown nucleotides (N); 4) Removing low quality reads containing more than 50% of low quality (Q-value≤20) bases
Short reads alignment tool Bowtie2 (2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads were then removed. The remaining reads were further used in assembly and analysis of transcriptome.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 and other parameters set as a default.
After aligned with reference genome, unmapped reads (or mapped very poorly) were then re-aligned with Bowtie2, the enriched unmapped reads were split into smaller segments which were then used to find potential splice sites. The section and the section position of these short segments were predicted as well. A set of splice sites was built with initial unmapped reads  without relying on the known genes annotation. Not only be used for identifying expressed genes and their quantitative expression, the sequence alignment will also be helpful to find alternative splicing and new transcripts.
Assembly: Oncorhynchus mykiss USDA_OmykA_1.1
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Oncorhynchus mykiss

source_name: Skin tissues

growth_protocol: Healthy rainbow trout (85 ± 0.5 g) used in this study were obtained from a fish farm in Gansu Province, and acclimatized for two weeks. These fish are six-month old road style rainbow trout and are full siblings. The fish were cultivated in 1000 L tanks at water temperatures of 12 ± 1℃. During the fish experiments, the pH ranged from 7.6 to 7.8 and the dissolved oxygen was about 8.5 mg/L. Feeding with commercial dry feed pellets (Shandong Hanye Biotechnology Co., Ltd, China) was performed twice daily, a rate of 2% of their body weight.

extract_protocol:
The total RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Two weeks after rainbow trout were suspended, healthy rainbow trout were randomly divided into three groups, including normoxia, moderate hypoxia, and severe hypoxia groups, the oxygen levels were maintained at 8.5 ± 0.1, 4.5 ± 0.1, and 3.0 ± 0.1 mg/L, respectively, and the low oxygen environment was created by mixing oxygen and nitrogen.

value: Skin tissues

value: control group_IHNV challenged

tag: time


title: SCT-2-3

description:
Library name: Sample 36
SCT2-vs-SCT1.all.annot.txt

value: vaccine group_IHNV challenged


title: SCT-1-2

description:
Library name: Sample 32
SCC-vs-SCT2.all.annot.txt

value: P-APS+vaccine group_IHNV challenged


title: SCT-1-3

description:
Library name: Sample 33
SCC-vs-SCT2.all.annot.txt


title: SCC-3

description:
Library name: Sample 30
SCC-vs-SCT1.all.annot.txt


title: SCC-1

description:
Library name: Sample 28
SCC-vs-SCT1.all.annot.txt


title: SI LBW HFHP 5

description: Library name: C5


title: SI LBW HFHP 3

description: Library name: C3


title: SI LBW HFHP 4

description: Library name: C4


title: ST-2-2

description:
Library name: Sample 26
ST2_vs_SC.all.annot.txt

value: vaccine

value: 7 d


title: SI LBW HFHP 6

description: Library name: C6


title: SI NBW 8

description: Library name: B8


title: SI NBW 5

description: Library name: B5


title: SI NBW 6

description: Library name: B6


title: SI NBW 2

description: Library name: B2


title: ST-2-1

description:
Library name: Sample 25
ST2_vs_SC.all.annot.txt


title: GCT-1-3

description:
Library name: Sample 15
GCT2-vs-GCT1.all.annot.txt

source_name: Gill tissues

value: Gill tissues


title: GCT-1-2

description:
Library name: Sample 14
GCT2-vs-GCT1.all.annot.txt


title: SI NBW HFHP 5

description: Library name: A5


title: GT-2-1

description:
Library name: Sample 7
GT2_vs_GC.all.annot.txt


title: GT-1-2

description:
Library name: Sample 5
GT1_vs_GT2.all.annot.txt

value: P-APS+vaccine


title: GT-2-2

description:
Library name: Sample 8
GT2_vs_GC.all.annot.txt


title: GCC-1

description:
Library name: Sample 10
GCC-vs-GCT1.all.annot.txt


title: SCT-2-1

description:
Library name: Sample 34
SCT2-vs-SCT1.all.annot.txt


title: SI NBW HFHP 3

description: Library name: A3


title: SI NBW 1

description: Library name: B1


title: SCT-1-1

description:
Library name: Sample 31
SCC-vs-SCT2.all.annot.txt


title: GC-2

description:
Library name: Sample 2
GT1_vs_GC.all.annot.txt

value: control


title: SC-3

description:
Library name: Sample 21
ST1_vs_SC.all.annot.txt


title: SC-2

description:
Library name: Sample 20
ST1_vs_SC.all.annot.txt


title: SCT-2-2

description:
Library name: Sample 35
SCT2-vs-SCT1.all.annot.txt


title: ST-1-2

description:
Library name: Sample 23
ST1_vs_ST2.all.annot.txt


title: GCT-2-2

description:
Library name: Sample 17
GCC-vs-GCT2.all.annot.txt


title: GCT-2-1

description:
Library name: Sample 16
GCC-vs-GCT2.all.annot.txt


title: SC-1

description:
Library name: Sample 19
ST1_vs_SC.all.annot.txt


title: GCC-3

description:
Library name: Sample 12
GCC-vs-GCT1.all.annot.txt


title: ST-1-3

description:
Library name: Sample 24
ST1_vs_ST2.all.annot.txt


title: A_1

city: Wuhan

first: Zhuo-ran

last: Yang

state: Hubei

address: No. 1037 Luoyu Road, Hongshan District

department: Hubei Engineering Research Center for Biomaterials and Medical Protective Materials, School of Chemistry and Chemical Engineering

institute: Huazhong University of Science and Technology (HUST)

description: Library name: Sample 1

data_processing:
The FASTQ files were processed and aligned to  reference genome using the BD Rhapsody WTA Analysis Pipeline (version 2.0) with unique molecular identifier (UMI) counts ummarized for each barcode. The UMI count matrix was then analyzed using Seurat (version 4.0.0) R package. Subsequently, we applied DoubletFinder package (version 2.0.3) to assess notential doublet and multiplets. To obtain the normalized gene expression data, library size normalization was implemented by the NormalizeData function.
Assembly: rn6
Supplementary files format and content: Tab-separated values files and matrix files

organism: Rattus norvegicus

source_name: nucleus pulposus

extract_protocol:
Upon completion of the in vivo experiments, intervertebral disc tissues were harvested from both the degenerative group and the B2M-ApoEV/DFS@HMs-treated group, followed by meticulous isolation of NP tissues. The NP specimens were uniformly minced into approximately 0.5 mm³ fragments and subsequently subjected to enzymatic digestion to obtain single-cell suspensions. Cell concentration and viability were quantitatively assessed using a Luna automated cell counter.
Single cell RNAsequencing was conducted by Shanghai OE Biotech Co., Ltd. utilizing the BD Rhapsody™ platform. Following the manufacturer’s recommendations, the single cell suspension was adjusted to the appropriate volume for loading and capture using the BD Rhapsody™ Enhanced Cartridge Reagent Kit and BD Rhapsody™ Cartridge Kit. Reverse transcription was performed using the BD Rhapsody™ cDNA kit. BD Rhapsody™ WTA Amplification Kit was used for DNA library construction. High-throughput sequencing was performed with the PE-150 mode.

value: nucleus pulposus

value: primary cells

value: nucleus pulposus cells

value: 100uM TBHP


title: B_2

description: Library name: Sample 4

value: 100uM TBHP+2uL B2M-ApoEV/DFS@HMs


title: ST-1-1

description:
Library name: Sample 22
ST1_vs_ST2.all.annot.txt


title: GCT-2-3

description:
Library name: Sample 18
GCC-vs-GCT2.all.annot.txt


title: ST-2-3

description:
Library name: Sample 27
ST2_vs_SC.all.annot.txt


title: MOLM-14 cells, RX-5902, 6 hours, biological replicate #2

city: Boston

first: WEI

last: NI

state: MA

address: 450 Brookline Ave, Bldg MA-0543

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description:
Library name: sample 11
Column name in all_samples_RX5902_6hrs_counts.txt: RX-5902_2

data_processing:
Reads were trimmed with Trim Galore (v0.6.7) to remove adapters and low-quality ends (Phred score < 30). The reference index for the human genome was built using STAR (v2.7.9a) with the GRCh38 primary assembly and its corresponding annotation file from GENCODE release 41 (https://www.gencodegenes.org/human/release_41.html). Reads were aligned to the reference genome using STAR (v2.7.9a), and alignment quality was assessed using Picard (v2.8.0). Uniquely aligned reads were summarized into gene-level counts using the featureCounts function from Subread (v2.0.3). The above steps were conducted on the O2 high-performance computing cluster at Harvard Medical School. Gene-level counts obtained from featureCounts were analyzed for differential expression locally in R (v4.4.2) using the DESeq2 package (v1.46.0), with metadata specifying the experimental groups. Normalized counts were generated through DESeq2’s internal factor-size estimation.
Assembly: Release 41 (GRCh38.p13)
Supplementary files format and content: tab-delimited text file includes raw counts for all samples in DDX5 knockdown experiment
Supplementary files format and content: tab-delimited text file includes raw counts for all samples in RX-5902 treatment experiemnt

growth_protocol: MOLM-14 cells were cultured in RPMI-1640 medium (ThermoFisher Scientific) supplemented with 10% heat-inactivated fetal bovine serum (ThermoFisher Scientific) and 1% Penicillin-Streptomycin (ThermoFisher Scientific), at 37°C with 5% CO2.

extract_protocol:
RNA was extracted using Trizol reagent (ThermoFisher Scientific) with chloroform, and purified using Rneasy mini plus kit (Qiagen) with on-column genomic DNA removal by RNase-free DNase (Qiagen).
RNA libraries for RNA-seq were prepared using MGIEasy Fast RNA Library Prep Set following manufacturer's protocols.

treatment_protocol: For DDX5 knockdown experiment, MOLM-14 cells transduced with control shRNA (shControl) or DDX5-targeting shRNA (shDDX5) by spinoculation, and then cells were collected 96 hours post lentiviral infection. For RX-5902 treatment experiment, MOLM-14 cells treated with DMSO (0.1%) or RX-5902 (100 nM) for 6 hours, and then cells were harvested for RNA extraction.

value: human AML cell line


title: MOLM-14 cells, DMSO, 6 hours, biological replicate #3

description:
Library name: sample 9
Column name in all_samples_RX5902_6hrs_counts.txt: DMSO_3

value: DMSO


title: MOLM-14 cells, DMSO, 6 hours, biological replicate #2

description:
Library name: sample 8
Column name in all_samples_RX5902_6hrs_counts.txt: DMSO_2


title: MOLM-14 cells, shControl, 96 hours, biological replicate #3

description:
Library name: sample 3
Column name in all_samples_DDX5_KD_counts.txt: shControl_3

value: shControl


title: GCT-1-1

description:
Library name: Sample 13
GCT2-vs-GCT1.all.annot.txt


title: MOLM-14 cells, shDDX5, 96 hours, biological replicate #3

description:
Library name: sample 6
Column name in all_samples_DDX5_KD_counts.txt: shDDX5_3


title: GT-2-3

description:
Library name: Sample 9
GT2_vs_GC.all.annot.txt


title: MOLM-14 cells, shControl, 96 hours, biological replicate #1

description:
Library name: sample 1
Column name in all_samples_DDX5_KD_counts.txt: shControl_1


title: GCC-2

description:
Library name: Sample 11
GCC-vs-GCT1.all.annot.txt


title: GC-1

description:
Library name: Sample 1
GT1_vs_GC.all.annot.txt


title: GT-1-1

description:
Library name: Sample 4
GT1_vs_GT2.all.annot.txt


title: B_1

description: Library name: Sample 3


title: RNA-Seq of Homo sapiens: H1 cell differentiation

city: Guangzhou 510700, China

first: yu

last: liu

address: Guangzhou 510700, China

institute: Guangzhou Future Homo Sapiens Institute of Regenerative Medicine Co., Ltd

description:
Library name: H1_MSCs_1
Total RNA was extracted (TaKaRa, 9108), rRNA was removed using probe hybridization (MGI, 1000005953), and the RNA was purified. RNA library construction was performed using an RNA library preparation kit (MGI, 1000006383). The samples were sequenced using a gene sequencer (MGISEQ-2000) and an MGISEQ-2000RS high-throughput sequencing reagent kit (FCL PE150) (MGI, 1000012555) to determine the transcriptomic gene expression profiles of H1 cells, H1-iMSCs, and bone marrow-, adipose-, and umbilical cord-derived MSCs.

data_processing:
Raw data from second-generation sequencing were processed using Toil-Rnaseq software to obtain TPM values.
PCA between samples was performed using the PCA function from the FactoMineR package for data normalization and PCA computation.
The sample correlation coefficients were calculated using the Pearson statistical method with the Cor function.
DEGs were clustered by normalizing the data using the log2(TPM + 0.01) values. DEG analysis was performed using the Limma package with the selection criteria of a false discovery rate (FDR) < 0.05 and log fold change (FC) > 1.
Assembly: GRCh38
Supplementary files format and content: csv files include TPM values for each Sample

source_name: It's derived from H1 cells differentiation

value: Human mesenchymal stem cells

value: MSC differentiated from H1 cells


title: MOLM-14 cells, shDDX5, 96 hours, biological replicate #2

description:
Library name: sample 5
Column name in all_samples_DDX5_KD_counts.txt: shDDX5_2


title: GC-3

description:
Library name: Sample 3
GT1_vs_GC.all.annot.txt


title: RNA-Seq of Homo sapiens:adipose

description:
Library name: AD_MSCs_1
Total RNA was extracted (TaKaRa, 9108), rRNA was removed using probe hybridization (MGI, 1000005953), and the RNA was purified. RNA library construction was performed using an RNA library preparation kit (MGI, 1000006383). The samples were sequenced using a gene sequencer (MGISEQ-2000) and an MGISEQ-2000RS high-throughput sequencing reagent kit (FCL PE150) (MGI, 1000012555) to determine the transcriptomic gene expression profiles of H1 cells, H1-iMSCs, and bone marrow-, adipose-, and umbilical cord-derived MSCs.

source_name: adipose

value: adipose


title: GT-1-3

description:
Library name: Sample 6
GT1_vs_GT2.all.annot.txt


title: RNA-Seq of Homo sapiens:umbilical cord

description:
Library name: UC_MSCs_1
Total RNA was extracted (TaKaRa, 9108), rRNA was removed using probe hybridization (MGI, 1000005953), and the RNA was purified. RNA library construction was performed using an RNA library preparation kit (MGI, 1000006383). The samples were sequenced using a gene sequencer (MGISEQ-2000) and an MGISEQ-2000RS high-throughput sequencing reagent kit (FCL PE150) (MGI, 1000012555) to determine the transcriptomic gene expression profiles of H1 cells, H1-iMSCs, and bone marrow-, adipose-, and umbilical cord-derived MSCs.

source_name: umbilical cord

value: umbilical cord


title: MOLM-14 cells, shDDX5, 96 hours, biological replicate #1

description:
Library name: sample 4
Column name in all_samples_DDX5_KD_counts.txt: shDDX5_1


title: MOLM-14 cells, DMSO, 6 hours, biological replicate #1

description:
Library name: sample 7
Column name in all_samples_RX5902_6hrs_counts.txt: DMSO_1


title: MAL1_1

city: Sakyo-ku

first: Yumi

last: Inoue

state: Kyoto

address: 54 Shogoin Kawaramachi

country: Japan

institute: Kyoto University

description: Library name: PR1800_10A0608

data_processing:
Raw read data were mapped to the human reference genome using the DRAGEN Bio-IT Platform (version 3.5.7, Illumina), and transcript abundance was quantified in transcripts per million (TPM).
Assembly: DRAGEN Bio -IT Platforom, GRCh38, gencode.v34
Supplementary files format and content: The Excel file contains the Counts and TPM values for each sample

source_name: RPE

extract_protocol:
Total RNA was extracted using the RNeasy Mini Plus Kit (Qiagen, 74104) and treated with deoxyribonuclease I (DNases1) to eliminate genomic DNA contamination.
Sequencing was performed on an Illumina NovaSeq 6000 platform in 150-base paired-end mode.

value: RPE

value: MAL

value: iPSC-RPE


title: MAL1_POS(+)_2

description: Library name: PR1800_14A0703


title: MAL1_3

description: Library name: PR1800_12A0607


title: RNA-Seq of Homo sapiens:Embryo culture (blastocyst stage)

description:
Library name: H1_1
Total RNA was extracted (TaKaRa, 9108), rRNA was removed using probe hybridization (MGI, 1000005953), and the RNA was purified. RNA library construction was performed using an RNA library preparation kit (MGI, 1000006383). The samples were sequenced using a gene sequencer (MGISEQ-2000) and an MGISEQ-2000RS high-throughput sequencing reagent kit (FCL PE150) (MGI, 1000012555) to determine the transcriptomic gene expression profiles of H1 cells, H1-iMSCs, and bone marrow-, adipose-, and umbilical cord-derived MSCs.

source_name: It's derived from blastocyst stage

value: It's derived from blastocyst stage

value: Human embryonic stem cell


title: NOR1_2

description: Library name: PR1800_02A0508

value: NOR


title: MOLM-14 cells, RX-5902, 6 hours, biological replicate #1

description:
Library name: sample 10
Column name in all_samples_RX5902_6hrs_counts.txt: RX-5902_1


title: RNA-Seq of Homo sapiens:bone marrow

description:
Library name: BM_MSCs_1
Total RNA was extracted (TaKaRa, 9108), rRNA was removed using probe hybridization (MGI, 1000005953), and the RNA was purified. RNA library construction was performed using an RNA library preparation kit (MGI, 1000006383). The samples were sequenced using a gene sequencer (MGISEQ-2000) and an MGISEQ-2000RS high-throughput sequencing reagent kit (FCL PE150) (MGI, 1000012555) to determine the transcriptomic gene expression profiles of H1 cells, H1-iMSCs, and bone marrow-, adipose-, and umbilical cord-derived MSCs.

source_name: bone marrow

value: bone marrow


title: NOR1_POS(+)_1

description: Library name: PR1800_04A0507


title: MOLM-14 cells, shControl, 96 hours, biological replicate #2

description:
Library name: sample 2
Column name in all_samples_DDX5_KD_counts.txt: shControl_2


title: MAL1_POS(+)_3

description: Library name: PR1800_15A0705


title: NOR1_3

description: Library name: PR1800_03A0510


title: MAL1_POS(+)_1

description: Library name: PR1800_13A0702


title: NOR1_POS(+)_3

description: Library name: PR1800_06A0603


title: NOR1_1

description: Library name: PR1800_01A0511


title: NOR1_POS(+)_2

description: Library name: PR1800_05A0602


title: MAL1_2

description: Library name: PR1800_11A0610


title: Multiplexed sublibrary of all samples, hU6-targeted gRNA ClonMapper barcode capture; sublibrary 8

city: Austin

first: Amy

last: Brock

state: Texas

address: 107 W Dean Keaton St.

department: Biomedical Engineering

institute: University of Texas at Austin

description: Library name: CR-8

data_processing:
The Parse Pipeline v1.4.0 was used to generate single-cell read count matrices for whole transcriptome libraries from multiplexed raw .fastq files. The sample_loading_table.xlsx required to run the whole-transcriptome pipeline is included as a supplementary file, containing demultiplexing sample information required by the pipeline. The sample_metadata.csv contains sample names and corresponding information for each sample in the dataset, including treatment, cell line, and demultiplexing well ID. The median absolute deviation of each cell was calculated for fraction of counts from mitochondrial genes, total number of counts per cell, and total number of genes per cell, and cells with greater 5 median absolute deviations for any of these metrics were filtered out as low quality cells. Genes with nonzero expression in less than 20 cells were removed from the dataset. Normalized counts were calculated as log(CPM+1).
The Parse Pipeline v1.4.0 with --crispr switch was used to generate single-cell barcode count matricies for CRISPR-detect barcode libraries from multiplexed raw .fastq files. The required guides.csv required to run the CRISPR-detect pipeline is included as a supplementary file. For each cell from the filtered whole-transcriptome dataset, a ClonMapper barcode was assigned by high abundance in the CRISPR-detect dataset.
Assembly: GRCh38
Supplementary files format and content: wt.h5ad - Annotated data matrix containing genes as variables and cells as observations. Normalized counts are stored in .X. Raw counts are stored under .layers in 'raw_counts'. Cell line identity is stored under .obs in 'cell_line'. Treatment information is stored under .obs as 'treatment'. Replicate information is stored under .obs as 'replicate'. Cell barcode identities are stored under .obs in 'lineage'. Targeted sequencing counts of barcodes from each sample are included in .uns under 'targeted_seq_counts'.
Supplementary files format and content: bc.h5ad - Annotated data matrix containing barcodes as variables and cells as observations. Barcode counts are stored under .X. Cell line identity is stored under .obs in 'cell_line'.

source_name: Breast

growth_protocol: UACC-2087 and UACC-3199 were cultured in high glucose DMEM with L-glutamine and phenol red, supplemented with 5% fetal bovine serum, 1X insulin-transferrin-selenium, 5 μg/mL catalase, 3.6 μg/mL hydrocortisone, and 2 mM extra L-glutamine. 885512-J2-296-R-PDC was cultured as described by NIH PDMR SOP30103 in “complete DMEM/F12 media” as described by PDMR SOP30101 as Advanced DMEM/F12 supplemented with 5% fetal bovine serum, 400 ng/mL hydrocortisone, 10 ng/mL human epidermal growth factor, 24 ug/mL adenine, 1% penicillin/streptomycin, and 2mM L-glutamine. 885512-J2 was continuously cultured on culture dishes coated with 2.5% Matrigel as described in PDMR SOP30102.

extract_protocol:
After recovery to 1e6 cells/well, cells were washed with PBS and dissociated with TrypLE. Dissociated cells were fixed with Parse Evercode cell fixation kits.
Whole-transcriptome scRNA-seq libraries were generated from fixed cells with a Parse Evercode WT v3 kit. Single cell barcode sequencing libraries were generated from fixed cells with a Parse CRISPR-detect kit. Libraries were generated with a target of 2650 cells/sample for barcoded cells and 4150 cells/sample for unbarcoded cells. Both kits produced 8 sublibraries (WT and CR, respectively) for sequencing. WT libraries were split evenly across 3.2B reads and CR libraries were split evenly across 500M reads.

treatment_protocol: Cells were seeded at 1e6 cells/well in a 6 well plate. 24h after seeding, cell medium was replaced with therapy-containing medium for 72h. After 72h, medium was removed and replaced with standard culture medium until cells recovered to 1e6 cells/well. Doses used: UACC-2087: (olaparib - 438.9 uM, ipatasertib - 65.19 uM, palbociclib - 54.46 uM), UACC-3199: (olaparib - 114.26 uM, ipatasertib - 69.95 uM, palbociclib - 12.03 uM), 885512-J2: (olaparib - 3.428 uM, ipatasertib - 83.81 uM, palbociclib - 17.40 uM). Control cells were seeded at 0.2e6 cells/well and allowed to seed for 24h. Medium was replaced with standard culture medium for 72h, then replaced again, to mimic treated conditions.

value: Breast

value: Triple-negative breast cancer

tag: genetic modification

value: ClonMapper bacoded

value: Olaparib, ipatasertib, palbociclib

tag: batch

value: Female


title: Multiplexed sublibrary of all samples, hU6-targeted gRNA ClonMapper barcode capture; sublibrary 3

description: Library name: CR-3


title: Multiplexed sublibrary of all samples, hU6-targeted gRNA ClonMapper barcode capture; sublibrary 5

description: Library name: CR-5


title: Multiplexed sublibrary of all samples, hU6-targeted gRNA ClonMapper barcode capture; sublibrary 2

description: Library name: CR-2


title: Multiplexed sublibrary of all samples, hU6-targeted gRNA ClonMapper barcode capture; sublibrary 7

description: Library name: CR-7


title: Multiplexed sublibrary of all samples, hU6-targeted gRNA ClonMapper barcode capture; sublibrary 1

description: Library name: CR-1


title: Multiplexed sublibrary of all samples, hU6-targeted gRNA ClonMapper barcode capture; sublibrary 6

description: Library name: CR-6


title: Multiplexed sublibrary of all samples, whole-transcriptome poly-A capture; sublibrary 5

description: Library name: WT-5


title: Multiplexed sublibrary of all samples, whole-transcriptome poly-A capture; sublibrary 3

description: Library name: WT-3


title: Multiplexed sublibrary of all samples, whole-transcriptome poly-A capture; sublibrary 6

description: Library name: WT-6


title: Multiplexed sublibrary of all samples, hU6-targeted gRNA ClonMapper barcode capture; sublibrary 4

description: Library name: CR-4


title: Multiplexed sublibrary of all samples, whole-transcriptome poly-A capture; sublibrary 1

description: Library name: WT-1


title: Multiplexed sublibrary of all samples, whole-transcriptome poly-A capture; sublibrary 8

description: Library name: WT-8


title: Multiplexed sublibrary of all samples, whole-transcriptome poly-A capture; sublibrary 7

description: Library name: WT-7


title: Multiplexed sublibrary of all samples, whole-transcriptome poly-A capture; sublibrary 4

description: Library name: WT-4


title: Cells extracted from soft matrix, cells migrated from stiff matrix

first: Stephanie

middle: K

last: Seidlits

address: 107 W. Dean Keeton Street Austin

institute: The University of Texas

description: Library name: Stiff_Mi

data_processing:
Annotated count matricies were generated using Cell Ranger. Low quality data was removed using a median absolute deviation (MAD) threshold of 3 and a mitochrondrial gene fraction of > 0.2. Data was normalized by application of a shifted logarithm.
Samples in HK177 were assigned ClonMapper cell lineages present in the 'lineage' observation and assigned a migratory phenotype based on a bionomial distribution listed in the 'phenotype' observation.
Assembly: GRCh38
Supplementary files format and content: h5ad anndata

source_name: brain

growth_protocol: Cells were encapsulated in hyaluronic acid-based hydrogels for 2 weeks prior to sequencing and  cultured in DMEM/F12 media containing human FGF, human EGF, Gem21 NeuroPlex supplement and L-Glutamine at 37C 5% O2.

extract_protocol:
Cells were extracted from hydrogels using the human tumor kit and the GentleMACs human tumor dissociator from Miltenyi Biotec (130-095-929). Cells were washed 3X with 1X PBS and stained with 7aad (Invitrogen A1310) according to the manufacturer’s recommendations for dead cell identification. Cells were sorted using FACS to remove hydrogel particles and to ensure that only live cells were submitted for sequencing.
Samples were prepared with 10X Chromium Single Cell 3ʹ v3 kit.

value: brain

value: glioblastoma

value: ClonMapper Barcode


title: Cells extracted from soft matrix, stationary cells

description: Library name: Soft_Non


title: Cells extracted from soft matrix, cells migrated from soft matrix

description: Library name: Soft_Mi


title: Multiplexed sublibrary of all samples, whole-transcriptome poly-A capture; sublibrary 2

description: Library name: WT-2


title: Cells extracted from stiff matrix, stationary cells

description: Library name: Stiff_Non


title: A_2

description: Library name: Sample 2

value: nucleus pulposus

value: primary cells

value: nucleus pulposus cells

value: 100uM TBHP


title: Pt5_Bx_I1D021_GEX

city: Seattle

first: Aude

last: Chapuis

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Center

description:
Library name: Sample16
10x Genomics

data_processing:
Sequencing reads were processed using Cell Ranger (v6.1.1) for alignment, barcode assignment, and UMI counting.
Assembly: GRCh38 (with appended TCRMCC1 and MCPyV sequences)
Supplementary files format and content: matrix.mtx.gz – raw gene expression counts (genes × cells)
Supplementary files format and content: features.tsv.gz – gene annotation file corresponding to rows of the count matrix
Supplementary files format and content: barcodes.tsv.gz – cell barcodes corresponding to columns of the count matrix

source_name: Tumor

extract_protocol:
Cryopreserved PBMCs were thawed and washed in PBS with 0.04% BSA. Tumor biopsies were enzymatically dissociated, washed, and subjected to dead cell removal. Cells were counted and resuspended for single-cell capture.
Single-cell RNA-seq libraries were prepared using the 10x Genomics Chromium Next GEM Single Cell 5’ Reagent Kits v2 (Dual Index) following the manufacturer’s instructions.

tag: patient id

tag: infusion

tag: day

value: Tumor

tag: collection site

value: Skin

tag: treatment group

value: SFRT


title: Pt3_Bx_I1D048_GEX

description:
Library name: Sample15
10x Genomics

value: Flu/Cy


title: Pt6_Bx_I1D118_GEX

description:
Library name: Sample21
10x Genomics

value: Pelvic lymph node


title: Pt7_Bx_I1D014_GEX

description:
Library name: Sample22
10x Genomics

value: Left adrenal nodule


title: Pt6_Bx_I1D014_GEX

description:
Library name: Sample19
10x Genomics


title: Pt6_Bx_PreIFNg_GEX

description:
Library name: Sample17
10x Genomics

value: PreIFNg (-11)


title: Pt6_Bx_PostIFNg_GEX

description:
Library name: Sample18
10x Genomics

value: PostIFNg (-1)


title: Pt6_Bx_I1D052_GEX

description:
Library name: Sample20
10x Genomics


title: Pt2_Bx_I1D105_GEX

description:
Library name: Sample14
10x Genomics


title: Pt3_PBMC_I1D048_GEX

description:
Library name: Sample6
10x Genomics

source_name: PBMC

value: PBMC

value: Blood


title: Pt6_PBMC_I1D056_GEX

description:
Library name: Sample12
10x Genomics


title: Pt6_PBMC_I1D028_GEX

description:
Library name: Sample11
10x Genomics


title: Pt5_PBMC_I1D021_GEX

description:
Library name: Sample9
10x Genomics


title: Pt1_PBMC_I2D014_GEX

description:
Library name: Sample4
10x Genomics