title: cdc42 WT

city: Gwangju

first: Changduk

last: Jun

state: Not US or Canada

address: Bukgu oryongdong GIST

department: life science

institute: Gwangju institute of science and technology(GIST)

description: Library name: sample1

data_processing:
Raw sequencing reads were processed using Cell Ranger v3.0.2 (10x Genomics). The `cellranger count` pipeline was used to perform read alignment, barcode processing, and UMI counting. Reads were aligned to the mm10 mouse reference genome using the STAR aligner. Normalization and downstream analysis were performed using Seurat.
Assembly: mouse mm10
Supplementary files format and content: count matrix, marker DEG and metadata

source_name: Thymus

extract_protocol:
Thymuses were isolated from mice and mechanically dissociated into single-cell suspensions. The dissociated cells were filtered through a 40 µm cell strainer using PBS to remove debris. Red blood cells (RBCs) were lysed using an RBC lysis buffer, followed by washing with PBS. The remaining cells were then resuspended in PBS containing 1 mM EDTA and 2% FBS to maintain cell viability and prevent aggregation.
Single-cell RNA sequencing (scRNA-seq) libraries were generated using the 10x Genomics Chromium platform according to the manufacturer’s protocol. Library preparation was performed using the Chromium Next GEM Single Cell 3ʹ Kit. The resulting cDNA libraries were amplified and sequenced on an Illumina HiSeq 2000 platform, generating paired-end reads.

value: Thymus

value: Thymocyte


title: cdc42 KO

status: Public on Jul 09 2025

type: SRA

country: South Korea

description: Library name: sample2

library_source: transcriptomic single cell

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell type


title: LCN2 KO-IMQ 2

city: Xi'an

first: Kaixuan

last: Ren

address: Huangcheng West Road

country: China

institute: Xi'an jiaotong University

description:
L1EHB2701290--KO_IMQ_2.R
raw_counts.txt

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 Hisat
Reads Per kilobase of exon per Megabase of library size (TPM) were calculated using a protocol from the standardized method developed by Wagner et al. (2012).
Assembly: mm8
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

source_name: skin

growth_protocol: All experimental animals were maintained in a specific pathogen-free (SPF) environment.

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 ribosome minus RNAseq protocols

treatment_protocol: To induce a psoriasis-like disease model, 5% imiquimod (IMQ) cream (Sichuan Mingxin Pharmaceuticals Co., China) or vehicle control was applied daily to the shaved back for a consecutive period of six days.

value: skin

tag: genotype

value: LCN2 knockdown

tag: treatment

value: IMQ


title: LCN2 KO-Control 3

description:
L1EHB2701296--KO_con_3.R
raw_counts.txt


title: LCN2 KO-Control 2

description:
L1EHB2701295--KO_con_2.R
raw_counts.txt


title: LCN2 KO-Control 1

description:
L1EHB2701294--KO_con_1.R
raw_counts.txt


title: Healthy donor HD_02, frozen bone marrow, bulk-ATAC-seq

status: Public on Jul 10 2025

city: Ulsan

first: Dayoung

last: Kim

address: 50 Unist-gil

institute: UNIST

description: Library name: bulkATAC_HD_02

library_source: genomic

data_processing:
5 bp sequence at 5' end, and primer sequence at 3' end were trimmed using in-house script.
ATAC-seq reads were aligned to UCSC hg38 genome using Bowtie version 2.5.3.
MACS2 version 2.2.9.1 was used to call ATAC-seq narrowPeaks.
bigWig files were generated using genomicRanges R package.
Supplementary files format and content: narrowPeak files containing all MACS2 called peaks from each ATAC-seq mapped reads.
Supplementary files format and content: Normalized bigWig file to visualize the mapped read in genome-wide tracks.

molecule: genomic DNA

organism: Homo sapiens

source_name: Bone marrow

extract_protocol:
Cells were thawed using 37C CTL wash buffer, and apoptotic cells were discarded using MACS Annexin-V microbead Kit.
50,000 cells were used as starting material for Omni-ATAC-seq. For each library, the amplification cycle was determined using qPCR, but not to exceed 16 cycles in total. Before sequencing, the libraries were size selected at 200 bp or longer to remove excessive primer dimers.

value: Bone marrow

tag: individual

tag: disease state

value: Whole bone marrow


title: WT-IMQ 2

description:
L1EHB2701284--WT_IMQ_2.R
raw_counts.txt

value: WT


title: WT-IMQ 1

description:
L1EHB2701283--WT_IMQ_1.R
raw_counts.txt


title: LCN2 KO-IMQ 1

description:
L1EHB2701289--KO_IMQ_1.R
raw_counts.txt


title: WT-Control 1

description:
L1EHB2701280--WT_con_1.R
raw_counts.txt


title: WT-Control 2

description:
L1EHB2701281--WT_con_2.R
raw_counts.txt


title: KO8_1

city: Shenzhen

first: Jin-Tang

last: Dong

state: Guangdong

address: 1088 Xueyuan Blvd.

institute: Southern University of Science  and Technology

description:
Library name: sample4
Column name in TPMs_all_Samples.txt: KO8_1

data_processing:
Illumina Casava1.7 software used for basecalling.
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4). After that, Ericscript (v0.5.5) and rMATS (V3.2.5) were used to fusion genes and differential splicing genes (DSGs), respectively. Bowtie2 (v2.2.5) was applied to align the clean reads to the gene set, a database for this organism built by BGI, which known and novel, coding transcripts were included, then expression level of gene was calculated by RSEM (v1.2.12). Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05.
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: tab-delimited  text  file  includes  TPMs  for  each  Sample

extract_protocol:
Remove the supernatant and wash with PBS, 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.
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and pair end 150 bases reads were generated on MGI2000 platform (BGI-Shenzhen, China).

tag: cell line

value: prostate cancer cells

value: ZFHX3 knockout


title: WT-Control 3

description:
L1EHB2701282--WT_con_3.R
raw_counts.txt


title: CTL_2257

type: genomic

city: Washington

first: Kristen

last: Kocher

state: DC

address: 111 Michigan Ave NW

country: USA

institute: Children's National Hospital

description:
n/a
previously submitted in GSE229463
iScan

hyb_protocol: Illumina Methylation EPIC array (v1 and v2) kit

scan_protocol: iScan or NextSeq 550 with beadchip adapter

data_processing:
R/Rstudio (ChAMP, minfi, limma)
functional normalization of beta values extracted from raw idat files (XY, SNPs, cross-reactive probes filtered out)

label: other

source_name: buccal

label_protocol: cohort_patient ID

extract_protocol: buccal swabs were collected from newborns within the first month of life (using OC-175 pediatric buccal swabs, Genotek) and DNA was extracted using the L2Prep-It Kit (Genotek)

value: buccal

tag: Sex

value: F


title: CTL_2239

value: M


title: CTL_2238


title: CTL_2253


title: CTL_2230


title: CTl_2235


title: CTL_2227


title: testis, ICR, RNA-seq, rep1

city: Badalona

first: Tanya

last: Vavouri

state: BARCELONA

address: Ctra de Can Ruti, Cami de les Escoles, s/n

country: Spain

institute: Josep Carreras Leukemia Research Institute

description:
Library name: sample01
piRNAcluster_normCounts_ICR_RNAseq.tsv

data_processing:
Reads were mapped using HISAT2. For inbred strains, RNA-seq data was mapped to the indicated inbred strain genome. For samples from the outbred strain ICR, RNA-seq data was mapped to the reference mouse genome GRCm38/mm10.
Assembly: BL6 (GRCm38/mm10), C3H (C3H_HeJ_v1), 129S1 (129S1_SvImJ_v1), NOD (NOD_ShiLtJ_v1), CAST (CAST_EiJ_v1)
Supplementary files format and content: TSV file. DESeq2-normalized counts of reads mapping to piRNA clusters from Li et al. (2013)

source_name: testis

extract_protocol:
RNA was isolated using TRIzol® Reagent (Invitrogen) according to manufacturer's instructions.
RNA was sequenced using TruSeq Stranded Total RNA with Ribo-Zero H/M/R_Gold libraries. For spermatogonia samples, polyA molecules were selected.

value: testis

value: ICR

tag: batch


title: CTL_2217

description:
n/a
previously submitted in GSE229463
nextseq550_w_beadchip_adapter


title: CTL_2222


title: CTL_2216


title: CHD_2296

description:
2V
nextseq550_w_beadchip_adapter

value: DORV


title: CHD_2287

description:
SV
nextseq550_w_beadchip_adapter

value: HLHS


title: CHD_2298

description:
2V
nextseq550_w_beadchip_adapter

value: TOF


title: CHD_2293

description:
2V_TGA
nextseq550_w_beadchip_adapter

value: TGA


title: CHD_2294

description:
2V
nextseq550_w_beadchip_adapter

value: CoA


title: CHD_2284

description:
2V
nextseq550_w_beadchip_adapter

value: CAVC


title: WT-IMQ 3

description:
L1EHB2701286--WT_IMQ_3.R
raw_counts.txt

value: skin

value: IMQ


title: CHD_2282

description:
2V_TGA
nextseq550_w_beadchip_adapter


title: CHD_2278

description:
SV
nextseq550_w_beadchip_adapter


title: CHD_2275

description:
2V
nextseq550_w_beadchip_adapter


title: CTL_2246


title: CHD_2274

description:
SV
nextseq550_w_beadchip_adapter

value: TA


title: CHD_2272

description:
2V
nextseq550_w_beadchip_adapter

value: Shone's


title: CHD_2271

description:
2V_TGA
nextseq550_w_beadchip_adapter


title: CHD_2273

description:
2V_TGA
nextseq550_w_beadchip_adapter


title: CTL_2224


title: CHD_2269

description:
2V_TGA
nextseq550_w_beadchip_adapter


title: CHD_2268

description:
2V
nextseq550_w_beadchip_adapter

value: IAA VSD


title: CHD_2263

description:
2V
nextseq550_w_beadchip_adapter

value: Truncus


title: CHD_2255

description:
2V_TGA
iScan

value: buccal


title: CHD_2256

description:
SV
iScan

value: F


title: CHD_2262

description:
SV
nextseq550_w_beadchip_adapter

value: PA


title: CHD_2260

description:
2V
iScan


title: CHD_2250

description:
SV
iScan

value: M

value: HRH


title: CHD_2265

description:
SV
nextseq550_w_beadchip_adapter


title: CHD_2266

description:
SV
nextseq550_w_beadchip_adapter


title: CHD_2240

description:
SV
iScan


title: CHD_2232

description:
SV
iScan


title: CHD_2254

description:
2V_TGA
iScan


title: CHD_2229

description:
2V_TGA
iScan


title: CHD_2226

description:
2V
iScan


title: CHD_2242

description:
2V_TGA
iScan


title: CHD_2223

description:
SV
iScan


title: CHD_2276

description:
2V
nextseq550_w_beadchip_adapter


title: CHD_2280

description:
SV
nextseq550_w_beadchip_adapter


title: SCI, Vehicle, mucosa,rep3

city: Boston

first: Ali

last: Hashemi Gheinani

address: 300 Longwood

department: Urology

institute: Boston Children's Hospital

description:
Library name: Sample 18
SCI, Vehicle, mucosa,rep3

data_processing:
Raw RNA sequencing data in FASTQ format were processed using a standardized computational pipeline. Quality control of raw reads was first assessed using FastQC v0.11.9, and summary reports were compiled using MultiQC v1.13. Adapter sequences and low-quality bases were trimmed if necessary using Trim Galore v0.6.10 (optional step, not applied in our case).  The rat reference genome and gene annotation files were obtained from Ensembl (release 109, Rattus norvegicus Rnor_6.0). The genome FASTA (Rattus_norvegicus.Rnor_6.0.dna.toplevel.fa) and GTF annotation (Rattus_norvegicus.Rnor_6.0.109.gtf) were used to build the STAR genome index.  Reads were aligned to the rat reference genome using STAR v2.7.10a with the following parameters: --runThreadN 8, --outSAMtype BAM SortedByCoordinate, --readFilesCommand zcat, and --quantMode GeneCounts TranscriptomeSAM. STAR also outputs a transcriptome-aligned BAM for downstream transcript quantification if needed. For each sample, paired-end reads were aligned, and resulting BAM files were sorted and indexed using SAMtools v1.17.  Gene-level quantification was performed using featureCounts v2.0.3 from the Subread package. Aligned BAM files were processed using the corresponding Ensembl GTF file to generate a matrix of read counts per gene. Only uniquely aligned, properly paired reads were included in the analysis.
Assembly: All RNA-seq reads were aligned to the Rattus norvegicus reference genome assembly Rnor_6.0, as provided by Ensembl (release 109). The corresponding genome FASTA file (Rattus_norvegicus.Rnor_6.0.dna.toplevel.fa) and gene annotation file in GTF format (Rattus_norvegicus.Rnor_6.0.109.gtf) were used for genome indexing and read alignment. This assembly provides high-quality coverage and annotation for both coding and non-coding transcripts and is the current standard reference for Rattus norvegicus transcriptome analyses.
Supplementary files format and content: Tab-delimited text files containing raw read counts for each gene across all samples

organism: Rattus norvegicus

source_name: mucosa of urinary bladder

extract_protocol:
Tissues were lysed in TRIzol (Thermofisher) using Fast Prep Lysing matrix D beads (MP Biomedical). RNA was isolated and purified from the tissue lysates using miRNeasy columns (Qiagen) according to the manufacturer’s instructions. Multimodal RNA quantification and quality control was performed using NanoDrop (Thermofisher), Qubit RNA Broad-Range Assay kit (Thermofisher), and Agilent 2100 Bioanalyzer (Agilent).
Ribosomal RNA depletion and stranded RNA sequencing libraries were prepared using the KAPA Stranded RNA-Seq Kit with RiboErase (HMR) (Roche/KAPA Biosystems, Cat. No. KK8483 or KK8484), following the manufacturer’s instructions. This kit enables depletion of cytoplasmic (5S, 5.8S, 18S, 28S) and mitochondrial (12S, 16S) rRNA species from 100 ng to 1 µg of total RNA using a hybridization-based approach coupled with RNase H and DNase treatments. Following rRNA depletion, RNA was fragmented using heat and magnesium, and first-strand cDNA was synthesized with random priming. Second-strand synthesis incorporated dUTP to enable strand specificity. After A-tailing and ligation of indexed adapters compatible with Illumina platforms, libraries were PCR-amplified using KAPA HiFi HotStart ReadyMix to ensure high fidelity and low amplification bias.

value: mucosa of urinary bladder

value: WT

value: vehicle


title: SCI, Vehicle, mucosa,rep2

description:
Library name: Sample 17
SCI, Vehicle, mucosa,rep2


title: SCI, Vehicle, detrusor,rep3

description:
Library name: Sample 15
SCI, Vehicle, detrusor,rep3

source_name: detrusor of urinary bladder

value: detrusor of urinary bladder


title: SCI, Vehicle, mucosa,rep1

description:
Library name: Sample 16
SCI, Vehicle, mucosa,rep1


title: SCI, Inosine, mucosa,rep3

description:
Library name: Sample 12
SCI, Inosine, mucosa,rep3

value: inosine


title: SCI, Inosine, mucosa,rep1

description:
Library name: Sample 10
SCI, Inosine, mucosa,rep1


title: Amplicon sequencing of primer 4 (L1PA2-6) in human liver

city: Mainz

first: Marcel

last: Misak

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology (IMB)

description: Library name: Sample 4

data_processing:
Raw read quality was assessed with FASTQC v.0.11.8 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc) and reads were subsequently mapped to the hg38 human reference genome using Bowtie v.2.3.4 (http://bowtie-bio.sourceforge.net/bowtie2) with options “--very-sensitive --end-to-end --fr --maxins 1000”. Read pairs were filtered with SAMtools v1.17 (http://www.htslib.org) to retain only uniquely aligned fragments, and a BED file was compiled from intervals supported by at least three fragments in either the filtered or unfiltered alignments. These intervals were designated “amplified loci” and intersected with each of the four previously generated annotation tracks.
Assembly: hg38
Supplementary files format and content: BED files containing experimentally validated genomic regions amplified by the respective primers

source_name: Human liver cells

extract_protocol:
Genomic DNA from human liver cells was obtained from a commercial supplier (Amsbio CD563105).
DNA library preparation was performed using the NEBNext Ultra II DNA Library Prep Kit from Illumina (Version 6.0, 3/20).

value: Human liver cells


title: Amplicon sequencing of primer 2 (L1PA2-3) in human liver

description: Library name: Sample 2


title: Amplicon sequencing of primer 1 (L1HS/L1PA2) in human liver

description: Library name: Sample 1


title: Amplicon sequencing of primer 5 (L1PA16) in human liver

description: Library name: Sample 5


title: Amplicon sequencing of primer 3 (L1PA4-5) in human liver

description: Library name: Sample 3


title: SCI, Inosine, mucosa,rep2

description:
Library name: Sample 11
SCI, Inosine, mucosa,rep2


title: SCI, Inosine, detrusor,rep3

description:
Library name: Sample 9
SCI, Inosine, detrusor,rep3


title: Amplicon sequencing of primer 6 (L1PA17) in human liver

description: Library name: Sample 6


title: SCI, Inosine, detrusor,rep2

description:
Library name: Sample 8
SCI, Inosine, detrusor,rep2


title: control, mucosa,rep1

description:
Library name: Sample 4
control, mucosa,rep1


title: SCI, Inosine, detrusor,rep1

description:
Library name: Sample 7
SCI, Inosine, detrusor,rep1


title: control, mucosa,rep3

description:
Library name: Sample 6
control, mucosa,rep3


title: control, detrusor,rep3

description:
Library name: Sample 3
control, detrusor,rep3


title: control, detrusor,rep1

description:
Library name: Sample 1
control, detrusor,rep1


title: bladder,SCI,8weeks,R8,rep3

description:
Library name: Sample 18
bladder,SCI,8weeks,R8,rep3

data_processing:
Raw RNA sequencing data in FASTQ format were processed using a standardized computational pipeline. Quality control of raw reads was first assessed using FastQC v0.11.9, and summary reports were compiled using MultiQC v1.13. Adapter sequences and low-quality bases were trimmed if necessary using Trim Galore v0.6.10 (optional step, not applied in our case).  The rat reference genome and gene annotation files were obtained from Ensembl (release 109, Rattus norvegicus Rnor_6.0). The genome FASTA (Rattus_norvegicus.Rnor_6.0.dna.toplevel.fa) and GTF annotation (Rattus_norvegicus.Rnor_6.0.109.gtf) were used to build the STAR genome index.  Reads were aligned to the rat reference genome using STAR v2.7.10a with the following parameters: --runThreadN 8, --outSAMtype BAM SortedByCoordinate, --readFilesCommand zcat, and --quantMode GeneCounts TranscriptomeSAM. STAR also outputs a transcriptome-aligned BAM for downstream transcript quantification if needed. For each sample, paired-end reads were aligned, and resulting BAM files were sorted and indexed using SAMtools v1.17.  Gene-level quantification was performed using featureCounts v2.0.3 from the Subread package. Aligned BAM files were processed using the corresponding Ensembl GTF file to generate a matrix of read counts per gene. Only uniquely aligned, properly paired reads were included in the analysis.
Assembly: All RNA-seq reads were aligned to the Rattus norvegicus reference genome assembly Rnor_6.0, as provided by Ensembl (release 109). The corresponding genome FASTA file (Rattus_norvegicus.Rnor_6.0.dna.toplevel.fa) and gene annotation file in GTF format (Rattus_norvegicus.Rnor_6.0.109.gtf) were used for genome indexing and read alignment. This assembly provides high-quality coverage and annotation for both coding and non-coding transcripts and is the current standard reference for Rattus norvegicus transcriptome analyses.
Supplementary files format and content: ab-delimited text files containing raw read counts for each gene across all samples

source_name: full thickness urinary bladder

value: full thickness urinary bladder

value: full thickness bladder


title: bladder,SCI,16weeks,R1,rep1

description:
Library name: Sample 19
bladder,SCI,16weeks,R1,rep1


title: control, detrusor,rep2

description:
Library name: Sample 2
control, detrusor,rep2


title: bladder,SCI,16weeks,R4,rep3

description:
Library name: Sample 21
bladder,SCI,16weeks,R4,rep3


title: SCI, Vehicle, detrusor,rep2

description:
Library name: Sample 14
SCI, Vehicle, detrusor,rep2


title: bladder,SCI,16weeks,R2,rep2

description:
Library name: Sample 20
bladder,SCI,16weeks,R2,rep2


title: SCI, Vehicle, detrusor,rep1

description:
Library name: Sample 13
SCI, Vehicle, detrusor,rep1


title: bladder,SCI,8weeks,R12,rep2

description:
Library name: Sample 17
bladder,SCI,8weeks,R12,rep2


title: bladder,SCI,8weeks,R10,rep1

description:
Library name: Sample 16
bladder,SCI,8weeks,R10,rep1


title: bladder,SCI,2weeks,R20,rep3

description:
Library name: Sample 15
bladder,SCI,2weeks,R20,rep3


title: control, mucosa,rep2

description:
Library name: Sample 5
control, mucosa,rep2


title: bladder,control,16weeks,C23_2,rep2

description:
Library name: Sample 11
bladder,control,16weeks,C23_2,rep2


title: bladder,control,16weeks,C23_1,rep1

description:
Library name: Sample 10
bladder,control,16weeks,C23_1,rep1


title: bladder,control,8weeks,C15_2,rep2

description:
Library name: Sample 8
bladder,control,8weeks,C15_2,rep2


title: bladder,control,2weeks,C9_3,rep3

description:
Library name: Sample 6
bladder,control,2weeks,C9_3,rep3


title: bladder,control,16weeks,C23_3,rep3

description:
Library name: Sample 12
bladder,control,16weeks,C23_3,rep3


title: bladder,SCI,2weeks,R15,rep2

description:
Library name: Sample 14
bladder,SCI,2weeks,R15,rep2


title: bladder,SCI,2weeks,R14,rep1

description:
Library name: Sample 13
bladder,SCI,2weeks,R14,rep1


title: CHD_2243

description:
SV
iScan

value: HLHS


title: bladder,control,8weeks,C15_1,rep1

description:
Library name: Sample 7
bladder,control,8weeks,C15_1,rep1


title: bladder,control,8weeks,C15_3,rep3

description:
Library name: Sample 9
bladder,control,8weeks,C15_3,rep3


title: bladder,control,2weeks,C9_2,rep2

description:
Library name: Sample 5
bladder,control,2weeks,C9_2,rep2


title: 43_T0_2

city: Ramat-Gan

first: Ilana

last: Lebenthal-Loinger

address: Bar-Ilan University

department: The Mina & Everard Goodman Faculty of Life Sciences

country: Israel

institute: Bar-Ilan University

description:
Library name: sample 5
S5

data_processing:
Reads were aligned to P. aeruginosa PAO1 strain ( assembly GCF_000006765.1 ) using the bowtie2 aligner software (v2.3.2)
Raw read counts for 5708 gene-level features were determined using HTSeq-count with the intersection-strict mode
Normalized read counts were generated using  R Bioconductor package DESeq2
Assembly: P. aeruginosa PAO1 - GCF_000006765.1
Supplementary files format and content: tab-delimited text file includes DESeq2 normalized counts

organism: Pseudomonas aeruginosa PAO1

source_name: Bacterial cell

growth_protocol: Overnight bacterial cultures cultivated at either 37 °C or 43 °C were diluted 1:100 into fresh LB medium and cultured until reaching an optical density (OD) of 0.6 at 595nm from each sample

extract_protocol:
90 mg/mL Lysozyme (Roche), 10 mL Proteinase K (Qiagen), and 1 mL warm Tri-reagent 37°C (Sigma) were added to pelleted cells. After 5 min of incubation at 65°C, 200 mL chloroform was added. The solution was centrifuged for 15 min at 20,817 g, and the upper liquid phase was transferred into 80% ethanol. The RNA was then extracted using an RNeasy minikit (Qiagen) according to the manufacturer's protocol.
The library was constructed with NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (NEB) according to the manufacturer's instructions using 30 ng of depleted RNA.

value: Bacterial cell

value: Initial growth at 43 C, no recovery replicate 2


title: bladder,control,0weeks,C7_3,rep3

description:
Library name: Sample 3
bladder,control,0weeks,C7_3,rep3


title: bladder,control,0weeks,C7_1,rep1

description:
Library name: Sample 1
bladder,control,0weeks,C7_1,rep1


title: 37_T18_1

description:
Library name: sample 7
S7

value: Initial growth at 37 C, 18hr recovery replicate 1


title: bladder,control,0weeks,C7_2,rep2

description:
Library name: Sample 2
bladder,control,0weeks,C7_2,rep2


title: 43_T0_3

description:
Library name: sample 6
S6

value: Initial growth at 43 C, no recovery replicate 3


title: 37_T0_2

description:
Library name: sample 2
S2

value: Initial growth at 37 C, no recovery replicate 2


title: 37_T0_3

description:
Library name: sample 3
S3

value: Initial growth at 37 C,no recovery replicate 3


title: 43_T54_3

description:
Library name: sample 18
S18

value: Initial growth at 43 C, 54hr recovery replicate 3


title: Sample 32 Control, Ventral, 22 month

city: Moscow

first: Vasiliy

last: Akimov

email: VAkimov@cspfmba.ru, vasoakim@gmail.com

address: Pogodinskaya Street, 10, bld. 1

country: Russia

institute: Centre for Strategic Planning of FMBA of Russia

description:
Library name: Sample 32
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: ventral part of the hippocampus

extract_protocol:
Mouse dorsal and ventral hippocampus were dissected and incubated in RNAprotect Tissue Reagent (QIAGEN) at +4℃ overnight, after RNAprotect was removed samples were stored at −80°C. Nuclei were isolated separately from fresh frozen dorsal and ventral hippocampus with Chromium Nuclei Isolation Kit with RNase Inhibitor (10x Genomics) according to the Single Cell Gene Expression & Chromium Fixed RNA Profiling protocol (CG000505 Rev A). From 4 to 11 mg of tissue were used to isolate nuclei for each sample, after which nuclei were quantified using trypan blue solution 0.4% on a Countess II FL Automated Cell Counter (Thermo Fisher Scientific Inc.).
snRNAseq libraries were prepared from 16 500 nuclei for each sample using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10x Genomics) according to the manufacturer's instructions (CG000204 Rev D, CG000315 Rev F). Quality control of prepared libraries was measured using Qubit 4.0 Flourometer (Thermo Fisher Scientific Inc.) and Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific Inc.), 4200 TapeStation System (Agilent Technologies, Inc.) and D1000 ScreenTape, D1000 Reagents (Agilent Technologies, Inc.) kits. Sequencing was performed on NovaSeq6000 and NextSeq2000 platforms (Illumina, Inc.) with a recommended coverage of 20 thousand read pairs per 1 cell, an average of 200 million read pairs per 1 sample.

value: ventral part of the hippocampus

value: Hippocampal cells

tag: age

value: 22 month old

value: male

value: Wild type


title: Sample 29 5xFAD, Dorsal, 16 month

description:
Library name: Sample 29
10x Genomics

source_name: dorsal part of the hippocampus

value: dorsal part of the hippocampus

value: 16 month old


title: 43_T54_2

description:
Library name: sample 17
S17

value: Initial growth at 43 C, 54hr recovery replicate 2


title: Sample 30 5xFAD, Ventral, 16 month

description:
Library name: Sample 30
10x Genomics


title: 37_T0_1

description:
Library name: sample 1
S1

value: Initial growth at 37 C, no recovery replicate 1


title: Sample 28 Control, Ventral, 16 month

description:
Library name: Sample 28
10x Genomics


title: 43_T0_1

description:
Library name: sample 4
S4

value: Initial growth at 43 C, no recovery replicate 1


title: 37_T18_2

description:
Library name: sample 8
S8

value: Bacterial cell

value: Initial growth at 37 C, 18hr recovery replicate 2


title: bladder,control,2weeks,C9_1,rep1

description:
Library name: Sample 4
bladder,control,2weeks,C9_1,rep1

value: full thickness urinary bladder

value: full thickness bladder

value: WT


title: Sample 27 Control, Dorsal, 16 month

description:
Library name: Sample 27
10x Genomics


title: 37_T54_3

description:
Library name: sample 15
S15

value: Initial growth at 37 C, 54hr recovery replicate 3


title: 37_T54_2

description:
Library name: sample 14
S14

value: Initial growth at 37 C, 54hr recovery replicate 2


title: Sample 25 5xFAD, Dorsal, 22 month

description:
Library name: Sample 25
10x Genomics


title: 43_T54_1

description:
Library name: sample 16
S16

value: Initial growth at 43 C, 54hr recovery replicate 1


title: Sample 23 5xFAD, Dorsal, 22 month

description:
Library name: Sample 23
10x Genomics

value: Hippocampal cells


title: Sample 26 5xFAD, Ventral, 22 month

description:
Library name: Sample 26
10x Genomics

value: ventral part of the hippocampus

value: 22 month old


title: 43_T18_3

description:
Library name: sample 12
S12

value: Initial growth at 43 C, 18hr recovery replicate 3


title: 43_T18_2

description:
Library name: sample 11
S11

value: Initial growth at 43 C, 18hr recovery replicate 2


title: 37_T54_1

description:
Library name: sample 13
S13

value: Initial growth at 37 C, 54hr recovery replicate 1


title: Sample 21 Control, Dorsal, 22 month

description:
Library name: Sample 21
10x Genomics

value: dorsal part of the hippocampus

value: male

value: Wild type


title: 43_T18_1

description:
Library name: sample 10
S10

value: Bacterial cell

value: Initial growth at 43 C, 18hr recovery replicate 1


title: 37_T18_3

description:
Library name: sample 9
S9

value: Initial growth at 37 C, 18hr recovery replicate 3


title: Sample 22 Control, Ventral, 22 month

description:
Library name: Sample 22
10x Genomics


title: Sample 18 5xFAD, Ventral, 16 month

description:
Library name: Sample 18
10x Genomics

value: 16 month old


title: Sample 20 5xFAD, Ventral, 16 month

description:
Library name: Sample 20
10x Genomics


title: Sample 31 Control, Dorsal, 22 month

description:
Library name: Sample 31
10x Genomics


title: Sample 16 Control, Ventral, 16 month

description:
Library name: Sample 16
10x Genomics


title: S12

city: Manchester

first: Cathy

last: Tournier

address: Dover Street

department: Division of Cancer Sciences

country: United Kingdom

institute: The University of Manchester

description: Library name: S12

data_processing:
Briefly, fastp software (v0.20.0) was used to trim adaptor and remove low quality reads to get high quality clean reads. STAR software (v2.7.9a) was used to align the high-quality clean reads to the human reference genome (hg38). featureCounts software (v2.0) was used to get the raw gene levels with Ensembl GTF file (v104).
Assembly: GRCh38/hg38
Supplementary files format and content: raw counts and annotations in excel

extract_protocol:
Briefly, total RNA was extracted using Trizol Reagent (ThermoFisher, 15596026). The mRNAs were  purified using a NEBNext Poly(A) mRNA Magnetic Isolation Module Kit (NEB, E7490) according to the user manual.
mRNA libraries were constructed by using Illumina TrueSeq mRNA sample preparation kit (Cat. No. RS-122-2101) according to the manufacturer’s instructions. Library sequencing  was performed on an Illumina NovaSeq 6000 instrument with paired end reads.


title: Sample 17 5xFAD, Dorsal, 16 month

description:
Library name: Sample 17
10x Genomics


title: S13

description: Library name: S13


title: S15

description: Library name: S15

value: DMSO


title: Sample 15 Control, Dorsal, 16 month

description:
Library name: Sample 15
10x Genomics


title: Sample 19 5xFAD, Dorsal, 16 month

description:
Library name: Sample 19
10x Genomics


title: Sample 24 5xFAD, Ventral, 22 month

description:
Library name: Sample 24
10x Genomics


title: Sample 14 Control, Ventral, 16 month

description:
Library name: Sample 14
10x Genomics


title: S11

description: Library name: S11


title: S10

description: Library name: S10


title: Sample 13 Control, Dorsal, 16 month

description:
Library name: Sample 13
10x Genomics


title: Sample 10 Control, Ventral, 8 month

description:
Library name: Sample 10
10x Genomics

value: 8 month old


title: Sample 9 Control, Dorsal, 8 month

description:
Library name: Sample 9
10x Genomics


title: S14

description: Library name: S14


title: S8

description: Library name: S8


title: S5

description: Library name: S5


title: S9

description: Library name: S9


title: S7

description: Library name: S7


title: Sample 11 Control, Dorsal, 8 month

description:
Library name: Sample 11
10x Genomics


title: S2

description: Library name: S2


title: Sample 8 5xFAD, Ventral, 8 month

description:
Library name: Sample 8
10x Genomics


title: Sample 7 5xFAD, Dorsal, 8 month

description:
Library name: Sample 7
10x Genomics


title: Sample 5 5xFAD, Dorsal, 8 month

description:
Library name: Sample 5
10x Genomics


title: Sample 1 Control, Dorsal, 8 month

description:
Library name: Sample 1
10x Genomics


title: OCI-LY1 shRGC32-02

city: Jinan

first: xiyuan

last: zhang

state: Shandong

address: No.324, Jingwu Road

institute: Shandong Provincial Hospital, Shandong University

description:
Library name: Sample5
RGC32 knockdown

data_processing:
RNA-Seq
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5。
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. 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: hg38
Supplementary files format and content: A table containing the fpkm values of each sample

growth_protocol: OCI-LY1 cells were maintained in IMDM medium (Gibco, CA, USA) containing 10% fetal bovine serum (Gibco, CA, USA) under standard culture conditions (37°C, 5% CO2 humidified atmosphere).

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

value: Diffuse large B-cell lymphoma


title: OCI-LY1 shControl-03

description:
Library name: Sample3
Control


title: OCI-LY1 shRGC32-01

description:
Library name: Sample4
RGC32 knockdown


title: LLC, Rag1-/-, rep22

city: Shanghai

first: Minlin

last: Jiang

address: SiPing Road NO.1239

institute: Tongji University

description:
Library name: LLC-41
In mageck count, counts for all Rag1-/- group samples were set as replicates and therefore integrated into the Rag1-/- column.

data_processing:
cutadapt (version 4.2) was used to trim adaptor sequences and removed untrimmed reads.
Sequences that after 20-base gRNAs were cut using fastx-toolkit (version 0.0.14).
MAGeCK (version 0.5.9) was used to map gRNAs to reference annotation and generate read count tables. The default parameters were used. By applying the median normalization, we normalized count tables with the count function of MAGeCK. The MAGeCK's test function was utilized for significance testing of changes across different conditions.
Assembly: A customized CRISPR library comprising 3689 sgRNAs.
Supplementary files format and content: tab-delimited text files includes integrated raw counts of replicates for each group.
Library strategy: CRISPR Screen

source_name: Lewis lung carcinoma (LLC)

growth_protocol: LLC and KP cells were cultured in 10% FBS contained DMEM (Gibco) and RPMI 1640 Medium (Gibco) respectively. All cells were routinely tested negative for mycoplasma cytoplasma before use. For in vivo screen, both C57BL/6 wild type mice and C57BL/6 Rag1-/- mice were used. After two weeks of in vitro expansion, transduced LLC/KP-Cas9 cells were injected subcutaneously into the mice.

extract_protocol:
Tumors were harvested when they reached approximately 1000 mm3 in size. The QIAamp DNA Mini Kit (Qiagen) was used for genomic DNA extraction, followed by PCR for sgRNA amplification and NGS sequencing.
Using RNA-seq data from 22 patients, we identified DEGs associated with immunotherapy efficacy through edgeR. A total of 394 genes were significantly downregulated in DCR patients, with |LogFC|>1, p-value<0.05. These human genes were subsequently converted to their mouse orthologs, resulting in 332 mouse genes. For each gene, 6-10 sgRNAs were designed, culminating in a customized CRISPR library comprising 3689 sgRNAs.

treatment_protocol: Mice in each group were treated with either anti-PD-1 antibody or isotype IgG control two or three times per week from the seventh day after tumor cell implantation.

value: Lewis lung carcinoma (LLC)

value: Mouse lung cancer

value: IgG


title: S1

description: Library name: S1


title: Sample 3 5xFAD, Dorsal, 8 month

description:
Library name: Sample 3
10x Genomics

value: Hippocampal cells


title: LLC, Rag1-/-, rep21

description:
Library name: LLC-40
In mageck count, counts for all Rag1-/- group samples were set as replicates and therefore integrated into the Rag1-/- column.


title: OCI-LY1 shRGC32-03

description:
Library name: Sample6
RGC32 knockdown


title: OCI-LY1 shControl-02

description:
Library name: Sample2
Control


title: LLC, Rag1-/-, rep19

description:
Library name: LLC-38
In mageck count, counts for all Rag1-/- group samples were set as replicates and therefore integrated into the Rag1-/- column.


title: LLC, Rag1-/-, rep20

description:
Library name: LLC-39
In mageck count, counts for all Rag1-/- group samples were set as replicates and therefore integrated into the Rag1-/- column.


title: S6

description: Library name: S6


title: LLC, Rag1-/-, rep14

description:
Library name: LLC-33
In mageck count, counts for all Rag1-/- group samples were set as replicates and therefore integrated into the Rag1-/- column.


title: LLC, Rag1-/-, rep18

description:
Library name: LLC-37
In mageck count, counts for all Rag1-/- group samples were set as replicates and therefore integrated into the Rag1-/- column.


title: OCI-LY1 shControl-01

description:
Library name: Sample1
Control


title: LLC, Rag1-/-, rep13

description:
Library name: LLC-32
In mageck count, counts for all Rag1-/- group samples were set as replicates and therefore integrated into the Rag1-/- column.


title: Sample 4 5xFAD, Ventral, 8 month

description:
Library name: Sample 4
10x Genomics

value: ventral part of the hippocampus


title: EGCG-2

city: Suzhou

first: Rui

middle: xing

last: Hou

state: Jiangsu

address: No.5, Tayun Road, Wuzhong District

department: Key Laboratory of Hand Surgery

institute: Suzhou Ruihua Orthopedic Hospital

description: Library name: sample 2

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include readcount values for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: skin epidermal stem cells

growth_protocol: Epidermal stem cells (EpSCs) were isolated from human skin and cultured with KGM2 at 37°C in a 5% CO₂ incubator.

extract_protocol:
Total RNA was extracted from EpSCs treated with 2 μM EGCG or PBS using TRIzol reagent (Invitrogen).
RNA-seq

treatment_protocol: EpSCs were treated with 2 μM epigallocatechin gallate (EGCG) or an equal volume of PBS for 3 days.

value: skin epidermal stem cells

value: 2 μM epigallocatechin gallate (EGCG),3 days


title: NC-3

description: Library name: sample 6

value: PBS, 3 days


title: Sample 6 5xFAD, Ventral, 8 month

description:
Library name: Sample 6
10x Genomics

value: male


title: LLC, Rag1-/-, rep11

description:
Library name: LLC-30
In mageck count, counts for all Rag1-/- group samples were set as replicates and therefore integrated into the Rag1-/- column.


title: S3

description: Library name: S3


title: LLC, Rag1-/-, rep12

description:
Library name: LLC-31
In mageck count, counts for all Rag1-/- group samples were set as replicates and therefore integrated into the Rag1-/- column.


title: LLC, Rag1-/-, rep10

description:
Library name: LLC-29
In mageck count, counts for all Rag1-/- group samples were set as replicates and therefore integrated into the Rag1-/- column.


title: scRNAseq PT11_VDJ

city: Nashville

first: Justin

last: Balko

state: TN

address: 658 Preston Research Building

institute: Vanderbilt University

description:
Library name: DFCI_VDJ9
TCRseq, VDJ reads

data_processing:
Assembly: Human Hg38
Demutiplexing, barcoading, and gene count extraction was performed using CellRanger software
Supplementary files format and content: CellRanger output: Tab-separated values and matrix
Library strategy: TCR-Seq

source_name: PBMC

extract_protocol:
CITEseq+TCRseq: single cell RNA and TCR sequencing was performed on longitudinal peripheral blood immune cells collected from HR+ breast cancer patients treated with immune checkpoint inhibitors. Red blood cell lysis and magnetic bead dead cell removal was performed on cyroperserved PBMCs prior to RNA extraction and library preparation.
Samples (targeting 15,000 cells/sample for processing and 10,000 cells/sample for sequencing) will be processed for single cell 5' RNA, V(D)J, and Feature Barcode sequencing utilizing the 10X Chromium system. Sequencing will be performed on the Illumina NovaSeq 6000 targeting 50,000 reads per cell for the 5 assay and 5,000 reads per cell for the V(D)J and Feature Barcode assays.

value: PBMC


title: LLC, Rag1-/-, rep17

description:
Library name: LLC-36
In mageck count, counts for all Rag1-/- group samples were set as replicates and therefore integrated into the Rag1-/- column.


title: LLC, Rag1-/-, rep9

description:
Library name: LLC-28
In mageck count, counts for all Rag1-/- group samples were set as replicates and therefore integrated into the Rag1-/- column.


title: NC-2

description: Library name: sample 5


title: LLC, Rag1-/-, rep15

description:
Library name: LLC-34
In mageck count, counts for all Rag1-/- group samples were set as replicates and therefore integrated into the Rag1-/- column.


title: scRNAseq Week3_VDJ

description:
Library name: DFCI_VDJ6
TCRseq, VDJ reads


title: EGCG-1

description: Library name: sample 1


title: EGCG-3

description: Library name: sample 3


title: scRNAseq Week1_VDJ

description:
Library name: DFCI_VDJ11
TCRseq, VDJ reads


title: scRNAseq PT15_VDJ

description:
Library name: DFCI_VDJ5
TCRseq, VDJ reads


title: LLC, Rag1-/-, rep16

description:
Library name: LLC-35
In mageck count, counts for all Rag1-/- group samples were set as replicates and therefore integrated into the Rag1-/- column.


title: NC-1

description: Library name: sample 4


title: scRNAseq PT5_VDJ

description:
Library name: DFCI_VDJ10
TCRseq, VDJ reads


title: LLC, Rag1-/-, rep5

description:
Library name: LLC-24
In mageck count, counts for all Rag1-/- group samples were set as replicates and therefore integrated into the Rag1-/- column.


title: LLC, Rag1-/-, rep6

description:
Library name: LLC-25
In mageck count, counts for all Rag1-/- group samples were set as replicates and therefore integrated into the Rag1-/- column.


title: scRNAseq PT1_VDJ

description:
Library name: DFCI_VDJ1
TCRseq, VDJ reads


title: S4

description: Library name: S4


title: scRNAseq PT7_VDJ

description:
Library name: DFCI_VDJ3
TCRseq, VDJ reads


title: LLC, Rag1-/-, rep4

description:
Library name: LLC-23
In mageck count, counts for all Rag1-/- group samples were set as replicates and therefore integrated into the Rag1-/- column.


title: LLC, Rag1-/-, rep1

description:
Library name: LLC-20
In mageck count, counts for all Rag1-/- group samples were set as replicates and therefore integrated into the Rag1-/- column.


title: LLC, IgG, rep9

description:
Library name: LLC-19
In mageck count, counts for all IgG group samples were set as replicates and therefore integrated into the IgG column.


title: scRNAseq PT13_VDJ

description:
Library name: DFCI_VDJ4
TCRseq, VDJ reads


title: scRNAseq PT11_HTO

description:
Library name: DFCI_FB9
Feature barcode reads, 10X, processed data integrated in to sample features
S9_barcodes.tsv.gz
S9_features.tsv.gz
S9_matrix.mtx.gz

library_source: other

data_processing:
Assembly: Human Hg38
Demutiplexing, barcoading, and gene count extraction was performed using CellRanger software
Supplementary files format and content: CellRanger output: Tab-separated values and matrix
Library strategy: CITE-seq

molecule: protein

tag: hto

value: TotalSeq C251(Week3), TotalSeq C252(Week7), TotalSeq C253(Week15)


title: scRNAseq Week3_addition_VDJ

description:
Library name: DFCI_VDJ7
TCRseq, VDJ reads


title: LLC, Rag1-/-, rep3

description:
Library name: LLC-22
In mageck count, counts for all Rag1-/- group samples were set as replicates and therefore integrated into the Rag1-/- column.


title: scRNAseq PT5_HTO

description:
Library name: DFCI_FB10
Feature barcode reads, 10X, processed data integrated in to sample features
S10_barcodes.tsv.gz
S10_features.tsv.gz
S10_matrix.mtx.gz


title: scRNAseq Week1_HTO

description:
Library name: DFCI_FB11
Feature barcode reads, 10X, processed data integrated in to sample features
S11_barcodes.tsv.gz
S11_features.tsv.gz
S11_matrix.mtx.gz

value: TotalSeq C251(PT5), TotalSeq C252(PT11)


title: LLC, IgG, rep8

description:
Library name: LLC-18
In mageck count, counts for all IgG group samples were set as replicates and therefore integrated into the IgG column.


title: LLC, IgG, rep6

description:
Library name: LLC-16
In mageck count, counts for all IgG group samples were set as replicates and therefore integrated into the IgG column.


title: scRNAseq PT15_replicate_HTO

description:
Library name: DFCI_FB8
Feature barcode reads, 10X, processed data integrated in to sample features
S8_barcodes.tsv.gz
S8_features.tsv.gz
S8_matrix.mtx.gz

value: TotalSeq C251(Week1), TotalSeq C252(Week7), TotalSeq C253(Week15)


title: LLC, Rag1-/-, rep8

description:
Library name: LLC-27
In mageck count, counts for all Rag1-/- group samples were set as replicates and therefore integrated into the Rag1-/- column.


title: LLC, Rag1-/-, rep7

description:
Library name: LLC-26
In mageck count, counts for all Rag1-/- group samples were set as replicates and therefore integrated into the Rag1-/- column.


title: LLC, IgG, rep5

description:
Library name: LLC-15
In mageck count, counts for all IgG group samples were set as replicates and therefore integrated into the IgG column.


title: scRNAseq Week3_addition_HTO

description:
Library name: DFCI_FB7
Feature barcode reads, 10X, processed data integrated in to sample features
S7_barcodes.tsv.gz
S7_features.tsv.gz
S7_matrix.mtx.gz

value: TotalSeq C251(PT1), TotalSeq C252(PT7), TotalSeq C253(PT15)


title: LLC, IgG, rep7

description:
Library name: LLC-17
In mageck count, counts for all IgG group samples were set as replicates and therefore integrated into the IgG column.


title: scRNAseq PT13_HTO

description:
Library name: DFCI_FB4
Feature barcode reads, 10X, processed data integrated in to sample features
S4_barcodes.tsv.gz
S4_features.tsv.gz
S4_matrix.mtx.gz


title: scRNAseq PT7_HTO

description:
Library name: DFCI_FB3
Feature barcode reads, 10X, processed data integrated in to sample features
S3_barcodes.tsv.gz
S3_features.tsv.gz
S3_matrix.mtx.gz


title: LLC, IgG, rep2

description:
Library name: LLC-12
In mageck count, counts for all IgG group samples were set as replicates and therefore integrated into the IgG column.


title: scRNAseq Week3_HTO

description:
Library name: DFCI_FB6
Feature barcode reads, 10X, processed data integrated in to sample features
S6_barcodes.tsv.gz
S6_features.tsv.gz
S6_matrix.mtx.gz

value: TotalSeq C251(PT6), TotalSeq C252(PT13)


title: LLC, IgG, rep4

description:
Library name: LLC-14
In mageck count, counts for all IgG group samples were set as replicates and therefore integrated into the IgG column.


title: scRNAseq Week1

description:
Library name: DFCI_scRNA11
10X genomics


title: LLC, PD1, rep9

description:
Library name: LLC-9
In mageck count, counts for all PD1 group samples were set as replicates and therefore integrated into the PD1 column.


title: LLC, PD1, rep8

description:
Library name: LLC-8
In mageck count, counts for all PD1 group samples were set as replicates and therefore integrated into the PD1 column.


title: LLC, PD1, rep7

description:
Library name: LLC-7
In mageck count, counts for all PD1 group samples were set as replicates and therefore integrated into the PD1 column.


title: LLC, IgG, rep3

description:
Library name: LLC-13
In mageck count, counts for all IgG group samples were set as replicates and therefore integrated into the IgG column.


title: scRNAseq PT6_VDJ

description:
Library name: DFCI_VDJ2
TCRseq, VDJ reads


title: LLC, Rag1-/-, rep2

description:
Library name: LLC-21
In mageck count, counts for all Rag1-/- group samples were set as replicates and therefore integrated into the Rag1-/- column.


title: scRNAseq PT1_HTO

description:
Library name: DFCI_FB1
Feature barcode reads, 10X, processed data integrated in to sample features
S1_barcodes.tsv.gz
S1_features.tsv.gz
S1_matrix.mtx.gz


title: LLC, PD1, rep10

description:
Library name: LLC-10
In mageck count, counts for all PD1 group samples were set as replicates and therefore integrated into the PD1 column.


title: scRNAseq PT15_HTO

description:
Library name: DFCI_FB5
Feature barcode reads, 10X, processed data integrated in to sample features
S5_barcodes.tsv.gz
S5_features.tsv.gz
S5_matrix.mtx.gz


title: scRNAseq PT15_add

description:
Library name: DFCI_scRNA8
10X genomics


title: scRNAseq PT6_HTO

description:
Library name: DFCI_FB2
Feature barcode reads, 10X, processed data integrated in to sample features
S2_barcodes.tsv.gz
S2_features.tsv.gz
S2_matrix.mtx.gz


title: scRNAseq PT5

description:
Library name: DFCI_scRNA10
10X genomics


title: scRNAseq PT11

description:
Library name: DFCI_scRNA9
10X genomics


title: LLC, PD1, rep4

description:
Library name: LLC-4
In mageck count, counts for all PD1 group samples were set as replicates and therefore integrated into the PD1 column.


title: scRNAseq Week3_addition

description:
Library name: DFCI_scRNA7
10X genomics


title: LLC, PD1, rep5

description:
Library name: LLC-5
In mageck count, counts for all PD1 group samples were set as replicates and therefore integrated into the PD1 column.


title: scRNAseq PT13

description:
Library name: DFCI_scRNA4
10X genomics


title: LLC, PD1, rep2

description:
Library name: LLC-2
In mageck count, counts for all PD1 group samples were set as replicates and therefore integrated into the PD1 column.


title: LLC, PD1, rep1

description:
Library name: LLC-1
In mageck count, counts for all PD1 group samples were set as replicates and therefore integrated into the PD1 column.


title: scRNAseq Week3

description:
Library name: DFCI_scRNA6
10X genomics


title: scRNAseq PT6

description:
Library name: DFCI_scRNA2
10X genomics


title: LLC, IgG, rep1

description:
Library name: LLC-11
In mageck count, counts for all IgG group samples were set as replicates and therefore integrated into the IgG column.


title: LLC, PD1, rep3

description:
Library name: LLC-3
In mageck count, counts for all PD1 group samples were set as replicates and therefore integrated into the PD1 column.


title: scRNAseq PT1

description:
Library name: DFCI_scRNA1
10X genomics


title: KP, Rag1-/-, rep15

description:
Library name: KP-30
In mageck count, counts for all Rag1-/- group samples were set as replicates and therefore integrated into the Rag1-/- column.


title: scRNAseq PT7

description:
Library name: DFCI_scRNA3
10X genomics


title: KP, Rag1-/-, rep14

description:
Library name: KP-29
In mageck count, counts for all Rag1-/- group samples were set as replicates and therefore integrated into the Rag1-/- column.


title: SW480_S39

city: Toronto

first: Yuqing

last: Feng

state: ONTARIO

address: 4700 Keele Street

country: Canada

institute: York University

description: Library name: sample 6

data_processing:
FASTQs were aligned to the hg38 human reference genome using STAR 2.7.2b, aligner with default settings
Assembly: Expression levels of all transcripts were quantified using RSEM 1.3.0 with the GENCODE transcript reference version 31. RNA data quality metrics were collected using RNAseQC v1.1.8.
Supplementary files format and content: RSEM quantified normalized read counts per transcript were used as input for differential expression analyses. RSEM quantified gene expression raw counts were normalized using DESeq2

extract_protocol:
total RNA extraction was performed using  Purelink RNA mini kit (Invitrogen, cat# 12183018A) according to the manufacture’s protocol.
RNA extracted from various cell lines were sequenced at the Princess Margaret Genomic Centre, Toronto. Briefly, RNA libraries were prepared from 100ng of total RNA using the Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus. Libraries were sequenced with pair-end 100 cycles V3 using Illumina Novaseq6000 to a target depth of 40 million reads per sample

value: human colorectal adenocarcinoma

value: Wildtype

value: do not apply


title: HCT116_S40

description: Library name: sample 4

value: human colorectal carcinoma


title: KP, Rag1-/-, rep12

description:
Library name: KP-27
In mageck count, counts for all Rag1-/- group samples were set as replicates and therefore integrated into the Rag1-/- column.

value: Mouse lung cancer

value: IgG


title: MDA231_S42

description: Library name: sample 5

value: human breast adenocarcinoma


title: Daudi_S41

description: Library name: sample 3

source_name: Daudi

value: Daudi

value: human Burkitts lymphoma


title: KP, Rag1-/-, rep11

description:
Library name: KP-26
In mageck count, counts for all Rag1-/- group samples were set as replicates and therefore integrated into the Rag1-/- column.


title: LLC, PD1, rep6

description:
Library name: LLC-6
In mageck count, counts for all PD1 group samples were set as replicates and therefore integrated into the PD1 column.

value: Lewis lung carcinoma (LLC)


title: KP, Rag1-/-, rep10

description:
Library name: KP-25
In mageck count, counts for all Rag1-/- group samples were set as replicates and therefore integrated into the Rag1-/- column.


title: A549_S43

description: Library name: sample 2

value: human lung carcinoma


title: ChIP_input-DSS1-dTAG+OE-DSS1-W39R_Batch2

first: Aixia

last: Song

address: Dong'an Road

institute: Fudan University

description: Library name: Sample12

data_processing:
The raw ChIP-Rx reads were trimmed by Trim Galore v0.6.6 (Babraham Institute) and aligned to the human hg19 and mouse mm10 assemblies using Bowtie v2.3.5.1 with default parameters.
Low mapping quality reads (MAPQ < 30) and PCR duplicates were removed using SAMtools v1.9 and Picard v2.26.6 (Babraham Institute).
The read number for each of the ChIP-Rx sample were then collected using SAMtools v1.9, and the normalization factor was calculated as 1e6/spike-in_count.
Normalized bigwig files were generated by deeptools v3.5.0.
Assembly: hg19
Supplementary files format and content: bigWig

growth_protocol: Human DLD-1 cells were cultured in McCoy’s 5A medium (BasalMedia) supplemented with 10% fetal bovine serum (FBS; Yeasen) and 1× penicillin-streptomycin (Meilunbio).

extract_protocol:
Each immunoprecipitation (IP) utilized 1×107 cells, which were crosslinked with 1% formaldehyde (Sigma) for 10 minutes at room temperature. The crosslinking reaction was terminated by the addition of glycine (final concentration 125 mM) and subsequent incubation for 5 minutes. Cells were then rinsed twice with ice-cold PBS, scraped, and collected by centrifugation. The cell pellet was resuspended in Lysis buffer (50 mM HEPES pH 7.4, 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1x protease inhibitor (Roche)) and subjected to sonication (Qsonica) to fragment chromatin to an appropriate size range. The soluble fraction was collected by centrifugation and mixed with 25% of lysate from mouse embryonic stem cells (mESCs) processed identically as a spike-in for normalization. The mixed lysate was then incubated with antibodies overnight and BSA-blocked magnetic Protein A/G beads for 2 h, followed by three washes with High-salt Wash buffer (20 mM HEPES pH 7.4, 500 mM NaCl, 1 mM EDTA, 1.0% NP-40, 0.25% sodium deoxycholate), two washes with Low-salt Wash buffer (20 mM HEPES pH 7.4, 150 mM NaCl, 1 mM EDTA, 0.5% NP-40, 0.1% sodium deoxycholate), and a final wash with TE buffer containing 50 mM NaCl. Beads were then eluted with Elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1.0% SDS). The eluted samples were treated with Protease K, and DNA was purified using the Phenol/Chloroform/Isoamyl Alcohol extraction method.
Libraries for sequencing were prepared using the VAHTS Universal Plus DNA Library Prep Kit for Illumina (Vazymes).

value: Human colorectal adenocarcinoma epithelial cell

value: DSS1-dTAG overexpressing DSS1-W39R

value: 24h dTAG-V1

tag: chip antibody


title: KP, Rag1-/-, rep8

description:
Library name: KP-23
In mageck count, counts for all Rag1-/- group samples were set as replicates and therefore integrated into the Rag1-/- column.


title: 293T_S44

description: Library name: sample 1

value: human embryonic kidney


title: KP, Rag1-/-, rep9

description:
Library name: KP-24
In mageck count, counts for all Rag1-/- group samples were set as replicates and therefore integrated into the Rag1-/- column.


title: ChIP_input-DSS1-dTAG+OE-DSS1-WT_Batch2

description: Library name: Sample11

value: DSS1-dTAG overexpressing DSS1-WT


title: KP, Rag1-/-, rep7

description:
Library name: KP-22
In mageck count, counts for all Rag1-/- group samples were set as replicates and therefore integrated into the Rag1-/- column.


title: KP, Rag1-/-, rep6

description:
Library name: KP-21
In mageck count, counts for all Rag1-/- group samples were set as replicates and therefore integrated into the Rag1-/- column.


title: ChIP_input-DSS1-dTAG+OE-DSS1-WT_Batch1

description: Library name: Sample9


title: KP, Rag1-/-, rep16

description:
Library name: KP-31
In mageck count, counts for all Rag1-/- group samples were set as replicates and therefore integrated into the Rag1-/- column.


title: scRNAseq PT15

description:
Library name: DFCI_scRNA5
10X genomics

value: PBMC


title: KP, Rag1-/-, rep5

description:
Library name: KP-20
In mageck count, counts for all Rag1-/- group samples were set as replicates and therefore integrated into the Rag1-/- column.


title: ChIP_INTS3-DSS1-dTAG+OE-DSS1-W39R_Batch2

description: Library name: Sample7

value: INTS3 (Proteintech 16620-1-AP)


title: KP, Rag1-/-, rep3

description:
Library name: KP-18
In mageck count, counts for all Rag1-/- group samples were set as replicates and therefore integrated into the Rag1-/- column.


title: KP, Rag1-/-, rep2

description:
Library name: KP-17
In mageck count, counts for all Rag1-/- group samples were set as replicates and therefore integrated into the Rag1-/- column.


title: ChIP_PolII-NTD_DSS1-dTAG+OE-DSS1-W39R-rep2_Batch1

description: Library name: Sample4

value: PolII-NTD (CST 14958S)


title: KP, Rag1-/-, rep4

description:
Library name: KP-19
In mageck count, counts for all Rag1-/- group samples were set as replicates and therefore integrated into the Rag1-/- column.


title: KP, Rag1-/-, rep13

description:
Library name: KP-28
In mageck count, counts for all Rag1-/- group samples were set as replicates and therefore integrated into the Rag1-/- column.


title: KP, Rag1-/-, rep1

description:
Library name: KP-16
In mageck count, counts for all Rag1-/- group samples were set as replicates and therefore integrated into the Rag1-/- column.


title: ChIP_INTS3-DSS1-dTAG+OE-DSS1-WT_Batch2

description: Library name: Sample5


title: ChIP_PolII-NTD_DSS1-dTAG+OE-DSS1-W39R-rep1_Batch1

description: Library name: Sample3


title: ChIP_PolII-NTD_DSS1-dTAG+OE-DSS1-WT-rep2_Batch1

description: Library name: Sample2


title: KP, IgG, rep7

description:
Library name: KP-13
In mageck count, counts for all IgG group samples were set as replicates and therefore integrated into the IgG column.


title: KP, IgG, rep6

description:
Library name: KP-12
In mageck count, counts for all IgG group samples were set as replicates and therefore integrated into the IgG column.


title: CUTTag_HA-DSS1-dTAG+OE-HA-DSS1-W39R-rep2

description: Library name: Sample10

data_processing:
Raw CUT&Tag reads were trimmed using Trim Galore v.0.6.6 (Babraham Institute).
Trimmed reads were aligned to the human hg19 genome using Bowtie v.2.4.4 with the following parameters: “-N 1 -L 25 -X 700 --no-mixed --no-discordant”.
Duplicate reads were removed with Picard Tools v2.26.6 (Broad Institute).
The reads were then shifted to compensate for the offset in tagmentation site relative to the Tn5 binding site using the alignmentSieve function of deepTools v.3.5.1 with the ‘--ATACshift’ option.
The read number for each of the sample were then collected using SAMtools v1.9, and the normalization factor was calculated as 1e6/Ecoli_count. Normalized bigwig files were generated by deeptools v3.5.0.
Assembly: hg19
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

extract_protocol:
DLD-1 cells were harvested using Accutase (Thermo Fisher Scientific) to prevent overdigestion. For each CUTTag reaction, 5 × 105 cells were typically utilized to ensure sufficient DNA yield for subsequent library construction. Following centrifugation (600 g, 3 minutes) at room temperature, cells were washed twice with 800 μl of wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 1× protease inhibitor) and subsequently resuspended in 100 μl of wash buffer within low-retention PCR tubes. The concanavalin-A-coated magnetic beads (Smart-Lifesciences) were pre-activated and resuspended in an equal volume of binding buffer (20 mM HEPES pH 7.5, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). Subsequently, 10 μl of activated concanavalin A beads were added to 5 × 105 cells, followed by a 10-minute incubation period under gentle rotation. The bead-bound cells were magnetized to remove excess liquid, then resuspended in 50 μl of antibody buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 1× protease inhibitor, 0.05% digitonin, 0.01% NP-40, 2 mM EDTA). Next, 1 μg of either Flag (Abclonal) or HA (proteintech) antibody was added to facilitate DSS1 binding, and the mixture was rotated overnight at 4 ℃. For IgG control experiments, mouse or rabbit IgG was substituted accordingly. Following overnight incubation, the bead-bound cells were subjected to successive incubations with rabbit anti-mouse IgG (Solarbio, diluted 1:100) and mouse anti-rabbit IgG (Solarbio, diluted 1:100) in 100 μl of antibody buffer for 1 hour at room temperature. Subsequently, the cells were washed four times with dig-wash buffer (antibody buffer without 2 mM EDTA) to remove unbound antibodies. The pAG-Tn5 adapter complex was prepared in dig-300 buffer (20 mM HEPES pH 7.5, 300 mM NaCl, 0.5 mM spermidine, 1× protease inhibitors, 0.01% digitonin, 0.01% NP-40) to a final concentration of 0.2 μM. The bead-bound cells were resuspended in 100 μl of pAG-Tn5 mix and incubated at room temperature for 1 hour before supernatant removal. Following thorough washing, the tagmentation reaction was initiated in 40 μl of tagmentation buffer (10 mM TAPS-KOH pH 8.3, 10 mM MgCl2, 1% DMF) at 37 ℃ for 1 h. To halt the reaction, 1.5 μl of 0.5 M EDTA, 0.5 μl of 10% SDS, and 1 μl of 20 mg/ml protease K were added. After a 1-hour incubation at 55 ℃, DNA purification was performed using VAHTS DNA Clean Beads (Vazyme), with elution in 10 μl of 0.1% Tween-20.
DNA were mixed with 10 U of Bst 2.0 WarmStart DNA polymerase (NEB) and 1× Q5 polymerase reaction buffer (NEB) in a 20 μl reaction system. The reaction was carried out at 65 ℃ for 30 min, followed by an additional 20 min at 80 ℃ to inactivate the Bst 2.0 WarmStart DNA polymerase. The purified DNA was then subjected to amplification using Q5 high-fidelity DNA polymerase (NEB) with a universal i5 primer and a uniquely barcoded i7 primer. The exact number of PCR cycles was determined by qPCR prior to amplification, with 11–12 cycles typically sufficient to yield an adequate library for sequencing. Following library size-selection with 0.56–0.85 VAHTS DNA Clean Beads to achieve library sizes ranging from 200 to 700 bp.

tag: cut&tag antibody

value: HA (Proteintech 51064-2-AP)


title: ChIP_PolII-NTD_DSS1-dTAG+OE-DSS1-WT-rep1_Batch1

description: Library name: Sample1


title: CUTTag_HA-DSS1-dTAG+OE-HA-DSS1-W39R-rep1

description: Library name: Sample9


title: KP, IgG, rep9

description:
Library name: KP-15
In mageck count, counts for all IgG group samples were set as replicates and therefore integrated into the IgG column.


title: CUTTag_HA-DSS1-dTAG+OE-HA-DSS1-WT-rep2

description: Library name: Sample8


title: KP, IgG, rep4

description:
Library name: KP-10
In mageck count, counts for all IgG group samples were set as replicates and therefore integrated into the IgG column.


title: CUTTag_Flag-DSS1-dTAG-dTAGV1-rep2

description: Library name: Sample6

value: Flag (Abclonal AE005)


title: CUTTag_Flag-DSS1-dTAG-dTAGV1-rep1

description: Library name: Sample5


title: KP, IgG, rep5

description:
Library name: KP-11
In mageck count, counts for all IgG group samples were set as replicates and therefore integrated into the IgG column.

value: Mouse lung cancer


title: KP, IgG, rep3

description:
Library name: KP-9
In mageck count, counts for all IgG group samples were set as replicates and therefore integrated into the IgG column.

value: IgG


title: CUTTag_HA-DSS1-dTAG+OE-HA-DSS1-WT-rep1

description: Library name: Sample7


title: KP, IgG, rep2

description:
Library name: KP-8
In mageck count, counts for all IgG group samples were set as replicates and therefore integrated into the IgG column.


title: KP, IgG, rep1

description:
Library name: KP-7
In mageck count, counts for all IgG group samples were set as replicates and therefore integrated into the IgG column.


title: CUTTag_Flag-DSS1-dTAG-DMSO-rep1

description: Library name: Sample3

value: DMSO


title: KP, PD1, rep6

description:
Library name: KP-6
In mageck count, counts for all PD1 group samples were set as replicates and therefore integrated into the PD1 column.


title: KP, PD1, rep4

description:
Library name: KP-4
In mageck count, counts for all PD1 group samples were set as replicates and therefore integrated into the PD1 column.


title: KP, PD1, rep5

description:
Library name: KP-5
In mageck count, counts for all PD1 group samples were set as replicates and therefore integrated into the PD1 column.


title: KP, IgG, rep8

description:
Library name: KP-14
In mageck count, counts for all IgG group samples were set as replicates and therefore integrated into the IgG column.


title: CUTTag_IgG-DSS1-dTAG-DMSO-rep1

description: Library name: Sample1

value: IgG (Solarbio SPA231)


title: KP, PD1, rep3

description:
Library name: KP-3
In mageck count, counts for all PD1 group samples were set as replicates and therefore integrated into the PD1 column.


title: KP, PD1, rep1

description:
Library name: KP-1
In mageck count, counts for all PD1 group samples were set as replicates and therefore integrated into the PD1 column.


title: HAP1 cells, Evercode sublibrary 6

city: Trondheim

first: Magnar

last: Bjørås

address: Erling Skjalgsons gate 1

country: Norway

institute: NTNU

description:
Library name: HAP1_Evercode_Lib6
HAP1 cells, Evercode sublibrary 6

data_processing:
The Split-pipe pipeline (version 1.3.1, Parse Biosciences) was utilized for the preprocessing of the single-cell RNA sequencing data. The resulting count matrix was filtered for empty droplets and to include only the features used during alignment of the NAxtra-based RNA sequencing data (GEO accession number: GSE284534).
Analysis of the count matrix was performed utilizing the Seurat package (version 5.2.1). Cells were further filtered based on the distribution of counts per cell, unique genes per cell, and the percentage of mitochondrial genes expressed per cell. The filtered raw counts contained 886 cells and were normalized using log-normalization.
Assembly: hg38
Supplementary files format and content: RDS objects containing either filtered raw counts for each cell or normalized counts for each cell, as indicated by file name.

growth_protocol: HAP1 cells were cultured in IMDM medium (Gibco) supplemented with 5% fetal bovine serum (Sigma-Aldrich), 1% l-glutamine (200 mM, Sigma-Aldrich) and 1% Penicillin (10,000 U/mL) Streptomycin (10,000 µg/mL) (Gibco) at 37°C with 5% CO2.

extract_protocol:
Fixation of the HAP1 cells was conducted according to the Evercode Cell Fixation v2 (Parse Biosciences) protocol.
The RNA of fixed the HAP1 cells was prepared for sequencing according to the Evercode Whole Transcriptome v2 Kit (Parse Biosciences) protocol.

value: WT


title: HAP1 cells, Evercode sublibrary 8

description:
Library name: HAP1_Evercode_Lib8
HAP1 cells, Evercode sublibrary 8


title: endomypcardial biopsy tissue, after

city: Saint Louis

first: Pan

last: Ma

state: United States

address: CSRB, Room 9918, 425 S Euclid, Saint Louis, MO, 63110

institute: Washington University in Saint Louis

description:
Library name: after
Parrafin Spatial Transcriptomics

data_processing:
Raw sequecing data were processed using the 10X Genomics Space Ranger pipeline to generate FASTQ files.
Sequecing were aligned to GRC-h38 genome to generate gene expression could using Space Ranger's default settings.
Gene expression level of Refseq coding genes were quantified using  Space      Rnager's default settings.
Assembly: GRC-h38
Supplementary files format and content: aligned_fiducials.jpg
Supplementary files format and content: barcodes.tsv.gz
Supplementary files format and content: detected_tissue_image.jpg
Supplementary files format and content: features.tsv.gz
Supplementary files format and content: matrix.mtx.gz
Supplementary files format and content: scalefactors_json.json
Supplementary files format and content: tissue_hires_image.png
Supplementary files format and content: tissue_lowres_image.png
Supplementary files format and content: tissue_positions.csv
Library strategy: Spatial Transcriptomics

source_name: endomypcardial biopsy tissue

extract_protocol:
10um Parrafin sections were cut with microtome with the biopsy FFPE blocks
Spatial transcriptome sequencing libraries were prepared with 10X Genomics Visium with CytoAssit platform according to manufacturer's construction.

value: endomypcardial biopsy tissue

value: after rilonacept


title: ChIP_input-DSS1-dTAG+OE-DSS1-W39R_Batch1

description: Library name: Sample10

value: Human colorectal adenocarcinoma epithelial cell


title: KP, PD1, rep2

description:
Library name: KP-2
In mageck count, counts for all PD1 group samples were set as replicates and therefore integrated into the PD1 column.


title: endomypcardial biopsy tissue, before

description:
Library name: before
Parrafin Spatial Transcriptomics

value: before rilonacept


title: HAP1 cells, Evercode sublibrary 7

description:
Library name: HAP1_Evercode_Lib7
HAP1 cells, Evercode sublibrary 7


title: HAP1 cells, Evercode sublibrary 5

description:
Library name: HAP1_Evercode_Lib5
HAP1 cells, Evercode sublibrary 5


title: HAP1 cells, Evercode sublibrary 2

description:
Library name: HAP1_Evercode_Lib2
HAP1 cells, Evercode sublibrary 2


title: HAP1 cells, Evercode sublibrary 1

description:
Library name: HAP1_Evercode_Lib1
HAP1 cells, Evercode sublibrary 1


title: 2iL KO , anti-RBBP4

city: Guangzhou

first: shuhui

last: xu

address: 190 Kaiyuan Avenue, Huangpu District

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

description: Library name: 2iL KO RBBP4

data_processing:
Sequenced reads were aligned to the mouse reference genome (mm10) using Bowtie2 with the parameters: --end-to-end--very-sensitive--local--no-mixed--no-discordant--no-unal--phred33-I10-X700. Then, Sambamba was used to remove duplicate reads and samtools was used to sort the data. Peaks were called using MACS2 (v.2.2.7.1) with the following parameters: --SPMR--nomodel--extsize 200--keep-dup all--q 0.001. Reads that mapped to mitochondrial DNA or unassigned sequences were discarded. For paired-end sequencing data, only transformed into read coverage files (bigwig format) using deepTools with RPKM normalization. For the sample without repeats, differential binding region was analysis by manorm (v.1.3.0) with P-value <= 0.05.
Assembly: mm10
Supplementary files format and content: bw
Library strategy: CUT&Tag

source_name: ESCs

extract_protocol:
For CUT&Tag library construction, NovoNGS® CUT&Tag 3.0 High-Sensitivity Kit for Illumina (Novoprotein, N259-YH01) was used. Around 1×105 living cells were collected for each sample, and the CUT&Tag library was sequenced on a illumina nova6000, carried out by CNGB.
CUT&Tag

treatment_protocol: Around 100000 living cells were collected for each sample CUT&Tag library construction.

value: ESCs

value: Tsc1 KO


title: CUTTag_IgG-DSS1-dTAG-DMSO-rep2

description: Library name: Sample2


title: HAP1 cells, Evercode sublibrary 4

description:
Library name: HAP1_Evercode_Lib4
HAP1 cells, Evercode sublibrary 4


title: N2B2740h WT , anti-RBBP4

description: Library name: N2B2740h WT RBBP4

value: Tsc1 WT


title: p62.1_miRNA_d

city: Schlieren

first: Hans-Dietmar

last: Beer

state: ZH

address: Wagistrasse 18

department: Dermatology

country: Switzerland

institute: USZ

description:
Library name: 179_3_miRNA
179_3_Plate_2874_12_S5_R1_001.fastq

data_processing:
High Throughput Sequencing (NGS) was performed on Illumina Novaseq 6000. Raw reads were quality-checked using FastQC. mRNA reads were mapped to the human transcriptome using salmon version 1.9.0. The quantified transcripts were imported into R and collapsed to the gene level using the R package “tximport”
Mature and hairpin microRNA quantification was performed using the nf-core/smrnaseq pipeline v2.3.0 (10.5281/zenodo.3456879
Differential expression analysis of mRNA and miRNA was performed using the R package DESeq2
Assembly: hg38; GRCh38
Supplementary files format and content: CSV files

source_name: cutaneous squamous cell carcinoma

growth_protocol: SCC12 were grown in serum-free keratinocyte medium (KSFM, Thermo Fisher Scientific, USA) supplemented with epidermal growth factor (EGF) and bovine pituitary extract (BPE).

extract_protocol:
Total RNA was isolated using the miRNeasy Mini Kit (217004, Qiagen).
For mRNA sequencing, libraries were prepared with TruSeq RNA (Illumina), while miRNA libraries utilized RealSeq®-AC (somagenics), following standard protocols at the Functional Genomics Centre Zurich (FGCZ).

value: cutaneous squamous cell carcinoma

value: CRISPR/Cas9 knockout (p62.1 - protein only)


title: ESCs 2iL , anti-IgG

description: Library name: ESCs 2iL IgG


title: p62.2K_miRNA_d

description:
Library name: 179_4_miRNA
179_4_Plate_2874_2_S9_R1_001.fastq

value: CRISPR/dCas9-KRAB knockout (p62.2K - mRNA and protein)


title: N2B2740h KO , anti-TFE3

description: Library name: N2B2740h KO TFE3

value: N2B27 40h+AAV-Cre


title: N2B2740h KO , anti-RBBP4

description: Library name: N2B2740h KO RBBP4


title: N2B2740h WT , anti-TFE3

description: Library name: N2B2740h WT TFE3


title: 2iL KO , anti-TFE3

description: Library name: 2iL KO TFE3


title: CUTTag_Flag-DSS1-dTAG-DMSO-rep2

description: Library name: Sample4

value: Flag (Abclonal AE005)


title: CT_miRNA_d

description:
Library name: 179_2_miRNA
179_2_Plate_2874_11_S4_R1_001.fastq

value: CT, empty (CRISPR/dCas9-KRAB)


title: 2iL WT , anti-RBBP4

description: Library name: 2iL WT RBBP4


title: p62.2K_miRNA_c

description:
Library name: 178_4_miRNA
178_4_Plate_2874_10_S7_R1_001.fastq


title: p62.1_miRNA_c

description:
Library name: 178_3_miRNA
178_3_Plate_2874_9_S3_R1_001.fastq


title: CT_miRNA_c

description:
Library name: 178_2_miRNA
178_2_Plate_2874_7_S6_R1_001.fastq


title: p62.2K_miRNA_b

description:
Library name: 177_5_miRNA
177_5_Plate_2874_8_S10_R1_001.fastq


title: p62.1_miRNA_b

description:
Library name: 177_4_miRNA
177_4_Plate_2874_6_S12_R1_001.fastq


title: DRs, Penk KO, pooled

city: La Jolla

first: Stanislav

last: Dikiy

state: CA

address: 10550 North Torrey Pines Road

department: Immunology

institute: Scripps Research

description:
Library name: SampleD
fixed sample scRNA-seq (FLEX)

data_processing:
Downstream analysis of snRNA-seq data was conducted in R using the Seurat pipeline, following quality control and clustering workflow previously described. Cells/nuclei were retained for analysis if they expressed more than 500 unique genes, had mitochondrial gene content below 10%, and fewer than 20,000 total unique molecular identifiers.
Assembly: MRCm39 (mm39)
Supplementary files format and content: cellranger produced matrix files of gene x cell expression counts

source_name: dorsal root ganglion

extract_protocol:
Cervical region of spinal cord was isolated from mice and immediately fixed in 4% PFA overnight at 4 °C. Following PBS washes, dorsal root ganglia (DRGs) from spinal levels C2 to C7 were bilaterally dissected. Tissue from each mouse was pooled and mechanically homogenized in 1 ml of pre-warmed RPMI 1640 medium containing collagenase I (3000 U/ml; Worthington Biochemical Corporation) for 20 minutes at 250 rpm and 37 °C in a shaking incubator. Additional dissociation was performed using a Dounce homogenizer at room temperature until the majority of DRGs were dissociated. The resulting cell suspension was filtered through a 70 µm mini cell strainer (pluriSelect #43-10070-40) and centrifuged at 850 g for 5 minutes at room temperature. The supernatant was discarded, and pellet was resuspended in 1 ml of quenching buffer (10x Genomics, PN 2000516).
Library preparation was performed using the Chromium Next GEM Single Cell Fixed RNA Profiling Kit for multiplexed samples, following the manufacturer's protocol (Mouse Transcriptome Kit #PN-1000496, Chromium Next GEM Chip Q Single Cell Kit #PN-1000418, and Dual Index Kit TS Set A #PN-1000251). Reads were aligned to the mouse reference genome (GRCm39) using Cell Ranger v7.0 (10x Genomics).

value: dorsal root ganglion

value: Foxp3 CreER; Penk fl/fl

value: tamoxifen


title: CT_miRNA_b

description:
Library name: 177_3_miRNA
177_3_Plate_2874_4_S2_R1_001.fastq


title: MeRIP-seq input, Young mouse, Replicate 3

city: Dongguan

first: xia

last: jing

state: None Selected

address: Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, Xin Cheng Avenue 1#, Songshan Lake, Dongguan 523808, P. R. China

institute: Guangdong Medical College - Dongguan Campus

description: Library name: young-9H-Input

data_processing:
Cutadapt (v2.5) was used to trim adapters and filter for sequences, remaining reads were then aligned to the mouse Ensemble genome GRCm38 using Hisat2 aligner (v2.1.0) under parameters: “--rna-strandness RF”. m6A peaks were identified using exomePeak R package (v2.13.2) under parameters: “PEAK_CUTOFF_PVALUE=0.05,PEAK_CUTOFF_FDR=NA,FRAGMENT_LENGTH=200”. Differential m6A peak were identified using exomePeak R package under parameters: “PEAK_CUTOFF_PVALUE=NA,PEAK_CUTOFF_FDR=0.05,FRAGMENT_LENGTH=200” . GO and KEGG analysis were performed using clusterProfiler R package (v3.6.0). m6A-RNA-related genomic features were visualized using Guitar R package (v1.16.0). Identified m6A peaks which p value <0.05 were chosen for the de novo motif analysis using homer (v4.10.4) under parameters:”-len 6 -rna”.
Assembly: GRCm38
Supplementary files format and content: peak files
Library strategy: MeRIP-Seq

source_name: heart

extract_protocol:
Total RNA was extracted using TRIzol™ Reagent (Invitrogen, 15596018).
10 μg total RNA was fragmented into 100-200 nt RNA fragments using 10X RNA Fragmentation Buffer (100 mM Tris-HCl, 100 mM ZnCl2 in nuclease-free H2O). The reaction was stopped by adding 10X EDTA (0.5M EDTA). Methylated RNA immunoprecipitation was performed using EpiTM m6A immunoprecipitation kit (Epibiotek, R1804). Briefly, the fragmented RNA was incubated with anti-m6A monoclonal antibody (abcam,ab208577) for 3 h at 4℃ and then with protein A/G magnetic beads (Invitrogen, 8880210002D/10004D) at 4 ℃ for an additional 2 h to obtain immunoprecipitated RNA fragments. The m6A-enriched RNA was purified using TRIzol™ Reagent (Invitrogen, 15596018). The library was prepared by smart-seq method.

value: heart


title: MeRIP-seq IP, Young mouse, Replicate 2

description: Library name: young-32H-IP


title: p62.2K_miRNA_a

description:
Library name: 170_5_miRNA
170_5_Plate_2874_5_S8_R1_001.fastq


title: MeRIP-seq input, Young mouse, Replicate 2

description: Library name: young-32H-Input


title: MeRIP-seq IP, Young mouse, Replicate 1

description: Library name: young-12H-IP


title: p62.1_miRNA_a

description:
Library name: 170_4_miRNA
170_4_Plate_2874_3_S11_R1_001.fastq


title: p62.1_mRNA_d

description:
Library name: 179_3_mRNA
179_3_Plate_2850_10_S9_R1_001.fastq


title: MeRIP-seq IP, Old mouse, Replicate 2

description: Library name: old-21H-IP


title: MeRIP-seq IP, Old mouse, Replicate 3

description: Library name: old-22H-IP


title: MeRIP-seq input, Old mouse, Replicate 2

description: Library name: old-21H-Input


title: MeRIP-seq input, Old mouse, Replicate 3

description: Library name: old-22H-Input


title: CT_miRNA_a

description:
Library name: 170_3_miRNA
170_3_Plate_2874_1_S13_R1_001.fastq


title: 2iL WT, anti-TFE3

description: Library name: 2iL WT TFE3


title: MeRIP-seq IP, Old mouse, Replicate 1

description: Library name: old-20H-IP


title: MeRIP-seq input, Old mouse, Replicate 1

description: Library name: old-20H-Input


title: p62.2K_mRNA_c

description:
Library name: 178_4_mRNA
178_4_Plate_2850_8_S12_R1_001.fastq


title: p62.2K_mRNA_d

description:
Library name: 179_4_mRNA
179_4_Plate_2850_12_S3_R1_001.fastq


title: CT_mRNA_d

description:
Library name: 179_2_mRNA
179_2_Plate_2850_9_S5_R1_001.fastq


title: MeRIP-seq IP, Young mouse, Replicate 3

description: Library name: young-9H-IP


title: BatfKO_Ezh2

city: Kanazawa

first: Sotaro

last: Fujisawa

state: Ishikawa

address: 13-1 Takara-machi

country: Japan

institute: Kanazawa University

description: Library name: Sample 50

data_processing:
Sequence data were assessed using FastQC, and trimmed for adapter and loq-quality bases using fastp.
Reads were aligned to the GRCm38/mm10 reference genome using Bowtie v2.3.5.
Unmapped, unpaired, low-quality reads, and mitochondrial reads were removed using samtools.
ENCODE blacklist regions were removed, and PCR duplicates were removed using Picard.
BED file was created using bamtobed function of BedTools.
Data were normalized by mapping the reads to E. coli DNA, the carry-over from purification of pAG-MNase (Meers et al., 2019) and normalized bigwig files were created using deepTools bamCoverage
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&Run

source_name: CD8+ T cells

extract_protocol:
DNA fragment of TF-bound regions were extracted using pAG-MNase.
Sequence libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina

value: CD8+ T cells

value: BatfKO

tag: antibody

value: Ezh2 (CST, D2C9)


title: DRGs, Penk ctrl, pooled

description:
Library name: SampleC
fixed sample scRNA-seq (FLEX)

value: Foxp3 CreER; Penk fl/WT


title: WT_Ezh2

description: Library name: Sample 49

value: WT


title: CT_mRNA_b

description:
Library name: 177_3_mRNA
177_3_Plate_2850_2_S10_R1_001.fastq


title: CT_mRNA_c

description:
Library name: 178_2_mRNA
178_2_Plate_2850_5_S11_R1_001.fastq


title: BatfKO_H3K27me3

description: Library name: Sample 48


title: WT_H3K27me3

description: Library name: Sample 47


title: p62.2K_mRNA_a

description:
Library name: 170_5_mRNA
170_5_Plate_2850_3_S1_R1_001.fastq


title: IRF4KO_2

description: Library name: Sample 20

data_processing:
Sequence data were assessed using FastQC, and trimmed for adapter and loq-quality bases using fastp.
Reads were aligned to the GRCm38/mm10 reference genome using Bowtie v2.3.5.
Unmapped, unpaired, low-quality reads, and mitochondrial reads were removed using samtools.
ENCODE blacklist regions were removed, and PCR duplicates were removed using Picard.
BED file was created using bamtobed function of BedTools and ATAC shift was corrected as described (https://github.com/wherrylab/jogiles_ATAC).
Peak calling was performed using MACS v2 using the narrowPeak setting with q value cut-off of 0.01, -f BEDPE.
Peaks from all samples in each experiment were combined and merged using BedTools merge, and the numbers of reads in each peak was quantified using BedTools coverage
Assembly: mm10
Supplementary files format and content: bigwig

extract_protocol:
DNA fragment of open chromatin regions were extracted using Tn5 transposase (Illumina)
Sequence libraries were prepared using NEBNext High Fidelity 2x PCR Master Mix

value: Irf4 RV


title: p62.1__mRNA_a

description:
Library name: 170_4_mRNA
170_4_Plate_2850_1_S8_R1_001.fastq


title: CT_mRNA_a

description:
Library name: 170_3_mRNA
170_3_Plate_2850_11_S7_R1_001.fastq


title: MeRIP-seq input, Young mouse, Replicate 1

description: Library name: young-12H-Input


title: IRF4KO_1

description: Library name: Sample 19


title: p62.1_mRNA_c

description:
Library name: 178_3_mRNA
178_3_Plate_2850_7_S2_R1_001.fastq


title: ADSCs-2,day 14

city: Haikou

first: Denggao

last: Huang

state: Hainan

address: No.43 avenue Renmin Road

institute: Haikou people hospital

description: Library name: D14hADSCs_2

data_processing:
fastp software were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp. We used HISAT2 to map reads to the reference genome of Homo sapiens GRCh38. The mapped reads of each sample were assembled using StringTie  with default parameters.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: All transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare . After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM × exon_length(kB)]). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR

source_name: cell line

extract_protocol:
Total RNA was isolated and purified via TRIzol reagent according to the manufacturer's protocol(Vazyme)
RNA libraries for RNA-seq were prepared using Illumina NovaSeq™ 6000 according to the manufacturer's recommended protocol.

value: cell line

value: ADSCs

value: stromal stem cells

value: wt

value: day 14


title: ADSCs-1,day 14

description: Library name: D14hADSCs_1


title: T24-3,day 14

description: Library name: D14T24_3

value: tumor cell


title: NTM-infected mouse lung tissue – Atg7 cKO, scRNAseq

city: Seoul

first: Yeonju

last: Lee

address: 500-1 Anam-dong, Seongbuk-gu

institute: Sungkyunkwan University

description: Library name: CR_24_15075_TS_C_SS3_1

data_processing:
Raw sequencing reads were processed using Cell Ranger v8.0.1 (10x Genomics), with alignment to the mouse reference genome mm10-2020-A. Gene-barcode matrices were generated, and low-quality cells with fewer than 200 detected genes were filtered out. Downstream analysis was performed using the Seurat package. Unsupervised clustering identified 22 distinct cell types, which were annotated based on differentially expressed genes and canonical markers, with reference to the PanglaoDB database.
Assembly: Mouse genome reference: mm10-2020-A, aligned using Cell Ranger v8.0.1 (10x Genomics)
Supplementary files format and content: The processed data are provided in the standard output format from the 10x Genomics Cell Ranger pipeline. (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz)

source_name: Lung

extract_protocol:
Mouse lung tissues were harvested at 21 days post-infection (dpi) from Mav-infected Atg7 conditional wild-type (cWT) and Atg7 conditional knockout (cKO) mice. The tissues were enzymatically dissociated into single-cell suspensions using Liberase TL (Roche, #05401020001), following the manufacturer’s instructions. Cell viability and total cell count were assessed using the LUNA-FX7™ Automated Cell Counter (Logos Biosystems) with Acridine Orange/Propidium Iodide staining.
Single-cell suspensions were processed using the Chromium Next GEM Single Cell 3’ Kit v3.1 (PN: 1000268) and Chromium Next GEM Chip G Single Cell Kit (PN: 1000120), along with the Dual Index Kit TT Set A (PN: 1000215), according to the manufacturer’s protocols (10x Genomics). Single-cell RNA-seq libraries were generated and subsequently sequenced on an Illumina NovaSeq 6000 platform using the NovaSeq 5000/6000 S2 Reagent Kit v1.5 (200 cycles, PN: 20028315). Sequencing was performed in paired-end mode with the following cycle configuration: Read1: 28 cycles, Read2: 90 cycles, i7 Index: 10 cycles, and i5 Index: 10 cycles.

value: Lung

value: Lung epithelial cells, Stromal cells, Immune cells

value: Atg7fl/fl LysM-Cre+/+

value: NTM infection


title: p62.2K_mRNA_b

description:
Library name: 177_5_mRNA
177_5_Plate_2850_6_S4_R1_001.fastq

value: cutaneous squamous cell carcinoma

value: CRISPR/dCas9-KRAB knockout (p62.2K - mRNA and protein)


title: Stat1-ChIP, DSS-treated T748A, rep.3

city: Kanagawa

first: Kazuki

last: Okuyama

address: 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama

department: IMS

institute: RIKEN Yokohama

description: Library name: DSS T748A, rep.3

data_processing:
Adapter sequences were trimmed from the reads by Cutadapt (v4.0)
Mapping to the mm10 genome using bowtie2 (v2.5.0)
Removing reads with low mapping quality (MAPQ<30) , mitochondrial reads, and improperly paired reads using Filter BAM (v2.5.2)
Removing PCR duplicates by MarkDuplicates (v2.18.2.3)
Peak calling using MACS2 callpeak (v2.2.7.1) with default settings
Generate BigWig files from BedGraph using Convert BedGraph to BigWig (v1.0.1)
Regions were extended 100bp for both directions from summits while keeping the most significant summit when nearby regions were overlapped and assigned as peaks
Assembly: mm10
Supplementary files format and content: BigWig files

source_name: Colon

extract_protocol:
Cross-linking was quenched with 1.375 M glycine for 5 minutes at room temperature. Nuclei were isolated, and chromatin was enzymatically sheared using micrococcal nuclease for 17 minutes at 37 °C. Five percent of the sheared chromatin was reserved as input, and the remainder was subjected to immunoprecipitation using anti–STAT1 antibody (1:50 dilution). Immunocomplexes were reverse cross-linked overnight at 65 °C with Proteinase K, and DNA was purified using phenol/chloroform extraction.
ChIP DNA libraries were prepared using the KAPA Hyper Prep Kit (KAPA Biosystems) according to the manufacturer’s instructions. Paired-end sequencing (2 × 101 bp) was performed on an Illumina NovaSeq 6000 platform (Illumina Inc., San Diego, CA, USA). Adapter trimming was conducted with Cutadapt (v4.8), using the following adapter sequences: Read 1: 5′-AGATCGGAAGAGCACACGTCTGAACTCCAGTCA-3′; Read 2: 5′-AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT-3′. Read quality was assessed using FastQC (default settings). Trimmed reads were aligned to the mouse reference genome (mm10) using Bowtie2 (v2.5.3) with the “very sensitive end-to-end” preset. BAM files were further processed using the Galaxy platform. Low-quality reads (MAPQ < 30), improperly paired reads, mitochondrial reads, and PCR duplicates were removed using ‘Filter’ (v2.4.2) and ‘MarkDuplicates’ (v3.1.1.0). Peak calling was performed using MACS2 callpeak (v2.2.9.1).

treatment_protocol: Briefly, IECs were isolated from DSS-treated Wt and Stat1T748A littermate mice and cross-linked with 3.7% formaldehyde for 10 minutes at room temperature.

value: Colon

value: Intestinal epithelial cells

value: Stat1 T748A/T748A

value: Stat1 (D1K9Y) Rabbit mAb


title: NTM-infected mouse lung tissue – Atg7 WT (control), scRNAseq

description: Library name: CR_24_15074_TS_C_SS3_1

value: Lung Epithelial cells, Stromal cells, Immune cells

value: Atg7fl/fl LysM-Cre-/-


title: T24-2,day 14

description: Library name: D14T24_2

value: cell line


title: NTM-infected mouse lung tissue – Atg7 WT (control), spatial transcriptomics

description:
Library name: ATG7_WT_Mav1_CR_23_15193_FP_R_SSV_1
FFPE tissue sample

data_processing:
Sequencing reads were processed using the Space Ranger software (10x Genomics) and aligned to the mouse reference genome mm10 (2020-A).
Feature-barcode matrices and spatial image files were generated as outputs from Space Ranger.
Aggregated HDF5 matrices were imported into R and split by sample.
Spots with fewer than 300 detected genes were excluded from further analysis.
Downstream analysis was performed using the Seurat package.
Assembly: mm10 (2020-A)
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz : list of gene IDs
Supplementary files format and content: matrix.mtx.gz : gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg
Supplementary files format and content: aligned_tissue_image.jpg
Supplementary files format and content: cytassist_image.tiff
Supplementary files format and content: detected_tissue_image.jpg
Supplementary files format and content: scalefactors_json.json
Supplementary files format and content: spatial_enrichment.csv
Supplementary files format and content: tissue_hires_image.png
Supplementary files format and content: tissue_lowres_image.png
Supplementary files format and content: tissue_positions.csv
Library strategy: Spatial Transcriptomics

source_name: lung

extract_protocol:
Tissue samples were processed using Visium CytAssist Spatial Gene Expression for FFPE protocol. Lung tissues from Mav-infected Atg7 cWT and Atg7 cKO mice (21 dpi) were fixed in 10% neutral buffered formalin, embedded in paraffin, and sectioned at 5 µm thickness using a microtome. Sections were placed on Visium CytAssist slides and processed following the manufacturer’s protocol (10x Genomics #CG000409). RNA was extracted using the RNeasy FFPE Kit (Qiagen #73504) after deparaffinization (Qiagen Deparaffinization Solution #19093). RNA integrity was assessed using Agilent TapeStation (High Sensitivity RNA ScreenTape #5067-5579) by measuring DV200 values.
Libraries were prepared from FFPE tissue sections using the Visium Spatial Gene Expression for FFPE Kit, Mouse Transcriptome v1 (10x Genomics #1000521) and Dual Index Kit TS Set A (10x Genomics #1000251) following the manufacturer’s instructions. H&E staining was performed prior to permeabilization using standard reagents (Xylene, Ethanol, Eosin Y, Mayer's Hematoxylin, Bluing Reagent), and imaging was conducted using Nikon Eclipse Ti2 microscope (QC at 4X, Visium at 20X).

value: lung


title: T24-CM-3,day 14

description: Library name: D14T24CM_3

value: wt

value: ADSCs-derived conditioned medium


title: Stat1-ChIP, DSS-treated T748A, rep.2

description: Library name: DSS T748A, rep.2


title: p62.1_mRNA_b

description:
Library name: 177_4_mRNA
177_4_Plate_2850_4_S6_R1_001.fastq

value: CRISPR/Cas9 knockout (p62.1 - protein only)


title: T24-1,day 14

description: Library name: D14T24_1

value: tumor cell

value: day 14


title: T24-CM-2,day 14

description: Library name: D14T24CM_2


title: Stat1-ChIP, DSS-treated Wt, rep.3

description: Library name: DSS WT, rep.3

value: Stat1 +/+


title: T24-CM-1,day 14

description: Library name: D14T24CM_1


title: Stat1-ChIP, DSS-treated Wt, rep.1

description: Library name: DSS WT, rep.1


title: ADSCs:T24(10:1)-3,day 14

description: Library name: D14CoC101_3

value: stromal stem cells and tumor cell

value: co-culture


title: Stat1-ChIP, untreated WT748A, rep.3

description: Library name: Untreated T748A, rep.3