title: HPF cell, PBS, 72hrs, LIGHT, 24 hrs, rep1

description: Library name: 231107_NG_Sample_4

value: PBS 72 hrs and LIGHT 24 hrs


title: MCF7_CTRL_RNA-seq_Rep1

status: Public on Jul 10 2025

type: SRA

city: Berkeley

first: Robert

last: Tjian

state: CA

address: University of California, Berkeley 450 Li Ka Shing #3370

department: MCB

country: USA

institute: UC Berkeley

library_source: transcriptomic

data_processing:
RNA-seq read quantification: Kalisto
RNA-seq gene differentiatial expression analysis: Sleuth
Assembly: hg38
Supplementary files format and content: h5 is a HDF5 binary file containing run info, abundance esimates, bootstrap estimates, and transcript length information length.

molecule: total RNA

organism: Homo sapiens

source_name: Breast Adenocarcinoma

growth_protocol:
Eagle's Minimum Essential Medium (EMEM; ATCC 30-2003), 10% FBS
Cells were grown according to ATCC recommendations (details in the Sample section above)

extract_protocol:
Total RNA extraction with TRIzol reagent followed by rRNA depletion (NEBNext® rRNA Depletion Kit (Human/Mouse/Rat) with RNA Sample Purification Beads (cat. E6350L)
RNA-seq libraries were prepared with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (cat. E7760S). Library concentration, quality and fragment size were assessed by Qubit fluorometric quantification (Qubit™ dsDNA HS Assay Kit, InvitrogenTM Q32851) qPCR and Fragment analyzer™. 10 multiplexed libraries were pooled and sequenced in one lane on the Illumina HiSeq4000 sequencing platform (100-bp, paired-end reads)

treatment_protocol: 20 uM Nutlin-3a (dissolved in EtOH) or the same volume of pure ethanol (mock-teated) for 4 hours.

tag: tissue

value: Breast Adenocarcinoma

tag: cell line

tag: cell type

value: Cancer, Metastasis

tag: treatment

value: mock-treated

tag: molecule subtype

value: rRNA-depleted RNA


title: MCF7_NUT_RNA-seq_Rep1


title: HPF cell, PBS, 72hrs, LIGHT, 24 hrs, rep2

city: La Jolla

first: Jeamin

last: Jung

address: 9420 Athena Cir

department: Bioinformatics Core

institute: La Jolla Institute for Immunology

description: Library name: 231107_NG_Sample_5

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.1.2
Filtered reads were mapped against the human GRCh38 reference using STAR v2.6.1
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using FeatureCount v1.6.5 (“union” option) and features with 0 counts across all samples were removed
Assembly: GRCh38
Supplementary files format and content: tsv counts matrix with rows as genes and columns as samples

molecule: polyA RNA

source_name: Lung

growth_protocol: Human pulmonary fibroblasts were cultured in fibroblast media, serum starved prior  cytokine treatment

extract_protocol:
Zymo Direct-zol
NEB mRNA Directional

treatment_protocol: Human pulmonary fibroblasts (HPF) stimulated with 50 ng/ml LIGHT, 25 ng/ml IL-13, and 100 ng/ml IL-17A and in combination of IL13 or Il17A with LIGHT. HPF were also pretreated with 50 ng/ml of IL13/ IL17A followed by 50 ng/ml LIGHT treatment.

value: Lung

value: HPF

value: Fibroblasts

tag: batch


title: HPF cell, PBS, 72hrs, LIGHT, 24 hrs, rep3

description: Library name: 231107_NG_Sample_6


title: HPF cell, IL13, 72 hrs, LIGHT, 24 hrs, rep3

description: Library name: 231107_NG_Sample_12

value: IL13 72hrs followed by LIGHT 24hrs


title: HPF cell, PBS, 96 hrs, rep3

description: Library name: 231107_NG_Sample_3

value: PBS 96 hrs


title: GM12878_CTRL_RNA-seq_Rep1

source_name: B-Lymphocyte

growth_protocol:
RPMI-1640 (Gibco 11875085), 10% FBS
Cells were grown according to ATCC recommendations (details in the Sample section above)

value: B-Lymphocyte

value: Normal


title: HPF cell, IL17A, 72 hrs, rep1

description: Library name: 231107_NG_Sample_13

value: IL17A 72 hrs


title: HPF cell, PBS, 96 hrs, rep1

description: Library name: 231107_NG_Sample_1


title: HPF cell, PBS, 96 hrs, rep2

description: Library name: 231107_NG_Sample_2


title: A549_NUT_RNA-seq_Rep1

source_name: NSCKC Adenocarcinoma

growth_protocol:
F12-K Medium (Kaighn's Modification of Ham's F-12 medium; ATCC 30-2004), 10% FBS
Cells were grown according to ATCC recommendations (details in the Sample section above)

value: NSCKC Adenocarcinoma

value: Cancer, Primary


title: U2OS_CTRL_RNA-seq_Rep1

source_name: Osteosarcoma

growth_protocol:
McCoy's 5A Medium (ATCC 30-2007), 10% FBS
Cells were grown according to ATCC recommendations (details in the Sample section above)

value: Osteosarcoma


title: HPF cell, LIGHT and IL17A, 24 hrs, rep3

description: Library name: 230428_NG_Sample_18

value: IL17A and LIGHT 24 hrs


title: HCT116_NUT_RNA-seq_Rep1

source_name: Colorectal Adenocarcinoma

value: Colorectal Adenocarcinoma


title: U2OS_NUT_RNA-seq_Rep1


title: HPF cell, IL17A, 24 hrs, rep3

description: Library name: 230428_NG_Sample_15

value: IL17A 24 hrs


title: Input of H1048 NOTCH2-WT TRIM28-HA Overexpressing cells

city: Boston

first: Yixiang

last: Li

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

description: Library name: 1048_Input

library_source: genomic

data_processing:
Sequenced read were aligned to the UCSC hg38 or mm10 reference genome assembly using BWA(v0.7.15) and peaking calling performed using MACS3.
Assembly: mm10 and hg38
Supplementary files format and content: bw files except for input samples

molecule: genomic DNA

growth_protocol: Murine SCLC cells were cultured with RPMI-1640 with 10% FBS, P/S, and HITES (10 nM hydrocortisone (Sigma Aldrich # H0135), Insulin-Transferrin-Selenium (Gemini #400-145), and 10 nM beta-estradiol (Sigma Aldrich# E2257), 100 U/mL of penicillin (P), and 100 μg/mL of streptomycin (S)] and culture with 5% CO2 at 37C.  NCI-H1048 cells were cultured with DMEM F12 with 5% FBS, P/S, and HITES (10 nM hydrocortisone (Sigma Aldrich # H0135), Insulin-Transferrin-Selenium (Gemini #400-145), and 10 nM beta-estradiol (Sigma Aldrich# E2257), 100 U/mL of penicillin (P), and 100 μg/mL of streptomycin (S)] and culture with 5% CO2 at 37C.

extract_protocol:
Cells were  collected, and centrifuged. The supernatant was removed and the cells were washed once in PBS. For the TRIM28-HA ChIP experiments, cells were cross-linked by incubation with 2 mM disuccinimidyl glutarate (DSG) with rocking for 30 minutes at room temperature prior to fixation step. Then, for all ChIP experiments, cells were fixed in 1% paraformaldehyde diluted in PBS for 10 minutes at room temperature. Excess formaldehyde was quenched by dropwise addition of freshly made Glycine at a final concentration 1.25 M followed by rocking the cells for an additional 5 minutes at room temperature. The paraformaldehyde/glycine was then removed by spinning at 400 x g for 5 minutes at 4°C and the cells were washed twice with ice cold PBS.     The cells were then resuspended in 1 mL of lysis buffer (50 mM Hepes-NaOH pH 8, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% TX-100 supplemented with a protease inhibitors and phosphatase inhibitors) and incubated by rotating for 10 minutes at 4°C. Intact nuclei were then collected by centrifugation at 1900 x g for 5 minutes at 4°C. The supernatant was then gently aspirated and the pellet was resuspended in 1 mL of wash buffer (10mM Tris-HCl pH 8.0, 200mM NaCl, 1mM EDTA, supplemented with a protease inhibitor cocktail and phosphatase inhibitors) and incubated by rotating for 10 minutes at 4°C. The nuclei were again collected by centrifugation at 1900 x g for 5 minutes at 4°C. The supernatant was then gently aspirated and the tube was rinsed with 500 μL of shearing buffer (0.1% SDS, 1 mM EDTA, 10 mM Tris-HCl pH 8.0 supplemented with protease inhibitors and phosphatase inhibitors). The nuclei were again collected by centrifugation at 1900 x g for 5 minutes at 4°C, the supernatant was carefully removed, and the pellet was gently resuspended in 1mL shearing buffer and transferred to a 1 mL AFA fiber tube (Covaris #520130). The chromatin was then sonicated using a Covaris E220 sonicator at 100 peak incident power, 10% duty cycles, 200 cycles per burst, water level 15 (left indicator)/10 (right indicator) for 900 seconds. The samples were then transferred to 1.5 mL Eppendorf tubes and centrifuged in an Eppendorf microcentrifuge at 15,900 x g for 5 minutes at 4°C. 900 μL of the supernatants were transferred to a new Eppendorf tube, to which 1% Triton X-100 and 150 mM NaCl were added. 20μl of Dynabeads Protein G (ThermoFisher #10004D), prewashed with Shearing Buffer, was then added and samples were rotated for 1 hour at 4°C to pre-clear the sonicated chromatin. The Dynabeads were then removed using a magnetic stand and the supernatants were transferred to new tubes. 5% of the total lysate was removed to make genomic DNA to be used for the ChIP-sequencing input DNA. The TRIM28-HA ChIPs were performed separately also using 5% input and 95% for ChIP. 10 μg of the rabbit anti-HA (CST #3724) primary antibodies were added. For the H3K9me3 and H3K27ac ChIPs, the remaining lysate (95% of total) were equally distributed into two Eppendorf tubes to perform the H3K9me3 and H3K27ac ChIPs. 5 μg of the rabbit anti-H3k9me3 (EPR16601) (Abcam, # ab176916) or 5 μg of the rabbit anti-H3K27ac (Diagenode# C15410196) primary antibodies were added. All samples were incubated overnight while rotating at 4°C. The following morning, 50 μL of Dynabeads, prewashed with Shearing buffer, were added and the samples were incubated for another 2 hours while rotating at 4°C. A magnetic stand was used to isolate the Dynabeads. The supernatant was removed and the Dynabeads were washed once in 1 mL of low salt immune complex wash buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 0.1% SDS, 1% TX-100, 2 mM EDTA) and incubated for 5 minutes while rotating at 4°C. The beads were again isolated using a magnetic stand. Following removal of the supernatant the Dynabeads were washed once in 1 mL of high salt immune complex wash buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 0.1% SDS, 1% TX-100, 2 mM EDTA) and incubated for 5 minutes while rotating at 4°C. The beads were again pelleted with a magnetic stand. Following removal of the supernatant, the Dynabeads were washed once in 1 mL of Lithium Chloride immune complex wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1% SDS, 1% NP-40, 1 mM EDTA) and incubated for 5 minutes while rotating at 4°C. The beads were then washed twice in TE pH8 at room temperature and the beads were then resuspended in 100μL TE pH8. RNase A (Qiagen #19101) was then added to a final concentration of 0.2 mg/mL and the samples were incubated for 30 minutes at 37°C. To reverse the formaldehyde crosslinking and remove protein, Proteinase K was then added to a final concentration of 0.8 mg/mL and the samples were incubated for 30 minutes at 42°C and then an additional 6 hours at 65°C. 300 μL QG buffer and 100 μL of isopropanol was then added to each sample and a magnetic stand was used to pellet the Dynabeads. The supernatant was then collected and DNA was isolated using QIAquick gel extraction kit (Qiagen #28706) according to the manufacturer’s instructions.
ChIPseq libraries were prepared using IDT XGen DNAseq library prep reagents on a Beckman Coulter Biomek i7 liquid handling platform from approximately 1ng of DNA according to manufacturer’s protocol and 14 cycles of PCR amplification. Finished sequencing libraries were quantified by Qubit fluorometer and Agilent TapeStation 2200.  Library pooling and indexing was evaluated with shallow sequencing on an Illumina MiSeq. Subsequently, libraries were sequenced on an Illumina NovaSeq X Plus targeting 40 million 150bp read pairs.

treatment_protocol: For the ChIP-seq of H3K9me3 and H3K27ac, murine 1014 TRIM28-dTAG-HA knock-in NOTCH2-isogenic cells (NOTCH2-WT or NOTCH2-inactivated) treated with 100 nM dTAG-V1 for 72 hours to degrade TRIM28 or with DMSO as a control.

value: SCLC cell line

tag: genotype

value: sgControl;TRIM28-HA overexpression


title: HPF cell, LIGHT and IL17A, 24 hrs, rep2

description: Library name: 230428_NG_Sample_17


title: HPF cell, LIGHT and IL17A, 24 hrs, rep1

description: Library name: 230428_NG_Sample_16


title: HPF cell, LIGHT and IL13, 24 hrs, rep3

description: Library name: 230428_NG_Sample_12

value: IL13 and LIGHT 24 hrs


title: SKNSH_NUT_RNA-seq_Rep1

source_name: Neuroblastoma

value: Neuroblastoma

value: SKSNH

value: Cancer, Metastasis

value: rRNA-depleted RNA


title: HPF cell, IL17A, 24 hrs, rep1

description: Library name: 230428_NG_Sample_13

value: Lung

value: HPF

value: Fibroblasts


title: HCT116_CTRL_RNA-seq_Rep1

value: mock-treated


title: HA ChIP-seq on H1048 NOTCH2-WT TRIM28-HA Overexpressing cells Rep2

description: Library name: 1048_TRIM28_HA_Rep2

tag: chip antibody

value: HA Cell Signaling Technology 3724


title: HPF cell, LIGHT and IL13, 24 hrs, rep2

description: Library name: 230428_NG_Sample_11


title: SKNSH_CTRL_RNA-seq_Rep1


title: HA ChIP-seq on H1048 NOTCH2-WT TRIM28-HA Overexpressing cells Rep1

description: Library name: 1048_TRIM28_HA_Rep1


title: HPF cell, LIGHT and IL13, 24 hrs, rep1

description: Library name: 230428_NG_Sample_10


title: GM12878_NUT_RNA-seq_Rep1

value: B-Lymphocyte

value: Normal


title: A549_CTRL_RNA-seq_Rep1

value: NSCKC Adenocarcinoma

value: Cancer, Primary


title: IMR90_NUT_RNA-seq_Rep1

source_name: Lung fibroblasts

value: Lung fibroblasts


title: HPF cell, IL13, 24 hrs, rep1

description: Library name: 230428_NG_Sample_7

value: IL13 24 hrs


title: HepG2_NUT_RNA-seq_Rep1

source_name: Hepatocellular Carcinoma

growth_protocol:
Dulbecco's Modified Eagle Medium (DMEM; Gibco 10566016), 10% FBS
Cells were grown according to ATCC recommendations (details in the Sample section above)

value: Hepatocellular Carcinoma


title: HPF cell, IL13 24 hrs, rep3

description: Library name: 230428_NG_Sample_9


title: HPF cell, IL13, 24 hrs, rep2

description: Library name: 230428_NG_Sample_8


title: IMR90_CTRL_RNA-seq_Rep1


title: Erythroid cells ffrom alpha thalassemia major donor, transduced with A2 UV renamed EV-a-UV

city: Los Angeles

first: Eva

last: Segura

address: Terasaki Life Sciences Building, Room 3163

department: Department of Microbiology, Immunology & Molecular Genetics

institute: University of California, Los Angeles

description:
Library name: A2 UV LV
10x Genomics

library_source: transcriptomic single cell

data_processing:
Single-cell RNA sequencing (scRNA-Seq) of in vitro differentiated red blood cells (RBCs) was performed to ensure robust quality control, sample demultiplexing, barcode processing, alignment, and single-cell 3′ gene counting. Further QA/QC steps were conducted using the Partek™ Flow™ software, v12.3. Gene and feature annotation was performed using hg38_ensembl_release90_v2. Genes detected in fewer than 10 cells or cells expressing fewer than 100 genes were excluded to minimize noise in downstream analyses. Normalization of individual samples was performed using cell RNA content, as implemented by the cell ranger count pipeline. For comparative analyses, only genes detected in at least ten cells were included. Further, counts per million (CPM) normalization was applied to all samples using Partek™ Flow™ v12.3. Downstream differential analyses were performed using Partek™ Flow™ v12.3 software for cell clustering, gene expression and pathway analysis. Principal Component Analysis (PCA) was applied to the normalized, log-transformed, centered, and scaled gene-barcode matrix to reduce dimensionality. Data was visualized in a two-dimensional space using t-distributed Stochastic Neighbor Embedding (t-SNE). Cell clustering was based on their PCA space projections using both graph-based and k-means clustering methods. Cluster classification and annotation were performed based on known marker genes for distinct erythroid lineage stages (e.g., GYPA, HBB, ALAS2, and other relevant cell-specific markers). Differentially expressed genes (DEG) in specific erythroid lineages were identified relative to all other clusters using ANOVA. Gene set enrichment analysis on sample-wise DEG comparisons was performed using Gene Ontology enrichment analysis and visualization tool (GOrilla) wherein the enrichment scores were plotted in a heatmap. Individual gene expression data was shown in forms of tSNE gradient (low to high) and violin dot plots at the single-cell level.
Assembly: Gene and feature annotation was performed using hg38_ensembl_release90_v2.
Supplementary files format and content: filtered_feature_bc_matrix.h5, barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz processed files have been generated for each sample

source_name: bone marrow

growth_protocol: CD34+ HSPCs cells were plated overnight (1E5-1E6 cells/mL) in a 96-well plate pre-coated with RetroNectin (TakaraBio, Cat.#T100B). Cells were cultured in 100uL X-VIVO 15 medium (Lonza), supplemented with glutamine, penicillin, streptomycin (PSG) (Gibco, Grand Island, NY, USA, Lot #2587132 ), and human stem cell factor (hSCF) (Thermo Fisher Scientific, Cat#300-07), human Flt-3 ligand (Thermo Fischer, Cat#300-19), human thrombopoietin (hTPO) (Thermo Fischer, Cat #300-18), and human IL-3 (Thermo Fisher Scientific, Cat#200-03), as previously detailed by Romero et al26.  Transduction was performed on the day after plating (day 1) using concentrated vector particles at different concentrations, ranging from 1E5 - 2E7 TU/mL. Erythroid differentiation was conducted over 18-21 days. Differentiation medium contained Iscove’s Modified Dulbecco’s Medium (IMDM) (Life Technologies), 1% PSG, 330 μg/mL of holo-transferrin (Sigma Aldrich) (reconstituted with Na2HPO4, NaH2PO4, NaCl, and water), 10 μg/mL recombinant human insulin (Sigma-Aldrich), 2 IU/mL heparin (Hikma Pharmaceuticals), and 5% inactivated human plasma (Sigma-Aldrich). On days 2–7, cells were cultured at a density ranging from 5e5-2e6 cells/mL, and supplemented  with 1uM hydrocortisone (Sigma-Aldrich), 5 ng/mL IL-3 (Thermo Fischer), 100ng/mL hSCF (Thermo Fischer), and 3 U/mL of erythropoietin (EPO) . Cells were then transferred to flasks containing a pre-formed adherent stromal cell layer (MS-5, murine stromal cell line, provided by Gay Crooks, UCLA), and cultured with EPO until days 11 and without EPO until days 18 – 21. ). On day 16 of erythroid differentiation, 10,000 cells were collected for single cell RNA sequencing.

extract_protocol:
On day 16 of in vitro erythroid differentiation, 120,000 cells were collected and resuspended in 100uL of Phosphate Buffered Saline (PBS) (Corning) with 0.05% Bovine Serum Albumin (BSA) (Sigma Aldrich, Cat# A7979-12) for single cell RNA sequencing conducted by the UCLA Technology Center for Genomics and Bioinformatics
Single-cell libraries were constructed using the Chromium Next GEM Single Cell 3' Kit v.3.1 (10X Genomics) targeting 10k cells, following manufacturer's protocol. The libraries were sequenced on the Illumina NovaSeq X+ paired-end platform (on a 10B flow cell with 150+10+24+150 cycles) and data de-multiplexing was performed using BCLConvert software v4.3.13 (Illumina).

treatment_protocol: Hematopoietic stem and progenitors cells that were derived from the bone marrow of two healthy donors and a donor with alpha thalassemia major were pre-stimulated with proper cytokines, and some were transduced, afterwhich all underwent an erythroid differentiation for 14 days. Cells were collected for single cell RNA sequencing and analysis.

value: bone marrow

value: hematopoietic stem and progenitors

value: erythroid

value: alpha globin loci knockout

value: Lentiviral vector EV-a-UV


title: Erythroid cells from alpha thalassemia major donor, transduced with A2 Globe renamed EV-a

description:
Library name: A2 Globe LV
10x Genomics

value: Lentiviral vector EV-a


title: HPF cell, LIGHT, 24 hrs, rep1

description: Library name: 230428_NG_Sample_4

value: Lung

value: HPF

value: LIGHT 24 hrs


title: HPF cell, LIGHT, 24 hrs,rep3

description: Library name: 230428_NG_Sample_6

value: Fibroblasts


title: HepG2_CTRL_RNA-seq_Rep1

value: mock-treated

value: rRNA-depleted RNA


title: HPF cell, LIGHT, 24 hrs, rep2

description: Library name: 230428_NG_Sample_5


title: Erythroid cells from alpha thalassemia major donor

description:
Library name: ATM
10x Genomics


title: Erythroid cells from healthy donor 1

description:
Library name: HD1
10x Genomics

value: WT


title: U2OS_NUT_p53_Rep1

data_processing:
Read quality control with FastQC
Read trimmed with Cutadapt
Read mapping with bowtie2
Peak calling: MACS2
bigwig files converted from MACS2 output bedGraph files with BedGraphToBigWig converter
Assembly: hg38
Supplementary files format and content: bigwig file with ChIP-seq genome coverage
Supplementary files format and content: bed files of p53 ChIP-seq peaks induced by Nutlin3a treatment in each cell line (ENCODE narrowPeak format)

extract_protocol:
After Nutlin-3a or mock treatment, cells were cross-linked 6’ at room temperature with 1% formaldehyde-containing medium; cross-linking was stopped by PBS-glycine (0.125 M final). Cells were washed twice with ice-cold PBS, scraped, centrifuged for 10’ and pellets were flash-frozen. Cell pellets were thawed and resuspended in cell lysis buffer (5 mM PIPES, pH 8.0, 85 mM KCl, and 0.5% NP-40, 1 ml/15 cm plate) w/ protease inhibitors and incubated for 10’ on ice. Lysates were centrifuged for 10’ at 4000 rpm and nuclear pellets resuspended in 6 volumes of sonication buffer (50 mM Tris-HCl, pH 8.1, 10 mM EDTA, 0.1% SDS) w/ protease inhibitors, incubated on ice for 10’, and sonicated to obtain DNA fragments below 2000 bp in length (Covaris S220 sonicator, 20% Duty factor, 200 cycles/burst, 150 peak incident power, 7-16 cycles 30” on and 30" off). Sonicated lysates were cleared by centrifugation and chromatin (100-800 ug per antibody) was diluted in RIPA buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS, 0.1% Na-deoxycholate, 140 mM NaCl) w/ protease inhibitors to a final concentration of 0.8 ug/ul, precleared with Protein G sepharose (GE Healthcare) for 2 hours at 4°C and immunoprecipitated overnight with 1 ug of specific antibodies per 100 ug of chromatin. About 4% of the precleared chromatin was saved as input. Immunoprecipitated DNA was purified with the Qiagen QIAquick PCR Purification Kit, eluted in 45 ul of 0.1X TE (1 mM Tris-HCl pH 8.0, 0.01 mM EDTA) and analyzed by qPCR together with 2% of the input chromatin prior to ChIP-seq library preparation.
ChIP-seq libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB E7645) according to manufacturer instructions with a few modifications. 20 ng of ChIP input DNA (as measured by Nanodrop) and 25 ul of the immunoprecipitated DNA were used as a starting material. The recommended reagents’ volumes were cut in half. The NEBNext Adaptor for Illumina was diluted 1:5 to 1:10 in Tris/NaCl, pH 8.0 (10 mM Tris-HCl pH 8.0, 10 mM NaCl) and the ligation step extended to 30’. After ligation, a single purification step with 0.9X volumes of Agencourt AMPure XP PCR purification beads (Beckman Coulter A63880) was performed, eluting DNA in 22 ul of 10 mM Tris-HCl pH 8.0. 20 ul of the eluted DNA were used for the library enrichment step, performed with the KAPA HotStart PCR kit (Roche Diagnostics KK2502) in 50 ul of total reaction volume (10 ul 5X KAPA buffer, 1.5 ul 10 mM dNTPs, 0.5 ul 10 uM NEB Universal PCR primer, 0.5 ul 10 uM NEB index primer, 1 ul KAPA polymerase, 16.5 ul nuclease-free water and 20 ul sample). Samples were enriched with 10-12 PCR cycles (98 'C, 45”; [98 'C, 15”; 60 'C, 10”] x 9; 72 'C, 1’; 4 'C, hold), purified with 0.9 volumes of AMPure XP PCR purification beads and eluted with 33 ul of 10 mM Tris-HCl pH 8.0. Library concentration, quality and fragment size were assessed by Qubit fluorometric quantification (Qubit™ dsDNA HS Assay Kit, InvitrogenTM Q32851) qPCR and Fragment analyzer™. 10 multiplexed libraries were pooled and sequenced in one lane on the Illumina HiSeq4000 sequencing platform (50-bp, single-end reads)

value: Osteosarcoma

value: Cancer, Primary

value: anti-p53, Cell Signalling #9282


title: HPF cell, PBS, 24 hrs, rep3

description: Library name: 230428_NG_Sample_3

value: PBS 24 hrs


title: HPF cell, IL17A, 24 hrs, rep2

description: Library name: 230428_NG_Sample_14

value: IL17A 24 hrs


title: U2OS_NUT_p53_Rep2


title: Patient AML_11, frozen bone marrow, bulk-ATAC-seq

city: Ulsan

first: Dayoung

last: Kim

address: 50 Unist-gil

country: South Korea

institute: UNIST

description: Library name: bulkATAC_AML_11

data_processing:
5 bp sequence at 5' end, and primer sequence at 3' end were trimmed using in-house script.
ATAC-seq reads were aligned to UCSC hg38 genome using Bowtie version 2.5.3.
MACS2 version 2.2.9.1 was used to call ATAC-seq narrowPeaks.
bigWig files were generated using genomicRanges R package.
Supplementary files format and content: narrowPeak files containing all MACS2 called peaks from each ATAC-seq mapped reads.
Supplementary files format and content: Normalized bigWig file to visualize the mapped read in genome-wide tracks.

source_name: Bone marrow

extract_protocol:
Cells were thawed using 37C CTL wash buffer, and apoptotic cells were discarded using MACS Annexin-V microbead Kit.
50,000 cells were used as starting material for Omni-ATAC-seq. For each library, the amplification cycle was determined using qPCR, but not to exceed 16 cycles in total. Before sequencing, the libraries were size selected at 200 bp or longer to remove excessive primer dimers.

value: Bone marrow

tag: individual

tag: disease state

value: acute myeloid leukemia

value: Whole bone marrow


title: HPF cell, PBS, 24 hrs, rep2

description: Library name: 230428_NG_Sample_2


title: Patient AML_09, frozen bone marrow, bulk-ATAC-seq

description: Library name: bulkATAC_AML_09


title: Patient AML_13, frozen bone marrow, bulk-ATAC-seq

description: Library name: bulkATAC_AML_13


title: Erythroid cells from healthy donor 2

description:
Library name: HD2
10x Genomics

value: bone marrow

value: hematopoietic stem and progenitors

value: erythroid


title: Patient AML_12, frozen bone marrow, bulk-ATAC-seq

description: Library name: bulkATAC_AML_12


title: Patient AML_07, frozen bone marrow, bulk-ATAC-seq

description: Library name: bulkATAC_AML_07


title: U2OS_NUT_input_Rep2


title: Patient AML_06, frozen bone marrow, bulk-ATAC-seq

description: Library name: bulkATAC_AML_06


title: Patient AML_08, frozen bone marrow, bulk-ATAC-seq

description: Library name: bulkATAC_AML_08


title: Patient AML_05, frozen bone marrow, bulk-ATAC-seq

description: Library name: bulkATAC_AML_05


title: U2OS_CTRL_p53_Rep2


title: HPF cell, PBS, 24 hrs, rep1

description: Library name: 230428_NG_Sample_1

value: Lung

value: HPF


title: Patient AML_01, frozen bone marrow, bulk-ATAC-seq

description: Library name: bulkATAC_AML_01


title: Patient AML_02, frozen bone marrow, bulk-ATAC-seq

description: Library name: bulkATAC_AML_02


title: U2OS_CTRL_input_Rep1


title: MA9GMP_WT_rep4

type: RNA

city: Bronx

first: Shira

middle: Gabriella

last: Glushakow-Smith

state: NY

address: 1300 Morris Park Ave, CH410

institute: Albert Einstein College of Medicine

hyb_protocol: Total RNA was amplified and hybridized to the Gene Chip Mouse Transcriptome Pico Assay 1.0 using the GeneChip Hybridization, Wash, and Stain Kit

scan_protocol: standard Affymetrix protocol

data_processing: Affymetrix Mouse Transcriptome Array 1.0

label: biotin

organism: Mus musculus

source_name: MA9 LSCs WT

label_protocol: standard Affymetrix protocol

extract_protocol: RNA was extracted using ARCTURUS PicoPure RNA Isolation Kit following manufacturers instructions


title: Patient AML_10, frozen bone marrow, bulk-ATAC-seq

description: Library name: bulkATAC_AML_10


title: U2OS_NUT_input_Rep1


title: SKSNH_NUT_p53_Rep2

value: Neuroblastoma

value: SKSNH

value: Cancer, Metastasis


title: Patient MDS_23, frozen bone marrow, bulk-ATAC-seq

description: Library name: bulkATAC_MDS_23

value: high-risk myelodysplastic syndrome

tag: response group

value: Responder


title: Patient MDS_21, frozen bone marrow, bulk-ATAC-seq

description: Library name: bulkATAC_MDS_21


title: MA9GMP_WT_rep5

value: WT


title: Patient MDS_22, frozen bone marrow, bulk-ATAC-seq

description: Library name: bulkATAC_MDS_22


title: Patient MDS_20, frozen bone marrow, bulk-ATAC-seq

description: Library name: bulkATAC_MDS_20


title: Patient MDS_18, frozen bone marrow, bulk-ATAC-seq

description: Library name: bulkATAC_MDS_18


title: Patient AML_04, frozen bone marrow, bulk-ATAC-seq

description: Library name: bulkATAC_AML_04


title: SKSNH_NUT_p53_Rep1

value: anti-p53, Cell Signalling #9282


title: SKSNH_NUT_input_Rep2


title: U2OS_CTRL_p53_Rep1

value: Osteosarcoma

value: Cancer, Primary

value: mock-treated


title: Patient MDS_17, frozen bone marrow, bulk-ATAC-seq

description: Library name: bulkATAC_MDS_17

value: Bone marrow


title: U2OS_CTRL_input_Rep2


title: Patient MDS_19, frozen bone marrow, bulk-ATAC-seq

description: Library name: bulkATAC_MDS_19

value: Whole bone marrow


title: Patient AML_03, frozen bone marrow, bulk-ATAC-seq

description: Library name: bulkATAC_AML_03

value: acute myeloid leukemia


title: MA9GMP_WT_rep2


title: MA9GMP_WT_rep3


title: MA9GMP_Pik3caKO_rep3

source_name: MA9 LSCs Pik3caKO


title: SKSNH_NUT_input_Rep1


title: Patient MDS_16, frozen bone marrow, bulk-ATAC-seq

description: Library name: bulkATAC_MDS_16

value: Non-responder


title: Patient MDS_12, frozen bone marrow, bulk-ATAC-seq

description: Library name: bulkATAC_MDS_12


title: MA9GMP_Pik3caKO_rep2


title: T-5547

city: New York

first: Osama

last: Al Dalahmah

address: 622 West 168th Street

department: Pathology & Cell Biology

institute: Columbia University Irving Medical Center

description:
Library name: T-5547
iRepertoire

data_processing:
TCR sequence data were processed using the iRmap pipeline provided by iRepertoire. Raw reads were demultiplexed based on Illumina dual indices and internal barcodes. Paired-end reads were merged and aligned to germline TCR V, D, J, and C genes using the IMGT reference database.
CDR3 regions were extracted and translated in all three reading frames, with productive CDR3 sequences identified using canonical amino acid motifs. To reduce sequencing and PCR errors, reads sharing identical CDR3 and UMI combinations were collapsed into a single count. For each sample, clonotypes were defined based on V/J gene pairing and CDR3 sequence identity.
Assembly: Mapping of immune receptor sequences was performed against the IMGT reference database for human T-cell receptor genes, which provides curated germline V, D, J, and C gene segment annotations. This reference serves as the standard for immune repertoire alignment and annotation in AIRR-seq studies
Supplementary files format and content: Includes V/J sequence and read counts

source_name: Substantia Nigra

extract_protocol:
RNA was extracted from postmortem human brain tissue obtained from the New York Brain Bank, including the cingulate cortex and substantia nigra of individuals with Parkinson’s disease, dementia with Lewy bodies, or without neuropathological findings (controls). Each tissue sample was dissected fresh-frozen at autopsy and immediately processed. RNA integrity was assessed, and only samples with an RNA integrity number (RIN) greater than 7 were used. For in-house α-chain library preparation, 500 ng of total RNA per sample served as input. For RepSeq+ libraries prepared by iRepertoire, 5 µL of RNA was submitted per sample.
For α-chain–only libraries, we followed the iRepertoire Bulk Reagent Universal User Manual (V20200818) using HTAIvc barcode kits. After reverse transcription and amplification, libraries were pooled, spiked with 10% PhiX, and sequenced on an Illumina NextSeq 550.
For RepSeq+ libraries, iRepertoire used a targeted amplicon approach to amplify TCR α and β chains simultaneously. The protocol employed gene-specific primers for the constant (C) and variable (V) regions, with unique molecular identifiers (UMIs) incorporated during reverse transcription. Following SPRIselect bead purification steps, a second round of amplification used V-gene primers. Final libraries incorporated Illumina dual-index adapters, a 10-nt UMI, and an 8-nt internal barcode for sample tracking. Sequencing captured regions spanning from framework 1 to the constant region, including CDR1, CDR2, and CDR3.

value: Substantia Nigra

tag: Sex

value: F

tag: age

tag: condition

value: Control


title: T-5498

description:
Library name: T-5498
iRepertoire

value: M

value: PD


title: SKSNH_CTRL_p53_Rep1

value: Neuroblastoma

value: SKSNH

value: Cancer, Metastasis


title: Patient MDS_11, frozen bone marrow, bulk-ATAC-seq

description: Library name: bulkATAC_MDS_11

value: high-risk myelodysplastic syndrome


title: Patient MDS_15, frozen bone marrow, bulk-ATAC-seq

description: Library name: bulkATAC_MDS_15

value: Responder


title: SKSNH_CTRL_p53_Rep2

value: anti-p53, Cell Signalling #9282


title: SKSNH_CTRL_input_Rep2


title: Patient MDS_10, frozen bone marrow, bulk-ATAC-seq

description: Library name: bulkATAC_MDS_10


title: Patient MDS_13, frozen bone marrow, bulk-ATAC-seq

description: Library name: bulkATAC_MDS_13


title: Patient MDS_14, frozen bone marrow, bulk-ATAC-seq

description: Library name: bulkATAC_MDS_14


title: T-5385

description:
Library name: T-5385
iRepertoire


title: T-5359

description:
Library name: T-5359
iRepertoire


title: MA9GMP_WT_rep1

value: WT


title: Patient MDS_09, frozen bone marrow, bulk-ATAC-seq

description: Library name: bulkATAC_MDS_09


title: SKSNH_CTRL_input_Rep1

value: mock-treated


title: T-5227

description:
Library name: T-5227
iRepertoire


title: T-5259

description:
Library name: T-5259
iRepertoire


title: Patient MDS_06, frozen bone marrow, bulk-ATAC-seq

description: Library name: bulkATAC_MDS_06

value: Bone marrow


title: MCF7_NUT_p53_Rep2

value: Breast Adenocarcinoma


title: T-4938

description:
Library name: T-4938
iRepertoire


title: T-5133

description:
Library name: T-5133
iRepertoire


title: Patient MDS_08, frozen bone marrow, bulk-ATAC-seq

description: Library name: bulkATAC_MDS_08

value: Whole bone marrow


title: Patient MDS_05, frozen bone marrow, bulk-ATAC-seq

description: Library name: bulkATAC_MDS_05

value: Non-responder


title: MCF7_NUT_p53_Rep1


title: MCF7_NUT_input_Rep2


title: Patient MDS_07, frozen bone marrow, bulk-ATAC-seq

description: Library name: bulkATAC_MDS_07


title: Patient MDS_04, frozen bone marrow, bulk-ATAC-seq

description: Library name: bulkATAC_MDS_04


title: Patient MDS_01, frozen bone marrow, bulk-ATAC-seq

description: Library name: bulkATAC_MDS_01


title: Patient MDS_02, frozen bone marrow, bulk-ATAC-seq

description: Library name: bulkATAC_MDS_02


title: Patient MDS_03, frozen bone marrow, bulk-ATAC-seq

description: Library name: bulkATAC_MDS_03


title: MCF7_NUT_input_Rep1


title: TECs, iPSC-derived, thymocyte co-culture

city: Kyoto

first: Yann

last: Pretemer

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

country: Japan

institute: Center for iPS Cell Research and Application, Kyoto University

description:
Library name: Sample 16
10x Genomics

data_processing:
Data were processed using Cell Ranger v6.1.2.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files.
Supplementary files format and content: RDS files containing Seurat objects of integrated samples from this Series, including their UMAP and cell annotations.

source_name: iPSC-derived (TECs) and thymus (thymocytes)

extract_protocol:
To isolate human thymic stromal cells, thymi were digested using 100 µg/ml Liberase TM and 200 µg/ml DNase I in RPMI 1640 with 1% FBS. Cells were resuspended in 83% v/v Percoll in PBS, and a lighter layer of 47% v/v Percoll in PBS and another layer of only PBS were overlaid. After centrifugation, the enriched stromal cell layer was collected and resuspended in buffer containing 1% FBS and 5 mM EDTA in PBS. Cells were incubated for 15 min on ice with 50 µl MojoSort Human CD45 Nanobeads per 1 x 10^8 cells in 1 ml buffer. After one wash, CD45+ cells were depleted on a MagniSort Magnet and the stromal fraction was frozen for future use. On the day of cell preparation for scRNA-seq, the frozen thymic stromal cells were defrosted and stained with antibodies at 1:50 dilution for 15 min on ice. After one wash, cells were passed through a cell strainer and analyzed using the BD FACSAria II. The EPCAM-CD45-CD235ab- and EPCAM+CD31-CD45-CD235ab- fractions were sorted and resuspended in 0.04% BSA in PBS, after which they were mixed 1:2 to enrich for TECs while also retaining other heterogeneous stromal cells. For the iPSC-derived cells, dissociation was performed using Accutase or Accumax, after which cells were washed in buffer containing 0.1% BSA in PBS. Cells were passed through a cell strainer and analyzed using the BD FACSAria II. The mCherry-, mCherry+(low), and mCherry+(high) fractions were sorted and resuspended in 0.04% BSA in PBS, after which they were mixed 1:1:2 to enrich for mCherry+ cells. For samples where no mCherry+ cells were detected (days 7, 11, and 18), the entire live fraction was sorted and resuspended in 0.04% BSA in PBS. For the co-cultured primary thymocytes and induced TECs, the organoids were dissociated using Accumax, washed in 1% FBS in PBS, and analyzed using the BD FACSymphony S6. The mCherry- and mCherry+ fractions were sorted and resuspended in 0.04% BSA in PBS, after which they were mixed at a ratio of 1:2.
10,000 cells per sample were applied to the Chromium Next GEM Chip K, after which reverse transcription, cDNA amplification, and library construction were performed using the Chromium Next GEM Single Cell 5' GEM Kit v2, Chromium Next GEM Single Cell 5' Gel Bead Kit v2, Library Construction Kit, and Dual Index Kit TT Set A according to the manufacturer's instructions (10x Genomics).

value: Thymic epithelial cell (TEC) and thymocyte

value: 1-6 months (thymocytes)

value: pooled male and female

tag: genetic modification

value: FOXN1-mCherry reporter (TECs)


title: MCF7_CTRL_p53_Rep2


title: U2OS_CTRL_MicroC_Rep2

data_processing:
*library strategy: Micro-C
Assembly: hg38
Micro-C: allValidPairs were generated by HiC-Pro package (>2.10 version)
Micro-C: mcool files were converted from allValidPairs by Cooler package
Supplementary files format and content: Micro-C: allValidParis file contains 1) read name, 2) chromosome of first locus, 3) read position of first locus,  4) strand of first locus, 5) chromosome of second locus, 6) read position of second locus, 7) strand of second locus, 8) DNA fragment lengh, 9) name of first restriction fragment, 10) name of second restiction fragment, 11) mapping quality of first read, 12) mapping quality of second read.
Supplementary files format and content: Micro-C: mcool file contains all valid Micro-C pairs stored in HDF5 format with mutiple resolutions

growth_protocol: Cells were grown according to ATCC recommendations (details in the Sample section above)

extract_protocol:
After Nutlin-3a or mock treatment, cells were cross-linked 10’ at room temperature with 1% formaldehyde-containing medium; cross-linking was stopped by Tris-glycine. Cells were washed twice with PBS and cross-linked for 45’ at room temperature with 3 mM DSG in PBS. Cross-linking was halted by Tris-glycine and cells were washed twice in PBS. Micro-C protocol was performed as the following steps: 1) digest crosslinked chromatin by MNase; 2) Repair fragment ends with biotin-dNTP; 3) Proximal ligation and purge unligated ends; 4) Purify ligated dinucleosomal DNA. Purified DNA with biotin-dNTPs was captured by Dynabeads® MyOne™ Streptavidin C1.
Micro-C libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB E7645) according to manufacturer instructions with a few modifications. The sequencing library was amplified by Kapa HiFi PCR enzyme with lowest possible cycles to reduce PCR duplicates. Library concentration, quality and fragment size were assessed by Qubit fluorometric quantification (Qubit™ dsDNA HS Assay Kit, InvitrogenTM Q32851) qPCR and Fragment analyzer™. 20 multiplexed libraries were pooled and sequenced in 6 lanes on the Illumina NovaSeq sequencing platform (100-bp, paired-end reads)

value: Osteosarcoma

value: Cancer, Primary

value: McCoy's 5A Medium (ATCC 30-2007), 10% FBS


title: U2OS_NUT_MicroC_Rep2


title: MCF7_CTRL_p53_Rep1

value: Cancer, Metastasis


title: T-4839

description:
Library name: T-4839
iRepertoire

value: Substantia Nigra

value: F

value: PD


title: T-4815

description:
Library name: T-4815
iRepertoire


title: HeLa_NUT_MicroC_Rep2

source_name: Cervical Adenocarcinoma

value: Cervical Adenocarcinoma

value: HeLa

value: Eagle's Minimum Essential Medium (EMEM; ATCC 30-2003), 10% FBS


title: HeLa_CTRL_MicroC_Rep2


title: HEK293_NUT_MicroC_Rep2

source_name: Embryonic Kidney

value: Embryonic Kidney

value: Immortalized

value: Dulbecco's Modified Eagle Medium (DMEM; Gibco 10566016), 10% FBS


title: MCF7_CTRL_input_Rep2

source_name: Breast Adenocarcinoma

value: Breast Adenocarcinoma

value: mock-treated


title: T-4695

description:
Library name: T-4695
iRepertoire


title: IMR90_NUT_MicroC_Rep2

value: Lung fibroblasts

value: Normal


title: MCF7_CTRL_input_Rep1


title: T-4530

description:
Library name: T-4530
iRepertoire

value: M


title: IMR-90_NUT_p53_Rep2

value: anti-p53, Cell Signalling #9282


title: IMR90_CTRL_MicroC_Rep2


title: T-4934

description:
Library name: T-4934
iRepertoire


title: HepG2_CTRL_MicroC_Rep2

value: Hepatocellular Carcinoma

value: Cancer, Primary


title: HepG2_NUT_MicroC_Rep2


title: T-4515

description:
Library name: T-4515
iRepertoire

value: Substantia Nigra


title: GM12878_NUT_MicroC_Rep2

value: B-Lymphocyte


title: IMR-90_NUT_p53_Rep1


title: GM12878_CTRL_MicroC_Rep2


title: A549_NUT_MicroC_Rep2

value: NSCKC Adenocarcinoma

value: F12-K Medium (Kaighn's Modification of Ham's F-12 medium; ATCC 30-2004), 10% FBS


title: T-4857

description:
Library name: T-4857
iRepertoire

value: Control


title: HEK293_CTRL_MicroC_Rep2


title: MA9GMP_Pik3caKO_rep1


title: T-4462

description:
Library name: T-4462
iRepertoire


title: IMR-90_NUT_input_Rep2


title: IMR-90_NUT_input_Rep1


title: HCT116_NUT_MicroC_Rep2

value: Colorectal Adenocarcinoma

value: McCoy's 5A Medium (ATCC 30-2007), 10% FBS


title: SKNSH_NUT_MicroC_Rep2

value: Neuroblastoma

value: SKSNH

value: Cancer, Metastasis

value: Eagle's Minimum Essential Medium (EMEM; ATCC 30-2003), 10% FBS


title: IMR-90_CTRL_p53_Rep2

value: Lung fibroblasts

value: mock-treated


title: SKNSH_CTRL_MicroC_Rep2


title: T-4235

description:
Library name: T-4235
iRepertoire

value: F


title: HCT116_CTRL_MicroC_Rep2


title: T-3998

description:
Library name: T-3998
iRepertoire

value: M


title: MCF7_NUT_MicroC_Rep2

value: Breast Adenocarcinoma


title: T-3870

description:
Library name: T-3870
iRepertoire


title: MCF7_CTRL_MicroC_Rep2


title: T-3799

description:
Library name: T-3799
iRepertoire


title: GM12878_NUT_MicroC_Rep1

value: Normal


title: IMR-90_CTRL_input_Rep1


title: HCT116_NUT_MicroC_Rep1

value: Cancer, Primary


title: HepG2_NUT_p53_Rep2

value: Hepatocellular Carcinoma

value: anti-p53, Cell Signalling #9282


title: A549_CTRL_MicroC_Rep2

value: NSCKC Adenocarcinoma

value: F12-K Medium (Kaighn's Modification of Ham's F-12 medium; ATCC 30-2004), 10% FBS


title: HEK293_NUT_MicroC_Rep1


title: HeLa_NUT_MicroC_Rep1

value: Cervical Adenocarcinoma

value: HeLa


title: T-2465

description:
Library name: T-2465
iRepertoire

value: Substantia Nigra

value: Control


title: T-4424

description:
Library name: T-4424
iRepertoire

value: PD


title: MCF7_NUT_MicroC_Rep1

value: Eagle's Minimum Essential Medium (EMEM; ATCC 30-2003), 10% FBS


title: IMR-90_CTRL_p53_Rep1

value: Lung fibroblasts


title: IMR90_NUT_MicroC_Rep1


title: HepG2_NUT_input_Rep2


title: T-2007

description:
Library name: T-2007
iRepertoire


title: A549_NUT_MicroC_Rep1


title: HepG2_NUT_MicroC_Rep1

value: Dulbecco's Modified Eagle Medium (DMEM; Gibco 10566016), 10% FBS


title: T-124

description:
Library name: T-124
iRepertoire


title: HepG2_NUT_p53_Rep1


title: GM12878_CTRL_MicroC_Rep1

value: B-Lymphocyte


title: U2OS_NUT_MicroC_Rep1

value: Osteosarcoma

value: McCoy's 5A Medium (ATCC 30-2007), 10% FBS


title: IMR-90_CTRL_input_Rep2

value: Normal

value: mock-treated


title: HepG2_NUT_input_Rep1

value: Hepatocellular Carcinoma

value: Cancer, Primary


title: A549_CTRL_MicroC_Rep1

value: NSCKC Adenocarcinoma


title: PDC098, TCR-seq

description: iRepertoire

data_processing:
raw paired-end fastq files were demultiplexed based on the internal 6-nt barcode sequences added during library construction. FLASH 1.2.11 (flash –M 250 –O) was used to merge the paired reads, which were aligned to the human genome (GRCh37) using the Burrows-Wheeler Aligner (bwa-mem)
Reads mapping to the T-cell receptor loci (TRA) and associated with V- and J-cassettes were extracted and translated in silico in all three readings. Reading frames containing a C...FGXG amino acid motif that was uninterrupted by a stop codon were identified as productive CDR3 amino acid sequences.
For each demultiplexed sample, all V- and J-cassettes were then reference-corrected and the number of reads identified with each unique combination of V- and J-cassettes encoding a CDR3 amino acid sequence were counted
Assembly: GRCh38
Supplementary files format and content: .filtJS.tsv file
Library strategy: T Cell Receptor Sequencing (TCRseq)

source_name: Cingulate Cortex and Substantia Nigra

extract_protocol:
iRepertoire Bulk Reagent Universal User Manual (V20200818). The starting material was 500ng RNA per sample. We used 9 barcodes - HTAIvc kits (HTAIvc01, HTAIvc02, HTAIvc03, HTAIvc04, HTAIvc05, HTAIvc06, HTAIvc07, HTAIvc08 and HTAIvc09).
We pooled one library from each of the barcoded kits together for each sequencing run. The libraries were pooled with 10% PhiX spike-in and sequenced with NextSeq High Output 300 Cycles kits (Illumina) on an Illumina NextSeq 550 (read 1: 155 cycles; read 2: 155 cycles). Five total sequencing runs were conducted.

value: Cingulate Cortex and Substantia Nigra

value: male and female

value: PD and Control


title: HCT116_CTRL_MicroC_Rep1

value: Colorectal Adenocarcinoma


title: T-2791

description:
Library name: T-2791
iRepertoire

value: Substantia Nigra

value: F

value: Control


title: HepG2_CTRL_p53_Rep2

value: anti-p53, Cell Signalling #9282


title: HeLa_CTRL_MicroC_Rep1

value: Cervical Adenocarcinoma

value: HeLa

value: Eagle's Minimum Essential Medium (EMEM; ATCC 30-2003), 10% FBS


title: HEK293_CTRL_MicroC_Rep1

value: Breast Adenocarcinoma

value: Cancer, Metastasis


title: PDC097, TCR-seq

description: iRepertoire


title: HepG2_CTRL_p53_Rep1

value: mock-treated


title: HepG2_CTRL_input_Rep2

value: Hepatocellular Carcinoma


title: MCF7_CTRL_MicroC_Rep1

value: Lung fibroblasts

value: Normal


title: SKNSH_CTRL_MicroC_Rep1

value: Neuroblastoma

value: SKSNH


title: IMR90_CTRL_MicroC_Rep1


title: PDC096, TCR-seq

description: iRepertoire

value: Cingulate Cortex and Substantia Nigra

value: male and female

value: PD and Control


title: PDC092, TCR-seq

description: iRepertoire


title: HepG2_CTRL_input_Rep1

value: Cancer, Primary


title: HepG2_CTRL_MicroC_Rep1

value: Dulbecco's Modified Eagle Medium (DMEM; Gibco 10566016), 10% FBS


title: TECs, iPSC-derived, day 133

description: 10x Genomics

source_name: iPSC-derived

value: iPSC-derived

value: Thymic epithelial cell (TEC)

value: Female

value: FOXN1-mCherry reporter


title: HeLa_NUT_p53_Rep2

value: Cervical Adenocarcinoma

value: HeLa

value: anti-p53, Cell Signalling #9282


title: U2OS_CTRL_MicroC_Rep1

value: Osteosarcoma

value: McCoy's 5A Medium (ATCC 30-2007), 10% FBS


title: PDC089, TCR-seq

description: iRepertoire


title: hBMSC, Serdemetan treatment

city: Seoul

first: Sol

last: Jeong

address: Gwanakgu, Gwanakro1

institute: SNU

description:
Library name: hBMSC_Ser
hBMSC_read count.csv

data_processing:
Sequenced reads were aligned to the reference genome with HISAT2 and analyzed using DESeq2
Assembly: GRCh38, GRCm39
Supplementary files format and content: Tab-delimited files containing normalized counts and DESeq2 output, including gene IDs, log2 fold change, and adjusted p-values.

extract_protocol:
RNA was harvested using Trizol (Invitrogen). 1 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Claretbio mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: bone marrow

value: human bone marrow-derived mesenchymal stromal cells

value: mesenchymal stromal cells

value: WT

value: Serdemetan treatment


title: HeLa_NUT_p53_Rep1


title: TECs, iPSC-derived, day 81, biological replicate 2

description: 10x Genomics


title: TECs, iPSC-derived, day 81, biological replicate 1

description: 10x Genomics


title: HeLa_NUT_input_Rep2


title: TEPs, iPSC-derived, day 63

description: 10x Genomics

value: Thymic epithelial progenitor (TEP)


title: TEPs, iPSC-derived, day 49

description: 10x Genomics


title: BMMs, Serdemetan treatment2

description:
Library name: Ser2
BMMs_read count.csv

value: mouse bone marrow-derived macrophage

value: macrophage


title: TEPs, iPSC-derived, day 38, biological replicate 2

description: 10x Genomics

value: iPSC-derived


title: HeLa_NUT_input_Rep1

value: Cancer, Primary


title: BMMs, Serdemetan treatment1

description:
Library name: Ser1
BMMs_read count.csv


title: TEPs, iPSC-derived, day 38, biological replicate 1

description: 10x Genomics

value: Female


title: TEPs, iPSC-derived, day 28

description: 10x Genomics

value: FOXN1-mCherry reporter


title: HeLa_CTRL_p53_Rep2

value: Cervical Adenocarcinoma

value: mock-treated


title: PE, iPSC-derived, day 18

description: 10x Genomics

value: Pharyngeal endoderm (PE)


title: BMMs, Rankl treatment2

description:
Library name: rankl2
BMMs_read count.csv

value: Rankl treatment


title: AFE, iPSC-derived, day 11

description: 10x Genomics

value: Anterior foregut endoderm (AFE)


title: HeLa_CTRL_p53_Rep1

value: HeLa

value: anti-p53, Cell Signalling #9282


title: BMMs, Rankl treatment1

description:
Library name: rankl1
BMMs_read count.csv

value: bone marrow


title: AFE, iPSC-derived, day 7

description: 10x Genomics


title: HeLa_CTRL_input_Rep2


title: TECs, primary, donor 3

description: 10x Genomics

source_name: Thymus

value: Thymus

value: Thymic epithelial cell (TEC)

value: 1-6 months

value: Male


title: TECs, iPSC-derived, day 98

description: 10x Genomics


title: TECs, primary, donor 2

description: 10x Genomics


title: hBMSC, OM control

description:
Library name: hBMSC_OM1
hBMSC_read count.csv

value: human bone marrow-derived mesenchymal stromal cells

value: mesenchymal stromal cells

value: WT

value: OM control


title: TECs, primary, donor 1

description: 10x Genomics

value: Female


title: HeLa_CTRL_input_Rep1

value: Cervical Adenocarcinoma

value: Cancer, Primary


title: MLC1800_2-fold_1

city: Baltimore

first: Luisa

last: Cochella

state: Maryland

address: 725 N. Wolfe Street, PCTB 803

institute: Johns Hopkins School of Medicine

description:
Library name: 100013
SR75 High

data_processing:
The gene expression profiles by Quant-seq were processed and analyzed in the same way as in (Gutierrez-Perez et al., 2021).
Briefly, UMIs were first extracted using UMI tools (Smith et al., 2017). Adaptors and first 4 bp of low quality of raw reads were trimmmed and reads were then mapped to the C. elegans genome (WBcel235) using STAR aligner (Dobin et al., 2013) with the parameter max_IntronL = 50000.
Duplicated mapped reads were discarded with UMI tools, and UMI counts were quantified using HTSeq count (Anders et al., 2015).
Differential expression between conditions was analyzed using the DESeq2 package (Love et al., 2014).
Assembly: C. elegans (WBcel235)
Supplementary files format and content: text file format for UMI count table

organism: Caenorhabditis elegans

source_name: Whole embryos

growth_protocol: C. elegans strains were grown at 20C on OP50 bacteria. Adult hermaphrodites were bleached to release embryos. 2-cell embryos were collected by mouth pipetting and allowed to develop to the relevant embryonic stage. 50 embryos were collected per replicate.

extract_protocol:
Total RNA was extracted using Trizol
Quant-seq library prep from Lexogen

value: Whole embryos


title: Normal_sample_S0079N_S72

city: Hsinchu

first: Jinn-Moon

last: Yang

address: 75 Po-Ai Street

country: Taiwan

institute: National Chiao Tung University

description: matrix column name is S0079N_S72

data_processing:
The quality of reads was examined using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
The reads were aligned to the human reference genome (hg38) using the HISAT2 package (v.2.1.1).
The reads from HISAT2 were mapped and assembled into transcripts using StringTie (v.2.1.4).
The expression level and fold change between tumor and normal samples of all genes were calculated using DESeq2 package (v. 1.42.1) in R (v. 4.3.3).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include normalized read counts for each Sample using DESeq2 package

source_name: Liver tissue

extract_protocol:
Total RNA of each sample was extracted using TRIzol Reagent (Invitrogen)/RNeasy Mini Kit (Qiagen)/other kits. 2μg total RNA with RIN value above 6.5 was used for following library preparation.
RNA libraries for RNA-seq were prepared using Agilent SureSelect Strand-Specific RNA Library Prep System following manufacturer's protocols.

value: Liver tissue

value: No

tag: alcoholism

tag: virus infection

value: Non-viral infection

tag: cirrhosis

tag: vital status

value: Alive

tag: pathology stage(ajcc_7th_edition)


title: MLC1800_Bean_2

description:
Library name: 100012
SR75 High

tag: tissue

tag: treatment

value: Bean


title: Normal_sample_S0076N_S70

description: matrix column name is S0076N_S70

value: Yes


title: HEK293_NUT_p53_Rep2

value: Embryonic Kidney

tag: cell line

tag: cell type

value: Immortalized

value: anti-p53, Cell Signalling #9282


title: Normal_sample_S0073N_S69

description: matrix column name is S0073N_S69

value: Male


title: HEK293_NUT_p53_Rep1

tag: chip antibody


title: Normal_sample_S0071N_S68

description: matrix column name is S0071N_S68


title: MLC1800_Bean_1

description:
Library name: 100011
SR75 High

tag: genotype

tag: batch


title: HEK293_NUT_input_Rep2


title: HCC_sample_S0070T_S67

description: matrix column name is S0070T_S67

value: IIIA


title: HCC_sample_S0069T_S66

description: matrix column name is S0069T_S66

value: Dead


title: MLC1800_190 cell_2

description:
Library name: 100010
SR75 High

value: 190 cell


title: HCC_sample_S0068T_S65

description: matrix column name is S0068T_S65

value: I


title: HEK293_NUT_input_Rep1


title: MLC1800_190 cell_1

description:
Library name: 100009
SR75 High


title: HCC_sample_S0067T_S64

description: matrix column name is S0067T_S64

value: HBV

value: II


title: MLC1800_2-fold_2

description:
Library name: 100014
SR75 High

value: Whole embryos


title: HCC_sample_S0063T_S62

description: matrix column name is S0063T_S62

value: Liver tissue


title: HCC_sample_S0062T_S61

description: matrix column name is S0062T_S61

value: Female

value: No

value: IIIB


title: HEK293_CTRL_p53_Rep1

value: mock-treated


title: HCC_sample_S0061T_S60

description: matrix column name is S0061T_S60

value: Non-viral infection

value: Alive


title: N2_2-fold_1

description:
Library name: 100007
SR75 High


title: N2_2-fold_2

description:
Library name: 100008
SR75 High


title: HEK293_CTRL_input_Rep2

value: Embryonic Kidney

value: Immortalized


title: Normal_sample_S0077N_S71

description: matrix column name is S0077N_S71


title: HCC_sample_S0059T_S58

description: matrix column name is S0059T_S58

value: Male

value: Yes


title: N2_Bean_2

description:
Library name: 100006
SR75 High

value: Bean


title: HCC_sample_S0058T_S57

description: matrix column name is S0058T_S57


title: HEK293_CTRL_input_Rep1


title: HCC_sample_S0057T_S56

description: matrix column name is S0057T_S56

value: Dead


title: HCC_sample_S0056T_S55

description: matrix column name is S0056T_S55


title: N2_Bean_1

description:
Library name: 100005
SR75 High


title: HCC_sample_S0055T_S54

description: matrix column name is S0055T_S54

value: HCV

value: IIIA


title: HCT116_NUT_p53_Rep1

source_name: Colorectal Adenocarcinoma

value: Colorectal Adenocarcinoma

value: Cancer, Primary

value: anti-p53, Cell Signalling #9282


title: N2_190 cell_2

description:
Library name: 100004
SR75 High

value: Whole embryos

value: 190 cell


title: HCT116_NUT_p53_Rep2


title: N2_190 cell_1

description:
Library name: 100003
SR75 High


title: HCC_sample_S0065T_S63

description: matrix column name is S0065T_S63

value: Liver tissue

value: Female

value: No

value: II


title: HEK293_CTRL_p53_Rep2

value: Embryonic Kidney

value: mock-treated


title: HCC_sample_S0054T_S53

description: matrix column name is S0054T_S53

value: Male

value: HBV


title: HCC_sample_S0053T_S52

description: matrix column name is S0053T_S52

value: Alive

value: I


title: HCC_sample_S0052T_S51

description: matrix column name is S0052T_S51

value: HCV

value: Dead


title: HCT116_NUT_input_Rep2

value: Colorectal Adenocarcinoma


title: Tumor Site Sample

first: Zhaorong

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

description: Library name: T357

data_processing:
Sequenced reads were aligned to GRCh38 reference genome and quantified using CellRanger (v 7.1) (47). Potential ‘doublet’ cells in each sample were predicted and removed with the software package “scrublet” (v 0.2.3). Cells that were either in the bottom 10% of UMI counts or in the bottom 10% of feature count (genes) were filtered out from each sample. Also, cells with more than 25% mitochondrial read content were removed. After filtering, 5,210 cells in the lymph node sample and 5,325 cells in the tumor sample were retained for further analysis.
Assembly: GRCh38
Supplementary files format and content: h5 files of cellranger output

source_name: Tumor Site

extract_protocol: We interrogated the availability of surgical specimens of patients who had received neo-adjuvant EGFR-TKIs at Dana-Farber Cancer Institute (Boston, MA, US), at Policlinico Universitario A. Gemelli IRCCS (Rome, Italy) and at Cochin Hospital AP-HP (Paris, France). All patients had signed an informed consent to participate to molecular studies and the studies were approved by the local institutional review boards.

value: Tumor Site

value: All cells


title: HCC_sample_S0051T_S50

description: matrix column name is S0051T_S50

value: Yes


title: HCT116_NUT_input_Rep1

value: Cancer, Primary


title: HCC_sample_S0060T_S59

description: matrix column name is S0060T_S59

value: Liver tissue

value: Non-viral infection


title: HCC_sample_S0050T_S49

description: matrix column name is S0050T_S49

value: No

value: IIIA


title: HCT116_CTRL_p53_Rep2

value: anti-p53, Cell Signalling #9282


title: Lymph Node Sample

description: Library name: N357

source_name: Lymph Node

value: Lymph Node


title: HCC_sample_S0048T_S47

description: matrix column name is S0048T_S47

value: Male

value: II


title: HCC_sample_S0047T_S46

description: matrix column name is S0047T_S46

value: Alive


title: HCC_sample_S0049T_S48

description: matrix column name is S0049T_S48


title: HCC_sample_S0046T_S45

description: matrix column name is S0046T_S45

value: I


title: HCC_sample_S0045T_S44

description: matrix column name is S0045T_S44

value: HCV


title: HCC_sample_S0044T_S43

description: matrix column name is S0044T_S43

value: Dead


title: HCT116_CTRL_input_Rep2

value: Colorectal Adenocarcinoma

value: mock-treated


title: WT Rpl18+ CD8+ cells sorted from D10 MC38 tumor 3

city: Pittsburgh

first: Lawrence

middle: P.

last: Kane

state: PA

address: 5051 Centre Ave.

department: Immunology

institute: University of Pittsburgh

description: Library name: WT_Tumor_3_S8

data_processing:
FASTq reads were quality checkedand  mapped with GRCm38 ref genome usingCLC genomics workbench V25 default setting
Map reads were quantified  using CLC genomics workbench
Raw count data was downloaded from CLC genomics and uploaded to Partekflow
Assembly: GRCm39
Supplementary files format and content: Excel file with individual sample read counts and normalization

source_name: Tumor

extract_protocol:
Illumina Stranded mRNA (PolyA+)
lumina DNA Prep kit (Illumina: 20060059)

treatment_protocol: Cells were isolated on day 10 from mice injected with MC38 tumor

value: Tumor

value: CD8 T cells

value: Day 10 post-MC38 Tumor injection


title: HCC_sample_S0043T_S42

description: matrix column name is S0043T_S42

value: Liver tissue

value: Yes

value: HBV


title: HCC_sample_S0042T_S41

description: matrix column name is S0042T_S41

value: Female

value: No


title: HCT116_CTRL_input_Rep1

value: Cancer, Primary


title: WT Rpl18+ CD8+ cells sorted from D10 MC38 tumor 4

description: Library name: WT_Tumor_4_S9


title: WT Rpl18+ CD8+ cells sorted from D10 MC38 tumor draining lymph node 4

description: Library name: WT_TDLN_4_S3

value: Lymph Node


title: HCC_sample_S0038T_S38

description: matrix column name is S0038T_S38

value: Male


title: GM12878_NUT_p53_Rep2

source_name: B-Lymphocyte

value: B-Lymphocyte

value: Normal

value: anti-p53, Cell Signalling #9282


title: HCC_sample_S0041T_S40

description: matrix column name is S0041T_S40

value: Alive

value: I


title: HCC_sample_S0039T_S39

description: matrix column name is S0039T_S39

value: Dead

value: II


title: WT Rpl18+ CD8+ cells sorted from D10 MC38 tumor draining lymph node 3

description: Library name: WT_TDLN_3_S2

value: CD8 T cells


title: GM12878_NUT_p53_Rep1


title: WT Rpl18+ CD8+ cells sorted from D10 MC38 tumor draining lymph node 1

description: Library name: WT_TDLN_1_S1

value: Day 10 post-MC38 Tumor injection


title: HCC_sample_S0035T_S35

description: matrix column name is S0035T_S35

value: Liver tissue


title: HCC_sample_S0036T_S36

description: matrix column name is S0036T_S36

value: Yes


title: GM12878_NUT_input_Rep2


title: HCC_sample_S0034T_S34

description: matrix column name is S0034T_S34

value: HBV


title: GM12878_NUT_input_Rep1


title: HCT116_CTRL_p53_Rep1

value: Colorectal Adenocarcinoma

value: mock-treated


title: KO Rpl18+ CD8+ cells sorted from D10 MC38 tumor 3

description: Library name: KO_Tumor_3_S12

value: Tumor


title: HCC_sample_S0032T_S32

description: matrix column name is S0032T_S32

value: HCV


title: KO Rpl18+ CD8+ cells sorted from D10 MC38 tumor 2

description: Library name: KO_Tumor_2_S11


title: HCC_sample_S0031T_S31

description: matrix column name is S0031T_S31

value: Male

value: No

value: Non-viral infection

value: IVB


title: GM12878_CTRL_p53_Rep2

value: B-Lymphocyte

value: Normal

value: anti-p53, Cell Signalling #9282


title: WT Rpl18+ CD8+ cells sorted from D10 MC38 tumor 1

description: Library name: WT_Tumor_1_S7


title: HCC_sample_S0030T_S30

description: matrix column name is S0030T_S30

value: Alive

value: II


title: KO Rpl18+ CD8+ cells sorted from D10 MC38 tumor 1

description: Library name: KO_Tumor_1_S10

value: CD8 T cells

value: Day 10 post-MC38 Tumor injection


title: GM12878_CTRL_p53_Rep1


title: HCC_sample_S0027T_S27

description: matrix column name is S0027T_S27

value: Liver tissue

value: Yes

value: Dead

value: I


title: HCC_sample_S0028T_S28

description: matrix column name is S0028T_S28

value: HBV


title: HCC_sample_S0037T_S37

description: matrix column name is S0037T_S37

value: Female


title: GM12878_CTRL_input_Rep2

value: mock-treated


title: HCC_sample_S0025T_S25

description: matrix column name is S0025T_S25

value: Male

value: No

value: HCV


title: KO Rpl18+ CD8+ cells sorted from D10 MC38 tumor draining lymph node 3

description: Library name: KO_TDLN_3_S6

value: Lymph Node


title: KO Rpl18+ CD8+ cells sorted from D10 MC38 tumor draining lymph node 2

description: Library name: KO_TDLN_2_S5


title: HCC_sample_S0026T_S26

description: matrix column name is S0026T_S26


title: GM12878_CTRL_input_Rep1

value: B-Lymphocyte

value: Normal


title: HCC_sample_S0023T_S23

description: matrix column name is S0023T_S23

value: Non-viral infection


title: A549_NUT_p53_Rep2

source_name: NSCKC Adenocarcinoma

value: NSCKC Adenocarcinoma

value: Cancer, Primary

value: anti-p53, Cell Signalling #9282


title: HCC_sample_S0022T_S22

description: matrix column name is S0022T_S22

value: Liver tissue

value: Alive

value: II


title: HCC_sample_S0033T_S33

description: matrix column name is S0033T_S33

value: Yes

value: Dead


title: HCC_sample_S0021T_S21

description: matrix column name is S0021T_S21


title: A549_NUT_p53_Rep1


title: A549_NUT_input_Rep2


title: KO Rpl18+ CD8+ cells sorted from D10 MC38 tumor draining lymph node, sample 3

description: Library name: G1_KO_TDLN_3_TCR

data_processing:
TRUST4 TCRseq
Assembly: GRCm39
Supplementary files format and content: Excel file with individual sample read counts and normalization
Library strategy: TCR-seq

extract_protocol:
Illumina Stranded mRNA (PolyA+)
TCR specific primers (Takara: 634403)

value: CD8 T cells

value: KO

value: Day 10 post-MC38 Tumor injection


title: KO Rpl18+ CD8+ cells sorted from D10 MC38 tumor, sample 3

description: Library name: G2_KO_Tumor_3_TCR

value: Tumor


title: HCC_sample_S0018T_S18

description: matrix column name is S0018T_S18

value: Male

value: No

value: I


title: KO Rpl18+ CD8+ cells sorted from D10 MC38 tumor, sample 2

description: Library name: F2_KO_Tumor_2_TCR


title: HCC_sample_S0017T_S17

description: matrix column name is S0017T_S17

value: Female

value: HBV

value: IIIB


title: HCC_sample_S0019T_S19

description: matrix column name is S0019T_S19

value: Non-viral infection


title: HCC_sample_S0029T_S29

description: matrix column name is S0029T_S29

value: HCV


title: HCC_sample_S0020T_S20

description: matrix column name is S0020T_S20

value: Liver tissue


title: HCC_sample_S0016T_S16

description: matrix column name is S0016T_S16


title: KO Rpl18+ CD8+ cells sorted from D10 MC38 tumor draining lymph node, sample 2

description: Library name: F1_KO_TDLN_2_TCR

value: Lymph Node


title: HCC_sample_S0015T_S15

description: matrix column name is S0015T_S15

value: Alive

value: II


title: KO Rpl18+ CD8+ cells sorted from D10 MC38 tumor, sample 1

description: Library name: E2_KO_Tumor_1_TCR


title: A549_CTRL_p53_Rep2

value: NSCKC Adenocarcinoma

value: Cancer, Primary

value: mock-treated

value: anti-p53, Cell Signalling #9282


title: HCC_sample_S0013T_S13

description: matrix column name is S0013T_S13

value: Dead


title: HCC_sample_S0014T_S14

description: matrix column name is S0014T_S14


title: A549_CTRL_p53_Rep1


title: KO Rpl18+ CD8+ cells sorted from D10 MC38 tumor draining lymph node, sample 1

description: Library name: E1_KO_TDLN_1_TCR

value: CD8 T cells

value: KO

value: Day 10 post-MC38 Tumor injection


title: WT Rpl18+ CD8+ cells sorted from D10 MC38 tumor, sample 4

description: Library name: D2_WT_Tumor_4_TCR

value: Tumor

value: WT


title: HCC_sample_S0010T_S10

description: matrix column name is S0010T_S10

value: Male

value: No

value: HBV

value: I


title: KO Rpl18+ CD8+ cells sorted from D10 MC38 tumor draining lymph node 1

description: Library name: KO_TDLN_1_S4

value: Lymph Node


title: HCC_sample_S009T_S9

description: matrix column name is S009T_S9

value: Liver tissue

value: Alive

value: IIIA


title: HCC_sample_S0024T_S24

description: matrix column name is S0024T_S24

value: Non-viral infection

value: II


title: HCC_sample_S0012T_S12

description: matrix column name is S0012T_S12

value: Yes


title: A549_CTRL_input_Rep1

value: NSCKC Adenocarcinoma

value: Cancer, Primary

value: mock-treated


title: HCC_sample_S008T_S8

description: matrix column name is S008T_S8

value: Female

value: HCV

value: Dead


title: HCC_sample_S007T_S7

description: matrix column name is S007T_S7

value: IIIB


title: A549_NUT_input_Rep1


title: WT Rpl18+ CD8+ cells sorted from D10 MC38 tumor draining lymph node, sample 4

description: Library name: D1_WT_TDLN_4_TCR

value: CD8 T cells

value: WT

value: Day 10 post-MC38 Tumor injection


title: HCC_sample_S006T_S6

description: matrix column name is S006T_S6

value: No


title: SKNSH_NUT_MicroC_Rep1

source_name: Neuroblastoma

value: Neuroblastoma

value: SKSNH

value: Cancer, Metastasis

value: Eagle's Minimum Essential Medium (EMEM; ATCC 30-2003), 10% FBS


title: P7_GCM_RNA_2

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

institute: Kyoto University, Graduate school of medicine

description: Library name: Sample12

data_processing:
Raw 3’ RNA-seq data were directly used with Salmon v1.4.0 (Patro et al., 2017) with default parameters and --noLengthCorrection to quantify the expression of GENCODE vM25 features on GRCm38.p6. Gene-level expression estimates were aggregated from transcript-level abundance using tximport v1.16.1 (Soneson et al., 2015).
Alternatively, all reads were processed with cutadapt v1.18 for trimming adaptor and poly-A, then mapped onto GRCm38.p6 transcript references using Tophat v2.1.1.
Resulting BAM files were processed with HTseq v0.9.1 to calculate read counts per gene.
Read counts per gene were divided by total read counts in all chromosomal genes to estimate RPM values for genes.
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include RPM values and read counts for each Sample

source_name: testis

extract_protocol:
Total RNA was extracted from cells using a RNeasy Micro kit (QIAGEN, 74004) according to the manufacturer’s instructions.
1 ng of extracted RNA was used for the reverse transcription and the cDNA amplification as previously described  (Nakamura et al, 2015). Sequencing libraries were generated from amplified cDNA as described previously   (Nakamura et al, 2015).

value: testis

value: Germ cells


title: HCC_sample_S004T_S4

description: matrix column name is S004T_S4

value: Liver tissue

value: HBV

value: Alive

value: II


title: P7_GCM_RNA_1

description: Library name: Sample11


title: HCC_sample_S005T_S5

description: matrix column name is S005T_S5

value: Female

value: Yes


title: HCC_sample_S003T_S3

description: matrix column name is S003T_S3

value: Male

value: HCV

value: Dead

value: I


title: WT Rpl18+ CD8+ cells sorted from D10 MC38 tumor draining lymph node, sample 3

description: Library name: C1_WT_TDLN_3_TCR

value: Lymph Node

value: CD8 T cells

value: WT

value: Day 10 post-MC38 Tumor injection


title: WT Rpl18+ CD8+ cells sorted from D10 MC38 tumor, sample 2

description: Library name: A2_WT Tumor_2_TCR

value: Tumor


title: HCC_sample_S001T_S1

description: matrix column name is S001T_S1

value: No


title: A549_CTRL_input_Rep2

value: NSCKC Adenocarcinoma

value: Cancer, Primary

value: mock-treated


title: SCO organoid, MMC 2 replicate 1, scRNAseq

first: Shaun

middle: M

last: Kunisaki

address: 1800 Orleans Street

department: Pediatric Surgery

institute: Johns Hopkins University School of Medicine

description: 10X genomics

data_processing:
Cell ranger 6.1.1 was used for alignment, filtering, barcode counting, and UMI counting.
All preprocessing, clustering, and cell identification was performed with Seurat in R.
RNA velocity utilized velocyto.py.
Assembly: GRCh38
Supplementary files format and content: UMI counts produced from cell ranger included as tab-separated value (TSV) files and matrices.
Supplementary files format and content: Fully processed Seurat also included as R object (Rds).

source_name: spinal cord organoid

extract_protocol:
For each line, 14 organoids were pooled and minced into <1 mm pieces. These pieces were enzymatically digested with papain dissociation system (Worthington) and incubated with DNase for 40min. Then, the organoids were mechanically dissociated with 5mL pipette, filtered with 40uM mesh, then centrifiged and washed with DMEM twice. After cell counting, the cells were suspened in DMEM/10% FBS at a concentration of 1000 cells/uL.
Library constructed with Chormium Next GEM Single Cell 3' Reagent Kits v 3.1. The cells were combined with RT reagents and loaded onto 10X Next GEM Chip with gel beads. ~100uL of emulsion was taken from the chip and incubated to generated barcoded cDNA from each cell. The samples were then cleaned with SPRI select beads.

value: spinal cord organoid

tag: disease

value: MMC


title: L3456-GM18278_ssSMF

city: Stanford

first: Georgi

middle: Kolev

last: Marinov

state: California

address: 279 Campus Drive West, Beckman Center, B-257A/259

department: Genetics

institute: STANFORD UNIVERSITY

description: Library name: L3456-GM18278_ssSMF

data_processing:
bwameth
Assembly: hg38
Supplementary files format and content: bedGraph of deamination levels, average over 10-bp windows

extract_protocol:
Cells were centrifuged at 1,000 g for 2 minutes, then resuspended in 1 mL 1xPBS with 27 uL 37% formaldehyde added (to a final concentration of 1%). Crosslinking was carried out for 15 minutes at room temperature on a rotator, then quenched with 100 uL 2.5 M glycine solution. Crosslinked cells were centrifuged at 1,000 g for 2 minutes, resuspended in 1 mL 1xPBS, and centrifuged again. Permeabilization was carried out either by resuspending cells in Lysis Buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% Igepal CA630) and incubating on ice for 10 minutes, then centrifuging for 2 minutes at 1,000 g. Cells (200,000 cells were used as input) were then resuspended in 1 mL of 1xAPOBEC Buffer  (from NEB EM-seq kit: NEB #E7120). Deamination treatment was carried out by adding 2 uL RNAse A and 10 uL PURExpress CseDa0, then incubating at 37C for 3 hours with shaking at 800 rpm in a Thermomixer. After deamination, cells were again pelleted by centrifugation at 1,500 g for 2 minutes, then resuspended in 200 uL IP Elution Buffer (1% SDS, 0.1 M NaHCO3); 2 uL Proteinase K were added, and reverse crosslinking was carried out overnight at 65C. DNA was then isolated using the MinElute kit (Qiagen) using 600 uL PB buffer and following the manufacturer's instructions, eluting in 52 uL EB buffer.
For single-stranded libraries construction, SMF DNA was first sheared using a Covaris E220 instrument to an average size of 400-500 bp, then the xGen Methyl-Seq DNA Library Prep Kit (IDT)) was used to generated Illumina-compatible libraries, which in turn were converted into Ultima-compatible libraries using a constant primer (CTGTGTGCCTTGGCAGTCTCAGCTCAGACGTGTGCTCTTCCGATC*T) and an index primer (CCATCTCATCCCTGCGTGTCTCCGACTGCACXXXXXXXXXXXGATCTACACGACGCTCTTCCGATC*T, where the portion indicated as ``XXXXXXXXXXX'' corresponds to the index sequences). For each library, ~10 ng were used as input, diluted in a 20 uL volume, then mixed with 2.5 uL of each primer and 25 uL of 2x NEB Next High Fidelity PCR Master Mix (NEB Cat \# M0541L). Libraries were amplified using initial denaturation at 98C for 45 seconds, then 7 cycles of 15 seconds at 98C, 30 seconds at 60C, and 60 seconds and 72C, followed by final extension for 10 minutes at 72C.


title: SCO organoid, Ctrl, scRNAseq

description: 10X genomics

value: control


title: L3454-GM18278_ssSMF

description: Library name: L3454-GM18278_ssSMF


title: Input of 1014 NOTCH2-Inactivated TRIM28-dTAG-HA knock-in  cells for HA-ChIP

description: Library name: 1014_N2_Inactivated_TRIM28_HA_Input

data_processing:
Sequenced read were aligned to the UCSC hg38 or mm10 reference genome assembly using BWA(v0.7.15) and peaking calling performed using MACS3.
Assembly: mm10 and hg38
Supplementary files format and content: bw files except for input samples

source_name: 1014 TRIM28-dTAG-HA knock-in

extract_protocol:
Cells were  collected, and centrifuged. The supernatant was removed and the cells were washed once in PBS. For the TRIM28-HA ChIP experiments, cells were cross-linked by incubation with 2 mM disuccinimidyl glutarate (DSG) with rocking for 30 minutes at room temperature prior to fixation step. Then, for all ChIP experiments, cells were fixed in 1% paraformaldehyde diluted in PBS for 10 minutes at room temperature. Excess formaldehyde was quenched by dropwise addition of freshly made Glycine at a final concentration 1.25 M followed by rocking the cells for an additional 5 minutes at room temperature. The paraformaldehyde/glycine was then removed by spinning at 400 x g for 5 minutes at 4°C and the cells were washed twice with ice cold PBS.     The cells were then resuspended in 1 mL of lysis buffer (50 mM Hepes-NaOH pH 8, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% TX-100 supplemented with a protease inhibitors and phosphatase inhibitors) and incubated by rotating for 10 minutes at 4°C. Intact nuclei were then collected by centrifugation at 1900 x g for 5 minutes at 4°C. The supernatant was then gently aspirated and the pellet was resuspended in 1 mL of wash buffer (10mM Tris-HCl pH 8.0, 200mM NaCl, 1mM EDTA, supplemented with a protease inhibitor cocktail and phosphatase inhibitors) and incubated by rotating for 10 minutes at 4°C. The nuclei were again collected by centrifugation at 1900 x g for 5 minutes at 4°C. The supernatant was then gently aspirated and the tube was rinsed with 500 μL of shearing buffer (0.1% SDS, 1 mM EDTA, 10 mM Tris-HCl pH 8.0 supplemented with protease inhibitors and phosphatase inhibitors). The nuclei were again collected by centrifugation at 1900 x g for 5 minutes at 4°C, the supernatant was carefully removed, and the pellet was gently resuspended in 1mL shearing buffer and transferred to a 1 mL AFA fiber tube (Covaris #520130). The chromatin was then sonicated using a Covaris E220 sonicator at 100 peak incident power, 10% duty cycles, 200 cycles per burst, water level 15 (left indicator)/10 (right indicator) for 900 seconds. The samples were then transferred to 1.5 mL Eppendorf tubes and centrifuged in an Eppendorf microcentrifuge at 15,900 x g for 5 minutes at 4°C. 900 μL of the supernatants were transferred to a new Eppendorf tube, to which 1% Triton X-100 and 150 mM NaCl were added. 20μl of Dynabeads Protein G (ThermoFisher #10004D), prewashed with Shearing Buffer, was then added and samples were rotated for 1 hour at 4°C to pre-clear the sonicated chromatin. The Dynabeads were then removed using a magnetic stand and the supernatants were transferred to new tubes. 5% of the total lysate was removed to make genomic DNA to be used for the ChIP-sequencing input DNA. The TRIM28-HA ChIPs were performed separately also using 5% input and 95% for ChIP. 10 μg of the rabbit anti-HA (CST #3724) primary antibodies were added. For the H3K9me3 and H3K27ac ChIPs, the remaining lysate (95% of total) were equally distributed into two Eppendorf tubes to perform the H3K9me3 and H3K27ac ChIPs. 5 μg of the rabbit anti-H3k9me3 (EPR16601) (Abcam, # ab176916) or 5 μg of the rabbit anti-H3K27ac (Diagenode# C15410196) primary antibodies were added. All samples were incubated overnight while rotating at 4°C. The following morning, 50 μL of Dynabeads, prewashed with Shearing buffer, were added and the samples were incubated for another 2 hours while rotating at 4°C. A magnetic stand was used to isolate the Dynabeads. The supernatant was removed and the Dynabeads were washed once in 1 mL of low salt immune complex wash buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 0.1% SDS, 1% TX-100, 2 mM EDTA) and incubated for 5 minutes while rotating at 4°C. The beads were again isolated using a magnetic stand. Following removal of the supernatant the Dynabeads were washed once in 1 mL of high salt immune complex wash buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 0.1% SDS, 1% TX-100, 2 mM EDTA) and incubated for 5 minutes while rotating at 4°C. The beads were again pelleted with a magnetic stand. Following removal of the supernatant, the Dynabeads were washed once in 1 mL of Lithium Chloride immune complex wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1% SDS, 1% NP-40, 1 mM EDTA) and incubated for 5 minutes while rotating at 4°C. The beads were then washed twice in TE pH8 at room temperature and the beads were then resuspended in 100μL TE pH8. RNase A (Qiagen #19101) was then added to a final concentration of 0.2 mg/mL and the samples were incubated for 30 minutes at 37°C. To reverse the formaldehyde crosslinking and remove protein, Proteinase K was then added to a final concentration of 0.8 mg/mL and the samples were incubated for 30 minutes at 42°C and then an additional 6 hours at 65°C. 300 μL QG buffer and 100 μL of isopropanol was then added to each sample and a magnetic stand was used to pellet the Dynabeads. The supernatant was then collected and DNA was isolated using QIAquick gel extraction kit (Qiagen #28706) according to the manufacturer’s instructions.
ChIPseq libraries were prepared using IDT XGen DNAseq library prep reagents on a Beckman Coulter Biomek i7 liquid handling platform from approximately 1ng of DNA according to manufacturer’s protocol and 14 cycles of PCR amplification. Finished sequencing libraries were quantified by Qubit fluorometer and Agilent TapeStation 2200.  Library pooling and indexing was evaluated with shallow sequencing on an Illumina MiSeq. Subsequently, libraries were sequenced on an Illumina NovaSeq X Plus targeting 40 million 150bp read pairs.

value: 1014 TRIM28-dTAG-HA knock-in

value: SCLC cell line


title: SCO organoid, MMC 1, scRNAseq

description: 10X genomics


title: L3453-GM18278_ssSMF

description: Library name: L3453-GM18278_ssSMF


title: WT P14 CD8+ T cells, TCR stimulated, not PI3Kδi treated, replicate 3

description: Library name: G2_WT_Stim_No_inhibitor__S21

source_name: Spleen

treatment_protocol: Splenocytes from P14 TCR Tg mice were stimulated with gp33 peptide (100ng/ml) for 24hrs and then CD8 T cells were sorted out and subject to sequencing

value: Spleen

value: WT P14tg

value: Il-2, IL-12, gp33 peptide stim


title: WT P14 CD8+ T cells, TCR stimulated, Treated with the PI3Kδ inhibitor, replicate 3

description: Library name: G3_WT_Stim_Plus_WITH_inhibitor_S27

value: Il-2, IL-12, gp33 peptide stim, PI3Kδi


title: T3

city: Chongqing

first: Tingting

last: Wang

address: Youyi road No.1

country: China

institute: The First Affiliated Hospital of chongqing Medical University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: HTR8/SVneo cells were purchased from ATCC. The cells were cultured in RPMI 1640 medium (Gibco, USA) supplemented with 10% fetal bovine serum (FBS) (PAN-Biotech, Germany) and 1% penicillin/streptomycin (Beyotime Biotechnology, China). It was kept and observed in an environment of 5% CO2 at 37 ℃.

extract_protocol:
Total RNA was extracted usingTrizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

treatment_protocol: Before each experiment, the storage solution was thawed in RPMI 1640 medium, diluted to the working concentration (3 μM) for 24 hours, and then used for detection.

value: human choriotrophoblast cells


title: L3452-GM18278_ssSMF

description: Library name: L3452-GM18278_ssSMF


title: Input of 1014 NOTCH2-WT TRIM28-dTAG-HA  knock-in cells for HA-ChIP

description: Library name: 1014_N2_WT_TRIM28_HA_Input


title: WT Rpl18+ CD8+ cells sorted from D10 MC38 tumor, sample 3

description: Library name: C2_WT_Tumor_3_TCR

value: CD8 T cells

value: WT


title: T2


title: WT P14 CD8+ T cells, TCR stimulated, not PI3Kδi treated, replicate 2

description: Library name: F2_WT_Stim_No_inhibitor__S20


title: WT P14 CD8+ T cells, not stimulated, not PI3Kδi treated, replicate 3

description: Library name: G1_WT_No_Stim_No_inhibitor_S15


title: L3449-GM18278_ssSMF

description: Library name: L3449-GM18278_ssSMF


title: Input of 1014 NOTCH2-WT TRIM28-dTAG-HA  knock-in cells witt dTAGV1

description: Library name: 1014_N2_WT_+dTAG_Input


title: L3455-GM18278_ssSMF

description: Library name: L3455-GM18278_ssSMF


title: L3451-GM18278_ssSMF

description: Library name: L3451-GM18278_ssSMF


title: WT P14 CD8+ T cells, not stimulated, not PI3Kδi treated, replicate 2

description: Library name: F1_WT_No_Stim_No_inhibitor_S14


title: HCC_sample_S002T_S2

description: matrix column name is S002T_S2

value: Liver tissue

tag: Sex

value: Male

value: HCV

value: Dead

value: II


title: Input of 1014 NOTCH2-WT TRIM28-dTAG-HA  knock-in cells with DMSO

description: Library name: 1014_N2_WT_-dTAG_Input


title: T1


title: WT P14 CD8+ T cells, TCR stimulated, Treated with the PI3Kδ inhibitor, replicate 2

description: Library name: F3_WT_Stim_Plus_WITH_inhibitor_S26


title: KO4, Input

city: Tel-Aviv

first: Boaz

last: Barak

address: Chaim Levanon street, 55

country: Israel

institute: Tel-Aviv University

description: Library name: KO4, Input

data_processing:
Uniquely mapped ChIP-Seq reads were mapped to the GRCm39 genome using Bowtie2.
Differential peak calling was performed using Macs2 (version 2.2.9.1) with the command line 'callpeak -t IP.bam -c Input.bam -g mm -f BAMPE -q 0.1 --nolambda --keep-dup all –B’, where immunoprecipitate (IP) over input scores were calculated.
Additional manual filtration was performed to exclude peaks with; q-value > 0.05, fragment size larger then 600bp and peaks that were mapped to mitochondrial DNA.
The Bedtools package (using the intersect and cluster tools) was employed to identify Tfii-i consensus peaks, defined as those present in at least three out of five samples in the Control group. Peaks were classified as "lost" if no overlap was observed between the KO group and the Tfii-i consensus peaks.
Assembly: mm39
Supplementary files format and content: bed files (IP files only)

source_name: OL-enriched primary cell culture

growth_protocol: DMEM/F12 supplemented with L-glutamine, penicillin-streptomycin and SM1 supplement (STEMCELL technologies, catalog no. 05711). To increase OPC differentiation into OLs, T3 (Sigma-Aldrich, catalog no. T5516) was added to the medium at a final concentration of 340 ng/mL.

extract_protocol:
Differentiated OLs from 4-5 P1 mice were pooled by genotype. At DIV7 cells were washed gently with PBS to remove cellular debris then harvested and pooled using Trypsin A (Sigma-Aldrich, catalog no. T4049). Trypsin activity was neutralized by adding DMEM/F12 supplemented with L-glutamine and 20% FBS. Cells were then centrifuged at 500 rpm for 5 minutes. The pellets were then crosslinked in 1% PFA for 10 minutes at room temperature. To avoid over-fixation, 100 µl of glycine (Cell Signaling, catalog no. 7005S) was added after 10 minutes. The lysates were then centrifuged at 5000 rpm for 5 minutes, and the supernatant was carefully removed. Three washing steps with PBS and centrifugation with the same parameters were then performed. Fresh sonication buffer containing 1% SDS, 50 mM Tris-HCl, pH 8.8, 20 mM EDTA, and a protease inhibitor in DEPC was then added to each sample. DNA shearing was performed by 9 rounds of sonication (Covaris) of 10 pulses each to obtain 200-800 bp DNA fragments.
Library preparation and paired-end sequencing using Illumina NovaSeq S1 (100 cycles) was performed at the Crown Genomics institute, Weizmann Institute of Science, Israel.

value: OL-enriched primary cell culture


title: C1

value: Ctrl


title: Input of 1014 NOTCH2-Inactivated TRIM28-dTAG-HA knock-in  cells with DMSO

description: Library name: 1014_N2_Inactivated_-dTAG_Input


title: H3K9me3 ChIP-seq on 1014 NOTCH2-Inactivated TRIM28-dTAG-HA  knock-in cells with dTAGV1 Rep1

description: Library name: 1014_N2_Inactivated_+dTAG_H3K9me3_Rep1

value: H3K9me3 Abcam ab176916


title: C3


title: SCO organoid, MMC 2 replicate 2, scRNAseq

description: 10X genomics

value: spinal cord organoid

value: MMC


title: WT Rpl18+ CD8+ cells sorted from D10 MC38 tumor draining lymph node, sample 1

description: Library name: A1_WT TDLN_1_TCR

value: Lymph Node

value: Day 10 post-MC38 Tumor injection


title: KO3, ChIP

description: Library name: KO3, ChIP

value: Tfii-I antibody (Cell Signaling, #4562)


title: C2


title: WT P14 CD8+ T cells, TCR stimulated, Treated with the PI3Kδ inhibitor, replicate 1

description: Library name: E3_WT_Stim_Plus_WITH_inhibitor_S25

value: Spleen

value: WT P14tg

value: Il-2, IL-12, gp33 peptide stim, PI3Kδi


title: H3K9me3 ChIP-seq on 1014 NOTCH2-Inactivated TRIM28-dTAG-HA  knock-in cells with dTAGV1 Rep2

description: Library name: 1014_N2_Inactivated_+dTAG_H3K9me3_Rep2

value: 1014 TRIM28-dTAG-HA knock-in

value: SCLC cell line


title: KO4, ChIP

description: Library name: KO4, ChIP


title: TrIP KO P14 CD8+ T cells, TCR stimulated, not PI3Kδi treated, replicate 3

description: Library name: C2_KO_Stim_No_inhibitor__S18

value: CD8 T cells

value: TrIP KO P14tg

value: Il-2, IL-12, gp33 peptide stim


title: TrIP KO P14 CD8+ T cells, not stimulated, not PI3Kδi treated, replicate 3

description: Library name: C1_KO_No_Stim_No_inhibitor_S12


title: Input of 1014 NOTCH2-Inactivated TRIM28-dTAG-HA  knock-in cells witt dTAGV1

description: Library name: 1014_N2_Inactivated_+dTAG_Input


title: WT P14 CD8+ T cells, TCR stimulated, not PI3Kδi treated, replicate 1

description: Library name: E2_WT_Stim_No_inhibitor__S19


title: PH129, Exercised

city: Tarrytown

first: Michael

last: Stec

address: 777 Old Saw Mill River Rd

institute: Regeneron Pharmaceuticals

description: Fresh Frozen Saptial Transcriptomic Sequencing

data_processing:
Raw sequencing data were processed using the 10X Genomics Space Ranger (V2) to generate FASTQ files
Sequences were aligned to GRCh38 genome to gene expression count using Space Ranger's default setting
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of spatial  barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: Skeletal Muscle

extract_protocol:
Muscle biopsies were cryosectioned at 10µm thickness onto SuperFrost Plus charged slides and stored at -80°C until staining and processing via the Visium CytAssist pipeline.
The 10x Genomics Visium CytAssist Spatial Gene Expression for FFPE platform was used for spatial transcriptomics experiments. Tissue sections mounted on standard glass slides were hybridized to the 10x Genomics human transcriptome probe set for CytAssist (v2) according to the manufacturer’s protocol (10x Genomics). The CytAssist machine was used to transfer hybridized probes from the tissue sections to Visium 6.5mm slides.

value: Skeletal Muscle

value: Exercised

tag: developmental stage

value: young


title: PH083, Exercised


title: KO3, Input

description: Library name: KO3, Input

value: OL-enriched primary cell culture


title: PH083, Sedentary

value: Sedentary


title: TrIP KO P14 CD8+ T cells, TCR stimulated, Treated with the PI3Kδ inhibitor, replicate 2

description: Library name: B3_KO_Stim_Plus_WITH_inhibitor_S23


title: L3450-GM18278_ssSMF

description: Library name: L3450-GM18278_ssSMF


title: WT P14 CD8+ T cells, not stimulated, not PI3Kδi treated, replicate 1

description: Library name: E1_WT_No_Stim_No_inhibitor_S13


title: H3K9me3 ChIP-seq on 1014 NOTCH2-Inactivated TRIM28-dTAG-HA  knock-in cells with DMSO Rep2

first: Yixiang

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

description: Library name: 1014_N2_Inactivated_-dTAG_H3K9me3_Rep2

value: H3K9me3 Abcam ab176916


title: TrIP KO P14 CD8+ T cells, TCR stimulated, Treated with the PI3Kδ inhibitor, replicate 3

description: Library name: C3_KO_Stim_Plus_WITH_inhibitor_S24


title: KO1, ChIP

description: Library name: KO1, ChIP


title: KO2, Input

description: Library name: KO2, Input


title: H3K9me3 ChIP-seq on 1014 NOTCH2-WT TRIM28-dTAG-HA  knock-in cells with DMSO Rep1

description: Library name: 1014_N2_WT_-dTAG_H3K9me3_Rep1


title: PH072, Exercised


title: PH106, Exercised


title: H3K9me3 ChIP-seq on 1014 NOTCH2-WT TRIM28-dTAG-HA  knock-in cells with dTAGV1 Rep2

description: Library name: 1014_N2_WT_+dTAG_H3K9me3_Rep2


title: KO2, ChIP

description: Library name: KO2, ChIP


title: PH072, Sedentary


title: TrIP KO P14 CD8+ T cells, TCR stimulated, not PI3Kδi treated, replicate 2

description: Library name: B2_KO_Stim_No_inhibitor__S17


title: H3K9me3 ChIP-seq on 1014 NOTCH2-WT TRIM28-dTAG-HA  knock-in cells with dTAGV1 Rep1

description: Library name: 1014_N2_WT_+dTAG_H3K9me3_Rep1


title: PH106, Sedentary


title: Control6, ChIP

description: Library name: Control6, ChIP

value: Control


title: PH129, Sedentary


title: PH078, Exercised


title: KO1, Input

description: Library name: KO1, Input


title: H3K9me3 ChIP-seq on 1014 NOTCH2-WT TRIM28-dTAG-HA knock-in  cells with DMSO Rep2

description: Library name: 1014_N2_WT_-dTAG_H3K9me3_Rep2


title: TrIP KO P14 CD8+ T cells, TCR stimulated, not PI3Kδi treated, replicate 1

description: Library name: A2_KO_Stim_No_inhibitor__S16


title: H3K9me3 ChIP-seq on 1014 NOTCH2-Inactivated TRIM28-dTAG-HA  knock-in cells with DMSO Rep1

description: Library name: 1014_N2_Inactivated_-dTAG_H3K9me3_Rep1


title: TrIP KO P14 CD8+ T cells, not stimulated, not PI3Kδi treated, replicate 2

description: Library name: B1_KO_No_Stim_No_inhibitor_S11


title: TrIP KO P14 CD8+ T cells, not stimulated, not PI3Kδi treated, replicate 1

description: Library name: A1_KO_No_Stim_No_inhibitor_S10


title: H3K27ac ChIP-seq on 1014 NOTCH2-Inactivated TRIM28-dTAG-HA knock-in  cells with dTAGV1 Rep2

description: Library name: 1014_N2_Inactivated_+dTAG_H3K27ac_Rep2

value: H3K27ac Diagenode C15410196


title: H3K27ac ChIP-seq on 1014 NOTCH2-Inactivated TRIM28-dTAG-HA  knock-in cells with dTAGV1 Rep1

description: Library name: 1014_N2_Inactivated_+dTAG_H3K27ac_Rep1


title: H3K27ac ChIP-seq on 1014 NOTCH2-Inactivated TRIM28-dTAG-HA  knock-in cells with DMSO Rep1

description: Library name: 1014_N2_Inactivated_-dTAG_H3K27ac_Rep1