title: RES.control.HiC

city: Los Angeles

first: Ye

last: Wang

state: California

address: 611 Charles E Young Dr E

department: Bioinformatics

institute: UCLA

data_processing:
For Hi-C, data is processed following 4DN in-situ Hi-C data processing pipeline (https://data.4dnucleome.org/resources/data-analysis/hi_c-processing-pipeline) to generate cool file as input for IGM modeling.
For oxaliplatin damage-seq, paired-ended data was trimmed by trimmomatic (v0.39) (29), oxaliplatin damage-seq data were generated as previously described. They were aligned to the human genome GRCh38 with HISAT2 (30) (v2.2.0) using parameter --rna-strandness RF --pen-noncansplice 1000000. Samtools (v1.0) (31) was used to convert the sam to bam files. After fixing mate pair with -mc parameter using samtools fixmate and sorting coordinates using samtools sort, reads were deduplicated by samtools markup. After PCR deduplication, only reads whose 5’ start are GG (for plus strand) or CC (for minus strand) are saved as potential cisplatin modified sites. R codes to extract the reads starting with GG and CC are described in Yimit et. al (32) and can be downloaded from https://github.com/yuchaojiang/damage_repair.
Assembly: hg38
Supplementary files format and content: Hi-C: mcool file that save the counts of genome-wide 2D contact map.
Supplementary files format and content: Damage-seq:bedgraph file that save the number of damage counts at particular genomic loci.

growth_protocol: Oxaliplatin sensitive HCT116 cell line (HCT116 OxS cell) is purchased from ATCC (https://www.atcc.org/products/ccl-247), Oxaliplatin resistant HCT116 cell line (HCT116 OxR cell) was obtained from MD Anderson Cancer Center Characterized Cell Line Core, supplied and generated by the Dr. Lee Ellis Laboratory. Both HCT116 OxS and HCT116 OxR were cultured in McCoy’s 5A cell culture medium (Gibco) with 10% (v/v) fetal bovine serum (FBS) and 1% (v/v) PenStrep. Cells are grown at 37°C in a humidified 5% CO2 incubator. Both cells were screened for Mycoplasma contamination with MycoStrip (InvivoGen, rep-mys-10) and tested negative.

extract_protocol:
For in-situ Hi-C, proximal ligated DNA is purified according to manufacturer’s protocol in Arima-HiC kit (Arima Genomics, #A510008, Document #A160134 v01). For damage-seq, cell pellet is resuspended in 200uL PBS with 10uL RNase A (Thermo #EN0531), 20uL Proteinase K and 200uL Buffer AL (both are from QIAGEN #69504). The suspension was then incubated at 55°C for 20 mins, followed by purification with the QIAGEN DNeasy Blood & Tissue Kit (QIAGEN #69504) according to manufacturer’s instruction.
In-situ Hi-C and Damage-seq
For in-situ Hi-C, HCT116 OxR control cells Hi-C library was generated with the Arima-HiC kit (Arima Genomics, #A510008, Document #A160134 v01) and Arima Library Prep Module (Arima Genomics, Cat #A303011, Document #A160432 v02) following manufacturer’s instruction.
For oxaliplatin damage-seq, cell pellet is resuspended in 200uL PBS with 10uL RNase A (Thermo #EN0531), 20uL Proteinase K and 200uL Buffer AL (both are from QIAGEN #69504). The suspension was then incubated at 55°C for 20 mins, followed by purification with the QIAGEN DNeasy Blood & Tissue Kit (QIAGEN #69504) according to manufacturer’s instruction. The purified genomic DNA is subsequently sonicated into 200-700bp fragments with Covaris sonicator. The fragmented genomic DNA (~2ug) was used for End repair, 5’ phosphorylation and dA-Tailing using 3uL End Prep Enzyme Mix and 7uL End Prep Reaction Buffer (NEB #E7546 or as included in NEB #E7645), at 20°C for 30 mins and then 65°C for 30 mins, before cooling down to room temperature. Following this, annealed AD1 adapter (500 pmol) was ligated to End Prepped DNA with 30uL Ligation Master Mix and 1uL Ligation Enhancer (NEB #E7595 or as included in NEB #E7645) at 16°C overnight. AD1 ligated DNA was purified with 1.2x AMPure XP beads and eluted in 50uL nuclease free water. Before the incubation with antibody coated beads, AD1 ligated DNA was denatured into ssDNA with 20uL 8M urea at 95°C for 1min, then placed on ice for 1min, and immediately incubated with antibody coated beads.
To prepare the antibody coated beads, 40uL anti-rat Dynabeads (Thermo, #11035) was washed three times with 1mL 1x PEXB buffer (1x PBS, 2mM EDTA, 0.01% Triton X-100 and 0.025% albumin). The beads were then incubated with 10ug salmon sperm DNA (Thermo, #AM9680) and 1.5uL anti-cisplatin modified DNA antibody (Abcam, #ab103261) in 100uL 1x PEXB buffer at 4°C with rotation for 3 hours. After incubation, antibody coated beads were then washed three times by 1mL 1x PEXB buffer and incubated with denatured, AD1 ligated DNA and 10ug salmon sperm DNA overnight at 4°C, to capture the oxaliplatin damaged DNA.
The beads were then washed subsequently with 400uL Wash Buffer U (20mM Tris-HCl (pH=8), 2mM EDTA, 1% Triton X-100, 2M urea), 400uL Wash Buffer II (20mM Tris-HCl (pH=8), 2mM EDTA, 1% Triton X-100, 0.5M NaCl, 0.1% SDS), 400uL Wash Buffer III (10mM Tris HCl (pH=8), 1mM EDTA, 150mM LiCl, 1% IGEPAL CA-630, 1% Na deoxycholate), 400uL Wash Buffer IV (100mM Tris-HCl (pH=8), 1mM EDTA, 500mM LiCl, 1% IGEPAL CA-630, 1% Na deoxycholate), and 400uL 1x TE (10mM Tris-HCl, 1mM EDTA). The oxaliplatin damaged DNA fragments were then eluted from beads with 100uL Elution buffer (50mM NaHCO3, freshly prepared, 1% (w/w) SDS) at 65°C for 10 mins. The eluted DNA was then precipitated by adding 10uL 3M sodium acetate solution, 1uL glycogen (Thermo #R0561), and 300uL ethanol at -80°C overnight.
Ethanol precipitated DNA is dissolved in 7uL nuclease free water. To this solution, Bio3U primer (30 pmol), 10uL Q5 Master Mix (NEB #M0544 or included in NEB #E7645) and nuclease free water were added to reach a total volume of 20uL. Primer extension is performed at 98°C for 45s, followed by 65°C for 5 min, and then placed on ice for cooling. Next, 2uL Exo I (NEB, M0293S) was added to remove the excessive primers at 37°C for 10 min. The primer extended DNA is then purified with 2x AMPure XP beads, and eluted with 30uL water. The DNA elute was denatured at 95°C for 90s, and then immediately placed on ice for 2 min. The denatured DNA is subsequently incubated with 5uL Streptavidin C1 beads (Thermo, #65001) in 30uL 2x B&W buffer (B&W final concentration (1x): 5mM Tris HCl (pH=7.5), 1mM EDTA, 1M NaCl) at 4°C for 1 hour to allow the biotinylated dsDNA being captured by C1 bead. The bead is then washed first with 100uL 1x B&W buffer, and then with 100uL 1x TE buffer. Finally the DNA was released from C1 beads into 18uL 0.1x TE by adding 2uL USER enzyme (NEB, #M5505) and incubating at 37°C for 25 min. The beads were washed by 25uL 1x B&W, and the supernatant was combined with the 20uL DNA elute obtained from the previous step.
To eliminate Bio3U extended DNA strand that read through the intact DNA fragment without damage (subtractive hybridization), Oligo SH (20 pmol) was added, followed by denaturing at 95°C for 1 min and naturally cooling down to room temperature to allow hybridization.  Oligo SH hybridized product was then captured by adding 10uL Streptavidin C1 beads (resuspended in 60uL 1x B&W) for 1 hour at 4°C. DNA was purified by ethanol precipitation at -80°C overnight.
To added second adapter to the 3’end, purified DNA was incubated with annealed AD2 (40 pmol) in 10uL 1x hybridization buffer (10mM Tris‐HCl, pH7.5,100mM NaCl, 0.1mM EDTA) at 65°C for 10min, and then 16°C for 5min. After adding 10uL ligation mix (From Thermo #EL0013, 2uL 10x ligation buffer, 1uL T4 DNA ligase (HC), 1uL 50% PEG solution, 1uL nuclease free water), the AD2 ligation reaction is incubated at 16°C overnight. The ligation product was then purified by 2x AMPure XP beads and PCR amplified by Q5 Master Mix (NEB #M0544 or included in NEB #E7645S) for 13-16 cycles. The PCR products were purified with AMPure XP beads.

treatment_protocol: Cells were cultured until they reached 70% confluency before treatment. Oxaliplatin (Sigma, #O9512) was dissolved in DMF to create a 4mM stock solution, which was then added to the medium to achieve a final concentration of 50uM. After added oxaliplatin, cells were further incubated for either 3 hours or 24 hours at incubator. Following incubation, the cells were washed with PBS and collected via trypsin digestion. The resulted cell pellets were then frozen at -80°C. For in-vitro experiments, 2ug genomic DNA was treated with 50uM oxaliplatin in an aqueous solution at 37°C for 15 mins. The DNA was then purified using 2x AMPure XP beads (Beckman, #A63881) for damage-seq library preparation.

value: Human colorectal cancer cell line

tag: sample group


title: Lung33_PDO_Tcells_6E7F1

status: Public on May 14 2025

type: SRA

city: Shanghai

first: Dongxi

last: Xiang

address: No. 25, Lane 2200, Xietu Road

country: China

institute: Shanghai Cancer Institute

library_source: transcriptomic single cell

data_processing:
Analysis of the sequencing data was performed using the Rhapsody Sequence Analysis Pipeline (v2.0) with default parameters, employing the RhapRef_Human_WTA_2023-02 transcriptome for mapping. Quality control, dimensionality reduction, and clustering were conducted using Seurat (v4.0.3). For each sample, cells with high quality, defined as expressing at least 200 genes and up to 7500 genes, with less than 20% mitochondrial genes and less than 5% red blood cell genes, were retained. Additionally, genes had to be expressed in at least 3 cells for retention. Doublet cells identified by DoubletFinder (v2.0.2) were excluded.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every cell in each sample

molecule: total RNA

organism: Homo sapiens

source_name: Lung

extract_protocol:
Organoids of each treated group were harvested and dissociated into single cells. Organoids were dissociated in Matrigel with TrypLE Express (Gibco) for 1~3min via mechanical pipetting. The cells were washed twice till Matrigel was cleared out, and then resuspended with cold PBS. Subsequently, the cells were stained with Trypan Blue (Gibco) and the viability of the cells was evaluated using phase contrast light microscopy (Olympus,Japan). The viability of the cells was preferably above 80%, and about 30000-50000 cells were needed to generate scRNA-seq.
Single-cell RNA-seq libraries were generated using the BD Rhapsody™ WTA Amplification Kit (No. 633801).

tag: tissue

value: Lung

tag: group

tag: cell type

value: NSCLC


title: M4-134, PLCG2 Knockout, 5xFAD, 7.5Month, Cortex, male

city: Indianapolis

first: Evan

last: Messenger

state: IN

address: 320 W 15th St

country: USA

institute: Stark Neuroscience Research Institute

description:
Library name: 7-5M_M4-134_P2KOHOM_5xFAD_Ctx
Column name in raw-counts.txt and normalized counts.csv: 7-5M_M4-134_P2KOHOM_5xFAD_Ctx

library_source: transcriptomic

data_processing:
Libraries of RNA samples with at least RIN 8 were prepared using KAPA mRNA Hyperprep Kit. Paired-end RNA sequencing (100bp) with ∼100 million reads coverage.
FASTQ files were aligned to the reference mouse genome mm10 with UCSC refGene annotation using STAR (v.2.7.10a), and gene read counts were generated using featureCounts (v. 2.0.3).
No trimming required.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: CSV file includes effective length, expected count, TPM, and FPKM for each sample

organism: Mus musculus

source_name: Cortex

extract_protocol:
RNA was extracted using the PureLink RNA mini kit (Invitrogen). 100ng of RNA were used.
KAPA mRNA Hyperprep Kit

value: Cortex

tag: genotype

value: PLCG2 Knockout


title: SEN.oxa.damage.24hrs.rep2

library_source: genomic

data_processing:
Library strategy: Damage-seq
For Hi-C, data is processed following 4DN in-situ Hi-C data processing pipeline (https://data.4dnucleome.org/resources/data-analysis/hi_c-processing-pipeline) to generate cool file as input for IGM modeling.
For oxaliplatin damage-seq, paired-ended data was trimmed by trimmomatic (v0.39) (29), oxaliplatin damage-seq data were generated as previously described. They were aligned to the human genome GRCh38 with HISAT2 (30) (v2.2.0) using parameter --rna-strandness RF --pen-noncansplice 1000000. Samtools (v1.0) (31) was used to convert the sam to bam files. After fixing mate pair with -mc parameter using samtools fixmate and sorting coordinates using samtools sort, reads were deduplicated by samtools markup. After PCR deduplication, only reads whose 5’ start are GG (for plus strand) or CC (for minus strand) are saved as potential cisplatin modified sites. R codes to extract the reads starting with GG and CC are described in Yimit et. al (32) and can be downloaded from https://github.com/yuchaojiang/damage_repair.
Assembly: hg38
Supplementary files format and content: Hi-C: mcool file that save the counts of genome-wide 2D contact map.
Supplementary files format and content: Damage-seq:bedgraph file that save the number of damage counts at particular genomic loci.

molecule: genomic DNA

tag: cell line

tag: chip antibody

value: anti-cisplatin modified DNA antibody (Abcam, #ab103261)


title: M2-110, PLCG2 Knockout, 5xFAD, 7.5Month, Cortex, male

description:
Library name: 7-5M_M2-110_P2KOHOM_5xFAD_Ctx
Column name in raw-counts.txt and normalized counts.csv: 7-5M_M2-110_P2KOHOM_5xFAD_Ctx


title: SEN.oxa.damage.24hrs.rep1


title: SEN.oxa.damage.24hrs.rep3


title: RES.oxa.damage.24hrs.rep1


title: F2-44, Trem2 Knockout, 5xFAD, 7.5Month, Cortex, female

description:
Library name: 7-5M_F2-44_T2KO_5xFAD_Ctx
Column name in raw-counts.txt and normalized counts.csv: 7-5M_F2-44_T2KO_5xFAD_Ctx

value: Trem2 Knockout


title: RES.oxa.damage.24hrs.rep3


title: SK-3-DMSOcontrol

city: Gainesville

first: Alberto

last: Riva

state: FL

address: 2033 Mowry Rd

department: ICBR

institute: University of Florida

data_processing:
Reads acquired from the Illumina NovaSeq 6000 platform were cleaned up with the trimmomatic program to trim off sequencing adaptors and low-quality bases with a quality phred-like score <20. Reads <50 bases were excluded from RNA-seq analysis.
The cleaned reads of each sample were mapped to the reference sequence using the STAR read mapper (Spliced Transcripts Alignment to a Reference, v2.7.9a) (Dobin et al., 2013).
The mapping results were processed with RSEM, samtools, and scripts developed in house at UF ICBR to count uniquely mapped reads for gene expression analysis.
Differential gene expression analysis was performed with a DESeq2-based R pipeline to identify genes showing significant differential expression.
Assembly: GRCh38
Supplementary files format and content: Raw counts table
Supplementary files format and content: Fold change and P-values for all genes in the Tumonolide vs DMSO comparison.

source_name: Large intestine; Colon

growth_protocol: DMEM plus 10% FBS in a humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 250 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEB Ultra II Directional RNA-seq library preparation kit for Illumina according to manufacturer's protocol

treatment_protocol: compound or vehicle control (0.5% DMSO) for 12 h after overnight seeding

value: Large intestine; Colon

value: colorectal carcinoma

value: wt

tag: treatment

value: 0.5% DMSO


title: SEN.oxa.damage.3hrs.rep1


title: SEN.oxa.damage.3hrs.rep2


title: RES.oxa.damage.3hrs.rep3


title: M3-45, Trem2 Knockout, 5xFAD, 7.5Month, Cortex, male

description:
Library name: 7-5M_M3-45_T2KO_5xFAD_Ctx
Column name in raw-counts.txt and normalized counts.csv: 7-5M_M3-45_T2KO_5xFAD_Ctx


title: RES.oxa.damage.24hrs.rep2


title: M2-41, Trem2 Knockout, 5xFAD, 7.5Month, Cortex, male

description:
Library name: 7-5M_M2-41_T2KO_5xFAD_Ctx
Column name in raw-counts.txt and normalized counts.csv: 7-5M_M2-41_T2KO_5xFAD_Ctx


title: RES.oxa.damage.3hrs.rep2


title: F1-42, Trem2 Knockout, 5xFAD, 7.5Month, Cortex, female

description:
Library name: 7-5M_F1-42_T2KO_5xFAD_Ctx
Column name in raw-counts.txt and normalized counts.csv: 7-5M_F1-42_T2KO_5xFAD_Ctx


title: M1-40, Trem2 Knockout, 5xFAD, 7.5Month, Cortex, male

description:
Library name: 7-5M_M1-40_T2KO_5xFAD_Ctx
Column name in raw-counts.txt and normalized counts.csv: 7-5M_M1-40_T2KO_5xFAD_Ctx


title: F2-1189, WT, 5xFAD, 7.5Month, Cortex, female

description:
Library name: 7-5M_F2-1189_WT_5xFAD_Ctx
Column name in raw-counts.txt and normalized counts.csv: 7-5M_F2-1189_WT_5xFAD_Ctx

value: WT


title: F3-1190, WT, 5xFAD, 7.5Month, Cortex, female

description:
Library name: 7-5M_F3-1190_WT_5xFAD_Ctx
Column name in raw-counts.txt and normalized counts.csv: 7-5M_F3-1190_WT_5xFAD_Ctx


title: Invitro.oxa.damage.15min.rep3


title: RES.oxa.damage.3hrs.rep1


title: F1-1180, WT, 5xFAD, 7.5Month, Cortex, female

description:
Library name: 7-5M_F1-1180_WT_5xFAD_Ctx
Column name in raw-counts.txt and normalized counts.csv: 7-5M_F1-1180_WT_5xFAD_Ctx


title: Invitro.oxa.damage.15min.rep2


title: Invitro.oxa.damage.15min.rep1


title: M2-1181, WT, 5xFAD, 7.5Month, Cortex, male

description:
Library name: 7-5M_M2-1181_WT_5xFAD_Ctx
Column name in raw-counts.txt and normalized counts.csv: 7-5M_M2-1181_WT_5xFAD_Ctx


title: M3-130, PLCG2 Knockout, 5xFAD, 7.5Month, Cortex, male

description:
Library name: 7-5M_M3-130_P2KOHOM_5xFAD_Ctx
Column name in raw-counts.txt and normalized counts.csv: 7-5M_M3-130_P2KOHOM_5xFAD_Ctx


title: LGE,  Latently infected cells with uninfected bystanders, GEX

city: New York City

first: Benjamin

last: Chen

state: New York

address: 1468 Madison Avenue

department: Infectious Disease

institute: Icahn School of Medicine at Mount Sinai

description:
10x Genomics
Sample2_GEX

data_processing:
Raw read data were demultiplexed, aligned and preliminarily analyzed by 10X Cell Ranger Count (v6.1.2) using default parameters. In order to identify HIV sequences, pHR_SIN_CS(RG)W and CreI_11036 sequences were added to 10X's standard  human and mouse reference (refdata-gex-GRCh38-and-mm10-2020-A) with annotations for SFFV/dsRed/EGFP/WPRE regions on pHR SIN_CS(RG)W and six regions on CreI_11036 based on HIV splice donor and acceptors (Leon-Rivera, Morsey et al. 2020). Each region is annotated as a gene for Cell Ranger to call its UMIs individually.  These reads then underwent an additional quality control (QC) filtering process, which included the removal of adapter sequences, read trimming and mapping to the genome within the Cell Ranger interface or with custom STAR alignment tools. Results were viewed using the Loupe Cell Browser.
10xGenomics CellRanger (v.6.21.) https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_in
Seurat v4.3 (https://satijalab.org/seurat/)
Assembly: GRCh38 and mm10
Supplementary files format and content: CellRanger output files (HTO): barcodes.tsv, features.tsv, matrix.mtx
Supplementary files format and content: CellRanger output files (RNA): barcodes.tsv, features.tsv, matrix.mtx

source_name: CD4+ T-cells

growth_protocol: PBMCs were isolated from buffy coats obtained from the New York Blood Center by ficoll gradient centrifugation followed by isolation of CD4+T cell by magnetic bead separation (Miltenyi). Primary CD4+T cells were activated by co-culturing with irradiated feeder PBMCS in the presence of phytohaemagglutinin (PHA; 2 μg/ml, Sigma) and IL-2 (50 IU/ml, Roche) for 48-72 hours. Activated cells were spinoculated with pHRSIN CS(RG)W virus and after 48 hours, infected with CreI virus. 48-72 hours post infection cells were analyzed by flow cytometry.

extract_protocol:
The sorted cells were counted after trypan blue staining for estimating the proportion of viable cells and introduced into the 10X Genomics Chromium platform workflow for high throughput scRNAseq library preparation (V2 3’ GEX assay). For sequencing, batched libraries were run on an Illumina NovaSeq S4 flowcell (2 x 100 nt paired-end read length) with a target of 50,000-100,000 reads per cell.
FACS sorting followed by Genomics Chromium Next GEM Single Cell 3’ Reagent Kits v.3.1 (CG000204 Rev D) protocol

value: CD4+ T-cells

tag: library type

value: mRNA


title: M1-62, PLCG2 Knockout, 5xFAD, 7.5Month, Cortex, male

description:
Library name: 7-5M_M1-62_P2KOHOM_5xFAD_Ctx
Column name in raw-counts.txt and normalized counts.csv: 7-5M_M1-62_P2KOHOM_5xFAD_Ctx


title: F3-46, Trem2 Knockout, 5xFAD, 7.5Month, Cortex, female

description:
Library name: 7-5M_F3-46_T2KO_5xFAD_Ctx
Column name in raw-counts.txt and normalized counts.csv: 7-5M_F3-46_T2KO_5xFAD_Ctx


title: M1-1177, WT, 5xFAD, 7.5Month, Cortex, male

description:
Library name: 7-5M_M1-1177_WT_5xFAD_Ctx
Column name in raw-counts.txt and normalized counts.csv: 7-5M_M1-1177_WT_5xFAD_Ctx


title: E6_S46_Th17n_Methanol_Div.1

city: Berkeley

first: Allon

last: Wagner

state: CA

address: 378 Stanley Hall

institute: UC Berkeley

description: Library name: E6_S46_R1_combined

data_processing:
Reads were trimmed with Trimmomatic and pseudoaligned with Kallisto to generate a TPM matrix.
Assembly: mm10
Supplementary files format and content: csv file containing a table of TPM expression values

molecule: polyA RNA

growth_protocol: T cells were pre-labeled with carboxyfluorescein succinimidyl ester (CFSE) prior to culture and cell division is determined by the intensity of CFSE labeling using flow cytometry. Each division will half the CFSE intensity. Two samples were generated for each condition: without sorting (Total) and cells that have gone exactly one division (Div.1).

extract_protocol:
Cultured cells were lysed in RLT buffer and subjected to RNA extraction (Qiagen)
Illumina
polyA tail capture

tag: divisions

value: Methanol


title: ACM, Actively infected Cells with uninfected bystanders, HTO

description:
10x Genomics
Sample1_HTO

library_source: other

molecule: protein

value: HTO


title: H7_S77_Th17n_DHEA_Total

description: Library name: H7_S77_R1_combined

value: Total

value: DHEA


title: LNCaP95_mouse liver metastasis-gHoxB13-3

city: Durham

first: Qianben

address: 905 S. Lasalle Street

institute: Duke University

description: LNCaP95 metastasis_all genes

data_processing:
RNA-seq quality control was performed by Trim Galore
Raw RNA-seq reads were mapped to human hg19 or hg38 genome by HISAT2
The expression counts were computed by htseq-count or featureCounts
The Differentially Expressed Genes were identified by DESeq2
Assembly: hg19 for RNA-seq analysis in 293FT cells; hg38 for RNA-seq analysis in LNCaP95 mouse liver metastasis
Supplementary files format and content: Tab-delimited text file contains raw/normalized counts for each sample

source_name: mouse liver metastasis

extract_protocol:
RNeasy Mini Kit from Qiagen following manufacturer's instructions
Libraries were prepared with NEBNext®Ultra™II Directional RNA Library Prep Kit for Illumina following manufacturer's instructions

value: mouse liver metastasis

value: HoxB13 knockdown

value: LNP treatment


title: LNCaP95_mouse liver metastasis-gHoxB13-1

description: LNCaP95 metastasis_all genes


title: G9_S69_Th17n_DHEA_Div.1

description: Library name: G9_S69_R1_combined


title: LNCaP95_mouse liver metastasis-gCtrl-2

description: LNCaP95 metastasis_all genes


title: H2_S72_Th17n_EGCG_Total

description: Library name: H2_S72_R1_combined

value: EGCG


title: M3-1182, WT, 5xFAD, 7.5Month, Cortex, male

description:
Library name: 7-5M_M3-1182_WT_5xFAD_Ctx
Column name in raw-counts.txt and normalized counts.csv: 7-5M_M3-1182_WT_5xFAD_Ctx

value: Cortex


title: LNCaP95_mouse liver metastasis-gCtrl-3

description: LNCaP95 metastasis_all genes


title: C4_S24_Th17p_EGCG_Div.1

description: Library name: C4_S24_R1_combined


title: A5_S5_Th17p_DMSO_Div.1

description: Library name: A5_S5_R1_combined

value: DMSO


title: B4_S14_Th17p_DMSO_Total

description: Library name: B4_S14_R1_combined


title: 293FT_gHoxB13_rep3 24h

description: 293FT_all genes

value: human embryonal kidney cells

value: HoxB13 knockdown cells

value: transfection


title: D3_S33_Th17p_EGCG_Total

description: Library name: D3_S33_R1_combined


title: A4_S4_Th17n_DMSO_Div.1

description: Library name: A4_S4_R1_combined


title: 293FT_gHoxB13_rep1 24h

description: 293FT_all genes


title: ACE, Actively infected Cells with uninfected bystanders, GEX

description:
10x Genomics
Sample1_GEX


title: 293FT_gCtrl_rep4 24h

description: 293FT_all genes

value: Control cells


title: G3_S63_Th17n_EGCG_Div.1

description: Library name: G3_S63_R1_combined


title: 293FT_gCtrl_rep3 24h

description: 293FT_all genes


title: D9_S39_Th17p_DHEA_Total

description: Library name: D9_S39_R1_combined


title: F9_S59_Th17n_Methanol_Total

description: Library name: F9_S59_R1_combined


title: F6_S56_Th17n_Methanol_Total

description: Library name: F6_S56_R1_combined


title: E3_S43_Th17n_DMSO_Div.1

description: Library name: E3_S43_R1_combined


title: LNCaP95_mouse liver metastasis-gHoxB13-2

description: LNCaP95 metastasis_all genes


title: G6_S66_Th17n_DHEA_Div.1

description: Library name: G6_S66_R1_combined


title: Pool_IP_4

city: CAMBRIDGE

first: Nicholas

last: Haradhvala

state: MA

address: 75 Ames St

institute: Broad Institute

data_processing:
cellranger count v6.0.1
cellbender v0.2.0
souporcell v2020.7
Assembly: hg38
Supplementary files format and content: Cellranger mtx

source_name: Peripheral Blood

extract_protocol:
After resuspension in PBS with 0.04% BSA at a concentration of 1,000 cells per μl, a total of 40,000 cells were loaded onto a 10x Genomics Chromium instrument (10x Genomics) according to the manufacturer’s instructions. Using Chromium single-cell 5′ library and gel bead kit v.2, the scRNA-seq libraries were processed and coupled scTCR-seq libraries were obtained using the chromium single-cell V(D) J enrichment kit (human T cell) (10x Genomics). For the Quality control of amplified cDNA libraries and final sequencing libraries the Bioanalyzer High Sensitivity DNA Kit (Agilent) was used. ScRNA-seq and scTCR-seq libraries were both normalized to 4 nM concentration and pooled in a volume ratio of 4:1.
Libraries were contructed acording to the 10x chromium v3 gene expression protocol

value: Peripheral Blood

value: Pooled infusion products for Patient1,Patient2,Patient3,Patient4,Patient5


title: 293FT_gCtrl_rep2 24h

description: 293FT_all genes


title: C1_S21_Th17p_EGCG_Div.1

description: Library name: C1_S21_R1_combined


title: 293FT_gCtrl_rep1 24h

description: 293FT_all genes


title: 293FT_gHoxB13_rep4 24h

description: LNCaP95 metastasis_all genes


title: D6_S36_Th17p_DHEA_Total

description: Library name: D6_S36_R1_combined


title: LNCaP95_mouse liver metastasis-gCtrl-1

description: LNCaP95 metastasis_all genes

value: WT


title: B1_S11_Th17p_DMSO_Total

description: Library name: B1_S11_R1_combined


title: Patient9-CART

value: Sorted CAR+ cells for Patient9


title: 293FT_gHoxB13_rep2 24h

description: 293FT_all genes


title: Pool_IP_2

value: Pooled infusion products for Patient7,Patient8,Patient9,Patient10,Patient11


title: Pool_IP_1


title: LCM, Latently infected cells with uninfected bystanders, HTO

description:
10x Genomics
Sample2_HTO

value: CD4+ T-cells

value: HTO


title: Pool_IP_3


title: E9_S49_Th17n_Methanol_Div.1

description: Library name: E9_S49_R1_combined

value: Methanol


title: F10_S60_Th17n_Methanol_Total

description: Library name: F10_S60_R1_combined

value: Total


title: Patient5-CART

value: Sorted CAR+ cells for Patient5


title: G4_S64_Th17n_EGCG_Div.1

description: Library name: G4_S64_R1_combined

value: EGCG


title: Patient7-CART

value: Sorted CAR+ cells for Patient7


title: B3_S13_Th17p_DMSO_Total

description: Library name: B3_S13_R1_combined

value: DMSO


title: Patient8-CART

value: Sorted CAR+ cells for Patient8


title: F4_S54_Th17n_DMSO_Total

description: Library name: F4_S54_R1_combined


title: D4_S34_Th17p_EGCG_Total

description: Library name: D4_S34_R1_combined


title: Patient3-CART

value: Sorted CAR+ cells for Patient3


title: Patient4-CART

value: Sorted CAR+ cells for Patient4


title: Patient19-CART

value: Sorted CAR+ cells for Patient19


title: Patient18-CART

value: Peripheral Blood

value: Sorted CAR+ cells for Patient18


title: H8_S78_Th17n_DHEA_Total

description: Library name: H8_S78_R1_combined

value: DHEA


title: C3_S23_Th17p_EGCG_Div.1

description: Library name: C3_S23_R1_combined


title: Patient16-CART

value: Sorted CAR+ cells for Patient16


title: D1_S31_Th17p_EGCG_Total

description: Library name: D1_S31_R1_combined


title: C6_S26_Th17p_DHEA_Div.1

description: Library name: C6_S26_R1_combined


title: Patient11-CART

value: Sorted CAR+ cells for Patient11


title: G1_S61_Th17n_EGCG_Div.1

description: Library name: G1_S61_R1_combined


title: Pool_CARneg_6

value: Pooled sorted CAR-negative cells for Patient7,Patient8,Patient9,Patient10,Patient11


title: F1_S51_Th17n_DMSO_Total

description: Library name: F1_S51_R1_combined


title: A6_S6_Th17p_Methanol_Div.1

description: Library name: A6_S6_R1_combined


title: Pool_CARneg_5


title: E1_S41_Th17n_DMSO_Div.1

description: Library name: E1_S41_R1_combined


title: A10_S10_Th17p_Methanol_Div.1

description: Library name: A10_S10_R1_combined


title: Patient10-CART

value: Sorted CAR+ cells for Patient10


title: Pool_CARneg_4

value: Pooled sorted CAR-negative cells for Patient1,Patient2,Patient3,Patient4,Patient5


title: B9_S19_Th17p_Methanol_Total

description: Library name: B9_S19_R1_combined

value: Total

value: Methanol


title: Pool_CARneg_2

value: Pooled sorted CAR-negative cells for Patient16,Patient17,Patient18,Patient19


title: Pool_CARneg_3


title: C9_S29_Th17p_DHEA_Div.1

description: Library name: C9_S29_R1_combined


title: E4_S44_Th17n_DMSO_Div.1

description: Library name: E4_S44_R1_combined


title: Pool_CARneg_1


title: B6_S16_Th17p_Methanol_Total

description: Library name: B6_S16_R1_combined


title: Patient17-CART

value: Sorted CAR+ cells for Patient17


title: H5_S75_Th17n_EGCG_Total

description: Library name: H5_S75_R1_combined

value: EGCG


title: G10_S70_Th17n_DHEA_Div.1

description: Library name: G10_S70_R1_combined


title: LesionB_Dermis

first: Jennifer

middle: Yunyan

last: Zhang

state: NC

address: 3 Genome Ct, rm4130

department: Dermatology

description: Single-cell suspensions were loaded on the 10x Genomics system, and mRNA was converted to cDNA library.

data_processing:
Alignment, counting, filtering, of single cell RNA-Seq of cells from each sample , using 10X Cellranger v3.0.1 with default parameters.
Genome_build: GRCh38-3.0.0
Supplementary_files_format_and_content: raw read counts in gene-barcode matrix

source_name: Dermis

extract_protocol:
Freshly collected human skin biopsies were immediately washed with cold PBS and digested with 1X dispase (Thermo Fisher Scientific) overnight at 4 °C. The epidermis and the dermis were separated from each other using forceps and then digested at 37 °C with 0.25% trypsin/EDTA. Digestion efficiency was monitored every 5 minutes by microscopic examination of cell counts in solution. The epidermal and dermal cell suspensions were passed through 70 µm and then 40 µm cell strainers, precipitated via centrifugation at 300 g centrifugal force for 5 minutes, washed, and suspended in cold 0.4%BSA in keratinocyte serum free media (Thermo Fisher Scientific).
Single-cell suspensions were loaded on the 10x Genomics system, and mRNA was converted to cDNA library using 10x 3’ scRNAseq kit, v3 and S1 flow cell with reads 28x8x91

value: Dermal cell-enriched skin cells

tag: disease state

value: graft-versus-host disease (GVHD)


title: Normal_Dermis

value: Epidermal cell-enriched skin cells

value: control


title: H4_S74_Th17n_EGCG_Total

description: Library name: H4_S74_R1_combined


title: Patient1-CART

value: Peripheral Blood

value: Sorted CAR+ cells for Patient1


title: A9_S9_Th17p_Methanol_Div.1

description: Library name: A9_S9_R1_combined


title: A7_S7_Th17p_Methanol_Div.1

description: Library name: A7_S7_R1_combined


title: Normal_Epi

source_name: Epidermis


title: LesionB_Epi


title: A3_S3_Th17p_DMSO_Div.1

description: Library name: A3_S3_R1_combined

value: DMSO


title: H10_S80_Th17n_DHEA_Total

description: Library name: H10_S80_R1_combined

value: DHEA


title: H1_S71_Th17n_EGCG_Total

description: Library name: H1_S71_R1_combined


title: Lesion A1

data_processing:
Alignment, counting, filtering, of single cell RNA-Seq of LesionA1  and LesionA2 Epidermal cells , using 10X Cellranger v3.0.1 with default parameters.
Genome_build: GRCh38-3.0.0
Supplementary_files_format_and_content: Cellranger output files (raw read counts in gene-barcode matrix)

extract_protocol:
Freshly collected human skin biopsies were immediately washed with cold PBS and digested with 1X dispase (Thermo Fisher Scientific) overnight at 4 °C. The epidermis was separated from the dermis, and then digested with 0.25% trypsin/EDTA for 20-30 minutes with frequent monitoring. Cell suspensions were passed through 70 µm and then 40 µm cell strainers, precipitated via centrifugation at 300g force, washed, and suspended in 0.4%BSA in keratinocyte serum free media (Thermo Fisher Scientific).
Single-cell suspensions were loaded on the 10x Genomics system, and mRNA was converted to cDNA library using 10x 3’ scRNAseq kit, v3 and S1 flow cell with reads 28x8x91

value: Epidermis

value: cutaneous graft-versus-host disease (GVHD)


title: C8_S28_Th17p_DHEA_Div.1

description: Library name: C8_S28_R1_combined


title: CD8 T cell GFP total donor 3

city: Amsterdam

first: Kaspar

last: Bresser

address: Plesmanlaan 125

department: Hematopoeisis

country: Netherlands

institute: Sanquin

description: Library name: SONAR_27

data_processing:
Sequencing reads (read2) were trimmed using cutadapt, removing 39 5’ bases and 57 3’ bases.
Resulting sequences were aligned to the UTR library using bowtie2 in local mode (using the --very-sensitive flag).
Read counts were obtained using htseq-count
sequence motifs detected with less than 40 reads across all samples were excluded from the analysis, and individual libraries were normalized to 10,000 reads
Supplementary files format and content: read count table in tsv format

source_name: Primary CD8+ T cells

extract_protocol:
Retroviral library was produced by transfecting 4.5 ug of the library plasmid DNA into FLYRD18 retroviral packaging cells, as described above. HEK and HeLa cells were cultured to a density of 60% prior to addition of virus-containing supernatants, and subsequently expanded for 10 days. PBMCs were activated with αCD3/ αCD28 and spinfected with virus-containing supernatants, as described above, and expanded for 10 days in RPMI supplemented with 10% fetal bovine serum (FBS; Bodinco), 2 mM L-glutamine, 20 IU/mL penicillin G sodium salts, 20 μg/mL streptomycin sulfate (all Sigma Aldrich), Non-Essential Amino Acids (Gibco), Sodium pyruvate (Gibco), 50 IU/mL recombinant human (rh) IL-2 (Proleukin, Novartis), 5 ng/mL rhIL-15 (Peprotech), and 10 ng/mL rhIL7 (Miltenyi). Transduction efficiencies were kept between 5-10% in order to minimize multiple transgene integrations. After expansion cells were harvested and stained with Near-IR live/dead marker (Life Technologies) for dead cell exclusion, in addition to anti-CD8-AF700 (Biolegend) and anti-CD4-BV510 (Biolegend) in the case of the T cell assay. The top and bottom 15% GFP expressing cells, in addition to the full GFP-positive fraction, were sorted on a FACS Aria II (BD Biosciences). The sorted cells were subsequently pelleted and resuspended in 1 µl DirectPCR Lysis Reagent (Viagen) per 2,500 cells, supplemented with 0.5 mg/ml proteinase K (Viagen). The obtained lysate was incubated at 55 C for 3 hours, followed by 85 C for 45 minutes, and 95 C for 5 minutes.
An initial pre-amplification of the synthetic 3’UTRs was performed on 10 µl lysate (±50,000 cells) in a 50 µl reaction volume using the NEBnext (NEB) and 10 µM forward (5’-AAAGACCCCAACGAGAAGC-3’) and reverse (5’-AGTCTATAGCTACTAGGCG-3’) primers. An initial touchdown stage was performed dropping the annealing temperature 1°C per cycle from 58°C to 50°C (8 cycles), followed by 6 cycles at 50°C. Extension time was kept at 20 seconds. PCR products were purified using Cytiva Sera-Mag™ Select at a 1.2:1 Sera-Mag:PCR-product ratio, following manufacturers protocol. Each of these samples were subsequently used as template for a second PCR, with primers (Forward: 5’-ACACTCTTTCCCTACACGACGCTCTTCCGATCTAGACCCCAACGAGAAGCGCGATCAC-3’, Reverse: 5’-GACTGGAGTTCAGACGTGTGCTCTTCCGATCTAGTCTATAGCTACTAGGCGATA-3’) designed to amplify the product and attach partial Illumina adapters. This second PCR was performed using the NEBnext (NEB) and consisted of 10 cycles with a constant annealing temperature of 65 °C and extension time of 30 sec. Correct products (±275 base pairs) were purified using Cytiva Sera-Mag™ Select at a 1.2:1 Sera-Mag:PCR-product ratio, following manufacturers protocol. Purified products were sequenced at the genomics core facility of the Netherlands Cancer institute.

value: Primary CD8+ T cells


title: CD8 T cell GFP low donor 3

description: Library name: SONAR_26


title: Lesion A2


title: B8_S18_Th17p_Methanol_Total

description: Library name: B8_S18_R1_combined


title: CD8 T cell GFP high donor 3

description: Library name: SONAR_25


title: B7_S17_Th17p_Methanol_Total

description: Library name: B7_S17_R1_combined


title: CD8 T cell GFP total donor 2

description: Library name: SONAR_24


title: CD8 T cell GFP low donor 2

description: Library name: SONAR_23


title: C7_S27_Th17p_DHEA_Div.1

description: Library name: C7_S27_R1_combined


title: A8_S8_Th17p_Methanol_Div.1

description: Library name: A8_S8_R1_combined


title: CD8 T cell GFP high donor 2

description: Library name: SONAR_22


title: B10_S20_Th17p_Methanol_Total

description: Library name: B10_S20_R1_combined


title: CD8 T cell GFP total donor 1

description: Library name: SONAR_21


title: A2_S2_Th17p_DMSO_Div.1

description: Library name: A2_S2_R1_combined


title: CD8 T cell GFP low donor 1

description: Library name: SONAR_20


title: HEK GFP low batch 3

description: Library name: SONAR_18

source_name: Human Embryonic Kidney

value: Human Embryonic Kidney


title: B2_S12_Th17p_DMSO_Total

description: Library name: B2_S12_R1_combined

value: Total


title: HEK GFP total batch 3

description: Library name: SONAR_19


title: F5_S55_Th17n_DMSO_Total

description: Library name: F5_S55_R1_combined


title: HEK GFP total batch 2

description: Library name: SONAR_16


title: HEK GFP high batch 3

description: Library name: SONAR_17


title: C2_S22_Th17p_EGCG_Div.1

description: Library name: C2_S22_R1_combined


title: D5_S35_Th17p_EGCG_Total

description: Library name: D5_S35_R1_combined


title: HEK GFP low batch 2

description: Library name: SONAR_15


title: HEK GFP high batch 2

description: Library name: SONAR_14


title: G7_S67_Th17n_DHEA_Div.1

description: Library name: G7_S67_R1_combined


title: D7_S37_Th17p_DHEA_Total

description: Library name: D7_S37_R1_combined


title: D10_S40_Th17p_DHEA_Total

description: Library name: D10_S40_R1_combined


title: CD8 T cell GFP high donor 1

description: Library name: SONAR_11


title: HEK GFP total batch 1

description: Library name: SONAR_13


title: H9_S79_Th17n_DHEA_Total

description: Library name: H9_S79_R1_combined


title: HEK GFP high batch 1

description: Library name: SONAR_10


title: CD4 T cell GFP total donor 3

description: Library name: SONAR_9

source_name: Primary CD4+ T cells

value: Primary CD4+ T cells


title: CD4 T cell GFP low donor 3

description: Library name: SONAR_8


title: B5_S15_Th17p_DMSO_Total

description: Library name: B5_S15_R1_combined


title: G5_S65_Th17n_EGCG_Div.1

description: Library name: G5_S65_R1_combined


title: CD4 T cell GFP total donor 2

description: Library name: SONAR_6


title: F2_S52_Th17n_DMSO_Total

description: Library name: F2_S52_R1_combined


title: CD4 T cell GFP low donor 2

description: Library name: SONAR_5


title: G2_S62_Th17n_EGCG_Div.1

description: Library name: G2_S62_R1_combined


title: E2_S42_Th17n_DMSO_Div.1

description: Library name: E2_S42_R1_combined


title: HEK GFP low batch 1

description: Library name: SONAR_12


title: A1_S1_Th17p_DMSO_Div.1

description: Library name: A1_S1_R1_combined


title: C10_S30_Th17p_DHEA_Div.1

description: Library name: C10_S30_R1_combined


title: E8_S48_Th17n_Methanol_Div.1

description: Library name: E8_S48_R1_combined

value: Methanol


title: CD4 T cell GFP total donor 1

description: Library name: SONAR_3


title: zf_akr7a3_hom9

city: Mannheim

first: Xin

address: Ludolf-Krehl-Str. 13-17

country: Germany

institute: Medical Faculty Mannheim

description: Library name: 8522307005478

data_processing:
Raw sequence data with adapter sequences or low-quality sequences was filtered.
Filtered reads were aligned to the Zebrafish reference genome (GRCz11)
Raw counts levels were quantified using FeatureCounts (v2.0.3)
Assembly: GRCz11
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

organism: Danio rerio

source_name: eye

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit(QIAGEN), 3ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using DNBSEQ Eukaryotic Strand-specific mRNA library.

value: eye


title: H3_S73_Th17n_EGCG_Total

description: Library name: H3_S73_R1_combined

value: EGCG


title: CD4 T cell GFP low donor 1

description: Library name: SONAR_2


title: D8_S38_Th17p_DHEA_Total

description: Library name: D8_S38_R1_combined


title: C5_S25_Th17p_EGCG_Div.1

description: Library name: C5_S25_R1_combined


title: F7_S57_Th17n_Methanol_Total

description: Library name: F7_S57_R1_combined


title: E10_S50_Th17n_Methanol_Div.1

description: Library name: E10_S50_R1_combined


title: zf_akr7a3_hom8

description: Library name: 8522307005477


title: H6_S76_Th17n_DHEA_Total

description: Library name: H6_S76_R1_combined


title: E7_S47_Th17n_Methanol_Div.1

description: Library name: E7_S47_R1_combined


title: CD4 T cell GFP high donor 1

description: Library name: SONAR_1


title: zf_akr7a3_hom5

description: Library name: 8522307005475


title: zf_akr7a3_hom4

description: Library name: 8522307005474


title: zf_akr7a3_hom1

description: Library name: 8522307005473


title: F8_S58_Th17n_Methanol_Total

description: Library name: F8_S58_R1_combined


title: CD4 T cell GFP high donor 2

description: Library name: SONAR_4


title: G8_S68_Th17n_DHEA_Div.1

description: Library name: G8_S68_R1_combined


title: zf_akr7a3_wt6

description: Library name: 8522307005483


title: Th17p_25mM_Mo1

description: Library name: CW_Glu_6

data_processing:
Cellranger 3.1.0 was used to demultiplex BCL files (cellranger mkfastq), followed by UMI collapsing, barcode filtering for cell-associated barcodes, and feature counting (cellranger count), and lastly output aggregation (cellranger aggr)
Assembly: mm10
Supplementary files format and content: sparse matrix (MEX format) of UMI counts associated with a feature (row) and a barcode (column), filtered to include only cell-associated barcodes

extract_protocol:
Single cell suspension is further prepared using 10x genomics, GEM single cell expression 5' kit
10x genomics library construction kit

tag: animal id

tag: glucose concentration


title: Th17p_1mM_Mo2

description: Library name: CW_Glu_7


title: zf_akr7a3_wt4

description: Library name: 8522307005482


title: zf_akr7a3_hom7

description: Library name: 8522307005476


title: Th17p_1mM_Mo1

description: Library name: CW_Glu_5


title: zf_akr7a3_wt3

description: Library name: 8522307005481


title: zf_akr7a3_wt2

description: Library name: 8522307005480


title: Th17p_25mM_Mo2

description: Library name: CW_Glu_8


title: zf_akr7a3_wt1

description: Library name: 8522307005479


title: Th17n_25mM_Mo2

description: Library name: CW_Glu_4


title: Exp2,iNKT (WT mouse) and PITL enriched population sorts after CD8 depletion(MHC-T), VDJ

city: Hannover

first: Ahmed

last: Hassan

address: Carl-Neuberg-Straße 1

institute: Hannover Medical School

data_processing:
Cellranger-7.0.1
Assembly: mm10-2020-A, vdj-GRCm38-alts-ensembl-7.0.0
Supplementary files format and content: Cellranger output file: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: Cellranger output file: airr_rearrangement.tsv

molecule: other

source_name: Thymus

extract_protocol:
Cell were sorted and mixed then used to generate 5’end V1.1 or V2 GEMs following 10x genomics protocol
Following the recommendation of 10x genomics

value: Thymus


title: Exp3,iNKT (WT mouse) and PITL enriched population  (MHC-T) sorts, HTO_ADT


title: Exp1,iNKT (WT mouse) and PITL enriched population sorts after CD8 depletion(MHC-T), VDJ


title: Th17n_1mM_Mo2

description: Library name: CW_Glu_3


title: Exp2,iNKT (WT mouse) and PITL enriched population sorts after CD8 depletion(MHC-T), HTO_ADT


title: Th17n_25mM_Mo1

description: Library name: CW_Glu_2


title: Exp1,iNKT (WT mouse) and PITL enriched population sorts after CD8 depletion(MHC-T), HTO_ADT


title: Exp3,iNKT (WT mouse) and PITL enriched population  (MHC-T) sorts, GEX


title: upf1_ypd_rep3_slamseq_t15

city: stockholm

first: yujie

last: zhang

address: Tomtebodavägen 23

country: Sweden

institute: Karolinska institutet

data_processing:
Base-calling was done using bcl2fastq v2.20.0.422  and for demultiplex, we allowed one mismatch in index1 and one mismatch in index2
SLAM-Seq data analysed was performed with slamdunk (v0.4.3) provided by nfcore pipeline(v1.0.0)(https://nf-co.re/slamseq). Firstly, fastq compressed files (fastq.gz) were first converted to reverse complementary reads method in order to feed into slamdunk nf core pipeline as stranded libraries were prepared with dUTP.  Adapter contamination and low-quality bases were trimmed using TrimGalore(v 0.6.4) (trim length 27bp). Slamdunk was used for mapping, quantifying nucleotide-conversions and collapsing quantifications on gene level.  At least 2 T>C conversions per read was regarded as a confident call for labelled RNA reads. Genes with less than 10 reads were filter out. SNP masking was employed to distinguish filter T>C SNPs from converted nucleotides. T > C reads counts in each library were normalized to total library read counts. To calculate RNA half-lives , T>C conversions were normalized to chase-onset (t0). Curve fitting was performed followed by non-linear decay model equations in R using the minpack.lm package.  Degradation rate is calculated as 60 * ln(2) / t1/2 (t1/2 is half-time of gene).
Assembly: Saccharomyces cerevisiae R64-1-1
Supplementary files format and content: Bedgraph files for collapsed reads for positive and negative strand. Reads were collapsed to the first 5´nucleotide.

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: S. cerevisiae (wildtype and upf1 mutant) were grown to mid exponential phase (OD600~0.6) at 30 °C with rotating using YPD (1% yeast extract, 2% peptone, 2% glucose) or  Complete Supplement Mixture (CSM from Formedium™).

extract_protocol:
Metabolic labelling of newly synthesized RNA molecules was performed as previously described [PMID: 28945705, PMID: 36838506].  Briefly, 4tU (Sigma)  was dissolved in NaOH (83 mM) used for labelling RNA molecules. The final concentration of 4tU for YPD and CSM is 5mM (PMID: 26941319) and 0.2 mM (PMID: 30192227), respectively. MES buffer (pH 5.9) with a final concentration 10 mM was prepared with media to avoid the PH change due to 4tU addition. To perform pulse and chase experiment, RNA molecules were labelled with 4tU (prepared as above) for 1h during cell grown at mid exponential phase. Cells were washed and resuspend in prewarmed medium (YPD with MES buffer or CSM with MES buffer) without  4tU and time points were collected at 0, 15 and 30 mins by centrifugation and snap frozen in liquid nitrogen immediately.
To perform thiol(SH)-linked alkylation, the reaction including 5 μg of RNA  was incubated with iodoacetamide (final concentration at 0.5 M) at 50 oC for 15 minutes [PMID: 28945705]. The reaction was stopped by adding 0.1 M DTT (final concentration at 20 mM). RNA was then precipitated by 3 M of sodium acetate and pure ethanol.  Purified RNA was subjected for ribosomal RNA depletion using RiboPools Depletion Kit (siTOOLs Biotech). Libraries were prepared by  Ultra™ II Directional RNA Library Prep Kit for Illumina® following manufacture instructions.  Sequencing was performed on Illumina Nextseq 2000 sequencer with single end read length for 150 cycles.
OTHER: SLAM seq

treatment_protocol: Pulse for 1 h and chase for 15 min

value: yeast

value: upf1delta(MATa his3delta1 leu2delta0 met15delta0 ura3delta0 upf1delta)


title: zf_akr7a3_wt7

description: Library name: 8522307005484


title: Th17n_1mM_Mo1

description: Library name: CW_Glu_1


title: upf1_ypd_rep3_slamseq_t30

treatment_protocol: Pulse for 1 h and chase for 30 min


title: Exp2,iNKT (WT mouse) and PITL enriched population sorts after CD8 depletion(MHC-T), GEX


title: Exp1,iNKT (WT mouse) and PITL enriched population sorts after CD8 depletion(MHC-T), GEX


title: Exp3,iNKT (WT mouse) and PITL enriched population  (MHC-T) sorts, VDJ


title: upf1_ypd_rep3_slamseq_t0

treatment_protocol: Pulse for 1 h and chase for 0 min


title: BAC_NonDepleted_3

city: Rochester

first: Laura

last: Calvi

address: 601 Elmwood Avenue

institute: University of Rochester

data_processing:
MultiQC v1.7
Sequence reads were processed using FastP, An ultra-fast all-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...)
Read quantification by subread-2.0.1, featurecounts
Assembly: Trimmed sequences were aligned using STAR_2.7.9a to reference genome - GRCm39 + Gencode-M27 Annotation;
Supplementary files format and content: bcltofastq-2.19.1
Supplementary files format and content: StarFeature count matrix in txt format

source_name: BAC

growth_protocol: Bone marrow and MSC mesenchymal stem cells  were maintained in alpha MEM minus ascorbic acid supplemented with 10% fetal bovin serum and antibiotics in humidified atmosphere with 5% CO2 at 37°C in hypoxic conditions,

extract_protocol:
Cells were lysed using RLT plus buffer with BME. RNA was harvested using Rneasy mini plus kit (Qiagen). 50ng of total RNA was used for the construction of sequencing libraries.
Clontech Low input

treatment_protocol: BM cells were with or without flow sorting (CD45-/Ly6C-/F4/80-/CD51+/Sca-1+). BAC were with or without magnetic depletion (CD45-/F4/80-/Ly6C-)

value: BAC

value: Bone associated stromal cell

value: WT

value: Non-Depleted


title: upf1_ypd_rep2_slamseq_t30


title: BAC_NonDepleted_2


title: BAC_NonDepleted_1


title: BAC_Depleted_3

value: Magnetic Depletion


title: 66cl4 shEya3 KD2 + IKK2-SE Biological Replicate 3

city: AURORA

first: Etienne

last: Danis

state: CO

department: Cancer Center

institute: University of Colorado, Denver - Anschutz Medical Campus

description: Library name: 66cl4_shEya3_KD2_plus_IKK2_SE_3

data_processing:
The quality of fastq files was accessed using FastQC, and MultiQC.
The Illumina adapters and low quality reads were filtered using BBDuk with the parameters for paired-end reads.
Reads were aligned and quantified using STAR against the Ensembl mouse transcriptome (genome release 96).
Ensembl IDs were mapped to gene names and counts of genes with multiple IDs were aggregated.
Assembly: mm10
Supplementary files format and content: txt

growth_protocol: 66cl4 cells were maintained in DMEM High Glucose supplemented with 10% calf serum, 1% L-glutamine, and 1% NEAAs in a humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was extracted using the RNeasy Mini Plus RNA extraction kit (Qiagen)
RNA libraries for RNA-seq were prepared using the NuGEN Universal Plus mRNA-Seq with NuQuant for bulk RNA-seq following the manufacturer's protocols

treatment_protocol: Cells were maintained in 2.5ug/ml Puromycin after shRNA transduction. Empty Vector and IKK2-SE cells were selected by expression of mCherry

value: Murine triple negative breast cancer

value: shEya3 KD2 + IKK2-SE


title: BAC_Depleted_2


title: upf1_ypd_rep2_slamseq_t15


title: BAC_Depleted_1


title: BM_NonSorted_2

source_name: BM

value: BM

value: Bone marrow stromal cell

value: Non-Sorted


title: 66cl4 shEya3 KD2 + Empty Vector Biological Replicate 3

description: Library name: 66cl4_shEya3_KD2_plus_EV_3

value: shEya3 KD2 + Empty Vector


title: upf1_ypd_rep1_slamseq_t30


title: 66cl4 shEya3 KD2 + IKK2-SE Biological Replicate 2

description: Library name: 66cl4_shEya3_KD2_plus_IKK2_SE_2


title: 66cl4 shEya3 KD2 + IKK2-SE Biological Replicate 1

description: Library name: 66cl4_shEya3_KD2_plus_IKK2_SE_1


title: BM_Sorted_3

value: Sorted


title: BM_NonSorted_1


title: 66cl4 shEya3 KD2 + Empty Vector Biological Replicate 2

description: Library name: 66cl4_shEya3_KD2_plus_EV_2


title: BM_NonSorted_3


title: upf1_ypd_rep2_slamseq_t0


title: upf1_ypd_rep1_slamseq_t0


title: BM_Sorted_2


title: BM_Sorted_1


title: Raw246.7, MSA-DA3, 24h

city: Hangzhou

first: Yani

state: Zhejiang

address: No. 268, Kaixuan Rd.

institute: Zhejiang University

description: Library name: DA3

data_processing:
Bcl2fastq (v2.20.0.422)
Cutadapt (version 1.9.1)
Hisat2 (v2.2.1)
Assembly: GRCm39.107
Supplementary files format and content: raw counts and FPKM values for each Sample

extract_protocol:
RNA was harvested using Trizol(Takara). 1.3μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seg were prepared based on Illumina/MGI sequencing platform.

value: macrophage

value: LPS pretreated

value: cultured for 24 hours on MSA-DA hydrogels


title: 66cl4 shEya3 KD2 + Empty Vector Biological Replicate 1

description: Library name: 66cl4_shEya3_KD2_plus_EV_1


title: 66cl4 SCR+Empty Vector Biological Replicate 3

description: Library name: 66cl4_SCR_plus_EV_3

value: shScramble + Empty Vector


title: Raw246.7, MSA-DA2, 24h

description: Library name: DA2


title: Raw246.7, MSA-DA1, 24h

description: Library name: DA1


title: F3_S53_Th17n_DMSO_Total

description: Library name: F3_S53_R1_combined

value: Total

value: DMSO


title: Raw246.7, MSA-ZW2, 24h

description: Library name: ZW2

value: cultured for 24 hours on MSA-ZW hydrogels


title: Raw246.7, MSA-ZW3, 24h

description: Library name: ZW3

value: WT


title: upf1_csm_rep3_slamseq_t30

value: yeast

value: upf1delta(MATa his3delta1 leu2delta0 met15delta0 ura3delta0 upf1delta)


title: 66cl4 SCR+Empty Vector Biological Replicate 1

description: Library name: 66cl4_SCR_plus_EV_1

value: Murine triple negative breast cancer


title: Raw246.7, MSA-ZW1, 24h

description: Library name: ZW1


title: upf1_csm_rep3_slamseq_t15


title: upf1_csm_rep3_slamseq_t0


title: Lung-d14-Smad4ON_m4

city: New York

first: Yu-Jui

last: Ho

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

description: single-end sequencing

data_processing:
Illumina read quality was checked for each sample using FastQC v0.11.5.
Raw fastq files were analyzed by removing adaptor sequences using Trimmomatic (0.36), aligned to the mouse genome using STAR (2.5.3a), and quantified transcript counts using featureCounts (1.6.3).
Assembly: Reads were aligned to the mouse transcriptome (mm10, GRCm38.91)
Supplementary files format and content: Tab-delimited text file includes raw count table for each sample

source_name: PDAC Lung Metastasis

growth_protocol: For pancreatic tumors, mouse hosts were placed on doxycycline chow 5-7 days before transplantation. Mice were anesthetized and a survival surgery was performed to expose the pancreas. 1 x 10^5 tumor-derived cells were resuspended in 25 uL 1:1 DMEM (Gibco) : Matrigel (Corning) mix and injected in the tail of the pancreas of each mouse. For liver metastasis assays, mice were anesthetized and a survival surgery was performed to expose the spleen. 4 x 10^5 tumor-derived cells resuspended in 20 uL PBS were injected in the splenic parenchyma of each mouse, followed by removal of the spleen and cauterization (splenectomy). For lung metastasis assays, mice were restrained, and 2.5 x 10^5 tumor-derived cells resuspended in 250 uL PBS were injected in the tail vein of each mouse.

extract_protocol:
Total RNA was extracted using Trizol Total RNA was isolated using TRIzol LS (Thermo Fisher Scientific # 10296028) followed by column clean-up using an RNeasy kit (Qiagen #74106). the RNeasy Mini Kit (Qiagen)
100-500 ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA HT Kit, Illumina #20020595), with 15 cycles of PCR.
Samples were barcoded and run on a HiSeq (Illumina) in a 75-bp SE run, with an average of 50 million reads per sample.

treatment_protocol: Mouse hosts were fed Doxycycline chow. Where applicable, doxycycline withdrawal was done at 4 (pancreas), 5 (liver) or 6 weeks (lungs) post-injection by switching the food source to regular chow.

value: PDAC lung metastasis cells

tag: time

value: day 14


title: 66cl4 shEya3 KD2 Biological Replicate 3

description: Library name: 66c14_shEya3_KD2_3

treatment_protocol: Cells were maintained in 2.5ug/ml Puromycin after shRNA transduction

value: shEya3 KD2


title: Lung-d14-Smad4ON_m3

description: single-end sequencing


title: Lung-d14-Smad4ON_m2

description: single-end sequencing


title: 66cl4 shEya3 KD2 Biological Replicate 2

description: Library name: 66c14_shEya3_KD2_2


title: upf1_ypd_rep1_slamseq_t15


title: upf1_csm_rep2_slamseq_t30


title: Lung-d14-Smad4OFF_m4

description: single-end sequencing


title: Lung-d14-Smad4OFF_m3

description: single-end sequencing


title: upf1_csm_rep2_slamseq_t15


title: upf1_csm_rep2_slamseq_t0


title: Lung-d14-Smad4OFF_m2

description: single-end sequencing


title: Lung-d14-Smad4OFF_m1

description: single-end sequencing


title: 66cl4 shEya3 KD1 Biological Replicate 3

description: Library name: 66c14_shEya3_KD1_3

value: shEya3 KD1


title: Lung-d14-Smad4ON_m1

description: single-end sequencing


title: Liv-d14-Smad4ON_m3

description: single-end sequencing

source_name: PDAC Liver Metastasis

value: PDAC liver metastasis cells


title: upf1_csm_rep1_slamseq_t30


title: 66cl4 SCR+Empty Vector Biological Replicate 2

description: Library name: 66cl4_SCR_plus_EV_2


title: Liv-d14-Smad4ON_m2

description: single-end sequencing


title: 66cl4 shEya3 KD1 Biological Replicate 2

description: Library name: 66c14_shEya3_KD1_2


title: Liv-d14-Smad4ON_m1

description: single-end sequencing


title: 66cl4 shEya3 KD1 Biological Replicate 1

description: Library name: 66c14_shEya3_KD1_1


title: Liv-d14-Smad4OFF_m2

description: single-end sequencing


title: upf1_csm_rep1_slamseq_t15


title: upf1_csm_rep1_slamseq_t0


title: Liv-d14-Smad4OFF_m3

description: single-end sequencing


title: 66cl4 SCR Biological Replicate 2

description: Library name: 66c14_shScramble_2

value: shScramble


title: 66cl4 shEya3 KD2 Biological Replicate 1

description: Library name: 66c14_shEya3_KD2_1


title: by_ypd_rep3_slamseq_t15

value: BY4741(MATa his3delta1 leu2delta0 met15delta0 ura3delta0)


title: Panc-d14-Smad4ON_m2

description: single-end sequencing

source_name: PDAC Primary Tumor

value: PDAC primary tumor cells


title: Panc-d14-Smad4ON_m1

description: single-end sequencing


title: Panc-d14-Smad4ON_m3

description: single-end sequencing


title: 66cl4 SCR Biological Replicate 1

description: Library name: 66c14_shScramble_1


title: by_ypd_rep3_slamseq_t0


title: Lung-d7-Smad4ON_m2

description: single-end sequencing

value: day 7


title: Panc-d14-Smad4OFF_m1

description: single-end sequencing


title: Panc-d14-Smad4OFF_m2

description: single-end sequencing


title: by_ypd_rep2_slamseq_t30


title: laczc9

city: Halle

first: Razif

last: Gabdoulline

state: Sachsen-Anhalt

address: Ernst-Grube-Straße 40

department: Innere Medizin IV Haematologie und Onkologie

institute: Universitätsklinikum Halle

data_processing:
Sequencing quality check with FastQC (passed)
Alignment with STAR version 2.5.2b
Feature count/Read summarisation with Rsubread on Mouse_gencode_M22.gtf
Zero count features removed; other than protein_coding features removed
Fragments Per Kilobase of transcript per Million mapped reads (FPKM)
Assembly: mm10
Supplementary files format and content: Excel worksheet with gene expression values (FPKM) on columns for all samples

source_name: C57BL/6 cells

growth_protocol: mouse bone marrow cells were grown in vitro in Dubelcco's media supplemented with 15% FCS.

extract_protocol:
Rneasy mini kit (Qiagen)
Illumina

treatment_protocol: Cells were stimulated for 48 hours in Dulbecco’s modified Eagle medium (DMEM) (STEM cell Technologies, Cologne, Germany) supplemented with 15% fetal bovine serum (FBS) (Sigma-Aldrich, Munich, Germany), 10 ng/mL human interleukin-6 (hIL-6), 6 ng/mL murine interleukin-3 (mIL-3), and 20 ng/mL murine stem cell factor (mSCF; all from PeproTech, Hamburg, Germany).

value: mouse bone marrow

value: NUP98:NSD1 Clec12a wt

value: Control


title: Lung-d7-Smad4OFF_m4

description: single-end sequencing


title: by_ypd_rep2_slamseq_t15


title: laczc8


title: Lung-d7-Smad4ON_m1

description: single-end sequencing


title: Lung-d7-Smad4OFF_m3

description: single-end sequencing


title: Lung-d7-Smad4OFF_m2

description: single-end sequencing


title: 66cl4 SCR Biological Replicate 3

description: Library name: 66c14_shScramble_3


title: by_ypd_rep2_slamseq_t0


title: by_ypd_rep3_slamseq_t30


title: Liv-d14-Smad4OFF_m1

description: single-end sequencing


title: Liv-d7-Smad4ON_m3

description: single-end sequencing


title: laczc6


title: Lung-d7-Smad4OFF_m1

description: single-end sequencing


title: by_ypd_rep1_slamseq_t30


title: CT44C4

value: NUP98:NSD1 Clec12a knockout

value: Clec12a knockout


title: Liv-d7-Smad4ON_m1

description: single-end sequencing


title: CT44C1


title: Liv-d7-Smad4OFF_m2

description: paired-end sequencing


title: Liv-d7-Smad4OFF_m1

description: single-end sequencing


title: by_ypd_rep1_slamseq_t0

value: yeast


title: Panc-d7-Smad4ON_m1

description: single-end sequencing


title: syy-6

first: Shuowang

address: Yuhang Tang Street No.866

data_processing:
The libraries were sequenced on an Illumina NovaSeq 6000 platform, generating 150 bp paired-end reads. Approximately 40M raw reads for each sample were produced. The raw reads in FASTQ format were first processed using fastp to remove low-quality reads, thereby obtaining the clean reads. Subsequently, approximately 40 clean reads for each sample were retained for further analyses. These clean reads were then mapped to the reference genome using HISAT2. The FPKM (Fragments Per Kilobase of transcript per Million mapped reads) of each gene was calculated, and the read counts of each gene were obtained by HTSeq-count. PCA (Principal Component Analysis) was performed using R (v 3.2.0) to evaluate the biological duplication of the samples.
Differential expression analysis was performed using DESeq2. Q value < 0.05 and a fold change > 2 or < 0.5 were set as the thresholds for identifying significantly differentially expressed genes (DEGs). Hierarchical cluster analysis of DEGs was conducted using R (v 3.2.0) to illustrate the expression patterns of genes across different groups and samples. Additionally, a radar map of the top 30 genes was generated using the R package ggradar to visualize the expression levels of up-regulated and down-regulated DEGs.
Based on the hypergeometric distribution, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, Reactome, and WikiPathways enrichment analyses of differentially expressed genes (DEGs) were performed to identify significantly enriched terms using R (v 3.2.0). R (v 3.2.0) was also utilized to generate column diagrams, chord diagrams, and bubble diagrams to visualize the significantly enriched terms.
Gene Set Enrichment Analysis (GSEA) was performed using GSEA software. A predefined gene set was used, and the genes were ranked based on the degree of differential expression between the two types of samples. The analysis then tested whether the predefined gene set was significantly enriched at the top or bottom of the ranking list.
Assembly: GRCm39
Supplementary files format and content: txt format inculde the FPKM and row gene counts for each sample

source_name: CD4+T cell

extract_protocol:
Total RNA was extracted using TRIzol reagent (9109, TaKaRa, Kusatsu, Shiga, Japan) and reverse transcribed into cDNA using a cDNA synthesis kit (RR047A, TaKaRa) according to the manufacturer’s instructions.
RNA purity and quantification were assessed using a NanoDrop 2000 Spectrophotometer (Thermo Scientific, USA), while RNA integrity was evaluated with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The transcriptome library was constructed following the manufacturer's instructions using the VAHTS Universal V5 RNA-seq Library Prep Kit.

value: CD4+T cell


title: by_csm_rep3_slamseq_t30


title: Panc-d7-Smad4OFF_m3

description: single-end sequencing


title: syy-5


title: Panc-d7-Smad4OFF_m2

description: single-end sequencing


title: by_csm_rep3_slamseq_t15


title: Panc-d7-Smad4OFF_m1

description: single-end sequencing


title: CT44C5


title: syy-4


title: Lung-Smad4ON_m1

description: paired-end sequencing

data_processing:
Illumina read quality was checked for each sample using FastQC v0.11.5.
FASTQ files were trimmed with trimGalore and cutadapt (PMID: 28715235), and the filtered, pair-ended reads were aligned to mm10 with Bowtie2 (PMID: 22388286).
Peaks were called over input using MACS2 (PMID: 18798982), and only peaks with ap-value of ≤ 0.001 and outside the ENCODE blacklist region were kept. All peaks from all samples were merged by combining peaks within 500 bp of each.
featureCounts (PMID: 24227677)was used to count the mapped reads for each sample. The resulting peak atlas was normalized using DESeq2 (PMID: 25516281). For comparison to DepthNorm, samples were normalized to 10 million mapped reads. Normalized bigWig files were created using the normalization factors from DESeq2 as previously described (PMID: 30429377)and BEDTools genomeCoverageBed (PMID: 20110278). Dynamic ATAC peaks were called if they had an absolute log2-transformed fold change≥0.58 and FDR≤0.1.
Assembly: Reads were aligned to the mouse genome (mm10, GRCm38.91)
Supplementary files format and content: Tab-delimited text file includes raw count table for each sample

extract_protocol:
A total of 60,000 mKate2+cells were isolated by FACS, washed once with 50 μl cold PBS and resuspended in 50 μl cold lysis buffer. Cells were then centrifuged immediately for 10 min at 500gat 4°C, and the pellet of nuclei was subjected to transposition with Nextera Tn5 transposase (Illumina #FC-121–1030) for 30 min at 37°C, according to the manufacturer’s instructions. DNA was eluted using a DNA Clean & Concentrator Kit in 21 μl elution buffer (Zymo Research #D4013).
ATAC-seq libraries were prepared using the NEBNext High-Fidelity 2X PCR Master Mix (NEB M0541) as previously described (PMID: 25559105). Purified libraries were assessed using a Bioanalyzer High-Sensitivity DNA Analysis kit (Agilent).
Approximately 50 million paired-end 150-bp reads (25 million each side) were sequenced per replicate on a HiSeq instrument (Illumina).


title: syy-3


title: Lung-Smad4ON_m2

description: paired-end sequencing


title: by_csm_rep3_slamseq_t0


title: Liv-d7-Smad4ON_m2

description: single-end sequencing


title: Lung-Smad4ON_m3

description: paired-end sequencing


title: by_csm_rep2_slamseq_t30


title: Lung-Smad4OFF_m3

description: paired-end sequencing


title: syy-2


title: Lung-Smad4OFF_m2

description: paired-end sequencing


title: by_csm_rep2_slamseq_t15


title: Lung-Smad4OFF_m1

description: paired-end sequencing


title: by_ypd_rep1_slamseq_t15


title: Panc-d7-Smad4ON_m2

description: single-end sequencing


title: by_csm_rep2_slamseq_t0


title: Liv-Smad4ON_m1

description: paired-end sequencing


title: Sora_3

source_name: Th9 cell

value: Th9 cell


title: Liv-Smad4OFF_m2

description: paired-end sequencing


title: by_csm_rep1_slamseq_t30


title: Sora_2


title: Panc-Smad4ON_m3

description: paired-end sequencing


title: CD4 T cell GFP high donor 3

description: Library name: SONAR_7

value: Primary CD4+ T cells


title: Panc-Smad4ON_m2

description: paired-end sequencing


title: Panc-Smad4ON_m1

description: paired-end sequencing


title: Ctrl_3


title: D2_S32_Th17p_EGCG_Total

description: Library name: D2_S32_R1_combined

data_processing:
Reads were trimmed with Trimmomatic and pseudoaligned with Kallisto to generate a TPM matrix.
Assembly: mm10
Supplementary files format and content: csv file containing a table of TPM expression values

extract_protocol:
Cultured cells were lysed in RLT buffer and subjected to RNA extraction (Qiagen)
Illumina
polyA tail capture

value: Total

value: EGCG


title: by_csm_rep1_slamseq_t0


title: Sora_1


title: Panc-Smad4OFF_m3

description: paired-end sequencing


title: BY-CSM_Riboseq_rep3

data_processing:
Base-calling was done using bcl2fastq v2.20.0.422  and for demultiplex, we allowed one mismatch in index1 and one mismatch in index2
Ribosome profiling data were trimmed adapter using cutadapt by the following parameters : -a TGGAATTCTCGGGTGCCAAGG. To keep the minimum length, the cutoff set to 10 nt. After that the 4-nt random barcodes from both 5´ and 3’ ends of reads were extracted as UMIs. Ribo-seq reads and RNA seq reads were selected at 28-32 nt and 20-70 nt , respectively. Reads were mapped to reference genome (SGD R64-1-1 f) using star/2.7.0. Analysis of 5´ ends positions was performed using Fivepseq package as described above. The distribution of frames with respect to the size of the ribosome-protected fragments were determined using the riboSeqR package in R (v4.0.4).
Assembly: Saccharomyces cerevisiae R64-1-1
Supplementary files format and content: Bedgraph files for  collapsed reads for positive and negative strand. Reads were collapsed to the first 5´nucleotide.

growth_protocol: Yeast overnight cultures were diluted at 0.05 of OD600 of 0.05 in 1000 ml CSM medium ( 6.7g  YNB (without amino acid) and ammonium sulfate, 2% glucose,  1x Complete Supplement Mixture from Formedium) and grown at 30 °C. All cells were collected by vacuum filtration and freezing by liquid nitrogen.

extract_protocol:
To prepare lysate for ribosome profiling,  200 µl glass beads and 500 µl of freshly prepared lysis buffer (composed of 20 mM Tris pH 8.0, 140 mM KCl, 1.5 mM MgCl2, 1% Triton X-100, 0.1 mg/mL cycloheximide, 2 mM DTT, and an EDTA-free protease inhibitor tablet) were added. The cells were pulverized by vortexing using a Multimixer for 2 minutes, followed by a 5-minute incubation on ice. This process was repeated three times to maximize the yield of RNA. After adding an additional 200 µl of lysis buffer to compensate for volume loss, the lysate was then centrifuged at 3000 g for 5 minutes at 4°C. After quantifying RNA concentration, per 200 µg RNA was incubated with 2 µl 100 U/µl RNase I (Ambion) for 1 h at 22 °C with gentle agitation (700 rpm) and the reaction was inhibited by the addition of 15 µl SuperaseIn (Thermo Fisher).   To perform polysome profiling,  another 50 µg RNA from the lysate was kept on ice undigested for the usage. Linear sucrose gradient centrifugation and fractionation were then performed as described previously [PMID: 24893926], except we modified the 10X sucrose gradient buffer (consisting of 0.5 M Tris-Acetate pH 7.0, 0.5 M NH4Cl, and 0.12 M MgCl2) to make it suitable for yeast cells.   Total RNA was isolated by the standard phenol: chloroform method as described in Zhang & Pelechano, 2021 (PMID:35474692) .
RNA footprints were isolated at 20-35 nucleotide size using 15% TBE-urea gel. In order to further ligate 3’ adapter and 5’adapter, RNA samples were treated with PNK to obtain 5’ phosphorated and 3’ hydroxylated ends, followed by ribosomal RNA depletion by using the RiboPools Depletion Kit (siTOOLs Biotech). Small RNA library was prepared by Small RNA Sample Preparation Kit for NEXTFLEX® following manufacture instructions. Sequencing was performed with single end setting, read length 47 bp on Illumina Nextseq 2000 sequencer.
OTHER: Ribo-seq

treatment_protocol: Cells were collected at exponential phase after growing at CSM for overnight


title: Panc-Smad4OFF_m2

description: paired-end sequencing


title: by_csm_rep1_slamseq_t15


title: Panc-Smad4OFF_m1

description: paired-end sequencing


title: 4DNEXPTYCQQ1, H. sapiens - K562, condition2 - conditionE - anti-SON, B1 T1

city: Boston

last: DCIC

address: 10 Shattuck St

institute: 4D Nucleome - Data Coordination and Integration Center

description:
TSA-seq in K562 (H. sapiens), condition2 - conditionE - anti-SON, Biological replicate 1, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXPTYCQQ1/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBS92SO65R/, Results include counts in BigWig (.bw) format.
4DNEXPTYCQQ1

data_processing:
For detecting SON TSA-seq Type I and Type II peaks, the SON TSA-seq score (25 kb bins) first was smoothed using locally weighted regression (LOESS). Next, a local maximum filter with window size (w) was applied, which recorded the maximum SON TSA-seq score within this window for each genomic locus. Then the data after the maximum filter were subtracted from the original smoothed data. Peaks were retained only if they showed a reduction in value, which indicates true local peaks. A parameter optimization procedure was conducted in order to maximize the peak agreement between two SON TSA-seq replicates. As a result, a smoothing factor (span=0.005) and a window size (w=50) were selected. To distinguish local peaks into Type I and Type II, we overlapped them with Hi-C subcompartments (Rao et. al, 2014). Genomic loci overlapping A1 subcompartments were classified as Type I peaks, while those overlapping A2/B1 were designated as Type II peaks.
Assembly: GRCh38
Supplementary files format and content: Counts in BigWig (.bw) format

extract_protocol:
H1, HCT116, and HFF cells were cultured according to standard operation protocols established by the NIH 4D Nucleome Consortium (https://www.4dnucleome.org/cell-lines.html). K562 cells were cultured according to the ENCODE Consortium protocol (http://genome.ucsc.edu/ENCODE/protocols/cell/human/K562_protocol.pdf).
SON and MKI67IP TSA-Seq was performed using Condition E (labeling with 1:300 tyramide biotin, 50% sucrose and 0.0015% hydrogen peroxide) (Zhang et al., 2020) with the following minor modification: 150ul of Dynabeads M-270 streptavidin (Invitrogen, catalog no. 65306) was used to purify the biotinylated DNA. For LMNB1 TSA-Seq, Condition A2 (Zhang et al., 2020) (labeling with 1:10000 tyramide biotin, 50% sucrose, 0.0015% hydrogen peroxide and reaction time 20 min at RT) was used.

value: immortalized cell line

value: condition2 - conditionE - anti-SON


title: Ctrl_1


title: syy-1


title: 4DNEXGMLP5SR, H. sapiens - K562, input - condition2 - conditionE - anti-SON, B1 T1

description:
TSA-seq in K562 (H. sapiens), input - condition2 - conditionE - anti-SON, Biological replicate 1, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXGMLP5SR/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBS92SO65R/
4DNEXGMLP5SR


title: Liv-Smad4ON_m2

description: paired-end sequencing

value: PDAC liver metastasis cells


title: BY-CSM_Riboseq_rep2

value: BY4741(MATa his3delta1 leu2delta0 met15delta0 ura3delta0)


title: 4DNEXI7XUWFK, H. sapiens - HFFc6, input - condition2 - conditionE - anti-SON, B1 T1

description:
TSA-seq in HFFc6 (H. sapiens), input - condition2 - conditionE - anti-SON, Biological replicate 1, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXI7XUWFK/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBS2G8G185/
4DNEXI7XUWFK


title: BY-CSM_Riboseq_rep1


title: Exp4,PITL enriched population  (Cd1dko) sorts, VDJ

value: Thymus


title: 4DNEXIRQ3TRW, H. sapiens - HFFc6, input - condition2 - conditionE - anti-SON, B2 T1

description:
TSA-seq in HFFc6 (H. sapiens), input - condition2 - conditionE - anti-SON, Biological replicate 2, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXIRQ3TRW/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSOS2TZMM/
4DNEXIRQ3TRW


title: Liv-Smad4OFF_m1

description: paired-end sequencing


title: BY-CSM_RNAseq_rep3


title: 4DNEX6U8TS3Y, H. sapiens - HFFc6, condition2 - conditionE - anti-SON, B1 T1

description:
TSA-seq in HFFc6 (H. sapiens), condition2 - conditionE - anti-SON, Biological replicate 1, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEX6U8TS3Y/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBS2G8G185/, Results include counts in BigWig (.bw) format.
4DNEX6U8TS3Y


title: 4DNEXJYIQ1LL, H. sapiens - HFFc6, condition2 - conditionE - anti-SON, B2 T1

description:
TSA-seq in HFFc6 (H. sapiens), condition2 - conditionE - anti-SON, Biological replicate 2, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXJYIQ1LL/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSOS2TZMM/, Results include counts in BigWig (.bw) format.
4DNEXJYIQ1LL


title: BY-CSM_RNAseq_rep2


title: 4DNEX5CWKK1V, H. sapiens - HCT116, input - condition2 - conditionE - anti-SON, B2 T1

description:
TSA-seq in HCT116 (H. sapiens), input - condition2 - conditionE - anti-SON, Biological replicate 2, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEX5CWKK1V/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSGYPCZ4H/
4DNEX5CWKK1V


title: Exp4,PITL enriched population  (Cd1dko) sorts, HTO_ADT


title: Ctrl_2


title: 4DNEXI5ZVEAW, H. sapiens - HCT116, input - condition2 - conditionE - anti-SON, B1 T1

description:
TSA-seq in HCT116 (H. sapiens), input - condition2 - conditionE - anti-SON, Biological replicate 1, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXI5ZVEAW/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSN217ZO7/
4DNEXI5ZVEAW


title: 4DNEX7F9CBFH, H. sapiens - HCT116, condition2 - conditionE - anti-SON, B2 T2

description:
TSA-seq in HCT116 (H. sapiens), condition2 - conditionE - anti-SON, Biological replicate 2, Technical replicate 2, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEX7F9CBFH/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSGYPCZ4H/, Results include counts in BigWig (.bw) format.
4DNEX7F9CBFH


title: BY-CSM_RNAseq_rep1


title: C5

city: taian

first: dejie

last: zhu

address: Shandong Agricultural University

institute: Shandong Agricultural University

data_processing:
The original data format of the off-line data sequenced by Nanopore is fast5 format, which contains all the original sequencing signals. After Base Calling analysis by GUPPY (version: 5.0.16) software, the data in fast5 format is converted into fastq format.
The quality of ONT original sequencing data is controlled. According to the quality value of sequencing data (the threshold value is 7 by default), those above the threshold value are pass and those below the threshold value are fail.
The original sequencing data is filtered to get clean reads, which are still stored in FASTQ format.
Use NanoFilt (version: 2.8.0; Parameter: -q 7 -l 50)(De Coster et al., 2018) filters the original fastq data to obtain valid data for subsequent analysis, and uses SeqKit (version: 0.12.0; Parameter: default)(Shen et al., 2016) statistics.
Identification of full-length sequences in valid sequencing data by Pychopper software
Assembly: According to minimap2 (version: 2.17-r941；; Parameters: -ax splice -uf -k14)(Li, 2018) The filtered full-length sequence was compared with the reference gene.
Supplementary files format and content: README

organism: Ovis aries

source_name: Pituitary

extract_protocol:
Experimental steps of RNA extraction：（1）Weighing 15mg-30mg of sample, grinding with liquid nitrogen, adding TRK Lysis Buffer or adding TRK Lysis Buffer to homogenize with homogenizer, transferring the lysate to a homogenizing column, putting the homogenizing column into a 2mL centrifuge tube, centrifuging at room temperature of 14,000xg for 2min to remove insoluble impurities, and collecting filtrate;(2) adding 70% ethanol with the same volume into the filtrate, and vortex mixing;(3) Put the RNA binding column into a collection tube, transfer the mixed solution obtained in the second step (the mixed solution transferred each time is less than or equal to 700 L), centrifuge at room temperature of 10000xg for 1min, and discard the filtrate;(4) repeat step 3 until all the mixed solution is bound to the RNA binding column;(5) Put the RNA binding column into the collection tube, add 500µl RNA Wash Buffer I into the binding column, centrifuge at 10000xg for 30s, and discard the filtrate;(6) Put the RNA binding column back into the collection tube, add 500µl RNA Wash Buffer II into the binding column, centrifuge at 10000xg for 1min, and discard the filtrate;(7) repeat step 6;(8) Put the RNA binding column back into the collection tube, and centrifuge at 10000xg for 2 min;(9) Put the RNA binding column into a new 1.5mL centrifuge tube, add 30-70L Nuclease-Free Water into the binding column, and centrifuge at 10000xg for 2min to elute RNA;(10)Nanodrop, Qbuit and electrophoretic quality inspection.
Steps for building a full-length transcription library (using ONT's kit: SQK-PCS109+SQK-PBK004): (1) Take 500 ng of Total RNA samples qualified in quality inspection, and adjust the volume to 9 ul by using Nuclease Free Water; (2) connecting a reverse transcription primer; (3). Reverse transcription reaction; (4) amplification reaction; (5) purifying with AMPure beads magnetic beads; (6) sequencing linker connection; (7) configuring a computer library; (8) On the computer: the library was Loading into the R9.4 sequencing chip, and the Prometheon Sequencer (Oxford Nano Pore Technologies, Oxford, UK) was used for sequencing for 48-72 hours.

value: Pituitary


title: C4


title: 4DNEX4ANWWVQ, H. sapiens - HCT116, condition2 - conditionE - anti-SON, B2 T1

description:
TSA-seq in HCT116 (H. sapiens), condition2 - conditionE - anti-SON, Biological replicate 2, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEX4ANWWVQ/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSGYPCZ4H/, Results include counts in BigWig (.bw) format.
4DNEX4ANWWVQ


title: CON_CD8TB

city: hangzhou

first: huan

last: chen

address: Hangzhou, Zhejiang Province, China

institute: Zhejiang Chinese Medical University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter-Quality limit:0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters-mismath cost:2 insertion cost 3length fraction:0.8 similarity fraction:0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited txst files include count values for each Sample

source_name: T cell

growth_protocol: JAML+/- CD8+ T cells were isolated from murine hepatocellular carcinoma using flow cytometric sorting.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3ug of total RNA was used for the construstion of sequencing livraries
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufactruer's protocols

value: T cell

value: WT


title: JAML_CD8TA


title: C6


title: SC_rep1

data_processing:
Base-calling was done using bcl2fastq v2.20.0.422  and for demultiplex, we allowed one mismatch in index1 and one mismatch in index2
HT5Pseq reads were demultiplexed using bcl2fastq (v2) and  trimmed 3’-sequencing adapter using cutadapt V1.16 (http://gensoft.pasteur.fr/docs/cutadapt/1.6/index.html). After that the 8-nt random barcodes located on the 5´ ends of reads were extracted and added to the fastq file header as UMIs using UMI-tools (Smith, Heger and Sudbery, 2017). Reads were mapped to the reference genome (SGD R64-1-1 for S. cerevisiae genome, GCF_000009045.1_ASM904v1 for B. subtilis  genome) by star/2.7.0 (Dobin et al., 2013) with the parameter --alignEndsType Extend5pOfRead1 to exclude soft-clipped bases on the 5´ end. Duplicated 5´ ends of read introduced by PCR during library preparation were removed based on random barcodes sequences using UMI-tools (Smith, Heger and Sudbery, 2017).
Analysis of 5´ ends positions was performed using Fivepseq package (Nersisyan, Ropat and Pelechano, 2020) (http://pelechanolab.com/software/fivepseq). This included analysis of the relative positions of the 5' ends of the mRNA reads with respect to the start codon, stop codon, and codon-specific pausing. Specifically, the unique 5´mRNA reads in biological samples were averaged and normalized to reads per million (rpm). The relative position of 5´mRNA reads at each codon were summed up  and used for all additional analyses. Metagene plots for frame preference were showed as the sum value (in rpm) of each frame versus the relative from the sliding window's average (in rpm) for 20 codons located at the beginning, middle, and end of each gene.
Assembly: Saccharomyces cerevisiae R64-1-1, GCA_000009045.1 for B. subtilis
Supplementary files format and content: Bedgraph files for UMI collapsed reads for positive and negative strand. Reads were collapsed to the first 5´nucleotide.

growth_protocol: All yeast experiments were performed using Saccharomyces cerevisiae strain BY4741 (MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0). S. cerevisiae was grown to mid exponential phase (OD600~0.6) at 30 °C with rotating using YPD (1% yeast extract, 2% peptone, 2% glucose), Complete Supplement Mixture (CSM from Formedium™) or Synthetic Complete (SC from MP Biomedicals™) medium. Bacteria of the strain B. subtilis 168 (trpC2) were pre-cultivated at 37°C with rotating in LB and minimal growth medium (per 50 ml:  5X minimal salts solution,10 ml;  glucose (50% (w/v)), 0.5 ml; casamino acids (2% (w/v)), 0.5 ml; tryptophan (10 mg/ml), 0.1 ml; iron ammonium citrate (2.2 mg/ml), 0.05 ml, demonized water, 39 ml) with tryptophan supplementation at OD600 < 0.8. Cultures were diluted to  OD600~0.05 and collected until reaching the mid-exponential phase (OD600~0.6).

extract_protocol:
Total RNA was isolated by the standard phenol chloroform method and DNA was removed by DNase I treatment, as described in Zhang & Pelechano, 2021 (PMID:33870233). RNA concentration was measured with Qubit and RNA quality was checked by 1.2% Agarose Gel or on a BioAnalyzer using an RNA Nano 6000 chip according (Agilent Technologies).
HT-5Pseq libraries were prepared following a previously established protocol (Zhang & Pelechano, 2021) if not stated otherwise. To briefly summarize, 6 μg of RNA was subjected to DNase treatment, and the resulting DNA-free total RNA was ligated with an RNA/RNA oligo containing UMI (RNA rP5_RND oligo). The ligated RNA was reverse transcribed using Illumina PE2 compatible oligos with random hexamers and oligo-dT as primers. To eliminate RNA in RNA/DNA hybrids, samples were treated with sodium hydroxide at 65°C for 20 minutes. Ribosomal RNAs were depleted using DSN (Duplex-specific nuclease) and a mixture of ribosomal DNA probes. To deplete Ribosomal RNAs in B. subtilis 168 (trpC2), we used the in-house rRNA DNA oligo depletion mixes described previously (Huch, Nersisyan et.al, doi.org/10.1101/2021.04.08.439066). Finally, the samples were amplified by PCR and sequenced on an Illumina NextSeq 2000 instrument using average of 45 cycles for read1.
OTHER: 5PSeq

treatment_protocol:
Cells were harvested at exponential growth after being growing overnight in a SC (Synthetic Complete) media
Stress-induced S. cerevisiae cells were subjected to heat shock (42°C for 30 minutes), oxidative stress (0.2 mM H2O2 for either 5 or 30 minutes), and amino acid deprivation (CSM medium lacking amino acids for 30 mins). S. cerevisiae cells grown with amino acid addition were individually supplemented with arginine, proline, and serine as single amino acids to achieve a comparable concentration to that of SC medium. The concentration of each added amino acid ranged from 50 to 85.6 mg/L for arginine and from 0 to 85.6 mg/L for proline and serine. For B. subtilis,  cells were grown in both LB and minimal media. Cells were fast spined down and flash-frozen in liquid nitrogen.


title: CON_CD8TA


title: JAML_CD8TB


title: YPD_ctrl_rep3

treatment_protocol:
Cells grew in YPD medium to exponential phase as a control for stress condition
Stress-induced S. cerevisiae cells were subjected to heat shock (42°C for 30 minutes), oxidative stress (0.2 mM H2O2 for either 5 or 30 minutes), and amino acid deprivation (CSM medium lacking amino acids for 30 mins). S. cerevisiae cells grown with amino acid addition were individually supplemented with arginine, proline, and serine as single amino acids to achieve a comparable concentration to that of SC medium. The concentration of each added amino acid ranged from 50 to 85.6 mg/L for arginine and from 0 to 85.6 mg/L for proline and serine. For B. subtilis,  cells were grown in both LB and minimal media. Cells were fast spined down and flash-frozen in liquid nitrogen.


title: YPD_ctrl_rep2


title: 4DNEXY7SLH9Y, H. sapiens - H1-hESC, input - condition2 - conditionE - anti-SON, B2 T1

description:
TSA-seq in H1-hESC (H. sapiens), input - condition2 - conditionE - anti-SON, Biological replicate 2, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXY7SLH9Y/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSW8I39OS/
4DNEXY7SLH9Y

value: stem cell derived cell line


title: SC_rep2


title: Sorted Thy1.1+ (Areg-producing) Lung Treg cells, Bleomycin, Bulk RNA-seq, Sample 3

last: Arpaia

state: NY

department: Microbiology & Immunology

institute: Columbia University

description:
BulkBleo_counts.txt
BulkBleo_normalizedcounts.txt

data_processing:
Libraries were sequenced using Illumina NovaSeq 6000, yielding paired-end 100bp reads
RTA (Illumina) for base calling and bcl2fastq2 (v2.19) for converting BCL to fastq, Trim Galore for adapter trimming
Pseudoalignment using Salmon (1.10.2) from transcriptomic data (Ensembl v96, Mouse GRCm38 p6)
DESeq2 for analysis
Assembly: Ensembl v96, Mouse GRCm38.p6
Supplementary files format and content: tab delimited .txt file with raw counts for each gene/sample
Supplementary files format and content: tab delimited .txt file with normalized DESeq2 values for each gene/sample

source_name: lung

extract_protocol:
Cells were lysed with Trizol Reagent, and RNA was extracted using a Qiagen kit
PolyA pulldown of RNA, then cDNA library synthesis with NexteraXT Kit

treatment_protocol: Thy1.1- (Areg non-producing) and Thy1.1+ (Areg-producing) lung Treg cells were sorted and prepared for bulk RNA-seq.

value: lung

value: Treg cells

value: C57BL/6 male; Foxp3GFPAregThy1.1/Thy1.1

value: Bleomycin


title: 4DNEXYZL3Q53, H. sapiens - HFFc6, condition2 - conditionE - anti-SON, B1 T2

description:
TSA-seq in HFFc6 (H. sapiens), condition2 - conditionE - anti-SON, Biological replicate 1, Technical replicate 2, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXYZL3Q53/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBS2G8G185/, Results include counts in BigWig (.bw) format.
4DNEXYZL3Q53


title: C2


title: C3


title: YPD_ctrl_rep1

value: yeast


title: 4DNEX2JUPDUP, H. sapiens - H1-hESC, condition2 - conditionE - anti-SON, B2 T1

description:
TSA-seq in H1-hESC (H. sapiens), condition2 - conditionE - anti-SON, Biological replicate 2, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEX2JUPDUP/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSW8I39OS/, Results include counts in BigWig (.bw) format.
4DNEX2JUPDUP


title: Exp4,PITL enriched population  (Cd1dko) sorts, GEX


title: Sorted Thy1.1- (Areg-non-producing) Lung Treg cells, Bleomycin, Bulk RNA-seq, Sample 3


title: C1


title: 4DNEXUUZ3QJY, H. sapiens - H1-hESC, condition2 - conditionE - anti-SON, B1 T1

description:
TSA-seq in H1-hESC (H. sapiens), condition2 - conditionE - anti-SON, Biological replicate 1, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXUUZ3QJY/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSZAY3C84/, Results include counts in BigWig (.bw) format.
4DNEXUUZ3QJY


title: YPD_HS_t30_rep3

treatment_protocol:
Cells grew in YPD medium to exponential phase and exposed to 42°C for 30 minutes
Stress-induced S. cerevisiae cells were subjected to heat shock (42°C for 30 minutes), oxidative stress (0.2 mM H2O2 for either 5 or 30 minutes), and amino acid deprivation (CSM medium lacking amino acids for 30 mins). S. cerevisiae cells grown with amino acid addition were individually supplemented with arginine, proline, and serine as single amino acids to achieve a comparable concentration to that of SC medium. The concentration of each added amino acid ranged from 50 to 85.6 mg/L for arginine and from 0 to 85.6 mg/L for proline and serine. For B. subtilis,  cells were grown in both LB and minimal media. Cells were fast spined down and flash-frozen in liquid nitrogen.


title: Sorted Thy1.1+ (Areg-producing) Lung Treg cells, Bleomycin, Bulk RNA-seq, Sample 2


title: 4DNEXCAJWM6W, H. sapiens - HCT116, condition2 - conditionE - anti-SON, B1 T1

description:
TSA-seq in HCT116 (H. sapiens), condition2 - conditionE - anti-SON, Biological replicate 1, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXCAJWM6W/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSN217ZO7/, Results include counts in BigWig (.bw) format.
4DNEXCAJWM6W


title: YPD_HS_t30_rep2


title: 4DNEXZ8L4YL6, H. sapiens - H1-hESC, input - condition2 - conditionE - anti-SON, B1 T1

description:
TSA-seq in H1-hESC (H. sapiens), input - condition2 - conditionE - anti-SON, Biological replicate 1, Technical replicate 1, 4DN experiment: https://data.4dnucleome.org/experiments-tsaseq/4DNEXZ8L4YL6/, 4DN Biosample: https://data.4dnucleome.org/biosamples/4DNBSZAY3C84/
4DNEXZ8L4YL6