title: Using  IRBP peptide and CFA for 2 weeks rep3

description: Library name: EAU3

value: EAU


title: Using  IRBP peptide and CFA for 2 weeks rep2

status: Public on Dec 22 2024

type: SRA

city: Wu Han

first: Zhen

last: Chen

state: Hu bei

address: Zhangzhidong Road

country: China

institute: Renmin Hospital of Wuhan University

description: Library name: EAU2

library_source: transcriptomic

data_processing:
Data filtering The sequencing data was filtered with SOAPnuke  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
RNA identification Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8)  according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5)  (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
Gene Annotation To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) .
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include gene count values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Retina

extract_protocol:
1. Experimental Procedures 1.1 Sample Lysis 1.1.1 Transfer appropriate tissue sample into corresponding tissue grinding tube (tissue≤30 mg, cell≤1×107). 1.1.2 Add 600 μL Buffer RLT Plus. Homogenize the lysate for using a rotor–stator homogenizer, stay at room temperature for 5 min. 1.1.3 Centrifuge at 12,000×g for 3 min in room temperature, transfer the supernatant to AllPrep DNA spin column. 1.1.4 Centrifuge 12,000×g for 30 s in room temperature, transfer the solution from the collection tube for the RNA purification. 1.1.5 Transfer the DNA spin column to the new collection tube for DNA purification. 1.2 DNA Purification 1.2.1 Add 500μL Buffer AW1 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate. 1.2.2 Add 500μL Buffer AW2 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate. 1.2.3 Centrifuge at 16,000×g for 2 min, transfer the AllPrep DNA spin column to 1.5mL centrifuge tube. 1.2.4 Add 50μL Buffer EB to AllPrep DNA spin column, stay at room temperature for 1 min. 1.2.5 Centrifuge at 16,000×g for 2 min and collect the DNA. 1.3 RNA Purification 1.3.1 Add the equal volume of 70% ethanol to the collection tube, mix by pipetting. 1.3.2 Transfer 700 μL mixed solution, to a RNeasy spin column placed in a 2 mL collection tube. 2.3.3 Centrifuge at 10,000×g for 30 s and allow it to empty by gravity flow. 1.3.4 Add 700 μL Buffer RW1 to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.5 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.6 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.7 Centrifuge at 16,000×g for 2 min and transfer the RNeasy spin column to the 1.5 mL centrifuge tube. 1.3.8 Add 35 μL RNase-free water to RNeasy spin column. Stay at room temperature for 1min. 1.3.9 Centrifuge at 16,000×g for 2 min at room temperature to collect RNA.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

tag: tissue

value: Retina

tag: genotype

tag: treatment


title: Using  IRBP peptide and CFA for 2 weeks rep1

description: Library name: EAU1


title: Using IRBP peptide and CFA for an additional 2 weeks, followed with CSD for  4 week rep1

description: Library name: CSD-EAU1

value: CSD-EAU


title: Chronic sleep deprivation treatment for 4 weeks rep2

description: Library name: CSD-CON2

value: CSD-CON


title: W4 (ATAC-seq)

status: Public on Dec 23 2024

city: Changsha

first: Mei

last: Yang

address: 139 Middle Renmin Road

institute: The Second Xiangya Hospital, Central South University

library_source: genomic

data_processing:
Raw reads were filtered and trimmed by Trimmomatic
The clean reads were then aligned to reference genome sequences using the bwa program
callpeak with cutoff qvalue<0.05 was performed with macs2 software
reads distributions across gene were analyzed by deeptools, and bedtools were employed to annotate peaks
Differential peak analysis of two conditions/groups was performed using the DESeq2 R package (1.6.3). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with a FDR < 0.01 and foldchange ≥ 2 found by DESeq2 were assigned as differentially expressed.
Assembly: GRCm38_release95
Supplementary files format and content: tab-delimited text file includes raw counts and normalized values for each Sample
Supplementary files format and content: merged bigwig file for WT and KO respectively

molecule: genomic DNA

source_name: skeletal muscle

extract_protocol:
Instantly frozen muscle from mice were used to collect nuclei for transposition by Tn5 Transposase. The samples were then purified using a Qiagen MinElute PCR Purification Kit (Qiagen)
Purified DNA were amplified using 1X NEBNext High-Fidelity PCR Master Mix (New England Biolabs, MA) for library construction, which were again purified using the Qiagen MinElute PCR Purification Kit (Qiagen)

value: skeletal muscle

tag: cell type

value: quadriceps femoris


title: Chronic sleep deprivation treatment for 4 weeks rep3

description: Library name: CSD-CON3


title: Healthy Control rep3

description: Library name: CON3

value: CON

value: Healthy Control rep3


title: Chronic sleep deprivation treatment for 4 weeks rep1

description: Library name: CSD-CON1


title: Healthy Control rep1

description: Library name: CON1

value: Healthy Control rep1


title: Human PGCLC generated from hiPSC-A4, Hi-C seq

city: Charlestown

first: Toshihiro

last: Shioda

state: MA

address: Building 149 - 7th Floor, 13th Street

department: Center for Cancer Research

country: USA

institute: MGH Cancer Center

description:
Library name: hPGCLC-A4
proximally ligated DNA

data_processing:
Libraries were sequenced using Illumina NovaSeq 6000. FASTQ reads (150 + 150 paired-end) were generated from the BCL files using Illumina bcl2fastq for NovaSeq.
Hi-C seq FASTQ reads were subjected to trimGalore (0.6.0) with -q 20 --trim1 --paired options.
Trimmed FASTQ reads were aligned to the GRCh38/hg38 human genome reference sequence using Hi-C Pro (2.11.1) using the default setting.
Hi-C Pro (2.11.1) generated matrix files (.matrix) and the index files (_abs.bed) were used to further generate ICE-normalized matrix files (_iced.matrix) by Hi-C Pro.
Assembly: GRCh38/hg38 (human reference genome)
Supplementary files format and content: Matrix files (.matrix), matrix index files (_abs.bed), and ICE-normalized matrix files (_iced.matrix) contain chromatin contact information.

organism: Homo sapiens

growth_protocol: Human iPSCs were grown in the mTeSR Plus medium. Human PGCLCs were generated from iPSCs and FACS-enriched as CD38+ cells.

extract_protocol:
Cell cultures were exposed to formaldehyde for proximal ligation and lysed following the protocol of Arima Genomics Hi-C kit (Cat# A510008).
Illumina compatible Hi-C libraries were prepared using Arima Genomics Hi-C kit (Cat# A510008).

tag: cell line

value: PGCLC culture

tag: Sex

value: male


title: Human PGCLC generated from hiPSC-A5, Hi-C seq

description:
Library name: hPGCLC-A5
proximally ligated DNA


title: WT_37_A

city: College Park

first: Jiqiang

last: Ling

state: MD

address: 2202 Microbiology Bldg., 4062 Campus Dr.

department: Cell Biology and Molecular Genetics

institute: The University of Maryland, College Park

description: Library name: Sample 1

data_processing:
Raw counts of sequence reads (FKPM) were analyzed by Novogene according to standard protocol using HISAT2 software.
Assembly: Reads were mapped to the reference genome (Saccharomyces cerevisiae S288c GCA_000146045.2) using HISAT2 software by Novogene.
Supplementary files format and content: Excel sheet. FKPM.

organism: Saccharomyces cerevisiae

source_name: Cell pellet

extract_protocol:
Total RNA extraction using QiaGen RNAeasy kit according to manufacture's protocol
Constructed by Novogene according to standard protocol

value: Cell pellet

value: Yeast


title: Healthy Control rep2

description: Library name: CON2

value: Healthy Control rep2


title: Human naive iPSC, clone A6, Hi-C seq

description:
Library name: hiPSC-A6
proximally ligated DNA

value: Naive iPSC culture


title: Human naive iPSC, clone A4, Hi-C seq

description:
Library name: hiPSC-A4
proximally ligated DNA


title: Human PGCLC generated from hiPSC-A6, Hi-C seq

description:
Library name: hPGCLC-A6
proximally ligated DNA


title: Human naive iPSC, clone A5, Hi-C seq

description:
Library name: hiPSC-A5
proximally ligated DNA


title: PBMCs, Japanese cohort, B010_L002, H146

city: Singapore

first: Boxiang

last: Liu

address: 12 Science Drive 2, MD1 - Tahir Foundation Building, Level 5

country: Singapore

institute: National University of Singapore

description: Library name: JP_RIK_B010_L002_5GEX_H146

library_source: transcriptomic single cell

data_processing:
The DRAGEN Single-Cell RNA pipeline in the Illumina DRAGEN v3.8.4 software (version 07.021.602.3.8.4-20-g74395e76) was used for pre-processing of paired-end FASTQ files from each individual scRNA-seq gene expression library. Reads from each pool were mapped to GENCODE Release 32 (GRCh38, Ensembl 98, date 2019-09-05).  The count data was processed and analyzed in R. Within each pool, every cell (barcode) and read was assigned to an individual within that pool using Genotype Data (provided) in DRAGEN v3.8.4.
Assembly: GRCh38/hg38
Supplementary files format and content: Raw data were processed from fatsq files, which contain cDNA sequences. Single-cell expression data were processed using *rds file containing single cell expression and metadata matrix.

molecule: polyA RNA

source_name: blood

extract_protocol:
Eight ml of blood was drawn from each donor using CPT tubes with sodium heparin (BD Vacutainer CPT, cat. no. 362753). PBMC isolation followed a standardized protocol across sites, using FBS (Sigma-Aldrich cat. no. F2442, lot 19G014 and 20A363) for cell isolation, pooling, and washing. Blood samples were processed within 2 hours at room temperature via density-gradient centrifugation (1,500 x g, 30 min, 20°C, with soft acceleration/deceleration). Plasma was aspirated, and PBMCs were pelleted at 300 x g for 15 min, then resuspended in ACK lysing buffer (Thermo Fisher, cat. no. A10492). Cells were washed twice (PBS pH 7.4, 1% FBS, 1 mM EDTA) and cryopreserved in CryoStor CS10 (STEMCELL Technologies, cat. no. 079555). Cryovials were stored at -80°C before transfer to liquid nitrogen. The full protocol is available on Protocols.io: https://www.protocols.io/view/pbmcs-isolation-from-cpt-tube-b8r9rv96.
Both AIDA and LONZA individuals were sequenced in pools of 16 individuals, including 15 AIDA samples and 1 LONZA control sample (chosen from 5 LONZA PBMC samples). Chromium Next GEM Single Cell 5’ Kit v2 was used for library construction

value: blood

value: human

value: PBMCs


title: PBMCs, Caucasian, B010_L002, LONZA3038306

description: Library name: JP_RIK_B010_L002_5GEX_LONZA3038306


title: PBMCs, Japanese cohort, B010_L002, H145

description: Library name: JP_RIK_B010_L002_5GEX_H145


title: PBMCs, Japanese cohort, B010_L002, H149

description: Library name: JP_RIK_B010_L002_5GEX_H149


title: PBMCs, Japanese cohort, B010_L002, H143

description: Library name: JP_RIK_B010_L002_5GEX_H143


title: PBMCs, Japanese cohort, B010_L002, H147

description: Library name: JP_RIK_B010_L002_5GEX_H147


title: PBMCs, Japanese cohort, B010_L002, H144

description: Library name: JP_RIK_B010_L002_5GEX_H144


title: PBMCs, Japanese cohort, B010_L002, H140

description: Library name: JP_RIK_B010_L002_5GEX_H140


title: PBMCs, Japanese cohort, B010_L002, H139

description: Library name: JP_RIK_B010_L002_5GEX_H139


title: PBMCs, Japanese cohort, B010_L002, H137

description: Library name: JP_RIK_B010_L002_5GEX_H137


title: Tumor 3 PG1lo

city: Kyoto

first: Yoshifumi

last: Ueda

address: Katsura, Kyoto-daigaku

department: Department of Synthetic Chemistry and Biological Chemistry

country: Japan

institute: Graduate School of Engineering, Kyoto University

data_processing:
Each obtained read was mapped to the human genome version GRCh37/hg19 with STAR (v2.6.0c) using default parameters.
To normalize the expression data, trimmed mean of M values (TMM) were calculated based on edgeR R package.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: tab-delimited text files include TMM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: NCI-N87 subcutaneous tumor (day 21)

growth_protocol: 2 x 10^6 NCI-N87 tumor cells in PBS containing 50 % Growth Factor Reduced Matrigel (BD Biosciences) were injected subcutaneously into the flank of each nude mouse.

extract_protocol:
Freshly isolated NCI-N87 tumors were enzymatically digested and the dissociated cells were sorted according to the fluorescence of PG1 and AF647. Total RNA isolation was performed with the Qiagen RNeasy micro kit.
A cDNA library was prepared using a SMART-Seq v4 Ultra Low Input RNA kit for Sequencing (Takara Bio) and a Nextera XT Index Kit v2 SetA/B/C/D (Illumina).

treatment_protocol: 21 days after the inoculation, mice were injected with PTA through tail vein.

tag: pg1 fluorescence

tag: sample number

value: Tumor 3


title: PBMCs, Japanese cohort, B010_L002, H148

description: Library name: JP_RIK_B010_L002_5GEX_H148


title: PBMCs, Caucasian, B010_L001, LONZA3038306

description: Library name: JP_RIK_B010_L001_5GEX_LONZA3038306


title: PBMCs, Japanese cohort, B010_L002, H141

description: Library name: JP_RIK_B010_L002_5GEX_H141


title: PBMCs, Japanese cohort, B010_L001, H149

description: Library name: JP_RIK_B010_L001_5GEX_H149


title: PBMCs, Japanese cohort, B010_L002, H142

description: Library name: JP_RIK_B010_L002_5GEX_H142


title: PBMCs, Japanese cohort, B010_L001, H148

description: Library name: JP_RIK_B010_L001_5GEX_H148


title: PBMCs, Japanese cohort, B010_L002, H136

description: Library name: JP_RIK_B010_L002_5GEX_H136


title: PBMCs, Japanese cohort, B010_L001, H146

description: Library name: JP_RIK_B010_L001_5GEX_H146


title: PBMCs, Japanese cohort, B010_L001, H145

description: Library name: JP_RIK_B010_L001_5GEX_H145


title: PBMCs, Japanese cohort, B010_L001, H143

description: Library name: JP_RIK_B010_L001_5GEX_H143


title: PBMCs, Japanese cohort, B010_L001, H142

description: Library name: JP_RIK_B010_L001_5GEX_H142


title: PBMCs, Japanese cohort, B010_L001, H140

description: Library name: JP_RIK_B010_L001_5GEX_H140


title: PBMCs, Japanese cohort, B010_L001, H141

description: Library name: JP_RIK_B010_L001_5GEX_H141


title: PBMCs, Japanese cohort, B010_L001, H138

description: Library name: JP_RIK_B010_L001_5GEX_H138


title: PBMCs, Japanese cohort, B010_L001, H144

description: Library name: JP_RIK_B010_L001_5GEX_H144


title: PBMCs, Japanese cohort, B010_L001, H139

description: Library name: JP_RIK_B010_L001_5GEX_H139


title: PBMCs, Japanese cohort, B010_L001, H136

description: Library name: JP_RIK_B010_L001_5GEX_H136


title: PBMCs, Japanese cohort, B010_L002, H138

description: Library name: JP_RIK_B010_L002_5GEX_H138


title: PBMCs, Japanese cohort, B009_L002, H134

description: Library name: JP_RIK_B009_L002_5GEX_H134


title: PBMCs, Japanese cohort, B009_L002, H132

description: Library name: JP_RIK_B009_L002_5GEX_H132


title: PBMCs, Japanese cohort, B009_L002, H131

description: Library name: JP_RIK_B009_L002_5GEX_H131


title: PBMCs, Caucasian, B009_L002, LONZA3038097

description: Library name: JP_RIK_B009_L002_5GEX_LONZA3038097


title: PBMCs, Japanese cohort, B009_L002, H129

description: Library name: JP_RIK_B009_L002_5GEX_H129


title: PBMCs, Japanese cohort, B009_L002, H128

description: Library name: JP_RIK_B009_L002_5GEX_H128


title: PBMCs, Japanese cohort, B009_L002, H133

description: Library name: JP_RIK_B009_L002_5GEX_H133


title: PBMCs, Japanese cohort, B010_L001, H147

description: Library name: JP_RIK_B010_L001_5GEX_H147


title: PBMCs, Japanese cohort, B009_L002, H124

description: Library name: JP_RIK_B009_L002_5GEX_H124


title: PBMCs, Japanese cohort, B009_L002, H121

description: Library name: JP_RIK_B009_L002_5GEX_H121


title: PBMCs, Japanese cohort, B009_L002, H123

description: Library name: JP_RIK_B009_L002_5GEX_H123


title: PBMCs, Caucasian, B009_L001, LONZA3038097

description: Library name: JP_RIK_B009_L001_5GEX_LONZA3038097


title: PBMCs, Japanese cohort, B009_L002, H125

description: Library name: JP_RIK_B009_L002_5GEX_H125


title: PBMCs, Japanese cohort, B009_L002, H122

description: Library name: JP_RIK_B009_L002_5GEX_H122


title: PBMCs, Japanese cohort, B009_L001, H135

description: Library name: JP_RIK_B009_L001_5GEX_H135


title: PBMCs, Japanese cohort, B009_L001, H134

description: Library name: JP_RIK_B009_L001_5GEX_H134


title: PBMCs, Japanese cohort, B010_L001, H137

description: Library name: JP_RIK_B010_L001_5GEX_H137


title: PBMCs, Japanese cohort, B009_L001, H132

description: Library name: JP_RIK_B009_L001_5GEX_H132


title: PBMCs, Japanese cohort, B009_L001, H133

description: Library name: JP_RIK_B009_L001_5GEX_H133


title: PBMCs, Japanese cohort, B009_L001, H131

description: Library name: JP_RIK_B009_L001_5GEX_H131


title: PBMCs, Japanese cohort, B009_L001, H130

description: Library name: JP_RIK_B009_L001_5GEX_H130


title: PBMCs, Japanese cohort, B009_L002, H130

description: Library name: JP_RIK_B009_L002_5GEX_H130


title: PBMCs, Japanese cohort, B009_L001, H126

description: Library name: JP_RIK_B009_L001_5GEX_H126


title: PBMCs, Japanese cohort, B009_L002, H126

description: Library name: JP_RIK_B009_L002_5GEX_H126


title: PBMCs, Japanese cohort, B009_L001, H124

description: Library name: JP_RIK_B009_L001_5GEX_H124


title: PBMCs, Caucasian, B008_L002, LONZA3038016

description: Library name: JP_RIK_B008_L002_5GEX_LONZA3038016


title: PBMCs, Japanese cohort, B008_L002, H117

description: Library name: JP_RIK_B008_L002_5GEX_H117


title: PBMCs, Japanese cohort, B008_L002, H113

description: Library name: JP_RIK_B008_L002_5GEX_H113


title: PBMCs, Japanese cohort, B009_L002, H127

description: Library name: JP_RIK_B009_L002_5GEX_H127


title: PBMCs, Japanese cohort, B008_L002, H120

description: Library name: JP_RIK_B008_L002_5GEX_H120


title: PBMCs, Japanese cohort, B009_L001, H127

description: Library name: JP_RIK_B009_L001_5GEX_H127


title: PBMCs, Japanese cohort, B009_L001, H129

description: Library name: JP_RIK_B009_L001_5GEX_H129


title: PBMCs, Japanese cohort, B008_L002, H119

description: Library name: JP_RIK_B008_L002_5GEX_H119


title: PBMCs, Japanese cohort, B009_L001, H123

description: Library name: JP_RIK_B009_L001_5GEX_H123


title: PBMCs, Japanese cohort, B009_L002, H135

description: Library name: JP_RIK_B009_L002_5GEX_H135


title: PBMCs, Japanese cohort, B009_L001, H125

description: Library name: JP_RIK_B009_L001_5GEX_H125


title: PBMCs, Japanese cohort, B008_L002, H111

description: Library name: JP_RIK_B008_L002_5GEX_H111


title: PBMCs, Japanese cohort, B008_L002, H109

description: Library name: JP_RIK_B008_L002_5GEX_H109


title: PBMCs, Japanese cohort, B009_L001, H128

description: Library name: JP_RIK_B009_L001_5GEX_H128


title: PBMCs, Japanese cohort, B009_L001, H122

description: Library name: JP_RIK_B009_L001_5GEX_H122


title: PBMCs, Japanese cohort, B008_L002, H107

description: Library name: JP_RIK_B008_L002_5GEX_H107


title: PBMCs, Japanese cohort, B009_L001, H121

description: Library name: JP_RIK_B009_L001_5GEX_H121


title: PBMCs, Japanese cohort, B008_L002, H118

description: Library name: JP_RIK_B008_L002_5GEX_H118


title: PBMCs, Japanese cohort, B008_L001, H119

description: Library name: JP_RIK_B008_L001_5GEX_H119


title: PBMCs, Japanese cohort, B008_L002, H108

description: Library name: JP_RIK_B008_L002_5GEX_H108


title: PBMCs, Japanese cohort, B008_L001, H117

description: Library name: JP_RIK_B008_L001_5GEX_H117


title: PBMCs, Japanese cohort, B008_L002, H114

description: Library name: JP_RIK_B008_L002_5GEX_H114


title: PBMCs, Japanese cohort, B008_L002, H115

description: Library name: JP_RIK_B008_L002_5GEX_H115


title: PBMCs, Japanese cohort, B008_L001, H118

description: Library name: JP_RIK_B008_L001_5GEX_H118


title: PBMCs, Japanese cohort, B008_L002, H106

description: Library name: JP_RIK_B008_L002_5GEX_H106


title: PBMCs, Japanese cohort, B008_L002, H116

description: Library name: JP_RIK_B008_L002_5GEX_H116


title: PBMCs, Japanese cohort, B008_L002, H112

description: Library name: JP_RIK_B008_L002_5GEX_H112


title: PBMCs, Caucasian, B008_L001, LONZA3038016

description: Library name: JP_RIK_B008_L001_5GEX_LONZA3038016


title: PBMCs, Japanese cohort, B008_L001, H120

description: Library name: JP_RIK_B008_L001_5GEX_H120


title: PBMCs, Japanese cohort, B008_L001, H115

description: Library name: JP_RIK_B008_L001_5GEX_H115


title: PBMCs, Japanese cohort, B008_L001, H114

description: Library name: JP_RIK_B008_L001_5GEX_H114


title: PBMCs, Japanese cohort, B008_L002, H110

description: Library name: JP_RIK_B008_L002_5GEX_H110


title: PBMCs, Japanese cohort, B008_L001, H113

description: Library name: JP_RIK_B008_L001_5GEX_H113


title: PBMCs, Japanese cohort, B008_L001, H112

description: Library name: JP_RIK_B008_L001_5GEX_H112


title: PBMCs, Japanese cohort, B008_L001, H110

description: Library name: JP_RIK_B008_L001_5GEX_H110


title: PBMCs, Japanese cohort, B008_L001, H111

description: Library name: JP_RIK_B008_L001_5GEX_H111


title: PBMCs, Japanese cohort, B008_L001, H108

description: Library name: JP_RIK_B008_L001_5GEX_H108


title: PBMCs, Japanese cohort, B008_L001, H109

description: Library name: JP_RIK_B008_L001_5GEX_H109


title: ETH04_IPO323_R30C_3

city: Zurich

first: Cecile

last: Lorrain

state: Zurich

address: Universistätstrasse 2

department: Plant PAthology

country: Switzerland

institute: ETH Zurich

description: Library name: Unknown_BW591-001U0061

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomaticv0.35
Transcript abundances were quantified using Kallisto v0.46.1
Read counts were summarized using tximport v1.2.0
Read abundance normalization and differential gene expression analysis were performed with the R package DESeq2
Assembly: IPO323 reference strain (Goodwin et al. 2011) and annotations from Lapalu et al. 2023
Supplementary files format and content: tab-delimited txi.kallisto abundance counts for all samples

molecule: nuclear RNA

organism: Zymoseptoria tritici

source_name: Spores

extract_protocol:
The frozen samples were sent for RNA extraction and sequencing to Biomarker Technologies GmbH (BMKgene, Münster, Germany)
Ribosomal RNA was depleted by poly A enrichment, and DNA libraries were sequenced with Illumina NovaSeq 6000 at Novogene Europe
Libraries were prepared by Biomarker Technologies GmbH (BMKgene, Münster, Germany)

value: Spores

tag: time

value: 90 hours

value: GPL pH 7  30°C 15h + 18°C 75h


title: ETH04_IPO323_R0C_2

description: Library name: Unknown_BW591-001U0036

value: GPL pH 7  0°C 15h + 18°C 75h


title: ETH04_IPO323_18C_3

description: Library name: Unknown_BW591-001U0053

value: GPL pH 7 18°C 15h + 18°C 75h


title: ETH04_IPO323_S30C_3

description: Library name: Unknown_BW591-001U0058

value: 15 hous

value: GPL pH 7 30°C 15h


title: ETH04_IPO323_R0C_3

description: Library name: Unknown_BW591-001U0062


title: PBMCs, Japanese cohort, B008_L001, H106

description: Library name: JP_RIK_B008_L001_5GEX_H106


title: ETH04_IPO323_S0C_3

description: Library name: Unknown_BW591-001U0059

value: GPL pH 7 0°C 15h


title: PBMCs, Japanese cohort, B008_L001, H116

description: Library name: JP_RIK_B008_L001_5GEX_H116


title: ETH04_IPO323_R30C_2

description: Library name: Unknown_BW591-001U0035


title: ETH04_IPO323_S18C_3

description: Library name: Unknown_BW591-001U0060

value: GPL pH 7 18°C 15h


title: ETH04_IPO323_S18C_2

description: Library name: Unknown_BW591-001U0034


title: ETH04_IPO323_S0C_2

description: Library name: Unknown_BW591-001U0033


title: PBMCs, Caucasian, B007_L002, LONZA3038306

description: Library name: JP_RIK_B007_L002_5GEX_LONZA3038306


title: PBMCs, Japanese cohort, B007_L002, H105

description: Library name: JP_RIK_B007_L002_5GEX_H105


title: PBMCs, Japanese cohort, B007_L002, H104

description: Library name: JP_RIK_B007_L002_5GEX_H104


title: ETH04_IPO323_S30C_2

description: Library name: Unknown_BW591-001U0032


title: PBMCs, Japanese cohort, B007_L002, H101

description: Library name: JP_RIK_B007_L002_5GEX_H101


title: PBMCs, Japanese cohort, B007_L002, H102

description: Library name: JP_RIK_B007_L002_5GEX_H102


title: PBMCs, Japanese cohort, B007_L002, H103

description: Library name: JP_RIK_B007_L002_5GEX_H103


title: ETH04_IPO323_R0C_1

description: Library name: Unknown_BW591-001U0010


title: PBMCs, Japanese cohort, B008_L001, H107

description: Library name: JP_RIK_B008_L001_5GEX_H107


title: PBMCs, Japanese cohort, B007_L002, H100

description: Library name: JP_RIK_B007_L002_5GEX_H100


title: ETH04_IPO323_R30C_1

description: Library name: Unknown_BW591-001U0009


title: PBMCs, Japanese cohort, B007_L002, H099

description: Library name: JP_RIK_B007_L002_5GEX_H099


title: ETH04_IPO323_S18C_1

description: Library name: Unknown_BW591-001U0008


title: ETH04_IPO323_S0C_1

description: Library name: Unknown_BW591-001U0007


title: PBMCs, Japanese cohort, B007_L002, H098

description: Library name: JP_RIK_B007_L002_5GEX_H098


title: ETH04_IPO323_S30C_1

description: Library name: Unknown_BW591-001U0006


title: PBMCs, Japanese cohort, B007_L002, H094

description: Library name: JP_RIK_B007_L002_5GEX_H094


title: 2457t_rpos_exp2

city: Ulsan

first: Donghyuk

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

country: South Korea

institute: UNIST

data_processing:
Sequencing: Illumina platform
Mapping: Sequence reads generated from RNA-seq were mapped onto the reference genome (NC_004741.1) using bowtie.
SAM: SAM files generated from bowtie.
Genome_build: Genome build: reference genome (NC_004741.1)
Supplementary_files_format_and_content: ChIP-exo reads were aligned to the NC_004741 genome reference sequence using using bowtie v1.0.0 with parameters -S. MACE software (https://code.google.com/p/chip-exo/) was used to detect peaks with aligned output from bowtie mapping. BAM files were generated by Samtools and GFF files were made by in-house python scripts. Tab-delimited text files in gff format which has 8 columns: sequence id, source(empty), feature (+/- strand), start position, end position, intensity score, strand(+/-), frame(.), attribute(.).

organism: Shigella flexneri

source_name: bacteria

growth_protocol: glycerol stocks of S. flexneri strains were inoculated into M9 minimal media with 0.2% (w/v) glucose. M9 minimal media was also supplemented with 1 ml trace element solution (100X) containing 1 g EDTA, 29 mg ZnSO4.7H2O, 198 mg MnCl2.4H2O, 254 mg CoCl2.6H2O, 13.4 mg CuCl2, and 147 mg CaCl2. The culture was incubated at 37 oC overnight with agitation, and then was used to inoculate the fresh media (1/200 dilution). The volume of the fresh media was 150 mL for each biological replicate. The fresh culture was incubated at 37 oC with agitation to the exponential phase (OD600 ≈ 0.5).

extract_protocol:
Lysates were clarified from sonicated transcription factor-DNA complexes were isolated with myc antibody.
ChIP-exo experiment was performed following the procedures:  to identify each TF candidate binding maps in vivo, we isolated the DNA bound to each TF candidate from formaldehyde cross-linked S. flexneri cells by chromatin immunoprecipitation (ChIP) with the specific antibodies that specifically recognizes myc tag (9E10, Santa Cruz Biotechnology), and Dynabeads Pan Mouse IgG magnetic beads (Invitrogen) followed by stringent washings as described previously. ChIP materials (chromatin-beads) were used to perform on-bead enzymatic reactions of the ChIP-exo method. Briefly, the sheared DNA of chromatin-beads was repaired by the NEBNext End Repair Module (New England Biolabs) followed by the addition of a single dA overhang and ligation of the first adaptor (5’-phosphorylated) using dA-Tailing Module (New England Biolabs) and NEBNext Quick Ligation Module (New England Biolabs), respectively. Nick repair was performed by using PreCR Repair Mix (New England Biolabs). Lambda exonuclease- and RecJf exonuclease-treated chromatin was eluted from the beads and the protein-DNA cross-link was reversed by overnight incubation at 65℃. RNAs- and Proteins-removed DNA samples were used to perform primer extension and second adaptor ligation with following modifications. The DNA samples incubated for primer extension as described previously were treated with dA-Tailing Module (New England Biolabs) and NEBNext Quick Ligation Module (New England Biolabs) for second adaptor ligation. The DNA sample purified by GeneRead Size Selection Kit (Qiagen) was enriched by polymerase chain reaction (PCR) using Phusion High-Fidelity DNA Polymerase (New England Biolabs). The amplified DNA samples were purified again by GeneRead Size Selection Kit (Qiagen) and quantified using Qubit dsDNA HS Assay Kit (Life Technologies). Quality of the DNA sample was checked by running Agilent High Sensitivity DNA Kit using Agilent 2100 Bioanalyzer (Agilent) before sequenced using MiSeq (Illumina) in accordance with the manufacturer’s instructions. Each modified step was also performed in accordance with the manufacturer’s instructions. ChIP-exo experiments were performed in biological duplicate.
ChIP-exo

value: rpoS knock-out

tag: myc-tagging

value: myc-tagging cells

tag: chip-exo antibody

value: c-myc(9E10) mouse monoclonal IgG1, sc-40, lot#J2413, SantaCruz Biotechnology

tag: strain

value: Shigella flexneri 2a str. 2457T


title: 2457t_rpos_exp1


title: PBMCs, Japanese cohort, B007_L002, H095

description: Library name: JP_RIK_B007_L002_5GEX_H095

value: blood


title: PBMCs, Japanese cohort, B007_L002, H096

description: Library name: JP_RIK_B007_L002_5GEX_H096

value: human


title: 2457t_rpon_exp1

value: rpoN knock-out


title: 2457t_rpon_exp2


title: ETH04_IPO323_18C_2

description: Library name: Unknown_BW591-001U0027


title: PBMCs, Japanese cohort, B007_L002, H092

description: Library name: JP_RIK_B007_L002_5GEX_H092

value: PBMCs


title: PBMCs, Japanese cohort, B007_L002, H093

description: Library name: JP_RIK_B007_L002_5GEX_H093


title: PBMCs, Japanese cohort, B007_L002, H091

description: Library name: JP_RIK_B007_L002_5GEX_H091


title: 2457t_rpob_exp2

value: rpoB knock-out


title: 2457t_rpod_exp1

value: rpoD knock-out


title: PBMCs, Japanese cohort, B007_L001, H105

description: Library name: JP_RIK_B007_L001_5GEX_H105


title: 2457t_rpob_exp1


title: 2457t_rna_exp2

data_processing:
Sequencing: Illumina platform
Mapping: Sequence reads generated from RNA-seq were mapped onto the reference genome (NC_004741.1) using bowtie.
SAM: SAM files generated from bowtie.
Genome_build: Genome build: reference genome (NC_004741.1)
Supplementary_files_format_and_content: Sequenced reads were mapped onto NC_004741 reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S. SAM files generated from bowtie, then, were then used for Cufflinks (http://cufflinks.cbcb.umd.edu/) to calculate fragments per kilobase of exon per million fragments (FPKM). Cufflinks was run with default options with the library type of dUTP RNA-seq and the default normalization method (classic-fpkm). Besides, BAM files were generated by Samtools and GFF files were made by in-house python scripts. Tab-delimited text files in gff format which has 8 columns: sequence id, source(empty), feature (+/- strand), start position, end position, intensity score, strand(+/-), frame(.), attribute(.).

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and genomic DNA was removed by gDNA Eliminator spin column in the RNeasy Plus Mini Kit. RNA quality and concentration was determined by analysis with a NanoDrop 1000 (Thermo Scientific Inc., Wilmington, DE, USA).  RNA libraries were prepared for sequencing using standard Illumina protocols
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cell culture was treated with the RNAprotect reagent (Qiagen)


title: PBMCs, Caucasian, B007_L001, LONZA3038306

description: Library name: JP_RIK_B007_L001_5GEX_LONZA3038306


title: Input

city: Perugia

first: Elisabetta

last: Albi

state: Italy

address: Via Romana

department: Department of Pharmaceutical Sciences

country: Italy

institute: Università degli studi di Perugia

description: Genomic input DNA as a reference

data_processing:
Basecalls performed using the ShortRead R/Biocoductor package
ChIP-seq reads were aligned to the hg38 genome assembly using bowtie2 version 2.3.4.3 with default configuration for unpaired reads
Duplicate reads were flagged using samtools but no duplicates were removed
peaks were called using MACS2 version 2.1.1 with the following setting: ChIP threshold (0.2).
Assembly: hg38
Supplementary files format and content: bedgraph files were generated with bedtools from a MACS2 generated BED3+2 format file containing the peak locations together with peak name and fold-enrichment

source_name: Panc-1 spheroids

growth_protocol: A total of 1600 cells were suspended in a Matrigel solution (20 μL 0.1% FBS-DMEM F-12, 60 μL 2.5% v/v reduced-growth factors Matrigel (Corning, USA)Matrigel, Corning, USA) and plated on coverslips in 35-mm tissue culture plates

extract_protocol:
Cells were fixed with 1% formaldeyde for 15 min at room temperature and then quenched with 5 ml of PBS/GLYCINE for 5 min at room temperature. Matrigel was melted and Cells were lysed in 0.1 ml ChIP lysis buffer (50 mM Hepes-KOH, pH 7.5, 140 mM NaCl, 1% Triton X-100, and 0.1% deoxycholate with 0.1 mM PMSF and the EDTA-free Protease Inhibitor Cocktail). Samples were incubated on ice for 10 min and then centrifuged at 3,000 rpm for 3 min at 4°C. The pellet was resuspended in 500 µl lysis buffer 2 (10 mM Tris, pH 8.0, 200 mM NaCl with 0.1 mM PMSF and the EDTA-free Protease Inhibitor Cocktail) and incubated at room temperature for 10 min. Samples were centrifuged at 3,000 rpm for 5 min at 4°C. Next, the pellet was resuspended in 300 µl lysis buffer 3 (10 mM Tris, pH 8.0, 100 mM NaCl, 0.5% deoxycholate, and 0.1% SDS with 0.1 mM PMSF and the EDTA-free Protease Inhibitor Cocktail). Cells were sonicated using a Biorupter (Diagenode) for 15 min (30 s on, 1 min off). Next, 30 µl of 10% Triton X-100 was added to each tube, and then samples were centrifuged at max speed for 15 min at 4°C. The supernatant was transferred to new tubes, and the DNA concentration was quantified. Samples were precleared for 1 h at 4°C on a rotator using 8 µl protein A Dynabeads (Zymo) in ChIP lysis buffer. Samples were centrifuged at max speed for 15 min at 4°C, after which the supernatant was transferred to a new tube. 1/100 input was collected. 3 µg Antibodies were added O/N. 8 µl of protein A Dynabeads were added and chromatin was immunoprecipitated for 2h at 4°C. The following washes were performed for 15 min each by rotating for 15 min at 4°C: ChIP lysis buffer (twice), ChIP lysis buffer + 0.65 M NaCl, wash buffer (10 mM Tris-HCl, pH 8.0, 250 mM LiCl, 0.5% NP-30, 0.5% DOC, and 1 mM EDTA, pH 8.0), and TE (10 mM Tris-HCl, pH 8.0, and 1 mM EDTA, pH 8.0). Beads were incubated with RNASEA solution (100ul TE/2ul Rnasi A (10mg/ml). DNA was eluted by adding to the beads 100ul of TES (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, pH 8.0, and 1% SDS) for 15 min at 65°C with brief vortexing every 2 min. Reversal of cross-linking was performed by incubating samples overnight at 65°C: transfer into 0.5ml tubes and place in termocycler. Proteins were digested using 150ug of proteinase K (0.5ul proteinase K) by incubating at 37°C for 5h. Finally, the DNA was purified using the Zymo Research Kit and eluted 2 times in 40ul H20.
Sonicated DNA underwent End repair and A-tailing steps (MGI Tech Co., Shenzen, China). Adapters ligation was performed following the instructions of the MGIEasy DNA Adapters kit, and cleaned up with the provided DNA Clean Beads. PCR amplification was carried out and cleaned-up again using magnetic beads. After quality control of DNA, purified PCR products were denaturated and ligated to generate single-strand circular DNA libraries. Barcoded libraries were then pooled in equal amounts to make DNA Nanoballs (DNB)
DNA nanoballs

treatment_protocol: 3D culture

value: Panc-1 spheroids

value: PDAC

value: 3D culture


title: 2457t_rna_exp1

value: Shigella  2a str. 2457T


title: PBMCs, Japanese cohort, B007_L001, H104

description: Library name: JP_RIK_B007_L001_5GEX_H104


title: PBMCs, Japanese cohort, B007_L001, H103

description: Library name: JP_RIK_B007_L001_5GEX_H103


title: H3K27ac WT

description: H3K27ac ChIP-seq

value: WT


title: HFF_si_NORAD_24h_rep4

city: Haifa

first: Tamar

last: Lahav

address: Zor

department: Biology

country: Israel

institute: Technion

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using catadapt
Trimmed sequence reads were mapped to GRCh38 or GRCm39 using STAR
Assembly: GRCh38/GRCm39.104
Supplementary files format and content: tab-delimited text files include read counts for each sample

source_name: HFF

extract_protocol:
RNA was extracted using Tri-reagent
RNA libraries for 3' RNA sequencing were prepared using the CEL-seq2 protocol

value: HFF

tag: time point

value: 24 hours


title: H3K27ac KO

description: H3K27ac ChIP-seq


title: HFF_si_NORAD_24h_rep3


title: ETH04_IPO323_18C_1

description: Library name: Unknown_BW591-001U0001

value: Spores

value: 90 hours

value: GPL pH 7 18°C 15h + 18°C 75h


title: PBMCs, Japanese cohort, B007_L002, H097

description: Library name: JP_RIK_B007_L002_5GEX_H097


title: HFF_si_NORAD_24h_rep1


title: HFF_si_control_24h_rep3


title: 2457t_rpod_exp2

value: myc-tagging cells

value: c-myc(9E10) mouse monoclonal IgG1, sc-40, lot#J2413, SantaCruz Biotechnology

value: Shigella flexneri 2a str. 2457T


title: HFF_si_control_24h_rep2


title: Entero_muscle_3

city: Seoul

first: Jeung Hee

last: An

address: 47 Kkachisan-ro 24-gil, Gangseo-gu

institute: Gangseo University

description: Library name: Entero_muscle_3

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastp), then mapped to GRCm39 whole genome using STAR
Calculation mapped reads using salmon
CPM + TMM calculation using conorm
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include Read count values for each Sample

source_name: muscle

growth_protocol: The animals were housed under standardized conditions, maintaining a temperature of 21–22 °C, a 12-h light/dark cycle, and 70% humidity, with ad libitum access to chow and water.

extract_protocol:
Total RNA was extracted from the cells with the use of a TruSeq Stranded mRNA Kit (Illumina) .
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: All animal procedures were approved by the Institutional Animal Care and Use Committee of Daejeon University (approval number: DJUARB2022-026). Six-week-old male C57BL/6 mice were sourced from Raon Bio Inc. (Gyeonggi-do, Korea) and maintained under controlled conditions with free access to food and water. After a one-week acclimation period, mice were assigned to five treatment groups (n = 8/group): (1) normal, (2) MPTP-intoxicated at 20 mg/kg (Sigma-Aldrich, St. Louis, MA, USA), (3) MPTP + levodopa at 2 mg/kg (Sigma-Aldrich), and (4) MPTP + low-dose En. faecium FBL1 (109 log CFU·mL-1·day-1), and (5) MPTP + high-dose En. faecium FBL1 (10¹⁰ log CFU·mL-1·day-1). The normal group was fed a standard diet for 28 days, while the MPTP group received MPTP for the first seven days, followed by a standard diet for 28 days. Groups 3–5 underwent MPTP treatment for seven days, after which they were treated with levodopa or En. faecium FBL1 for 28 days (Fig. 3a). Upon completion of the treatment period, the mice were sacrificed and their brain and muscle tissues were collected for molecular analyses.

value: muscle

value: 6 week

value: male

value: 1 weeks of stabilization, MPTP treatment for 1 week followed by oral injection of Enterococcus faecium for 4 weeks.


title: Entero_muscle_2

description: Library name: Entero_muscle_2


title: PBMCs, Japanese cohort, B007_L001, H101

description: Library name: JP_RIK_B007_L001_5GEX_H101

value: blood

value: human

value: PBMCs


title: HFF_si_control_24h_rep1


title: Entero_muscle_1

description: Library name: Entero_muscle_1


title: HFF_si_control_16h_rep4

value: 16 hours


title: HFF_si_control_24h_rep4


title: PBMCs, Japanese cohort, B007_L001, H100

description: Library name: JP_RIK_B007_L001_5GEX_H100


title: HFF_si_NORAD_16h_rep4


title: PBMCs, Japanese cohort, B007_L001, H099

description: Library name: JP_RIK_B007_L001_5GEX_H099


title: HFF_si_control_16h_rep3


title: PBMCs, Japanese cohort, B007_L001, H098

description: Library name: JP_RIK_B007_L001_5GEX_H098


title: HFF_si_NORAD_16h_rep3


title: HFF_si_NORAD_24h_rep2


title: Levo_muscle_1

description: Library name: Levo_muscle_1

value: 1 weeks of stabilization, MPTP treatment for 1 week followed by intraperitoneal injection of levodopa for 4 weeks.


title: PBMCs, Japanese cohort, B007_L001, H097

description: Library name: JP_RIK_B007_L001_5GEX_H097


title: HFF_si_control_16h_rep1

value: HFF


title: HFF_si_control_16h_rep2


title: HFF_si_NORAD_16h_rep1


title: PBMCs, Japanese cohort, B007_L001, H096

description: Library name: JP_RIK_B007_L001_5GEX_H096


title: MPTP_muscle_3

description: Library name: MPTP_muscle_3

value: 1 weeks of stabilization, MPTP treatment for 1 week followed by Normal diet for 4 weeks


title: HFF_si_NORAD_8h_rep2

value: 8 hours


title: HFF_si_control_8h_rep2


title: MPTP_muscle_2

description: Library name: MPTP_muscle_2


title: PBMCs, Japanese cohort, B007_L001, H095

description: Library name: JP_RIK_B007_L001_5GEX_H095


title: MPTP_muscle_1

description: Library name: MPTP_muscle_1


title: PBMCs, Japanese cohort, B007_L001, H094

description: Library name: JP_RIK_B007_L001_5GEX_H094


title: PBMCs, Japanese cohort, B007_L001, H102

description: Library name: JP_RIK_B007_L001_5GEX_H102


title: HFF_si_NORAD_8h_rep1


title: ES_si_NORAD_rep4

source_name: ES

value: ES

value: 72 hours


title: Levo_muscle_3

description: Library name: Levo_muscle_3


title: ES_si_NORAD_rep3


title: Levo_muscle_2

description: Library name: Levo_muscle_2


title: ES_si_control_rep4


title: PBMCs, Japanese cohort, B007_L001, H093

description: Library name: JP_RIK_B007_L001_5GEX_H093


title: PBMCs, Japanese cohort, B007_L001, H092

description: Library name: JP_RIK_B007_L001_5GEX_H092


title: ES_si_NORAD_rep2


title: HFF_si_NORAD_16h_rep2


title: ES_si_control_rep2


title: Con_muscle_2

description: Library name: Con_muscle_2

value: 1 weeks of stabilization, Normal diet for 5 weeks


title: ES_si_control_rep3


title: ES_si_control_rep1


title: PBMCs, Japanese cohort, B007_L001, H091

description: Library name: JP_RIK_B007_L001_5GEX_H091


title: MEF_si_Norad_rep3

source_name: MEF

value: MEF

value: 24 hours


title: Con_muscle_1

description: Library name: Con_muscle_1

value: muscle


title: PBMCs, Caucasian, B006_L002, LONZA3038099

description: Library name: JP_RIK_B006_L002_5GEX_LONZA3038099


title: ES_si_NORAD_rep1


title: MEF_si_Norad_rep2


title: HFF_si_control_8h_rep1


title: PBMCs, Japanese cohort, B006_L002, H090

description: Library name: JP_RIK_B006_L002_5GEX_H090


city: shanghai

first: Beibei

last: Hu

address: No 1678, Dongfang Road, Pudong New Area

institute: shanghai children's medical center

description: Library name: macrophages-non_depleted_sorbs2_mutant_e18.5_biol rep 2

data_processing:
CLC Genomics W orkbench v 11.0.1
Assembly: GRCm39
Supplementary files format and content: tab-delimted text file includes raw counts for each Sample

source_name: heart

extract_protocol:
RNA was harvested using trizol.1.5 ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq Library Prep Kit following manufacture's protocols.

value: heart

tag: developmental stage


description: Library name: macrophages-non_depleted_sorbs2_mutant_e18.5_biol rep 1


title: MEF_si_Norad_rep1


title: MEF_si_control_rep2


title: PBMCs, Japanese cohort, B006_L002, H089

description: Library name: JP_RIK_B006_L002_5GEX_H089


title: MEF_si_control_rep3


title: Con_muscle_3

description: Library name: Con_muscle_3

value: 6 week

value: male


description: Library name: macrophages-depleted_sorbs2 mutant_e18.5_biol rep 2


title: PBMCs, Japanese cohort, B006_L002, H088

description: Library name: JP_RIK_B006_L002_5GEX_H088

value: blood


title: MEF_si_control_rep1


title: AT3 p.8

city: Tel-Aviv

first: Amit

last: Levon

address: Ramat Aviv

institute: Tel-Aviv University

data_processing:
The processed reads were aligned to the mouse genome (mm10) using Rsubread v2.0.0 ‘align’ function (sortReadsByCoordinates=True, detectSV=False), with the mouse GENCODE mm10 vM10 GTF as an external annotation file.
Every sample (currently 4 bam files each - L001/L002/L003/L004) was merged into a single bam file, using the Samtools v1.3.1 ‘merge’ command.
Gene expression was calculated using Rsubread ‘featureCounts’ (countMultiMappingReads=False) to count the number of reads that map to each gene, with the GENCODE mm10 vM10 GTF as an external annotation file.
The reads were then normalized by TPM (Transcripts Per Kilobase Million) using the total exonic length acquired from the same GENCODE database.
In order to remain with only genes that have been robustly expressed in the samples, we continued only with genes that have a value of at least 1.0 TPM in all replicates of at least one biological condition in the dataset.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample (txt file).
Supplementary_files_format_and_content: Matrix table with TPM normalized gene counts for every gene and every sample (txt file).
Supplementary_files_format_and_content: Matrix table with TPM normalized gene counts only for genes that have a value of at least 1.0 TPM in all replicates of at least one biological condition in the dataset (txt file).

source_name: Primary lung fibroblasts

growth_protocol: Cells were grown in complete Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 15% fetal bovine serum (FBS), 1% (v/v) penicillin/streptomycin and 1% (v/v) L-glutamine. The cultures were maintained at 37°C in a humidified atmosphere with 5% CO2 and 3% O2

extract_protocol:
Total RNA was isolated using Qiazol Lysis Reagent (QIAGEN) and purified with the MiRNeasy Kit (QIAGEN), according to the manufacturer’s protocol. The RNA purity (260/230 and 280/260) was measured by nanodop. RNA concentration was measured by Qbit and the integrity was measured using the Tapstation instrument. The purified RNA was used for subsequent library preparation and sequencing.
TrueSeq RNA sample prep

treatment_protocol: For IR-induced senescence, cells were exposed to 10Gy X-rays using the Faxitron (X-ray) cabinet providing 0.5 Gy/min, and harvested 10 days later .

value: No treatment

value: Atm-/-

value: Primary lung fibroblasts


description: Library name: macrophages-depleted_sorbs2 mutant_e18.5_biol rep 1


title: PBMCs, Japanese cohort, B006_L002, H087

description: Library name: JP_RIK_B006_L002_5GEX_H087

value: human

value: PBMCs


title: AT1 p.8


title: PBMCs, Japanese cohort, B006_L002, H086

description: Library name: JP_RIK_B006_L002_5GEX_H086


title: WT1 p.8

value: Atm+/+


title: WT3 p.8


title: PBMCs, Japanese cohort, B006_L002, H085

description: Library name: JP_RIK_B006_L002_5GEX_H085


description: Library name: macrophages-non_depleted_sorbs2_mutant_e12.5_biol rep 2


description: Library name: macrophages-non_depleted_sorbs2_mutant_e12.5_biol rep 1


description: Library name: macrophages-non_depleted_sorbs2_mutant_e12.5_biol rep 3


title: PBMCs, Japanese cohort, B006_L002, H084

description: Library name: JP_RIK_B006_L002_5GEX_H084


title: AT2 p.2


title: AT1 p.2


title: WT2 p.8


title: AT3 p.2


title: PBMCs, Japanese cohort, B006_L002, H083

description: Library name: JP_RIK_B006_L002_5GEX_H083


description: Library name: macrophages-depleted_sorbs2 mutant_e18.5_biol rep 3


title: AT2 p.8


title: WT1 p.2


description: Library name: macrophages-depleted_sorbs2_mutant_e12.5_biol rep 5


title: WT3 p.2


title: PBMCs, Japanese cohort, B006_L002, H082

description: Library name: JP_RIK_B006_L002_5GEX_H082


description: Library name: macrophages-depleted_sorbs2_mutant_e12.5_biol rep 4


title: PBMCs, Japanese cohort, B006_L002, H081

description: Library name: JP_RIK_B006_L002_5GEX_H081


title: WT2 p.2


title: IR3 p.2

value: Irradiated with 10 Gy X-ray


title: IR2 p.2


description: Library name: macrophages-depleted_sorbs2_mutant_e12.5_biol rep 3


title: IR1 p.2


title: mg1655_rna_exp2

data_processing:
Sequencing: Illumina platform
Mapping: Sequence reads generated from RNA-seq were mapped onto the reference genome (NC_000913.2) using bowtie.
SAM: SAM files generated from bowtie.
Genome_build: Genome build: reference genome (NC_000913.2)
Supplementary_files_format_and_content: Sequenced reads were mapped onto NC_000913.2 reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S. SAM files generated from bowtie, then, were then used for Cufflinks (http://cufflinks.cbcb.umd.edu/) to calculate fragments per kilobase of exon per million fragments (FPKM). Cufflinks was run with default options with the library type of dUTP RNA-seq and the default normalization method (classic-fpkm). Besides, BAM files were generated by Samtools and GFF files were made by in-house python scripts. Tab-delimited text files in gff format which has 8 columns: sequence id, source(empty), feature (+/- strand), start position, end position, intensity score, strand(+/-), frame(.), attribute(.).

organism: Escherichia coli

growth_protocol: glycerol stocks of E. coli strains were inoculated into M9 minimal media with 0.2% (w/v) glucose. M9 minimal media was also supplemented with 1 ml trace element solution (100X) containing 1 g EDTA, 29 mg ZnSO4.7H2O, 198 mg MnCl2.4H2O, 254 mg CoCl2.6H2O, 13.4 mg CuCl2, and 147 mg CaCl2. The culture was incubated at 37 oC overnight with agitation, and then was used to inoculate the fresh media (1/200 dilution). The volume of the fresh media was 150 mL for each biological replicate. The fresh culture was incubated at 37 oC with agitation to the exponential phase (OD600 ≈ 0.5).

value: Escherichia coli K-12 substr. MG1655


description: Library name: macrophages-depleted_sorbs2_mutant_e12.5_biol rep 2


title: PBMCs, Japanese cohort, B006_L002, H080

description: Library name: JP_RIK_B006_L002_5GEX_H080


title: PBMCs, Japanese cohort, B006_L002, H079

description: Library name: JP_RIK_B006_L002_5GEX_H079


title: mg1655_rna_exp1


title: PBMCs, Japanese cohort, B006_L002, H078

description: Library name: JP_RIK_B006_L002_5GEX_H078


description: Library name: macrophages-depleted_sorbs2_mutant_e12.5_biol rep 1


title: sorbs2 mutant_e18.5_biol rep 4

description: Library name: sorbs2 mutant_e18.5_biol rep 4


title: sorbs2 mutant_e18.5_biol rep 3

description: Library name: sorbs2 mutant_e18.5_biol rep 3


title: K562 CYTOR KD1-1

city: New York

first: Avi

last: Ma'ayan

state: NY

address: One Gustave L. Levy Place, Box 1603

department: Pharmacological Sciences

institute: Icahn School of Medicine at Mount Sinai

description:
Library name: CYTOR KD1-1
k562CYTOR11

data_processing:
The samples containing sgRNAs that silenced lncRNA CYTOR, along with the NC, were produced in four replicates were quantified by 3’ CEL-seq. Samples were barcoded and pooled before linear amplification of mRNA. During sample preparation, each mRNA transcript was tagged with a Unique Molecular Identifies (UMI).
The sequences obtained from the CEL-seq were aligned and matched to their appropriate gene. The number of reads per gene was recorded for each of the samples. Genes with less than 10 reads overall were filtered out. Analysis was done in R language, using the Remove Unwanted Variation (RUV) package to adjust for systematic errors of unknown origin.
Differential Gene Expression Analysis using limma was done using Biojupies.
Assembly: Sequencing reads were aligned to the human genome reference GRCh38 primary assembly.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: K562 leukemia cells were maintained in Roswell Park Memorial Institute (RPMI) 1640 medium (Gibco), supplemented with 10% fetal calf serum (FCS), 1% L-Glutamine, and 1% pen strep antibiotics (Biological Industries)

extract_protocol:
RNA was extracted with the PureLink RNA Mini Kit (Thermo Fisher Scientific). The quality of the extracted RNA was validated by 1.5% agarose gel (120V for 45 min).
RNA samples were quantified using Qubit Flex (Invitrogen) using the RNA HS assay kit (cat no. Q32855). The quality of the RNA was evaluated using the TapeStation 4200 (Agilent) with the RNA kit (cat no. 5067- 5576). The RINe values of all samples were in the range of 9.5-10.0, indicating high quality. CEL-Seq2 sequencing libraries were prepared as published by Hashimshony et al. [REF: 27121950], with one modification- instead of single cells as input, 2 ng purified RNA was taken as input for library preparation.

treatment_protocol: Lentiviral transfection was performed using Polyjet In Vitro Transfection Reagent (SignaGen, Frederick, MD, USA) following the manufacturer protocol. The synthesized viruses where then used to transduce k562 cells. Positive cells were selected according to BFP fluorescence using the BD FACS Aria-IIIU Sorter.

value: human chronic myelogenous leukemia

value: CYTOR Knockdown


title: K562 CYTOR KD1-2

description:
Library name: CYTOR KD1-2
k562CYTOR12


title: K562 CYTOR KD3-2

description:
Library name: CYTOR KD3-2
k562CYTOR32


title: PBMCs, Japanese cohort, B006_L002, H076

description: Library name: JP_RIK_B006_L002_5GEX_H076


title: K562 WT 4

description:
Library name: NC10010-4
k562100104

value: WT


title: K562 WT 3

description:
Library name: NC10010-3
k562100103


title: K562 WT 2

description:
Library name: NC10010-2
k562100102


title: K562 CYTOR KD3-1

description:
Library name: CYTOR KD3-1
k562CYTOR31


title: K562 WT 1

description:
Library name: NC10010-1
k562100101


title: PBMCs, Caucasian, B006_L001, LONZA3038099

description: Library name: JP_RIK_B006_L001_5GEX_LONZA3038099


title: sorbs2 mutant_e18.5_biol rep 2

description: Library name: sorbs2 mutant_e18.5_biol rep 2


title: OVCAR-8, BLU 250 nM, rep3

city: Buffalo

first: Jianxin

last: Wang

address: 665 Elm Street

department: Molecular and Cellular Biology

institute: Roswell Park Comprehensive Cancer Center

data_processing:
nf-core/rnaseq  version 3.3.
Assembly: GRCh38
Supplementary files format and content: Tab delimited text files, contain raw read counts at isoform level.

extract_protocol:
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads
After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: ovarian cancer


title: sorbs2 mutant_e18.5_biol rep 1

description: Library name: sorbs2 mutant_e18.5_biol rep 1


title: PBMCs, Japanese cohort, B006_L001, H090

description: Library name: JP_RIK_B006_L001_5GEX_H090


title: OVCAR-8, BLU 250 nM, rep1


title: OVCAR-8, BLU 250 nM, rep2


title: ctrl_e18.5_biol rep 3

description: Library name: ctrl_e18.5_biol rep 3


title: PBMCs, Japanese cohort, B006_L001, H089

description: Library name: JP_RIK_B006_L001_5GEX_H089


title: OVCAR-8, DMSO, rep 3

value: DMSO


title: ctrl_e18.5_biol rep 2

description: Library name: ctrl_e18.5_biol rep 2

value: heart


title: PBMCs, Japanese cohort, B006_L001, H088

description: Library name: JP_RIK_B006_L001_5GEX_H088


title: OVCAR-8, DMSO, rep 1


title: ctrl_e18.5_biol rep 1

description: Library name: ctrl_e18.5_biol rep 1


title: PBMCs, Japanese cohort, B006_L001, H087

description: Library name: JP_RIK_B006_L001_5GEX_H087


title: MDA-MB-157, BLU 100 nM, rep 2

value: triple negative breast cancer


title: PBMCs, Japanese cohort, B006_L002, H077

description: Library name: JP_RIK_B006_L002_5GEX_H077


title: MDA-MB-157, BLU 100 nM, rep 1


title: MDA-MB-157, DMSO, rep 3


title: PBMCs, Japanese cohort, B006_L001, H085

description: Library name: JP_RIK_B006_L001_5GEX_H085


title: sorbs2 mutant_e15.5_biol rep 3

description: Library name: sorbs2 mutant_e15.5_biol rep 3


title: MDA-MB-157, DMSO, rep 1


title: MDA-MB-157, DMSO, rep 2


title: sorbs2 mutant_e15.5_biol rep 2

description: Library name: sorbs2 mutant_e15.5_biol rep 2


title: Kuramochi, BLU 125 nM, rep3

source_name: Kuramochi

value: Kuramochi


title: PBMCs, Japanese cohort, B006_L001, H084

description: Library name: JP_RIK_B006_L001_5GEX_H084

value: blood


title: OVCAR-8, DMSO, rep 2


title: PBMCs, Japanese cohort, B006_L001, H086

description: Library name: JP_RIK_B006_L001_5GEX_H086


title: PBMCs, Japanese cohort, B006_L001, H083

description: Library name: JP_RIK_B006_L001_5GEX_H083


title: Kuramochi, DMSO,  rep 2


title: Kuramochi, BLU 125 nM, rep1


title: ctrl_e15.5_biol rep 3

description: Library name: ctrl_e15.5_biol rep 3


title: Kuramochi, DMSO,  rep 1


title: sorbs2 mutant_e15.5_biol rep 1

description: Library name: sorbs2 mutant_e15.5_biol rep 1


title: Kuramochi, DMSO,  rep 3


title: PRDM16 KO day 32 organoids repeat 3 [95_D32_3]

city: Rehovot

first: Tsviya

last: Olender

address: 234 Herzl St.

department: Molecular Genetics

institute: The Weizmann Institute

data_processing:
Data were trimed from their adapter using cutadapt and aligned to the human genome (hg38)
using STAR. Normalization, and test for differential expression was done with DESeq2.
All the analyses were performed using the UTAP pipeline (Kohen R. et. al., BMC Bioinformatics. 2019 Mar 25;20(1):154).
Assembly: hg38
Supplementary files format and content: crude read count, normalized read count, statistical tests

source_name: NIHhESC-10-0079 WIBR3

growth_protocol: About 9000 ES cells per well were dispensed into low adhesive v-shaped 96-well plates and aggregates were formed. Forebrain differentiation media, containing wnt inhibitor and TGFb inhibitor, was exchanged every other day. At day 18, organoids were transferred to a 10-cm non-cell adhesive plate and cultured in suspension, in a second forebrain media. Organoids were collected after two weeks, at day 32.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen) under the manufacturer’s protocols. RNA was extracted from forebrain organoids on day 32. Three repeats were taken. Total of 5-8 organoids for each repeat.

value: NIHhESC-10-0079 WIBR3

value: Forebrain organoids

value: PRDM16 KO


title: PBMCs, Japanese cohort, B006_L001, H082

description: Library name: JP_RIK_B006_L001_5GEX_H082

value: human


title: PBMCs, Japanese cohort, B006_L001, H081

description: Library name: JP_RIK_B006_L001_5GEX_H081

value: PBMCs


title: PRDM16 KO day 32 organoids repeat 2 [95_D32_2]


title: Kuramochi, BLU 125 nM, rep2


title: control day 32 organoids repeat 3 [W3_D32_3]

value: control


title: PBMCs, Japanese cohort, B006_L001, H080

description: Library name: JP_RIK_B006_L001_5GEX_H080


title: ctrl_e15.5_biol rep 2

description: Library name: ctrl_e15.5_biol rep 2


title: sorbs2 mutant_e15.5_biol rep 4

description: Library name: sorbs2 mutant_e15.5_biol rep 4


title: MDA-MB-157, BLU 100 nM, rep 3


title: control day 32 organoids repeat 2 [W3_D32_2]


title: ctrl_e15.5_biol rep 1

description: Library name: ctrl_e15.5_biol rep 1


title: sorbs2 mutant_e12.5_biol rep 3

description: Library name: sorbs2 mutant_e12.5_biol rep 3


title: control day 32 organoids repeat 1 [W3_D32_1]


title: sorbs2 mutant_e12.5_biol rep 4

description: Library name: sorbs2 mutant_e12.5_biol rep 4


title: PBMCs, Japanese cohort, B006_L001, H079

description: Library name: JP_RIK_B006_L001_5GEX_H079


title: PBMCs, Japanese cohort, B006_L001, H078

description: Library name: JP_RIK_B006_L001_5GEX_H078


title: PBMCs, Japanese cohort, B006_L001, H077

description: Library name: JP_RIK_B006_L001_5GEX_H077


title: ctrl_e12.5_biol rep 4

description: Library name: ctrl_e12.5_biol rep 4


title: PBMCs, Japanese cohort, B006_L001, H076

description: Library name: JP_RIK_B006_L001_5GEX_H076


title: 12w_tumor_Rep5_AB657

city: Tel Aviv

first: Merav

last: Cohen

address: Chaim Levanon St 55

department: Clinical microbiology and immunology

institute: Tel Aviv University

data_processing:
We generated FASTQ files from the raw BCL files using the bcl2fastq software provided by Illumina (v.2.20.0.422) with default parameters.
Sequences were mapped to the mouse genome (GRCm39) using STAR (v.2.7.1a). Reads with multiple mapping positions were excluded. We then assigned gene names for exonic, genomic and mitochondrial regions using featureCounts (v.2.0.0), processed the resulting BAM file using samtools (v.1.10) and finally created gene-cell UMI matrices using the UMI-tools software package (v.1.1.2). Using the Scanpy package (v.1.9.1), we loaded these files to a unified data object.
Assembly: GRCm39
Supplementary files format and content: FASTQ, R1 contains genomic data and R2 contains 8BP of cell barcode and 7BP of UMI barcode.

source_name: Mammary gland

growth_protocol: All mice were maintained under specific pathogen-free conditions

extract_protocol:
Mammary gland: The fourth pair of mammary glands was collected from MMTV-PyMT oncogene carrier and non-carrier females along 6 developmental and cancerous time points: postnatal day 10, and weeks 3, 6, 8, 10 and 12. The lymph nodes were removed from the dissected mammary glands. Both healthy and cancerous mammary tissues were suspended in Dulbecco’s modified Eagle medium/F12 medium (01-170-1A, Biological Industries) supplemented with collagenase IV (1 mg/ml, Worthington LS004188), collagenase II (1 mg/ml, Worthington LS004176), hyaluronidase I-S (800 U/ml, Sigma H3506) and DNase I (1.2 U/ml, Sigma D5021-15KU), cut into small pieces, mechanically dissociated by pipetting using different sizes of needles and incubated at 37ºC with agitation of 100 rpm for 30 minutes. Then, cells were washed with ice-cold sorting buffer (PBS supplemented with 0.2mM ethylene diamine tetra-acetic acid (EDTA), pH 8, and 0.5% BSA), filtered through a 100 µm cell strainer and centrifuged at 1500 rpm for 5 minutes at 4ºC. Flow cytometry was performed on the BD FACSAria III Cell sorter or BD FACSymphony S6, using a 100 µm nozzle, analyzed with BD FACSDIVA software (BD Biosciences) and FlowJo software. Cells suspended in ice-cold sorting buffer were incubated with anti-mouse CD16/32 (BD Bioscience) to block Fc receptors before labeling with fluorescent antibodies against cell-surface epitopes. Cells were stained with DAPI (Biolegend) and then with the following antibodies: eFLuor450-conjugated TER-119 (eBioscience), FITC-conjugated CD45 (Biolegend), APC-conjugated CD45 (Biolegend), PE-conjugated CD45 (Biolegend), APC/Cy7-conjugated EpCAM (, Biolegend), APC-conjugated EpCAM (Biolegend), FITC-conjugated F4/80 (Biolegend), FITC-conjugated Ly6G (Biolegend), PE-conjugated Ly6G (Biolegend), FITC-conjugated CD31 (Biolegend), PE-conjugated Pdgfr-a (Bioloegend), FITC-conjugated I-A/I-E (MHC II, Biolegend). For sorting, dead cells (DAPI+) and erythrocytes (TER119+) were excluded. First, total immune cells (CD45+) and non-immune cells (CD45-) were sorted from DAPI-/TER119- gate (Live cells). For enrichment of immune-epithelial/cancer cell PICs, we sorted the double positive population from live cells by using immune and epithelial markers (CD45+EpCAM+) and their respective singlet background, singlet immune (CD45+EpCAM-) and epithelial cells (CD45-EpCAM+). For enrichment of neutrophils-epithelial PICs, we gated the Ly6G+EpCAM+ population from general immune-tumor cell PICs (CD45+EpCAM+). For enrichment of singlet neutrophils, we sorted Ly6G+ cells from CD45+ gate. Singlet EpCAM+ cells used for analysis as tumor cell background were isolated from tumor carrier mice as described above. Singlets and PICs were sorted into 384-well cell capture plates. These plates contain 2μl of lysis solution along with barcoded poly (T) reverse-transcription primers for single-cell RNA-seq. As no-cell control for the data analysis, four wells were left empty. Immediately after sorting, each plate was spun down and stored at -80°C until further processing. Peripheral blood: Peripheral blood was collected by cardiac puncture from MMTV-PyMT+ female mouse. Peripheral blood was diluted in PBS and layered on top of Histopaque-1077, centrifuge at 400g, 30min, no break and acceleration. Buffy coat was diluted 10 times with PBS, centrifuged at 400 g, 7min at 4°C and resuspended in FACS buffer. Peripheral blood neutrophils were stained and sorted (CD45+ or CD45+Ly6G+).
The library preparation was conducted following the previously reported protocol {Jaitin, 2014}. In brief, mRNA from cells sorted into capture plates was barcoded and converted into cDNA. The resulting cDNA was pooled and amplified by T7 in vitro transcription. Then, the RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during the ligation, reverse transcription and PCR steps. The library's quality was evaluated and concentration was assessed as described in the MARS-seq2.0 protocol {Jaitin, 2014}. Primer barcodes and genes were used according to MARS-seq2.0 protocol for both library preparations and qPCR validations.

treatment_protocol: Mice were sacrified by CO2. For depletion/isotype samples, MMTV-PyMT+ female mice at the age of 10.5 weeks old were treated daily for 9 days via intraperitoneal injection with 12.5 μg per mouse of rat anti-Ly6G antibody (BioXcell, clone 1A8, BE0075-1-5AC) in PBS or rat IgG2a isotype control (BioXcell, BE0089-25AC).

value: Mammary gland

value: EPCAM

value: FVB/n MMTV-PyMT+

tag: age


title: 12w_tumor_Rep5_AB656


title: Peripheral_blood_11w_tumor_Rep1_AB302

source_name: Peripheral blood

value: Peripheral blood


title: 12w_tumor_Rep5_AB652


title: 12w_tumor_Rep5_AB653


title: Peripheral_blood_11w_tumor_Rep2_AB390


title: 12w_tumor_Rep5_AB654


title: sorbs2 mutant_e12.5_biol rep 2

description: Library name: sorbs2 mutant_e12.5_biol rep 2


title: PRDM16 KO day 32 organoids repeat 1 [95_D32_1]


title: PBMCs, Caucasian, B005_L002, LONZA3038016

description: Library name: JP_RIK_B005_L002_5GEX_LONZA3038016


title: Peripheral_blood_11w_tumor_Rep1_AB299


title: ctrl_e12.5_biol rep 3

description: Library name: ctrl_e12.5_biol rep 3


title: 12w_tumor_CD45+_Rep4_AB543


title: PBMCs, Japanese cohort, B005_L002, H075

description: Library name: JP_RIK_B005_L002_5GEX_H075


title: ctrl_e12.5_biol rep 2

description: Library name: ctrl_e12.5_biol rep 2


title: 12w_tumor_EPCAM_Rep4_AB541


title: 12w_tumor_EPCAM-CD45_Rep4_AB542


title: PBMCs, Japanese cohort, B005_L002, H074

description: Library name: JP_RIK_B005_L002_5GEX_H074


title: 12w_tumor_LY6G_Rep4_AB540


title: ctrl_e12.5_biol rep 1

description: Library name: ctrl_e12.5_biol rep 1


title: 12w_tumor_EPCAM-LY6G_Rep4_AB538


title: PBMCs, Japanese cohort, B005_L002, H073

description: Library name: JP_RIK_B005_L002_5GEX_H073


title: 12w_tumor_EPCAM-LY6G_Rep4_AB539


title: 12w_tumor_CD45+_Rep3_AB529


title: sorbs2 mutant_e12.5_biol rep 1

description: Library name: sorbs2 mutant_e12.5_biol rep 1


title: PBMCs, Japanese cohort, B005_L002, H072

description: Library name: JP_RIK_B005_L002_5GEX_H072


title: 12w_tumor_EPCAM-CD45_Rep3_AB528


title: 12w_tumor_EPCAM_Rep3_AB527


title: liver immune cells, LPS treated, PND4 mice 1, VDJ

city: Aachen

first: Hieu

middle: Trong

last: Nguyen

address: Pauwelstrasse 30

country: Germany

institute: RWTH Aachen University Hospital

description:
Library name: d4_LPS_VDJ
Cells were pooled from 3 individual feature barcoded animals

data_processing:
Firstly, filter for %mitochondrial mapped reads less than 10% were applied. Doublets were removed using feature barcoding hashtag antibodies. After quality control, a myeloid immune cell subset was developed by removing T and B cell lymphocytes.
Assembly: mm10
Supplementary files format and content: csv
Supplementary files format and content: h5

source_name: liver

extract_protocol:
Single hepatic immune cells were isolated and sorted (n=3) of 4 days old untreated SPF mice . Cell sorting was performed on a FACS ARIA II (BD) equipped with a 100 mm nozzle for live CD45+ cells and using the BD FACS DIVA 8.0.1 software. Liver immune cells were further processed using the Chromium Next GEM Single Cell 5’ Reagent Kits v3.1 according to manufacturer’s instruction (10x Genomics, Inc., United States). 15000 single immune cells were aimed for sequencing. Single-cell sequencing on High-Output flow cells using 100 cycles was performed on an Illumina NovaSeq6000 platform.
Live liver immune cells cells were further processed using the Chromium Next GEM Single Cell 5’ Reagent Kits with Feature Barcoding v2 according to manufacturer’s instruction. Single-cell sequencing on High-Output flow cells using 100 cycles was performed on an Illumina NovaSeq platform with a NovaSeq S2 cartridge. The fragment size of the final libraries was determined using the Bioanalyzer High-Sensitivity DNA Kit (Agilent). Library concentration was determined using the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific).

value: liver

value: liver immune cells

value: WT

value: P1 to P4 daily oral LPS (2.5µg/g BW)


title: 12w_tumor_LY6G_Rep3_AB526


title: PBMCs, Japanese cohort, B005_L002, H070

description: Library name: JP_RIK_B005_L002_5GEX_H070


title: 12w_tumor_EPCAM-LY6G_Rep3_AB522


title: 12w_tumor_LY6G_Rep3_AB525


title: 12w_tumor_EPCAM-LY6G_Rep3_AB523


title: PBMCs, Japanese cohort, B005_L002, H071

description: Library name: JP_RIK_B005_L002_5GEX_H071


title: 12w_tumor_EPCAM-LY6G_Rep3_AB524


title: liver immune cells, WT, PND4 mice 1, GEX

description:
Library name: d4_SPF_GEX
Cells were pooled from 3 individual feature barcoded animals


title: 10d_normal_EPCAM-CD45_Rep3_AB434

value: FVB/n MMTV-PyMT-


title: 10w_tumor_Rep6_AB1302


title: PBMCs, Japanese cohort, B005_L002, H068

description: Library name: JP_RIK_B005_L002_5GEX_H068


title: PBMCs, Japanese cohort, B005_L002, H067

description: Library name: JP_RIK_B005_L002_5GEX_H067


title: 10d_normal_LY6G_Rep3_AB435


title: 10w_normal_Rep7_AB1300


title: 10w_tumor_Rep6_AB1301


title: 10d_normal_EPCAM_Rep3_AB432


title: 10d_tumor_EPCAM_Rep3_AB430


title: 10d_tumor_EPCAM-CD45_Rep3_AB429


title: 10w_normal_Rep7_AB1299


title: liver immune cells, LPS treated, PND4 mice 1, GEX

description:
Library name: d4_LPS_GEX
Cells were pooled from 3 individual feature barcoded animals


title: 10d_normal_CD45+_Rep3_AB420


title: liver immune cells, WT, PND4 mice 1, VDJ

description:
Library name: d4_SPF_VDJ
Cells were pooled from 3 individual feature barcoded animals


title: PBMCs, Japanese cohort, B005_L002, H069

description: Library name: JP_RIK_B005_L002_5GEX_H069


title: PBMCs, Japanese cohort, B005_L002, H064

description: Library name: JP_RIK_B005_L002_5GEX_H064


title: 10w_normal_Rep7_AB1298


title: 10d_normal_EPCAM-CD45_Rep3_AB418


title: 10w_normal_Rep6_AB1297


title: 10d_tumor_CD45+_Rep3_AB417


title: PBMCs, Japanese cohort, B005_L002, H063

description: Library name: JP_RIK_B005_L002_5GEX_H063


title: 10d_normal_EPCAM_Rep3_AB419


title: 10w_normal_Rep6_AB1296


title: 10d_tumor_CD45+_Rep3_AB414


title: PBMCs, Japanese cohort, B005_L002, H062

description: Library name: JP_RIK_B005_L002_5GEX_H062


title: 10d_tumor_LY6G_Rep3_AB431


title: 3w_normal_CD45+_Rep5_AB413


title: 3w_normal_EPCAM-CD45_Rep5_AB412


title: PBMCs, Japanese cohort, B005_L002, H066

description: Library name: JP_RIK_B005_L002_5GEX_H066


title: 10w_normal_Rep6_AB1294


title: 3w_normal_EPCAM_Rep5_AB411


title: PBMCs, Japanese cohort, B005_L002, H061

description: Library name: JP_RIK_B005_L002_5GEX_H061


title: 3w_tumor_EPCAM-CD45_Rep5_AB410


title: 10w_normal_Rep6_AB1293


title: 10w_tumor_EPCAM_Rep4_AB409


title: 6w_normal_EPCAM_Rep3_AB408


title: PBMCs, Japanese cohort, B005_L001, H075

description: Library name: JP_RIK_B005_L001_5GEX_H075


title: 10d_tumor_EPCAM-CD45_Rep3_AB416


title: 10d_tumor_EPCAM_Rep3_AB415


title: 8w_tumor_Rep4_AB1210


title: 6w_tumor_EPCAM_Rep3_AB407


title: 3w_normal_CD45+_Rep5_AB406


title: 3w_normal_EPCAM_Rep5_AB405


title: 8w_tumor_Rep4_AB1209


title: 8w_tumor_Rep4_AB1208


title: 3w_tumor_CD45+_Rep5_AB403


title: 3w_normal_EPCAM-CD45_Rep5_AB404


title: 8w_tumor_Rep4_AB1207


title: PBMCs, Japanese cohort, B005_L001, H074

description: Library name: JP_RIK_B005_L001_5GEX_H074


title: PBMCs, Japanese cohort, B005_L001, H073

description: Library name: JP_RIK_B005_L001_5GEX_H073


title: 3w_tumor_CD45+_Rep5_AB402


title: 10w_normal_Rep6_AB1295


title: 3w_tumor_EPCAM_Rep5_AB401


title: 3w_tumor_EPCAM_Rep5_AB400


title: PBMCs, Caucasian, B005_L001, LONZA3038016

description: Library name: JP_RIK_B005_L001_5GEX_LONZA3038016


title: PBMCs, Japanese cohort, B005_L001, H071

description: Library name: JP_RIK_B005_L001_5GEX_H071


title: 3w_tumor_EPCAM-CD45_Rep5_AB399


title: Peripheral_blood_12w_tumor_Rep2_AB1206


title: 10w_normal_CD45-_Rep5_AB398


title: PBMCs, Japanese cohort, B005_L001, H070

description: Library name: JP_RIK_B005_L001_5GEX_H070


title: 10w_tumor_LY6G_Rep5_AB396


title: 10w_tumor_CD45-_Rep5_AB397


title: PBMCs, Japanese cohort, B005_L001, H069

description: Library name: JP_RIK_B005_L001_5GEX_H069


title: 10w_tumor_EPCAM-LY6G_Rep5_AB395


title: Isotype daily-12w_tumor_Rep3_AB1204

description: Isotype daily-12w_tumor_Rep3


title: 10w_tumor_EPCAM_Rep5_AB394


title: 10w_tumor_EPCAM-CD45_Rep5_AB393


title: PBMCs, Japanese cohort, B005_L001, H072

description: Library name: JP_RIK_B005_L001_5GEX_H072


title: PBMCs, Japanese cohort, B005_L001, H067

description: Library name: JP_RIK_B005_L001_5GEX_H067


title: PBMCs, Japanese cohort, B005_L001, H068

description: Library name: JP_RIK_B005_L001_5GEX_H068


title: 10w_tumor_EPCAM-CD45_Rep5_AB392


title: Isotype daily-12w_tumor_Rep3_AB1203

description: Isotype daily-12w_tumor_Rep3


title: 10w_tumor_CD45+_Rep5_AB391


title: 12w_tumor_Rep5_AB655


title: 8w_normal_EPCAM-CD45_Rep3_AB377


title: PBMCs, Japanese cohort, B005_L001, H066

description: Library name: JP_RIK_B005_L001_5GEX_H066


title: 12w_tumor_Rep6_AB1201


title: 12w_tumor_Rep6_AB1202


title: 8w_normal_CD45+_Rep3_AB376


title: 8w_normal_CD45+_Rep3_AB375


title: PBMCs, Japanese cohort, B005_L001, H064

description: Library name: JP_RIK_B005_L001_5GEX_H064


title: 8w_normal_EPCAM-CD45_Rep3_AB373


title: PBMCs, Japanese cohort, B005_L001, H065

description: Library name: JP_RIK_B005_L001_5GEX_H065


title: Isotype daily-12w_tumor_Rep3_AB1205

description: Isotype daily-12w_tumor_Rep3


title: 8w_normal_EPCAM_Rep3_AB374


title: Isotype daily-12w_tumor_Rep3_AB1199

description: Isotype daily-12w_tumor_Rep3


title: Isotype daily-12w_tumor_Rep3_AB1200

description: Isotype daily-12w_tumor_Rep3


title: PBMCs, Japanese cohort, B005_L001, H063

description: Library name: JP_RIK_B005_L001_5GEX_H063


title: 8w_tumor_CD45+_Rep3_AB372


title: Depletion daily-12w_tumor_Rep4_AB1198

description: Depletion daily-12w_tumor_Rep4


title: 8w_tumor_EPCAM_Rep3_AB370


title: 8w_tumor_EPCAM_Rep3_AB371


title: 8w_tumor_CD45+_Rep3_AB369


title: Depletion daily-12w_tumor_Rep4_AB1197

description: Depletion daily-12w_tumor_Rep4


title: 8w_tumor_EPCAM-CD45_Rep3_AB368


title: 10w_tumor_EPCAM-LY6G_Rep4_AB378


title: PBMCs, Japanese cohort, B005_L001, H062

description: Library name: JP_RIK_B005_L001_5GEX_H062


title: 8w_tumor_LY6G_Rep3_AB366


title: PBMCs, Japanese cohort, B005_L001, H061

description: Library name: JP_RIK_B005_L001_5GEX_H061


title: 8w_tumor_EPCAM-CD45_Rep3_AB367


title: Depletion daily-12w_tumor_Rep4_AB1195

description: Depletion daily-12w_tumor_Rep4


title: PBMCs, Japanese cohort, B004_L002, H060

description: Library name: JP_RIK_B004_L002_5GEX_H060


title: 8w_tumor_EPCAM-LY6G_Rep3_AB365


title: Depletion daily-12w_tumor_Rep4_AB1196

description: Depletion daily-12w_tumor_Rep4


title: PBMCs, Japanese cohort, B004_L002, H059

description: Library name: JP_RIK_B004_L002_5GEX_H059


title: 10w_tumor_CD45+_Rep4_AB341


title: Depletion daily-12w_tumor_Rep4_AB1194

description: Depletion daily-12w_tumor_Rep4


title: 10w_tumor_EPCAM-LY6G_Rep4_AB340


title: 10w_tumor_EPCAM-CD45_Rep4_AB339


title: PBMCs, Japanese cohort, B004_L002, H058

description: Library name: JP_RIK_B004_L002_5GEX_H058


title: Peripheral_blood_12w_tumor_Rep1_AB1193


title: Isotype daily-12w_tumor_Rep2_AB1192

description: Isotype daily-12w_tumor_Rep2


title: 10w_tumor_EPCAM-CD45_Rep4_AB337


title: PBMCs, Japanese cohort, B004_L002, H057

description: Library name: JP_RIK_B004_L002_5GEX_H057


title: PD1_687_Tumor_d13

city: Philadelphia

first: Michael

last: Klichinsky

state: Pennsylvania

address: 3675 Market Street Ste. 401

institute: Carisma Therapeutics

description: Library name: PD1_687_Tumor_d13

data_processing:
Data processing was performed by Adaptive Biotechnologies according to their pipeline
Assembly: MM10
Supplementary files format and content: tab-delimited text file with TCR sequences, counts, frequencies, and VDJ gene predictions
Library strategy: TCR-Seq

source_name: Tumor

extract_protocol:
Extraction performed by Adaptive Biotechnologies
Library construction performed by Adaptive Biotechnologies

value: Tumor


title: 10w_tumor_EPCAM-LY6G_Rep4_AB338


title: 3w_normal_CD45+_Rep4_AB336


title: PBMCs, Japanese cohort, B004_L002, H056

description: Library name: JP_RIK_B004_L002_5GEX_H056

data_processing:
The DRAGEN Single-Cell RNA pipeline in the Illumina DRAGEN v3.8.4 software (version 07.021.602.3.8.4-20-g74395e76) was used for pre-processing of paired-end FASTQ files from each individual scRNA-seq gene expression library. Reads from each pool were mapped to GENCODE Release 32 (GRCh38, Ensembl 98, date 2019-09-05).  The count data was processed and analyzed in R. Within each pool, every cell (barcode) and read was assigned to an individual within that pool using Genotype Data (provided) in DRAGEN v3.8.4.
Assembly: GRCh38/hg38
Supplementary files format and content: Raw data were processed from fatsq files, which contain cDNA sequences. Single-cell expression data were processed using *rds file containing single cell expression and metadata matrix.

source_name: blood

value: blood


title: Peripheral_blood_12w_tumor_Rep2_AB1191


title: Peripheral_blood_12w_tumor_Rep2_AB1190


title: PBMCs, Caucasian, B004_L002, LONZA3038099

description: Library name: JP_RIK_B004_L002_5GEX_LONZA3038099


title: 10w_tumor_EPCAM_Rep4_AB343


title: PBMCs, Japanese cohort, B004_L002, H055

description: Library name: JP_RIK_B004_L002_5GEX_H055


title: PD1_677_Tumor_d13

description: Library name: PD1_677_Tumor_d13


title: 3w_normal_EPCAM_Rep4_AB335


title: 3w_normal_EPCAM-CD45_Rep4_AB334


title: 10w_tumor_CD45+_Rep4_AB342


title: PBMCs, Japanese cohort, B004_L002, H054

description: Library name: JP_RIK_B004_L002_5GEX_H054


title: PD1_677_Blood_d13

description: Library name: PD1_677_Blood_d13

source_name: Blood

value: Blood


title: PD1_593_Tumor_d13

description: Library name: PD1_593_Tumor_d13


title: PBMCs, Japanese cohort, B004_L002, H053

description: Library name: JP_RIK_B004_L002_5GEX_H053


title: Isotype daily-12w_tumor_Rep3_AB1186

description: Isotype daily-12w_tumor_Rep3


title: PD1_593_Blood_d13

description: Library name: PD1_593_Blood_d13


title: Depletion daily-12w_tumor_Rep4_AB1185

description: Depletion daily-12w_tumor_Rep4


title: 3w_tumor_EPCAM-CD45_Rep4_AB331


title: PBMCs, Japanese cohort, B004_L002, H052

description: Library name: JP_RIK_B004_L002_5GEX_H052


title: Isotype daily-12w_tumor_Rep3_AB1184

description: Isotype daily-12w_tumor_Rep3


title: PD1_687_Blood_d13

description: Library name: PD1_687_Blood_d13


title: PBMCs, Japanese cohort, B004_L002, H050

description: Library name: JP_RIK_B004_L002_5GEX_H050


title: PBMCs, Japanese cohort, B004_L002, H051

description: Library name: JP_RIK_B004_L002_5GEX_H051


title: PD1_559_Tumor_d13

description: Library name: PD1_559_Tumor_d13


title: PD1_559_Blood_d13

description: Library name: PD1_559_Blood_d13


title: Isotype daily-12w_tumor_Rep3_AB1188

description: Isotype daily-12w_tumor_Rep3


title: 12w_tumor_Rep1_AB1183


title: 12w_normal_CD45+_Rep2_AB329


title: PD1_546_Tumor_d13

description: Library name: PD1_546_Tumor_d13


title: PBMCs, Japanese cohort, B004_L002, H049

description: Library name: JP_RIK_B004_L002_5GEX_H049


title: Isotype daily-12w_tumor_Rep3_AB1187

description: Isotype daily-12w_tumor_Rep3


title: Depletion daily-12w_tumor_Rep4_AB1182

description: Depletion daily-12w_tumor_Rep4


title: 3w_tumor_CD45+_Rep4_AB333


title: PD1_546_Blood_d13

description: Library name: PD1_546_Blood_d13


title: PBMCs, Japanese cohort, B004_L002, H048

description: Library name: JP_RIK_B004_L002_5GEX_H048


title: 3w_tumor_EPCAM_Rep4_AB332


title: Depletion daily-12w_tumor_Rep4_AB1181

description: Depletion daily-12w_tumor_Rep4


title: CTRL_689_Tumor_d13

description: Library name: CTRL_689_Tumor_d13

value: CTRL


title: 12w_normal_EPCAM_Rep2_AB327


title: PBMCs, Japanese cohort, B004_L002, H047

description: Library name: JP_RIK_B004_L002_5GEX_H047


title: 12w_tumor_Rep1_AB1180


title: PBMCs, Japanese cohort, B004_L002, H046

description: Library name: JP_RIK_B004_L002_5GEX_H046


title: CTRL_689_Blood_d13

description: Library name: CTRL_689_Blood_d13


title: 3w_tumor_EPCAM-CD45_Rep4_AB330


title: 12w_normal_EPCAM_Rep2_AB326


title: 12w_normal_EPCAM-CD45_Rep2_AB325


title: Isotype daily-12w_tumor_Rep2_AB1179

description: Isotype daily-12w_tumor_Rep2


title: PBMCs, Caucasian, B004_L001, LONZA3038099

description: Library name: JP_RIK_B004_L001_5GEX_LONZA3038099


title: CTRL_556_Tumor_d13

description: Library name: CTRL_556_Tumor_d13


title: PBMCs, Japanese cohort, B004_L001, H060

description: Library name: JP_RIK_B004_L001_5GEX_H060


title: CTRL_556_Blood_d13

description: Library name: CTRL_556_Blood_d13


title: 12w_normal_EPCAM-CD45_Rep2_AB324


title: Depletion daily-12w_tumor_Rep4_AB1177

description: Depletion daily-12w_tumor_Rep4


title: 12w_tumor_EPCAM_Rep2_AB323


title: Isotype daily-12w_tumor_Rep2_AB1176

description: Isotype daily-12w_tumor_Rep2


title: PBMCs, Japanese cohort, B004_L001, H059

description: Library name: JP_RIK_B004_L001_5GEX_H059


title: CTRL_488_Blood_d13

description: Library name: CTRL_488_Blood_d13


title: 12w_tumor_EPCAM_Rep2_AB322


title: CTRL_488_Tumor_d13

description: Library name: CTRL_488_Tumor_d13


title: Isotype daily-12w_tumor_Rep2_AB1175

description: Isotype daily-12w_tumor_Rep2


title: PBMCs, Japanese cohort, B004_L001, H058

description: Library name: JP_RIK_B004_L001_5GEX_H058


title: 12w_tumor_CD45+_Rep2_AB321


title: 12w_normal_CD45+_Rep2_AB328


title: CTRL_484_Tumor_d13

description: Library name: CTRL_484_Tumor_d13


title: Isotype daily-12w_tumor_Rep2_AB1174

description: Isotype daily-12w_tumor_Rep2


title: PBMCs, Japanese cohort, B004_L001, H056

description: Library name: JP_RIK_B004_L001_5GEX_H056


title: PBMCs, Japanese cohort, B004_L001, H057

description: Library name: JP_RIK_B004_L001_5GEX_H057


title: CTRL_484_Blood_d13

description: Library name: CTRL_484_Blood_d13


title: Depletion daily-12w_tumor_Rep4_AB1178

description: Depletion daily-12w_tumor_Rep4


title: Isotype daily-12w_tumor_Rep2_AB1173

description: Isotype daily-12w_tumor_Rep2


title: 12w_tumor _CD45+_Rep2_AB320


title: 12w_tumor_EPCAM-CD45_Rep2_AB319


title: Depletion daily-12w_tumor_Rep3_AB1172

description: Depletion daily-12w_tumor_Rep3


title: 12w_tumor_EPCAM-CD45_Rep2_AB318


title: CTRL_482_Blood_d13

description: Library name: CTRL_482_Blood_d13


title: CTRL_482_Tumor_d13

description: Library name: CTRL_482_Tumor_d13


title: PBMCs, Japanese cohort, B004_L001, H055

description: Library name: JP_RIK_B004_L001_5GEX_H055


title: 6w_normal_EPCAM-CD45_Rep3_AB177


title: PBMCs, Japanese cohort, B004_L001, H054

description: Library name: JP_RIK_B004_L001_5GEX_H054


title: PBMCs, Japanese cohort, B004_L001, H053

description: Library name: JP_RIK_B004_L001_5GEX_H053


title: Depletion daily-12w_tumor_Rep3_AB1171

description: Depletion daily-12w_tumor_Rep3


title: CAR+PD1_699_Tumor_d13

description: Library name: CAR+PD1_699_Tumor_d13


title: CAR+PD1_699_Blood_d13

description: Library name: CAR+PD1_699_Blood_d13


title: PBMCs, Japanese cohort, B004_L001, H052

description: Library name: JP_RIK_B004_L001_5GEX_H052


title: Depletion daily-12w_tumor_Rep3_AB1169

description: Depletion daily-12w_tumor_Rep3


title: 12w_normal_EPCAM-CD45_Rep1_AB173


title: CAR+PD1_545_Tumor_d13

description: Library name: CAR+PD1_545_Tumor_d13


title: Depletion daily-12w_tumor_Rep3_AB1170

description: Depletion daily-12w_tumor_Rep3


title: 6w_tumor_EPCAM-CD45_Rep3_AB174


title: Depletion daily-12w_tumor_Rep3_AB1168

description: Depletion daily-12w_tumor_Rep3


title: PBMCs, Japanese cohort, B004_L001, H051

description: Library name: JP_RIK_B004_L001_5GEX_H051


title: 12w_tumor_EPCAM-CD45_Rep1_AB172


title: PBMCs, Japanese cohort, B005_L002, H065

description: Library name: JP_RIK_B005_L002_5GEX_H065


title: PBMCs, Japanese cohort, B004_L001, H050

description: Library name: JP_RIK_B004_L001_5GEX_H050


title: Depletion daily-12w_tumor_Rep3_AB1167

description: Depletion daily-12w_tumor_Rep3


title: 6w_normal_CD45-_Rep3_AB171


title: CAR+PD1_545_Blood_d13

description: Library name: CAR+PD1_545_Blood_d13


title: Depletion daily-12w_tumor_Rep3_AB1166

description: Depletion daily-12w_tumor_Rep3


title: CAR+PD1_539_Tumor_d13

description: Library name: CAR+PD1_539_Tumor_d13


title: CAR+PD1_539_Blood_d13

description: Library name: CAR+PD1_539_Blood_d13


title: 6w_normal_CD45+_Rep3_AB169


title: CAR+PD1_527_Tumor_d13

description: Library name: CAR+PD1_527_Tumor_d13


title: PBMCs, Japanese cohort, B004_L001, H047

description: Library name: JP_RIK_B004_L001_5GEX_H047


title: PBMCs, Japanese cohort, B004_L001, H048

description: Library name: JP_RIK_B004_L001_5GEX_H048


title: Depletion daily-12w_tumor_Rep2_AB1164

description: Depletion daily-12w_tumor_Rep2


title: 6w_normal_CD45+_Rep3_AB168


title: PBMCs, Japanese cohort, B004_L001, H046

description: Library name: JP_RIK_B004_L001_5GEX_H046


title: PBMCs, Japanese cohort, B004_L001, H049

description: Library name: JP_RIK_B004_L001_5GEX_H049


title: Depletion daily-12w_tumor_Rep2_AB1163

description: Depletion daily-12w_tumor_Rep2


title: 6w_normal_EPCAM_Rep3_AB167


title: CAR+PD1_521_Tumor_d13

description: Library name: CAR+PD1_521_Tumor_d13


title: 6w_normal_CD45-_Rep3_AB170


title: PBMCs, Caucasian, B003_L002, LONZA3038099

description: Library name: JP_RIK_B003_L002_5GEX_LONZA3038099


title: Isotype-6w_tumor_Rep1_AB1161


title: CAR+PD1_521_Blood_d13

description: Library name: CAR+PD1_521_Blood_d13


title: Depletion daily-12w_tumor_Rep2_AB1162

description: Depletion daily-12w_tumor_Rep2


title: 6w_tumor_CD45-_Rep3_AB166


title: PBMCs, Japanese cohort, B003_L002, H045

description: Library name: JP_RIK_B003_L002_5GEX_H045


title: Depletion daily-12w_tumor_Rep2_AB1165

description: Depletion daily-12w_tumor_Rep2


title: 6w_tumor_CD45-_Rep3_AB165


title: CAR_599_Tumor_d13

description: Library name: CAR_599_Tumor_d13

value: CAR


title: PBMCs, Japanese cohort, B003_L002, H044

description: Library name: JP_RIK_B003_L002_5GEX_H044

value: human


title: Isotype-6w_tumor_Rep1_AB1160


title: PBMCs, Japanese cohort, B003_L002, H043

description: Library name: JP_RIK_B003_L002_5GEX_H043

value: PBMCs


title: PBMCs, Japanese cohort, B003_L002, H042

description: Library name: JP_RIK_B003_L002_5GEX_H042


title: Isotype-6w_tumor_Rep1_AB1159


title: Isotype-6w_tumor_Rep1_AB1158


title: 6w_tumor_CD45+_Rep3_AB163


title: CAR_588_Tumor_d13

description: Library name: CAR_588_Tumor_d13


title: 6w_tumor_EPCAM_Rep3_AB162


title: CAR_588_Blood_d13

description: Library name: CAR_588_Blood_d13


title: Depletion-6w_tumor_Rep1_AB1157


title: CAR+PD1_527_Blood_d13

description: Library name: CAR+PD1_527_Blood_d13


title: PBMCs, Japanese cohort, B003_L002, H041

description: Library name: JP_RIK_B003_L002_5GEX_H041


title: 12w_normal_EPCAM_Rep1_AB161


title: Depletion-6w_tumor_Rep1_AB1156


title: PBMCs, Japanese cohort, B003_L002, H039

description: Library name: JP_RIK_B003_L002_5GEX_H039


title: 12w_normal_CD45-_Rep1_AB160


title: CAR_572_Blood_d13

description: Library name: CAR_572_Blood_d13


title: PBMCs, Japanese cohort, B003_L002, H038

description: Library name: JP_RIK_B003_L002_5GEX_H038


title: Depletion-6w_tumor_Rep1_AB1155


title: CAR_572_Tumor_d13

description: Library name: CAR_572_Tumor_d13


title: CAR_569_Tumor_d13

description: Library name: CAR_569_Tumor_d13


title: 12w_normal_CD45-_Rep1_AB159


title: Depletion-6w_tumor_Rep1_AB1154


title: 6w_tumor_CD45+_Rep3_AB164


title: PBMCs, Japanese cohort, B003_L002, H037

description: Library name: JP_RIK_B003_L002_5GEX_H037


title: CAR_599_Blood_d13

description: Library name: CAR_599_Blood_d13


title: 12w_normal_CD45+_Rep1_AB158


title: Isotype-6w_tumor_Rep1_AB1153


title: 12w_normal_CD45+_Rep1_AB157


title: Isotype-6w_tumor_Rep1_AB1152


title: CAR_569_Blood_d13

description: Library name: CAR_569_Blood_d13


title: CAR_492_Blood_d13

description: Library name: CAR_492_Blood_d13


title: PBMCs, Japanese cohort, B003_L002, H035

description: Library name: JP_RIK_B003_L002_5GEX_H035


title: PBMCs, Japanese cohort, B003_L002, H036

description: Library name: JP_RIK_B003_L002_5GEX_H036


title: 12w_tumor_CD45-_Rep1_AB155


title: CAR_492_Tumor_d13

description: Library name: CAR_492_Tumor_d13


title: 12w_tumor_EPCAM_Rep1_AB156


title: Isotype-6w_tumor_Rep1_AB1151


title: PBMCs, Japanese cohort, B003_L002, H040

description: Library name: JP_RIK_B003_L002_5GEX_H040


title: S27_716 IR 10d

data_processing:
The processed reads were aligned to the mouse genome (mm10) using Rsubread v2.0.0 ‘align’ function (sortReadsByCoordinates=True, detectSV=False), with the mouse GENCODE mm10 vM10 GTF as an external annotation file.
Gene expression was calculated using Rsubread ‘featureCounts’ (countMultiMappingReads=False) to count the number of reads that map to each gene, with the GENCODE mm10 vM10 GTF as an external annotation file.
The reads were then normalized by TPM (Transcripts Per Kilobase Million) using the total exonic length acquired from the same GENCODE database.
In order to remain with only genes that have been robustly expressed in the samples, we continued only with genes that have a value of at least 1.0 TPM in all replicates of at least one biological condition in the dataset.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample (txt file).
Supplementary_files_format_and_content: Matrix table with TPM normalized gene counts for every gene and every sample (txt file).
Supplementary_files_format_and_content: Matrix table with TPM normalized gene counts only for genes that have a value of at least 1.0 TPM in all replicates of at least one biological condition in the dataset (txt file).

extract_protocol:
Total RNA was isolated using Qiazol Lysis Reagent (QIAGEN) and purified with the MiRNeasy Kit (QIAGEN), according to the manufacturer’s protocol. The RNA purity (260/230 and 280/260) was measured by nanodop.  RNA concentration was measured by Qbit and the integrity was measured using the Tapstation instrument. The purified RNA was used for subsequent library preparation and sequencing.
TruSeq RNA sample prep

treatment_protocol: Cells were treated with either KU60019 or DMSO at a final concentration of 3uM for 15 or 35 days.For IR-induced senescence, cells were exposed to 10Gy X-rays using the Faxitron (X-ray) cabinet providing 0.5 Gy/min, and harvested 10 days later .

value: Wild-type

value: 10Gy IR + incubation for 10 days

value: Primary lung fibroblasts


title: Isotype-6w_tumor_Rep1_AB1150

value: Mammary gland

value: FVB/n MMTV-PyMT+


title: 12w_tumor_CD45-_Rep1_AB154


title: 12w_tumor_CD45+_Rep1_AB153


title: Depletion-6w_tumor_Rep1_AB1149


title: PBMCs, Japanese cohort, B003_L002, H033

description: Library name: JP_RIK_B003_L002_5GEX_H033

extract_protocol:
Eight ml of blood was drawn from each donor using CPT tubes with sodium heparin (BD Vacutainer CPT, cat. no. 362753). PBMC isolation followed a standardized protocol across sites, using FBS (Sigma-Aldrich cat. no. F2442, lot 19G014 and 20A363) for cell isolation, pooling, and washing. Blood samples were processed within 2 hours at room temperature via density-gradient centrifugation (1,500 x g, 30 min, 20°C, with soft acceleration/deceleration). Plasma was aspirated, and PBMCs were pelleted at 300 x g for 15 min, then resuspended in ACK lysing buffer (Thermo Fisher, cat. no. A10492). Cells were washed twice (PBS pH 7.4, 1% FBS, 1 mM EDTA) and cryopreserved in CryoStor CS10 (STEMCELL Technologies, cat. no. 079555). Cryovials were stored at -80°C before transfer to liquid nitrogen. The full protocol is available on Protocols.io: https://www.protocols.io/view/pbmcs-isolation-from-cpt-tube-b8r9rv96.
Both AIDA and LONZA individuals were sequenced in pools of 16 individuals, including 15 AIDA samples and 1 LONZA control sample (chosen from 5 LONZA PBMC samples). Chromium Next GEM Single Cell 5’ Kit v2 was used for library construction


title: S25_705 IR 10d


title: PBMCs, Japanese cohort, B003_L002, H032

description: Library name: JP_RIK_B003_L002_5GEX_H032


title: 12w_tumor_CD45+_Rep1_AB152


title: PBMCs, Caucasian, B003_L001, LONZA3038099

description: Library name: JP_RIK_B003_L001_5GEX_LONZA3038099


title: Depletion-6w_tumor_Rep1_AB1148

value: EPCAM


title: Depletion-6w_tumor_Rep1_AB1146


title: Depletion-6w_tumor_Rep1_AB1147


title: PBMCs, Japanese cohort, B003_L002, H031

description: Library name: JP_RIK_B003_L002_5GEX_H031


title: S24_716 -KU 20d (35)

value: Removal of KU60019 after 35d and incubation for 20d


title: 3w_normal_CD45-_Rep2_AB151


title: PBMCs, Japanese cohort, B003_L002, H034

description: Library name: JP_RIK_B003_L002_5GEX_H034


title: S23_715 -KU 20d (35)


title: Isotype-12w_tumor_Rep1_AB1145


title: 3w_normal_EPCAM_Rep2_AB149


title: 3w_normal_CD45-_Rep2_AB150


title: S22_705 -KU 20d (35)


title: PBMCs, Japanese cohort, B003_L001, H044

description: Library name: JP_RIK_B003_L001_5GEX_H044


title: Depletion-12w_tumor_Rep1_AB1144


title: PBMCs, Japanese cohort, B003_L001, H045

description: Library name: JP_RIK_B003_L001_5GEX_H045


title: S20_715 -DMSO 20d (35)

value: Removal of DMSO after 35d and incubation for 20d


title: 3w_normal_CD45+_Rep2_AB147


title: S26_715 IR 10d


title: Isotype-12w_tumor_Rep1_AB1143


title: PBMCs, Japanese cohort, B003_L001, H043

description: Library name: JP_RIK_B003_L001_5GEX_H043


title: 3w_normal_CD45+_Rep2_AB148


title: S19_705 -DMSO 20d (35)


title: S18_716 +KU 35d

value: KU60019 for 35 days


title: Isotype-12w_tumor_Rep1_AB1142


title: 3w_tumor_CD45-_Rep2_AB146


title: PBMCs, Japanese cohort, B003_L001, H041

description: Library name: JP_RIK_B003_L001_5GEX_H041


title: Isotype-12w_tumor_Rep1_AB1141


title: S17_715 +KU 35d


title: 3w_tumor_CD45-_Rep2_AB145


title: PBMCs, Japanese cohort, B003_L001, H040

description: Library name: JP_RIK_B003_L001_5GEX_H040


title: Isotype-12w_tumor_Rep1_AB1140


title: PBMCs, Japanese cohort, B003_L001, H039

description: Library name: JP_RIK_B003_L001_5GEX_H039


title: 3w_tumor_EPCAM_Rep2_AB144


title: S21_716 -DMSO 20d (35)


title: Isotype-12w_tumor_Rep1_AB1139


title: PBMCs, Japanese cohort, B003_L001, H038

description: Library name: JP_RIK_B003_L001_5GEX_H038