title: Raji ATAC-seq RGS-SE knockout replicate 1

city: Matsudo City

first: Jinichi

last: Mori

state: Chiba

address: 107-1 Kanegasaku

institute: Chibanishi General Hospital

description:
Library name: ATACseq_RGSSEKO_1
ATACseq_WT-RGSSEKO_DESeq2_annotated.txt

data_processing:
RNA-seq: Reads were trimmed using Trim Galore, Trimmomatic, and cutadapt. Trimmed reads were aligned to GRCh38 (hg38) using STAR. Read counts were generated using featureCounts. FPKM values were calculated and differentially expressed genes were identified using DESeq2 (base mean > 5; fold-change < 0.25 or > 4).
ATAC-seq: Reads were aligned to the human reference genome GRCh38 (hg38) using Bowtie2. Peak calling was performed using HOMER (findPeaks). Read counts at merged peak regions were compared between wild-type and RGS-SE knockout cells using DESeq2. Peaks were annotated with gene information using HOMER (annotatePeaks.pl): peaks located within the promoter region (TSS -1 kb to +100 bp) were assigned to the corresponding gene; peaks outside promoter regions were assigned to the nearest gene by shortest distance to TSS. Differentially accessible peaks were defined as padj < 0.05 with fold change > 2 or < -2.
Assembly: hg38 (GRCh38)
Supplementary files format and content: RNAseq_gene-WT-RGSSEKO_DESeq2.txt: Tab-delimited text file. DESeq2 differential expression results (wild-type vs RGS-SE knockout Raji cells). Columns: gene symbol, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj.
Supplementary files format and content: ATACseq_WT-RGSSEKO_DESeq2_annotated.txt: Tab-delimited text file. DESeq2 differential chromatin accessibility results between wild-type and RGS-SE knockout Raji cells, with HOMER gene annotation. Columns: Merged_Peak (peak coordinates, chr_start_end format), baseMean, log2FoldChange, lfcSE, stat, pvalue, padj, Annotation, Detailed Annotation, Distance to TSS, Nearest PromoterID, Entrez ID, Nearest Unigene, Nearest Refseq, Nearest Ensembl, Gene Name, Gene Alias, Gene Description, Gene Type.

source_name: Raji

growth_protocol: The human Burkitt lymphoma cell line Raji was cultured in RPMI-1640 medium (Wako) supplemented with 10% fetal bovine serum (FBS; Biological Industries) and 1% penicillin-streptomycin (FUJIFILM Wako Chemicals). Cells were maintained at 37 degrees C in a humidified atmosphere containing 5% CO2.

extract_protocol:
For RNA-seq: Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen) per the manufacturer's protocol, treated with DNase I (Nippon Gene), and purified using TRIzol Reagent (Thermo Fisher Scientific). Poly(A)+ RNA was enriched using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs). For ATAC-seq: Approximately 50,000 Raji cells were lysed and transposition was performed using Tn5 transposase (Illumina, #FC121-1030) for 30 min at 37 degrees C. The reaction was purified using the MinElute PCR Purification Kit (Qiagen).
For RNA-seq: Libraries were prepared with the SMARTer Stranded RNA-Seq Kit v2 (Takara Bio). Sequencing was performed on a DNBSEQ-G400 with paired-end reads. For ATAC-seq: Five PCR cycles were performed using custom Nextera primers with NEBNext Q5 Hot Start HiFi PCR Master Mix (New England BioLabs). Additional cycles were determined by qPCR of partially amplified products. Libraries were purified using Agencourt AMPure XP beads (Beckman Coulter, A63881) with double size selection (left 1.4, right 0.5). Sequencing was performed on a DNBSEQ-G400.

treatment_protocol: RGS-SE knockout (RGS-SEKO) Raji cells were generated by CRISPR/Cas9-mediated deletion of the super-enhancer region between RGS1 and RGS13 (chr1:192,515,157-192,741,754, hg38). Cells were electroporated with Cas9 expression vector and two sgRNA plasmids using a Neon NxT Electroporation System (Invitrogen) at 1300 V, 30 ms, 1 pulse, selected with puromycin (2.5 ug/mL, 24 h), and single clones were confirmed by PCR and Sanger sequencing.

value: Raji

value: B lymphoblast

value: RGS-SE knockout (CRISPR-Cas9)


title: Control 2

status: Public on Jun 30 2026

type: RNA

city: São Paulo

first: Helena

last: Malvezzi

state: São Paulo

address: Av. Morumbi

department: Research

country: Brazil

institute: Hospital Israelita Albert Einstein

data_processing: The calculations of the relative gene expression of the samples were made using the ΔΔCt method with the housekeeping gene 18S, ACTB and GAPDH as normalizer. The normalizer was determined based on the coefficient of variation (CV) obtained in similar datasets.

label: Taqman

molecule: total RNA

organism: Homo sapiens

source_name: Control 2.eds

label_protocol: cDNA synthesis and Real-Time Polymerase Chain Reaction (RT-PCR in Real time)  Reverse transcription of RNA samples was performed using the SuperScript VILO MasterMix (Invitrogen, ThermoFisher Scientific, Waltham, MA, USA) with oligo-dT primers. The final reaction volume was 14μL per sample. The samples were placed in a thermocycler (Master Cycler – Nexus, Eppendorf Sigma Aldrich, MERK SA, Darmstadt, Germany) at 50ºC for 50 minutes. The sequences of genes analysed and synthesized by Invitrogen Brazil were: Gene Name: 18S; ACTB; AIM2; BCL2; BIRC2; BIRC3; BLC2L1; CARD18; CARD6; CASP1; CASP4; CASP5; CASP8; CCL2; CCL5; CCL7; CD40LG; CFLAR; CHUK; CIITA; CTSB;CXCL1; CXCL2; FADD; GAPDH; GSDMD; HSP90AA1; HSP90AB1; HSP90B1; IFNB1; IFNG; IKBKB; IKBKG; IL10; IL12A; IL12B; IL17A; IL18; IL1B; IL33; IL4; IL6; IRAK1; IRF1; IRF2; LDHB; MAP3K7; MAPK1; MAPK11; MAPK12; MAPK13; MAPK3; MAPK8; MAPK9; MEFV; MOK; MYD88; NAIP; NFKB1; NFKBIA; NFKBIB; NLRC4; NLRC5; NLRP1; NLRP12; NLRP3;NLRP4; NLRP5; NLRP6; NLRP9; NLRX1; NOD2; P2RX7; PANX1; PEA15; PSTPIP1; PTGS2; PYCARD; PYDC1; RELA; RIPK2; SUGT1; TAB1; TAB2; TIRAP; TLR2; TLR3; TLR4; TLR9; TNF; TNFFS4; TNFSF11; TNFSF14; TRAF6; TXNIP; XIAP  Real-time amplification was performed according to the Taqman Array assay protocol (Thermo Fisher Scientific, Waltham, MA, USA). Briefly, 1.5μL of cDNA was added to 13.5μL of the mix, totalling the final volume of 15μL of reaction per well of the plate.

extract_protocol: RNA extraction   The PicoPure RNA Isolation Kit (Life Technologies, MERK SA, Darmstadt, Germany) was used to extract RNA from whole biopsy samples. The extracted total RNA was quantified by spectrophotometry using a NanoDrop One Microvolume UV-Vis Spectrophotometer (ThermoFisher Scientific, Waltham, MA, USA) at an absorbance of 260nm and frozen at -80ºC.

tag: sample group

value: Control

tag: subject status

value: Non-endometriosis

tag: tissue

value: Peritoneal Fluid


title: Control 1

source_name: Control 1.eds


title: S3-FPKM

type: SRA

city: Yangling

first: ningxin

last: guo

address: No. 3, Taicheng Road

country: China

institute: Northwest A&F University

description: Library name: Sample 6

library_source: transcriptomic

data_processing:
HISAT2 was used to compare the quality-controlled clean reads to the oat reference genome (https://plants.ensembl.org/Avena_sativa_OT3098/Info/Index), and gene expression was quantified using StringTie and Ballgown software. Differentially expressed genes (DEG) were selected using the criteria of |log2FC| ≥1 and FDR ≤ 0.05, and the DEGs were enriched by KEGG analysis.
Assembly: Avena_sativa_OT3098
Supplementary files format and content: txt file includes FPKM values for eacd sample and genes annotations

organism: Avena sativa

source_name: seeds

extract_protocol:
Total RNA from peeled seeds of shading treatment for 4 days and non-shading treatment of BY 9 was extracted using Trizol reagent (Invitrogen, USA) for RNA-seq analysis, on the PacBio Sequel Ⅱ sequencing platform (Xi’an Haorui Genomics Technology Company Limited, Shaanxi, China).
First-strand cDNA was synthesized using fragmented mRNA as templates and random oligonucleotides as primers in the M-MuLV reverse transcriptase system. The RNA strand was then degraded with RNaseH, followed by second-strand cDNA synthesis using dNTPs as substrates in a DNA polymerase I system. The purified double-stranded cDNA underwent end repair, A-tailing, and adapter ligation. cDNA fragments of approximately 250-300 bp were size-selected using AMPure XP beads, then PCR-amplified, and the PCR products were purified again with AMPure XP beads to generate the final library. The library was constructed using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina®.

value: seeds

tag: cell line

value: Ear of Baiyan No.9

tag: cell type

value: peeled seeds

tag: treatment

value: ear shading


title: NR2, with ketamine

city: Cleveland

first: Wanpeng

last: Cui

state: OH

address: Room E765, Robbins Building,, 10900 Euclid Ave, Department of Neurosciences,

department: Neurosciences

country: USA

institute: Case Western Reserve University

description: Library name: sample2

data_processing:
Data quanlity control, alignment
Gene expression level analysis
differential gene expression analysis
Assembly: mm10
Supplementary files format and content: xlsx, DEGlist of downregulated genes
Supplementary files format and content: downregulated genes

molecule: polyA RNA

organism: Mus musculus

source_name: Brain (PFC)

growth_protocol: C57bl/6j male mice were siblings, and group house, 3 mice/cage

extract_protocol:
Total RNA were extracted from the prefrontal cortex of each mice.
RNA library was constructed according to SMARTER RNA libarary prep kit

treatment_protocol: ketamine, i.p., 10 mg/kg, 24 hours before sacrifice

value: Brain (PFC)

value: brian cells

value: all kind of brain cells

tag: genotype

value: NR, nonresponders to ketamine

value: 24 hours after ketamine

tag: batch

tag: strain

value: C57bl/6j male


title: Raji ATAC-seq wild-type replicate 2

country: Japan

description:
Library name: ATACseq_WT_2
ATACseq_WT-RGSSEKO_DESeq2_annotated.txt

library_source: genomic

molecule: genomic DNA

value: wild-type


title: S2-FPKM

description: Library name: Sample 5


title: S1-FPKM

description: Library name: Sample 4


title: NR1, with ketamine

description: Library name: sample1


title: CK3-FPKM

description: Library name: Sample 3

value: no shading


title: Raji ATAC-seq wild-type replicate 1

description:
Library name: ATACseq_WT_1
ATACseq_WT-RGSSEKO_DESeq2_annotated.txt

value: Raji

value: B lymphoblast


title: Tumor_FFPE_P16_Post

city: Philadelphia

first: Nelson

last: Freeburg

state: PA

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania

description:
Library name: Tumor_FFPE_P16_Post
Column = P16_Post_1

data_processing:
FASTQ files aligned and preprocessed using 10x Genomics CellRanger Multi v8.0.1 pipeline
For Single-cell, single-nucleus gene expression: Ambient RNA contamination removed using CellBender Remove-Background (CellBender v0.3.0).
For single-cell, single-nucleus gene expression, cellbender-adjusted counts imported intor seurat. Genes and cells were filtered for quality and expression thresholds, and data were lognormalized. Cells were annotated manually based on marker gene expression.
For bulk RNA sequencing, Fastq files were trimmed with umi_tools (v1.1.6) to extract UMIs. Cutadapt (v5.2) was used to trim nonbiological sequences from reads. Reads were aligned using the STAR aligner (v2.7.9a). Reads were deduplicated based on UMI identity using umi_tools (v1.1.6) and counted using FeatureCounts (v2.1.1). Normalized counts are in transcripts per milliion (TPM). Raw counts are also provided.
Assembly: GRCh38
Supplementary files format and content: Processed gene expression data is in .h5 format and contains CellBender-processed gene expression counts.
Supplementary files format and content: Processed V(D)J data is the output of CellRanger and in .csv format. It contains cell barcode and TCR A a B chain sequence as DNA and protein.
Supplementary files format and content: Supplementary .rds files contain Seurat objects for single-cell CSF, single-cell Infusion product, and single-nucleus tumor samples

source_name: Glioblastoma tumor

extract_protocol:
Tumors (single-nucleus): Single cell supsensions produced by tumor sample dissociation with gentleMACS Octo Dissociator and filtered through 75 uM strainer before single nucleus prep with CHAPS; Cerebrospinal and infusion product: Cells or nucei input directly into 10x genomics single cell library preparation protocol. Tumors (Bulk RNAseq from FFPE). Malignant cell-enriched regions were extracted from slides using laser-capture microdissection. RNA was extracted using a Qiagen RNA FFPE kit.
Chromium GEM-X Single Cell 5' Kit v3 with Chromium Single Cell Human TCR Amplification kit (single-cell, single-nucleus). SMART-Seq® Total RNA Pico Input with UMIs (ZapR™ Mammalian) (Bulk RNA sequencing)

treatment_protocol: 5e6, 1e7 or 2.5e7 bivalent CAR T cells targeting EGFR and IL13RA2 administered intracerebroventricularly

value: Glioblastoma tumor

value: Primary cells

value: GBM tumor cells

value: EGFR amplified

value: 5e6 bivalent CAR T cells (EGFR, IL13RA2)


title: MDA-MB-231_ZSWIM8_KD_2_cells expressing the ZSWIM targeting sgRNA_2

city: Milano

first: Francesco

last: Nicassio

address: Via Adamello 16

department: Center for genomic science

country: Italy

institute: Istituto Italiano di Tecnologia

data_processing:
FASTQ data were trimmed using cutadapt-1.9.1; then trimmed data was aligned to custom sequence libraries listing all isoforms of small RNA molecules by using Bowtie with --best and -v 0 switches and saved in .map output format.
Isomirage software was used to count the number of occurrences in the .map file of each isoform listed in the .genome file
Raw counts were converted into TPM and all templated forms for each miRNA were summed together
Assembly: custom genome, containing all human microRNAs (canonical and Isoforms)
Supplementary files format and content: TPM_counts.xlsx: excel file that includes normalized reads (transcript per million reads, TPM, normalized  to the size of each library) for all miRNAs in all samples

extract_protocol:
Total RNA, including microRNAs, was isolated through the miRNeasy mini kit (Qiagen).
1000 nanograms of total RNA were used to prepare Small RNA libraries following the Illumina TruSeqTM Small RNA kit instructions

treatment_protocol: Cells were treated infected with lentivirus expressing the sgRNAs and then treated with 1 ug/mL doxycycline, to activate the dCas9-KRAB transgene, for 7 passages

value: BREAST CANCER

value: ZSWIM8 knock down


title: MDA-MB-231_ZSWIM8_KD_1_cells expressing the ZSWIM targeting sgRNA_1


title: CK2-FPKM

description: Library name: Sample 2

value: seeds

value: Ear of Baiyan No.9

value: peeled seeds


title: CK1-FPKM

description: Library name: Sample 1


title: aortic cells isolated from knock-in mice

city: Los Angeles

first: Xinjiang

last: Cai

state: CA

department: Medicine/Cardiology

institute: University of California, Los Angeles

description:
Library name: Knock-in-1-month
10X Genomics

library_source: transcriptomic single cell

data_processing:
CellRanger v 7.1.0 was used
Assembly: Mus musculus genome
Supplementary files format and content: Tab separated value files and matrix files

source_name: Aorta

extract_protocol:
Aortic cell isolation was performed with both male and female wild-type and MGP-KI mice at one month old as previously described.38 After the mice were sacrificed and perfused with 10 ml of warm 1xPBS without Ca2+ and Mg2+, aortas were isolated and adventitia were removed under a dissecting microscope. The dissected aortas were then cut into small pieces and incubated with 1 mL of digestion buffer containing DNase1 (Qiagen), 10 mM HEPES, Liberase (Millipore-Sigma), and 1X HBSS at 37°C for 25 mins. Isolated cells in a single cell suspension were washed three times and passed through a 40 mm cell strainer (Corning). The final cell suspension was resuspended in 1xPBS containing 1% FBS and 0.05% BSA. Dead cells, identified by DAPI positivity (Sigma-Aldrich, 1:5,000), were removed by FACS. The remaining live cells were sent for scRNA-seq
Library was contructed per 10X Genomics instructions

value: Aorta

value: aortic cells

value: knock-in


title: aortic cells isolated from wild-type mice

description:
Library name: Wild-type-1-month
10X Genomics

value: wild-type


title: LCMV D30 fresh control effector memory rep 56

city: Cambridge

first: Nir

last: Hacohen

state: MA

address: 415 Main Street, Room 6032

department: Cell Circuits Program / Center for Cell Circuits

institute: Broad Institute

description:
Library name: day30_mem_fresh_control_EM_rep_56
Column name in day30_mem_normalized_counts.tsv: day30_mem_fresh_EM_56

data_processing:
Salmon NumReads were summed to gene-level counts, rounded, filtered to nonzero-count genes, normalized with DESeq2.
Assembly: GRCm38/mm10 mouse reference; GENCODE vM25 annotation for transcript-to-gene assignment.
Supplementary files format and content: naive_lenti_activated_normalized_counts.tsv: tab-delimited gene-by-sample matrix containing complete DESeq2-normalized expression values for the 27 CD8 T cell state bulk RNA-seq libraries. Rows are genes; columns are submitted sample/library identifiers.
Supplementary files format and content: day30_mem_normalized_counts.tsv: tab-delimited gene-by-sample matrix containing complete DESeq2-normalized expression values for the 59 day-30 memory P14 CD8 T cell bulk RNA-seq libraries. Rows are genes; columns are submitted sample/library identifiers.

source_name: spleen

growth_protocol: P14 CD8 T cells were isolated from mouse spleen and lymph node. For the lenti naive condition, naive P14 CD8 T cells were transduced using the naive-state-preserving lentiviral workflow and maintained without TCR stimulation before transfer. For the lenti-activated condition, P14 CD8 T cells were transduced and activated with anti-CD3/CD28 before transfer. Experimental donor populations were mixed with freshly isolated congenically marked naive P14 CD45.1+CD45.2+ CD8 T cells as cotransferred controls, and recipient mice were infected with LCMV Armstrong after transfer.

extract_protocol:
T cell populations were sorted on a Sony cell sorter into 96-well plates at 1,000 cells per well in lysis buffer consisting of TCL buffer supplemented with 1% 2-mercaptoethanol, then frozen before RNA capture and cDNA synthesis. RNA was isolated using SPRI beads and eluted directly into oligo-dT/dNTP-containing reverse-transcription mix.
Full-length cDNA was generated using the Smart-seq2 protocol with SuperScript II reverse transcriptase, a template-switching oligonucleotide, and RNase inhibitor. cDNA was amplified by whole-transcriptome amplification using KAPA HiFi HotStart ReadyMix, purified with SPRI beads, quantified, and assessed by Bioanalyzer or TapeStation. Sequencing libraries were prepared from amplified cDNA using Nextera XT tagmentation with indexed adapters, pooled, and sequenced on Illumina NextSeq platforms at the Broad Institute Genomics Platform.

value: spleen

value: effector memory CD8 T cells

value: day 30 post infection baseline; fresh control; Thy1.1 not applicable


title: LCMV D30 fresh control effector memory rep 52

description:
Library name: day30_mem_fresh_control_EM_rep_52
Column name in day30_mem_normalized_counts.tsv: day30_mem_fresh_EM_52


title: LCMV D30 fresh control effector memory rep 48

description:
Library name: day30_mem_fresh_control_EM_rep_48
Column name in day30_mem_normalized_counts.tsv: day30_mem_fresh_EM_48


title: BU-LF-160

city: Jacksonville

last: Zhao

state: FL

address: 4500 San Pablo Rd S

department: Neuroscience

institute: Mayo Clinic

description: Library name: BU-LF-160

data_processing:
RNA sequencing reads were processed through the Mayo Clinic RNA sequencing analytic pipeline, MAPRSeq Version 3.1.3. Briefly, reads were aligned to the mouse reference genome mm10 using STAR version 2.6.1c. Quality control (QC) was performed using RSeQC version 2.6.4. Gene counts were generated using featureCounts version 1.5.1. Genes were filtered out from further analyses if there were not at least four samples with 10 counts of the gene.
Conditional quantile normalization (CQN) was performed on the raw gene counts to correct for gene length differences, GC bias, and global technical variations and to obtain similar quantile-by-quantile distributions of gene expression levels across samples.
Based on the bimodal distribution of the CQN-normalized and log2-transformed reads per kilobase per million (RPKM) gene expression values, genes with log2 RPKM ≥ 2 in all samples were considered expressed. Using this selection threshold, 18,592 genes were included in the downstream analysis.
Assembly: mm10
Supplementary files format and content: .tsv of raw gene counts

source_name: Cortical RNA

extract_protocol:
Total RNA was extracted from the cortex using Trizol reagent and cleaned using RNeasy spin columns with DNase treatment to remove contaminating genomic DNA.
RNA libraries were prepared from 200 ng of total RNA using the TruSeq Stranded RNA Sample Prep Kit (Illumina, San Diego, CA) according to the manufacturer’s instructions, employing poly-A mRNA enrichment using oligo-dT magnetic beads. The final adaptor-modified cDNA fragments were enriched by 15 cycles of PCR using Illumina TruSeq PCR primers. The concentration and size distribution of the completed libraries were determined using an Agilent Tape Station, (Agilent, Santa Clara, CA) and Qubit fluorometer (Invitrogen, Carlsbad, CA).
Libraries from all samples were sequenced on Illumina’s NovaSeq 6000 at 50 million fragment reads/sample following Illumina’s standard protocol on two S2 flow cells. S2 flow cells were sequenced at 101 x 2 paired end reads using a NovaSeq S2 sequencing kit, NovaSeq Control Software v1.7.0 and base-calling was analyzed using Illumina’s RTA version 3.4.4.

treatment_protocol: For each APOE genotype group, 12-month-old mice were assigned to one of two feeding regimens for 32 weeks: AL feeding with a normal diet or 30% CR with a normal diet. CR feeding was provided daily during a fixed time slot (3–4 pm).

value: Cortical RNA

value: CR

tag: Sex

value: Female


title: Raji RNA-seq wild-type replicate 2

description:
Library name: RNAseq_WT_2
RNAseq_gene-WT-RGSSEKO_DESeq2.txt

value: Raji

value: B lymphoblast


title: LCMV D30 fresh control effector memory rep 44

description:
Library name: day30_mem_fresh_control_EM_rep_44
Column name in day30_mem_normalized_counts.tsv: day30_mem_fresh_EM_44


title: BU-LF-158

description: Library name: BU-LF-158


title: LCMV D30 fresh control central memory rep 59

description:
Library name: day30_mem_fresh_control_CM_rep_59
Column name in day30_mem_normalized_counts.tsv: day30_mem_fresh_CM_59

value: central memory CD8 T cells


title: Raji RNA-seq wild-type replicate 1

description:
Library name: RNAseq_WT_1
RNAseq_gene-WT-RGSSEKO_DESeq2.txt


title: BU-LF-155

description: Library name: BU-LF-155

value: male


title: HcoFi Passage 26

city: Suwon

first: Soon Sang

last: Park

address: Worldcup-Ro 206

country: South Korea

institute: Ajou University School of Medicine

description: Library name: Passage 26

data_processing:
fastq files are processed with Altanalyze.
Assembly: hg38
Supplementary files format and content: csv files containing raw counts for each sample

source_name: Colon

extract_protocol:
RNA was extracted using RNA extraction kit (MN) 1ug of total RNA was used for RNA library generation.
The 1 mg of total RNA was processed for preparing mRNA sequencing library using MGIEasy RNA Directional Library Prep Kit (MGI) according to manufacturer’s instruction.

value: Colon

value: HCoFi

value: Fibroblast

value: Wild type


title: LCMV D30 fresh control central memory rep 47

description:
Library name: day30_mem_fresh_control_CM_rep_47
Column name in day30_mem_normalized_counts.tsv: day30_mem_fresh_CM_47


title: MRR, 2004118

city: Budapest

first: <Up loaded by Bioinformatics core  facility>

last: <PI shown in the article>

address: Szigony st 43.

country: Hungary

institute: HUN-REN Institute of Experimental Medicine

description:
Library name: 2004118
MRR

data_processing:
Read quality was checked with fastqc
Trimmed adapter seq and low phredscore 3’ ends; if a read became shorter than 50 bp it and it’s pair was removed; read pairs where one at least on of the reads consisted of only 3 type of nucleotides were removed
STAR aligner (2.7.10a) was used to align reads to the reference and to count reads mapped to genes; reads mapped to introns were not considered valid
Assembly: Mouse genome mm39 with ensEMBL annotation v110 was supplemented with Addgene_pAAV-EF1a-DIO-mCherry (Plasmid #50459); Cre (NCBI/Nucleotide:NC_005856.1); and sYFP (NCBI/Nucleotide:GQ221700.1).
Supplementary files format and content: A tab separated count matrix on a gene level consisting of genes as rows and samples as columns

source_name: MRR

growth_protocol: We used vGluT2-iRES-Cre adult (at least 6 weeks-old) mice that had access to food and water ad libitum and were housed in a vivarium (3-5 mice/cage) until used in experiments. Mice were injected with AAVretro-EF1a-DIO-mCherry into bilateral LHb (60 nl per site) then were placed into separate cages. After 2-5 weeks of incubation time mice were sacrificed during the light phase and 200-250 μm thick horizontal slices were made from the pontine region of the brainstem of vGLuT2-Cre mice.

extract_protocol:
Mice were decapitated under deep anesthesia and slices were prepared in ice-cold cutting solution (85 mM NaCl, 75 mM sucrose, 2.5 mM KCl, 25 mM glucose, 1.25 mM NaH2PO4, 4 mM MgCl2, 0.5 mM CaCl2, and 24 mM NaHCO3) using a VT1200S vibratome (Leica). Slices were incubated at 35 °C for ~30 min and then kept at room temperature until use. During recordings the slices are kept at 35 °C in continuously perfused with artificial cerebrospinal fluid (126 mM NaCl, 2.5 mM KCl, 26 mM NaHCO3, 2 mM CaCl2, 2 mM MgCl2, 1.25 mM NaH2PO4, and 10 mM glucose, saturated with carbogen,) Fluorescently labeled MRR neurons were visualized in an upright microscope (Eclipse FN-1; Nikon) with epifluorescent illumination (Lambda FLED @ 530 nm; Sutter Instrument) combined with a CMOS camera (DaVinci 1k, RedShirtImaging). The neurons were patched with thin-wall borosilicate pipettes (pipette resistance: 3.69±0.09 MΩ, BF150-117-10, Sutter Instrument) filled with small amount (~1 µl) of intracellular solution containing 133.5 mM K-gluconate, 1.8 mM NaCl, 1.7 mM MgCl2, 0.05 mM EGTA, 10 mM HEPES, 2 mM Mg-ATP, 0.4 mM Na2-GTP, 10 mM phosphocreatine, and 8 mM biocytin (pH 7.25;  290-300 mOsm). Pipette capacitance and the bridge balance were carefully compensated in all current clamp recordings. For the RNA harvesting, the recordings were made using a HEKA EPC800 amplifier (HEKA Elektronik) digitized with a Digidata1440A A/D converter (Molecular Devices). The data acquisition was controlled by the pClamp10 software package. After patching the identified neurons, we measured the basic electrophysiological parameters of the cells including the resting membrane potential, the spontaneous synaptic activity, and the firing pattern. The length of the recording session was limited to 5 min from the break-in. The cytosol together with the nucleus was extracted from the neuron by the application of small negative pressure to the pipette. The tip of the quickly removed pipette was gently pushed into a microtube containing ice cold reaction buffer (lysis buffer with RNase inhibitor, Takara SMART-Seq HT PLUS Kit). The sample containing tubes was spun briefly and snap-frozen on dry ice. To suppress RNase contamination, the workplace including parts of the experimental setup was cleaned each day before the start of the sample collection with RNase AWAY (Thermo Fisher).
Sample collection: After electrophysiological recordings, the cells’ cytosol was aspirated via the same recording glass pipette that used for recording, and using a positive pressure, expelled into microtubes containing 1 µl of 1x lysis buffer with RNase inhibitor (SMART-Seq HT PLUS Kit, Takara). The samples were immediately frozen on dry ice and stored at -80°C until further processing. cDNA and library preparation for next-generation sequencing: Single-cell mRNA processing was performed using the SMART-Seq HT PLUS Kit (Takara) and according to manufacturer’s protocol. In brief, samples were reverse transcribed to cDNA, amplified, and purified with AMPure XP beads (Beckman Coulter). The quantity and the quality of the purified cDNA was assessed using Fragment Analyzer (Advanced Analytical). Subsequently, the cDNA was fragmented and adapters including indices for cell identification were added to the fragments. The quality and quantity were again assessed using Fragment Analyzer. For library preparation, the single cell samples with unique index adapters were pooled in equal amounts. The sequencing was performed on a NovaSeq 6000 (Illumina) instrument using 150 bp paired end configuration and a full SP-flowcell. Processing of sequencing data: After sequencing, raw reads were de-multiplexed with Illumina’s bcl2fastq2 (v2.20).

treatment_protocol: All vGluT2-Cre mice were injected with AAVretro-EF1a-DIO-mCherry into bilateral LHb (60 nl per site) to label MRR vGluT2 neurons.

value: MRR


title: BU-LF-154

description: Library name: BU-LF-154

value: AL


title: HcoFi Passage 24

description: Library name: Passage 24


title: LCMV D30 fresh control effector memory rep 58

description:
Library name: day30_mem_fresh_control_EM_rep_58
Column name in day30_mem_normalized_counts.tsv: day30_mem_fresh_EM_58


title: BU-LF-144

description: Library name: BU-LF-144


title: LCMV D30 fresh control effector memory rep 54

description:
Library name: day30_mem_fresh_control_EM_rep_54
Column name in day30_mem_normalized_counts.tsv: day30_mem_fresh_EM_54


title: HcoFi Passage 22

description: Library name: Passage 22


title: LCMV D30 fresh control effector memory rep 50

description:
Library name: day30_mem_fresh_control_EM_rep_50
Column name in day30_mem_normalized_counts.tsv: day30_mem_fresh_EM_50


title: BU-LF-143

description: Library name: BU-LF-143


title: LCMV D30 fresh control effector memory rep 46

description:
Library name: day30_mem_fresh_control_EM_rep_46
Column name in day30_mem_normalized_counts.tsv: day30_mem_fresh_EM_46


title: HcoFi Passage 16

description: Library name: Passage 16


title: LCMV D30 fresh control effector memory rep 42

description:
Library name: day30_mem_fresh_control_EM_rep_42
Column name in day30_mem_normalized_counts.tsv: day30_mem_fresh_EM_42


title: LCMV D30 fresh control central memory rep 57

description:
Library name: day30_mem_fresh_control_CM_rep_57
Column name in day30_mem_normalized_counts.tsv: day30_mem_fresh_CM_57


title: HcoFi Passage 15

description: Library name: Passage 15


title: LCMV D30 fresh control central memory rep 49

description:
Library name: day30_mem_fresh_control_CM_rep_49
Column name in day30_mem_normalized_counts.tsv: day30_mem_fresh_CM_49


title: HcoFi Passage 14

description: Library name: Passage 14


title: BU-LF-139

description: Library name: BU-LF-139


title: LCMV D30 fresh control central memory rep 41

description:
Library name: day30_mem_fresh_control_CM_rep_41
Column name in day30_mem_normalized_counts.tsv: day30_mem_fresh_CM_41


title: LCMV D30 post-transduction with stimulation effector memory rep 40

description:
Library name: day30_mem_lenti_stim_EM_rep_40
Column name in day30_mem_normalized_counts.tsv: day30_mem_activated_EM_40

value: day 30 post infection post-transduction with stimulation; Thy1.1 positive


title: HcoFi Passage 6

description: Library name: Passage 6


title: LCMV D30 post-transduction with stimulation effector memory rep 36

description:
Library name: day30_mem_lenti_stim_EM_rep_36
Column name in day30_mem_normalized_counts.tsv: day30_mem_activated_EM_36

value: spleen


title: BU-LF-134

description: Library name: BU-LF-134


title: HcoFi Passage 4

description: Library name: Passage 4


title: BU-LF-142

description: Library name: BU-LF-142


title: LCMV D30 post-transduction with stimulation effector memory rep 32

description:
Library name: day30_mem_lenti_stim_EM_rep_32
Column name in day30_mem_normalized_counts.tsv: day30_mem_activated_EM_32

value: effector memory CD8 T cells


title: LCMV D30 fresh control central memory rep 53

description:
Library name: day30_mem_fresh_control_CM_rep_53
Column name in day30_mem_normalized_counts.tsv: day30_mem_fresh_CM_53

value: day 30 post infection baseline; fresh control; Thy1.1 not applicable


title: BU-LF-141

description: Library name: BU-LF-141

value: Cortical RNA


title: BU-LF-128

description: Library name: BU-LF-128

value: CR


title: LCMV D30 post-transduction with stimulation effector memory rep 28

description:
Library name: day30_mem_lenti_stim_EM_rep_28
Column name in day30_mem_normalized_counts.tsv: day30_mem_activated_EM_28


title: LCMV D30 fresh control central memory rep 45

description:
Library name: day30_mem_fresh_control_CM_rep_45
Column name in day30_mem_normalized_counts.tsv: day30_mem_fresh_CM_45


title: Human, TMCi, Veh6h_1

city: Fukuoka

first: Keisuke

last: Ikegami

address: Nishi-ku Motooka 744

institute: Kyushu University

description: Library name: HTMCi_Veh6h_1

data_processing:
FASTQ files were received from the sequencing provider.
Quality control, mapping, and differential gene expression analysis were performed using RaNAseq and BioJupies.
Differentially expressed genes were identified by comparing NE- or DEX-treated samples with vehicle-treated control samples at the corresponding exposure time points.
Assembly: To be confirmed based on the reference genome used for mapping in RaNAseq/BioJupies.
Supplementary files format and content: Processed data files contain gene-level expression values and differential expression analysis results generated from the RNA-seq data.

source_name: Immortalized Trabecular meshwork cell line

growth_protocol: Immortalized human primary trabecular meshwork cells (abm; T0371)  were plated in Type I collagen-coated 6-well plates and cultured until they reached 80–90% confluence. The medium was then replaced with serum-free trabecular meshwork cell medium (TMCM; ScienCell; #6591), and cells were incubated for 24 hours before treatment.

extract_protocol:
At the indicated time points, culture medium was aspirated, and cells were gently washed with 1 mL of ice-cold PBS. Cells were lysed by adding 0.2 mL of lysis reagent from the NucleoSpin RNA/Protein kit (Takara Bio) and detached using a cell scraper. RNA was extracted according to the manufacturer's protocol and quantified using a NanoDrop One spectrophotometer.
RNA sequencing library preparation and sequencing were performed by an external service provider using the submitted RNA samples.

treatment_protocol: After 24 hours in serum-free TMCM, cells were treated with norepinephrine (NE; final concentration, 1 µM) or dexamethasone (DEX; final concentration, 0.1 µM). Vehicle-treated control cells received DMSO. Cells were harvested 6 hours after treatment.

value: Trabecular meshwork

value: Immortalized Trabecular meshwork cell type


title: LCMV D30 post-transduction with stimulation effector memory rep 24

description:
Library name: day30_mem_lenti_stim_EM_rep_24
Column name in day30_mem_normalized_counts.tsv: day30_mem_activated_EM_24


title: HcoFi Passage 3

description: Library name: Passage 3


title: Endometriosis 15

source_name: Endometriosis 15.eds

value: Case

value: Endometriosis

value: Peritoneal Fluid


title: BU-LF-125

description: Library name: BU-LF-125

value: Female


title: LCMV D30 post-transduction with stimulation central memory rep 39

description:
Library name: day30_mem_lenti_stim_CM_rep_39
Column name in day30_mem_normalized_counts.tsv: day30_mem_activated_CM_39

value: central memory CD8 T cells


title: Endometriosis 14

source_name: Endometriosis 14.eds


title: Posterior hNTOrg day 6, rep3

city: Barcelona

first: Elisa

last: Martí

address: C/ Baldiri Reixac, 4-8, Torre R, 3era Planta

country: Spain

institute: Institut de Biologia Molecular de Barcelona

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using SOAPnuke v2.1.7 (parameters: -l 15 -q 0.2 -n 0.05)
Trimmed sequence reads were mapped to GRCh38 using HISAT2 v2.1.0 (parameters: --sensitive –no-discordant --no-mixed -I 1 -X 1000 -p 8 --rna-strandness RF)
Read count extraction was performed using FeatureCounts v.2.0.3 (parameters: -p --countReadPairs -t exon -g gene_id -O -T 8)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw count values for all samples extracted from FeatureCounts

source_name: Posterior hNTOrg

growth_protocol: To generate the hNTOrg, small clumps of hESC were seeded in matrigel droplets and culture the first 24h with mTeSR1 and from that point on with N2B27 with the different drug tratments.

extract_protocol:
Total RNA extraction using Trizol reagent
RNA libraries for RNA-seq were prepared using DNBSEQ eukaryotic stranded mRNA Library Prep Kit following manufacturer’s protocols.

treatment_protocol:
Anterior hNTOrg were cultured in neural induction medium (N2B27) with transient inhibition of BMP and TGFb signaling (from day 2 to day 3)
Posterior hNTOrg were cultured in neural induction medium (N2B27) with transient activation of WNT (first 24 hours) and subsequent activation of WNT, FGF and RA activation and inhibition of BMP the following 48 hours.

value: Neural

value: NPCs

value: WT

value: WNT, FGF and RA activation and BMP inhibition

tag: organoid

value: Posterior hNTOrg


title: BU-LF-122

description: Library name: BU-LF-122

value: male


title: LCMV D30 post-transduction with stimulation central memory rep 35

description:
Library name: day30_mem_lenti_stim_CM_rep_35
Column name in day30_mem_normalized_counts.tsv: day30_mem_activated_CM_35

value: spleen

value: day 30 post infection post-transduction with stimulation; Thy1.1 positive


title: Endometriosis 11

source_name: Endometriosis 11.eds


title: Posterior hNTOrg day 6, rep2


title: LCMV D30 post-transduction with stimulation central memory rep 31

description:
Library name: day30_mem_lenti_stim_CM_rep_31
Column name in day30_mem_normalized_counts.tsv: day30_mem_activated_CM_31


title: Endometriosis 10

source_name: Endometriosis 10.eds


title: LCMV D30 post-transduction with stimulation central memory rep 27

description:
Library name: day30_mem_lenti_stim_CM_rep_27
Column name in day30_mem_normalized_counts.tsv: day30_mem_activated_CM_27


title: BU-LF-119

description: Library name: BU-LF-119

value: Cortical RNA


title: LCMV D30 post-transduction with stimulation central memory rep 23

description:
Library name: day30_mem_lenti_stim_CM_rep_23
Column name in day30_mem_normalized_counts.tsv: day30_mem_activated_CM_23


title: Posterior hNTOrg day 6, rep1


title: LCMV D30 untransduced cotransfer control effector memory rep 38

description:
Library name: day30_mem_untransduced_cotransfer_control_EM_rep_38
Column name in day30_mem_normalized_counts.tsv: day30_mem_activated_EM_38

value: effector memory CD8 T cells

value: day 30 post infection baseline; untransduced cotransfer control; Thy1.1 negative


title: LCMV D30 untransduced cotransfer control effector memory rep 34

description:
Library name: day30_mem_untransduced_cotransfer_control_EM_rep_34
Column name in day30_mem_normalized_counts.tsv: day30_mem_activated_EM_34


title: BU-LF-117

description: Library name: BU-LF-117

value: CR


title: Anterior hNTOrg day 6, rep3

source_name: Anterior hNTOrg

value: BMP and TGFb inhibition

value: Anterior hNTOrg


title: BU-LF-114

description: Library name: BU-LF-114


title: LCMV D30 untransduced cotransfer control effector memory rep 30

description:
Library name: day30_mem_untransduced_cotransfer_control_EM_rep_30
Column name in day30_mem_normalized_counts.tsv: day30_mem_activated_EM_30


title: LCMV D30 untransduced cotransfer control effector memory rep 26

description:
Library name: day30_mem_untransduced_cotransfer_control_EM_rep_26
Column name in day30_mem_normalized_counts.tsv: day30_mem_activated_EM_26


title: Anterior hNTOrg day 6, rep2


title: LCMV D30 untransduced cotransfer control effector memory rep 22

description:
Library name: day30_mem_untransduced_cotransfer_control_EM_rep_22
Column name in day30_mem_normalized_counts.tsv: day30_mem_activated_EM_22


title: BU-LF-113

description: Library name: BU-LF-113


title: Raji ATAC-seq RGS-SE knockout replicate 2

description:
Library name: ATACseq_RGSSEKO_2
ATACseq_WT-RGSSEKO_DESeq2_annotated.txt

source_name: Raji

value: Raji

value: B lymphoblast

value: RGS-SE knockout (CRISPR-Cas9)


title: LCMV D30 untransduced cotransfer control central memory rep 37

description:
Library name: day30_mem_untransduced_cotransfer_control_CM_rep_37
Column name in day30_mem_normalized_counts.tsv: day30_mem_activated_CM_37

value: central memory CD8 T cells


title: Anterior hNTOrg day 6, rep1

value: Neural

value: NPCs


title: LCMV D30 untransduced cotransfer control central memory rep 29

description:
Library name: day30_mem_untransduced_cotransfer_control_CM_rep_29
Column name in day30_mem_normalized_counts.tsv: day30_mem_activated_CM_29


title: BU-LF-112

description: Library name: BU-LF-112

value: Female


title: LCMV D30 untransduced cotransfer control central memory rep 25

description:
Library name: day30_mem_untransduced_cotransfer_control_CM_rep_25
Column name in day30_mem_normalized_counts.tsv: day30_mem_activated_CM_25


title: Control 3

source_name: Control 3.eds

value: Control

value: Non-endometriosis

value: Peritoneal Fluid


title: Osteosarcoma_Metastasis_2

city: Osaka

first: Thuy

middle: Thi Thanh

last: Le

state: Osaka

address: 1-4-3 Asahimachi, Abeno-ku

department: Department of Global Education and Medical Sciences

institute: Osaka Metropolitan University Graduate School of Medicine

description:
Library name: M2
10x Genomics

data_processing:
The demultiplexing and gene expression quantification were performed using the Cell Ranger v7.1.0 (10x Genomics)
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separared values files and matrix files

source_name: Lung

extract_protocol:
Single-cell suspensions were prepared from human frozen bone tissues using the 10x Genomics Chromium Next GEM Single Cell Fixed RNA Profiling (FLEX) workflow. Specimens were categorized into four clinical groups: naïve (n = 2), treated (n = 2), recurrent (n = 2), and metastasis (n = 2). Tissue dissociation and fixation were performed using the Chromium Next GEM RNA Profiling Sample Fixation Kit (10x Genomics, PN-1000414, CA, USA) according to the manufacturer’s protocol. Briefly, tissues were weighed to calculate fixation buffer volume (1 mL per 25 mg of tissue), minced on a prechilled glass dish, and incubated in fixation buffer at 4 °C for 16–24 hours. Following centrifugation at 850 × g for 5 min at room temperature (RT), pellets were washed twice with chilled PBS and resuspended in resuspension buffer. Dissociation solution (10x Genomics) was prewarmed at 37 °C for 10 min, and 2 mL was added to each sample, which was then transferred to Miltenyi C tubes (Miltenyi Biotec, Cat#130-093-237) and processed using GentleMACS Octo Dissociator with Heater (Cat#130-096-427). Resulting suspensions were filtered with MACS SmartStrainers 30 μm (Cat#130-098-458), and viable cells were counted using trypan blue or propidium iodide staining (Sigma, Cat#P4170). Single-cell suspensions were stored at –80°C in Quenching Buffer supplemented with Enhancer and glycerol for later use in downstream steps including barcoding, library preparation, and sequencing.
Gene expression profiling was conducted using the Chromium Fixed RNA Profiling Reagent Kit for Singleplexed Samples (10x Genomics, CG000477 Rev C), employing the Human Transcriptome Probe Set. Approximately 2,000,000–3,000,000 fixed cells were hybridized for 18 hours at 42 °C with whole-transcriptome probe pairs. After post-hybridization washes, cells were encapsulated in gel beads-in-emulsion (GEMs) using the Chromium X system and Chip Q. Within each GEM, ligated probe pairs were barcoded with 10x GEM Barcodes and Unique Molecular Identifiers (UMIs), followed by heat denaturation and recovery. The barcoded products underwent pre-amplification and purification using SPRIselect beads. Final libraries were generated via sample index PCR using the Dual Index Kit TS Set A and were further purified by size selection. Library quality was assessed using an Agilent Bioanalyzer, and concentrations were determined using the KAPA Library Quantification Kit (Roche). Libraries were sequenced on the DNBSEQ-G400RS platform (MGI Tech) in paired-end mode, using 28 bp for Read 1 (containing the 16 bp GEM barcode and 12 bp UMI) and 100 bp for Read 2 (capturing the probe insert). Demultiplexing and gene expression quantification were performed using Cell Ranger v7.1.0 (10x Genomics), which aligns reads to the human reference genome and generates filtered feature‒barcode matrices for downstream analyses.

value: Lung

value: all bone cell types

tag: age

value: female

value: Chemotherapy, surgery


title: LCMV D30 untransduced cotransfer control central memory rep 21

description:
Library name: day30_mem_untransduced_cotransfer_control_CM_rep_21
Column name in day30_mem_normalized_counts.tsv: day30_mem_activated_CM_21

value: spleen

value: day 30 post infection baseline; untransduced cotransfer control; Thy1.1 negative


title: BU-LF-111

description: Library name: BU-LF-111

value: Cortical RNA

value: CR

value: male


title: LCMV D30 post-transduction no stimulation effector memory rep 8

description:
Library name: day30_mem_lenti_no_stim_EM_rep_08
Column name in day30_mem_normalized_counts.tsv: day30_mem_lenti_EM_08

value: effector memory CD8 T cells

value: day 30 post infection post-transduction with no stimulation; Thy1.1 positive


title: Osteosarcoma_Metastasis_1

description:
Library name: M1
10x Genomics


title: LCMV D30 post-transduction no stimulation effector memory rep 4

description:
Library name: day30_mem_lenti_no_stim_EM_rep_04
Column name in day30_mem_normalized_counts.tsv: day30_mem_lenti_EM_04


title: BU-LF-109

description: Library name: BU-LF-109


title: LCMV D30 post-transduction no stimulation effector memory rep 16

description:
Library name: day30_mem_lenti_no_stim_EM_rep_16
Column name in day30_mem_normalized_counts.tsv: day30_mem_lenti_EM_16


title: BU-LF-105

description: Library name: BU-LF-105


title: LCMV D30 post-transduction no stimulation effector memory rep 12

description:
Library name: day30_mem_lenti_no_stim_EM_rep_12
Column name in day30_mem_normalized_counts.tsv: day30_mem_lenti_EM_12


title: Osteosarcoma_Recurrent_2

description:
Library name: R2
10x Genomics

source_name: Soft tissue

value: Soft tissue


title: LCMV D30 post-transduction no stimulation effector memory rep 20

description:
Library name: day30_mem_lenti_no_stim_EM_rep_20
Column name in day30_mem_normalized_counts.tsv: day30_mem_lenti_EM_20


title: LCMV D30 post-transduction no stimulation central memory rep 7

description:
Library name: day30_mem_lenti_no_stim_CM_rep_07
Column name in day30_mem_normalized_counts.tsv: day30_mem_lenti_CM_07

value: central memory CD8 T cells


title: BU-LF-103

description: Library name: BU-LF-103


title: Osteosarcoma_Recurrent_1

description:
Library name: R1
10x Genomics


title: Osteosarcoma_Treated_2

description:
Library name: T2
10x Genomics

source_name: Bone

value: Bone


title: LCMV D30 post-transduction no stimulation central memory rep 3

description:
Library name: day30_mem_lenti_no_stim_CM_rep_03
Column name in day30_mem_normalized_counts.tsv: day30_mem_lenti_CM_03


title: BU-LF-101

description: Library name: BU-LF-101

value: AL


title: LCMV D30 post-transduction no stimulation central memory rep 19

description:
Library name: day30_mem_lenti_no_stim_CM_rep_19
Column name in day30_mem_normalized_counts.tsv: day30_mem_lenti_CM_19


title: Raji RNA-seq RGS-SE knockout replicate 2

description:
Library name: RNAseq_RGSSEKO_2
RNAseq_gene-WT-RGSSEKO_DESeq2.txt

value: Raji

value: B lymphoblast

value: RGS-SE knockout (CRISPR-Cas9)


title: LCMV D30 fresh control effector memory rep 60

description:
Library name: day30_mem_fresh_control_EM_rep_60
Column name in day30_mem_normalized_counts.tsv: day30_mem_fresh_EM_60

value: day 30 post infection baseline; fresh control; Thy1.1 not applicable


title: LCMV D30 post-transduction no stimulation central memory rep 15

description:
Library name: day30_mem_lenti_no_stim_CM_rep_15
Column name in day30_mem_normalized_counts.tsv: day30_mem_lenti_CM_15


title: LCMV D30 untransduced cotransfer control effector memory rep 6

description:
Library name: day30_mem_untransduced_cotransfer_control_EM_rep_06
Column name in day30_mem_normalized_counts.tsv: day30_mem_lenti_EM_06


title: BU-LF-98

description: Library name: BU-LF-98

value: Female


title: LCMV D30 post-transduction no stimulation central memory rep 11

description:
Library name: day30_mem_lenti_no_stim_CM_rep_11
Column name in day30_mem_normalized_counts.tsv: day30_mem_lenti_CM_11


title: Osteosarcoma_Treated_1

description:
Library name: T1
10x Genomics

value: all bone cell types

value: Chemotherapy, surgery


title: LCMV D30 untransduced cotransfer control effector memory rep 2

description:
Library name: day30_mem_untransduced_cotransfer_control_EM_rep_02
Column name in day30_mem_normalized_counts.tsv: day30_mem_lenti_EM_02

value: spleen

value: day 30 post infection baseline; untransduced cotransfer control; Thy1.1 negative


title: Raji RNA-seq RGS-SE knockout replicate 1

description:
Library name: RNAseq_RGSSEKO_1
RNAseq_gene-WT-RGSSEKO_DESeq2.txt


title: Osteosarcoma_Naive_2

description:
Library name: N2
10x Genomics

value: Surgery


title: BU-LF-96

description: Library name: BU-LF-96

value: Cortical RNA

value: male


title: LCMV D30 untransduced cotransfer control effector memory rep 18

description:
Library name: day30_mem_untransduced_cotransfer_control_EM_rep_18
Column name in day30_mem_normalized_counts.tsv: day30_mem_lenti_EM_18

value: effector memory CD8 T cells


title: LCMV D30 untransduced cotransfer control effector memory rep 14

description:
Library name: day30_mem_untransduced_cotransfer_control_EM_rep_14
Column name in day30_mem_normalized_counts.tsv: day30_mem_lenti_EM_14


title: Osteosarcoma_Naive_1

description:
Library name: N1
10x Genomics

value: female


title: LCMV D30 untransduced cotransfer control effector memory rep 10

description:
Library name: day30_mem_untransduced_cotransfer_control_EM_rep_10
Column name in day30_mem_normalized_counts.tsv: day30_mem_lenti_EM_10


title: BU-LF-93

description: Library name: BU-LF-93


title: BU-LF-91

description: Library name: BU-LF-91

value: CR


title: LCMV D30 untransduced cotransfer control central memory rep 9

description:
Library name: day30_mem_untransduced_cotransfer_control_CM_rep_09
Column name in day30_mem_normalized_counts.tsv: day30_mem_lenti_CM_09

value: central memory CD8 T cells


title: LCMV D30 fresh control central memory rep 55

description:
Library name: day30_mem_fresh_control_CM_rep_55
Column name in day30_mem_normalized_counts.tsv: day30_mem_fresh_CM_55


title: LCMV D30 untransduced cotransfer control central memory rep 1

description:
Library name: day30_mem_untransduced_cotransfer_control_CM_rep_01
Column name in day30_mem_normalized_counts.tsv: day30_mem_lenti_CM_01


title: S6_BR.snRNAseq

city: Phoenix

first: John

last: Fryer

email: jfryer@tgen.org, kolney@tgen.org

address: 445 N 5th St

institute: TGen

description:
Library name: S6
paired-end single nucleus RNAseq
Ecoli_pigs_snRNA_object.rds

data_processing:
Samples were QC’d on the Agilent Tapestation, and bulk RNAseq libraries prepared with TruSeq stranded mRNA (cat # 20020594) and sequenced to a depth of ~50M paired-end reads on an Illumina NovaSeq S4 instrument at the Mayo Clinic Genome Sequencing Core. FASTQ files were trimmed for adapter content and polyA/polyG artifacts using BBDuk, part of the BBMap package (48).FastQC and MultiQC were used to assess read quality before and after trimming (49, 50). Trimmed reads were aligned to the Ensembl reference genome Sscrofa11.1 v107 using STAR 2.7.11b (51). Quantification estimates for each sample were obtained using STAR following the twopassMode alignment and quantMode to get the read counts for each geneID. A count matrix of gene rows by sample columns was created and read into R for analysis. Mitochondrially-encoded genes (MT-genes) were excluded during the normalization pipeline to prevent highly abundant mitochondrial transcripts from masking more subtle nuclear-encoded differential expressions, and only protein-coding genes were retained. Lowly expressed genes were removed from the analysis by keeping only genes with a count greater than or equal to one count per million (CPM) in all samples within at least one group, 13,692 protein coding genes were retained for downstream differential expression analysis. The edgeR package converted library sizes into effective library sizes using the Trimmed Mean of M-values (TMM) (52). Differential expression was performed using the limma/voom pipeline (53, 54). A model was created to compare E. coli and saline where each coefficient corresponds to a group mean and minutes from injection till the killing was added as a covariate. P-values were adjusted for multiple tests using the Benjamin-Hochberg correction, denoted as q-value. Specifically, the q-value is derived by adjusting the distribution of p-values across all tested genes to control the expected proportion of false positives among the set of significant findings. There is no fixed raw p-value cutoff that corresponds to q < 0.05. Instead, the effective p-value threshold depends on the overall p-value distribution. We used a logarithm base 2 of the fold change (log2FC) to denote the ratio of change between experimental and control animals. Genes were identified as differentially expressed when the absolute log2FC exceeded 1.0  and the q-value < 0.05. This strict criterion guarantees that the detected changes are not only statistically reliable after adjusting for multiple testing, but also biologically robust in magnitude.
Assembly: Ensembl reference genome Sscrofa11.1 v107
Supplementary files format and content: rds or txt file contains sample counts, gene information, and sample information

molecule: nuclear RNA

organism: Sus scrofa

source_name: brain

extract_protocol:
Brain (prefrontal cortex) samples were collected post-mortem and flash-frozen immediately at −80°C or fixed in formalin for subsequent analysis
A total of 0.5 grams of forebrain tissue was used to prepare total brain RNA from n = 4 E. coli pigs and n = 4 saline-treated pigs with the Qiagen RNeasy Mini Kit (cat # 74104). Samples were QC’d on the Agilent Tapestation, and bulk RNAseq libraries prepared with TruSeq stranded mRNA (cat # 20020594) and sequenced to a depth of ~50M paired-end reads on an Illumina NovaSeq S4 instrument at the Mayo Clinic Genome Sequencing Core.

treatment_protocol: Animals were group-housed with ad libitum access to water and Purina Lab Porcine Grower Diet 5084. Adult males were not included in these experiments as they are too large and aggressive for safe housing and handling. At experiment onset, anesthesia was induced with intramuscular glycopyrrolate (0.02 mg/Kg), telazol (5 mg/Kg), and xylazine (2 mg/Kg), followed by maintenance anesthesia with continuous isoflurane (1.5-2.5%). Once anesthetized, cannulas were surgically placed in the jugular vein and carotid artery for clinical monitoring and infusion procedures. A continuous i.v. infusion of E. coli (clinical isolate 41949 obtained from Brigham and Women’s Hospital, Crimson Biorepository) was initiated for a target dose of 1.2x10^9 colony forming units (CFU)/Kg over a maximum of 6 hours, while saline controls received an equivalent volume of 0.9% normal saline (1.00 mL/h). Time to euthanasia varied among pigs exposed to E. coli (199 – 362 minutes) due to individual differences in the progression of septic shock. In contrast, all saline control pigs were euthanized at 300 minutes, having exhibited no signs of organ dysfunction.

value: brain

value: Sus scrofa

value: Saline


title: S3_BR.snRNAseq

description:
Library name: S3
paired-end single nucleus RNAseq
Ecoli_pigs_snRNA_object.rds


title: BU-LF-86

description: Library name: BU-LF-86

value: AL


title: S2_BR.snRNAseq

description:
Library name: S2
paired-end single nucleus RNAseq
Ecoli_pigs_snRNA_object.rds


title: LCMV D30 untransduced cotransfer control central memory rep 5

description:
Library name: day30_mem_untransduced_cotransfer_control_CM_rep_05
Column name in day30_mem_normalized_counts.tsv: day30_mem_lenti_CM_05

source_name: spleen


title: BU-LF-85

description: Library name: BU-LF-85

source_name: Cortical RNA


title: LCMV D30 untransduced cotransfer control central memory rep 17

description:
Library name: day30_mem_untransduced_cotransfer_control_CM_rep_17
Column name in day30_mem_normalized_counts.tsv: day30_mem_lenti_CM_17


title: LCMV D30 untransduced cotransfer control central memory rep 13

description:
Library name: day30_mem_untransduced_cotransfer_control_CM_rep_13
Column name in day30_mem_normalized_counts.tsv: day30_mem_lenti_CM_13


title: LCMV D30 fresh control central memory rep 51

description:
Library name: day30_mem_fresh_control_CM_rep_51
Column name in day30_mem_normalized_counts.tsv: day30_mem_fresh_CM_51

value: day 30 post infection baseline; fresh control; Thy1.1 not applicable


title: subcutaneous white adipose, Sphk2 deleted anti-H3K27 acetylation repicate 3

city: Richmond

first: Christopher

last: Green

state: Virginia

address: 1101 E. Marshall St.

institute: Virginia Commonwealth University

description:
Library name: RB23
H3K27ac_IgG_counts.csv

data_processing:
Fastq files were subsequently generated with Illumina BaseSpace.
Reads were aligned using Bowtie2 with parameters --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700 to the mouse mm39 (GRCm39) version 30 reference genome.
To account for spike-in calibration, reads were also aligned to the E. coli genome using Bowtie2 with the --end-to-end mode and the same sensitivity and filtering parameters.
Peak calling was performed using the SEACR (Sparse Enrichment Analysis for CUT&RUN) package.
Differential peak analysis based on read counts across peaks between conditions was performed using DESeq2, and caniddate enriched peaks were identified using an adjusted p-value (FDR) threshold of 0.05.
Assembly: mm39vM30
Supplementary files format and content: CSV file: differential peak analysis based on read counts across peaks between conditions
Library strategy: CUT&Tag

source_name: subcutaneous white adipose

extract_protocol:
Single nuclei were isolated using Minute Single Nuclei and Cytosol Isolation Kit (#AN-029, Invent Biotechnologies). 5000 nuclei for each sample that was used as the input for Hyperactive Universal Cleavage Under Targets and Tagmentation (CUT&Tag) Assay Kit for Illumina Pro (#TD904, Vazyme). 0.05 pg E. coli lamda DNA spike-in diluted in 10% SDS was added. Activated DNA Extract Beads Pro were added to the transposase-treated nuclei-bead complexes to extract the DNA.
Libraries were amplified by PCR for 15 cycles with a unique combination of N5XX and N7XX dual-index adapters (#TD202, Vazyme). The PCR products were purified with VAHTS DNA Clean Beads (#N411, Vazyme). Quality and concentration of the DNA libraries were assessed by a high sensitivity dsDNA kit (#5067-4626, Agilent) run on a 2100 Bioanalyser (#G2939A, Agilent). Sequencing was performed using an Illumina NextSeq 2000 Sequencer (Illumina, RRID:SCR_023614) with PE 2x61 base pair settings.

treatment_protocol: Mice were fed Western diet for 18 weeks.

value: subcutaneous white adipose

value: Sphk2 deleted

tag: cut&tag antibody

value: anti-H3K27ac (Abcam, #ab4729)

tag: spike-in control

value: 0.05 pg E. coli lamda DNA spike-in


title: S1_BR.snRNAseq

description:
Library name: S1
paired-end single nucleus RNAseq
Ecoli_pigs_snRNA_object.rds


title: subcutaneous white adipose, Sphk2 deleted anti-H3K9 acetylation repicate 3

description:
Library name: RB22
H3K9ac_IgG_counts.csv

value: anti-H3K9ac (Abcam, #ab10812)


title: 1_13_19_TWB2_C_CGCCTG_R1

city: Brookings

first: Anne

last: Fennell

state: SD

address: Raven Precision Ag Building Box 2100A

department: Agronomy, Horticulture & Plant Science

institute: South Dakota State University

description:
Library name: 12685_5751_144718_HW3JMBGXJ_NSF023_E07_1_13_19_TWB2_C_CGCCTG_R1
Total RNA single illumina

data_processing:
1. Quality Control of Raw Reads- Raw RNA-seq reads were assessed for quality using FastQC, and summary reports across all samples were generated using MultiQC.
2. Adapter Trimming and Filtering- Adapter sequences and low-quality bases were removed using Trimmomatic. Since the data consisted of single-end reads, the TruSeq2 single-end adapter file was used during trimming.
3. Reference Genome Preparation- The Vitis vinifera 12Xv2 reference genome assembly and V2.20 GFF3 annotation file were downloaded and prepared for downstream analysis.
4. Genome Index Generation - Genome indices were generated using STAR to facilitate efficient alignment of RNA-seq reads.
5. Read Alignment - Trimmed reads were aligned to the Vitis vinifera reference genome using STAR, producing BAM alignment files for each sample.
Assembly: 6. Gene Expression Quantification- Gene-level read counts were generated using featureCounts  with the V2.20 GFF3 annotation file, retaining gene IDs for downstream expression analysis.
Supplementary files format and content: The processed data file consists of a tab-delimited text matrix file generated by featureCounts. The matrix contains raw, un-normalized digital gene-level counts, where rows correspond to specific unique Gene IDs derived from the Vitis vinifera 12Xv2 (V2.20 GFF3) reference annotation, and columns represent the individual biological samples (replicates) mapped using single-end RNA-seq reads. No normalized values (such as FPKM or TPM) are included in this specific file.

organism: Vitis hybrid cultivar

source_name: Bud

growth_protocol: Standard commercial vineyard management, Tuckers Walk, Garretson SD.

extract_protocol:
Total RNA was extracted from grapevine bud tissue using a modified CTAB protocol or standard commercial RNA isolation kit optimized for woody plant tissues. RNA quality and quantity were assessed using an Agilent Bioanalyzer or NanoDrop spectrophotometer to ensure high-quality material prior to library preparation.
Sequencing libraries were constructed using the Illumina TruSeq RNA Library Prep Kit following the manufacturer's standard protocols. Poly-A selected mRNA was fragmented, converted to cDNA, ligated with TruSeq adapters, and PCR amplified to generate single-end sequencing libraries.

treatment_protocol: Controled chilling (4ºC) in dark.  Field natural chilling temperatures.

value: Bud

value: Controlled Chilling

value: total RNA

value: single


title: mSIorg_36h_1

city: Basel

first: Prisca

last: Liberali

address: Klingelbergstrasse 48

department: D-BSSE

country: Switzerland

institute: ETHZ

description: Library name: mSIorg_36h_1

data_processing:
Raw sequencing reads were processed using the Alevin module of Salmon (v1.2.0) (Patro et al., 2017; Srivastava et al., 2019). Reads were quantified in paired-end mode (-l ISR) using the 10x Genomics Chromium v3 protocol specification (--chromiumV3). Multiple sequencing lanes per sample were combined at the FASTQ level prior to quantification. Quantification was performed against a spliced–unspliced “gentrome” reference derived from GENCODE mouse release M24 (GRCm38), enabling simultaneous estimation of spliced and intronic counts for RNA velocity–compatible analyses. Gene-level quantification was obtained using a transcript-to-gene mapping file (--tgMap), and feature-level output (spliced/unspliced) was generated using the --dumpFeatures option. Cell barcode whitelisting and UMI deduplication were handled internally by Alevin. Quantification uncertainty was estimated using 50 bootstrap replicates (--numCellBootstraps 50). All runs were executed using 32 threads per sample. Quantification outputs were imported into R using tximeta (v1.12.4) (Love et al., 2020), with inferential replicates discarded (dropInfReps = TRUE). Spliced and unspliced counts were separated using splitSE, and spliced counts were used as the primary assay for downstream analyses. Cell barcodes were prefixed with sample identifiers, sample metadata were appended, and samples were merged into a single SingleCellExperiment object (v1.16.0) containing 54,446 features across 43,684 cells.
Gene annotations were added from GENCODE release M24, including gene biotype, gene symbol, Entrez ID and chromosome. Mitochondrial genes were annotated based on chromosome “chrM” and MitoCarta3.0, and ribosomal protein genes were annotated using GO:0003735 with org.Mm.eg.db (v3.14.0) (Rath et al., 2021). Genes were retained if annotated as protein-coding, immunoglobulin, T cell receptor, mitochondrial rRNA or mitochondrial tRNA genes; all other gene biotypes were removed before downstream analysis. Per-cell and per-feature quality control metrics were calculated using scater (v1.22.0) (McCarthy et al., 2017). Cells were retained if they contained >1,200 detected genes and <22% mitochondrial counts. Library-size normalization was performed using scran (v1.22.1) (Lun et al., 2016). Cells were first grouped into coarse clusters using quickCluster, and deconvolution size factors were estimated with computeSumFactors using min.mean = 0.5. Cells with size factors <0.1 were excluded. Log-normalized expression values were computed with logNormCounts and used for downstream analyses.
To preserve transcriptional heterogeneity and ensure representation of rare cell populations, cells were subsampled using geometric sketching as previously applied in large-scale single-cell analyses (Oost, Kahnwald et al., bioRxiv, 2023). In brief, we used sketchR (v0.1.4), an R interface to the geometric sketching strategy described by Hie et al. (2019). PCA was first computed on log-normalized expression values using 100 components, and representative cells were selected with geosketch using a target sketch size corresponding to approximately 10% of cells, with a minimum of 2,000 cells and capped at the total number of cells. Highly variable genes were identified using modelGeneVar in scran with an FDR threshold of 0.05. Variable genes were identified globally and within each experimental condition, and the union of condition-wise variable genes was used for dimensionality reduction. PCA was computed using 30 components. t-SNE embeddings were generated with snifter/FIt-SNE, and UMAP embeddings were generated using uwot (Linderman et al., 2019; McInnes et al., 2018).
Cell type identities were assigned using marker gene set scoring, graph-based clustering and manual annotation. Curated intestinal marker gene sets were scored separately within culture conditions using swissknife::normGenesetExpression, with non-variable genes used as the background set. Sketched cells were converted to a Seurat object (v4.1.0), and a shared nearest-neighbor graph was constructed in the sketch PCA space using FindNeighbors with k = 20 and 30 principal components (Hao et al., 2021). Cells were clustered using FindClusters across resolutions 0.4–4.0, and resolution 3.5 was used for annotation. Clusters were annotated based on marker gene expression, marker gene set scores and timepoint distribution. One mixed enterocyte cluster was split by timepoint, with 24–48 hour cells annotated as enterocyte reprogramming cells and 60–108 hour cells annotated as mature enterocytes. Cluster labels from sketched cells were transferred to the full dataset by 1-nearest-neighbor classification in sketch PCA space. Final annotations were collapsed into intestinal epithelial cell states, including reprogramming, regenerative, stem/progenitor, secretory and enterocyte-lineage populations.
Assembly: GRCm38/mm10
Supplementary files format and content: barcodes.tsv.gz: gzipped, tab-separated text file with column annotation of the (sparse) alignment count table (genes versus cells). The columns correspond to cell_id (cell identifier), culture medium (intesticult/enr), timepoint (0h, 24h, 36h, 48h, 60h, 72h, 84h, 108h), cell_type (annotated celltype label), TSNE1 (first coordinate for TSNE embedding), TSNE2 (second coordinate for TSNE embedding), UMAP1 (first coordinate for UMAP embedding), UMAP2 (second coordinate for UMAP embedding).
Supplementary files format and content: features.tsv.gz: gzipped, tab-separated text file with row annotation of the (sparse) alignment count table (genes versus cells). The columns correspond to gene symbol, gene_id (ensembl_id), is_variable (logical specifying variable genes used).
Supplementary files format and content: matrix.mtx.gz: gzipped, tab-separated text file with the number of mRNA counts per gene (row) and cell (column), as a sparse matrix in MatrixMarket format.
Supplementary files format and content: matrix_logcounts.mtx.gz: gzipped, tab-separated text file with the log-transformed and normalized expression per gene (row) and cell (column), as a sparse matrix in MatrixMarket format.

source_name: mouse small intestinal organoids

growth_protocol: Small intestinal organoids were derived from the duodenum of a 10-week-old male C57BL/6 wild-type mouse as described in Sato et al, Nature 2009. For amplification and maintenance, organoids were cultured in IntestiCult Organoid Growth Medium (STEMCELL Technologies) with 100 μg/ml Penicillin-Streptomycin. Organoid timecourses were started by performing a single-cell dissociation of the maintenance cultures. Specifically, organoids were collected 6 days after passaging and digested with TripLE (Invitrogen) with 10 μM Y-27632 (ROCK inhibitor; STEMCELL Technologies) for 20 min at 37 °C. Dissociated cells were passed through a cell strainer with a pore size of 30 µm and stained with DRAQ7 dye (Invitrogen). Single cells were isolated by fluorescence-activated cell sorting (FACS; SONY MA900 Cell Sorter) by gating for live (DRAQ7-negative) single cells. Cells were seeded into Matrigel (Corining) droplets (1:1 ratio Matrigel:ENR medium) at a density of 600 cell/ul, marking the start of the organoid timecourse. ENR medium consisted of Advanced DMEM/F-12 with 15 mM HEPES (STEM CELL Technologies) supplemented with 100 μg/ml Penicillin and Streptomycin, 1x Glutamax (Thermo Fisher Scientific), 1x B27 (Thermo Fisher Scientific), 1x N2 (Thermo Fisher Scientific), 1 mM N-acetylcysteine (Sigma), 500 ng/ml R-Spondin (kind gift from Novartis), 100 ng/ml Noggin (PeproTech) and 100 ng/ml murine EGF (R&D Systems). For the first 24 hr of the timecourse, ENR was supplemented with 25% Wnt3a-conditioned medium (Wnt3a-CM), 10 μM Y-27632 (ROCK inhibitor, STEMCELL Technologies) and 3 µM of CHIR99021 (STEMCELL Technologies). From 24 to 72 hr, ENR was supplemented with 25% Wnt3a-CM and 10 μM Y-27632 (ROCK inhibitor, STEMCELL Technologies). From 72 to 108 hr, only ENR was added to the organoids. Wnt3a-CM was produced in-house by Wnt3a L-cells (kind gift from Novartis).

extract_protocol:
Organoids were collected at baseline (0h) and at 12-hour intervals throughout the regeneration timecourse (24-108h) for single cell RNA sequencing. For each timepoint, organoids were collected and digested to a single-cell suspension and FACS sorted as described above. For single-cell RNA sequencing library preparation, 13k cells were sorted per collection vial per timepoint.
Single-cell libraries were prepared using the 10x Genomics Chromium Single Cell 3′ Reagent Kit v2 according to the manufacturer’s protocol. Gel bead-in-emulsion (GEM) generation, reverse transcription, cDNA amplification, and library construction were performed following standard procedures. Libraries were sequenced on an Illumina NextSeq 500 platform using a 75-cycle kit with paired-end configuration (Read 1: 26 bp; Read 2: 56 bp; single index: 8 bp). Base calling was performed using Illumina RTA (v2.4.11), and FASTQ files were generated using bcl2fastq2 (v2.17).

value: mouse small intestinal organoids

value: intestinal epithelial cells

value: wildtype


title: BU-LF-84

description: Library name: BU-LF-84

value: Cortical RNA

value: CR

value: Female


title: E8_BR.snRNAseq

description:
Library name: E8
paired-end single nucleus RNAseq
Ecoli_pigs_snRNA_object.rds

value: brain

value: female

value: Sus scrofa

value: E coli


title: subcutaneous white adipose, Sphk2 deleted IgG control repicate 3

description:
Library name: RB21
H3K9ac_IgG_counts.csv
H3K27ac_IgG_counts.csv

value: subcutaneous white adipose

value: Sphk2 deleted

value: IgG (Abcam, #ab171870)


title: subcutaneous white adipose, wild-type anti-H3K27 acetylation repicate 3

description:
Library name: RB19
H3K27ac_IgG_counts.csv

value: wild-type

value: anti-H3K27ac (Abcam, #ab4729)

value: 0.05 pg E. coli lamda DNA spike-in


title: LCMV D30 fresh control central memory rep 43

description:
Library name: day30_mem_fresh_control_CM_rep_43
Column name in day30_mem_normalized_counts.tsv: day30_mem_fresh_CM_43

value: spleen

value: central memory CD8 T cells

value: day 30 post infection baseline; fresh control; Thy1.1 not applicable


title: subcutaneous white adipose, wild-type anti-H3K9 acetylation repicate 3

description:
Library name: RB18
H3K9ac_IgG_counts.csv

value: anti-H3K9ac (Abcam, #ab10812)


title: BU-LF-83

description: Library name: BU-LF-83

value: Cortical RNA

value: AL


title: BU-LF-82

description: Library name: BU-LF-82

value: CR

value: male


title: subcutaneous white adipose, Sphk2 deleted anti-H3K27 acetylation repicate 2

description:
Library name: RB15
H3K27ac_IgG_counts.csv


title: subcutaneous white adipose, wild-type IgG control repicate 3

description:
Library name: RB17
H3K9ac_IgG_counts.csv
H3K27ac_IgG_counts.csv


title: E4_BR.snRNAseq

description:
Library name: E4
paired-end single nucleus RNAseq
Ecoli_pigs_snRNA_object.rds

value: brain

value: female


title: E6_BR.snRNAseq

description:
Library name: E6
paired-end single nucleus RNAseq
Ecoli_pigs_snRNA_object.rds

value: Sus scrofa

value: E coli


title: subcutaneous white adipose, Sphk2 deleted anti-H3K9 acetylation repicate 2

description:
Library name: RB14
H3K9ac_IgG_counts.csv

value: subcutaneous white adipose

value: Sphk2 deleted


title: BU-LF-81

description: Library name: BU-LF-81

value: Female


title: E1_BR.snRNAseq

description:
Library name: E1
paired-end single nucleus RNAseq
Ecoli_pigs_snRNA_object.rds


title: subcutaneous white adipose, Sphk2 deleted IgG control repicate 2

description:
Library name: RB13
H3K9ac_IgG_counts.csv
H3K27ac_IgG_counts.csv

value: IgG (Abcam, #ab171870)


title: subcutaneous white adipose, wild-type anti-H3K27 acetylation repicate 2

description:
Library name: RB11
H3K27ac_IgG_counts.csv

value: wild-type

value: anti-H3K27ac (Abcam, #ab4729)

value: 0.05 pg E. coli lamda DNA spike-in


title: BU-LF-76

description: Library name: BU-LF-76


title: subcutaneous white adipose, wild-type anti-H3K9 acetylation repicate 2

description:
Library name: RB10
H3K9ac_IgG_counts.csv


title: subcutaneous white adipose, wild-type IgG control repicate 2

description:
Library name: RB9
H3K9ac_IgG_counts.csv
H3K27ac_IgG_counts.csv


title: BU-LF-74

description: Library name: BU-LF-74


title: htz-1(tm2469), young adult, rep 4

city: Bonn

first: Daniele

last: Bano

state: NRW

address: Venusberg Campus 1/99

country: Germany

institute: DZNE, German Center for Neurodegenerative Diseases

description: Library name: Sample12

data_processing:
RNA sequencing was performed using 75 bp paired-end reads (PE75) on a NovaSeq X Plus (Illumina) with a 10B flow cell. Total RNA was extracted using the miRNeasy Micro Kit and quality-controlled for concentration and size distribution on a TapeStation 4200 system using RNA ScreenTape.
Libraries were prepared following the bulk SMART-Seq2 protocol from 200 pg input RNA and assessed using D1000 ScreenTape on the TapeStation 4200. Sequencing reads were pseudo-aligned to the C. elegans reference genome (Ensembl release 109) using Kallisto (v0.48).
Assembly: WBcel235
Supplementary files format and content: csv file includes normalized counts for each sample.

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Nematode animals were cultured on OP50-1 E. coli at 20 ℃.

extract_protocol:
Young adult worms were collected and dissolved in 1ml Trizol (Invitrogen). Total RNA was extracted using miRNeasy Micro Kit (Qiagen).
Libraries were prepared using SMART-Seq2 protocol (Picelli et al., 2014).

value: whole animal


title: subcutaneous white adipose, Sphk2 deleted anti-H3K27 acetylation repicate 1

description:
Library name: RB7
H3K27ac_IgG_counts.csv


title: htz-1(tm2469), young adult, rep 3

description: Library name: Sample11


title: htz-1(tm2469), young adult, rep 2

description: Library name: Sample10


title: subcutaneous white adipose, Sphk2 deleted IgG control repicate 1

description:
Library name: RB5
H3K9ac_IgG_counts.csv
H3K27ac_IgG_counts.csv


title: BU-LF-71

description: Library name: BU-LF-71


title: subcutaneous white adipose, Sphk2 deleted anti-H3K9 acetylation repicate 1

description:
Library name: RB6
H3K9ac_IgG_counts.csv

value: anti-H3K9ac (Abcam, #ab10812)


title: subcutaneous white adipose, wild-type anti-H3K27 acetylation repicate 1

description:
Library name: RB3
H3K27ac_IgG_counts.csv


title: BU-LF-70

description: Library name: BU-LF-70

value: Cortical RNA


title: htz-1(tm2469), young adult, rep 1

description: Library name: Sample9


title: subcutaneous white adipose, wild-type IgG control repicate 1

description:
Library name: RB1
H3K9ac_IgG_counts.csv
H3K27ac_IgG_counts.csv


title: BU-LF-69

description: Library name: BU-LF-69

value: AL


title: Bcell-3

city: kisarazu

first: Keiko

last: Nakano

state: chiba

address: kazusa-kamatari 2-6-7

institute: Kazusa DNA Research institute

description:
Library name: Bcell-3
Column name in CPM_count1.tsv: Bcell-3

data_processing:
For 3' mRNA sequencing (QuantSeq), single-end reads (101 bp) were processed using fastp (version 0.23.4) to remove adapter sequences and poly(A) tails.
Clean reads were aligned using STAR (version 2.7.10a) to the following reference genomes: - Mus musculus: GRCm39 (mm39; GCA_000001635.9) - Homo sapiens: GRCh38 (hg38; GCA_000001405.15)
Gene-level read counts were generated using Subread featureCounts (version 2.0.6) at the meta-feature (exon) level using Ensembl annotations: - Mus musculus: Ensembl release 113 (Mus_musculus.GRCm39.113.gtf) - Homo sapiens: Ensembl release 115 (Homo_sapiens.GRCh38.115.gtf)
Counting was performed with strand-specific settings (forward), assigning reads to gene_id.
CPM values were calculated for each sample using a scaling factor (1,000,000 divided by the total assigned reads).
Assembly: Mus musculus: GRCm39 (Ensembl release 113 / GCA_000001635.9) Homo sapiens: GRCh38 (Ensembl release 115 / GCA_000001405.15)
Supplementary files format and content: Excel files include CPM values for each Sample

source_name: B cell

extract_protocol:
See method in article
Quant-Seq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen)

value: B cell

value: WT


title: Bcell-2

description:
Library name: Bcell-2
Column name in CPM_count1.tsv: Bcell-2


title: htz-1(ok3099), young adult, rep 4

description: Library name: Sample8


title: subcutaneous white adipose, wild-type anti-H3K9 acetylation repicate 1

description:
Library name: RB2
H3K9ac_IgG_counts.csv


title: BU-LF-66

description: Library name: BU-LF-66


title: htz-1(ok3099), young adult, rep 3

description: Library name: Sample7


title: Tcell-2

description:
Library name: Tcell-2
Column name in CPM_count1.tsv: Tcell-2

source_name: T cell

value: T cell


title: BU-LF-65

description: Library name: BU-LF-65

value: CR

value: male


title: Bcell-1

description:
Library name: Bcell-1
Column name in CPM_count1.tsv: Bcell-1


title: Tcell-1

description:
Library name: Tcell-1
Column name in CPM_count1.tsv: Tcell-1


title: htz-1(ok3099), young adult, rep 2

description: Library name: Sample6


title: BU-LF-63

description: Library name: BU-LF-63


title: D56_GFP_Runx1 Input

city: Rochester

first: Aditya

last: Bhagwate

state: MN

address: 200 1st Street SW

description: Library name: Input-D56-G-11

data_processing:
Paired end reads were mapped to mm10 reference genome using BWA.
Uniquely mapped read pairs were retained using samtools.
Peaks were called using MACS2
Assembly: mm10
Supplementary files format and content: macs2 peaks files

extract_protocol:
Single cells were isolated from lungs and fixed in 1% formaldehyde for 10 min. After quencing, cells were frozen at -80C until further processing.
Libraries were prepared from purified ChIP and input DNAs using NEBNext High-Fidelity PCR mix (NEB) with Nextera PCR primers with molecular indices (Nextera DNA Sample Preparation Kit). DNA size was analyzed by the Fragment Analyzer (Agilent, Santa Clara, CA) using the High Sensitivity NGS Fragment Analysis Kit (Cat. #DNF-486).

value: Lung

value: Fibroblast

value: Bleomycin injury

tag: chip antibody


title: BU-LF-61

description: Library name: BU-LF-61


title: ID_423

city: New York City

first: Ragavi

last: Vijayakumar

state: New York

address: 430 E 67th St

department: Developmental Biology

institute: Sloan Kettering Institute

description:
Library name: Sample 48
Ribodepleted bulk RNA_seq

data_processing:
The fastq files were processed using salmon to generate the "quant" files
The "quant" files were used as input for Rstudio (deseq2 package)
Assembly: mm10
Supplementary files format and content: Salmon-outputs

source_name: Diversity Outbred

extract_protocol:
Frozen cells were lysed in 1mL TRIzol Reagent (ThermoFisher catalog # 15596018) and phase separation was induced with 200 µL chloroform. RNA was extracted from 350 µL of the aqueous phase using the miRNeasy Micro or Mini Kit (Qiagen catalog # 217084/217004) on the QIAcube Connect (Qiagen) according to the manufacturer’s protocol. Samples were eluted in 20-35 µL RNase-free water.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 71-500 ng of total RNA with RIN values of 9.5-10 underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit, catalog # RS-122-2102), with 8 cycles of PCR. Samples were barcoded and run on a NovaSeq 6000 in a PE100 run, using the NovaSeq 6000 S2 or S4 NovaSeq Reagent Kit (200 or 300 Cycles) (Illumina).  An average of 69 million paired reads was generated per sample. Ribosomal reads represented 0.1-1.7% of the total reads generated and the percent of mRNA bases averaged 91%.

value: Diversity Outbred

value: Neural Progenitor Cells


title: htz-1(ok3099), young adult, rep 1

description: Library name: Sample5


title: D56_GFP_Runx1 ChIP

description: Library name: D56-G-X1-5

value: Runx1 (Abcam, Cat. # ab23980)


title: htz-1(bon101), young adult, rep 4

description: Library name: Sample4


title: D14_GFP_Runx1 ChIP

description: Library name: D14-G-X1-3


title: Sham_GFP_Runx1 Input

description: Library name: Input-Sham-G-7

value: Sham injury


title: BU-LF-59

description: Library name: BU-LF-59

value: Female


title: Sham_GFP_Runx1 ChIP

description: Library name: Sham-G-X1-1


title: D14_GFP_Runx1 Input

description: Library name: Input-D14-G-9


title: RNA_6_KO4_Treg_melanoma_RbpdeltaFoxp3a

city: Heraklion

first: Matthieu

middle: David

last: Lavigne

address: Nikolaou Plastira 100

country: Greece

institute: IMBB-FORTH

description:
Library name: RNA_6_KO4
KO4.BAM
Rbpj_RNAseq_countdata.csv

data_processing:
For full-length mRNA-seq, Raw sequence data were quality-controlled using FastQC version 0.12.0 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Adapter sequences and poor-quality bases were removed with Cutadapt version 1.1656. Paired-end reads were aligned to the mouse genome GRCm38 using Rsubread version 2.12.3. Alignments were performed using default parameters. Reads associated with annotated genes were counted using the Rsubread function ‘featureCount’. Differentially expressed genes were identified using an FDR cut-off below 0.05 after normalization in EdgeR version 3.40.2 (PMID: 19910308)
Quant-seq: The quality of the FASTQ files was assessed with the FastQC software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were aligned to the mouse (mm10) genome  with the Hisat2 aligner (hisat2 -p32 -x $REFERENCE_GENOME -q fastq/$FILE_ID.fastq -S $FILE_ID.sam --score-min L,0,-0.5 -k 2). Htseq-counts was utilized to summarize reads at the gene level (htseq-count -f bam -s yes-igene_idbam/$FILE_ID.bamdata/refs/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf>$COUNTS_DIR/NGS$FILE_ID). Differential expression analysis (DEA) was conducted by running EdgeR via SARTools 1.5.0. For each comparison, DEGs were defined by applying the following thresholds adj. p-value <0.05, which was considered statistically significant.
Read quality was assessed using FastQC version 0.12.0 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Adapters and poor-quality bases were trimmed using fastp version 0.23.4 (PMID: 30423086). Samples were aligned to the mouse reference genome GRCm38 using default parameters in Rsubread version 2.12.3 (PMID: 30783653).  Mitochondrial reads were removed using SAMtools version 1.18. PCR duplicates were removed using the ‘MarkDuplicates’ function in Picard Tools version 17.0.13 (Java) (http://broadinstitute.github.io/picard/). Open chromatin was detected using MACS2 version 2.2.9.1 with an FDR < 0.05. The number of reads in each peak was determined using featureCounts embedded in Rsubread version 2.12.3. Differentially accessible peaks were identified using an FDR cut-off below 0.05 after normalization in DESeq2 version 1.38.3 (PMID: 25516281). Peaks were annotated using the ‘annotatePeak’ function using ChIPseeker version 1.34.1.  The bamCoverage function from deepTools version 3.5.6 was used to generate coverage track (BigWig) files. Trackplot version 1.6.0 was utilized to create IGV-style track plots (also known as locus plots) from BigWig files. Pheatmap version 1.0.12 was used to generate the heatmap of differentially accessible regions (DARs).
Assembly: mm10
Supplementary files format and content: Quant-seq: raw_counts_table_LTvT_quant-seq.txt, This matrix includes  counts of reads in ESMUSG Ensemble genes id  for 3 biological replicates (sample LT1,LT2,LT3 - TDLN_Treg cells_Foxp3EGFP mice; sample T1, T2, T345 - tumor_Treg cells_Foxp3EGFP mice)
Supplementary files format and content: ATAC-seq count matrix (Rbpj_ATACseq_counts_table.csv: This matrix excludes blacklisted regions, mitochondrial reads, and peaks detected in only one sample  (WT1, WT2, WT3:  biological Replicates of Tregs from Foxp3YFPcre;   KO1, KO2, KO3: biological Replicates of Tregs from Foxp3YFPcre RbpjΔFoxp3)
Supplementary files format and content: full length mRNA-seq raw count data (Rbpj_RNAseq_countdata.csv): Row names correspond to gene IDs, and column names represent the samples: (WT1, WT2, WT3:  biological Replicates of Tregs from Foxp3YFPcre;   KO2 KO3, KO4: biological Replicates of Tregs from Foxp3YFPcre RbpjΔFoxp3)

source_name: tumor melamoma

growth_protocol: murine B16.F10 melanoma, were cultured at 37°C under 5% CO2 in complete medium [RPMI-1640 medium (GlutaMAXTM, Gibco, #61870) supplemented with 10% foetal bovine serum (FBS, Gibco, #10270), 0.1% β-mercaptoethanol (Gibco, #31350) and 1% of a mix of Penicillin/Streptomycin (P/S, Gibco, #15140)]. B16.F10 melanoma and MB49 urothelial cancer cells were split at 90%–100% confluence.

extract_protocol:
For Full length strand-specific mRNA-seq, Treg cells (CD45+CD4+ Foxp3YFP+) were FACS-sorted from melanoma tumors of Foxp3YFPcre or RbpjΔFoxp3and RNA was extracted using the ArcturusTM PicoPure TM RNA isolation kit (Thermo Fisher, #12204-01) according to the manufacturer’s protocol. For Quant-seq (T1-345, LT1-3), total RNA was extracted from FACS-sorted Tregs cells derived TDLNs or tumors of Foxp3EGFP melanoma-bearing mice, using NucleoSpin RNA XS (Macherey-Nagel; cat. #740955.50) as per the manufacturer’s protocol. The quantity and quality of RNA samples were analyzed using Agilent RNA 6000 Nano kit with the bioanalyzer from Agilent.
For Full length strand-specific mRNA-seq, RNA-seq libraries were prepared using NEBNext Ultra™ II Directional RNA Library Prep Kit for Illumina with NEBNext Poly(A) mRNA Magnetic Isolation Module according to manufacturer’s instructions and starting with three replicates per group and 50-120 ng of pure total RNA extracted from 18-28.000 sorted cells. Libraries were prepared using sample specific combinations of i5 and i7 indexed adapters, amplified for 16-18 cycles according to qPCR estimates and were size selected for sizes around 400 bp. Paired-end reads (2*111) were sequenced on an Illumina NextSeq 2000 at Genecore EMBL, DE. For Quant-seq (T1-345, LT1-3,) RNA samples with RNA integrity number (RIN)>7 were used for library construction using the 3′ mRNA-Seq Library Prep Kit FWD for Illumina (QuantSeq-LEXOGEN) as per the manufacturer’s instructions. Amplification was controlled for obtaining optimal unbiased libraries across samples by assessing the number of cycles (ranging from 19-20 cycles) required by qPCR. DNA High Sensitivity Kit for bioanalyzer was used to assess the quantity and quality of libraries, according to the manufacturer’s instructions (Agilent). Libraries were multiplexed and sequenced on an Illumina Nextseq 500 at the genomics facility of IMBB FORTH, GR. according to the manufacturer’s instructions.
The ATAC-seq protocol was performed as previously described57,58. In brief, 2-5 x 104 Treg cells were FACS-sorted (CD45+CD4+Foxp3YFP+) from melanoma tumors of Foxp3YFPcre or RbpjΔFoxp3, washed with ice-cold PBS and resuspended in lysis buffer [0.1% NP-40, 0.1% Tween-20, 0.01% Digitonin in Resuspension Buffer (10mM Tris-HCl, 10mM NaCl, 3mM MgCl2)]. Cell nuclei were washed (0.1% Tween-20 in Resuspension Buffer) and the transposition reaction was performed by using Tn5 Transposase in tagmentation buffer (Illumina Tagment DNA enzyme and Buffer, #20034210), 10%Tween-20, 1%Digitonin and incubating for 30min at 37oC. DNA was purified with the the MinElute Cleanup Kit (Qiagen, #28204) and amplified using the NEBNext High-Fidelity PCR Master Mix (New England BioLabs) and Nextera PCR primers with sample specific combinations of i5 and i7 indexes. Library were size selected for sizes between 200 and 500 bp using AMPure XP beads (Beckman Coulter). Paired-end reads (2*111) were sequenced on an Illumina NextSeq 2000 at Genecore EMBL, Heidelberg.

treatment_protocol: melanoma tumors growth in Foxp3YFPcre, RbpjΔFoxp3 and  Foxp3EGFP mice was monitored after implanting subcutaneously on the back 3 x 10^5 B16.F10 melanoma cells in each tested mouse.

value: tumor melamoma

value: Treg

value: subcutaneous implantation 3 x 10^5 B16.F10 melanoma cells


title: htz-1(bon101), young adult, rep 2

description: Library name: Sample2

value: whole animal


title: RNA_5_KO3_Treg_melanoma_RbpjdeltaFoxp3a

description:
Library name: RNA_5_KO3
KO3.BAM
Rbpj_RNAseq_countdata.csv


title: BU-LF-56

description: Library name: BU-LF-56

value: Cortical RNA


title: RNA_4_KO2_Treg_melanoma_RbpjdeltaFoxp3a

description:
Library name: RNA_4_KO2
KO2.BAM
Rbpj_RNAseq_countdata.csv


title: BU-LF-52

description: Library name: BU-LF-52


title: RNA_3_WT3_Treg_melanoma_Foxp3YFPcre

description:
Library name: RNA_3_WT3
WT3.BAM
Rbpj_RNAseq_countdata.csv


title: RNA_2_WT2_Treg_melanoma_Foxp3YFPcre

description:
Library name: RNA_2_WT2
WT2.BAM
Rbpj_RNAseq_countdata.csv


title: RNA_1_WT1_Treg_melanoma_Foxp3YFPcre

description:
Library name: RNA_1_WT1
WT1.BAM
Rbpj_RNAseq_countdata.csv


title: ATAC_6_KO3_Treg_melanoma_RbpjdeltaFoxp3a

description:
Library name: ATAC_6_KO3
KO3.bam
Rbpj_ATACseq_counts_table.csv


title: BU-LF-50

description: Library name: BU-LF-50

value: AL


title: NFkB_2_screen_A549_rep1

city: Vienna

first: Tomas

last: Pachano

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

description:
Library name: Sample 19
164bp

data_processing:
Adapters were trimmed using trim galore
Trimmed reads were aligned with Bowtie2 to a custom dictionary indexes of BCs, where each BC is associated to its assigned ORF
The resulting BAM file was used to construct a raw count matrix for each BC
The resulting BC count matrix was used as an input to MAGeCK tool (https://doi.org/10.1186/s13059-014-0554-4) to identify ORFs that are enriched in each screen.
Assembly: custom Dictionary of BC-eORFs
Supplementary files format and content: tab-delimited text file includes raw counts for each BC id. Each BC id contains a number and the id of its associated ORF (e.g. BC23_1893 correspond to the BC 23 of ORF 1893, and the ORF id can be associated to a specific ORF through table S1).

growth_protocol: A549 cells were cultured at 37ºC in DMEM (In-house) supplemented with 10% heat inactivated FBS (Gibco, S0615), L-glutamine (Gibco, 25030081) and penicillin-streptomycin (Gibco, 15140122) and passaged every 3 days. U937 cells were cultured at 37ºC in RPMI (Gibco, 11875093) supplemented with 10% FBS (Gibco, S0615) and passaged every 3 days.

extract_protocol:
Genomic DNA (gDNA) was isolated by lysing cell pellets overnight at 55°C in a buffer containing 10 mM Tris-HCl (pH 8.0), 5 mM EDTA, 100 mM NaCl, 1% SDS, and 0.5 mg/ml proteinase K. The lysate was then treated with RNase A (Qiagen) for 2 hours at 37°C. Subsequently, gDNA was purified through two sequential extractions with phenol:chloroform:isoamyl alcohol followed by a final extraction with chloroform:isoamyl alcohol. For barcode (BC) recovery, the entire gDNA yield from sorted/selected samples and 40 µg of gDNA from input samples were used as templates.
To generate NGS libraries,  40 individual PCR reactions were performed for each gDNA sample. The PCR adds Illumina adaptors and indexes for each sample. Following amplification, all PCR reactions for a given sample were pooled. The pooled amplicons were concentrated and purified using the Monarch PCR & DNA Cleanup Kit (NEB), using six columns for each input sample and one column for each sorted/selected sample. The final purified barcode amplicons were gel-extracted and submitted for next-generation sequencing.

treatment_protocol: For each biological replicate, cells were transduced at a multiplicity of infection (MOI) below 0.2 to ensure single-copy integration while maintaining a library representation of at least 10,000-fold. Twenty-four hours post-transduction, cells were selected with 1 µg/ml puromycin, after which eORF expression was induced with 1 µg/ml doxycycline for 24 hours. For the reporter-based screens, procedures were as follows: for the NF-κB activation screen, a baseline sample of 15 million cells was collected as the "input" control before the remaining cells were sorted for the GFP-positive population (top 5%) using a BD FACSAria III sorter. For the inhibition screens, cells were first treated with either 20 ng/mL TNFα (NF-κB inhibition) or 2.5 µM Nutlin (p53 inhibition) for 16 hours. After this treatment, the 15 million cell "input" sample was collected, and the remaining cells were sorted to isolate the GFP-low or mCherry-low populations (bottom 5%), respectively, using a BD FACSAria III sorter. For the apoptosis inhibition screen, transduced A549-Eco cells were split post-induction into two conditions: a control group maintained in doxycycline and a treatment group cultured with both doxycycline and etoposide (0.1 uM). These populations were maintained for 10 days, splitting them at a 1:4 ratio upon reaching confluency. At the conclusion of each screen, genomic DNA was isolated from all collected cell populations (input, sorted, or treated) for subsequent barcode analysis (see below). All screens were performed in two independent biological replicates.

value: screen


title: NFkB_2_screen_A549_rep2

description:
Library name: Sample 20
164bp


title: ATAC_5_KO2_Treg_melanoma_RbpjdeltaFoxp3a

description:
Library name: ATAC_5_KO2
KO2.bam
Rbpj_ATACseq_counts_table.csv


title: ATAC_3_WT3_Treg_melanoma_Foxp3YFPcre

description:
Library name: ATAC_3_WT3
WT3.bam
Rbpj_ATACseq_counts_table.csv


title: NFkB_2_input_A549_rep2

description:
Library name: Sample 18
164bp

value: input


title: NFkB_2_input_A549_rep1

description:
Library name: Sample 17
164bp


title: BU-LF-46

description: Library name: BU-LF-46

value: CR


title: ATAC_2_WT2_Treg_melanoma_Foxp3YFPcre

description:
Library name: ATAC_2_WT2
WT2.bam
Rbpj_ATACseq_counts_table.csv