title: MTB20_17_V3_MTB_TCRB.tsv

description: Library name: MTB20_17_V3_MTB_TCRB.tsv


title: testis_BP_5

status: Public on Jul 07 2025

type: SRA

city: Changchun

first: Tong

last: Chen

state: Jilin

address: No. 5333, Xi'an Road, Lvyuan District

country: China

institute: Jilin University

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

molecule: total RNA

organism: Mus musculus

source_name: testis

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: testis

tag: treatment

value: PBS+Busulfan


title: Differentiated, KDi, biol rep 2

city: Bethesda

first: Alison

middle: Anne

last: McBride

state: MD

address: 33 North Drive

department: DIR

country: USA

institute: NIAID

description:
Library name: Sample 7
D3_KDi_2_S7

library_source: genomic

data_processing:
Eight ATAC samples were pooled and subjected to 2 x 100 bp paired-end read sequencing on the Illumina NextSeq 2000 P2 platform
All the samples had Q30 bases above 93% and yields between 103 and 141 million pass filter reads.
Reads were trimmed for adapters using Cutadapt v1.18 and aligned to the human reference genome using Bowtie 2 v2.3.4.1 with flag -k 10
Peaks were called using Genrich v0.6 (https://github.com/jsh58/Genrich) with the following flags: -j -y -r -v -d 150 -m 5 -e chrM, chrY. Genrich-produced bedgraphs were normalized by library size (reads per million sequenced reads, RPM) for visualization.
Assembly: hg19
Supplementary files format and content: BigWig files of ATAC-seq peaks.

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: CIN612-9E cervical keratinocytes were grown in Rheinwald-Green F-medium (3:1 Ham’s F-12/high-glucose Dulbecco’s modified Eagle’s medium [DMEM], 5% fetal bovine serum [FBS], 0.4 µg/ml hydrocortisone, 8.4 ng/ml cholera toxin, 10 ng/ml epidermal growth factor, 24 µg/ml adenine, 2mM glutamine, 6 µg/ml insulin, 100 U/ml penicillin, and 100 µg/ml streptomycin) on a layer of lethally irradiated J2/3T3 mouse fibroblast cells. J2/3T3 fibroblasts were grown in DMEM, 10% newborn calf serum, 2 mM glutamine,100 U/ml penicillin, and 100 µg/ml streptomycin. For ATAC-seq, cells were seeded onto 10 cm plates at 6x10e5 and 1.5x10e6 cells per plate for the growing and differentiated conditions, respectively. Cells were cryopreserved in 5% DMSO/F-media two- (growing cells) and seven-days (differentiated cells) post-seeding. For cellular differentiation, confluent cells were cultured in complete KGM™ Keratinocyte Growth Medium (Lonza, CC-4131), excluding GA-1000, for 24 hours and then cultured in KBM™ Keratinocyte Basal Medium (Lonza, CC-3101) supplemented with 1.5 mM CaCl2 for 72 hours.

extract_protocol:
Omni-ATAC protocol, https://doi.org/10.1038/nmeth.4396
Omni-ATAC protocol, https://doi.org/10.1038/nmeth.4397

treatment_protocol: Differentiated cells were stimulated with 0.5 µM keratinocyte differentiation inducer (KDi, CK2 inhibitor IV, Santa Cruz, CAS 863598-09-8, Sc-311368, lot E3012) or DMSO vehicle control for 48 hours prior to harvesting total RNA.

tag: cell line

tag: cell type

value: HPV31-positive cervical keratinocytes

tag: genotype

value: WT

value: 0.5 µM keratinocyte differentiation inducer (KDi), differentiated cells

tag: time

value: 48 hour KDi; 72 hour Ca2+


title: Xeno_GV_plus Pat1MSC_6

city: Rochester

first: Sanjay

last: Misra

state: MN

address: 200 First Street SW

department: Radiology

institute: Mayo Clinic

data_processing:
BAM files were imported into the RNA-Seq pipeline of hg38. Exclusions included a minimum RPKM value of 0.01.
Assembly: hg38
Supplementary files format and content: Xeno Pat_1 MSC_RAW.XLS

source_name: Outflow vein received MSCs (MSC)

extract_protocol:
AVF outflow vein was harvested three days after AVF creation and RNA was isolated using miRNeasy kit (qiagen).
0.5 μg of total RNA was subjected to library synthesis using the TruSeq V2 RNA-Seq kit.
Libraries were sequenced at four samples per lane following Illumina’s standard protocol using the Illumina cBot and HiSeq 3000/4000 PE Cluster Kit. The flow cell was sequenced as 100 X 2 paired end reads on an Illumina HiSeq 4000 using HiSeq 3000/4000 sequencing kit and HD 3.4.0.38 collection software. Base-calling was performed using Illumina’s RTA version 2.7.7.

treatment_protocol: Immediately after AVF creation, 250000 MSCs in 5 ul of ringer lactate solution were layered on the AVF outflow vein.

tag: strain/genotype

value: Fox N1 nude mouse

value: AVF outflow veins

value: MSC


title: P4329_4

city: Montreal

first: Marc

middle: J

last: Servant

state: Quebec

address: P.O. Box 6128, Downtown Station

department: Faculty of Pharmacy

country: Canada

institute: Université de Montréal

description: Library name: P4329_4

data_processing:
RNA-seq
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.20 allowing 1 mismatch in the index.
Sequenced reads were trimmed for sequencing adapters and low quality extremities and mapped to the reference genome using STAR version 2.7.1a
Readcounts were computed by STAR during sequence alignment based on gene annotations from Gencode version 40 (based on Ensembl 106)
Expression values were also computed using RSEM version 1.3.2 based on Gencode version 40
Assembly: GRCh38
Supplementary files format and content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned
Supplementary files format and content: RSEM: Tab-delimited file where columns correspond to a standard RSEM output for gene values (first line identifies the column)

molecule: polyA RNA

source_name: Skin

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) + RNeasy mini kit (Qiagen, #74106)
cDNA libraries were prepared from total RNA using a PolyA selection and the KAPA RNA Hyperprep Kit and were further amplified for sequencing.

value: Skin

value: puromycine resistant HaCat cell population

value: immortalized human keratinocytes

value: cell population stably transfected with the pMRX plasmid

value: LPA 60 min


title: MTB20_17_V1_PT_TCRB.tsv

city: La Jolla

first: Bjoern

last: Peters

state: CA

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

description: Library name: MTB20_17_V1_PT_TCRB.tsv

data_processing:
Raw reads were aligned and quantified using the Cell Ranger Multi pipeline (version 5.0.0) against the GRCh38 (2020-A) human reference genome and the VDJ was aligned with refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0. GEX and HTO data were aggregated as feature/barcode matrices and imported into the R environment using Seurat where additional QCs and downstream analysis were conducted. Before creating the Seurat object, in the GEX matrix, TCR genes belonging to each category of TCR alpha, beta, gamma and delta were averaged across the cells to prevent the formation of individual TCR gene expression clusters in downstream analysis.
Supplementary files format and content: tab-delimited text file includes template counts for each sample
Library strategy: TCR-seq

source_name: PBMC

extract_protocol:
Cells were harvested on day 14. CD4 T cells were purified from the ex vivo samples using the EasySep™ Human CD4 Positive Selection Kit II (STEM cellTM Technologies), according to the manufacturer’s instructions. DNA extraction (DNeasy Blood and Tissue kit; Qiagen) was performed according to the manufacturer’s instructions for both the purified CD4 T cells and the cultured cells.
TCR sequencing of the V-β chain was performed by Adaptive Biotechnologies and their ImmunoSeq platform. Ex vivo samples were sequenced at a higher depth   than cultured samples for greater sensitivity to detect rare clonotypes and to assess a broader range of the repertoire.

value: PBMC

tag: library type

value: TCR


title: all mix sample 5

city: Calgary

first: Esteban

middle: Enrique

last: Elias

state: Alberta

address: 3300 Hospital Dr

department: Medicine

institute: University of Calgary

description:
Library name: E12K5
Parse Bioscience

library_source: transcriptomic single cell

data_processing:
The resulting FASTQ files were analyzed using the Parse Biosciences data analysis pipeline (v1.1) (https://www.parsebiosciences.com) which demultiplexes reads and assigns cells and samples. Reads were aligned to the mouse genome (mm10).
Assembly: Mouse mm10
Supplementary files format and content: .csv, .mtx

source_name: kidney

extract_protocol:
Euthanized mice were perfused with chilled 1× PBS via the left ventricle. After removing the renal capsule and fat, kidneys were minced into approximately 1 mm3 cubes and digested using Multi-Tissue Dissociation kit (Miltenyi, 130-110-201). Up to 250 mg of tissue was digested with 50 μl of enzyme D, 25 μl of enzyme R, and 6.75 μl of enzyme A in 1 ml of RPMI and incubated for 30 min at 37 °C. Digestion was deactivated by 10% fetal bovine serum (FBS). The suspension was passed through a 70 μm cell strainer. After centrifugation at 400 ×g for 5 min, cell pellet was incubated with 1 ml of RBC lysis buffer on ice for 3 min and washed again. Cells were resuspended in PBS and passed through a 40 μm cell strainer. Cells were resuspended in staining buffer (1× PBS, 1% BSA, 2 mM EDTA) for further analysis.
Kidneys were collected from C57BL/6 mice subjected to ischemia-reperfusion injury (IRI) or left untreated as controls (n=3 per condition). Single-cell suspensions were prepared from pooled kidneys (3 mice per condition), and live leukocytes were enriched by fluorescence-activated cell sorting (FACS) using SYTOX™ Blue exclusion and forward/side scatter gating. Cell viability was confirmed by Trypan Blue exclusion (>80%). Live cells were fixed using the Evercode™ Cell Fixation Kit (V2) (Parse Biosciences) and stored at –80 °C. Fixed cells were thawed and processed with the Evercode™ WT (V2) kit for single-cell library preparation according to manufacturer protocols. Libraries were sequenced at ~50,000 reads per cell on a NovaSeq 6000 platform (Illumina) with 5% PhiX spike-in, performed by Novogene.

treatment_protocol: ischemia reperfusion injury +/- entospletinib

value: kidney


title: Differentiated, KDi, biol rep 1

description:
Library name: Sample 6
D3_KDi_1_S6


title: Xeno_GV_plus Pat1MSC_5


title: MTB20_17_V1_MTB_TCRB.tsv

description: Library name: MTB20_17_V1_MTB_TCRB.tsv


title: Xeno_GV_plus Pat1MSC_4


title: Differentiated, DMSO, biol rep 3

description:
Library name: Sample 5
D2_3_S5

value: DMSO vehicle control, differentiated cells

value: 48 hour DMSO; 72 hour Ca2+


title: all mix sample 3

description:
Library name: E12K3
Parse Bioscience


title: Differentiated, DMSO, biol rep 2

description:
Library name: Sample 4
D2_2_S4

value: HPV31-positive cervical keratinocytes


title: Xeno_GV_plus Pat1MSC_3


title: MTB20_8_V3_PT_TCRB.tsv

description: Library name: MTB20_8_V3_PT_TCRB.tsv


title: Differentiated, DMSO, biol rep 1

description:
Library name: Sample 3
D2_1_S3

value: WT


title: MTB20_8_V3_MTB_TCRB.tsv

description: Library name: MTB20_8_V3_MTB_TCRB.tsv


title: all mix sample 1

description:
Library name: E12K1
Parse Bioscience


title: Xeno_GV_plus Pat1MSC_2


title: Growing, untreated, biol rep 2

description:
Library name: Sample 2
G1_2_S2

value: Untreated growing cells

value: 0 hour


title: Xeno_GV_plus Pat1MSC_1

value: Fox N1 nude mouse


title: Growing, untreated, biol rep 1

description:
Library name: Sample 1
G1_1_S1


title: MTB20_8_V1_MTB_TCRB.tsv

description: Library name: MTB20_8_V1_MTB_TCRB.tsv


title: Invitro_W7_rep3

city: shanghai

first: danjun

last: li

address: No. 639 Zhizaoju Road

institute: Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine

description: Library name: Sample 12

data_processing:
Quality control and alignment: First, Trimmomatic (version 0.33) was used to remove adapters and low-quality bases from all bisulfite sequencing reads. Next, the paired-end reads that passed quality control were mapped to the mouse reference genome (GRCm39) in paired-end mode using bismark (version 0.16.3). The single-end reads that passed quality control were mapped to the reference genome in single-end mode. Then, Samtools and Picard were used to sort the reads and remove PCR duplicate reads.
DNA methylation level analysis: Before determining the DNA methylation status, all sequencing reads containing incompletely converted non-CpG cytosines were removed. To extract the methylation status of cytosines, bismark_methylation_extractor was applied to both paired-end and single-end reads. For each CpG site, the methylation level was determined by the ratio of the number of methylated cytosines in the reads covering that CpG to the total number of reads covering that CpG.
Assembly: GRCm39
Supplementary files format and content: Fastq

source_name: Tail DNA of 7-week-old mice born from in vitro blastocyst transfer

extract_protocol:
The genomic DNA was fragmented by sonication, followed by end-repair, adenine tailing, and adapter ligation.
According to the manufacturer's instructions, the genomic DNA was subjected to bisulfite treatment using the EZ DNA Methylation Kit (D5001; Zymo Research), and subsequent PCR amplification was carried out.

value: Muscle tissue and Connective tissue

value: somatic cell

value: in vitro embryo tranfer


title: MTB20_49_V3_PT_TCRB.tsv

description: Library name: MTB20_49_V3_PT_TCRB.tsv


title: Invitro_W7_rep2

description: Library name: Sample 11


title: Xeno_GV_M_5

source_name: No treatment  control (C)

value: AVF outflow veins

value: Control


title: Xeno_GV_M_3


title: PED05_ALG_WT_CM, rep4, group7, day21

city: Madison

first: Matthew

middle: E

last: Brown

state: WI

address: 600 Highland Avenue, H4/733 CSC

institute: University of Wisconsin-Madison

description:
Library name: 5WT-4-neg_S5
WT_CM_3

data_processing:
Raw fastq reads were trimmed using skewer v0.2.2b for adapter sequence and low quality sequences
Trimmed reads where aligned to the reference genome using STAR v2.5.3a
Reads were quantified using RSEM v1.2.31
Assembly: GRCh37
Supplementary files format and content: Tab-delimited text file includes transcript length, RSEM-determined expected counts, TPM, and FPKM for each sample

source_name: iPSC line

extract_protocol:
Qiagen
TruSeq Stranded mRNA

value: iPSC line

value: iPSC-derived cardiomyocytes

value: ALG WT

value: Cardiomyocyte differentiation

tag: batch


title: MTB20_49_V3_MTB_TCRB.tsv

description: Library name: MTB20_49_V3_MTB_TCRB.tsv

value: PBMC

value: TCR


title: all mix sample 4

description:
Library name: E12K4
Parse Bioscience

value: kidney


title: MTB20_49_V1_PT_TCRB.tsv

description: Library name: MTB20_49_V1_PT_TCRB.tsv


title: PED05_ALG_WT_CM, rep3, group7, day21

description:
Library name: 5WT-3-neg_S3
WT_CM_2


title: Xeno_GV_M_2


title: PED05_ALG_WT_CM, rep6, group7, day21

description:
Library name: 5WT-6-neg_S7
WT_CM_4


title: Invivo_W7_rep2

description: Library name: Sample 8

source_name: Tail DNA of 7-week-old mice born from in vivo blastocyst transfer

value: in vivo embryo tranfer


title: all mix sample 2

description:
Library name: E12K2
Parse Bioscience


title: Xeno_GV_M_1


title: MTB20_49_V1_MTB_TCRB.tsv

description: Library name: MTB20_49_V1_MTB_TCRB.tsv


title: PED05_ALG_WT, rep4, group9, day8

description:
Library name: WT-4-neg_S46
WT_iPS_4

value: induce Pluripotent Stem Cells (iPSCs)

value: undifferentiated


title: PED05_ALG_WT_CM, rep1, group7, day21

description:
Library name: 5WT-1-neg_S1
WT_CM_1


title: Invitro_W1_rep3

description: Library name: Sample 6

source_name: Tail DNA of 1-week-old mice born from in vitro blastocyst transfer


title: Invivo_W7_rep1

description: Library name: Sample 7


title: Xeno_GV_M_6


title: MTB20_35_V3_PT_TCRB.tsv

description: Library name: MTB20_35_V3_PT_TCRB.tsv


title: Mouse_MSC_3

data_processing:
Libraries were sequenced at four samples per lane following Illumina’s standard protocol using the Illumina cBot and HiSeq 3000/4000 PE Cluster Kit. The flow cell was sequenced as 100 X 2 paired end reads on an Illumina HiSeq 4000 using HiSeq 3000/4000 sequencing kit and HD 3.4.0.38 collection software. Base-calling was performed using Illumina’s RTA version 2.7.7.
BAM files were imported into the RNA-Seq pipeline of mm10. Exclusions included a minimum RPKM value of 0.01.
Genome_build: mm10
Supplementary_files_format_and_content: RPKM

source_name: Adipose derived mesenchymal stem cells (MSC)

growth_protocol: MSCs isolated from adult mouse fat pads and cultured in advanced MEM supplimented with 10% FBS as described in methods.

extract_protocol:
RNA was isolated using miRNeasy kit (qiagen).
0.5 μg of total RNA was subjected to library synthesis using the TruSeq V2 RNA-Seq kit.

tag: strain


title: Invitro_W1_rep2

description: Library name: Sample 5


title: PED05_ALG_WT, rep3, group9, day8

description:
Library name: WT-3-neg_S44
WT_iPS_3


title: Mouse_MSC_2

value: Adipose derived mesenchymal stem cells (MSC)


title: PED05_ALG_WT, rep2, group9, day8

description:
Library name: WT-2-neg_S42
WT_iPS_2


title: Invitro_W7_rep1

description: Library name: Sample 10


title: MTB20_8_V1_PT_TCRB.tsv

description: Library name: MTB20_8_V1_PT_TCRB.tsv


title: MTB20_35_V1_PT_TCRB.tsv

description: Library name: MTB20_35_V1_PT_TCRB.tsv


title: Mouse_MSC_1


title: Invitro_W1_rep1

description: Library name: Sample 4


title: Invivo_W7_rep3

description: Library name: Sample 9


title: PED05_ALG_WT, rep1, group9, day8

description:
Library name: WT-1-neg_S40
WT_iPS_1


title: MTB20_35_V1_MTB_TCRB.tsv

description: Library name: MTB20_35_V1_MTB_TCRB.tsv


title: MSC_4

description: MSC

data_processing:
Libraries were sequenced at four samples per lane following Illumina’s standard protocol using the Illumina cBot and HiSeq 3000/4000 PE Cluster Kit. The flow cell was sequenced as 100 X 2 paired end reads on an Illumina HiSeq 4000 using HiSeq 3000/4000 sequencing kit and HD 3.4.0.38 collection software. Base-calling was performed using Illumina’s RTA version 2.7.7.
BAM files were imported into the RNA-Seq pipeline of mm10. Exclusions included a minimum RPKM value of 0.01.
Genome_build: mm10
Supplementary_files_format_and_content: The average RPKMs of each group (KI-A or KI-V) were calculated and KI-A/KI-V was considered as fold change.  The genes that were >1.5 or <0.75 were considered as differentially expressed genes and the genes that were <1.5 or > 0. 75 were excluded. A simple t-test was performed to determine the P value and P<0.05 was considered as significant different compared to KI-V and the genes that were >0.05 were excluded.

source_name: Vein

extract_protocol:
Extraction protocol 0.5 μg of total RNA was subjected to library synthesis using the TruSeq V2 RNA-Seq kit.
0.5 μg of total RNA was subjected to library synthesis using the TruSeq V2 RNA-Seq kit.

treatment_protocol: Chronic Kidney disease created to a C57BL6J mouse as described in methods. 28days later an arteriovenous fistula was clreated by ligation of carotid artery and jugular vein. immidiatly after AVF creation, 250000 MSCs from C57 donor mouse of same gender were layred on the adventitia of the AVF outflow veins. 3 days after AVF creation, animals were euthanized and the outflow veins of AVFs were harvested.

tag: disease state

value: chronic kidney disease model

value: MSC Treatment


title: Invivo_W1_rep3

description: Library name: Sample 3

source_name: Tail DNA of 1-week-old mice born from in vivo blastocyst transfer

value: Muscle tissue and Connective tissue

value: somatic cell


title: PED05_ALG_CD54KO, rep4, group1, day8

description:
Library name: KO-4-neg_S38
KO_iPS_4

value: ALG CD54KO


title: Invivo_W1_rep2

description: Library name: Sample 2


title: MSC_3

description: MSC

value: AVF outflow veins


title: PED05_ALG_CD54KO, rep3, group1, day8

description:
Library name: KO-3-neg_S36
KO_iPS_3

value: iPSC line


title: MTB20_55_V3_MTB_TCRB.tsv

description: Library name: MTB20_55_V3_MTB_TCRB.tsv


title: MSC_2

description: MSC


title: Invivo_W1_rep1

description: Library name: Sample 1


title: MTB20_35_V3_MTB_TCRB.tsv

description: Library name: MTB20_35_V3_MTB_TCRB.tsv


title: MTB20_55_V1_MTB_TCRB.tsv

description: Library name: MTB20_55_V1_MTB_TCRB.tsv


title: Bone marrow of tumor-bearing (KP) mice; Nfe2l2:Ms4a3Cre (KO) (scATAC-seq)

city: New York

first: Laszlo

last: Halasz

state: NY

address: 1470 Madison Avenue

department: Department of Oncological Sciences

institute: Mount Sinai Icahn School of Medicine

description:
Library name: mm_scATAC_BM_KP_Nfe2l2_KO
10x Genomics

library_source: genomic single cell

data_processing:
scRNA-seq: Fastq reads from scRNA-seq samples were aligned to the mm10 reference transcriptome followed by count matrix generation using the default CellRanger multi workflow, using the ‘raw’ matrix output. Following alignment, barcodes matching cells that contained > 500 unique molecular identifiers (UMIs) were extracted. From these cells, those with transcripts > 25% mitochondrial genes were filtered from downstream analyses.
scATAC-seq: Fastq reads from scATAC-seq samples were aligned to mouse genome reference mm10 using cellranger-atac v2.0.0. Fragment files were parsed with ArchR v1.0.2 and initial quality control was applied based on sequencing depth and transposition quality (minTSS = 8, minFrags = 5000). FRIP scores were also used for filtering data prior to downstream analyses.
Assembly: Mouse:mm10
Supplementary files format and content: scRNA-seq, scATAC-seq: cellranger processed outputs (barcode, peak/feature matrix).

source_name: Bone marrow

extract_protocol:
Mouse: myeloid cells were sorted from respective tissues (Lung/BM/blood) based on markers described in Methods section. For scRNA-seq, cells were encapsulated following 10x Genomics Chromium Next GEM Single Cell 3ʹ v3.1 protocol. For scATAC-seq, cells were subjected to nuclei isolation following 10x Genomics Chromium Next GEM Single Cell ATAC v1.1 protocol. Nuclei quality was verified by brightfield microscopy prior to loading. A target recovery number of 8000~10000 nuclei or cells were loaded onto each lane of a 10X Chromium chip according to manufacturer’s instructions.
Mouse: Libraries were prepared according to manufacturer’s instructions. All libraries were quantified via Agilent 2100 hsDNA Bioanalyzer. scRNA-seq libraries were sequenced at a targeted depth of minimum 25,000 read pairs per cell pooled on the Illumina NovaSeq 6000 S2 100 cycle kit. scATAC-seq libraries were sequenced at a targeted depth of minimum 25,000 read pairs per cell using the Illumina NovaSeq 6000 S2 100 cycle kit.

treatment_protocol: Mouse: myeloid cells excluding mature neutrophils were sorted from processed tissues (Lung/BM/blood) of naïve or KP Tumor-bearing mice in PBS+0.04% BSA, based on surface markers described in Methods section.

value: Bone marrow

value: immune

value: Tumor-bearing

value: late

value: DNA


title: PED05_ALG_CD54KO, rep2, group1, day8

description:
Library name: KO-2-neg_S34
KO_iPS_2


title: PED05_ALG_CD54KO, rep1, group1, day8

description:
Library name: KO-1-neg_S32
KO_iPS_1


title: C4

description: NT

value: Vehicle


title: MTB20_43_V3_MTB_TCRB.tsv

description: Library name: MTB20_43_V3_MTB_TCRB.tsv

value: PBMC

value: TCR


title: MTB20_43_V3_PT_TCRB.tsv

description: Library name: MTB20_43_V3_PT_TCRB.tsv


title: Lung of tumor-bearing (KP) mice; Nfe2l2:Ms4a3Cre (KO) (scRNA-seq): CMO

description:
Library name: mm_scRNAseq_Lung_KP_Nfe2l2_KO_CMO
10x Genomics
mm_scRNAseq_Lung_KP_Nfe2l2_KO_pool1_filtered_feature_bc_matrix.h5
mm_scRNAseq_Lung_KP_Nfe2l2_KO_pool2_filtered_feature_bc_matrix.h5
mm_scRNAseq_Lung_KP_Nfe2l2_KO_pool3_filtered_feature_bc_matrix.h5

source_name: Lung

value: Lung

tag: cmo

value: HTO


title: C3

description: NT

value: chronic kidney disease model


title: C2

description: NT


title: Lung of tumor-bearing (KP) mice; Nfe2l2:Ms4a3Cre (KO) (scRNA-seq): GEX

description:
Library name: mm_scRNAseq_Lung_KP_Nfe2l2_KO_GEX
10x Genomics
mm_scRNAseq_Lung_KP_Nfe2l2_KO_pool1_filtered_feature_bc_matrix.h5
mm_scRNAseq_Lung_KP_Nfe2l2_KO_pool2_filtered_feature_bc_matrix.h5
mm_scRNAseq_Lung_KP_Nfe2l2_KO_pool3_filtered_feature_bc_matrix.h5

value: mRNA


title: MTB20_6_V3_PT_TCRB.tsv

description: Library name: MTB20_6_V3_PT_TCRB.tsv


title: Bone marrow of tumor-bearing (KP) mice; Nfe2l2:fl/fl (WT) (scATAC-seq)

description:
Library name: mm_scATAC_BM_KP_Nfe2l2_WT
10x Genomics


title: MTB20_55_V3_PT_TCRB.tsv

description: Library name: MTB20_55_V3_PT_TCRB.tsv


title: Lung of tumor-bearing (KP) mice; Nfe2l2:fl/fl (WT) (scRNA-seq): CMO

description:
Library name: mm_scRNAseq_Lung_KP_Nfe2l2_WT_CMO
10x Genomics
mm_scRNAseq_Lung_KP_Nfe2l2_WT_pool1_filtered_feature_bc_matrix.h5
mm_scRNAseq_Lung_KP_Nfe2l2_WT_pool2_filtered_feature_bc_matrix.h5
mm_scRNAseq_Lung_KP_Nfe2l2_WT_pool3_filtered_feature_bc_matrix.h5


title: C1

description: NT


title: MTB20_6_V1_PT_TCRB.tsv

description: Library name: MTB20_6_V1_PT_TCRB.tsv


title: Lung of tumor-bearing (KP) mice; Nfe2l2:fl/fl (WT) (scRNA-seq): GEX

description:
Library name: mm_scRNAseq_Lung_KP_Nfe2l2_WT_GEX
10x Genomics
mm_scRNAseq_Lung_KP_Nfe2l2_WT_pool1_filtered_feature_bc_matrix.h5
mm_scRNAseq_Lung_KP_Nfe2l2_WT_pool2_filtered_feature_bc_matrix.h5
mm_scRNAseq_Lung_KP_Nfe2l2_WT_pool3_filtered_feature_bc_matrix.h5


title: embryo, prdm1a_sibling_homeostasis_rep3

city: Kansas City

first: Shiyuan

middle: (Cynthia)

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

data_processing:
Raw sequencing data were processed using 10X Genomics Cell Ranger pipeline. Reads were demultiplexed into Fastq file format using cellranger mkfastq. Genome index was built by cellranger mkref using zebrafish genome danRer11, ensembl 98 gene model. Data were aligned by STAR aligner and cell counts tables were generated using cellranger count function with default parameters.
Assembly: danRer11
Supplementary files format and content: single cell  count matrix in hdf5 format, raw data in bam format.

organism: Danio rerio

source_name: embryo

extract_protocol:
600 each prdm1a mutant and sibling embryos of the Tg (she:H2A-mCherry)psi56Tg lateral line marker line were separately dissociated in 4.5ml 0.25% Trypsin-EDTA (Gibco) for 3.5 minutes on ice by triturating with a 1ml pipette repeatedly. Supernatant containing cells was filtered through a 70μm Cup Filcon (BD Biosciences) and cells were pelleted by centrifugation at 720g for five minutes at 4C. Cells were washed in cold PBST by resuspending the pellet and pelleted again at 720g for five minutes at 4C. Cells were filtered through a 35μm strainer (Falcon-Corning), and stained with Draq5 (BioStatus) at a dilution of 1:500. Cells were then sorted on a BD Influx Cell Sorter (BD Biosciences). mCherry and Draq5 double positive cells were sorted into 90% MeOH for fixation.
FAC-sorted MeOH fixed cells prepared above were processed according to 10X Genomics standard protocols. Cells were rehydrated in 1% BSA and 0.5 U/μl RNase-inhibitor in ice-cold DPBS. A volume of 34ul was loaded onto the Chromium Controller, targeting ~12,000 cells per sample. Library prep was performed using the Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1. Two independent replicates were sequenced for both prdm1a mutant and sibling conditions. Libraries were pooled and sequenced on an Illumina instrument in High Output mode, with 28 bp, 8bp, and 91 bp for read 1, i7 index, and read 2 respectively.
scRNA-seq (10x Genomics)

value: embryo

tag: timepoints

value: Homostasis

value: Wildtype


title: embryo, prdm1a_sibling_homeostasis_rep2


title: Bone marrow of tumor-bearing (KP) mice; Nfe2l2:Ms4a3Cre (KO) (scRNA-seq): CMO

description:
Library name: mm_scRNAseq_BM_KP_Nfe2l2_KO_CMO
10x Genomics
mm_scRNAseq_BM_KP_Nfe2l2_KO_pool1_filtered_feature_bc_matrix.h5
mm_scRNAseq_BM_KP_Nfe2l2_KO_pool2_filtered_feature_bc_matrix.h5
mm_scRNAseq_BM_KP_Nfe2l2_KO_pool3_filtered_feature_bc_matrix.h5


title: MTB20_55_V1_PT_TCRB.tsv

description: Library name: MTB20_55_V1_PT_TCRB.tsv


title: Hi-C_BWX4310_42C_IPTG30min

city: Bloomington

first: Xindan

last: Wang

state: IN

address: 1001 E 3rd St

department: Biology

institute: Indiana University at Bloomington

data_processing:
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
For Bacillus subtilis Hi-C, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) independently by Bowtie version 2.1.0 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts.  For ChIP-seq and WGS, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) using CLC genomics workbench 8.0, and exported .csv file.
For Hi-C, the two resulting SAM files were then merged together. Unaligned reads were discarded.
For Hi-C, the Bacillus subtilis (PY79) genome was divided into HindIII restriction fragments. Each aligned read was sorted into its corresponding restriction fragment. We inferred that a DNA fragment resulted from non-ligation or self-ligation if reads from both ends were from the same restriction fragment; these reads were discarded. Only DNA fragments for which the reads came from different restriction fragments were retained and used for construction of a Hi-C contact map.
For Hi-C, the genomes of Bacillus subtilis (PY79) was then divided into bins 10 kb and the remaining reads were allocated to their corresponding bin. We then counted the number of fragments having reads with in different bins. A raw Hi-C contact map is the matrix of read counts in which each entry, mij, indicates the number of fragments with ends mapping to bins i and j. The raw Hi-C contact map/matrix is biased due to the uneven distribution of restriction enzyme sites and, to a lesser extent, differences in GC content and the mappability of individual reads. We normalized raw contact maps using an iterative normalization procedure (Imakaev et al., 2012 PMID: 22941365). Essentially, we converted the number of interactions, or read counts, into Hi-C scores by applying the following equation and iteratively repeating it for the resulting contact map after each cycle:  mij =mij * (total reads) / (total reads in bin i * total reads in bin j). The iterative procedure was repeated until the maximum relative error of the total number of Hi-C scores in a bin was less than 10-5. Resulting matrices were normalized so that Hi-C scores for each row and column sum to 1. Subsequent analysis and visualization was done using R scripts.
Assembly: Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1)
Supplementary files format and content: Files ending with .matrix.txt: tab-delimited text files of the iteratively-corrected Hi-C contact maps/matrices. Files ending with .csv files are comma-separated values files of ChIP-seq/WGS results.

organism: Bacillus subtilis PY79

source_name: Bacillus subtilis PY79

extract_protocol:
Wild type and mutant cells of Bacillus subtilis PY79 growing in CH were crosslinked using 3% formaldehyde and then lysed by treatment of lysosome and 1% SDS as previouly discribed (Wang et al 2015).
Standard library construction protocol was used for Illumina Nextseq500/Nextseq2000 sequencing platforms. Illumina Truseq indexes were used.

value: Bacillus subtilis PY79

value: Bacterial

value: parSdelta9 no a.b., deltaspo0J (remains wt parS at -1degree)::spec, yvbJ::Pspank spo0J (deltaparS) (cat), dnaB134 (ts) zhb-83::Tn917 (erm)

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 30min. Then 1mM IPTG was added into the cell culture and the cells were incubated at 42degreeC for another 30min


title: MSC_1

description: MSC

value: AVF outflow veins

value: MSC Treatment


title: MTB20_6_V1_MTB_TCRB.tsv

description: Library name: MTB20_6_V1_MTB_TCRB.tsv


title: embryo, prdm1a_sibling_homeostasis_rep1


title: MTB20_38_V3_PT_TCRB.tsv

description: Library name: MTB20_38_V3_PT_TCRB.tsv


title: Bone marrow of tumor-bearing (KP) mice; Nfe2l2:Ms4a3Cre (KO) (scRNA-seq): GEX

description:
Library name: mm_scRNAseq_BM_KP_Nfe2l2_KO_GEX
10x Genomics
mm_scRNAseq_BM_KP_Nfe2l2_KO_pool1_filtered_feature_bc_matrix.h5
mm_scRNAseq_BM_KP_Nfe2l2_KO_pool2_filtered_feature_bc_matrix.h5
mm_scRNAseq_BM_KP_Nfe2l2_KO_pool3_filtered_feature_bc_matrix.h5

value: Bone marrow

value: immune

value: Tumor-bearing

value: late


title: Hi-C_BWX4310_42C_IPTG15min_HPUra15min

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min. Then 1mM IPTG was added into the cell culture and the cells were incubated at 42degreeC for 15min. Finally 162 µM HPUra was added into the cell culture and cells were incubated at 42degreeC for another 15min


title: MTB20_38_V3_MTB_TCRB.tsv

description: Library name: MTB20_38_V3_MTB_TCRB.tsv

value: PBMC

value: TCR


title: embryo, prdm1a_mutant_homeostasis_rep3

value: Mutant


title: Hi-C_BWX4310_42C_IPTG15min

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min. Then 1mM IPTG was added into the cell culture and the cells were incubated at 42degreeC for another 15min


title: embryo, prdm1a_mutant_homeostasis_rep2

value: embryo

value: Homostasis


title: Bone marrow of tumor-bearing (KP) mice; Nfe2l2:fl/fl (WT) (scRNA-seq): CMO

description:
Library name: mm_scRNAseq_BM_KP_Nfe2l2_WT_CMO
10x Genomics
mm_scRNAseq_BM_KP_Nfe2l2_WT_pool1_filtered_feature_bc_matrix.h5
mm_scRNAseq_BM_KP_Nfe2l2_WT_pool2_filtered_feature_bc_matrix.h5
mm_scRNAseq_BM_KP_Nfe2l2_WT_pool3_filtered_feature_bc_matrix.h5

value: HTO


title: MTB20_26_V3_PT_TCRB.tsv

description: Library name: MTB20_26_V3_PT_TCRB.tsv


title: Bone marrow of tumor-bearing (KP) mice; Nfe2l2:fl/fl (WT) (scRNA-seq): GEX

description:
Library name: mm_scRNAseq_BM_KP_Nfe2l2_WT_GEX
10x Genomics
mm_scRNAseq_BM_KP_Nfe2l2_WT_pool1_filtered_feature_bc_matrix.h5
mm_scRNAseq_BM_KP_Nfe2l2_WT_pool2_filtered_feature_bc_matrix.h5
mm_scRNAseq_BM_KP_Nfe2l2_WT_pool3_filtered_feature_bc_matrix.h5

value: mRNA


title: MTB20_6_V3_MTB_TCRB.tsv

description: Library name: MTB20_6_V3_MTB_TCRB.tsv


title: embryo, prdm1a_mutant_homeostasis_rep1


title: MTB20_26_V3_MTB_TCRB.tsv

description: Library name: MTB20_26_V3_MTB_TCRB.tsv


title: Invitro_rep3-1

description:
B3
A single inner cell mass of a blastocyst-stage embryo in vitro-3

data_processing:
The raw data were processed by Skewer (v0.2.2), and the data quality was assessed by FastQC v0.11.2. The sequencing reads had a length of 2×150 bp. The gene expression level was calculated as fragments per kilobase of transcript per million mapped reads (FPKM). DESeq2 was used to screen differentially expressed genes (DEGs) among the different groups (P < 0.05 and |log2-fold change| ≥1). Gene Ontology (GO) term and KEGG pathway enrichment analyses were conducted through the DAVID Bioinformatics Resources and OmicShare CloudTools, respectively.
Assembly: GRCm39

source_name: Inner cell mass

extract_protocol:
For RNA sequencing, RNA extraction was carried out using a total RNA microextraction kit (Zymo Research).
Library preparation was performed using the TruePrep DNA Library Prep Kit V2 for Illumina (TD202; Vazyme Biotech, Nanjing, China) according to the manufacturer’s instructions.

value: Blastocysts

value: Embryonic stem cell

value: in vitro culture


title: Invitro_rep2-1

description:
B2
A single inner cell mass of a blastocyst-stage embryo in vitro-2


title: sair1-1, flg22,  Rep2  (RNA-seq)

city: Beijing

first: Qiangsheng

last: Yu

address: Tsinghua university

department: School of life sciences

institute: Tsinghua university

description: Library name: BFR2

data_processing:
For RNA-seq data, reads were mapped to the tair10 genome using STAR (version 2.7.3a) with parameter "--outSAMmultNmax 1". Read mapped to CDS annotated in tair10 were counted using featureCounts (version 1.6.2).
For RIP-seq data, low-quality and adapter sequences were trimmed using fastp (version 0.19.11) software. Subsequently, the cleaned reads were aligned to the Arabidopsis reference genome (TAIR10) using BWA (v 0.7.12). Reads that did not overlap with rRNA annotations were extracted from the resulting BAM files using SAMtools (version 1.7-16) and converted into BED files using BEDtools (v2.27.1-1). The BED-format alignment data served as input for the Piranha peak caller (v1.2.1) with the parameters ‘‘-z 50 -s -v’’, using the 35S::GFP sample as a covariant.
For ribo-seq data, reads without 3’ adapter, with 5’ adapter, or with low sequencing quality were discarded. Reads mapped to rRNA and tRNA by bowtie (version 1.0.1) were also excluded. Cleaned reads were mapped to tair10 genome using STAR (version 2.7.3a) with parameters "--outFilterType BySJout --outFilterMismatchNmax 2 --outFilterMultimapNmax 1 --outSAMmultNmax 1 --outFilterMatchNmin 16 --alignEndsType EndToEnd". Number of reads overlap with tair10 CDSs were determined by featureCounts (version 1.6.2)".
Assembly: tair10
Supplementary files format and content: RNA-seq.counts.txt, count matrix of RNA-seq samples without paired Ribo-seq data;paired.RNA-seq.counts.txt: RNA-seq count matrix of samples with paired Ribo-seq data;Ribo-seq.counts.txt: count matrix of Ribo-seq samples.
Supplementary files format and content: RIP-seq.rep1.bed,RIP-seq.rep2.bed: peaks of RIP-seq in bed format

organism: Arabidopsis thaliana

source_name: leaves

extract_protocol:
Leaves of 3-week-old plants grown on soil was ground with liquid nitrogen, and the powder was used to extract RNA
The RNA was dissolved with 20 μL RNase-free water. Library construction was carried out by Novogene Corporation (Beijing, China).

value: leaves


title: MTB20_26_V1_PT_TCRB.tsv

description: Library name: MTB20_26_V1_PT_TCRB.tsv


title: HiC_BWX5529_42C_T30

value: Bacillus subtilis PY79

value: Bacterial

value: parSdelta9 no a.b., -59degree parS no a.b, dnaB134 (ts) zhb-83::Tn917 (erm)

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC for 15min, finally shifted up to 42degreeC for 15min


title: MTB20_26_V1_MTB_TCRB.tsv

description: Library name: MTB20_26_V1_MTB_TCRB.tsv


title: sair1-1, mock,  Rep2  (RNA-seq)

description: Library name: BMR2

value: Mock


title: HiC_BWX5529_42C_T20

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC for 15min, finally shifted up to 42degreeC for 5min


title: sair1-1, flg22 , Rep1  (RNA-seq)

description: Library name: BFR1


title: Invitro_rep1-1

description:
B1
A single inner cell mass of a blastocyst-stage embryo in vitro-1


title: Invivo_rep3-1

description:
A3
A single inner cell mass of a blastocyst-stage embryo in vivo-3

value: in vivo development


title: Invivo_rep2-1

description:
A2
A single inner cell mass of a blastocyst-stage embryo in vivo-2


title: HiC_BWX5529_42C_T25

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC for 15min, finally shifted up to 42degreeC for 10min


title: HiC_BWX5529_30C_T15

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC for 15min


title: sair1-1, mock , Rep1  (RNA-seq)

description: Library name: BMR1


title: HiC_BWX5529_30C_T10

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC for 10min


title: hiPSC kucg-2 CRIPSRi Ribo-Seq ZNF598 KD GCN2i disome rep2

city: Martinsried

first: Danny

last: Nedialkova

address: Am Klopferspitz 18

country: Germany

institute: Max Planck Institute of Biochemistry

description: Library name: Sample 18

library_source: other

data_processing:
Sequencing libraries were demultiplexed and adapter-trimmed with Cutadapt v2.5. Trimmed reads longer than 10 nt were aligned to a human ribosomal RNA reference using Bowtie v1.2.2 (Langmead 2009) with the following options: -p 40 -S --best. rRNA-filtered reads were aligned to GRCh38.p13 using STAR v2.6.1c (Dobin 2013) with the following options: --outFilterMultimapNmax 1 --outSAMtype BAM SortedByCoordinate --outFilterMismatchNmax 0 --alignEndsType Local --seedSearchStartLmax 14 --alignIntronMax 10000 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --quantMode TranscriptomeSAM --outSAMattributes NH HI AS nM NM MD.
A custom reference transcriptome annotation was built for the GRCh38.p13 genome based on the Matched Annotation from the NCBI and EMBL-EBI (MANE) and the best scoring transcript annotated in APPRIS (Rodriguez 2013)(https://apprisws.bioinfo.cnio.es/pub/current_release/datafiles/homo_sapiens/GRCh38/appris_data.appris.txt). For all the genes, we extrapolate the MANE-annotated transcript. For genes without a MANE-annotated transcript, the best-scoring transcript in APPRIS was chosen as the principal isoform. For multiple best-scoring transcripts associated with the same gene, the longest isoform was selected. When multiple best-scoring transcripts had the same length, a random one was chosen as the principal isoform. This reference set was further filtered for transcripts with coding regions ending with a UAG/UAA/UGA stop codon, having a three-base periodicity, and not containing unidentified bases in the open reading frame. We retained known transcripts with non-AUG start codons (e.g., EIF4G2) or containing UGA codons re-coded as selenocysteine, and curated the remaining set by manually removing mis-annotations that resulted in multiple transcripts per Ensembl gene ID. and filtering out 18 transcripts associated with pseudoautosomal regions on the Y chromosome (PAR_Y). The resulting reference contained 19,759 protein-coding transcripts and was used for ribosome footprint and matched RNA-seq read alignment.
Assembly: GRCh38
Supplementary files format and content: csv; read counts for protein-coding genes
Library strategy: Ribo-Seq

molecule: other

source_name: cell line

extract_protocol:
Cells were quickly washed with ice cold PBS supplemented with 100 µg/ml cycloheximide (CHX) and snap-frozen in liquid nitrogen. Plates were thawed on ice and cells were scraped off the plate in 400 µl polysome lysis buffer (20 mM Tris pH=7.4, 150 mM NaCl, 5 mM MgCl2, 1% Triton-X100, 1 mM DTT, 100 µg/ml CHX, 25 U/ml Turbo DNase), 0.1% NP-40, 10 µg/ml aprotinin, 20 µM leupeptin, 2.5 µM pepstatin A, 0.5 mM AEBSF and 1x Phosphatase Inhibitor Cocktail. Samples were vortexed vigorously, triturated through a 26G gauge needle, and spun down for 7 minutes at 16,000xg/ 4°C. Supernatant was transferred to a new tube. 20 µg RNA in 200 µl polysome lysis buffer were digested with 50 U RNase I for 45 minutes at 2,000 rpm/22°C.
Ribosome footprint libraries were prepared essentially as described (McGlincy and Ingolia, 2017; Wu 2019) with minor modifications. RNase I digestion was stopped by addition of 100 U Superase In and extracts were loaded on a sucrose cushion. The pellet was dissolved in 400 µl LiDS/LET lysis buffer and RNA was extracted with the acid phenol protocol. Fragments in the range of 19 to 32 nucleotides (monosomes) or 50 to 80 nt (disomes) were isolated by gel size selection, with T4 PNK and ligated to pre-adenylated adapters containing 5 random nucleotides at their 5’ ends (McGlinzy 2017) with T4 RNA Ligase 2 (truncated KQ). Adapter-ligated RNA was subjected to rRNA depletion using the Ribo-Seq riboPOOL h/m/r depletion kit (siTOOLs). The rRNA-depleted footprints were reverse-transcribed with Protoscript II and cDNA was circularized with recombinant TS2126 RNA ligase 1 (commercially available as CircLigase). Libraries were constructed from circularized cDNA with KAPA HiFi DNA Polymerase and single-end sequencing was performed on a NextSeq 550 platform (Illumina).

value: kucg-2 CRISPRi hiPSC

value: Human induced pluripotent stem cells


title: Invivo_rep1-1

description:
A1
A single inner cell mass of a blastocyst-stage embryo in vivo-1


title: hiPSC kucg-2 CRIPSRi Ribo-Seq ZNF598 KD GCN2i disome rep1

description: Library name: Sample 17


title: Col-0, flg22,  Rep2  (RNA-seq)

description: Library name: CFR2


title: HiC_BWX5529_T0

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min


title: Col-0, flg22 , Rep1  (RNA-seq)

description: Library name: CFR1


title: 9E cells, extrachromosomal HPV31, biol rep1

description:
Library name: Sample 1
Sample ID SM159

data_processing:
Reads were trimmed and filtered using cutadapt version 1.18. Following trimming, reads were processed using HiC-Pro version 2.11.1. Reads were aligned to a joint reference genome of hg38 autosome and sex chromosomes and HPV31. The genome was digested by the HiC-Pro script digest_genome.py using an “mboi” digestion pattern. Contact maps were created at window sizes of 500 kb and 1 Mb.
Trans-interactions were called using MHiC version 0.5.0 (R/3.6.1). First, data from chromosomes Y and M were removed from the 1 Mb raw matrix file and matching coordinate bed file. Next, MHiC was used to call all trans-interactions using default parameters.
Assembly: hg38
Supplementary files format and content: SM159/SM163.allValidPairs.hic; Juicer-associated format of the HiC-Pro contact matrices
Supplementary files format and content: SM159/SM163_500000_iced.matrix files; (Hi-C contact matrices) interaction frequencies between pairs of loci from the associated regions files (SM159/SM163_500000_abs.bed) generated using HiC-Pro.
Supplementary files format and content: SM159/SM163_1000000_noYM_mhic_output_table_sig.txt; trans-interactions called using MHiC and default paramters.

growth_protocol: CIN612-9E cervical keratinocytes were grown in Rheinwald-Green F-medium (3:1 Ham’s F-12/high-glucose Dulbecco’s modified Eagle’s medium [DMEM], 5% fetal bovine serum [FBS], 0.4 µg/ml hydrocortisone, 8.4 ng/ml cholera toxin, 10 ng/ml epidermal growth factor, 24 µg/ml adenine, 2mM glutamine, 6 µg/ml insulin, 100 U/ml penicillin, and 100 µg/ml streptomycin) on a layer of lethally irradiated J2/3T3 mouse fibroblast cells. J2/3T3 fibroblasts were grown in DMEM, 10% newborn calf serum, 2 mM glutamine,100 U/ml penicillin, and 100 µg/ml streptomycin.

extract_protocol:
In situ Hi-C was performed with 5 million cells per experiment and restriction enzyme MboI. After end-repair and washes, Dynabeads (Thermo Fisher Scientific) with bound DNA were resuspended in 10 mM Tris, 0.1 mM EDTA pH8.0.
Sequencing libraries were created from bound DNA using the Ovation Ultralow Library System V2 kit (NuGEN) with one modification. After adapter ligation, because DNA is still attached to the beads, water instead of SPRI beads was added to the reaction. DNA bound to the beads was purified with a magnet, washed, and the beads were resuspended in 10 mM Tris, 0.1 mM EDTA pH8.0. After library amplification, SPRI beads were used to purify the amplified DNA.

value: Cervical keratinocytes containing extrachromosomal HPV31

value: WT

value: Untreated


title: reaction_6_HTO

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

data_processing:
BCL files were converted to Fastq using bcl2fastq v. 2.19.0 (Illumina)
Salmon Alevin v1.9.045 and Alevin-fry v0.7.046 were used to perform pseudo-alignment of the RNA and hashtag oligos (HTO) library.
RNA library was pseudo-aligned to a custom reference transcriptome, distinguishing between spliced and unspliced transcripts, modified from the ensemble GRCm38 reference, using the salmon index tool (version 1.5.0).
Following pseudo-alignment, mapping steps were performed using the Alevin-fry framework (v.0.7.0)
Assembly: GRCm38
Supplementary files format and content: matrix files with read counts, text files with gene names and cellular barcodes
Supplementary files format and content: csv file with metadata for droplets with a single nucleus

source_name: full liver (L), collagenase-digested hepatocytes (CS) and cultured hepatocytes (PH)

extract_protocol:
Nucleus pellets were suspended in 110 µL nuclei buffer (PBS; w/o MgCl₂ and CaCl₂ [20012068; Invitrogen]), 1 % BSA (SRE0036-25 ml; Sigma), 2 mM MgCl2 (M1028-100 ml; Sigma), and 0.1 % Protector RNase inhibitor 40 U/μl (3335399001; Sigma), and the solution was passed through a 40 μm strainer (43-10040-40; pluriSelect life Science, Germany). For each sample, 10 µL was recovered and mixed with 10 µL trypan blue solution. 93595-50 ml, Sigma) for counting nuclei in a counting chamber. The remaining 100 µL were added 1 µL of individual TotalSeq-A antibodies (BioLegend, San Diego, CA), for a final concentration of 5 ng/µL to enable multiplexing. Samples were washed, centrifuged, re-suspended and stored.
Using a SH800S Cell Sorter (SONY), 6,000 nuclei from each of the 24 samples was sorted. From two of the liver samples, only 3,005 and 4,015 nuclei could be recovered. Nuclei from four samples were mixed resulting in a total of six pools. Each pool containing 24,000 nuclei were loaded on a 10X reaction using 10X Genomics Chromium single-cell 3′ reagent kits (version 3.1). Single-cell cDNA libraries were produced according to the manufacturer’s instructions and sequenced on an Illumina NovaSeq 6000 (Illumina, San Diego, CA) using 2x S1 flow cells

tag: reaction number


title: HiC_BWX5529_42C_T40

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC for 15min, finally shifted up to 42degreeC for 25min


title: Col-0, mock,  Rep2  (RNA-seq)

description: Library name: CMR2

value: leaves


title: HiC_BWX5297_42C_IPTG40min_T40

value: Bacillus subtilis PY79

value: Bacterial

value: parSdelta9 no a.b., -59degree parS no a.b, deltaspo0J::spec, yvbJ::Pspank spo0J (deltaparS) (cat), dnaB134 (ts) zhb-83::Tn917 (erm)

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min, then shifted down to 30degreeC with the treatment of 1mM IPTG for 15min, finally shifted up to 42degreeC for 25min


title: 9E cells, extrachromosomal HPV31, biol rep 4

description:
Library name: Sample 7
S15_9E_4_EcoRI, has processed data file for viewpoints 1-3 (VP1-3)

data_processing:
Viral-host genome contact profiles were mapped for the three viewpoint reading primers (VP1: AACAACACCACCACATCG; VP2: CAAGGCGCAGGTTTTGGAAT; VP3: GATTGTCCTCCATTAGAATT) using the pipe4C pipeline, which generated three contact maps per sample (viewpoint 1-3, VP1-3)
R1 and R2 reads were processed independently using pipe4C version 1.1.6. Reads were aligned to a joint reference genome of hg38 autosome and sex chromosomes and HPV31. Read counts per fragment in the pipe4C output files were combined for R1 and R2. Normalized read counts were calculated using the same steps as in the pipe4C code. Specifically, read counts in genomic regions were normalized to reads per million, excluding the top highest two values to mitigate outliers. Normalized counts were then collapsed into 50 kb windows using GenomicRanges and BSgenome.Hsapiens.UCSC.hg38.
Assembly: hg38
Supplementary files format and content: Bedgraph files of 4C-seq signal
Library strategy: 4C-Seq

growth_protocol: CIN612 cervical keratinocytes were grown in Rheinwald-Green F-medium (3:1 Ham’s F-12/high-glucose Dulbecco’s modified Eagle’s medium [DMEM], 5% fetal bovine serum [FBS], 0.4 µg/ml hydrocortisone, 8.4 ng/ml cholera toxin, 10 ng/ml epidermal growth factor, 24 µg/ml adenine, 2mM glutamine, 6 µg/ml insulin, 100 U/ml penicillin, and 100 µg/ml streptomycin) on a layer of lethally irradiated J2/3T3 mouse fibroblast cells. J2/3T3 fibroblasts were grown in DMEM, 10% newborn calf serum, 2 mM glutamine,100 U/ml penicillin, and 100 µg/ml streptomycin. For each 4C-seq sample, approximately 5 million cells were crosslinked in situ with 2% formaldehyde for 10 min at room temperature and quenched for 5 min with 0.125 M glycine.

extract_protocol:
Cells were lysed using 0.2-0.5% Igepal CA-630, centrifuged at 3,000 x g for 5 min at 4°C and the resulting nuclei permeabilized in 0.3-0.7% SDS for 1 hour at 37°C, with shaking at 900 rpm, followed by sequestration of SDS by 2% Triton X-100 for 1 hour at 37°C, 900 rpm. Nuclei were washed twice with 1X EcoRI buffer (NEB; 100 mM Tris-HCl, 50 mM NaCl, 10 mM MgCl2, 0.025% Triton X-100, pH 7.5 @ 25°C) to remove SDS and digested overnight with 400U EcoRI (NEB, R3101M) at 37°C, with shaking at 900 rpm. An additional 300U EcoRI was added and the nuclei incubated for a further 4 hours prior to heat inactivation at 65°C for 20 min. Digested samples were ligated overnight in 7 ml 1X ligase buffer (NEB; 50 mM Tris-HCl, 10 mM MgCl2, 1 mM ATP, 10 mM DTT, pH 7.5 at 25°C) containing 400 cohesive-end units (CEU) T4 DNA ligase (NEB, M0202L) at 16°C, 500 rpm, and crosslinks reversed overnight at 56°C, 500 rpm, in the presence of 0.04 mg/ml proteinase K. Samples were then incubated with 0.04 mg/ml RNase A for 30 min at 37°C, 500 rpm. For sample S14, the primary ligation was performed overnight at 16°C, 1,400 rpm, in 50 µl 1X ligase buffer (NEB), supplemented with 0.1% Triton X-100 and 670 CEU T4 DNA ligase (NEB, M0202L), and crosslinks reversed overnight at 56°C in the presence of 0.2 mg/ml proteinase K. Samples were then incubated with 0.3 mg/ml RNase A for 30 min at 37°C. DNA was purified by phenol:chloroform:isoamyl alcohol (25:24:1, v/v; Invitrogen, 15593-031) and chloroform (Macron Fine Chemicals) extractions  and digested with 150U DpnII (NEB, R0543M) overnight at 37°C, with shaking at 900 rpm, prior to heat inactivation at 65°C for 20 min. Digested DNA samples were ligated and purified by phenol:chloroform and chloroform extractions, followed by and additional purification step using the QIAquick PCR Purification Kit (QIAGEN, 28106).
Purified DNA was subjected to inverse PCR using the Expand Long Template PCR System (Roche, 11681842001) and primers that target three viewpoints within the HPV31 genome. PCR products for the three viewpoints were pooled for each sample, purified using the QIAquick PCR Purification Kit (QIAGEN, 28106) and subjected to 2 x 100 bp paired-end read sequencing to a sequencing depth of >387 million read pairs per sample. Sequencing libraries were generated using the Truseq DNA Nano kit (Illumina) and subjected to size selection to remove fragments >1,000 bp that typically represent undigested or self-ligated products. To ensure high sequence diversity of the 4C-seq libraries, a PhiX spike-in control of 30% the sequencing run was included.


title: reaction_4_HTO

value: full liver (L), collagenase-digested hepatocytes (CS) and cultured hepatocytes (PH)


title: Col-0, mock , Rep1 (RNA-seq)

description: Library name: CMR1

value: Mock


title: HiC_BWX5297_42C_IPTG35min_T35

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min, then shifted down to 30degreeC with the treatment of 1mM IPTG for 15min, finally shifted up to 42degreeC for 20min


title: sair1-1, flg22,  Rep2

description: Library name: BFS2

data_processing:
For RNA-seq data, reads were mapped to the tair10 genome using STAR (version 2.7.3a) with parameter "--outSAMmultNmax 1". Read mapped to CDS annotated in tair10 were counted using featureCounts (version 1.6.2).
For RIP-seq data, low-quality and adapter sequences were trimmed using fastp (version 0.19.11) software. Subsequently, the cleaned reads were aligned to the Arabidopsis reference genome (TAIR10) using BWA (v 0.7.12). Reads that did not overlap with rRNA annotations were extracted from the resulting BAM files using SAMtools (version 1.7-16) and converted into BED files using BEDtools (v2.27.1-1). The BED-format alignment data served as input for the Piranha peak caller (v1.2.1) with the parameters ‘‘-z 50 -s -v’’, using the 35S::GFP sample as a covariant.
For ribo-seq data, reads without 3’ adapter, with 5’ adapter, or with low sequencing quality were discarded. Reads mapped to rRNA and tRNA by bowtie (version 1.0.1) were also excluded. Cleaned reads were mapped to tair10 genome using STAR (version 2.7.3a) with parameters "--outFilterType BySJout --outFilterMismatchNmax 2 --outFilterMultimapNmax 1 --outSAMmultNmax 1 --outFilterMatchNmin 16 --alignEndsType EndToEnd". Number of reads overlap with tair10 CDSs were determined by featureCounts (version 1.6.2)".
Assembly: tair10
Supplementary files format and content: RNA-seq.counts.txt, count matrix of RNA-seq samples without paired Ribo-seq data;paired.RNA-seq.counts.txt: RNA-seq count matrix of samples with paired Ribo-seq data;Ribo-seq.counts.txt: count matrix of Ribo-seq samples.
Supplementary files format and content: RIP-seq.rep1.bed,RIP-seq.rep2.bed: peaks of RIP-seq in bed format
Library strategy: Ribo-Seq


title: 9E cells, extrachromosomal HPV31, biol rep 3

description:
Library name: Sample 6
S14_9E_3_EcoRI, has processed data file for viewpoints 1-3 (VP1-3)


title: reaction_3_HTO


title: sair1-1, flg22 , Rep1

description: Library name: BFS1


title: HiC_BWX5297_42C_IPTG30min_T30

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min, then shifted down to 30degreeC with the treatment of 1mM IPTG for 15min, finally shifted up to 42degreeC for 15min


title: 9E cells, extrachromosomal HPV31, biol rep 2

description:
Library name: Sample 5
S13_9E_2_EcoRI, has processed data file for viewpoints 1-3 (VP1-3)


title: reaction_2_HTO


title: 9E cells, extrachromosomal HPV31, biol rep2

description:
Library name: Sample 2
Sample ID SM163


title: sair1-1, mock,  Rep2

description: Library name: BMS2


title: HiC_BWX5297_42C_IPTG25min_T25

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min, then shifted down to 30degreeC with the treatment of 1mM IPTG for 15min, finally shifted up to 42degreeC for 10min


title: HiC_BWX5529_42C_T35

value: parSdelta9 no a.b., -59degree parS no a.b, dnaB134 (ts) zhb-83::Tn917 (erm)

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC for 15min, finally shifted up to 42degreeC for 20min


title: reaction_1_HTO


title: sair1-1, mock , Rep1

description: Library name: BMS1


title: 9E cells, extrachromosomal HPV31, biol rep 1

description:
Library name: Sample 4
S12_9E_1_EcoRI, has processed data file for viewpoints 1-3 (VP1-3)


title: 6E cells, integrated HPV31, biol rep 3

description:
Library name: Sample 3
S11_6E_3_EcoRI, has processed data file for viewpoint 1 (VP1) only

value: Cervical keratinocytes containing integrated HPV31


title: HiC_BWX5297_42C_IPTG20min_T20

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min, then shifted down to 30degreeC with the treatment of 1mM IPTG for 15min, finally shifted up to 42degreeC for 5min


title: reaction_6_RNA

value: WT


title: reaction_5_HTO


title: HiC_BWX5297_30C_IPTG10min_T10

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min, then shifted down to 30degreeC with the treatment of 1mM IPTG for 10min


title: Col-0, flg22,  Rep2

description: Library name: CFS2


title: 6E cells, integrated HPV31, biol rep 2

description:
Library name: Sample 2
S10_6E_2_EcoRI, has processed data file for viewpoint 1 (VP1) only

value: Untreated


title: HiC_BWX5297_42C_IPTG25min_HPUra10min_T25

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min, then shifted down to 30degreeC with the treatment of 1mM IPTG for 15min. Next, 162 µM HPUra was added into the cell culture and the cells were incubated at 42degreeC for 10min


title: 6E cells, integrated HPV31, biol rep 1

description:
Library name: Sample 1
S9_6E_1_EcoRI, has processed data file for viewpoint 1 (VP1) only


title: reaction_5_RNA


title: reaction_4_RNA


title: Col-0, flg22 , Rep1

description: Library name: CFS1

value: leaves


title: HiC_BWX5297_42C_IPTG20min_HPUra5min_T20

value: Bacillus subtilis PY79

value: Bacterial

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min, then shifted down to 30degreeC with the treatment of 1mM IPTG for 15min. Next, 162 µM HPUra was added into the cell culture and the cells were incubated at 42degreeC for 5min


title: NTN

city: Hefei, Anhui

first: dou

last: yin

address: 81 Meishan Road

department: Department of Pathophysiology School of Basic Medical Sciences

institute: Anhui Medical University

description:
Library name: smaple7
NTN_fpkm

data_processing:
The core of RNA-seq is the significance analysis of gene expression differences, using statistical methods to compare the gene expression differences under two or more conditions, find out the specific genes related to the conditions, and then further analyze the biological significance of these specific genes, including quality control, comparison, quantification, differential significance analysis, functional enrichment and other links. In addition, alternative splicing, variation sites, and fusion gene prediction are also important analyses for RNA-seq. At the same time, according to different research needs, Novo Zhiyuan has launched personalized transcriptome analysis content, such as gene co-expression network construction (WGCNA), somatic mutation detection, etc.
Data Quality Control1.Sequencing data description 2.Sequencing error rate distribution 3.GC content distribution 4.Sequencing data filtering 5.Data Quality Summary 6.Quality Control FAQs and Answers
Reference genome alignment Sequencing fragments are randomly interrupted by mRNA, and in order to determine which genes transcribe these segments, the QC clean reads need to be aligned to the reference genome. Use HISAT2 software to quickly and accurately align Clean Reads to the reference genome to obtain the localization information of the Reads on the reference genome。 Official manual for HISAT2 software. If the reference genome is well assembled, and the species tested are consistent with the reference genome, and there is no contamination in the relevant experiments, then the proportion of sequencing reads generated by the experiment will be higher than 70% (Total Mapped Reads or Fragments). The reference genome used in this project is XX, and the download address is XX. Genome structure annotation file: XX.
Quantitative analysis Based on the location information of the gene alignment on the reference genome, the number of reads covered by each gene (including the new predicted gene) from start to end can be counted. Separately filter out the comparison quality values below10 reads, reads on non-contrasting pairs, reads aligned to multiple regions of the genome. This part of the analysis uses the featureCounts tool in the subread software.
Difference Analysis After the gene expression quantification is completed, the expression data needs to be statistically analyzed to screen for genes with significant differences in expression levels in different states. There are three main steps to a variance analysis. First, the original readcount is normalized, mainly to correct the sequencing depth. The statistical model then calculates the hypothesis test probability (pvalue). Finally, multiple hypothesis testing correction is performed to obtain the FDR value (false discovery rate, padj is the common form)。 For different experimental situations, we selected appropriate software to analyze the significance of gene expression differences.
Enrichment analysis After we have obtained the differential gene based on the gene expression analysis, we must further fall on the function of the gene. For transcriptome analysis, thousands of genes are often involved, which can complicate the analysis. The solution is to divide a list of genes into multiple parts, thereby reducing the complexity of the analysis. In order to solve the problem of how to classify different classes, enrichment analysis of gene function is usually carried out, with the expectation of discovering the biological pathways that play a key role in biological processes, so as to reveal and understand the basic molecular mechanisms of biological processes. Functional enrichment assays can divide hundreds or thousands of genes, proteins, or other molecules into different pathways to reduce the complexity of the analysis. In addition, under two different experimental conditions, the activated pathway is clearly more convincing than a simple list of genes or proteins. Gene function enrichment analysis should first construct a gene set (such as GO and KEGG databases), that is, genome annotation information for classification. Then map our target gene set (differential gene set or other gene set) to the background gene set, taking care to distinguish between annotation and enrichment. We used clusterProfiler software to perform GO functional enrichment analysis and KEGG pathway enrichment analysis for differential gene sets. The enrichment analysis is based on the principle of hypergeometric distribution, in which the differential gene set is the gene set of the differentially significant genes analyzed and annotated to the GO or KEGG database, and the background gene set is all the genes that have been significantly analyzed and annotated to GO or KEGGGene set of the database. The results of enrichment analysis were the enrichment of all differential gene sets, up-regulated differential gene sets, and down-regulated differential gene sets for each differential comparison combination. The table presented in this report shows the results of the enrichment analysis for a certain combination of comparisons, and the picture shows the results of the enrichment analysis for all combinations.
Alternative Splicing Analysis In addition to expression analysis, RNA-seq data can also be used to analyze variant sites such as alternative splicing and SNP/indel based on the alignment of reads to the reference genome. Alternative splicing (AS) is a common gene expression modality in most eukaryotic cells. The gene sequence of eukaryotic cells consists of introns and exons, which are removed by RNA sciploids after the gene is transcribed into mRNA precursors, while exons remain in mature mRNA. An unsheared RNA can have multiple exon splice forms, so that a gene can translate different proteins at different times and in different environments, thereby increasing the complexity or adaptability of the system under its physiological conditions.
Analysis of variant sites SNPs stand for Single Nucleotide Polymorphisms, which refer to genetic markers formed by single nucleotide mutations on the genome, which are numerous and polymorphic. In general, SNPs refer to single nucleotide variants with a variation frequency greater than 1%. InDel(insertion-deletion) refers to an indel that occurs in a sample of a small fragment relative to the reference genome, which may contain one or more bases. Variant site analysis is an important part of RNA-seq structure analysis, which mainly includes the detection of congenital mutation sites and acquired somatic cell mutation sites, which is of great significance for tumor research. We used GATK software to analyze the variant loci in the sample data and annotate the variant loci with SnpEff software
List of fusion genes The list of fusion genes is shown below. Among them, JunctionReads and SpanningFrags were the main indicators for the detection of fusion genes. In paired-end sequencing, read1 and read2 can be regarded as the two ends of a fragment (250bp-300bp), and if read1 or read2 crosses the breakpoint of the fusion event, such reads are calledJunctionRead。 The gap region between read1 and read2 spans the breakpoint of the fusion event.
Supplementary files format and content: all_compare.xls_and_all_compare(1).xls

source_name: Breast tissue

growth_protocol: MDA-MB-468 and BT-474 cells were cultured with DMEM/F12 complete medium containing 10%FBS. The medium used for human preadipocytes cells was a high-glucose DMEM medium containing 10% FBS. Human preadipocytes were induced to differentiate with 10% FBS, 0.5 mM IBMX, 1 µM dexamethasone, and 10 µg/mL insulin for 3 days, followed by further differentiation in DMEM with 10% FBS and 10 µg/mL insulin for 3 days. Cells were then cultured in DMEM with 10% FBS for 4 days to form mature adipocytes enriched with lipid droplets. All cells were cultured in a constant temperature cell incubator containing 5% carbon dioxide at 37 ° C

extract_protocol:
Novogene uses standard extraction methods to extract RNA from tissues or cells, and then strictly controls the RNA samples, and the quality control standards mainly include the following three aspects. 1.Agarose gelelectrophoresis: Samples are analyzed for RNA integrity and the presence of DNA contamination. 2.NanoPhotometer spectrophotometer：Detection of RNA purity（OD260/280and OD260/230）。 3.Agilent 2100 bioanalyzer：Accurate detection of RNA integrity. Note: RNA integrity and total volume were used as the main reference indicators
There are two main ways to obtain mRNA: one is to use the structural feature that most of the mRNA in eukaryotes has polyA tails, and enrich mRNAs with polyA tails through Oligo(dT) magnetic beads. The second is to remove ribosomal RNA from total RNA to obtain mRNA. Subsequently, the mRNA obtained was randomly interrupted with divalent cations in the NEB Fragmentation Buffer, and the library was created according to the normal NEB library preparation method or the strand-specific library preparation method.  1.NEB common library construction: The first cDNA strand was synthesized in M-MuLV reverse transcriptase system using fragmented mRNA as template and random oligonucleotides as primer, then the RNA strand was degraded by RNaseH, and the second cDNA strand was synthesized using dNTPs as raw material in DNA polymerase I system. The purified double-stranded cDNA was end-repaired, A-tail was added, and sequencing joints were connected. cDNA of about 250-300bp was screened by AMPure XP beads for PCR amplification, and PCR products were purified by AMPure XP beads again, and finally A library was obtained. The NEBNext® Ultra™ RNA Library Prep Kit was used for Illumina®.2.Chain specific database: The method for synthesizing the first strand of cDNA by reverse transcription is the same as the common library building method of NEB. The difference is that when synthesizing the second strand, dTTP in dNTPs is replaced by dUTP, and then the cDNA end repair, A-tail addition, sequencing joint connection and length screening are also carried out. Then, USER enzyme was used to degrade the second strand of cDNA containing U, and PCR amplification was performed to obtain the library. Chain specific library has many advantages, such as the same amount of data can obtain more effective information; More accurate gene quantitative, localization and annotation information can be obtained. It provides antisense transcripts and a single exon expression level in each isoform. The NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® was used.
NEB common library construction: The first cDNA strand was synthesized in M-MuLV reverse transcriptase system using fragmented mRNA as template and random oligonucleotides as primer, then the RNA strand was degraded by RNaseH, and the second cDNA strand was synthesized using dNTPs as raw material in DNA polymerase I system. The purified double-stranded cDNA was end-repaired, A-tail was added, and sequencing joints were connected. cDNA of about 250-300bp was screened by AMPure XP beads for PCR amplification, and PCR products were purified by AMPure XP beads again, and finally A library was obtained. The NEBNext® Ultra™ RNA Library Prep Kit was used for Illumina®. Chain specific database: The method for synthesizing the first strand of cDNA by reverse transcription is the same as the common library building method of NEB. The difference is that when synthesizing the second strand, dTTP in dNTPs is replaced by dUTP, and then the cDNA end repair, A-tail addition, sequencing joint connection and length screening are also carried out. Then, USER enzyme was used to degrade the second strand of cDNA containing U, and PCR amplification was performed to obtain the library. Chain specific library has many advantages, such as the same amount of data can obtain more effective information; More accurate gene quantitative, localization and annotation information can be obtained. It provides antisense transcripts and a single exon expression level in each isoform. The NEBNext® Ultra™ Directional RNA Library Prep Kit was used for Illumina

treatment_protocol: The pre-cultured breast cancer cells MDA-MB-468 and BT-474 were uniformly inoculated into the chamber, and after the cells were attached to the bottom of the chamber, the co-culture chamber was picked up with tweezer and placed in the six-well plate of the induced mature adipose cells. The co-culture model of breast cancer cells and adipose cells was constructed for 72 hours. Subsequently, breast cancer cells were collected in a small chamber for following experiments.

value: Breast tissue

value: Non-triple-negative breast cancer


title: HiC_BWX5297_30C_IPTG15min_T15

value: parSdelta9 no a.b., -59degree parS no a.b, deltaspo0J::spec, yvbJ::Pspank spo0J (deltaparS) (cat), dnaB134 (ts) zhb-83::Tn917 (erm)

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min, then shifted down to 30degreeC with the treatment of 1mM IPTG for 15min


title: NTN_CO

description:
Library name: smaple9
NTN_CO_fpkm


title: reaction_3_RNA

value: full liver (L), collagenase-digested hepatocytes (CS) and cultured hepatocytes (PH)


title: Col-0, mock , Rep1

description: Library name: CMS1

value: Mock


title: reaction_2_RNA


title: MDA468_CO_3

description:
Library name: smaple6
MDA468_CO_3_fpkm

value: Triple-negative breast cancer


title: HiC_BWX5297_42C_HPUraIPTG25min_T50

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min, then shifted down to 30degreeC for 15min, next shifted up to 42degreeC for 10min. Then 1mM IPTG and 162 µM HPUra were added into the cell culture and the cells were  incubated at 42degreeC for another 25min


title: MDA468_CO_2

description:
Library name: smaple5
MDA468_CO_2_fpkm


title: SAIR1-YFP-OX2, Rep2 (total RNA for BDR2)

description: Library name: TBDR2

value: Input


title: reaction_1_RNA

value: WT


title: SAIR1-YFP-OX2, Rep1 (total RNA for BDR1)

description: Library name: TBDR1


title: HiC_BWX5297_42C_HPUraIPTG20min_T45

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min, then shifted down to 30degreeC for 15min, next shifted up to 42degreeC for 10min. Then 1mM IPTG and 162 µM HPUra were added into the cell culture and the cells were  incubated at 42degreeC for another 20min


title: MDA468_CO_1

description:
Library name: smaple4
MDA468_CO_1_fpkm


title: 35S-GFP, Rep2 (total RNA for CDR2)

description: Library name: TCDR2


title: HiC_BWX5297_42C_noreplisome_IPTG25min_T25

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min. Then 1mM IPTG was added into the cell culture and the cells were incubated at 42degreeC for another 25min


title: Stag3_WT_8w

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

data_processing:
Read data generated from samples labeled with Cell Multiplexing Oligo were processed with cellranger v6.0.1 with “multi” option.
Assembly: GRCm38.p3
Supplementary files format and content: Cellranger output, tab-delimitted barcodes, features, and matrix files.

source_name: Testis

extract_protocol:
RNA extraction was integrated in "library construction protocol" process.
Testes were dissociated as previously described with some modifications (Nakagawa). Briefly, dissociated testicular tubules were incubated with collagenase type IV (1 mg/ml) at 37°C in a water bath for 15 minutes with intermittent tapping. Nine milliliters of HBSS was added, and the tube was spun down quickly. After aspirating the supernatant, 1 ml of trypsin was added, pipetted 15 times, and incubated at 37°C in a water bath for 3 minutes. Following vigorous pipetting for dissociation, trypsin was quenched by adding 9 ml of HBSS with 2% FBS, and the cells were centrifuged at 300 g for 5 minutes. The samples were then washed with HBSS containing 2% FBS. In P15 testes, after filtration, the cells were directly analyzed and sorted by FACS (AriaII, BD). In 8-week adult testes, following further incubation with antibodies (Brilliant Violet 421 anti-mouse/human CD324 (E-Cadherin) antibody (1:1000) (BioLegend, 147319); Alexa Fluor® 647 anti-mouse CD9 antibody (1:500) (BioLegend, 124810); PE/Cyanine7 anti-mouse CD117 (c-Kit) antibody (1:200) (BioLegend, 105814)), the samples were analyzed and sorted by FACS. Subsequent 10X scRNA-seq library preparation (10X Genomics, Single Cell 3' Kit v. 3 and v. 3.1) and sequencing on a NovaSeq 6000 platform (Illumina) were performed following the manufacturers’ instructions.

value: Testis

value: Undifferentiated Spermatogonia


title: MDA468_C3

description:
Library name: smaple3
MDA468_C3_fpkm


title: HiC_BWX5297_42C_HPUraIPTG15min_T40

value: Bacillus subtilis PY79

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min, then shifted down to 30degreeC for 15min, next shifted up to 42degreeC for 10min. Then 1mM IPTG and 162 µM HPUra were added into the cell culture and the cells were  incubated at 42degreeC for another 15min


title: 35S-GFP, Rep1 (total RNA for CDR1)

description: Library name: TCDR1

value: leaves


title: Col-0, mock,  Rep2

description: Library name: CMS2


title: Stag3_KO_8w

value: Stag3 KO


title: SAIR1-YFP-OX2, Rep2

description: Library name: BDR2

value: IP


title: Stag3_KO_P15_1

value: Whole tesis


title: MDA468_C2

description:
Library name: smaple2
MDA468_C2_fpkm

value: Breast tissue


title: Stag3_KO_P15_2


title: MDA468_C1

description:
Library name: smaple1
MDA468_C1_fpkm


title: Stag3_WT_P15_2


title: 35S-GFP, Rep2

description: Library name: CDR2


title: DLD-1 EVs 3/3 RNase R

city: Newark

first: Mona

last: Batish

state: Delaware

address: 15 Innovation Way

institute: University of Delaware

data_processing:
Reads from control samples were aligned to transcripts from Gencode v32 using Kallisto v0.44.0
Reads from RNase R treated samples were aligned to hg38 using STAR v2.7.10b and circRNAs were extracted from chimeric junction files using circExplorer2 v2.3.8
Assembly: hg38
Supplementary files format and content: tab-delimited file containing raw counts of linear RNAs or circRNAs for each sample

growth_protocol: Cells were grown in DMEM media supplemented with 10% detal bovine serum (FBS) and antibiotics and incubated in a humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was isolated using phenol-chloroform and Zymo-Spin columns
Libraries were prepared using Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus following manufacturer's protocol

treatment_protocol: 1 ug of RNA was treated with 1 unit of RNase R and incubated at 37C for 30 minutes

tag: fraction

value: EV

value: Colorectal cancer

value: RNase R


title: Stag3_WT_P15_1


title: SAIR1-YFP-OX2, Rep1

description: Library name: BDR1


title: DLD-1 EVs 2/3 RNase R


title: Dhx16_CKO5

city: Chongqing

first: Zhigang

last: Li

state: China

address: NO.30 GaotanYan  Street, Shapingba District

institute: Southwest Hospital, Army Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.9.
Reads Per Kilobase of exon per Megabase of library size (RPKM) was performed with Cufflinks v2.1.1, aligned reads were counted with HTSeq.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include RPKM values for each Sample ...

extract_protocol:
About 5000 HSC (Lin-Sca-1+c-Kit+CD48-CD150+) were isolated by FACS and the mRNA library constructed using Smart-Seq V4 Ultra Low Input RNA Kit for sequencing (Takara) according to the manufacturer’s instruction RNA libraries were prepared for sequencing using standard Illumina protocols
The mRNA library constructed using Smart-Seq V4 Ultra Low Input RNA Kit for sequencing (Takara) according to the manufacturer’s instruction.RNA libraries were prepared for sequencing using standard Illumina protocols

value: Bone marrow

value: primary cell

value: Hematopoietic stem cells (HSC)

value: KO


title: HiC_BWX4310_42C_HPUraIPTG30min_T45

value: Bacterial

value: parSdelta9 no a.b., deltaspo0J (remains wt parS at -1degree)::spec, yvbJ::Pspank spo0J (deltaparS) (cat), dnaB134 (ts) zhb-83::Tn917 (erm)

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min, then shifted down to 30degreeC for 15min, finally shifted up to 42degreeC with the treatment of 1mM IPTG and 162 µM HPUra for 30min


title: HiC_BWX5297_42C_noreplisome_IPTG20min_T20

value: Bacillus subtilis PY79

value: parSdelta9 no a.b., -59degree parS no a.b, deltaspo0J::spec, yvbJ::Pspank spo0J (deltaparS) (cat), dnaB134 (ts) zhb-83::Tn917 (erm)

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min. Then 1mM IPTG was added into the cell culture and the cells were incubated at 42degreeC for another 20min


title: SAIR1-YFP-OX2, DC3000, Rep2

description: Library name: SD2

value: leaves


title: HiC_BWX4310_42C_HPUraIPTG25min_T40

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min, then shifted down to 30degreeC for 15min, finally shifted up to 42degreeC with the treatment of 1mM IPTG and 162 µM HPUra for 25min


title: HiC_BWX4310_42C_HPUraIPTG20min_T35

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min, then shifted down to 30degreeC for 15min, finally shifted up to 42degreeC with the treatment of 1mM IPTG and 162 µM HPUra for 20min


title: Dhx16_CKO4


title: DLD-1 EVs 1/3 RNase R

value: WT


title: DLD-1 EVs 3/3 control

value: EV

value: Control


title: HiC_BWX5297_42C_noreplisome_IPTG15min_T15

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min. Then 1mM IPTG was added into the cell culture and the cells were incubated at 42degreeC for another 15min


title: Dhx16_CKO3

value: Bone marrow


title: HiC_BWX4310_42C_HPUraIPTG15min_T30

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min, then shifted down to 30degreeC for 15min, finally shifted up to 42degreeC with the treatment of 1mM IPTG and 162 µM HPUra for 15min


title: sair1-1, DC3000, Rep2

description: Library name: BD2


title: DLD-1 EVs 2/3 control

value: Colorectal cancer


title: Dhx16_CKO2

value: primary cell

value: Hematopoietic stem cells (HSC)

value: KO


title: HiC_BWX4310_42C_IPTG30min_T45

value: Bacterial

value: parSdelta9 no a.b., deltaspo0J (remains wt parS at -1degree)::spec, yvbJ::Pspank spo0J (deltaparS) (cat), dnaB134 (ts) zhb-83::Tn917 (erm)

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min, then shifted down to 30degreeC for 15min, finally shifted up to 42degreeC with the treatment of 1mM IPTG for 30min


title: Dhx16_CKO1


title: sair1-1, DC3000, Rep1

description: Library name: BD1


title: DLD-1 EVs 1/3 control


title: HiC_BWX5297_T0

value: Bacillus subtilis PY79

value: parSdelta9 no a.b., -59degree parS no a.b, deltaspo0J::spec, yvbJ::Pspank spo0J (deltaparS) (cat), dnaB134 (ts) zhb-83::Tn917 (erm)

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min.


title: HiC_BWX4310_42C_IPTG25min_T40

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min, then shifted down to 30degreeC for 15min, finally shifted up to 42degreeC with the treatment of 1mM IPTG for 25min


title: DLD-1 cells 3/3 RNase R

value: cell

value: WT


title: Col-0, DC3000, Rep2

description: Library name: WTD2

value: leaves


title: 35S-GFP, Rep1

description: Library name: CDR1

value: IP


title: HiC_BWX4310_42C_IPTG20min_T35

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min, then shifted down to 30degreeC for 15min, finally shifted up to 42degreeC with the treatment of 1mM IPTG for 20min


title: Dhx16_fl4

value: Bone marrow


title: DLD-1 cells 2/3 RNase R

value: Colorectal cancer

value: RNase R


title: Col-0, DC3000, Rep1

description: Library name: WTD1


title: SAIR1-YFP-OX2, DC3000, Rep1

description: Library name: SD1


title: SAIR1-YFP-OX2, mock, Rep1

description: Library name: SN1

value: Mock


title: HiC_BWX4310_42C_IPTG15min_T30

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min, then shifted down to 30degreeC for 15min, finally shifted up to 42degreeC with the treatment of 1mM IPTG for 15min


title: Dhx16_fl2

value: primary cell

value: Hematopoietic stem cells (HSC)


title: SAIR1-YFP-OX2, mock, Rep2

description: Library name: SN2


title: DLD-1 cells 3/3 control


title: Dhx16_fl3


title: HiC_BWX5230_42C_T30

value: Bacterial

value: parSdelta9 no a.b., -27degree parS no a.b., dnaB134 (ts) zhb-83::Tn917 (erm)

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC for 15min, finally shifted up to 42degreeC for 15min


title: DLD-1 cells 2/3 control

value: Control


title: Dhx16_fl1


title: PBMCs from NSCLC Patient HD5 ATAC (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_PBMC_HD5_ATAC

data_processing:
multiome (RNA + ATAC): Fastq files from human scATAC-seq and 10x Genomics multiome samples were aligned to human genome reference hg38 using cellranger-atac v2.0.0 or cellranger-arc v2.0.0 respectively. Fragment files were parsed with ArchR v1.0.2 and initial quality control was applied based on sequencing depth and transposition quality (minTSS = 8, minFrags = 3000). FRIP scores were also used for filtering data prior to downstream analyses.
Assembly: Human: hg38
Supplementary files format and content: scRNA-seq, scATAC-seq and 10x Multiome (RNA + ATAC): cellranger processed outputs (barcode, peak/feature matrix).

source_name: Blood

extract_protocol:
Human: PBMCs were subjected to nuclei isolation following 10x  Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol in the presence of RNAse inhibitor (Sigma) and DTT (Sigma) to prevent RNA degradation. In case of low-input samples (with <100,000 cells), we utilized 0.2 ml PCR tubes and centrifuged at 4C using swinging rotor buckets to maximize nuclear recovery. Nuclei quality was verified by brightfield microscopy prior to loading. A target recovery number of 8000~10000 nuclei were loaded onto each lane of a 10X Chromium chip according to manufacturer’s instructions.
Human: Libraries were prepared according to manufacturer’s instructions. All libraries were quantified via Agilent 2100 hsDNA Bioanalyzer. Libraries were sequenced at a targeted depth of minimum 25,000 read pairs per cell using the Illumina NovaSeq 6000 S2 100 cycle kit.

treatment_protocol: Human: CD34 positive cells were bead-enriched or sorted (based on surface markers described in Methods section) from isolated PBMCs of patients with NSCLC or healthy donors, and combined with the original isolated PBMCs.

value: Blood

value: healthy donor


title: HiC_BWX5230_42C_T40

value: Bacillus subtilis PY79

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC for 15min, finally shifted up to 42degreeC for 25min


title: HiC_BWX5230_42C_T35

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC for 15min, finally shifted up to 42degreeC for 20min


title: sair1-1, mock, Rep1

description: Library name: BN1

value: leaves


title: HiC_BWX5230_42C_T20

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC for 15min, finally shifted up to 42degreeC for 5min


title: DLD-1 cells 1/3 control

value: cell

value: Colorectal cancer

value: WT


title: HiC_BWX5230_42C_T25

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC for 15min, finally shifted up to 42degreeC for 10min


title: PBMCs from NSCLC Patient HD4 ATAC (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_PBMC_HD4_ATAC


title: P14 control and sgIcos_GDO

first: Alice

last: Kamphorst

state: New York

address: 1425 Madison Avenue

department: Immunology and immunotherapy

institute: Icahn school of medicine at Mount Sinai

description: Guide-derived oligonucleotide (GDO)

data_processing:
Raw fastq files were aligned to the mm10 reference genome (2020-A) and demultiplexed using Cell Ranger v7.0.1 (10x Genomics).
Each biologic sample was split in half and barcoded differently
Guidederived oligo (CMO) assigments were as follows: CTL002={CMO301:ATGAGGAATTCCTGC; or CMO302:CATGCCAATAGAGCG}; CTL003={CMO303:CCGTCGTCCAAGCAT; or CMO304:AACGTTAATCACTCA}; CTL005={CMO305:CGCGATATGGTCGGA; or CMO306:AAGATGAGGTCTGTG}; sglcos006={CMO307:AAGCTCGTTGGAAGA; or CMO308:CGGATTCCACATCAT}; sglcos007={CMO309:GTTGATCTATAACAG; or CMO310:GCAGGAGGTATCAAT}; sglcos010={CMO311:GAATCGTGATTCTTC; or CMO312:ACATGGTCAACGCTG}
Downstream analysis was performed in R v4.3.2 using Seurat v5 package (Hao et al., 2024).  Cells with greater than 5% mitochondrial transcript unique molecular identifier (UMI) counts, greater than 3000 total transcript UMI count, or less than 1100 transcript UMI count were excluded. In total, we retained 12,654 cells for analysis. Standard analysis was run: SCTransform RunPCA to identify the top 30 principal components, RunUMAP, FindNeighbors, FindClusters. Cell cycle scores (calculated using the CellCycleScoring function in Seurat) and mitochondrial percentage were selected as variables to regress out during SCTransform. Samples were integrated with 5000 variable genes chosen for the anchoring process. Clustering was visualized using Clustree (Zappia and Oshlack, 2018), and a cluster resolution of .09 was chosen for five main clusters. Tpex and effector-like cells were subset and re-clustered with the same pipeline as described above and clustered with a resolution of .17 and .09, respectively. SgIcos and sgCtrl samples were pseudobulked using function Seurat2PB. Differentially expressed genes were calculated with EdgeR using a generalized linear model quasi-likelihood F test and defined as having FDR < 0.05 and log2(FC) > 0.5. To annotate the defining genes of each cell cluster, we checked for the presence of well-characterized marker genes for T cells within the differentially expressed genes of a given cluster, and assigned each cluster an identity. Gene signature (Giles et al.) was analyzed using the VISION package
Assembly: mm10-2020-A
Supplementary files format and content: Gene name and raw counts for sequenced cells for each sample

source_name: spleen

extract_protocol:
Five weeks post infection, spleens were collected and single cell suspension from each mouse was surface stain with CD44 (FITC), CD8 (PerCP), PD-1 (PE-Dazzle), CD45.1 (APC) and live/dead IR for 30 min on ice. Samples were washed 3 times with PBS, 1%EDTA, 2% FBS. Then each single cell suspension was divided in two and stained with a unique cell multiplex oligonucleotide tag (CMO) from the 3’ CellPlex Kit set A (10x Genomics) and sort separately. P14 CD8 T cells were sorted as Live CD8+ CD45.1+ by FACS (BD Aria). Viability of the sorted cells was assessed using Acridine Orange/Propidium Iodide viability staining reagent (Nexcelom), showing a viability of 97%. Cells from all mice were then pooled in equal proportions.
ScRNA-seq was performed on the Chromium microfluidics platform (10x Genomics) using the 3’ gene expression (3’ GEX) V3.1 kit, targeting a recovery of 35,000 cells. Briefly, Gel-Bead in Emulsions (GEMs) were generated on the sample chip in the Chromium X system. Barcoded cDNA was extracted from the GEMs after Post-GEM RT-cleanup and amplified for 11 cycles. Full-length cDNA from poly-A mRNA transcripts underwent enzymatic fragmentation and size selection to optimize cDNA amplicon size (~400 bp) for library construction. The cDNA fragments were then subjected to end-repair, adapter ligation, and 10x-specific sample indexing according to the manufacturer’s protocol (10x Genomics). The concentration of the single-cell library was accurately quantified using qPCR (Kapa Biosystems) to achieve appropriate cluster counts for sequencing on the NovaSeq 6000 (Illumina), aiming for a sequencing depth of 25,000 reads per cell and 2,000 reads per CMO.

value: spleen

value: P14 (LCMV-specific CD8 T cell) mixed control and sgICOS

value: LCMV chronic infection (40DPI)

value: GDO


title: Col-0, mock, Rep2

description: Library name: WTN2

value: Mock


title: P14 terminal Tex ICOSneg #4

first: Dan

last: Filipescu

address: 1470 Madison Ave

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai

description:
Poly-A purified RNA, stranded
sorted P14 terminal Tex (CD45.1+ PD-1+ CD39+ CX3CR1neg)
TermDiff-sgICOS-2-2

data_processing:
Raw reads were quasi-mapped to the Gencode M25 (GRCm38.p6) gene set using salmon v.1.2.1 (Patro et al., 2017).
Assembly: Gencode M25 (GRCm38.p6)
Supplementary files format and content: .tar.gz - folder containing table of gene expression counts and TPM generated by salmon in .sf format

extract_protocol:
Cells were sorted in lysis reagent (QIAGEN). After addition of chloroform (Sigma) and centrifugation, RNA was isolated from the aqueous phase using an RNEasy Micro kit (QIAGEN).
1 ng RNA from 10,000 sorted cells was used as input for the NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina (NEB).

value: C57/BL6 P14 (LCMV-specific) primary CD8 T cell

value: terminal Tex

tag: genetic modification

value: Icos KO (Icos sgRNA #2)

tag: biological replicate

value: biol rep 2


title: P14 control and sgIcos_GEX

description: 10x Genomics, polyA RNA

tag: tissue

value: mRNA


title: Dhx16_fl5

value: Bone marrow

value: primary cell

value: Hematopoietic stem cells (HSC)


title: Col-0, mock, Rep1

description: Library name: WTN1

value: leaves

tag: treatment


title: HiC_BWX5230_30C_T10

tag: cell line

value: Bacillus subtilis PY79

value: Bacterial

value: parSdelta9 no a.b., -27degree parS no a.b., dnaB134 (ts) zhb-83::Tn917 (erm)

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted to 42degreeC for 45min, then shifted down to 30degreeC for 10min


title: P14 terminal Tex ICOSneg #3

description:
Poly-A purified RNA, stranded
sorted P14 terminal Tex (CD45.1+ PD-1+ CD39+ CX3CR1neg)
TermDiff-sgICOS-2-1

value: spleen

tag: cell type

value: biol rep 1


title: DLD-1 cells 1/3 RNase R

value: cell

value: Colorectal cancer

tag: genotype

value: WT

value: RNase R


title: PBMCs from NSCLC Patient Lu1032 ATAC (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_PBMC_Lu1032_ATAC

value: Blood

value: lung adenocarcinoma


title: sair1-1, mock, Rep2

description: Library name: BN2

value: Mock


title: PBMCs from NSCLC Patient Lu1027 ATAC (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_PBMC_Lu1027_ATAC


title: P14 terminal Tex ICOSneg #2

description:
Poly-A purified RNA, stranded
sorted P14 terminal Tex (CD45.1+ PD-1+ CD39+ CX3CR1neg)
TermDiff-sgICOS-1-2

value: C57/BL6 P14 (LCMV-specific) primary CD8 T cell

value: terminal Tex

value: Icos KO (Icos sgRNA #1)

value: biol rep 2

value: LCMV chronic infection (40DPI)


title: HiC_BWX5230_T0

value: Bacillus subtilis PY79

value: Bacterial

value: Cells were grown in CH medium at 30degreeC for 2h, then shifted up to 42degreeC for 45min


title: PBMCs from NSCLC Patient HD5 RNA (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_PBMC_HD5_RNA

molecule: nuclear RNA

value: healthy donor


title: PBMCs from NSCLC Patient Lu1024 ATAC (Multiome [RNA + ATAC])

description:
10x Genomics
hs_multiome_PBMC_Lu1024_ATAC