title: NPY_P01_G09

description: Library name: LigandScreen-P01-20230825-071_S71


title: vWT_rep3_DP

status: Public on Jun 25 2026

type: SRA

city: Greater Noida

first: Sanjeev

last: Galande

state: Uttar Pradesh

address: Center of Excellence in Epigenetics  Department of Life Sciences  School of Natural Sciences  Shiv Nadar Institute of Eminence  NH91, Tehsil Dadri

department: Biology

country: India

institute: Shiv Nadar University

description:
Library name: Sample6
column name in dp_wt_vko_counts.txt: WT3 DP

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10. HISATv2.0.1 was used to map the paired reads Count matrix were generated using feature counts of the SubRead package v1.0.1. DE was performed using Deseq2 in R v4.1.5
Assembly: mm10
Supplementary files format and content: Tab-delimited txt files including raw counts of each sample

molecule: polyA RNA

organism: Mus musculus

source_name: Thymus

extract_protocol:
RNA was extracted from 1-3 million sorted cells using TRIzol (Thermo F isher Scientific) for bulk RNA-seq. The Agilent 2100 Bioanalyzer was used to quantify and qualify the total RNA. Following this, 1 μg of total RNA was utilized to prepare the library.
The poly(A) mRNA magnetic isolation module was used to carry out the poly(A) mRNA isolation. First strand synthesis mix (NEB) was used to create first- strand cDNA, while second strand synthesis enzyme mix (NEB) was used to create second-strand cDNA. Three steps were taken with the isolated double-stranded cDNA: adapter ligation, 3'-dA tailing, and end repair. The number of PCR cycles was determined by qPCR. Ligated DNA was amplified using six to ten cycles with Illumina P5/P7 primers. PCR products were purified using magnetic beads and quantified using a Qubit 4.0 Fluorometer (Thermo Fisher Scientific). The resulting libraries were pooled and sequenced using 2×150 bp paired-end chemistry.

tag: tissue

value: Thymus

tag: cell line

value: Primary

tag: cell type

value: DP

tag: genotype

value: WT

tag: treatment

value: Tamoxifen

tag: batch


title: CHIP015, Input, FRDA, rep1

city: Philadelphia

first: Ricardo

middle: A

last: Linares Saldana

state: PA

address: 3400 civic center blvd

country: USA

institute: University of Pennsylvania

description:
LB1_PT.inpLg2_1kb.woTNR.e100.S10Kb.bw
LB1_PT.inpLg2_15kb.woTNR.e100.S75Kb.znormChr_15_woBlklst_domains.bed

library_source: genomic

data_processing:
Basecalls were performed using bcl2fastq v2.20.
ChIP-seq reads were deduplicated and trimmed using fastp v0.23.2. Low complexity reads were discarded.
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 2.5.1. Only uniquely mapping reads with a MAPQ >20 were retained using sambamba 1.0.0.
To create ChIP-seq coverage plots of LB1 and H3K9me2, the locations of the mapped ChIP-seq reads were extended to 100 bp to represent sequenced fragments, normalized (to counts per million, cpm) and log2 normalized against their corresponding inputs. The resulting bigwig files were generated using deeptools v3.1.3. Bigwigs for RAD21 were generated using macs2 version 2.2.6 representing a fold enrichment over their corresponding inputs. ENCODE blacklisted regions (hg38-blacklist.v2.bed) were excluded from analysis.
RAD21 peaks were called using MACS v2.2.6 with the significance cut-off q-value <=0.01. Broad domains for LB1 or H3K9me2 were identified using HMMDomainCaller doi:10.1038/s41588-021-00821-2.
Assembly: hg38
Supplementary files format and content: bigWig files with input normalized ChIP-seq signal for each condition as described above. Bed and narrowPeak files with domain calls per condition as described above.

molecule: genomic DNA

organism: Homo sapiens

source_name: FRDA fibroblast

growth_protocol: Human skin non-treatment control (NTC) fibroblasts and fibroblasts from a Freidrich's Ataxia patient (FRDA) fibroblast cells were cultured in DMEM (Gibco #11965084) supplemented with 10% fetal bovine serum (Cytiva SH30910.03), 1% penicillin/streptomycin (Invitrogen #15140122), and 1% non-essential amino acids (Invitrogen # 11140050) at 37C with 20% O2 and 5% CO2. RAD21-mAID-HCT116 cells were cultured in McCoys (Invitrogen #16600082) supplemented with 10% fetal bovine serum, and 1% penicillin/streptomycin at 37C with 20% O2 and 5% CO2.

extract_protocol:
Samples for ChIP were processed as previously described (3). Human NTC and FRDA fibroblasts and Rad21-mAID-HCT116 cells were cultured in 10cm dishes and crosslinked in culture using methanol-free formaldehyde for 10 min at RT with gentle rotation (final 1% v/v). Crosslinking was quenched by addition of glycine for 5 min at RT with gentle rotation (final 125mM). Cells were washed with 1x PBS once before collection via scraping and PBS removal by centrifugation (250xg for 5 minutes at RT). Resulting pellets were flash frozen on dry ice and stored at -80C. For each ChIP sample, 30µL protein G magnetic beads (Invitrogen #10004D) were washed 3 times in blocking buffer (0.5% BSA in 1x PBS) before beads were resuspended in 250µL blocking buffer and 2µg (anti-LaminB1 [Abcam #ab16048], anti-H3K9me2 [Active Motif #39239]) or 4µg (anti-RAD21 [Abcam, #ab992]) antibody and rotated at 4C overnight. Nuclei were isolated from frozen pellets as follows: pellets were resuspended in 10mL cold Lysis Buffer 1 (50mM HEPES-KOH pH7.5, 1mMEDTA, 140mM NaCl, 10% Glycerol, 0.5% NP-40, 0.25% TritonX-100, and protease inhibitor) and rotated at 4C for 10 min. Resuspended cells were centrifuged at 250xg for 5 min at RT and supernatant discarded. Remaining pellet was resuspended in 10mL cold Lysis buffer (220mM NaCl, 10mM Tris-HCl pH 8.0, 1mM EDTA, 0.5mM EGTA, and protease inhibitor) and rotated at 4C for 10 min. Resuspended cells were centrifuged at 250xg for 5 min at RT and supernatant discarded. Nuclei were resuspended in 1mL cold Lysis Buffer 3 (10mM Tris-HCl pH8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, and protease inhibitor). Samples were transferred to a pre-chilled 1mL Covaris AFA tube (Covaris #520130) and sonicated using a Covaris S220 sonicator (high cell chromatin shearing for 15 minutes). TrintonX-100 (final 1%) was added to lysates and centrifuged at top speed for 10 min at 4C. Supernatant was collected and protein concentration measured via Bradford assay. Antibody-conjugated beads were washed 3 times in blocking buffer and resuspended in 50µL blocking buffer before 500µg protein lysate was added and allowed to rotate overnight at 4C. For inputs, 50µg protein lysate was aliquoted and stored at -20C. The next day, antibody-conjugated beads with lysate were washed 5 times for 2 min each at 4C with rotation in 1mL RIPA buffer (50mM HEPES-KOH pH7.5, 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate). Beads were washed in 1mL Final Wash buffer (1XTE, 50mM NaCl) for 2 min with rotation at RT. Lastly, beads were resuspended in 210µL Elution Buffer (50mM Tris-HCl pH 8.0, 10mM EDTA, 1% SDS) and incubated at 65C for 30 min with agitation. 200µL eluate was removed and all samples were incubated at 65C with agitation for a minimum of 12 h, but no more than 18 h. 200µL of 1X TE was added the resulting samples followed by addition of RNase (final 0.2mg/mL, Sigma #10109169001) and incubated at 37C for 2 h. Proteinase K was subsequently added (final 0.2mg/mL, Roche #3115879001) and incubated at 55C for 2 h. DNA was isolated via phenol:chloroform extraction and resuspended in 10mM Tris-HCl pH8.0. DNA was quantified by Qubit.
ChIP-seq libraries were prepared using NEBNext Ultra II DNA library prep kit (NEB #E7770L). Samples were prepared with dual unique indices for multiplex sequencing using NEBNext Multiplex Oligos (NEB #E7630). Library quality was determined by BioAnalyzer or 2% agarose gel electrophoresis and quantified by qPCR using NEBNext Library Quant Kit (NEB #E7630S). Libraries were pooled, re-quantified, and single-end sequenced on the Illumina NextSeq500 or NextSeq1000/2000 platforms
Libraries were quantified and pooled for sequencing; input libraries were always run with associated ChIP samples. If possible, replicate samples were run together on the same sequencing run.

treatment_protocol: Human fibroblasts were grown in complete media (DMEM, 10% FBS, 1% penicillin/streptomycin) and plated at 40% confluency. The next day, dCas9-KRAB-FXN guide or dCas9-KRAB-Scramble guide was introduced into NTC fibroblasts for 2d followed by 2d selection in blasticidin. RAD21-mAID-HCT116 cells were propagated in standard medium (McCoy’s with 10% FBS and 1% penicillin/streptomycin) and plated in 10cm dishes at 40% density and grown overnight. The following morning, a time course was started for three conditions (DMSO control, triptolide-only, and auxin + triptolide). At time 0, DMSO control and triptolide-only cells were incubated in fresh media alone; auxin + triptolide cells were incubated in fresh media + 1μM auxin (5-Ph-IAA, Tocris Bioscience). After 1 hour, 200nM final triptolide (Selleckchem) was added to triptolide-only and auxin + triptolide cells. 12 hours post-triptolide, all cells were harvested for ChIP (see “ChIP and library preparation for sequencing”). DMSO was used as a vehicle control.

value: FRDA fibroblast

tag: chip antibody

value: Input

value: FRDA


title: NRG-1_P01_F09

city: Brisbane

first: James

last: Hudson

state: Queensland

address: 300 Herston Rd, Herston QLD 4006

country: Australia

institute: QIMR Berghofer Medical Research Institute

description: Library name: LigandScreen-P01-20230825-070_S70

data_processing:
Sequence reads were aligned using STAR (version 2.7.9a)
Counts matrix was generated using RSEM (version 1.3.1)
Assembly: Human reference, GRCh38 (Ensembl 98)
Supplementary files format and content: RSEM_Counts_Cardiopedia-Ligand.xlsx file includes raw counts for each sample

molecule: total RNA

extract_protocol:
Total RNA was isolated using the NuceloMag RNA kit (Macherey-Nagel) on the EpMotion 5075t
RNA libraries were prepared using the Illumina Stranded mRNA Prep Ligation kit (polyA RNA selection) on the EpMotion 5075t

treatment_protocol: hCO were stimulated with a library of 90 ligands (n = 2-5 hCO per ligand in final RNA-seq dataset after passing all quality control). After 24 hours, media was aspirated and hCO were washed with ice cold PBS- and lysed for RNAseq.


title: DK21052-HC-2-iPSC-MOsMPs

city: Yushima, Bunkyo-ku

first: FUMIKO

last: OZAKI

state: Tokyo

country: Japan

institute: Tokyo medical and dental university

description: all.rpm_DK21052-HC-iPSCs_Neutro_MOsMPs.xlsx

data_processing:
The mRNA profiles were compiled using Cufflinks (ver 2.2.1) software program and expressed as Reads per million mapped reads (PKM).
Assembly: hg38
Supplementary files format and content: xlsx files include RPM value for each sample

source_name: iPSCs derived cells

extract_protocol:
RNA was harvested using RNAeasy mini plus kit (Qiagen). In DK21052, 1 ng of total RNA was used to construct the sequencing library. For DK2220 and DK22223, 25 ng of total RNA was used, and for DK23067, 0.75 ng of total RNA was used.
Using the QuantSeq 3'mRNA-Seq Library Prep Kit, libraries for the NextSeq next-generation sequencer were prepared following the manual's protocol.

value: iPSCs derived cells

value: monocytes/macrophages

value: untreated


title: MCF7, Kaempferol, CM10, 6h, H12

city: Mason

first: Yuqing

last: Shan

state: Ohio

address: 8700 mason montgomery road

institute: Procter & Gamble

description: Library name: CM10_T7_D3_H12

data_processing:
TempO-Seq data are analyzed using the Tempo-SeqR software package using the statistical computing language R.
The input for TempO-Seq data analysis is a folder of zipped FASTQ files. Each FASTQ file contains the reads and quality scores for one sample.
Each FASTQ file is aligned using the Bowtie algorithm to a pseudo-transcriptome input by the user.
The output for TempO-Seq data analysis is a table of counts with each column representing a sample and each row representing a gene.
Assembly: hWTv2
Supplementary files format and content: txt file

source_name: Breast; Mammary gland

extract_protocol:
6h after treatment, 100uL of TempoSeq lysis buffer used to lyse cells per 96-well, which were then frozen and 2ul used for TempO-Seq library building
In TempO-Seq, each Detector Oligo (DO) consists of a sequence complementary to an mRNA target plus a universal (i.e. same for every targeted gene) primer binding site. They anneal in immediate juxtaposition to each other on the targeted RNA template such that they can be ligated together. Ligated detector oligos are PCR-amplified using a primer set (single-plex PCR reaction, with a single primer pair for each sample) that introduces both the adaptors required for sequencing and a sample-specific barcode. The barcode sequences flank the target sequence and are inserted appropriately into the standard Illumina adaptors to permit standard dual-index sequencing of the barcodes and deconvolution of sample-specific reads from the sequencing data using the standard Illumina software. All the PCR-amplified and barcoded samples are pooled into a single library for sequencing. Sequencing reads are demultiplexed using the standard sequencing instrument software for each sample using the barcodes to give a FASTQ file for each.

value: Breast; Mammary gland

value: epithelial cell

value: Adenocarcinoma

value: test


title: vWT_rep2_DP

description:
Library name: Sample5
column name in dp_wt_vko_counts.txt: WT2 DP


title: CTRL-WM_P03_A01

description: Library name: LigandScreen-P03-20230901-001_S97


title: HES3_Cortisol-1

city: New haven

first: Woo Sub

last: Yang

state: CT

address: 10 Amistad St, Room 214j

institute: Yale University

description:
Library name: RNA-seq sample4
truseq stranded mrna library

data_processing:
For RNA-seq, Sequencing reads were first quality-trimmed using fastp (v0.20.1) with adapter detection enabled and a minimum length cutoff of 25 bp. The quality of the trimmed reads was evaluated with FastQC (v0.11.9). Trimmed paired-end reads were aligned to the human reference genome (GRCh38) using STAR (v2.7.9a), with the primary assembly FASTA file and GTF annotations obtained from Ensembl (release 112). The alignment included both transcriptome and gene count quantification modes. Parameters allowed for a maximum of 20 multimapping reads and required a minimum overhang of 8 bp for splice junctions. Aligned reads were sorted and indexed using samtools (v1.10), and transcript quantification was performed with Salmon (v1.5.2) in alignment-based mode using the sorted BAM files, accounting for sequence and GC biases.  For scRNA-seq, The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1 (https://www.10xgenomics.com/support/software/cell-ranger/latest/tutorials/cr-tutorial-in)
Assembly: GRCh38
Supplementary files format and content: For RNA-seq, csv file including TPM. For scRNA-seq, matrix, features and barcode files.

source_name: Brain organoid

extract_protocol:
for RNAseq, RNA was extracted using RNeasy plus universal mini prep kit (Quiagen). 1 ug total RNA was used for construction of sequencing libraries. For scRNA-seq organoids were dissociated with Papain dissociation system (worthington biochemical). And total 20,000 cells were used for library contruction.
for RNA-seq, Truseq stranded mRNA library prep kit (Illumina) was used following manufacture's protocol. For scRNA-seq, Library prep was performed following 3P v4 (GEM-X)  protocol (10X Genomics)

value: Brain organoid

value: 10uM Cortisol


title: CHIP014, LMNB1, FRDA, rep2

value: LMNB1 (abcam, #ab16048)


title: LPA_P01_D09

description: Library name: LigandScreen-P01-20230825-068_S68


title: MCF7, Kaempferol, CM10, 6h, D04

description: Library name: CM10_T7_D3_D04


title: vWT_rep1_DP

description:
Library name: Sample4
column name in dp_wt_vko_counts.txt: WT1 DP

value: Thymus

value: Primary


title: LTB4_P01_C09

description: Library name: LigandScreen-P01-20230825-067_S67


title: CHIP013, LMNB1, FRDA, rep1


title: vKO_rep3_DP

description:
Library name: Sample3
column name in dp_wt_vko_counts.txt: cKO3 DP

value: DP

value: Satb1 KO


title: MCF7, Kaempferol, CM10, 6h, C07

description: Library name: CM10_T7_D3_C07


title: LIF_P01_B09

description: Library name: LigandScreen-P01-20230825-066_S66


title: MCF7, Kaempferol, CM10, 6h, A10

description: Library name: CM10_T7_D3_A10


title: TGF-β1_P01_D12

description: Library name: LigandScreen-P01-20230825-092_S92


title: CHIP010, Input, CRISPRi, rep1_part2

description:
LB1_iFXN.inpLg2_1kb.woTNR.e100.S10Kb.bw
LB1_iFXN.inpLg2_15kb.woTNR.e100.S75Kb.znormChr_15_woBlklst_domains.bed

source_name: WT fibroblast

value: WT fibroblast

value: Human fibroblast

value: CRISPRi


title: Leptin_P01_A09

description: Library name: LigandScreen-P01-20230825-065_S65


title: vKO_rep1_DP

description:
Library name: Sample1
column name in dp_wt_vko_counts.txt: cKO1 DP

value: Tamoxifen


title: CHIP008, LMNB1, CRISPRi, rep2_part2


title: IL-6_P01_H08

description: Library name: LigandScreen-P01-20230825-064_S64


title: MCF7, Kaempferol, CM10, 6h, H09

description: Library name: CM10_T7_D2_H09


title: MCF7, Kaempferol, CM10, 6h, G12

description: Library name: CM10_T7_D2_G12


title: CHIP006, LMNB1, CRISPRi, rep1_part2


title: IL-4_P01_G08

description: Library name: LigandScreen-P01-20230825-063_S63


title: DK21052-HC-1-E250Q-iPSC-neutrophils

value: iPSCs derived cells

value: neutrophils


title: M3-CKO, replicate 2, scRNA

city: Guangzhou

first: Kechen

last: Chen

state: Guangdong

address: Shatai South Road

country: China

institute: Southern Medical University

description: Library name: B1238

library_source: transcriptomic single cell

data_processing:
Raw reads were demultiplexed, mapped to the reference genome and gene counting using the 10X Genomics Cell Ranger pipeline
Assembly: mm10
Supplementary files format and content: Cell Ranger processed filtered feature bc matrix .h5 file

source_name: Trachea

extract_protocol:
The tracheal epithelial cells were isolated from 2 control mice (Mettl3fl/+; Krt5-CreERT2/+; R26R-tdTomato) and 2 Mettl3 conditional knockout mice (Mettl3fl/fl; Krt5-CreERT2/+; R26R-tdTomato) by dissecting tracheas, removing connective tissue, and mincing into small pieces followed by sequential enzymatic digestion in DMEM/F12 containing 2 mg/mL dispase (Sigma, D4693) at 37°C for 30 minutes and 0.5 mg/mL DNase I (Solarbio, D8071) at 37°C for 30 minutes, after which epithelial sheets were manually peeled and further dissociated into single cells using 0.25% Trypsin-EDTA (Thermo Fisher, 25200056) at 37°C for 5 minutes, with the resulting cell suspension filtered through a 70 μm strainer before preparing a 1:1 mixture of Krt5-lineage-traced tdTomato+ and non-traced tdTomato- cells for 3' droplet-based single-cell RNA sequencing (10x Genomics platform).
The cell suspension was loaded into 10x Chromium Chip (v3.1) and barcoded with a 10x Chromium Controller. RNA from the barcoded cells was subsequently reverse-transcribed, amplified and prepared into sequencing libraries with 10x Library Construction Kit (v3.1) according to the manufacturer’s instructions.

value: Trachea


title: M3-CKO, replicate 1,scRNA

description: Library name: B1216


title: IL-13_P01_E08

description: Library name: LigandScreen-P01-20230825-061_S61


title: M_HF_FL-3

city: College Station

first: Kartik

last: Shankar

email: kartik.shankar@cuanschutz.edu, kartikster@gmail.com, kartik.shankar@usda.gov, kartik.shankar@ag.tamu.edu

state: TX

address: 498 Olsen Blvd TAMU 2250 TAMU 2250

department: RAFSRU

institute: USDA ARS

data_processing:
All reads were trimmed for adapters, filtered based on quality score using FASTX trimmer and aligned to the mouse genome (mm9) using the Bowtie2 aligner using default settings. Resulting read alignments for each sample were imported in Seqmonk for gene level quantification as counts mapping to annotated genes. Gene counts were imported into R (v4.05) and analysis of differential expression between groups was done using the limma-vst pipeline
Supplementary files format and content: Processed data are provided as data matrix where rows are gene level quantitation (counts) and columns include samples. A single file is included for all samples.

source_name: Placenta

extract_protocol:
RNA was extracted from placenta tissue from MyD88-CKO dams fed either control or HFD. Biologically distinct pools were created in a genotype and sex-stratified manner (n = 3 per group). Total RNA was isolation using the TRI reagents and RNeasy Mini Kit per manufacturer’s instructions including on-column DNase digestion. Total RNA was quantified using a Qubit RNA BR Assay Kit and RNA integrity was assessed on an RNA ScreenTape.
mRNA-seq libraries (n = 3 per group) were prepared using a Nebnext Ultra reagents following mRNA isolation Dynabeads Oligo-Dt reagents. Manual bead cleanup was performed using AMPure XP Beads (Beckman Coulter, A63881) after the libraries were completed to remove primer-dimers. Qubit dsDNA BR Assay kit was used to determine the concentration of the completed library and a Fragment Analyzer Standard Sensitivity NGS Fragment Kit
Single-end, opposing starnd libraries

value: Placenta

value: Fl

tag: Sex

value: M

tag: diet

value: HF

tag: group


title: IFN-γ_P01_B08

description: Library name: LigandScreen-P01-20230825-058_S58


title: MCF7, Kaempferol, CM10, 6h, G09

description: Library name: CM10_T7_D1_G09

value: Breast; Mammary gland

value: epithelial cell

value: Adenocarcinoma

value: test


title: M_HF_FL-1


title: Ctrl, replicate 1, scRNA

description: Library name: B1231


title: MCF7, Kaempferol, CM10, 6h, F12

description: Library name: CM10_T7_D1_F12


title: IGF-1_P01_A08

description: Library name: LigandScreen-P01-20230825-057_S57


title: C57BL6J-KXA_F2 - snMultiome-RNA of saline-treated mouse: VISp

city: Seattle

first: Cindy

last: van Velthoven

state: WA

address: 615 Westlake Ave N

institute: Allen Institute

description:
Library name: SQ_MX2020-5
snMultiome-RNA

data_processing:
The snMultiome libraries were sequenced on the Illumina NovaSeq6000, and sequencing reads were aligned to the mouse references downloaded from 10x Genomics, which includes ensembl GRCm38 (v98) fasta and gencode (vM23) gtf file, using the 10x Genomics CellRanger Arc (v2.0) workflow with default parameters.
Assembly: ensembl GRCm38 (v98) fasta and gencode (vM23) gtf file
Supplementary files format and content: filter_feature_bc_matrix.h5 or atac_fragments.tsv.gz

source_name: VISp

extract_protocol:
Allen Institute for Brain Science. RAISINs (RNA-seq for Profiling Intact Nuclei with Ribosome-bound mRNA) Nuclei Isolation from Mouse CNS Tissue Protocol v1. Preprint at https://doi.org/10.17504/protocols.io.4r3l22n5pl1y/v1 (2023)
Allen Institute for Brain Science. 10x Multiome sample processing. Protocols.io https://doi.org/10.17504/protocols.io.bp2l61mqrvqe/v1 (2023)

value: VISp

value: wt/wt

value: ketamine


title: M_HF_CKO-3

value: CKO


title: IFN-β_P01_G07

description: Library name: LigandScreen-P01-20230825-055_S55


title: CHIP012, Input, CRISPRi, rep2_part2

value: WT fibroblast

value: Human fibroblast

value: Input

value: CRISPRi


title: M_HF_CKO-2


title: Histamine_P01_F07

description: Library name: LigandScreen-P01-20230825-054_S54


title: MCF7, Kaempferol, CM10, 6h, A07

description: Library name: CM10_T7_D1_A07


title: M_HF_CKO-1


title: HGF_P01_E07

description: Library name: LigandScreen-P01-20230825-053_S53


title: MCF7, 4-hydroxybenzophenone, CM10, 6h, H06

description: Library name: CM10_T6_D3_H06


title: C57BL6J-Sal_F1 - snMultiome-RNA of saline-treated mouse: VISp

description:
Library name: SQ_MX2019-3
snMultiome-RNA

value: saline


title: M_Con_FL-3

value: Placenta

value: control


title: MCF7, 4-hydroxybenzophenone, CM10, 6h, F09

description: Library name: CM10_T6_D3_F09


title: C57BL6J-KXA_F2 - snMultiome-ATAC of saline-treated mouse: VISp

description:
Library name: SQ_AT0025-9
snMultiome-ATAC

library_source: genomic single cell


title: GH_P01_D07

description: Library name: LigandScreen-P01-20230825-052_S52


title: M_Con_FL-2

value: Fl

value: M


title: GDNF_P01_C07

description: Library name: LigandScreen-P01-20230825-051_S51


title: MCF7, 4-hydroxybenzophenone, CM10, 6h, E12

description: Library name: CM10_T6_D3_E12

value: Breast; Mammary gland


title: C57BL6J-Sal_F2 - snMultiome-RNA of saline-treated mouse: VISp

description:
Library name: SQ_MX2019-4
snMultiome-RNA


title: C57BL6J-KXA_F1 - snMultiome-ATAC of saline-treated mouse: VISp

description:
Library name: SQ_AT0025-8
snMultiome-ATAC


title: M_Con_FL-1


title: Galectin-3_P01_A07

description: Library name: LigandScreen-P01-20230825-049_S49


title: C57BL6J-Sal_F2 - snMultiome-ATAC of saline-treated mouse: VISp

description:
Library name: SQ_AT0024-8
snMultiome-ATAC


title: FGF-2_P01_H06

description: Library name: LigandScreen-P01-20230825-048_S48


title: C57BL6J-Sal_F1 - snMultiome-ATAC of saline-treated mouse: VISp

description:
Library name: SQ_AT0024-7
snMultiome-ATAC


title: FGF-1_P01_G06

description: Library name: LigandScreen-P01-20230825-047_S47


title: M_Con_CKO-2


title: MCF7, 4-hydroxybenzophenone, CM10, 6h, G06

description: Library name: CM10_T6_D2_G06

value: epithelial cell


title: 5FU_d0_LK

city: New York

last: Swann

state: NY

address: 650 W 168th Street

institute: Columbia University

description:
Library name: EO070
10X Genomics v3

data_processing:
Raw fastq files were aligned and processed to count matrices using CellRanger v7.
Assembly: mm10
Supplementary files format and content: 10X Genomics: Tab-separated feature, barcode, and matrix files.
Supplementary files format and content: Hashing data: a key for totalseq B antibodies is provided as a comma separated file.

source_name: Bone marrow

growth_protocol: Mice were maintained in Columbia University Irving Medical Center facilities under SPF conditions.

extract_protocol:
Bone marrow was harvested by crushing bones in cold HBSS with 2% FBS (staining media, SM). All samples were filtered, treated with ACK red blood cell lysis buffer, magnetically enriched for cKit+ cells, and stained for surface protein expression. Live hematopoietic stem and progenitor cells were isolated on the basis of propridium iodide negativity and surface protein expression, either as lineage-/cKit+ cells (LK) or lineage-/cKit+/Sca-1+ cells (LSK). For hashing, 5 different hematopoietic stem and progenitor cell populations were FACS sorted, labelled with TotalSeq-B oligo-hashed antibodies, then pooled for sequencing.
Libraries were constructed following manufacturer's instructions for Chromium Single Cell 3' Library & Bead Kit v3.1 (10X Genomics). 5,000 cells were loaded for each sample and samples were sequenced in a NovaSeq 6000 sequencer (Illumina).

treatment_protocol: For 5-fluorouracil (5FU), mice were injected once i.p. with 150 mg/kg 5FU dissolved in sterile PBS, before killing on indicated days. For polyinosinic:polycytidylic acid (pIC), mice were injected i.p. with 10 mg/kg pIC dissolved in sterile PBS every 48 hours for indicated number of days. For IL-1b, mice were injected i.p. with 0.5 ug of IL-1b dissolved in PBS with 0.1% bovine serum albumin daily for 20 days (chronic) or 7 days (acute) treatment.

value: Bone marrow

value: Lineage-/cKit+

tag: strain


title: M_Con_CKO-1


title: CTRL-Ethanol_P01_F06

description: Library name: LigandScreen-P01-20230825-046_S46


title: MCF7, 4-hydroxybenzophenone, CM10, 6h, E09

description: Library name: CM10_T6_D2_E09

value: Adenocarcinoma

value: test


title: F_HF_FL-3

value: F

value: HF


title: Hashing_5FU_M

description:
Library name: 5FUM
10X Genomics v3

value: Sorted HSPCs

tag: time point


title: CTRL-Ethanol_P01_E06

description: Library name: LigandScreen-P01-20230825-045_S45


title: MCF7, 4-hydroxybenzophenone, CM10, 6h, D12

description: Library name: CM10_T6_D2_D12


title: Hashing_5FU_F

description:
Library name: 5FUF
10X Genomics v3


title: F_HF_FL-2


title: 5FU_d14_LSK

description:
Library name: EJ005
10X Genomics v3


title: MCF7, 4-hydroxybenzophenone, CM10, 6h, G03

description: Library name: CM10_T6_D1_G03


title: CTRL-DMSO_P01_C06

description: Library name: LigandScreen-P01-20230825-043_S43


title: F_HF_FL-1


title: CTRL-WM_P01_B06

description: Library name: LigandScreen-P01-20230825-042_S42


title: MCF7, 4-hydroxybenzophenone, CM10, 6h, F06

description: Library name: CM10_T6_D1_F06


title: 5FU_d12_LSK

description:
Library name: EJ004
10X Genomics v3


title: CTRL-WM_P01_A06

description: Library name: LigandScreen-P01-20230825-041_S41


title: MCF7, 4-hydroxybenzophenone, CM10, 6h, D09

description: Library name: CM10_T6_D1_D09


title: F_HF_CKO-3

value: CKO


title: 5FU_d10_LSK

description:
Library name: EJ003
10X Genomics v3


title: F_HF_CKO-2


title: M_Con_CKO-3


title: MCF7, 4-hydroxybenzophenone, CM10, 6h, A04

description: Library name: CM10_T6_D3_A04


title: FPP_P01_H05

description: Library name: LigandScreen-P01-20230825-040_S40


title: MCF7, 4-hydroxybenzophenone, CM10, 6h, C12

description: Library name: CM10_T6_D1_C12


title: F_HF_CKO-1


title: 5FU_d8_LSK

description:
Library name: EJ002
10X Genomics v3


title: MCF7, 4-hydroxybenzophenone, CM10, 6h, H03

description: Library name: CM10_T6_D2_H03


title: EGF_P01_G05

description: Library name: LigandScreen-P01-20230825-039_S39


title: MCF7, 2-hydroxybenzophenone, CM10, 6h, F03

description: Library name: CM10_T5_D3_F03


title: 5FU_d0_LSK

description:
Library name: EJ001
10X Genomics v3


title: F_Con_FL-3


title: ET-2_P01_E05

description: Library name: LigandScreen-P01-20230825-037_S37


title: MCF7, 2-hydroxybenzophenone, CM10, 6h, E06

description: Library name: CM10_T5_D3_E06


title: pIC_3dpIC_LK

description:
Library name: pICLK
10X Genomics v3

value: pIC


title: F_Con_FL-2


title: ET-1_P01_D05

description: Library name: LigandScreen-P01-20230825-036_S36


title: MCF7, 2-hydroxybenzophenone, CM10, 6h, C09

description: Library name: CM10_T5_D3_C09


title: F_Con_FL-1


title: pIC_Control_LK

description:
Library name: pICControl
10X Genomics v3


title: Dopamine_P01_C05

description: Library name: LigandScreen-P01-20230825-035_S35


title: MCF7, 2-hydroxybenzophenone, CM10, 6h, A12

description: Library name: CM10_T5_D3_A12


title: Acute_IL1_7dIL1_LSK

description:
Library name: AcuteIL1
10X Genomics v3


title: F_Con_CKO-3


title: CXCL12_P01_H04

description: Library name: LigandScreen-P01-20230825-032_S32


title: MCF7, 2-hydroxybenzophenone, CM10, 6h, H11

description: Library name: CM10_T5_D2_H11


title: Chronic_IL1_20dIL1_LSK

description:
Library name: EJ010
10X Genomics v3


title: CNTF_P01_F04

description: Library name: LigandScreen-P01-20230825-030_S30


title: F_Con_CKO-2


title: MCF7, 2-hydroxybenzophenone, CM10, 6h, E03

description: Library name: CM10_T5_D2_E03


title: Chronic_IL1_20dIL1_LK

description:
Library name: EJ009
10X Genomics v3


title: F_Con_CKO-1


title: MCF7, 2-hydroxybenzophenone, CM10, 6h, C06

description: Library name: CM10_T5_D2_C06


title: Chronic_IL1_Control_LSK

description:
Library name: EJ008
10X Genomics v3

value: PBS


title: BDNF_P01_D04

description: Library name: LigandScreen-P01-20230825-028_S28


title: HipC3

city: Pamplona

first: Maite

middle: G

last: Fernandez-Barrena

address: Pio XII 55

country: Spain

institute: CIMA

description: Library name: HipC3

data_processing:
Alignment with STAR 2.7
Read counts with Feature count (SubRead 2.0.6)
Assembly: GRCh38_Gencode48
Supplementary files format and content: Microsoft Excel file with raw counts

growth_protocol: The HuCCT-1 human iCCA cell line was cultured in DMEM-F12 culture medium supplemented with 10% fetal bovine serum, glutamine and antibiotics

extract_protocol:
Automated Maxwell system (Promega)
Illumina Stranded mRNA Prep Ligation kit

treatment_protocol: Cells were grown under hypoxic conditions (1% O2) using a Whitley H35 Hypoxystation (Don Whitley Scientific Ltd., Bingley, UK) for 24h

value: tumoral, iCCA

value: Normoxia/Hypoxia


title: BMP-4_P01_C04

description: Library name: LigandScreen-P01-20230825-027_S27


title: MCF7, 2-hydroxybenzophenone, CM10, 6h, B09

description: Library name: CM10_T5_D2_B09


title: Chronic_IL1_Control_LK

description:
Library name: EJ007
10X Genomics v3


title: HipC2

description: Library name: HipC2


title: BMP-2_P01_A04

description: Library name: LigandScreen-P01-20230825-025_S25


title: vKO_rep2_DP

description:
Library name: Sample2
column name in dp_wt_vko_counts.txt: cKO2 DP

value: Thymus

value: Primary

value: DP

value: Satb1 KO

value: Tamoxifen


title: MCF7, 2-hydroxybenzophenone, CM10, 6h, G11

description: Library name: CM10_T5_D1_G11

value: Breast; Mammary gland

value: epithelial cell


title: HipC1

description: Library name: HipC1


title: CD44 KO LysM mouse 3, Ethanol feeding

city: Nice

first: Philippe

last: Gual

address: 151 Route de Saint-Antoine

country: France

institute: INSERM U1065

description:
Library name: Etoh_LysM_04
Column name in gene_count_LysM.csv: Etoh_LysM_04

data_processing:
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end  clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b)  in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: ensembl_mus_musculus_grcm38_p6_gca_000001635_8
Supplementary files format and content: csv file include Raw counts for each samples

source_name: Liver

extract_protocol:
Total liver RNA was extracted using the RNeasy Mini Kit (Qiagen) and treated with Turbo DNA-free DNase (Thermo Fisher Scientific Inc) following the manufacturer’s protocol.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Liver

value: CD44 KO LysM


title: MCF7, 2-hydroxybenzophenone, CM10, 6h, D03

description: Library name: CM10_T5_D1_D03

value: Adenocarcinoma

value: test


title: BNP_P01_G03

description: Library name: LigandScreen-P01-20230825-023_S23


title: NormC3

description: Library name: NormC3


title: CD44 KO LysM mouse 2, Ethanol feeding

description:
Library name: Etoh_LysM_03
Column name in gene_count_LysM.csv: Etoh_LysM_03


title: β-CGRP_P01_E03

description: Library name: LigandScreen-P01-20230825-021_S21


title: MCF7, 2-hydroxybenzophenone, CM10, 6h, B06

description: Library name: CM10_T5_D1_B06


title: MCF7, Kaempferol, CM10, 6h, C04

description: Library name: CM10_T7_D2_C04


title: CD44 KO LysM mouse 1, Ethanol feeding

description:
Library name: Etoh_LysM_02
Column name in gene_count_LysM.csv: Etoh_LysM_02


title: NormC2

description: Library name: NormC2


title: MCF7, 2-hydroxybenzophenone, CM10, 6h, A09

description: Library name: CM10_T5_D1_A09


title: ATP_P01_D03

description: Library name: LigandScreen-P01-20230825-020_S20


title: WT mouse 3, Ethanol feeding

description:
Library name: Etoh_WT_04
Column name in gene_count_LysM.csv: Etoh_WT_04

value: WT


title: MCF7, Kaempferol, CM10, 6h, B07

description: Library name: CM10_T7_D2_B07


title: AA_P01_C03

description: Library name: LigandScreen-P01-20230825-019_S19


title: MCF7, 3-hydroxybenzophenone, CM10, 6h, H08

description: Library name: CM10_T4_D3_H08


title: M_HF_FL-2

value: Placenta

value: Fl

value: M

value: HF


title: Ctrl, replicate 2, scRNA

description: Library name: B1232

value: Trachea


title: NormC1

description: Library name: NormC1

value: tumoral, iCCA

value: Normoxia/Hypoxia


title: WT mouse 2, Ethanol feeding

description:
Library name: Etoh_WT_03
Column name in gene_count_LysM.csv: Etoh_WT_03


title: ApoE_P01_B03

description: Library name: LigandScreen-P01-20230825-018_S18


title: WT_systemic_Mock_30min_Rep3

city: Columbia

first: Sameep

last: Dhakal

state: MO

address: 1201 Rollins St.

department: Institute for data science and Informatics

institute: University of Missouri

description:
Library name: WT_S_M_3
Systemic tissue analyzed, local leaf treated with a mock

data_processing:
Read quality control was performed using Trim Galore v0.6.7 and FastQC v0.11.9. Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence. Subsequently, the processed reads were mapped to the Gmax_880_v6.0 whole genome using Hisat2 v2.2.1. Samtools v1.19 was used to sort the bam files which were subjected toranscript assembly and quantification using Cufflinks v2.2.1. Differential expression analysis was performed later using Cuffdiff v2.2.1, comparing control conditions with different stress and .
Assembly: Arabidopsis_thaliana TAIR10
Supplementary files format and content: processed data files are in format txt and it contains the gene names along with the fpkm values for each of the replicates.

organism: Arabidopsis

source_name: rosette leaf

growth_protocol: Plants were cultivated under controlled conditions consisting of 10h light/14h dark, light intensity of 50 µmol photons s−1 m−2, and ambient temperature of 21°C for four weeks.

extract_protocol:
RNA extractions were performed using Plant Rneasy kit (Qiagen)
RNA libraries were prepared through standard Illumina protocols

treatment_protocol: The local leaf of an Arabidopsis rosette was treated with either eATP, L-Glu, or a mock solution and the systemic rosette leaf was taken and immediately frozen in LN2 30 minutes post treatment of the local leaf

value: rosette leaf

value: Mock


title: MCF7, 3-hydroxybenzophenone, CM10, 6h, F11

description: Library name: CM10_T4_D3_F11


title: WT mouse 1, Ethanol feeding

description:
Library name: Etoh_WT_01
Column name in gene_count_LysM.csv: Etoh_WT_01


title: WT_systemic_Mock_30min_Rep2

description:
Library name: WT_S_M_2
Systemic tissue analyzed, local leaf treated with a mock


title: MCF7, Kaempferol, CM10, 6h, B04

description: Library name: CM10_T7_D1_B04


title: MCF7, 3-hydroxybenzophenone, CM10, 6h, C03

description: Library name: CM10_T4_D3_C03


title: AngII_P01_G02

description: Library name: LigandScreen-P01-20230825-015_S15


title: WT_systemic_Mock_30min_Rep1

description:
Library name: WT_S_M_1
Systemic tissue analyzed, local leaf treated with a mock


title: CD44 KO mouse 3, Ethanol feeding

description:
Library name: Etoh_G_KO_03
Column name in gene_count_CD44_KO_Ethanol.csv: Etoh_G_KO_03

value: CD44 KO


title: ANGPT-1_P01_F02

description: Library name: LigandScreen-P01-20230825-014_S14


title: ADM_P01_E02

description: Library name: LigandScreen-P01-20230825-013_S13


title: MCF7, 3-hydroxybenzophenone, CM10, 6h, A06

description: Library name: CM10_T4_D3_A06

value: Breast; Mammary gland


title: CD44 KO mouse 2, Ethanol feeding

description:
Library name: Etoh_G_KO_02
Column name in gene_count_CD44_KO_Ethanol.csv: Etoh_G_KO_02


title: WT_systemic_L-Glu_30min_Rep3

description:
Library name: WT_S_GLU_3
Systemic tissue analyzed, local leaf treated with L-Glu

value: 100mM L-Glu


title: C57BL6J-KXA_F1 - snMultiome-RNA of saline-treated mouse: VISp

description:
Library name: SQ_MX2020-4
snMultiome-RNA

value: VISp

value: wt/wt

value: ketamine


title: MCF7, 3-hydroxybenzophenone, CM10, 6h, H05

description: Library name: CM10_T4_D2_H05

value: epithelial cell

value: Adenocarcinoma

value: test


title: CD44 KO mouse 1, Ethanol feeding

description:
Library name: Etoh_G_KO_01
Column name in gene_count_CD44_KO_Ethanol.csv: Etoh_G_KO_01

value: Liver


title: WT_systemic_L-Glu_30min_Rep2

description:
Library name: WT_S_GLU_2
Systemic tissue analyzed, local leaf treated with L-Glu


title: Adrenaline_P01_D02

description: Library name: LigandScreen-P01-20230825-012_S12


title: Adipo_P01_C02

description: Library name: LigandScreen-P01-20230825-011_S11


title: WT_systemic_L-Glu_30min_Rep1

description:
Library name: WT_S_GLU_1
Systemic tissue analyzed, local leaf treated with L-Glu


title: MCF7, 3-hydroxybenzophenone, CM10, 6h, F08

description: Library name: CM10_T4_D2_F08


title: MCF7, 3-hydroxybenzophenone, CM10, 6h, E11

description: Library name: CM10_T4_D2_E11


title: Wild-type mouse 3, Ethanol feeding

description:
Library name: Etoh_G_WT_03
Column name in gene_count_CD44_KO_Ethanol.csv: Etoh_G_WT_03

value: WT


title: WT_systemic_ATP_30min_Rep3

description:
Library name: WT_S_ATP_3
Systemic tissue analyzed, local leaf treated with eATP

value: 300µM βγmeATP


title: Wild-type mouse 2, Ethanol feeding

description:
Library name: Etoh_G_WT_02
Column name in gene_count_CD44_KO_Ethanol.csv: Etoh_G_WT_02


title: Adenosine_P01_B02

description: Library name: LigandScreen-P01-20230825-010_S10


title: MCF7, 3-hydroxybenzophenone, CM10, 6h, B03

description: Library name: CM10_T4_D2_B03


title: Wild-type mouse 1, Ethanol feeding

description:
Library name: Etoh_G_WT_01
Column name in gene_count_CD44_KO_Ethanol.csv: Etoh_G_WT_01


title: WT_systemic_ATP_30min_Rep2

description:
Library name: WT_S_ATP_2
Systemic tissue analyzed, local leaf treated with eATP


title: Activin A_P01_A02

description: Library name: LigandScreen-P01-20230825-009_S9


title: MCF7, 3-hydroxybenzophenone, CM10, 6h, G05

description: Library name: CM10_T4_D1_G05


title: SL028_CBP_RH_HOMO

first: Laura

last: Pasqualucci

address: 1130 St Nicholas Avenue

department: Institute for Cancer Genetics

description: Library name: SL028_CBP_RH_HOMO

data_processing:
Sequencing data were acquired through the default Illumina pipeline using Casava V1.8.
Reads were aligned to the mouse genome (mm10) using HISAT2.
Reads were mapped to exons using FeatureCounts and a curated version of Gencode M19 (obtained by removing transcript types tagged as readthrough, antisense RNA, rRNA, miRNA) to produce count tables, which were converted to transcript per million (TPM) values using the sum of the exons as the transcript length.
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing the read counts per gene

source_name: Sorted germinal center B cells from mice immunized with SRBC

growth_protocol: Mice were immunized by intraperitoneal injection of sheep red blood cells. Analysis was performed 12 days after immunization.

extract_protocol:
Total RNA was isolated using the NucleoSpin RNA XS kit (Machery Nagel), according to the manufacturer's instructions.
Libraries were prepared using the TruSeq RNA Sample Preparation v2 kit (Illumina).

treatment_protocol: Germinal center B cells (B220+/PNA+/CD95+)  were isolated by cytofluorimetric sorting, after B cell isolation using the Miltenyi B cell isolation kit

value: Crebbp-RH/RH (homozygous)

value: Spleen

value: total RNA

value: SRBC immunization 10 days prior to collection

value: Crebbp-RH cohort


title: ACh_P01_H01

description: Library name: LigandScreen-P01-20230825-008_S8


title: MCF7, 3-hydroxybenzophenone, CM10, 6h, E08

description: Library name: CM10_T4_D1_E08


title: SL027_CBP_RH_HET

description: Library name: SL027_CBP_RH_HET

value: Sorted germinal center B cells from mice immunized with SRBC

value: Crebbp-RH/WT (heterozygous)


title: p2k1p2k2_systemic_Mock_30min_Rep3

description:
Library name: P2K_S_M_3
Systemic tissue analyzed, local leaf treated with a mock

value: rosette leaf

value: Mock


title: MCF7, 3-hydroxybenzophenone, CM10, 6h, D11

description: Library name: CM10_T4_D1_D11

value: Breast; Mammary gland


title: 7a,25-OHC_P01_G01

description: Library name: LigandScreen-P01-20230825-007_S7


title: p2k1p2k2_systemic_Mock_30min_Rep2

description:
Library name: P2K_S_M_2
Systemic tissue analyzed, local leaf treated with a mock


title: SL026_CBP_RH_HET

description: Library name: SL026_CBP_RH_HET


title: MCF7, 3-hydroxybenzophenone, CM10, 6h, A03

description: Library name: CM10_T4_D1_A03


title: CTRL-Ethanol_P01_F01

description: Library name: LigandScreen-P01-20230825-006_S6


title: p2k1p2k2_systemic_Mock_30min_Rep1

description:
Library name: P2K_S_M_1
Systemic tissue analyzed, local leaf treated with a mock


title: SL025_CBP_RH_WT

description: Library name: SL025_CBP_RH_WT

value: Crebbp-WT


title: CTRL-Ethanol_P01_E01

description: Library name: LigandScreen-P01-20230825-005_S5


title: Day 21 bleo NP-treated mouse 2

city: Ann Arbor

first: Hannah

last: Viola

state: Michigan

address: 1600 Huron Parkway

department: Biomedical Engineering

institute: University of Michigan - Ann Arbor

description:
Library name: 12757-HV-6
Column name in gene_expected_count.annot.txt: X12757.HV.6

data_processing:
BCL Convert Conversion Software v4.3.6 (Illumina) was used to generate de-multiplexed fastq files.
The reads were trimmed using Cutadapt v4.8 (Martin, 2011).  Martin,M. (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMB net.journal, 17, 10–12.
FastQC v0.11.8 was used to ensure the quality of data (Andrews, 2010)  Andrews,S. (2010) FastQC: A quality control tool for high throughput sequence data.
Fastq Screen v0.15.3 was used to screen for various types of contamination (Wingett and Andrews, 2018).  Wingett,S.W. and Andrews,S. (2018) Fastq screen: A tool for multi-genome mapping and quality control [version 1; referees: 3 approved, 1 approved with reservations]. F1000Research, 7, 1–13
Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR v2.7.8a (Dobin et al., 2013) and assigned count estimates to genes with RSEM v1.3.3 (Li and Dewey, 2011). Alignment options followed ENCODE standards for RNA-seq.  Dobin,A. et al. (2013) STAR: Ultrafast universal RNA-seq aligner. Bioinformatics, 29, 15–21. Li,B. and Dewey,C.N. (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics.
Multiqc v1.20 compiled the results from several of these tools and provided a detailed and comprehensive quality control report (Ewels et al., 2016)  Ewels,P. et al. (2016) MultiQC: Summarize analysis results for multiple tools and samples in a single report
Assembly: GRCm38
Supplementary files format and content: tab-delimited counts with genes on rows and samples on columns. First four columns contain Ensembl database terms "gene_id", "entrezgene_id", "external_gene_name", and "description", followed by counts columns for all samples.
Supplementary files format and content: gene_expected_count.annot.txt: raw counts
Supplementary files format and content: gene_FPKM_annot.txt: FPKM (Fragments Per Kilobase Million) normalized counts
Supplementary files format and content: gene_TPM_annot.txt: TPM (Transcripts Per Kilobase Million) normalized counts

source_name: Lung

extract_protocol:
Whole lung lobes were excised from large airway and trachea, and all 5 lobes were homogenized at 15000 rpm for 1-3 minutes in 1 mL TRIzol® reagent (Zymo Research) to achieve a pipetteable solution. This solution was spun to remove solids and 150 μL supernatant was diluted with 650 μL TRIzol®. Then, RNA was extracted using the Direct-Zol™ RNA MiniPrep Plus with Zymo-Spin™ IIICG Columns (Zymo Research Corporation R2070) according to manufacturer instructions.
A TruSeq-based kit was used during library preparation. The adapter sequences for this kit are
R1: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA
R2: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
The product name of the library preparation kit is NEB.
This pool was subjected to 151bp paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq 6000, Control Software Version: 1.8.1, RTA Version: v3.4.4).

treatment_protocol: We fabricated polymeric NPs comprised of a poly(lactide-co-glycolide) (PLG) core coated with the surfactant poly(ethylene-alt-maleic anhydride) (PEMA) using oil-in-water emulsion followed by solvent evaporation. NPs had a mean diameter of  609.22 ± 15.30 nm, polydispersity index (PDI) of 0.322 ± 0.099, and surface charge of -45.61 ± 5.48 mV across 5 independent batches. Pulmonary fibrosis was induced using the oropharyngeal bleomycin mouse model (0.0125 U/mouse ~ 0.5 U/kg). NPs were delivered intravenously via retro-orbital injection at 2 mg/dose in phosphate-buffered saline (Vehicle) beginning on day 14 post-bleomycin and daily until Day 18 for 5 total doses (2 mg/dose). Bulk RNA-sequencing was conducted on whole lung homogenates from 3 conditions: Day 14 (pre-treatment, n=4), Day 21 NP (n=4), and Day 21 Vehicle (n=4) (mean 44 ± 7.7 million reads/sample).

value: Lung

value: male

tag: age

value: 10 weeks

tag: time

value: Day 21

value: intravenous NPs


title: WT_systemic_ATP_30min_Rep1

description:
Library name: WT_S_ATP_1
Systemic tissue analyzed, local leaf treated with eATP

value: 300µM βγmeATP


title: MCF7, Avobenzone, CM10, 6h, G04

description: Library name: CM10_T1_D3_G04

value: epithelial cell

value: Adenocarcinoma

value: test


title: p2k1p2k2_systemic_L-Glu_30min_Rep3

description:
Library name: P2K_S_GLU_3
Systemic tissue analyzed, local leaf treated with L-Glu

value: 100mM L-Glu


title: SL023_CBP_RH_HOMO

description: Library name: SL023_CBP_RH_HOMO

value: Crebbp-RH/RH (homozygous)

value: Spleen

value: total RNA

value: SRBC immunization 10 days prior to collection

value: Crebbp-RH cohort


title: MCF7, Avobenzone, CM10, 6h, F07

description: Library name: CM10_T1_D3_F07

value: Breast; Mammary gland


title: CTRL-DMSO_P01_D01

description: Library name: LigandScreen-P01-20230825-004_S4


title: p2k1p2k2_systemic_L-Glu_30min_Rep2

description:
Library name: P2K_S_GLU_2
Systemic tissue analyzed, local leaf treated with L-Glu

value: rosette leaf


title: CTRL-DMSO_P01_C01

description: Library name: LigandScreen-P01-20230825-003_S3


title: p2k1p2k2_systemic_L-Glu_30min_Rep1

description:
Library name: P2K_S_GLU_1
Systemic tissue analyzed, local leaf treated with L-Glu


title: MCF7, Avobenzone, CM10, 6h, E10

description: Library name: CM10_T1_D3_E10


title: SL022_CBP_RH_HOMO

description: Library name: SL022_CBP_RH_HOMO

value: Sorted germinal center B cells from mice immunized with SRBC


title: SL021_CBP_RH_HET

description: Library name: SL021_CBP_RH_HET

value: Crebbp-RH/WT (heterozygous)


title: p2k1p2k2_systemic_ATP_30min_Rep3

description:
Library name: P2K_S_ATP_3
Systemic tissue analyzed, local leaf treated with eATP


title: CTRL-WM_P01_B01

description: Library name: LigandScreen-P01-20230825-002_S2


title: SL020_CBP_RH_HET

description: Library name: SL020_CBP_RH_HET


title: CTRL-WM_P01_A01

description: Library name: LigandScreen-P01-20230825-001_S1


title: MCF7, Avobenzone, CM10, 6h, H01

description: Library name: CM10_T1_D2_H01


title: MCF7, Avobenzone, CM10, 6h, F04

description: Library name: CM10_T1_D2_F04


title: HT29-MTX cells, MUC1-deltaMUC1, Salmonella infection, replicate 4

city: Utrecht

first: Karin

last: Strijbis

state: Utrecht

address: Yalelaan 1

department: Biomolecular Health Sciences

country: Netherlands

institute: Utrecht University

description: Library name: KO_wSal_4

data_processing:
RNA sequencing data analysis was performed according to a standardized RNA sequencing analysis pipeline. Briefly, quality control of all sequence reads was checked using FastQC (version 0.11.9) for raw sequence reads and MultiQC (version 1.13 (8dd46e3) for sequences after alignment. Sequencing reads were mapped to the human genome (assembly GRCh38.109) using the STAR RNA aligner (version 2.7.10b). Then, FeatureCounts was used to count the mapped reads (version 2.0.3). For differential expression genes (DEGs) analysis, transcript counts were analyzed using RStudio (RStudio 2023.03.1+446) package DEseq2 (version 1.46.0) for DEGs, and FDR-corrected values of p < 0.05 were considered statistically significant.
Assembly: human genome (assembly GRCh38.109)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: cell line

growth_protocol: The human colorectal carcinoma cell lines HT29-MTX (MUC1-WT), HT29-MTX-ΔMUC1 (ΔMUC1) [21], and HT29-MTX-MUC1-ΔCT (MUC1-ΔCT) (this study) were routinely cultured in 25 cm2 flasks in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal calf serum (FCS) at 37°C in 10% CO2.

extract_protocol:
Total RNA was extracted from HT29-MTX cultures using the TRIzol standard protocol (Thermo)
RNA was used for mRNA library preparation using the Stranded Total RNA Prep, Ligation with Ribo-Zero Plus (Illumina)

treatment_protocol: Salmonella was grown overnight on LB agar (Biotrading) and the next day, a single colony was picked and inoculated in 10 mL of LB medium (Biotrading) containing ampicillin (100 μg/ml) or kanamycin (50 μl/ml) and incubated overnight at 37°C while shaking at 160 rpm. To induce optimal SiiE expression, the overnight Salmonella culture was inoculated at 1:1000 dilution in 25 mL LB medium without antibiotics and incubated at 37°C while shaking at 160 rpm and grown till late logarithmic phase to an OD600 of 1. 1 ml of bacterial culture was centrifuged for 2 minutes at 8000 rpm and the pellet was resuspended in 1 ml DPBS.  Immediately after preparing the bacterial suspension, the bacteria were added to the confluent HT29-MTX cultures grown in 12-well plates in DMEM without FCS.

value: cell line

value: epithelial colorectal adenocarcinoma cells

value: Salomella infected


title: p2k1p2k2_systemic_ATP_30min_Rep2

description:
Library name: P2K_S_ATP_2
Systemic tissue analyzed, local leaf treated with eATP

value: 300µM βγmeATP


title: SL019_CBP_RH_WT

description: Library name: SL019_CBP_RH_WT

value: Crebbp-WT

value: Crebbp-KO cohort


title: HT29-MTX cells, MUC1-deltaMUC1, Salmonella infection, replicate 3

description: Library name: KO_wSal_3


title: MCF7, Avobenzone, CM10, 6h, E07

description: Library name: CM10_T1_D2_E07

value: epithelial cell

value: Adenocarcinoma

value: test


title: glr3.3glr3.6_systemic_Mock_30min_Rep3

description:
Library name: GLR_S_M_3
Systemic tissue analyzed, local leaf treated with a mock

value: Mock


title: p2k1p2k2_systemic_ATP_30min_Rep1

description:
Library name: P2K_S_ATP_1
Systemic tissue analyzed, local leaf treated with eATP


title: HT29-MTX cells, MUC1-deltaMUC1, Salmonella infection, replicate 2

description: Library name: KO_wSal_2


title: SL018_CBP_KO

description: Library name: SL018_CBP_KO

value: Crebbp-KO (homozygous)

value: Spleen

value: total RNA


title: MCF7, Avobenzone, CM10, 6h, D10

description: Library name: CM10_T1_D2_D10

value: Breast; Mammary gland


title: SL017_CBP_KO

description: Library name: SL017_CBP_KO

value: SRBC immunization 10 days prior to collection


title: glr3.3glr3.6_systemic_Mock_30min_Rep2

description:
Library name: GLR_S_M_2
Systemic tissue analyzed, local leaf treated with a mock

value: rosette leaf


title: HT29-MTX cells, MUC1-deltaMUC1, Salmonella infection, replicate 1

description: Library name: KOwSal1


title: Mouse medial prefrontal cortex tissue from LPS and sedanolide co-treated group replicate 5

city: hangzhou

first: fangla

last: luo

address: zhejiang university zijingang campus

institute: zhejiang university

description: Library name: LPS_SDN5

data_processing:
Raw sequencing reads were filtered using fastp. Clean reads were aligned to the mouse reference genome using HISAT2. Transcript assembly and quantification were performed using StringTie and RSEM. Differentially expressed genes were identified using DESeq2 and DEGseq.
Assembly: Mus musculus GRCm39release-109
Supplementary files format and content: Processed data files contain gene-level expression values quantified by RSEM and reported as TPM (transcripts per million). Differential expression analysis results generated using DESeq2/DEGseq are provided as tab-delimited text files.

source_name: medial prefrontal cortex

extract_protocol:
Total RNA was extracted from mouse medial prefrontal cortex tissues using TRIzol reagent according to the manufacturer's instructions. RNA quality was assessed using NanoDrop ND-2000 and Agilent 5300 Bioanalyzer.
RNA libraries were prepared using Illumina Stranded mRNA Prep, Ligation kit. Poly(A)-containing mRNA was enriched using oligo(dT) beads.

value: medial prefrontal cortex

value: brain tissue

value: WT

value: Sedanolide administration (20 mg/kg, i.g.) starting 3 days before LPS injection and continuing for 8 days; LPS (1 mg/kg, i.p.) injection for 5 consecutive days


title: NPY_P03_G09

description: Library name: LigandScreen-P03-20230901-071_S167


title: MCF7, Avobenzone, CM10, 6h, G01

description: Library name: CM10_T1_D1_G01


title: glr3.3glr3.6_systemic_Mock_30min_Rep1

description:
Library name: GLR_S_M_1
Systemic tissue analyzed, local leaf treated with a mock


title: MCF7, Avobenzone, CM10, 6h, E04

description: Library name: CM10_T1_D1_E04


title: HT29-MTX cells, MUC1-deltaCT, Salmonella infection, replicate 4

description: Library name: dCT_wSal_4

value: cell line

value: epithelial colorectal adenocarcinoma cells

value: Salomella infected


title: SL016_CBP_WT

description: Library name: SL016_CBP_WT

value: Sorted germinal center B cells from mice immunized with SRBC

value: Crebbp-WT

value: Crebbp-KO cohort


title: SL015_CBP_WT

description: Library name: SL015_CBP_WT


title: MCF7, Avobenzone, CM10, 6h, D07

description: Library name: CM10_T1_D1_D07

value: epithelial cell

value: Adenocarcinoma

value: test


title: SL013_CBP_KO

description: Library name: SL013_CBP_KO

value: Crebbp-KO (homozygous)

value: Spleen

value: total RNA


title: HT29-MTX cells, MUC1-deltaCT, Salmonella infection, replicate 3

description: Library name: dCT_wSal_3


title: Day 14 bleo mouse 4

description:
Library name: 12757-HV-4
Column name in gene_expected_count.annot.txt: X12757.HV.4

value: Lung

value: male

value: 10 weeks

value: Day 14


title: glr3.3glr3.6_systemic_L-Glu_30min_Rep3

description:
Library name: GLR_S_GLU_3
Systemic tissue analyzed, local leaf treated with L-Glu

value: rosette leaf

value: 100mM L-Glu


title: HT29-MTX cells, MUC1-deltaCT, Salmonella infection, replicate 2

description: Library name: dCT_wSal-2

value: cell line

value: epithelial colorectal adenocarcinoma cells


title: glr3.3glr3.6_systemic_L-Glu_30min_Rep2

description:
Library name: GLR_S_GLU_2
Systemic tissue analyzed, local leaf treated with L-Glu


title: MCF7, Avobenzone, CM10, 6h, B10

description: Library name: CM10_T1_D1_B10

value: Breast; Mammary gland


title: SL012_CBP_WT

description: Library name: SL012_CBP_WT

value: Sorted germinal center B cells from mice immunized with SRBC

value: Crebbp-WT

value: SRBC immunization 10 days prior to collection


title: glr3.3glr3.6_systemic_L-Glu_30min_Rep1

description:
Library name: GLR_S_GLU_1
Systemic tissue analyzed, local leaf treated with L-Glu


title: MCF7, DMSO, CM10, 6h, G08

description: Library name: CM10_DMSO_G08

value: epithelial cell

value: Adenocarcinoma

value: vehicle


title: CD8, rep3

city: Princeton

first: Yuri

last: Pritykin

state: NJ

address: 245 Carl Icahn Lab

department: QCB

institute: Princeton

description: Hi-C on sorted T cells

data_processing:
Hi-C reads were aligned to the mouse UCSC mm10 GRCm38 genome (chromosomes 1-19, X, Y) downloaded from the 4DNucleome (4DNFI2493SDN) using bwa mem version 0.7.17, with settings --SP5M. Pairs files were generated using pairtools parse version 0.3.0 with a min-mapq cutoff of 30 and --walks-policy 5unique, followed by pairtools dedup with default parameters, and pairtools select for the following pair types: UU, UR, and UR. Pairs files were mapped into cool files using cooler version 0.8.11. Hi-C data in these cool files was normalized using cooler balance with default parameters for each sample separately and for merged biological replicates of each condition across all conditions. This way, balancing normalization was applied to both intrachromosomal and interhcromosomal Hi-C signal.
Assembly: mm10
Supplementary files format and content: mcool: hi-c pairs at different resolutions

source_name: SLO

extract_protocol:
Mice: 6-week-old female C57BL/6J mice were obtained from The Jackson Laboratory (Bar Harbor, ME). Experiments using C57BL/6J mice were performed in accordance with a protocol (number 3063), which was reviewed and approved by the Institutional Animal Care and Use Committee (IACUC) of Princeton University.
Isolation and preparation of CD4 and CD8 T cells from mouse spleen: Mice were euthanized by intraperitoneal injection of ketamine/xylazine at a supratherapeutic dose. Spleens were collected and placed into 5 mL of serum-free Dulbecco’s Modified Eagle Media (DMEM, Thermo Fisher Scientific, Waltham, MA, 11995081). Individual spleens were placed on 100-μm strainers then mechanically dissociated using the plunger of a 3 mL syringe. The strainer was washed with 5 mL of serum-free DMEM in which the splenocytes were subsequently resuspended. The single cell suspension was centrifuged at 1,300 rpm for 5 min at 4°C, then the pellet was resuspended in 1x BD Pharm Lyse lysis buffer (BD Biosciences, Franklin Lakes, NJ, 55599) and incubated at room temperature in the dark for 15 min. Lysis was quenched using DMEM supplemented with 10% (v/v) FBS and 1% (v/v) penicillin-streptomycin. The splenocyte suspensions were spun at 1,300 rpm for 5 min at 4°C, then washed with FACS buffer (1% (v/v) FBS in PBS). The cells were counted using 0.4% trypan blue solution (Thermo Fisher Scientific, 15250061) and a hemocytometer, then resuspended at a concentration of 1 x 107 cells/mL. An aliquot of cells was set aside as an unstained control. Another aliquot of cells was set aside to generate the live/dead control in which half of the cells are heat shocked at 95°C for 5 min, set on ice for 2 min, and combined with the live cells.
Antibody staining and fluorescence-activated cell sorting: The following fluorophore-conjugated antibodies were used for flow cytometry: CD45-FITC (clone 30-F11, 1.25 μg/mL, BioLegend, San Diego, CA 103108), CD3-Alexa700 (clone 17A2, 1 μg/mL, Invitrogen, Waltham, MA, 56-0032-82), CD4-PE-Cy7 (clone RM4-5, 1 μg/mL, Invitrogen, 25-0042-82), CD8-BV510 (clone 53-6.7, 1 μg/mL, BioLegend, 100752). The antibody cocktail was prepared in FACS buffer, then incubated with cells for 30 min at 4°C in the dark. The splenocyte suspensions were washed 2x in FACS buffer. To serve as a viability marker, DAPI (1 μg /mL, Sigma-Aldrich, St. Louis, MO, D9542) was directly added to antibody-stained cells and the live/dead control 15 min prior to FACS acquisition. Compensation controls were prepared using AbC Total Antibody Compensation Bead Kit (Invitrogen, A10497). The FACSAria Fusion Flow Cytometer (BD Biosciences) or the MA-900 cell sorter (Sony Biotechnology, San Jose, CA) was used to perform cell sorting and acquired data were analyzed using BD FACSDiva or MA900 software. For collection of each T cell subset, the samples were gated as follows: for CD3+ T cells, CD45+ CD3+; for CD4+ T cells, CD45+ CD3+ CD4+ CD8- ; and for CD8+ T cells, CD45+ CD3+ CD4- CD8+. Cells were sorted into FACS buffer and maintained at 4°C.

value: SLO

value: Bulk CD8

value: WT


title: HT29-MTX cells, MUC1-deltaCT, Salmonella infection, replicate 1

description: Library name: dCTwSal1

value: Salomella infected


title: HT29-MTX cells, MUC1-WT, Salmonella infection, replicate 4

description: Library name: WT_wSal_4


title: MCF7, DMSO, CM10, 6h, F05

description: Library name: CM10_DMSO_F05


title: CD8, rep2

description: Hi-C on sorted T cells


title: glr3.3glr3.6_systemic_ATP_30min_Rep3

description:
Library name: GLR_S_ATP_3
Systemic tissue analyzed, local leaf treated with eATP

value: 300µM βγmeATP


title: glr3.3glr3.6_systemic_ATP_30min_Rep2

description:
Library name: GLR_S_ATP_2
Systemic tissue analyzed, local leaf treated with eATP


title: HT29-MTX cells, MUC1-WT, Salmonella infection, replicate 3

description: Library name: WT_wSal_3


title: CD8, rep1

description: Hi-C on sorted T cells


title: HT29-MTX cells, MUC1-WT, Salmonella infection, replicate 2

description: Library name: WT_wSal_2


title: MCF7, DMSO, CM10, 6h, C10

description: Library name: CM10_DMSO_C10


title: CD4, rep3

description: Hi-C on sorted T cells

value: Bulk CD4


title: glr3.3glr3.6_systemic_ATP_30min_Rep1

description:
Library name: GLR_S_ATP_1
Systemic tissue analyzed, local leaf treated with eATP

value: rosette leaf


title: MCF7, DMSO, CM10, 6h, D02

description: Library name: CM10_DMSO_D02


title: MCF7, DMSO, CM10, 6h, B12

description: Library name: CM10_DMSO_B12


title: CD4, rep2

description: Hi-C on sorted T cells


title: HT29-MTX cells, MUC1-WT, Salmonella infection, replicate 1

description: Library name: WTwSal1


title: Human macrophages, Infected L. interrogans Pomona 202100004, 6 hr, replicate 2

city: Paris

first: Alexandre

last: Giraud-Gatineau

address: 25-28 rue du docteur roux

department: Microbiology

institute: Institut Pasteur

description:
Library name: Sample 21
N89DPD_21_Infection_PO_rep_8

data_processing:
Quality of the fastq files was assessed using FastQC v0.12.1. Reads were then quality filtered using fastp v0.24.0 with poly-X tail trimming, 3' quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length requirement of 50 bp. Quality-filtered reads were aligned to the reference genome using STAR aligner v2.7.11 with non-canonical splice junction removal and output of unmapped reads, followed by coordinate sorting using samtools v1.22.1. PCR and optical duplicates were removed using UMI-based deduplication with UMIcollapse v1.1.0. Alignment quality metrics, strand specificity, and read distribution across genomic features were assessed using RSeQC v5.0.4 and Qualimap v2.3, with results aggregated into a comprehensive quality control report using MultiQC v1.32. Gene-level expression quantification was performed using featureCounts (subread package v2.1.1) with strand-specific counting, multi-mapping read fractional assignment, exons and three prime UTR as the feature identifiers, and grouped by gene_id. Final gene counts were annotated with gene biotype and other metadata extracted from the reference GTF file.  Sample-sample correlations for sample-sample heatmap and PCA were calculated on normalized counts (TMM, trimmed mean of M-values) using Pearson correlation. Differential expression was done with edgeR v4.0.16 using standard practice including filtering for low-expressed genes with edgeR::filterByExprwith default values. Functional enrichment, when available, is performed using gene set enrichment analysis with gseapy v0.12 using the MSigDB Hallmark gene set.
Assembly: Human samples: GRCh38_114; Murine samples: GRCm39_114
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
Total RNAs from human and murine macrophages at 6 hr post-infection were extracted using QIAzol lysis reagent (Qiagen) and purified using RNeasy mini kit (Qiagen) with a DNAse treatment.
RNA-seq libraries were prepared by Plasmidsaurus using their proprietary transcriptomics workflow. Briefly, mRNA was reverse-transcribed into complementary DNA (cDNA), followed by second-strand synthesis. The resulting cDNA was subjected to tagmentation, indexing, and PCR amplification to generate sequencing-ready libraries. This protocol is based on a 3′-end counting strategy, in which reads are generated from the 3′ end of transcripts to enable accurate and efficient quantification of gene expression while minimizing transcript length bias.

treatment_protocol: THP-1 cells (a human monocyte cell line; ATCC TIB-202) and Raw 264.7 cells (a murine macrophage cell line) were cultured in RPMI 1640 medium (Gibco) supplemented with 10% heat-inactivated fetal bovine serum (Sigma) and 2 mM L-glutamine (Gibco). THP-1 cells were differentiated/activated into macrophages by a treatment with 50 nM PMA for 2 days following by a 24 hr incubation without PMA. Macrophages were infected with L. interrogans at a multiplicity of infection (MOI) of 50 bacteria-per-cell during 6 hr. Cells were incubated in 5% CO2 at 37°C.


title: Human macrophages, Infected L. interrogans Pomona 202100004, 6 hr, replicate 1

description:
Library name: Sample 20
N89DPD_20_Infection_PO_rep_7

growth_protocol: THP-1 cells (a human monocyte cell line; ATCC TIB-202) and Raw 264.7 cells (a murine macrophage cell line) were cultured in RPMI 1640 medium (Gibco) supplemented with 10% heat-inactivated fetal bovine serum (Sigma) and 2 mM L-glutamine (Gibco). THP-1 cells were differentiated/activated into macrophages by a treatment with 50 nM PMA for 2 days following by a 24 hr incubation without PMA.


title: HT29-MTX cells, MUC1-deltaMUC1, No treatment, replicate 4

description: Library name: KO-Sal_4

value: uninfected


title: CD4, rep1

description: Hi-C on sorted T cells


title: iCAR, Myricetin, Ci11, 6h, G04

description: Library name: Ci11_T8_D3_G04

source_name: heart muscle cells

value: heart muscle cells

value: iCAR

value: human induced pluripotent stem cells (iPSCs)

value: iPSC-derived cardiomyocytes

value: test


title: Human macrophages, Infected L. interrogans Pomona 201902969, 6 hr, replicate 2

description:
Library name: Sample 19
N89DPD_19_Infection_PO_rep_6


title: HT29-MTX cells, MUC1-deltaMUC1, No treatment, replicate 3

description: Library name: KO-Sal_3

value: cell line

value: epithelial colorectal adenocarcinoma cells


title: iCAR, Myricetin, Ci11, 6h, F07

description: Library name: Ci11_T8_D3_F07


title: SL024_CBP_RH_WT

description: Library name: SL024_CBP_RH_WT

value: Sorted germinal center B cells from mice immunized with SRBC

value: Crebbp-WT

value: Spleen

value: total RNA

value: SRBC immunization 10 days prior to collection

value: Crebbp-RH cohort


title: Human macrophages, Infected L. interrogans Pomona 201902969, 6 hr, replicate 1

description:
Library name: Sample 18
N89DPD_18_Infection_PO_rep_5

value: WT


title: rLSL, rep3

description: Hi-C on sorted T cells

extract_protocol:
A cell suspension was made from pooled secondary lymphoid organs (spleen, pLNs and mLNs) of Foxp3GFP/LSL mice (cite PMID 15780990; 34426690) by meshing the organs through a 100-μm strainer (Corning, 07-201-432) with a syringe plunger. CD4+ T cells were enriched with the Dynabeads Flowcomp Mouse CD4 Kit (Thermo Fisher, 11461D) according to the manufacturer’s instructions, stained with antibodies, washed extensively, resuspended in isolation buffer (PBS with 2% FBS, 10 mM HEPES buffer, 1% l-glutamine and 2 mM EDTA), and sorted on a FACSAria (BD) instrument. Treg cells were sorted as TCRβ+CD4+CD8−NK1.1−Foxp3-GFP+Thy-1.1−, and naïve conventional CD4+ T cells as TCRβ+CD4+CD8−NK1.1−Foxp3-GFP−Thy-1.1−CD44loCD62Lhi. Wannabe Treg cells were sorted from Foxp3GFP/LSL mice as follows: naïve wannabe Treg cells: TCRβ+CD4+CD8−NK1.1−Foxp3-GFP−Thy-1.1+ CD44loCD62Lhi; activated wannabe Treg cells: TCRβ+CD4+CD8−NK1.1−Foxp3-GFP−Thy-1.1+CD44hiCD62L−; Treg cells and conventional CD4+ T cells were sorted from Foxp3DTR mice as follows: naïve Treg cells: TCRβ+CD4+CD8−NK1.1−Foxp3-DTR+ CD44loCD62Lhi; activated Treg cells: TCRβ+CD4+CD8−NK1.1−Foxp3-DTR+ CD44hiCD62L−; naïve conventional CD4+ T cells: TCRβ+CD4+CD8−NK1.1−Foxp3-DTR−CD44loCD62Lhi; activated conventional CD4+ T cells: TCRβ+CD4+CD8−NK1.1−Foxp3-DTR− CD44hiCD62L−. 100,000 cells were sorted for each population per replicate.
Hi-C for Tcon and Treg cells: Hi-C was performed as previously described (Viny et al., 2019). Briefly, sorted T cell populations (approximately 1x105) were cross-linked in 1% formaldehyde for 10 minutes and quenched in 125mM glycine. Cross-linked cells were lysed and chromatin was digested using the Arima HiC+ kit (Arima Genomics, San Diego, CA) using protocol adaptations for low cell input. Digested and reverse crosslinked DNA was eluted in 100uL and fragmented to 350 bps using a Covaris LE220Rsc sonicator (Covaris, Woburn, MA). Sheared genomic material was enriched for biotinylated DNA using streptavidin beads followed by library preparation using Arima protocol modifications for Accel-NGS 2S DNA plus library kit (IDT, Coralville, IA). After end repair and ligation, libraries were quantified using the KAPA library quantification kit (Roche, Indianapolis, IN) and PCR amplified for the number of cycles required to generate >4nM per library. Hi-C libraries were sequenced on an Illumina NovaSeq and raw sequencing data in the FASTQ format were obtained.

value: SLO

value: Resting Foxp3-KO (LSL) Treg


title: HT29-MTX cells, MUC1-deltaMUC1, No treatment, replicate 2

description: Library name: KO-Sal_2

value: uninfected


title: iCAR, Myricetin, Ci11, 6h, E10

description: Library name: Ci11_T8_D3_E10

value: heart muscle cells


title: rLSL, rep2

description: Hi-C on sorted T cells


title: Human macrophages, Infected L. interrogans Pomona 201700303, 6 hr, replicate 2

description:
Library name: Sample 17
N89DPD_17_Infection_PO_rep_4


title: iCAR, Myricetin, Ci11, 6h, A02

description: Library name: Ci11_T8_D3_A02

value: iCAR


title: Human macrophages, Infected L. interrogans Pomona 201700303, 6 hr, replicate 1

description:
Library name: Sample 16
N89DPD_16_Infection_PO_rep_3


title: rLSL, rep1

description: Hi-C on sorted T cells


title: HT29-MTX cells, MUC1-deltaCT, No treatment, replicate 4

description: Library name: dCT-Sal_4


title: iCAR, Myricetin, Ci11, 6h, H01

description: Library name: Ci11_T8_D2_H01

value: human induced pluripotent stem cells (iPSCs)


title: rTreg, rep3

description: Hi-C on sorted T cells

value: Resting Treg


title: Human macrophages, Infected L. interrogans Pomona 201801210, 6 hr, replicate 2

description:
Library name: Sample 15
N89DPD_15_Infection_PO_rep_2


title: rTreg, rep2

description: Hi-C on sorted T cells


title: iCAR, Myricetin, Ci11, 6h, F04

description: Library name: Ci11_T8_D2_F04

value: iPSC-derived cardiomyocytes

value: test


title: MCF7, Avobenzone, CM10, 6h, A02

description: Library name: CM10_T1_D3_A02

value: Breast; Mammary gland

value: epithelial cell

value: Adenocarcinoma


title: HT29-MTX cells, MUC1-deltaCT, No treatment, replicate 3

description: Library name: dCT-Sal_3

value: cell line

value: epithelial colorectal adenocarcinoma cells


title: rTreg, rep1

description: Hi-C on sorted T cells


title: HT29-MTX cells, MUC1-deltaCT, No treatment, replicate 2

description: Library name: dCT-Sal_2


title: Human macrophages, Infected L. interrogans Pomona 201801210, 6 hr, replicate 1

description:
Library name: Sample 14
N89DPD_14_Infection_PO_rep_1


title: iCAR, Myricetin, Ci11, 6h, D10

description: Library name: Ci11_T8_D2_D10


title: iCAR, Myricetin, Ci11, 6h, E07

description: Library name: Ci11_T8_D2_E07


title: Human macrophages, Infected L. interrogans Icterohaemorrhagiae 202102907, 6 hr, replicate 2

description:
Library name: Sample 13
N89DPD_13_Infection_IC_rep_10


title: rTcon, rep3

description: Hi-C on sorted T cells

value: Resting Tcon


title: HT29-MTX cells, MUC1-deltCT, No treatment, replicate 1

description: Library name: dCT-Sal1


title: Human macrophages, Infected L. interrogans Icterohaemorrhagiae 202102907, 6 hr, replicate 1

description:
Library name: Sample 12
N89DPD_12_Infection_IC_rep_9


title: iCAR, Myricetin, Ci11, 6h, G01

description: Library name: Ci11_T8_D1_G01


title: rTcon, rep2

description: Hi-C on sorted T cells


title: HT29-MTX cells, MUC1-WT, No treatment, replicate 3

description: Library name: WT-Sal_3


title: Human macrophages, Infected L. interrogans Icterohaemorrhagiae 202100001, 6 hr, replicate 2

description:
Library name: Sample 11
N89DPD_11_Infection_IC_rep_8


title: HT29-MTX cells, MUC1-WT, No treatment, replicate 4

description: Library name: WT-Sal_4


title: iCAR, Myricetin, Ci11, 6h, E04

description: Library name: Ci11_T8_D1_E04


title: rTcon, rep1

description: Hi-C on sorted T cells


title: Human macrophages, Infected L. interrogans Icterohaemorrhagiae 202100001, 6 hr, replicate 1

description:
Library name: Sample 10
N89DPD_10_Infection_IC_rep_7


title: iCAR, Myricetin, Ci11, 6h, D07

description: Library name: Ci11_T8_D1_D07


title: HT29-MTX cells, MUC1-WT, No treatment, replicate 2

description: Library name: WT-Sal_2


title: aLSL, rep3

description: Hi-C on sorted T cells

value: Active Foxp3-KO (LSL) Treg


title: Human macrophages, Infected L. interrogans Icterohaemorrhagiae 202102995, 6 hr, replicate 2

description:
Library name: Sample 9
N89DPD_9_Infection_IC_rep_6

value: WT


title: iCAR, Myricetin, Ci11, 6h, B10

description: Library name: Ci11_T8_D1_B10


title: iCAR, DMSO, Ci11, 6h, G08

description: Library name: Ci11_DMSO_G08

value: vehicle


title: aLSL, rep1

description: Hi-C on sorted T cells

value: SLO


title: Human macrophages, Infected L. interrogans Icterohaemorrhagiae 202102995, 6 hr, replicate 1

description:
Library name: Sample 8
N89DPD_8_Infection_IC_rep_5


title: iCAR, DMSO, Ci11, 6h, F05

description: Library name: Ci11_DMSO_F05


title: aTreg, rep3

description: Hi-C on sorted T cells

value: Active Treg


title: Lutein_3

city: Taipei

first: Tsung Ming

last: Chang

state: Please Select

address: Wuxing street No.250

country: Taiwan

institute: Taipei Medical University

description: Library name: Lu_3

data_processing:
Sequencing reads were quality-trimmed and adapter sequences removed using Trimmomatic (v.0.38). Clean reads were aligned to the human reference genome (GRCh38) using HISAT2 with default parameters. Gene-level quantification was performed using featureCounts, and expression values were normalized using both Relative Log Expression (RLE) and Trimmed Mean of M-values (TMM) methods. Differential expression analysis was conducted using DESeq2 (for biological replicates) or DEGseq (for samples without replicates), with genes considered differentially expressed if |fold change| > 2 and adjusted p-value < 0.05.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

extract_protocol:
RNA Purity and quantification were checked using SimpliNano™ - Biochrom Spectrophotometers (Biochrom, MA, USA). RNA degradation and integrity were monitored by Qsep 100 DNA/RNA Analyzer (BiOptic Inc., Taiwan)
A total amount of 1 μg total RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using KAPA mRNA HyperPrep Kit (KAPA Biosystems, Roche, Basel, Switzerland) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using magnetic oligo-dT beads. Captured mRNA was fragmented by incubating at a high temperature in the presence of magnesium in KAPA Fragment, Prime and Elute Buffer (1x). First strand cDNA was synthesized using random hexamer priming. Combined 2nd strand synthesis and A-tailing, which converts the cDNA:RNA hybrid to double-stranded cDNA (dscDNA), incorporated dUTP into the second cDNA strand, and added dAMP to the 3’ ends of the resulting dscDNA. dsDNA adapter with 3’dTMP overhangs were ligated to library insert fragments to generate the library fragments carrying the adapters. In order to select cDNA fragments of preferentially 300~400bp in length, the library fragments were purified with KAPA Pure Beads system (KAPA Biosystems, Roche, Basel, Switzerland). The library carrying appropriate adapter sequences at both ends was amplified using KAPA HiFi HotStart ReadyMix (KAPA Biosystems, Roche, Basel, Switzerland) along with library amplification primers. The strand marked with dUTP in not amplified, allowing strand-specific sequencing. At last, PCR products were purified using KAPA Pure Beads system and the library quality was assessed on the Qsep 100 DNA/RNA Analyzer (BiOptic Inc., Taiwan). The library quality was assessed on the Qubit@ 2.0 Fluorometer (Thermo Scientific) and Agilent Bioanalyzer 2100 system. At last, the library was sequenced on an Illumina NovaSeq6000 platform and 150 bp paired-end reads were generated.

value: Rheumatoid fibroblast-like synoviocyte

value: Lutein


title: Human macrophages, Infected L. interrogans Icterohaemorrhagiae 202102576, 6 hr, replicate 1

description:
Library name: Sample 6
N89DPD_6_Infection_IC_rep_3


title: Lutein_1

description: Library name: Lu_1


title: aTreg, rep2

description: Hi-C on sorted T cells


title: iCAR, DMSO, Ci11, 6h, D02

description: Library name: Ci11_DMSO_D02

extract_protocol:
6h after treatment, 100uL of TempoSeq lysis buffer used to lyse cells per 96-well, which were then frozen and 2ul used for TempO-Seq library building
In TempO-Seq, each Detector Oligo (DO) consists of a sequence complementary to an mRNA target plus a universal (i.e. same for every targeted gene) primer binding site. They anneal in immediate juxtaposition to each other on the targeted RNA template such that they can be ligated together. Ligated detector oligos are PCR-amplified using a primer set (single-plex PCR reaction, with a single primer pair for each sample) that introduces both the adaptors required for sequencing and a sample-specific barcode. The barcode sequences flank the target sequence and are inserted appropriately into the standard Illumina adaptors to permit standard dual-index sequencing of the barcodes and deconvolution of sample-specific reads from the sequencing data using the standard Illumina software. All the PCR-amplified and barcoded samples are pooled into a single library for sequencing. Sequencing reads are demultiplexed using the standard sequencing instrument software for each sample using the barcodes to give a FASTQ file for each.

value: heart muscle cells

value: iCAR

value: human induced pluripotent stem cells (iPSCs)


title: Human macrophages, Infected L. interrogans Icterohaemorrhagiae 202101402, 6 hr, replicate 2

description:
Library name: Sample 5
N89DPD_5_Infection_IC_rep_2


title: aTreg, rep1

description: Hi-C on sorted T cells


title: iCAR, DMSO, Ci11, 6h, C10

description: Library name: Ci11_DMSO_C10

value: iPSC-derived cardiomyocytes


title: Human macrophages, Infected L. interrogans Icterohaemorrhagiae 202101402, 6 hr, replicate 1

description:
Library name: Sample 4
N89DPD_4_Infection_IC_rep_1


title: Control_3

description: Library name: Control_3

value: Control


title: iCAR, DMSO, Ci11, 6h, B12

description: Library name: Ci11_DMSO_B12


title: aTcon, rep3

description: Hi-C on sorted T cells

value: Active Tcon


title: Control_2

description: Library name: Control_2


title: Control_1

description: Library name: Control_1


title: aTcon, rep2

description: Hi-C on sorted T cells


title: iCAR, Kaempferol, Ci10, 6h, H12

description: Library name: Ci10_T7_D3_H12

value: test


title: Human macrophages, Uninfected, 6 hr, replicate 2

description:
Library name: Sample 2
N89DPD_2_Uninfected_rep_2


title: hAO, Day 80

description:
Library name: scRNA-seq sample2
10x Genomics

extract_protocol:
for RNAseq, RNA was extracted using RNeasy plus universal mini prep kit (Quiagen). 1 ug total RNA was used for construction of sequencing libraries. For scRNA-seq organoids were dissociated with Papain dissociation system (worthington biochemical). And total 20,000 cells were used for library contruction.
for RNA-seq, Truseq stranded mRNA library prep kit (Illumina) was used following manufacture's protocol. For scRNA-seq, Library prep was performed following 3P v4 (GEM-X)  protocol (10X Genomics)

value: Brain organoid


title: iCAR, Kaempferol, Ci10, 6h, D04

description: Library name: Ci10_T7_D3_D04


title: Human macrophages, Uninfected, 6 hr, replicate 1

description:
Library name: Sample 1
N89DPD_1_Uninfected_rep_1


title: hAO, Day 40

description:
Library name: scRNA-seq sample1
10x Genomics


title: iCAR, Kaempferol, Ci10, 6h, C07

description: Library name: Ci10_T7_D3_C07


title: Val-1k, TPO/FL/SCF/IL3/IL6, 7d, donor2, batch3

city: Edogawa-ku

first: Kyungtaek

last: Lim

address: 1-16-13, Kitakasai

institute: Daiichi Sankyo Co., Ltd.

description: 10X Genomics

data_processing:
The cell ranger ATAC pipeline (v2.0) was used for demultiplexing, barcode processing, read mapping against GRCh38, generation of a fragment file (a file contains coordinates of tagmented fragments), peak calling, and peak-cell count matrix construction.
ArchR (v1.0.1) was applied to the resulting fragment files to collect per-cell quality control metrics in addition to those provided from the cell ranger ATAC pipeline.
Assembly: GRCh38
Supplementary files format and content: h5. Barcode-peak count matrix
Supplementary files format and content: TSV, Fragments
Supplementary files format and content: CSV, cellranger-atac per-barcode stats
Supplementary files format and content: CSV, ArchR per-barcode stats

source_name: bone marrow

growth_protocol: Primary human bone marrow CD34+ cells were cultured in StemSpan serum-free expansion medium (STEMCELL Technologies) in the presence of thrombopoietin (TPO, 50 ng/mL), TPO (50 ng/mL)/FLT3 ligand (FL, 100 ng/mL)/SCF (100 ng/mL), interleukin 3 (IL3, 20 ng/mL)/ interleukin 6 (IL6, 100 ng/mL), TPO (50 ng/mL)/IL3 (20 ng/mL)/IL6 (100 ng/mL), or TPO (50 ng/mL)/FL (100 ng/mL)/SCF (100 ng/mL)/IL3 (20 ng/mL)/IL6 (100 ng/mL) at 37 ℃ in a 5% CO2 incubator.

extract_protocol:
Cell nuclei were isolated following the standard protocol provided by 10x Genomics (Protocol number CG000169). In brief, 10,000 to 20,000 cells were lysed using 100 µL of lysis buffer (Tris-HCl pH7.4 10mM, NaCl 10mM, MgCl2 3mM, BSA 1%, Tween-20 0.1%, IGEPAL 0.1%, and Digitonin 0.01%) on ice for 5 minutes. Subsequent to lysis, cells were washed with chilled wash buffer (Tris-HCl pH7.4 10mM, NaCl 10mM, MgCl2 3mM, BSA 1%, Tween-20 0.1%). The cell suspension was centrifuged to pellet the nuclei, which were then resuspended in Nuclei Buffer (Chromium Single Cell ATAC Reagent Kits, 10x Genomics). The concentration of isolated nuclei was determined using a TC20 Automated Cell Counter (Bio-Rad).
Library preparation for scATAC-seq was performed by Chromium Next GEM Single Cell ATAC Reagent Kits v1.1 (10x Genomics) with manufacturer’s protocol.

treatment_protocol: Valemetostat or dimethyl sulfoxide was treated during the cell culture.

value: bone marrow

value: bone marrow CD34+ cells

value: valemetostat 1uM

tag: stimulation

tag: donor id

tag: experimental batch


title: Treg, rep2

description: Hi-C on sorted T cells

tag: tissue

value: Treg

value: WT


title: D3_cerv_SUMOi_2

city: Stanford

first: Paul

last: Khavari

state: CA

address: 269 Campus Dr

department: Dermatology

institute: Stanford University

description: Library name: D3_cerv_SUMOi_2

data_processing:
UMI extraction with UMI tools
read alignment to reference genome using STAR
featureCount generation
DESeq2 with apeGLM shrinkage,
Assembly: GRCh38
Supplementary files format and content: feature counts

source_name: cornea

growth_protocol: Cells were aquired from ATCC (PCS-480-011, grown in ATCC PCS-480-032 and PCS-480-042) (PCS-700-010, grown in ATCC PCS-700-040 and ATCC PCS-700-030)

extract_protocol:
Cells previously transfected with siRNA or treated with pharmacologic compounds were collected in RLT plus lysis buffer supplemented with 10uL/mL Beta-mercaptoethanol (ß-ME) and passed through QIAshredder (Qiagen) column. RNA was then extracted using the RNeasy Plus mini kit (Qiagen).
Libraries were prepared with 10-500ng input to the QuantSeq mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) following the manufacturer’s protocol. Libraries were quantified with KAPA Library Quantification Kit Illumina® Platforms (Roche) and sequenced on NovaSeq X+ with ~30 M paired-end, 150 bp reads per sample.

treatment_protocol: cells were treated with DMSO or NEDD8i for 16hrs then harvested

value: cornea

value: cervical epithelial cells


title: D3_cerv_SUMOi_1

description: Library name: D3_cerv_SUMOi_1


title: DMSO, TPO/FL/SCF/IL3/IL6, 7d, donor2, batch3

description: 10X Genomics

value: dimethyl sulfoxide 0.01%


title: iCAR, Kaempferol, Ci10, 6h, H09

city: Mason

first: Yuqing

last: Shan

address: 8700 mason montgomery road

institute: Procter & Gamble

description: Library name: Ci10_T7_D2_H09

data_processing:
TempO-Seq data are analyzed using the Tempo-SeqR software package using the statistical computing language R.
The input for TempO-Seq data analysis is a folder of zipped FASTQ files. Each FASTQ file contains the reads and quality scores for one sample.
Each FASTQ file is aligned using the Bowtie algorithm to a pseudo-transcriptome input by the user.
The output for TempO-Seq data analysis is a table of counts with each column representing a sample and each row representing a gene.
Assembly: hWTv2
Supplementary files format and content: txt file

tag: cell line


title: Treg, rep1

description: Hi-C on sorted T cells

value: SLO

tag: cell type


title: D3_cerv_NEDD8i_2

description: Library name: D3_cerv_NEDD8i_2


title: HT29-MTX cells, MUC1-deltaMUC1, No treatment, replicate 1

description: Library name: KO-Sal1

value: cell line

value: epithelial colorectal adenocarcinoma cells

tag: genotype

value: uninfected


title: Val-1k, TPO/FL/SCF, 7d, donor2, batch3

description: 10X Genomics

tag: treatment

value: TPO/FL/SCF


title: iCAR, Kaempferol, Ci10, 6h, G12

description: Library name: Ci10_T7_D2_G12

value: heart muscle cells

value: iCAR

value: human induced pluripotent stem cells (iPSCs)

value: iPSC-derived cardiomyocytes

tag: batch


title: D3_cerv_NEDD8i_1

description: Library name: D3_cerv_NEDD8i_1


title: DMSO, TPO/FL/SCF, 7d, donor2, batch3

description: 10X Genomics

value: bone marrow


title: iCAR, Kaempferol, Ci10, 6h, C04

description: Library name: Ci10_T7_D2_C04

value: test


title: Tcon, rep2

description: Hi-C on sorted T cells

value: Tcon


title: D3_cerv_DMSO_2

description: Library name: D3_cerv_DMSO_2


title: Val-1k, TPO/FL/SCF/IL3/IL6, 5d, donor2, batch3

description: 10X Genomics

value: bone marrow CD34+ cells

value: valemetostat 1uM


title: iCAR, Kaempferol, Ci10, 6h, B07

description: Library name: Ci10_T7_D2_B07


title: DMSO, TPO/FL/SCF/IL3/IL6, 5d, donor2, batch3

description: 10X Genomics


title: iCAR, Kaempferol, Ci10, 6h, G09

description: Library name: Ci10_T7_D1_G09


title: Tcon, rep1

description: Hi-C on sorted T cells

value: WT


title: D3_corneal_SUMOi_2

description: Library name: D3_corneal_SUMOi_2

value: cornea

value: corneal epithelial cells


title: Val-1k, TPO/FL/SCF, 5d, donor2, batch3

description: 10X Genomics


title: YT4

first: Julien

last: Couthouis

address: 279 Campus Dr

department: Genetics

data_processing:
illumina basecalling
STAR alignment
RSEM counts
DESeq2 normalization and analyzis
Full pipeline with settings used available on https://github.com/emc2cube/Bioinformatics/blob/master/sh_RNAseq.sh
Assembly: mm10
Supplementary files format and content: comma separated value text files with normalized abundance measurements (output from DESeq2)

source_name: hippocampus

extract_protocol:
RNA extracted using Qiagen Rneasy extraction
polyA enriched mRNA libraries (SureSelect Automated Strand-Specific RNA Library Prep, mRNA Library Prep for Illumina Paired-End Multiplexed Sequencing)

treatment_protocol: For CD8 depletion, Aged (22-24 months) mice were treated i.p. with 200 μm of InVivoMAb anti-mouse CD8a (2.43, BioXCell, BE0061) or InVivoMAb rat IgG2b isotype control (LTF-2, BioXCell, BE0090) in 200 μL PBS every 4 days until time of sacrifice. For adoptive transfer, B6.SJL-Ptprca Pepcb/BoyJ (4 months) mice were treated i.p. with 200 μm of InVivoMAb anti-mouse CD8a in 200 μL PBS day -11 and -7 to deplete resident CD8+ T cells. CD8+ T cells were isolated from single cell suspensions of spleenocytes and PBMCs from young (3-4 months) or aged (22-28 months) C57BL/6J mice using the CD8a+ T cell Isolation Kit (Miltenyi Biotech, 130-104-075) according to manufacturer instructions. For adoptive transfer of young or aged CD8+ T cells, cells were immediately resuspended at concentrations of 3e5 (first injection) or 3e6 (second injection) in 100 μL saline and injected via tail vein. Mice were anesthetized with 87.5 mg per kg ketamine and 12.5 mg per kg xylazine and transcardially perfused with ice-cold phosphate-buffered saline. To process the brains, the whole brain was sectioned in half along the sagittal plane. The hippocampus from one hemisphere was subdissected and flash frozen.

value: hippocampus

value: male

value: Young

value: Young CD8+ T Cell transfer


title: iCAR, Kaempferol, Ci10, 6h, F12

description: Library name: Ci10_T7_D1_F12


title: D3_corneal_SUMOi_1

description: Library name: D3_corneal_SUMOi_1


title: HT29-MTX cells, MUC1-WT, No treatment, replicate 1

description: Library name: WT-Sal1

value: cell line

value: epithelial colorectal adenocarcinoma cells

value: uninfected


title: DMSO, TPO/FL/SCF, 5d, donor2, batch3

description: 10X Genomics

value: dimethyl sulfoxide 0.01%

value: TPO/FL/SCF


title: YT23


title: iCAR, Kaempferol, Ci10, 6h, B04

description: Library name: Ci10_T7_D1_B04

value: heart muscle cells

value: iCAR

value: human induced pluripotent stem cells (iPSCs)

value: iPSC-derived cardiomyocytes


title: Human macrophages, Infected L. interrogans Icterohaemorrhagiae 202102576, 6 hr, replicate 2

description:
Library name: Sample 7
N89DPD_7_Infection_IC_rep_4


title: D3_corneal_NEDD8i_1

description: Library name: D3_corneal_NEDD8i_1


title: Lutein_2

description: Library name: Lu_2

value: Rheumatoid fibroblast-like synoviocyte

value: Lutein


title: iCAR, Kaempferol, Ci10, 6h, A07

description: Library name: Ci10_T7_D1_A07

value: test


title: D3_corneal_NEDD8i_2

description: Library name: D3_corneal_NEDD8i_2

value: cornea

value: corneal epithelial cells


title: YT21

value: hippocampus

value: male

value: WT


title: DMSO, TPO/FL/SCF/IL3/IL6, 3d, donor2, batch3

description: 10X Genomics

value: bone marrow

value: bone marrow CD34+ cells


title: D3_corneal_DMSO_2

description: Library name: D3_corneal_DMSO_2


title: Val-1k, TPO/FL/SCF, 3d, donor2, batch3

description: 10X Genomics

value: valemetostat 1uM


title: iCAR, 4-hydroxybenzophenone, Ci10, 6h, F09

description: Library name: Ci10_T6_D3_F09


title: YT10

value: Young

value: Young CD8+ T Cell transfer


title: iCAR, 4-hydroxybenzophenone, Ci10, 6h, E12

description: Library name: Ci10_T6_D3_E12

value: heart muscle cells


title: DMSO, TPO/FL/SCF, 3d, donor2, batch3

description: 10X Genomics

value: dimethyl sulfoxide 0.01%

value: TPO/FL/SCF


title: IG9

value: Aged

value: IgG2b isotype control


title: Val-1k, TPO/FL/SCF/IL3/IL6, 7d, donor1, batch3

description: 10X Genomics


title: iCAR, 4-hydroxybenzophenone, Ci10, 6h, A04

description: Library name: Ci10_T6_D3_A04

value: iCAR

value: human induced pluripotent stem cells (iPSCs)

value: iPSC-derived cardiomyocytes


title: CAL27_NEDD8i_1

description: Library name: CAL27_NEDD8i_1

data_processing:
UMIs were extracted using UMItools
Adapter trimming and polyA sequence removal were carried out with bbduk
Reads were aligned to the GRCh38 reference genome using STAR
gene-level counts were obtained using featureCounts with GENCODE v39 annotations.
Differential expression analysis was performed using DESeq2 with apeGLM shrinkage
Assembly: GRCh38
Supplementary files format and content: FeatureCounts

growth_protocol: Cells were grown subconfluently in appropriate cell culture media. Fresh media was added with drug treatments.

extract_protocol:
Cells previously treated with pharmacologic compounds were collected in RLT plus lysis buffer supplemented with 10uL/mL Beta-mercaptoethanol (ß-ME) and passed through QIAshredder (Qiagen) column. RNA was then extracted using the RNeasy Plus mini kit (Qiagen)
QuantSeq mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen)

treatment_protocol: 16hr drug treatments

value: cell line

value: squamous cell carcinoma


title: DMSO, TPO/FL/SCF/IL3/IL6, 7d, donor1, batch3

description: 10X Genomics


title: iCAR, 4-hydroxybenzophenone, Ci10, 6h, H03

description: Library name: Ci10_T6_D2_H03

value: test


title: IG6

value: hippocampus

value: male

value: WT


title: CAL27_DMSO_2

description: Library name: CAL27_DMSO_2

value: DMSO


title: iCAR, 4-hydroxybenzophenone, Ci10, 6h, G06

description: Library name: Ci10_T6_D2_G06


title: Val-1k, TPO/FL/SCF, 7d, donor1, batch3

description: 10X Genomics

value: bone marrow

value: bone marrow CD34+ cells

value: valemetostat 1uM


title: IG2


title: CAL27_DMSO_1

description: Library name: CAL27_DMSO_1


title: DMSO, TPO/FL/SCF, 7d, donor1, batch3

description: 10X Genomics

value: dimethyl sulfoxide 0.01%


title: A431_NEDD8i_2

description: Library name: A431_NEDD8i_2

value: human epidermoid carcinoma


title: IG12

value: Aged


title: iCAR, 4-hydroxybenzophenone, Ci10, 6h, D12

description: Library name: Ci10_T6_D2_D12

value: heart muscle cells


title: Val-1k, TPO/FL/SCF/IL3/IL6, 5d, donor1, batch3

description: 10X Genomics


title: cd8a7

value: CD8a depleting antibody


title: A431_NEDD8i_1

description: Library name: A431_NEDD8i_1


title: DMSO, TPO/FL/SCF/IL3/IL6, 5d, donor1, batch3

description: 10X Genomics


title: iCAR, 4-hydroxybenzophenone, Ci10, 6h, G03

description: Library name: Ci10_T6_D1_G03

value: iCAR

value: human induced pluripotent stem cells (iPSCs)


title: A431_DMSO_2

description: Library name: A431_DMSO_2

value: cell line


title: Val-1k, TPO/FL/SCF, 5d, donor1, batch3

description: 10X Genomics

value: TPO/FL/SCF


title: iCAR, 4-hydroxybenzophenone, Ci10, 6h, F06

description: Library name: Ci10_T6_D1_F06

value: iPSC-derived cardiomyocytes

value: test


title: cd8a3

value: hippocampus

value: male


title: A431_DMSO_1

description: Library name: A431_DMSO_1

value: DMSO