title: Primary human mammary epithelial cells

description: HMEC

hyb_protocol: A single GeneChip® Cartridge Array was used per cell line. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix).

data_processing: RMA-normalized expression was calculated using the R tool ‘oligo’ (Carvalho BS, Irizarry RA. “A Framework for Oligonucleotide Microarray Preprocessing” Bioinformatics (2010) 26(19), 2363-7).

label: Biotin

source_name: RNA isolated from cells in culture

growth_protocol: HS578T cells were grown in low-glucose DMEM containing 10% fetal calf serum, glutamine and insulin. BAS cells were grown in keratynocyte serum-free medium supplemented with human recombinant epidermal growth factor and bovine pituitary extract. MCF-7 and MDA-MB-231 cells were grown in low-glucose DMEM containing 10% fetal calf serum and glutamine. HMEC (primary human mammary epithelial cells; a pool from 3 isolates from normal reduction mammoplasties) and MCF-10A were grown in serum-free Mammary Epithelial Cell Growth Medium.

extract_protocol: Three biological replicates were used to isolate miRs with the miRCURY RNA isolation kit - Exiqon. RNA was pooled and labelled.

value: NORMAL breast

value: Primary human mammary epithelial cells


title: MDA-MB-231 cells - triple negative

status: Public on Jan 29 2023

type: RNA

city: London

first: Ernesto

last: Yague

address: Du Cane Road

department: Division of Cancer

country: United Kingdom

institute: Imperial College London

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G.

molecule: total RNA

organism: Homo sapiens

label_protocol: Affymetrix FlashTag Biotin HSR RNA Labeling Kit

tag: tissue

value: breast cancer

tag: cell line

value: MDA-MB-231 cells

tag: phenotype

value: triple negative


title: BAS cells - triple negative - metaplastic

description: BAS

value: BAS cells

value: triple negative - metaplastic


title: LX-2 cells, siADAMTS12, 48h, replicate 1

type: SRA

city: Rennes

first: Vincent

last: Legagneux

address: 2 avenue du Professeur Léon Bernard, Bâtiment 5

country: France

institute: Inserm

description:
SiTS12_1
FA_06_S21
LX-2_6_samples_norm_counts.csv

library_source: transcriptomic

data_processing:
FASTQ reads were aligned on the reference genome (GRCh38) using the STAR software and read counts per genes were computed using htseq-count. Read counts were normalized using the R-package DESeq2.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include normalized read count values for each Sample

growth_protocol: LX-2 cells were cultured in DMEM containing 4.5 g/l Glucose, Pyruvate, Glutamine, penicillin (100 IU/ml)-streptomycin (100 mg/ml) and supplemented with 10% fetal calf serum (Eurobio).

extract_protocol:
total RNA was extracted using TRIzol (Invitrogen) reagent according to the manufacturer’s instructions. RNA samples from siRNA-transfected or control LX-2 cells, and from mouse liver samples (see above) were quality controlled by RNA integrity number (RIN) measurement on a Bioanalyzer with RNA 6000 Nano assays (Agilent). RINs were comprised between 9.2 and 9.9.
RNA-sequencing libraries were prepared from 500ng total RNA and quality-controlled on TapesStation (fragment sizes of approximately 260 bp) by the GenoBiRD facility (Nantes, France) using the TruSeq® Stranded mRNA Library Prep (96 samples) from Illumina. Multiplexed (bar-coded) libraries were randomized and sequenced on a NovaSeq 6000.

treatment_protocol:
LX-2 cells were transfected with ADAMTS12 or control siRNAs for 48h using Lipofectamine® RNAiMAX Reagent according to the manufacturer’s instructions. Small interfering RNAs were provided by Eurogentec.
siADAMTS12 sequence (sense): GCCAAAGUUUGGAGGGAAAdTdT - siCTRL (negative control): Eurogentec reference SR-CL000-005.

tag: cell type

value: Activated Hepatic Stellate Cells

tag: genotype

value: WT

tag: treatment

tag: time


title: HS578T cells - paclitaxel resistant

description: HS-TX

value: HS578T cells

value: paclitaxel resistant


title: BC8_PBMC_TIL_CITESEQ.tar.gz

city: Pittsburgh

first: Anthony

middle: Richard

last: Cillo

state: PA

address: The Assembly, Room 4070C Bay 10, 5051 Centre Ave

department: Immunology

country: USA

institute: University of Pittsburgh

description: CITEseq feature barcode matrix

data_processing:
For demuliplexing of samples, bcl2fastq (v2.20.0) was used with the following settings for 3' v2 samples: --use-bases-mask=Y26,I8,Y98 \ --create-fastq-for-index-reads \ --minimum-trimmed-read-length=8 \ --mask-short-adapter-reads=8 \ --ignore-missing-positions \ --ignore-missing-controls \ --ignore-missing-filter \ --ignore-missing-bcls \ -barcode-mismatches=0. The following settings were used for 5' v1 samples: --use-bases-mask=Y28,I8,Y91 \ --create-fastq-for-index-reads \ --minimum-trimmed-read-length=8 \ --mask-short-adapter-reads=8 \ --ignore-missing-positions \ --ignore-missing-controls \ --ignore-missing-filter \ --ignore-missing-bcls \ -barcode-mismatches=0.
CellRanger (v3.1.0; 10X Genomics) was used to align gene expression data to the GRCh38 reference and generate feature barcode expression matrices using the default settings. CITEseqCount was used to align oligonucleotide tags to TotalSeqC (Biolegend) sequences to create citeseq feature barcode expression matrices using the following custom settings: -cbf 1 -cbl 16 -umif 17 -umil 26 \ -trim 10.
Genome_build: GRCh38
Supplementary_files_format_and_content: Each processed data file consists of a gzipped tar file containing either gene expression feature barcode matrices (GEX) or CITEseq feature barcode matrices (CITEseq).

molecule: other

source_name: Peripheral blood, tumor infiltrating leukocytes

extract_protocol:
Blood and tumors were obtained from patients undergoing surgical resection as treatment for breast cancer. Blood specimens were collected by venipuncture into EDTA collection tubes.  Peripheral blood mononuclear cells were isolated from whole blood by Ficoll-Hyapque density gradient centrifugation. Surgical specimens were collected in RPMI 1640 medium supplemented with 10% fetal bovine serum and 1% penicillin and streptomycin. Single cell suspensions were generated from tissues by manually micing tissues and incubating the resulting tissue fragments in serum-free RPMI 1640 with 50 ug/ml of Liberase DL and 1 mg/ml DNase I for 30 minutes. Live CD45+ cells (i.e. all immune cells) were then sorted using a MoFlo Astrios High Speed Sorter (Beckman Coulter). Cell hashing using oligonucleotide conjugated antibodies was performed to multiplex peripheral blood and tumor specimens from the same patients as indiciated in the sample records. Samples were run using either 3'- or 5'-based single-cell RNAseq as described in the samples records.
Libraries were prepared as per the manufacturer's protocol for 3'- and 5'-based single-cell RNAseq. For cell hashed samples, CITEseq libraries were generated as descibed by Stoeckius et al (Nature Biotechnology, 2017).

value: Live CD45+ cells

tag: cancer type

value: Breast cancer

tag: cancer subtype

value: IDC


title: BAScells -doxorubicin resistant

description: BAS-DOX

value: doxorubicin resistant


title: BC3_PBMC_TIL_CITEseq.tar.gz

description: CITEseq feature barcode matrix


title: HS578T cells -doxorubicin resistant

description: HS-DOX


title: MouseBrain_20um_100barcodes_H3K27ac

city: New Haven

first: Di

last: Zhang

state: CT

address: 55 Prospect St

department: Biomedical Engineering

institute: Yale University

data_processing:
Two constant linker sequences (linker 1 and linker 2)  were used to filter Read 2, the Read 2 was refined to extract the Barcode A, Barcode B, and UMI. ST pipeline v1.7.2 was used to map the processed read 1 against the mouse genome (GRCm38), which created the gene matrix for downstream analysis. The gene expression matrix contains information of genes and spatial locations (barcode A x barcode B).
Assembly: mm10
Supplementary files format and content: *tsv: Tab-delimited text files include counts for each pixels for each Sample.

organism: Mus musculus

source_name: Mouse brain P22

extract_protocol: The fresh frozen tissue section was fixed with formaldehyde. The adapters loaded Tn5/pA-Tn5 transposition containing a ligation linker was inserted into transposase accessible genomic DNA loci. The biotin decorated poly-T primer with a ligation linker was added to capture the mRNA for reverse transcription. In situ ligation was conducted by introducing distinct spatial barcode Ai (i = 1-50/100) to the adapters through an array of lateral microchannels. Then, distinct spatial barcode Bj (j = 1-50/100) were introduced through the longitudinal microchannels. Barcodes A and B with linkers were ligated to the 5’ end of the Tn5//pA-Tn5 oligo separately during each ligation. The tissue can be spatially barcoded with a distinct combination of barcodes Ai and Bj (i = 1-50/100, j = 1-50/100, n of barcoded pixels = 2,500/10,000). To correlate the spatially chromatin accessibility, transcriptome, and tissue morphology, the tissue was imaged after each ligation. Reverse crosslinking was then performed to collect barcoded cDNA and DNA fragments. The streptavidin beads were used to separate DNA and cDNA fragments. The cDNA fragments can be enriched with streptavidin beads and the DNA fragment was left in the supernatant. After separation, the DNA and cDNA libraries were constructed separately during PCR amplification. NGS sequencing was then performed using a NovaSeq 6000 sequencer with pair-end 150 bp mode.

value: Mouse brain

tag: spatial resolution

value: 20 um


title: ME13_50um [ATAC-Seq]

library_source: genomic

data_processing:
Two constant linker sequences (linker 1 and linker 2) were used to filter Read 2, and the sequences were converted to Cell Ranger ATAC format (10x Genomics). The genome sequences were in the newly formed Read 1, barcodes A and barcodes B were included in newly formed Read 2. Human reference (GRCh38) or mouse reference (mm10) were used to align the fastq files. The achieved BED like fragments were used to conduct downstream analysis. The fragments file includes fragments information on spatial locations (barcode A x barcode B) and genome.
Assembly: mm10
Supplementary files format and content: BED like fragments file for downstream analysis. The fragments file contains fragments information on the genome and tissue location (barcode A x barcode B).

molecule: genomic DNA

source_name: Mouse embryo E13

extract_protocol: The fresh frozen tissue section was fixed with formaldehyde. The adapters loaded Tn5 transposition containing a ligation linker was inserted into transposase accessible genomic DNA loci. The biotin decorated poly-T primer with a ligation linker was added to capture the mRNA for reverse transcription. In situ ligation was conducted by introducing distinct spatial barcode Ai (i = 1-50/100) to the adapters through an array of lateral microchannels. Then, distinct spatial barcode Bj (j = 1-50/100) were introduced through the longitudinal microchannels. Barcodes A and B with linkers were ligated to the 5’ end of the Tn5 oligo separately during each ligation. The tissue can be spatially barcoded with a distinct combination of barcodes Ai and Bj (i = 1-50/100, j = 1-50/100, n of barcoded pixels = 2,500/10,000). To correlate the spatially chromatin accessibility, transcriptome, and tissue morphology, the tissue was imaged after each ligation. Reverse crosslinking was then performed to collect barcoded cDNA and DNA fragments. The streptavidin beads were used to separate DNA and cDNA fragments. The cDNA fragments can be enriched with streptavidin beads and the DNA fragment was left in the supernatant. After separation, the DNA and cDNA libraries were constructed separately during PCR amplification. NGS sequencing was then performed using a NovaSeq 6000 sequencer with pair-end 150 bp mode.

value: Embryo

value: 50 um


title: BC9_PBMC_TIL_CITESEQ.tar.gz

description: CITEseq feature barcode matrix

value: ILC


title: U937 cells, shKDM6A+6B, ATAC-seq Replicate 2

city: Toronto

first: Alexander

middle: James

last: Murison

state: Ontario

address: 101 College Street, TMDT room 11-706

country: Canada

institute: University Health Network

data_processing:
Reads were mapped against the hg38 human reference genome using BWA with default parameters. All reads with Q<30, duplicate reads, and reads mapped to mitochondria, chrY, an ENCODE blacklisted region (ENCODE Project Consortium 2012) or an unspecified contig, were removed.
MACS 2.0.10 was used to call peaks.
Assembly: hg38
Supplementary files format and content: narrow Peak files for called peaks generated using MACS

source_name: Blood

growth_protocol: U937 cells were maintained in RPMI-1640 medium supplemented with 10% heat inactivated fetal bovine serum and 100 U/mL Penicillin, 100 μg/mL Streptomycin and 2 mM L-Glutamine (all from Gibco) at 37°C with 5% CO2.

extract_protocol:
Cells were lysed using cold lysis buffer. Nuclei were spun at 500g for 10 min using a refrigerated centrifuge. The pellet was resuspended in the transposase reaction mix. Directly following transposition the sample was purified using a Qiagen MinElute kit.
Libraries for ATAC-seq were prepared using Nextera DNA Sample Preparation kit (Illumina)

value: Blood

value: Adult acute monocytic leukemia

value: KDM6A and KDM6B knockdown


title: U937 cells, shKDM6A+6B, ATAC-seq Replicate 3


title: U937 cells, shKDM6B, ATAC-seq Replicate 1

value: KDM6B knockdown


title: BC2_PBMC_TIL_CITEseq.tar.gz

description: CITEseq feature barcode matrix


title: MCF7 cells - luminal type

value: breast cancer

value: MCF7 cells

value: luminal type


title: BC5_PBMC_TIL_CITESEQ.tar.gz

description: CITEseq feature barcode matrix


title: Peripheral Blood, GEX

city: Bethesda

first: Shouguo

last: Gao

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: National Institutes of Health

library_source: transcriptomic single cell

data_processing:
The raw data was processed using cellranger multi. Read counts for genes and proteins are saved in data_RNA.zip and data_ADT.zip
Sample demultiplexing, barcode processing, alignment, filtering, UMI counting,and csv files of TCR clonality were performed using the cellranger analysis pipeline.
Metadata for hashed samples and HTO oligo sequence are available in the file "HTO.csv"
Paired-end reads were mapped to the hg19 genome with cellranger for gene-level read counts
Data normalization, dimension reduction, and differential expression analysis were performed using R and the Seurat R package. Cells were clustered with PhenoGraph.
T cell receptor VDJ analysis: Cellranger vdj
VDJ of Tcells were infered with cellranger vdj pipeline to get TCR contig annotations.
Assembly: hg19
Supplementary files format and content: contig_annotations
Supplementary files format and content: counts
Supplementary files format and content: HTO.csv
Supplementary files format and content: metaData_GEO.csv

molecule: polyA RNA

source_name: Peripheral Blood

extract_protocol:
Cells from pre- and post-treatment of one patient were loaded into the 10XChromium Controller using the Single Cell 5' Library and Gel BeadKit (10X Genomics). The Chromium Single Cell V(D)J protocol was used to profile  gene expression and T cell receptor.
scRNA-seq + TCR +cell surface proteins

tag: library type

value: mRNA

tag: antibody


title: Peripheral Blood, ADT

library_source: other

molecule: protein

value: ADT

value: Anti-CD3/TotalSeq-C0034; Anti-CD4/TotalSeq-C0045; Anti-CD8/TotalSeq-C0046; Anti-CD19/TotalSeq-C0050; Anti-CD11c/TotalSeq-C0053; Anti-CD56/TotalSeq-C0047


title: U937 cells, shKDM6A, ATAC-seq Replicate 3

value: KDM6A knockdown


title: BAS cells - paclitaxel resistant

description: BAS-TX

value: BAS cells

value: paclitaxel resistant


title: BC14_TIL

description: gene expression feature barcode matrix

source_name: Tumor infiltrating leukocytes

value: Live CD45+ cells

value: Breast cancer

value: IDC


title: BC7_PBMC_TIL_CITESEQ.tar.gz

description: CITEseq feature barcode matrix

value: ILC


title: U937 cells, wild type, ATAC-seq Replicate 3

value: Blood

value: Wild type


title: MouseBrain_20um_rep2 ATAC

source_name: Mouse brain P21

value: Mouse brain

value: 20 um


title: U937 cells, shKDM6B, ATAC-seq Replicate 3

value: Adult acute monocytic leukemia

value: KDM6B knockdown


title: ME13_50um

value: Embryo

value: 50 um


title: U937 cells, wild type, ATAC-seq Replicate 2


title: HS578T cells - triple negative- metaplastic

value: breast cancer

value: HS578T cells

value: triple negative- metaplastic


title: BC4_PBMC_TIL_CITESEQ.tar.gz

description: CITEseq feature barcode matrix


title: BC11_TIL

description: gene expression feature barcode matrix


title: MouseBrain, 20um, 100barcodes, H3K4me3

data_processing:
Read 1 was first filtered by two constant linker sequences (linker 1 and linker 2). Then filtered sequences were processed to cellranger atac format (10x Genomics), where the new Read 1 was genome sequences and the new Read 2 includes barcodes A and barcodes B. Resulting fastq files were aligned to the mouse genome (mm10), filtered for duplicates and counted using cellranger atac, which generated the BED like fragments file for downstream analysis. The fragments file contains tissue location info (barcode A x barcode B) and fragments info on the genome. We developed a preprocessing pipeline using Snakemake workflow management system, which is shared at https://github.com/dyxmvp/spatial-CUT-Tag
Assembly: mm10
Supplementary files format and content: BED like fragments file for downstream analysis. The fragments file contains tissue location info (barcode A x barcode B) and fragments info on the genome.
Library strategy: CUT&Tag

extract_protocol: The fresh frozen tissue section was fixed with formaldehyde. The adapters loaded pA-Tn5 transposition containing a ligation linker was inserted into transposase accessible genomic DNA loci. The biotin decorated poly-T primer with a ligation linker was added to capture the mRNA for reverse transcription. In situ ligation was conducted by introducing distinct spatial barcode Ai (i = 1-50/100) to the adapters through an array of lateral microchannels. Then, distinct spatial barcode Bj (j = 1-50/100) were introduced through the longitudinal microchannels. Barcodes A and B with linkers were ligated to the 5’ end of the pA-Tn5 oligo separately during each ligation. The tissue can be spatially barcoded with a distinct combination of barcodes Ai and Bj (i = 1-50/100, j = 1-50/100, n of barcoded pixels = 2,500/10,000). To correlate the spatially chromatin accessibility, transcriptome, and tissue morphology, the tissue was imaged after each ligation. Reverse crosslinking was then performed to collect barcoded cDNA and DNA fragments. The streptavidin beads were used to separate DNA and cDNA fragments. The cDNA fragments can be enriched with streptavidin beads and the DNA fragment was left in the supernatant. After separation, the DNA and cDNA libraries were constructed separately during PCR amplification. NGS sequencing was then performed using a NovaSeq 6000 sequencer with pair-end 150 bp mode.

value: H3K4me3 (Active Motif, 39159)


title: MCF10A cells

value: MCF10A cells


title: Non-diabetic small RNAseq sample #4 [KC285_S36_R1_001]

city: Ithica

first: Praveen

last: Sethupathy

state: NY

address: Cornell University College of Veterinary Medicine, Box 17

institute: Cornell University

description:
Islet sample from a non-diabetic individual
processed data file:
DESeq_HP_smRNA_normalized_counts.csv

data_processing:
Sequencing was aligned and quantiitated using miRquant2.0 (small RNAseq) or aligned and quantified using Proseq.
Both sequencing types were processed with DESeq2.
Genome_build: hg19 (small RNAseq) or hg38 (RNAseq)
Supplementary_files_format_and_content: DESeq normalized counts of transcriptional regulatory elements, genes

source_name: Non-diabetic small RNAseq sample

extract_protocol:
Libraries were prepared according to the TriLink CleanTag Small RNA Library Preparation Kit protocol
Libraries were prepared using the TriLink CleanTag Small RNA Ligation kit (small RNAseq) or as per Dinh et el,  2020 (ChROseq)

value: islet

tag: subject status

value: a non-diabetic individual

tag: molecule subtype

value: small RNA


title: Non-diabetic small RNAseq sample #3 [2285_S41_R1_001]


title: U937 cells, shKDM6B, ATAC-seq Replicate 2


title: U937 cells, shKDM6A+6B, ATAC-seq Replicate 1

value: KDM6A and KDM6B knockdown


title: MouseBrain_20um_100barcodes_H3K27me3


title: BC8_PBMC_TIL

description: gene expression feature barcode matrix

value: Live CD45+ cells

value: Breast cancer

value: IDC


title: MouseBrain_20um_100barcodes_H3K4me3

value: Mouse brain

value: 20 um


title: BC1_PBMC_TIL_CITEseq.tar.gz

description: CITEseq feature barcode matrix

value: ILC


title: post burn day 3, scRNAseq

city: Cincinnati

first: Mike

last: Adam

state: Ohio

address: 240 Albert Sabin Way

department: CBDI

institute: Cincinnati Children's Hospital Research Foundation

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0  (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

source_name: post day 3 burn

extract_protocol:
Single-cell suspensions were processed through Chromium 10X to generate single-cell cDNA libraries attached to microbeads
Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA prepared for sequencing using a modified Nextera XT protocol

value: burn-injured skin

value: post day 3 burn

tag: age

value: 8-12 weeks


title: MouseBrain_20um_100barcodes_ATAC


title: U937 cells, wild type, ATAC-seq Replicate 1

value: Blood

value: Adult acute monocytic leukemia

value: Wild type


title: 24 hr wound beds, scRNAseq

first: Miller-Jensen

last: Lab

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (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

source_name: skin

extract_protocol:
Wound beds were digested for single-cell RNA sequencing analysis in a buffer of Roswell Park Memorial Institute (RPMI) medium with Glutamine (Gibco), Liberase Thermolysin Medium (TM) (Roche), DNase, N-2-hydroxyethylpiperazine-N-2-ethane sulfonic acid (HEPES) (Gibco), Sodium Pyruvate (Gibco), Non-essential amino acids (Gibco), and Antibiotic-Antimycotic (100X) (Gibco). Blood cells were removed with Ammonium-Chloride-Potassium (ACK) lysing buffer (Gibco). Cells were resuspended in Dulbecco's Modified Eagle's Medium (DMEM) (ATCC) with 0.1% Bovine Serum Albumin (BSA) for analysis.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).

value: skin

tag: Sex

value: male

tag: strain

value: wounded using using a 4 mm biopsy punch

value: 24 hours post-injury

value: 7-9 weeks old


title: 48 hr wound beds, scRNAseq

description: 10x Genomics

tag: tissue

value: 48 hours post-injury


title: MouseBrain, 20um, 100barcodes, H3K27ac


title: Non-diabetic small RNAseq sample #2 [17328_S37_R1_001]

value: islet

value: a non-diabetic individual

value: small RNA


title: BC6_PBMC_TIL

description: gene expression feature barcode matrix

value: Live CD45+ cells

value: Breast cancer

value: IDC


title: MouseBrain_20um_repATAC

value: Mouse brain

value: 20 um


title: BC12_TIL

description: gene expression feature barcode matrix

value: ILC


title: MouseBrain, 20um, 100barcodes, H3K27me3

value: H3K27me3 (Cell Signaling Technology, 9733)


title: Type2 diabetes small RNAseq sample #2 [18320_S39_R1_001]

description:
Islet sample from an individual with type2 diabetes
processed data file:
DESeq_HP_smRNA_normalized_counts.csv

source_name: Type2 diabetes small RNAseq sample

value: an individual with type2 diabetes


title: U937 cells, shKDM6A, ATAC-seq Replicate 2

value: Blood

tag: cell line

value: Adult acute monocytic leukemia

value: KDM6A knockdown


title: U937 cells, shControl, RNA-seq Replicate 3

data_processing:
Raw sequencing reads were aligned to human hg19 using STAR with annotations from gencode version 19
Assembly: hg19
Supplementary files format and content: STAR output of reads per transcript

extract_protocol:
Total RNA was isolated using TRIzol (Thermo Fisher Scientific). Genomic DNA contamination was removed by DNase I treatment of the isolated RNA using DNase I RNase free kit (Roche).
Libraries for RNA-seq were prepared using TruSeq RNA Sample Prep Kit v.2 (Illumina) following manufacturer's protocols.

value: Scrambled shRNA control


title: DIPG35

city: Stanford

first: Michelle

last: Monje

state: CA

address: 265 Campus Drive, SIM1 G3035

department: Neurology

institute: Stanford University

data_processing:
Reads were mapped to hg19 annotation using Tophat2 (Kim et al 2013) (version 2.0.13). Transcript expression was quantified against RefSeq gene annotations using featureCounts (Liao et al, 2014). Attached files indicate transcript expression via fpkm values.
Assembly: hg19
Supplementary files format and content: Raw fpkm counts of gene expression abundance for SU-DIPG20, SU-DIPG31, SU-DIPG35, and SU-DIPG48 (in csv format)
Supplementary files format and content: Metadata table with sample key (in csv format)

source_name: Primary human patient DIPG35 tumor tissue

extract_protocol:
RNA-seq samples were pelleted and lysed in Trizol reagent then subsequently precipitated. After extraction from Trizol, RNA-seq samples were poly(A) selected using Dynabeads mRNA Purification Kit (Life Tech) before fragmentation using Thermo AM8740 and Second Strand Synthesis. Libraries were sequenced at 1x75 on an Illumina NextSeq 500.
RNA-seq samples were poly(A) selected using Dynabeads mRNA Purification Kit (Life Tech) before fragmentation using Thermo AM8740 and Second Strand Synthesis.

value: Pons DIPG tumor

value: Primary DIPG cells


title: MouseBrain_20um_H3K27ac rep


title: DIPG48

source_name: Primary human patient DIPG48 tumor tissue


title: BC7_PBMC_TIL

description: gene expression feature barcode matrix


title: BC9_PBMC_TIL

description: gene expression feature barcode matrix


title: Type2 diabetes small RNAseq sample #1 [17300_S40_R1_001]

value: islet


title: U937 cells, shControl, RNA-seq Replicate 2


title: MouseBrain, 20um, H3K27ac, rep


title: Type2 diabetes ChROseq sample #2 [T2D_18320]

description:
Islet sample from an individual with type2 diabetes
processed data file:
DESeq_ChROseq_gene_normalized_b12.csv
DESeq_ChROseq_TRE_normalized_counts_b12.csv

data_processing:
library strategy: chromatin run-on and sequencing (ChRO-seq)
Sequencing was aligned and quantiitated using miRquant2.0 (small RNAseq) or aligned and quantified using Proseq.
Both sequencing types were processed with DESeq2.
Genome_build: hg19 (small RNAseq) or hg38 (RNAseq)
Supplementary_files_format_and_content: DESeq normalized counts of transcriptional regulatory elements, genes

source_name: Type2 diabetes ChROseq sample

extract_protocol:
Libraries were prepared according to Dinh et el, 2020.
Libraries were prepared using the TriLink CleanTag Small RNA Ligation kit (small RNAseq) or as per Dinh et el,  2020 (ChROseq)


title: DIPG31

source_name: Primary human patient DIPG31 tumor tissue


title: U937 cells, shControl, RNA-seq Replicate 1


title: U937 cells, shKDM6A, ATAC-seq Replicate 1


title: MouseBrain_20um


title: MouseBrain_20um_H3K27ac

data_processing:
Read 1 was first filtered by two constant linker sequences (linker 1 and linker 2). Then filtered sequences were processed to cellranger atac format (10x Genomics), where the new Read 1 was genome sequences and the new Read 2 includes barcodes A and barcodes B. Resulting fastq files were aligned to the mouse genome (mm10), filtered for duplicates and counted using cellranger atac, which generated the BED like fragments file for downstream analysis. The fragments file contains tissue location info (barcode A x barcode B) and fragments info on the genome. We developed a preprocessing pipeline using Snakemake workflow management system, which is shared at https://github.com/dyxmvp/spatial-CUT-Tag
Assembly: mm10
Supplementary files format and content: BED like fragments file for downstream analysis. The fragments file contains tissue location info (barcode A x barcode B) and fragments info on the genome.
Library strategy: CUT&TAG


title: MouseBrain 20um H3K27ac


title: Non-diabetic small RNAseq sample #1 [17307_S38_R1_001]

value: a non-diabetic individual


title: BC10_PBMC_TIL

description: gene expression feature barcode matrix


title: MouseBrain 20um


title: BC1_PBMC_TIL

description: gene expression feature barcode matrix


title: DIPG20

source_name: Primary human patient DIPG20 tumor tissue


title: BC5_PBMC_TIL

description: gene expression feature barcode matrix


title: U937 cells, shKDM6B, RNA-seq Replicate 1

value: KDM6B knockdown


title: CByB6F1 BMF untreated-6 [CTRL-6]

data_processing:
The raw data was processed through in-house perl scripts.
Paired-end reads were mapped to the mm10 genome with Hisat2 v2.0.5
Genome_build: mm10
Supplementary_files_format_and_content: gene counts

source_name: Mouse Bone Marrow

extract_protocol: NEBNext Ultra™ II RNA Library Prep Kit for Illumina

value: Female

value: 2-5 months

value: Bone Marrow

tag: markers

tag: sample group


title: Non-diabetic ChROseq sample #4 [ND_18074]

description:
Islet sample from a non-diabetic individual
processed data file:
DESeq_ChROseq_gene_normalized_b12.csv
DESeq_ChROseq_TRE_normalized_counts_b12.csv

source_name: Non-diabetic ChROseq sample


title: Type2 diabetes ChROseq sample #1 [T2D_17300]


title: ME13_100barcodes_25um

value: Embryo

value: 25 um


title: CByB6F1 BMF untreated-4 [CTRL-4]


title: ME13 100barcodes 25um


title: U937 cells, shKDM6B, RNA-seq Replicate 2

tag: cell type

tag: genotype


title: U937 cells, shKDM6B, RNA-seq Replicate 3

tag: treatment


title: MKL-1 TAZ F52A - Rep 3

city: Boston

first: Ashley

middle: K.

last: Gartin

state: MA

address: 450 Brookline Ave. Mayer 444

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Illumina basecalling was performed by Novogene.
Read quality was checked by FastQC.
Salmon version 1.2.0 was used to map the reads to concatenated GRch38p.13 version 102 human cDNA plus ViralProj28509 MCPyV isolate R17b cDNA, and to quantify transcript abundance. Concatenated human and MCPyV gDNA of the same versions was used as a decoy.
tximport version 1.18.0 was used with the latest Ensembl human transcript database to generate files for use by DESeq2. Analysis was restricted to transcripts with an Ensembl ID.
DESeq2 was used to generate normalized transcript count file and perform comparisons between treatment conditions.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table contains normalized transcript counts for all samples calculated by DESeq2. All _quant.txt files contain Salmon quantification of each sample's transcript abundance.

source_name: MKL-1 Merkel cell carcinoma cell line

growth_protocol: MKL-1 cells were maintained in RPMI medium with 10% FBS at 37 °C and 5% CO2.

extract_protocol:
Total RNA was extracted using a standard TRIzol/chloroform protocol.
mRNA libraries were generated using polyA capture and standard Illumina library preparation protocols.

treatment_protocol: Cells were plated at 50E4 cells/mL with 2 µg/mL doxycycline and harvested after 3 days.

tag: induction

value: TAZ F52A


title: MKL-1 TAZ F52A - Rep 1


title: U937 cells, shKDM6A+6B, RNA-seq Replicate 2

value: KDM6A and KDM6B knockdown


title: Non-diabetic ChROseq sample #6 [ND_KC285]


title: CByB6F1 BMF untreated-5 [CTRL-5]


title: Non-diabetic ChROseq sample #2 [ND_17307]


title: Non-diabetic ChROseq sample #5 [ND_2285]


title: BC4_PBMC_TIL

description: gene expression feature barcode matrix

source_name: Peripheral blood, tumor infiltrating leukocytes

value: Live CD45+ cells

tag: cancer type

value: Breast cancer

tag: cancer subtype

value: ILC


title: Non-diabetic ChROseq sample #1 [ND_107968]


title: MKL-1 TAZ - Rep 2

value: TAZ


title: U937 cells, shKDM6A+6B, RNA-seq Replicate 1

source_name: Blood

value: Blood

value: Adult acute monocytic leukemia


title: Non-diabetic ChROseq sample #3 [ND_17328]


title: U937 cells, shKDM6A+6B, RNA-seq Replicate 3


title: MKL-1 TAZ - Rep 3


title: BC2_PBMC_TIL

description: gene expression feature barcode matrix

value: IDC


title: BC3_PBMC_TIL

description: gene expression feature barcode matrix


title: CByB6F1 BMF RUX-treated-3 [RUX-3]


title: U937 cells, shKDM6A, RNA-seq Replicate 3

value: KDM6A knockdown


title: MKL-1 TAZ F52A - Rep 2


title: U937 cells, shKDM6A, RNA-seq Replicate 2


title: CByB6F1 BMF RUX-treated-2 [RUX-2]


title: MKL-1 YAP S94A - Rep 3

value: YAP S94A


title: MKL-1 TAZ - Rep 1


title: CByB6F1 BMF RUX-treated-1 [RUX-1]


title: BMDM treated with CCL26 [C2]

city: Chicago

first: Gye Young

last: Park

state: IL

address: 909 S. Wolcott Avenue CMRB 3080

department: Medicine

institute: University of Illinois at Chicago

description:
C2
counts_filtered.csv

data_processing:
Quality of sequencing data was verified using MultiQC software. Sequence alignment and quantification were performed using the STAR-featureCounts pipeline. Reads overlapping exons in the annotation of Genome Reference Consortium Mouse Build GRCm38 (mm10) were identified, and would be excluded from further downstream analysis if they failed to achieve raw read counts of at least 2 across all the libraries. The trimmed mean of M-values normalization method (TMM) was used for calculating normalized count data.
Genome_build: GRCm38
Supplementary_files_format_and_content: counts_filtered.csv: Read counts were generated by featureCounts. Features (genes) with low expression were discarded and keep holding the genes >=10 reads at least two samples.

source_name: Bone marrow

growth_protocol: Bone marrows were isolated from C57BL/6 mice and cultured in complete DMEM containing 15% L929 cell supernatant for 7 days.

extract_protocol:
Total RNA was isolated with RNeasy Mini kit (Qiagen) according to the manufacturer’s protocol.
Library was constructed by Novogene (Novogene Corporation Inc, Sacramento, CA) using NEBNext Ultra II RNA Library Prep kit.
Paired-end 150bp sequencing on Illumina NovaSeq 6000.

treatment_protocol: Cells were treated with 4 nM of bovine serum albumin (BSA), CX3CL1 or CCL26 and incubated for 4 hours before harvesting.

value: Wild type

value: 6 weeks

value: Bone marrow-derived macrophages


title: MKL-1 YAP S94A - Rep 2


title: BC13_PBMC

description: gene expression feature barcode matrix

source_name: Peripheral blood


title: BC15_PBMC

description: gene expression feature barcode matrix


title: BC15_TIL

description: gene expression feature barcode matrix

source_name: Tumor infiltrating leukocytes


title: MKL-1 YAP - Rep 3

value: YAP


title: BC13_TIL

description: gene expression feature barcode matrix


title: BMDM treated with CCL26 [C3]

description:
C3
counts_filtered.csv


title: BMDM treated with CX3CL1 [B3]

description:
B3
counts_filtered.csv


title: BMDM treated with BSA [A3]

description:
A3
counts_filtered.csv

value: BSA


title: MKL-1 YAP - Rep 2


title: U937 cells, shKDM6A, RNA-seq Replicate 1


title: MKL-1 GFP - Rep 3

value: GFP


title: MKL-1 YAP S94A - Rep 1


title: BMDM treated with CCL26 [C1]

description:
C1
counts_filtered.csv


title: SSc9_SiPN_plus

city: SAGA

first: Yasuhiro

last: Nanri

address: 5-1-1 Nabeshima

country: Japan

institute: Saga university

hyb_protocol: 0.6ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver3.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: RNA was prepared using theRNAiso plus kit (Takara Bio) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2200 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: SSc-DF


title: MKL-1 YAP - Rep 1


title: MKL-1 GFP - Rep 2


title: BMDM treated with CX3CL1 [B1]

description:
B1
counts_filtered.csv


title: BMDM treated with CX3CL1 [B2]

description:
B2
counts_filtered.csv


title: SCC-25, tuni 6h rep3, HTA 2.0

city: Chengdu

first: Chenzhou

last: Wu

address: Number 14, Unit 3, Renmin Nan Road,

country: China

institute: West china hospital of Stomatology, Sichuan university

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HTA 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Human oral cancer cell line SCC28 treated with tunicamycin (5μg/ml)

label_protocol: RNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

growth_protocol: SCC25 cells were maiteined in DMEM/F12 medium with 10% FBS

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cells were washed by PBS for 3 times, and added fresh medium containing tunicamycin (5μg/ml) or DMSO (0.1%) for 6 hours

value: tunicamycin


title: BMDM treated with BSA [A1]

description:
A1
counts_filtered.csv


title: MKL-1 GFP - Rep 1


title: SCC-25, tuni 6h rep1, HTA 2.0


title: 7- MEF Tfam+/-Zbp1-/-_rep1

status: Public on Jan 28 2023

city: Bar Harbor

first: Phillip

last: West

state: ME

address: 600 Main St

institute: The Jackson Laboratory

data_processing:
Illumina BaseSpace FASTQ Generation | Version: 1.0.0
Illumina BaseSpace RNA-Seq Alignment | Version: 2.0.0; Incroporates STAR Aligner (Version: 2.6.1a) and Salmon Quantification (Version 0.11.2)
Assembly: Mus_musculus (UCSC mm10)
Supplementary files format and content: MEF RNA_seq normalized counts.txt

source_name: mouse embryo

growth_protocol: MEFs were grown in DMEM media (Sigma D5796) supplemented with 10% FBS (screened for low endotoxin; VWR 97068-085).  After two passages, cells were harvested for RNA extraction.  Standard culture at 37C, 5% CO2 in a humidified incubator.

extract_protocol:
Total cellular RNA was prepared using the Quick-RNA microprep kit (Zymo Research).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mouse embryo

value: primary mouse embryonic fibroblasts


title: 6- MEF Zbp1-/-_rep2


title: 8- MEF Tfam+/-Zbp1-/-_rep2


title: BMDM treated with BSA [A2]

description:
A2
counts_filtered.csv


title: 3- MEF Tfam+/-_rep1

value: Tfam+/-


title: SCC-25, tuni 6h rep2, HTA 2.0


title: 4- MEF Tfam+/-_rep2


title: 2- MEF WT_rep2

value: WT


title: SSc9_SiSOX_plus


title: SCC-25, ctrl 6h rep3, HTA 2.0

source_name: Human oral cancer cell line SCC25 treated with DMSO  (0.1%)

value: DMSO


title: SSc9_PN_minus


title: SSc9_SiSOX11


title: SSc9_C_plus


title: 2_C_plus


title: 1_C_minus


title: SSc9_C_minus


title: SCC-25, ctrl 6h rep1, HTA 2.0


title: SCC-25, ctrl 6h rep2, HTA 2.0


title: 5- MEF Zbp1-/-_rep1


title: Cone 550

city: Los Angeles

first: David

last: Cobrinik

address: 4661 Sunset Blvd

institute: Childrens Hospital Los Angeles

data_processing:
Reads were trimmed with trim_galore; minimum read quality 20; minimum read length 20bp
Trimmed reads were aligned with HISAT2; penalty for a non-canonical splice site: 20; max and min penalties for mismatch: 1, 0; max and min penalties for soft-clipping: 3,1
Transcript quantitation with Stringtie quantified using reference transcripts from ensembl bulid 87
Count matrices assembled using tximport
Expression  converted to relative transcript counts with Census.
Assembly: GRCh38

source_name: Retina (Gestational week 19)

growth_protocol: Isolated retinae were cultured in retina culture medium (IMDM with 10% FBS, 55 uM β-mercaptoethanol, 0.28 u/ml insulin, glutamine, and penicillin/streptomycin), and media changed every 2-3  days.

extract_protocol:
Each cell group was fully dissociated, and single cells obtained via FACS at multiple time points. cDNA libraries were prepared via a minimized protocol based on the SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing User Manual (Takara Bio) (S Lee et al. in preparation.)
Libraries were generated with Nextera XT DNA library preparation kit (FC-131-1096, Illumina) and a modified protocol based on SMART-Seq® v4 Ultra® Low Input RNA Kit for the Fluidigm® C1TM System, IFCs User Manual (Takara Bio).

treatment_protocol:
Intact retinae were infected with lentivirus carrying OPN1LW-H2B-Cerulean for 4 days and partially dissociated and divided into three groups.
Each cell group was infected with lentivirus carrying either shSCR, shRB1-733 or shRB1-737.

value: Cone

tag: harvested day

value: Day 15

tag: cluster for cones


title: Cone 541


title: Rod 546

value: Rod


title: 100 µM Ebselen, biological rep 2

city: Lucknow

first: Prabhat

last: Singh

state: Uttar Pradesh

address: MG Marg

department: Toxicology

country: India

institute: Central Drug Research Institute

description: Gene expression data from Yeast cell culture treated with 100µM ebselen

hyb_protocol: Fragmentation of labeled aRNA prepares the target for hybridization to GeneChip® 3’ expression arrays. The labeled cRNA was purified, fragmented, and hybridized to the arrays at 45°C for 16 h with constant rotational mixing at 60 rpm.

scan_protocol: Washing and staining of the arrays was performed using the Affymetrix GeneChip Fluidics Station 450. Arrays were scanned using an Affymetrix GeneChip Scanner 3000 and GeneChip® Operating Software (GCOS).

data_processing: RMA

label: biotin

organism: Saccharomyces cerevisiae

source_name: Yeast cell culture treated with 100µM Ebselen

label_protocol: In vitro transcription was performed to synthesize biotin-modified aRNA with IVT labeling master mix generates multiple copies of biotin-modified aRNA from the double stranded cDNA templates (GeneChip® 3’ IVT Express Kit User Manual, Affymetrix)

growth_protocol: Yeast strains were grown in YPD (1% yeast extract, 2% peptone, and 2% dextrose) medium.

extract_protocol: Total RNA was isolated by heat/freeze method as described previously (Schmitt et al., 1990) with slight modification.

treatment_protocol: Yeast were grown in YPD medium till log phase reached at OD600, 0.6-0.8, and treated with 100 µM Ebselen for 3 hours.

value: wild type strain W1588-4c

value: 100 uM Ebselen


title: Cone 545


title: Control, biological rep 2

description: Gene expression data from Yeast cell culture treated with DMSO

source_name: Yeast cell culture treated with DMSO (as a control in which drug was dissolved)

value: control


title: Rod 544


title: Cone 549


title: Cone 537


title: Cone 542


title: Cone 539


title: Cone 547


title: Cone 538


title: 100 µM Ebselen, biological rep 1


title: 1- MEF WT_rep1


title: Cone 540


title: Control, biological rep 1


title: Cone 548


title: Cone 536


title: Rod 543


title: Cone 531


title: Rod-like cells 533

value: Rod-like cells


title: Rod 535


title: Rod 530


title: Rod 529


title: Rod 551


title: Rod 528


title: Cone 534


title: Cone 527


title: Rod 532


title: Rod 526


title: Cone 523


title: Cone 525


title: Rod-like cells 524


title: Cone 517


title: Rod-like cells 513


title: Cone 522


title: Rod 521


title: Rod 514


title: Cone 510


title: Rod 519


title: Cone 512


title: Rod 511


title: Cone 518


title: Rod 515


title: Cone 516


title: Rod 520


title: Rod-like cells 507


title: Rod 508


title: Rod 509


title: Rod 506


title: Rod 503

value: shSCR


title: Rod 505


title: Rod 500


title: Rod 499


title: Cone 498


title: Cone 497


title: Cone 496


title: Cone 494


title: Cone 495


title: Cone 493


title: Cone 491


title: Rod-like cells 492


title: Rod 490


title: Rod 487


title: Rod-like cells 488


title: Rod-like cells 504


title: Cone 484


title: Cone 483


title: Rod 456

value: Day 12


title: Cone 453


title: Cone 455


title: Cone 502


title: Cone 482


title: Rod-like cells 454


title: Cone 451


title: Rod 450


title: Rod-like cells 489


title: Rod-like cells 449


title: Rod 481


title: Rod 452


title: Rod 447


title: Rod 446


title: Cone 444


title: Rod 445


title: Cone 448


title: Cone 443


title: Cone 485


title: Rod 441


title: Rod 439


title: Cone 486


title: Cone 442


title: Cone 440


title: Rod 436


title: Rod 438


title: Cone 433


title: Cone 435


title: Rod 429


title: Rod 437


title: Rod 434


title: Cone 428


title: Cone 431


title: Rod 426


title: Cone 427


title: Cone 432


title: Rod 423


title: Rod 425


title: Rod 422


title: Cone 421


title: Rod 430


title: Cone 416


title: Rod-like cells 417


title: Cone 418


title: Cone 415


title: Rod 412


title: Cone 408


title: Cone 419


title: Rod 413


title: Cone 404


title: Rod 410


title: Cone 401


title: Cone 402


title: Cone 409


title: Cone 411


title: Cone 399


title: Cone 398


title: Cone 403


title: Cone 396


title: Cone 405


title: Rod 424


title: Cone 400


title: Rod 406


title: Cone 414


title: Cone 389


title: Cone 393


title: Rod 407


title: Cone 390


title: Rod 388


title: Rod 387


title: Cone 397


title: Cone 395


title: Rod 392


title: Cone 391


title: Cone 394


title: Rod 358

value: Day 9


title: Cone 359


title: Cone 386


title: Rod 360


title: Cone 361


title: Rod 355


title: Rod-like cells 352


title: Rod 356


title: Cone 349


title: Cone 354


title: Cone 357


title: Cone 351


title: Rod 353


title: Rod 347


title: Cone 350


title: Cone 346


title: Cone 345


title: Rod 340


title: Cone 341


title: Rod 344


title: Cone 343


title: Cone 342


title: Rod-like cells 337


title: Rod-like cells 339


title: Rod-like cells 338


title: Rod 335


title: Rod 334


title: Rod 336


title: Rod 333


title: Rod 329


title: Rod 348


title: Cone 332


title: Cone 330


title: Rod 328


title: Cone 331


title: Rod-like cells 325


title: Rod 321


title: Cone 323


title: Rod 320


title: Cone 322


title: Rod-like cells 317


title: Cone 318


title: Cone 319


title: Rod 313


title: Rod 314


title: Cone 312


title: Cone 316


title: Rod 308


title: Rod 305


title: Cone 307


title: Cone 304


title: Cone 327


title: Cone 315


title: Rod 298


title: Cone 303


title: Rod-like cells 296


title: Cone 301


title: Rod 311


title: Cone 326


title: Rod 306


title: Cone 295


title: Cone 300


title: Cone 310


title: Rod 269

value: Day 7


title: Rod-like cells 267


title: Cone 268


title: Rod 297


title: Rod 309


title: Rod 266


title: Rod 261


title: Cone 264


title: Cone 263


title: Rod 259


title: Cone 258


title: Cone 299


title: Cone 302


title: Cone 257


title: Rod 256


title: Cone 255


title: Rod-like cells 253


title: Rod 265


title: Cone 252


title: Cone 250


title: Cone 262


title: Cone 244


title: Cone 270


title: Cone 242


title: Cone 260


title: Rod 243


title: Rod 240


title: Rod 246


title: Rod-like cells 241


title: Rod-like cells 232


title: Cone 231


title: Rod-like cells 230


title: Cone 247


title: Cone 229


title: Rod 248


title: Rod 225


title: Cone 237


title: Rod 223


title: Rod 254


title: Cone 224


title: Cone 236


title: Cone 234


title: Cone 220


title: Cone 219


title: Cone 216


title: Rod 249


title: Rod 233


title: Cone 245


title: Rod-like cells 215


title: Cone 228


title: Rod 221


title: Cone 222


title: Cone 238


title: Rod 235


title: Rod-like cells 239


title: Cone 212


title: Rod 208


title: Cone 226


title: Cone 213


title: Rod 217


title: Rod 227


title: Rod-like cells 206


title: Rod 209


title: Cone 218


title: Cone 177

value: Day 5


title: Cone 207


title: Cone 211


title: Cone 204


title: Cone 178


title: Rod-like cells 172


title: Cone 205


title: Cone 167


title: Cone 214


title: Rod 159


title: Cone 210


title: Cone 158


title: Cone 176


title: Cone 168


title: Cone 156


title: Rod-like cells 155


title: Cone 152


title: Cone 150


title: Cone 165


title: Rod-like cells 171


title: Cone 151


title: Rod 169


title: Rod 146


title: Cone 162


title: Cone 174


title: Rod 166


title: Cone 153


title: Rod 157


title: Cone 175


title: Cone 143


title: Cone 140


title: Rod 139


title: Cone 173


title: Cone 154


title: Cone 138


title: Rod 141


title: Rod 170


title: Cone 164


title: Cone 160


title: Cone 163


title: Cone 129


title: Cone 147


title: Rod 136


title: Cone 127


title: Rod 124


title: Cone 149


title: Cone 161


title: Rod 137


title: Cone 145


title: Cone 148


title: Cone 144


title: Rod 142


title: Cone 116


title: Cone 133


title: Cone 132


title: Cone 135


title: Immune_p53 Off 2

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

description: 10x Genomics (3' kit, v2.0)

data_processing:
All scRNAseq data were processed into count matrices using 10x Genomics CellRanger All scRNAseq data were processed into count matrices using 10x Genomics CellRanger 6.0.0 with default parameters using reference mouse genome GRCm38/mm10 augmented with BioLegend TotalSeqB hashtag oligonucleotide barcode sequences for demultiplexing cellular compartments in downstream analysis oligonucleotide barcode sequences for demultiplexing cellular compartments in downstream analysis. Count matrices were processed to remove empty and low quality droplets by removing (in order): transcripts with more than 10 million or fewer than 100 total reads, droplets with library size greater than 150,000 or lower than 300 total read count, and droplets with fewer than 15 distinct expressed transcripts.
Potential doublets were removed using Solo version 1.2 (76) by training one doublet classification model per sample using default parameters for Solo and removing droplets using a threshold of 0.5. Subsequently, dead / dying cells were filtered by removing droplets with high mitochondrial RNA content (greater than 20% of transcript counts mapped to MT genes) or high ribosomal transcript count (greater than 15% of total transcript counts mapped to ribosomal genes). After pre-processing, poor quality samples with either low numbers of recovered cells or low number of distinct transcripts recovered were removed.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: liver tumor

growth_protocol: GFP-expressing NSP tumor cells were cultured off Dox to suppress p53 expression and orthotopically injected into liver of C57B/6 mice fed with Dox food. After 2-3 weeks tumor growth, the mice were randomized either keeping on Dox or removing Dox diet to control p53 expression in tumor cells

extract_protocol:
Single-cell encapsulation and scRNA-seq library prep of Flow cytometry-sorted cell suspensions was performed on the Chromium instrument (10x Genomics) following the user manual (Reagent Kit 3’ v2). Each sample loaded onto the cartridge contained approximately 40,000 cells at a final dilution of ~600 cells/μl. Transcriptomes of encapsulated cells were barcoded during reverse transcription.
cDNA was purified with DynaBeads, followed by amplification per the user manual (Reagent Kit 3’ v2). Next, the PCR-amplified product was fragmented, A-tailed, purified with 1.2X SPRI beads, ligated to sequencing adapters and indexed by PCR. Indexed DNA libraries were double-size purified (0.6–0.8X) with SPRI beads.
scRNA-seq (3' kit, v 2.0)

treatment_protocol: Liver tumors were harvested from the indicated mouse models and processed for FACS using Collagenase IV (1 mg/mL) & Dispase II (2 U/mL) mix digestion solution and Gentle-MACS dissociator (mTDK_1 protocol), followed by a 0.05% Trypsin-EDTA step. Cell suspensions were incubated with Fc block and CD45-APC or CD45-APC-Cy7 antibody to mark immune cells. Live immune cells from liver tumor (marked as GFP-negative, CD45-positive and DAPI-negative) were sorted using Sony or Aria 1 sorter, and collected in 2% 1x PBS buffer containing 2% fetal bovine serum (FBS).  Single-cell suspensions were spun down and resuspended in 0.05% BSA containing 1 U/µL Invitrogen Ambion RNase Inhibitor (AM2682, Thermo Fisher Scientific).

value: sorted primary immune cells (CD45+)

value: liver tumor

tag: condition

value: orthotopic liver injection

value: p53 Off

tag: sorting strategy

value: GFP-; Cd45+;DAPI-

tag: mouse strain

value: Female


title: Immune_p53 On 1

description: 10x Genomics (3' kit, v2.0)

value: p53 On 8 days

tag: Sex


title: Cone 121

value: Cone


title: Cone 134


title: Cone 113


title: Cone 122


title: Cone 128


title: Cone 114


title: Cone 123


title: Xrn1-WT 30 min NaCl, replicate 3

city: Barcelona

first: Juana

last: Díez

state: Barcelona

address: Carrer del Dr. Aiguader 88

department: Department of Experimental and Health Sciences

country: Spain

institute: Universitat Pompeu Fabra

data_processing:
RNA-sequencing reads were mapped to the sacCer3 genome build using TopHat2 (v2.1.0, settings: “--max-multihits 1 --library-type fr-firststrand --b2-very-sensitive --no-coverage-search”) and quantified using featureCounts (v1.5.1, “-Q 1 -s 2”)
Differential expression testing was performed using DESeq2 v1.22.2.
Genome_build: sacCer3
Supplementary_files_format_and_content: The file raw_counts_mRNA.tsv contains raw mRNA read counts from featureCounts. Each column represents one sample in lexicographical order.

source_name: whole cell

growth_protocol: Xrn1-AID cells were grown to log-phase on YPD medium at 30ºC (no stress) and then subjected to auxin (500 µM) for 30 minutes (Xrn1-AID) or not subjected to auxin (Xrn1-WT). Stressed samples were incubated with 0.4 M NaCl diluted in YAPD media for 10 and 30 min for both Xrn1-AID and Xrn1-WT cells.

extract_protocol:
The samples were treated with Proteinase K (New England Biolabs) to get rid of the proteins, and then total RNA was extracted by a phenol-chloropropane method. After, remaining DNA was digested by Turbo DNase (Ambion) and RNA was extracted again with acid phenol-chloroform method. RNA concentration was measured by Nanodrop.
Libraries were prepared using the protocol described in TrueSeq Stranded mRNA Sample kit (Illumina). The libraries were sequenced by HiSeq 2500 System (Illumina) in reads of 50 base-pair length (1x50).

treatment_protocol: Samples were treated with auxin (Xrn1-AID) or not (Xrn1-WT) before being osmostressed with NaCl (10 min NaCl; 30 min NaCl) or not (no stress).

tag: pretreatment

value: 30 min 0.4 M NaCl


title: Cone 125


title: Xrn1-WT 30 min NaCl, replicate 2


title: Cone 130


title: Cone 118


title: Cone 126


title: Cone 110


title: Rod 120

value: Rod


title: Immune_p53 Off 3

description: 10x Genomics (3' kit, v2.0)

tag: tissue


title: Cone 131


title: Cone 119


title: Xrn1-WT 30 min NaCl, replicate 1


title: Cone 108


title: Immune_p53 Off 1

description: 10x Genomics (3' kit, v2.0)


title: Immune_p53 On 2

description: 10x Genomics (3' kit, v2.0)


title: Cone 115


title: Cone 111


title: Cone 83

value: Day 3


title: Rod 84


title: Cone 82


title: Cone 112


title: CX3 3035

city: San Antonio

first: Kaira

middle: Adriana

last: Church

state: TX

address: One UTSA Circle 1.212

department: Molecular Microbiology and Immunology

institute: University of Texas at San Antonio

data_processing:
After the sequencing run, demultiplexing with Bcl2fastq2 was employed to generate the fastq file, with the average of 30M reads per sample
Raw reads were imported into CLC Genomics Workbench v21.0.5
Initially, adaptors were trimmed and remaining reads for each sample were mapped to the annotated mouse genome (GRCm39), followed by differential gene expression (DEG) analysis using the RNA-seq analysis tools within the CLC genomics software
Assembly: GRCm39
Supplementary files format and content: excel file outlining the differentially expressed genes in the comparison listed in the file name

source_name: Retina

extract_protocol:
RNA was isolated from enucleated retinas using the Qiagen RNeasy Kit following tissue homogenization using Zymo Research BashingBead lysis tubes.
Approximately 500ng of total RNA was used for stranded mRNA-seq library preparation by following the NEB Directional mRNA-seq sample preparation guide. The first step in the workflow involved purifying the poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads. Following purification, the mRNA was fragmented into small pieces using divalent cautions under elevated temperature. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP in the Second Strand Marking Mix (SMM). These cDNA fragments then went through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products were then purified and enriched with PCR to create the final RNA-seq library. Finally RNA-seq libraries were subjected to quantification process, pooled for cBot amplification and subsequent 100bp paired read sequencing run with Illumina NovaSeq 6000 platform.

value: Retina

value: WILD-TYPE

value: 10wks Diabetic + 2wks DTx + 2wks DTx recovery


title: Rod-like cells 80

value: Rod-like cells


title: Cone 117

value: shSCR


title: Cone 78


title: Cone 85


title: Cone 109

value: Day 5


title: CX3 3033


title: CX3 3032


title: Xrn1-WT, no stress, replicate 2


title: CX3 3034


title: Cone 79


title: CX3 2983

value: 10wks Diabetic + PBS


title: CX3 3031


title: Xrn1-WT 10 min NaCl, replicate 2

value: 10 min 0.4 M NaCl


title: Xrn1-WT, no stress, replicate 1


title: CX3 2981


title: Cone 74


title: Rod 81


title: Xrn1-WT 10 min NaCl, replicate 3


title: Xrn1-WT 10 min NaCl, replicate 1


title: CX3 2979


title: Xrn1-AID 30 min NaCl, replicate 2

value: 30 min 500 μM auxin


title: Cone 77


title: CX3 2982


title: Cone 73


title: Xrn1-AID 10 min NaCl, replicate 3


title: CX3 3029

value: 8wks Diabetic + 2wks DTx


title: Cone 75


title: Cone 76


title: Xrn1-AID 30 min NaCl, replicate 1


title: Cone 68


title: CX3 3028


title: CX3 2980


title: Xrn1-AID 10 min NaCl, replicate 2


title: CX3 3027


title: Xrn1-WT, no stress, replicate 3


title: Cone 70


title: Xrn1-AID, no stress, replicate 2


title: Cone 64


title: Cone 62


title: Cone 63


title: Xrn1-AID, no stress, replicate 3


title: Cone 71


title: CX3 2977

value: 8wks Diabetic + PBS


title: CX3 3026


title: Rod 56


title: Cone 72


title: CX3 2978


title: CX3 2974


title: Cone 53


title: Cone 51


title: CX3 3015

value: 6wks Diabetic


title: Cone 60


title: CX3 3014


title: Cone 67


title: Cone 65


title: Cone 66


title: Cone 69


title: CX3 2976


title: CX3 3013


title: OPC Ro25-6981, 2

city: Baltimore

first: Weifeng

last: Li

state: Maryland

address: 400 N Broadway

institute: Johns hopkins university

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Cells from each well were dissociated into single cells by treating with accutase for 45 minutes (just the cells that had migrated out from the spheres were collected, the spheres remain mostly intact). Single cells were passed through 40 uM cell strainers, washed once with PBS, cryopreserved in CTLC-ABC (NC9711917, Immunospot) buffer, and stored in -80 before shipping for single cell capture
The cryopreserved cells were thawed by following the instructions provided for CTLC-ABC. Cells were washed and counted on the DeNovex cell counter. Single cell capture, barcoding, post GEM-RT cleanup, cDNA amplification, and 3’ library construction was performed using the 10X genomics’ single-cell RNA-seq technology by following their detailed instructions

tag: cell line

value: hESC-derived OPC

value: wildtype


title: Cone 55

value: Cone


title: Xrn1-AID 10 min NaCl, replicate 1


title: Rod 54

value: Rod


title: CX3 3012


title: Xrn1-AID, no stress, replicate 1


title: Cone 58

value: Day 3


title: Rod 50


title: Cone 59


title: Cone 61


title: CX3 2975

value: Retina


title: Cone 57


title: CX3 3011

value: WILD-TYPE


title: Cone 52


title: Rod 47


title: Cone 49


title: Cone 45


title: OPC Ro25-6981, 1

description: 10x Genomics


title: Cone 46


title: Cone 48


title: Rod 42


title: CX3 3025

value: Non-Diabetic + 2wks DTx +2wks DTx recovery


title: Cone 44


title: Rod 43


title: Cone 41


title: Cone 38


title: Rod 40


title: OPC Ro1138452, 2

description: 10x Genomics


title: OPC SR2211, 1

description: 10x Genomics


title: CX3 3024


title: OPC SR2211, 2

description: 10x Genomics


title: Cone 37


title: CX3 3023


title: CX3 3022


title: Cone 36


title: OPC DMSO control, 3

description: 10x Genomics

value: DMSO


title: OPC Ro1138452, 1

description: 10x Genomics


title: Rod 35

value: shSCR


title: CX3 3021


title: Rod 33


title: Cone 34


title: Cone 32


title: OPC DMSO control, 2

description: 10x Genomics


title: OPC DMSO control, 1

description: 10x Genomics


title: CX3 3016

value: Non-Diabetic


title: Cone 39


title: Rod 31


title: Cone 30


title: CX3 3010


title: MH3

city: Shanghai

first: Wenjun

last: Wang

address: Huangpu District Fangxie Lu 419

institute: Obstetrics and Gynecology Hospital, Fudan University

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated
Raw data (raw reads) were processed using Trimmomatic.
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
DEGs were identified using the DESeq(2012) R package functions estimateSizeFactors and nbinomTest
Assembly: hg38
Supplementary files format and content: The txt file include FPKM values for each Sample
Supplementary files format and content: The txt file include counts values for each Sample

source_name: KGN cells, MH,1ug/ml, 72h

growth_protocol: KGN cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
RNA libraries for RNA-seq were prepared using VAHTS Universal V6 RNA-seq Library Prep following manufacturer's protocols.

treatment_protocol: KGN cells were  treated with solvent, 0.5ug/ml insulin or 1ug/ml insulin (Sigma) for 72h after fasting 12h

value: KGN cells

value: human ovarian granulosa cells

value: WT

value: 1ug/ml insulin


title: MH2


title: CX3 3008


title: Cone 28


title: M3

source_name: KGN cells, M,0.5ug/ml, 72h

value: 0.5ug/ml insulin


title: Cone 25


title: Cone 26


title: CX3 3009


title: Cone 29


title: Rod 27


title: Cone 23


title: M2


title: Cone 24


title: M1


title: Cone 19


title: Cone 18


title: MH1


title: Cone 21


title: Cone 20


title: CX3 3007


title: CX3 3006


title: Cone 17


title: C3

source_name: KGN cells, Control,solvent,72h

value: solvent


title: Hippocampus, TBI, 24-h rep1

first: Jianwei

last: Zhao

address: 600 Yishan Road

department: Department of Neurosurgery

institute: Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
In the current analysis, FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) method was adopted for quality control.
HISAT2 was used to align the raw RNA-seq reads to the mouse reference genome (Mus musculus, GRCm38)
StringTie was used to assemble and quantify the transcripts.
The DEGs between the TBI and sham groups were analyzed using the “DESeq2” R package
Assembly: GRCm38
Supplementary files format and content: tab-delimited txt file with raw counts matrix containing all samples

source_name: hippocampus

extract_protocol:
RNA was harvested using MolPure® Cell/Tissue Total RNA Kit (Yeasen Biotechnology (Shanghai) Co., Ltd). 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared for sequencing using standard Illumina protocols

tag: breed

value: hippocampus

tag: protocol

value: TBI

tag: time point

value: Male


title: Cone 22

tag: cell type

value: Cone


title: genomic DNA from DKO clone3

type: genomic

first: Weiya

middle: Stephanie

last: Ni

state: California

address: 1450 Biggy Street

institute: University of Southern California

hyb_protocol: The bisulfite-converted DNA was analyzed using Illumina EPIC BeadArrays, as described in Moran, 2016 (PMID: 26673039).

scan_protocol: The BeadArrays were scanned

data_processing:
The raw signal intensities were extracted from the *.IDAT files using the ‘noob’ function in the minfi R package.
Unmethylated and methylated signal intensities

label: cy3, cy5

source_name: DKO clone3

label_protocol: Standard Illumina Protocol

growth_protocol: HEK293T cells were grown according to ATCC protocol

extract_protocol: Genomic DNA was extracted from wt HEK293T cells and the three DKO clones using the Zymo Quick-DNA Miniprep kit (Zymo #D3024) and bisulfite-converted using the Zymo EZ DNA Methylation kit (Zymo #D5001) according to the manufacturer’s protocol.

tag: genotype

value: ZFX and ZNF711 DKO

tag: clone id

value: ZFX and ZNF711 DKO clone3


title: C1

tag: treatment


title: Hippocampus, TBI, 24-h rep3


title: SK-N-AS RNA-seq

city: Parkville

first: Jack

middle: Aatto Laasonen

last: Cooper

state: Victoria

address: 49 College Crescent

country: Australia

institute: University of Melbourne

description:
RNA-seq
PAR-CLIP RNA-seq control counts.csv

data_processing:
fastq files were quantified against a reference genome (hg19)
Salmon quants were aggregated into read counts and imported into R with tximport version 1.4.0
Read counts were normalised using DESeq2 version 1.16.1
hg19
KELLY NONO normalised counts.csv contains the read counts for each of the 12 samples in the NONO KD RNA-seq experiment, normalised with DESeq2. "PAR-CLIP RNA-seq control counts.csv" contains the read counts for the RNA samples sequenced alongside the PAR-CLIP experiment.

source_name: SK-N-AS

growth_protocol: KELLY cells were grown in 10% foetal bovine serum (FBS) and 100 U/mL penicillin streptomycin (PenStrep) RPMI media, while SK-N-AS and BEC2 cells were grown in 10% FBS and 100 U/mL PenStrep DMEM media. For RNA-seq, cells were grown in 6-well plates for 24 hours. For PAR-CLIP, cells were grown in 15cm dishes for 2 days. All culturing was done in a humidified incubator (37ºC; 5% carbon dioxide).

extract_protocol:
For NONO KD samples and total RNA samples (KELLY, BEC2 and SK-N-AS, cells were lysed using Nucleozol ™? by Machery-Nagel. For PAR-CLIP samples, after PAR-CLIP protocol was conducted (including immmunoprecipitation, phosphorus-32 treatment, SDS-PAGE electrophoresis and proteinase K treatment), samples were extracted using the Qiagen™? miRNeasy RNA extraction kit.
RNA extracted from PAR-CLIP was converted into cDNA using the TruSeq small RNA Kit v2 (illumina). RNA extracted from other samples was converted to cDNA with the TruSeq Stranded Total RNA Library Prep Kit (illumina) and rRNA depleted with the Ribo-Zero-Gold kit (illumina). All samples were sequenced on illumina Hiseq 2000 to obtain 50bp single end reads.

treatment_protocol: For siRNA treated samples, media was replaced with 4% FBS-RPMI media, and forward transfection of 10 nM siRNAs was conducted, with cells lysed for RNA extraction 72 hours later. Other RNA-seq samples were not treated and were lysed 48 hours after plating into 6-well plates. For PAR-CLIP, 40 µL of 50mM 4-thiouridine (4-SU) was added to each plate (for final concentration of 100µM 4-SU). Cells were left for another 14 hours, after which media was removed and plates were irradiated 0.15J/cm2 with 365 nm UV light. Cells were scraped off the plates using a cell scraper, suspended in PBS and centrifuged (6,000 x g for 5 minutes), with a pellet of cells remaining (and supernatant removed).

value: Immortalised neuroblastoma cells

tag: passages


title: Hippocampus, TBI, 24-h rep2


title: genomic DNA from wt HEK293T

source_name: wt HEK293T

value: wild type

value: wt HEK293T


title: C2


title: Hippocampus, Sham, 24-h rep3

value: sham


title: BEC2 RNA-seq


title: BEC2 NONO PAR-CLIP

description:
PAR-CLIP
BEC2 NONO clusters.csv

data_processing:
The PARpipe pipeline (https://github.com/ohlerlab/PARpipe)  was used for analysis of PAR-CLIP data, this pipeline uses the following steps:
Cutadapt version 1.14 was used to remove sequencing adapters and low quality reads (-n 1 -m 20)
Bowtie version 1.2.1.1 was used to align sequence reads to the reference genome (hg19)
Reads were aggregated into clusters using PARalyzer version 1.5 and the default settings
hg19
Cluster files contain clusters (peaks) called by PARalyzer, showing hg19 genomic coordinates as well as additional peak scoring information (see PARpipe https://github.com/ohlerlab/PARpipe)


title: genomic DNA from DKO clone1

source_name: DKO clone1

value: ZFX and ZNF711 DKO clone1


title: Hippocampus, Sham, 24-h rep2


title: Hippocampus, Sham, 24-h rep1


title: KF2_Fn14 si2 (biol rep2)

city: Guangzhou

first: Gu

last: Jingjing

address: No2. Road Lujing

institute: Dermatology Hospital, Southern Medical University

description: KF2_Fn14 si2

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 mm9 whole genome using hisat2 (v2.0.1)
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using stringtie-2.0.6 following the protocol from Pertea et al., Nature Protocols, 2016.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for all Sample.

source_name: keloid dermis

growth_protocol: Keloid fibroblasts were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was isolated from cells using TRIzol (Takara). Total RNA was quantified and qualified by Agilent 2100/2200 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).1.1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: keloid dermis

value: Primary cell

value: fibroblast

value: Fn14 knockdown

value: Transfected with Fn14-targeted siRNA 2 (Fn14 siRNA 2) for 72 h.


title: KELLY RNA-seq

source_name: KELLY


title: KELLY siR-NONO_2 3

description:
RNA-seq
KELLY NONO KD normalised counts.csv


title: KF2_siNC (biol rep2)

value: Fn14 siNC

value: Transfected with nontargeting control-siRNA (siNC) for 72 h.


title: KELLY siR-NONO_2 2


title: KELLY NONO PAR-CLIP

description:
PAR-CLIP
KELLY NONO clusters.csv


title: KF1_Fn14 si2 (biol rep1)

description: KF1_Fn14 si2


title: SK-N-AS NONO PAR-CLIP

description:
PAR-CLIP
SKNAS NONO clusters.csv


title: KELLY siR-NONO_1 2


title: KELLY siR-NONO_2 4


title: KF1_Fn14 si1 (biol rep1)

description: KF1_Fn14 si1

value: Transfected with Fn14-targeted siRNA 1 (Fn14 siRNA 1) for 72 h.


title: genomic DNA from DKO clone2

source_name: DKO clone2

value: ZFX and ZNF711 DKO clone2


title: KF2_Fn14 si1 (biol rep2)

description: KF2_Fn14 si1


title: KELLY siR-NONO_1 4


title: KELLY siR-NC 4


title: KELLY siR-NONO_1 1


title: KF1_siNC (biol rep1)


title: 2-m/o mouse liver, 4 day post-partial hepatectomy, rep2

city: Houston

first: Xiaoqin

last: Liu

address: 2121 W. Holcombe Blvd., Room 511

department: Center for translational cancer research

institute: Texas A&M University IBT

data_processing:
Model based Analysis of Bisulfite Sequencing data
The quality of raw WGBS data was determined using the fastqc V0.11.5 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and multiqc v0.9.dv0 (https://github.com/ewels/MultiQC) modules.
Qualified reads were mapped to the mouse GRCm38/mm10 reference genome using the BSMAP module.
Methylation calling was done using the MCALL module. DMCs and DMRs were identified using the MCOMP module, with credible methylation difference ∆b > 0.2 for hypermethylation or < -0.2 for hypomethylation, and p-value < 0.05.
Assembly: mm10
Supplementary files format and content: bedGraph

source_name: Liver

extract_protocol:
Genomic DNA was harvested using using the AllPrep DNA/RNA/Protein Mini kit (Qiagen, #80004). 1.3 ug of total RNA was used for the construction of sequencing libraries.
DNA fragments were end-repaired, A-tailed, and ligated with methylated paired-end adaptors using the NEBNext UltraTM II DNA Library Prep Kit (NEB, #E7645S/L). Adaptor-ligated DNA fragments were size-selected and bisulfite treated using the EZ DNA Methylation-LightningTM kit (Zymo, D5030T).
WGBS

treatment_protocol: baseline or 70% partial hepatectomy

value: Liver

tag: group

value: regeneration

value: female

value: 70% partial hepatectomy, day 4

tag: age


title: 2-m/o mouse liver, 4 day post-partial hepatectomy, rep4


title: 2-m/o mouse liver, 2 day post-partial hepatectomy, rep4

value: 70% partial hepatectomy, day 2


title: KELLY siR-NONO_1 3

value: Immortalised neuroblastoma cells


title: KELLY siR-NC 1


title: 2-m/o mouse liver, 4 day post-partial hepatectomy, rep3


title: KF2_TWEAK (biol rep2)

value: TWEAK stimulation

value: TWEAK-100ng/ml, 48h


title: 2-m/o mouse liver, 2 day post-partial hepatectomy, rep2


title: KF1_TWEAK (biol rep1)

value: keloid dermis


title: KELLY siR-NC 3


title: KELLY siR-NC 2


title: 2-m/o mouse liver, 4 day post-partial hepatectomy, rep1


title: 2-m/o mouse liver, 1 day post-partial hepatectomy, rep4

value: 70% partial hepatectomy, day 1


title: KELLY siR-NONO_2 1


title: KF2_no TWEAK(biol rep2)

value: Primary cell

value: fibroblast

value: WT

value: TWEAK-0ng/ml, 48h


title: 2-m/o mouse liver, 1 day post-partial hepatectomy, rep3


title: 2-m/o mouse liver, 2 day post-partial hepatectomy, rep3


title: BT549_Clone242_rep3

city: Ceriano Laghetto

first: Alberto

last: Gallo

state: District Of Columbia

address: Via Marconi 11/B

country: Italy

institute: Università degli Studi di Milano

description:
final_tab_BT549_raw_genes.txt
final_tab_BT549_norm_genes.txt
final_tab_BT549_norm_isoforms.txt

data_processing:
mRNA expression was calculated from FASTQ files with RSEM (version = 1.3.1)
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes gene-level expected counts for each Sample (raw_genes)
Supplementary files format and content: tab-delimited text file includes gene-level TPM values for each Sample (norm_genes)
Supplementary files format and content: tab-delimited text file includes isoform-level TPM values for each Sample (norm_isoforms)

extract_protocol:
RNA samples were extracted with the Tri-Reagent protocol (Sigma-Aldrich). 1 μg of total RNA was retrotranscribed to cDNA by the MMLV Reverse Transcription Mix (GeneSpin). RNA samples for RNA-Seq were extracted from three independent biological replicates for each cell line, treated with DNAse and checked for its quality by RNA ScreenTape Assay with TapeStation System.
BT549: mRNA was enriched using oligo(dT) beads cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) was added with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation. The final cDNA library was obtained after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR enrichment. SUM159PT: total RNA was depleted of ribosomal RNA and the RNAseq libraries were prepared with the Illumina TruSeq Stranded Total RNA kit following the manufacturer’s protocol. Amplified libraries were checked on a bioanalyzer 2100 and quantified with picogreen reagent.

value: Claudinlow Breast Cancer

value: NF-YA deltaEx3

value: CRISPR/spCas9D10A editing


title: MDA-MB-231 DSM OE, rep3

city: Gainesville

first: Daiqing

last: Liao

state: FL

address: 2033 Mowry Rd

department: Anatomy and Cell Biology

institute: University of Florida

hyb_protocol: Sense strand DNA was fragmented, biotinylated, and hybridized with rotation at 45°C for 16 hr to the GeneChip® Human Transcriptome Array 2.0.

scan_protocol: The arrays were washed and stained with streptavidin-phycoerythrin (SAPE) on an Affymetrix Fluidics Station 450, and scanned on a GeneChip® 7G Scanner (Affymetrix, Inc).

data_processing: We used the Affymetrix® Expression Console Software  (Version 1.3) to generate .txt files for each RNA hybridization.

source_name: MDA-MB-231 DSM OE

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA

growth_protocol: MDA-MB-231 cells were seeded in a well in a 6-well plate and cultured in complete DMEM medium for 24 hours

extract_protocol: Extraction of total RNA with the RNeasy mini kit was performed according to the manufacturer's instructions.

value: Cultured breast cancer cells

value: DSM OE


title: KF3_no TWEAK (biol rep3)


title: 2-m/o mouse liver, 2 day post-partial hepatectomy, rep1

value: Liver

value: regeneration

value: female


title: KF3_TWEAK (biol rep3)


title: KF1_no TWEAK (biol rep1)


title: BT549_Clone242_rep1


title: NSP_SEN_IFNG_1 ng_3

data_processing:
Illumina read quality was checked for each sample using FastQC v0.11.5.
Raw fastq files were analyzed by removing adaptor sequences using Trimmomatic (0.36), aligned to the mouse genome using STAR (2.5.3a), and quantified transcript counts using featureCounts (1.6.3).
Assembly: Reads were aligned to the mouse transcriptome (mm10, GRCm38.91)
Supplementary files format and content: Tab-delimited text file includes raw count table for each sample

source_name: in vitro senescent NSP cells + IFNg high dose

growth_protocol: NSP cells were cultured in DMEM supplemented with 10% FBS and 1% penicillin and streptomycin (GIBCO) on plates that were collagen-coated (PurCol, Advanced Biomatrix, 0.1 mg/ml) for 30’ at 37 C and maintained by the addition of 1 μg/ml doxycycline to suppr

extract_protocol:
PolyA mRNA was selected using beads coated with polyT oligonucleotides. Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.
For sequencing, pooled multiplexed libraries were run on a HiSeq 2500 machine on RAPID mode. Approximately 10 million 76bp single-end reads were retrieved per replicate  condition. Resulting RNA-Seq data was analyzed by removing adaptor sequences using Trimmomatic (29), aligning sequencing data to GRCh37.75(hg19) with STAR (30), and genome wide transcript counting using HTSeq (31) to generate a RPKM matrix of transcript counts.

value: Cell line

value: Doxycycline Off


title: NSP_SEN_IFNG_1 ng_2

growth_protocol: NSP cells were cultured in DMEM supplemented with 10% FBS and 1% penicillin and streptomycin (GIBCO) on plates that were collagen-coated (PurCol, Advanced Biomatrix, 0.1 mg/ml) for 30’ at 37 C and maintained by the addition of 1 μg/ml doxycycline to suppress p53 expression. In order to restore p53 expression and therefore induce senescence, doxycycline-containing media was replaced with doxycycline-free media for 6 days and senescent cells were seeded and collected on day 8 after doxycycline withdrawal. For IFN-γ of proliferating or senescent populations, the indicated doses of mouse recombinant IFN-γ was administrated to proliferating and senescent (p53-restored) NSP cells after 24 h of cell seeding and cells were harvested after 24 h of IFN-γ treatment.


title: BT549_Clone12_rep3


title: NSP_PRO_IFNG_1 ng_3

source_name: in vitro proliferating NSP cells + IFNg high dose

value: Doxycycline On


title: NSP_PRO_IFNG_1 ng_2


title: NSP_PRO_IFNG_1 ng_1


title: NSP_PRO_No IFNG_1

source_name: in vitro proliferating NSP cells + no IFNg


title: NSP_PRO_No IFNG_3


title: MDA-MB-231 DAXX OE, rep1

source_name: MDA-MB-231 DAXX OE

value: DAXX OE


title: 2-m/o mouse liver, 1 day post-partial hepatectomy, rep1

value: 70% partial hepatectomy, day 1


title: BT549_Clone242_rep2


title: MDA-MB-231 DSM OE, rep1


title: NSP_SEN_No IFNG_3

source_name: in vitro senescent NSP cells + no IFNg


title: 16-m/o mouse liver, baseline, rep2

value: aging

value: 16 months old


title: NSP_SEN_IFNG_1 ng_1


title: NSP_SEN_No IFNG_1


title: 16-m/o mouse liver, baseline, rep3


title: MDA-MB-231 DSM OE, rep2


title: NSP_SEN_No IFNG_2


title: MDA-MB-231 DAXX OE, rep3


title: 2-m/o mouse liver, 1 day post-partial hepatectomy, rep2


title: 16-m/o mouse liver, baseline, rep4


title: iPSC-CM HIF-1alpha mutant treated with LPS, replicate 1

city: Boston

first: Gabriela

middle: Venturini

last: Venturini da Silva

state: Massachusetts

address: 77 Avenue Louis Pasteur, New Research Bu

department: Department of Genetics

institute: Harvard Medical School

data_processing:
CLC Genomics Workbench v 11.0.1
Sequenced reads were aligned with STAR
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: iPSC-CM

extract_protocol:
RNA was harvested using Trizol and 1ug was used to prepare a library
RNA libraries for RNA-seq were prepared using Nextera RNA-Seq Library Prep Kit following manufacturer's protocols.

value: iPSC-CM

value: cardiomyocyte derived from iPSC

value: LPS

tag: time

value: 16 hours


title: BT549_Clone12_rep1

value: Claudinlow Breast Cancer

value: NF-YA deltaEx3

value: CRISPR/spCas9D10A editing


title: BT549_Clone12_rep2


title: iPSC-CM HIF-1alpha mutant treated with LPS, replicate 2


title: MDA-MB-231 DAXX OE, rep2

value: Cultured breast cancer cells


title: iPSC-CM treated with LPS, replicate 3

value: WT


title: BT549_WT_rep3

value: control


title: 16-m/o mouse liver, baseline, rep1

value: Liver

value: female


title: iPSC-CM HIF-1alpha mutant treated with LPS, replicate 3


title: iPSC-CM treated with LPS, replicate 2


title: NSP_PRO_No IFNG_2

value: Cell line

value: Doxycycline On


title: BT549_WT_rep2


title: 8-m/o mouse liver, baseline, rep4

value: 8 months old


title: iPSC-CM treated with LPS, replicate 1


title: BT549_WT_rep1


title: SUM159PT_Clone321_rep3

description:
final_tab_SUM159_raw_genes.txt
final_tab_SUM159PT_norm_genes.txt
final_tab_SUM159_norm_isoforms.txt


title: iPSC-CM unexposed to T. cruzi and filtered by FACS, replicate 1

value: FACS sorting


title: iPSC-CM infected by T. cruzi after 48 hours (only infected cells filtered by FACS), replicate 3

value: T. cruzi infection

value: 48 hours


title: 8-m/o mouse liver, baseline, rep2

value: aging


title: 8-m/o mouse liver, baseline, rep1


title: iPSC-CM unexposed to T. cruzi and filtered by FACS, replicate 2

value: iPSC-CM

value: cardiomyocyte derived from iPSC


title: iPSC-CM infected by T. cruzi after 48 hours (only infected cells filtered by FACS), replicate 1


title: SUM159PT_Clone321_rep2

value: Claudinlow Breast Cancer


title: 2-m/o mouse liver, baseline, rep4

value: 2 months old


title: iPSC-CM exposed over 48 hours to T. cruzi but not infected (filtered by FACS), replicate 1

value: T. cruzi exposure


title: iPSC-CM exposed over 48 hours to T. cruzi but not infected (filtered by FACS), replicate 3


title: iPSC-CM infected after 48 hours T. cruzi infection, replicate 3


title: 2-m/o mouse liver, baseline, rep2


title: iPSC-CM infected after 24 hours T. cruzi infection, replicate 3

value: 24 hours


title: 8-m/o mouse liver, baseline, rep3


title: iPSC-CM infected after 48 hours T. cruzi infection, replicate 1

value: WT


title: iPSC-CM infected after 24 hours T. cruzi infection, replicate 2


title: iPSC-CM exposed over 48 hours to T. cruzi but not infected (filtered by FACS), replicate 2


title: SUM159PT_Clone266_rep2

value: NF-YA deltaEx3

value: CRISPR/spCas9D10A editing


title: iPSC-CM infected by T. cruzi after 48 hours (only infected cells filtered by FACS), replicate 2


title: iPSC-CM infected after 48 hours T. cruzi infection, replicate 2


title: 2-m/o mouse liver, baseline, rep3

value: Liver

value: female


title: zebrafish_embryo_multiomics_ATAC

city: Hang Zhou

first: Tao

last: cheng

state: Zhe Jiang

address: 886 Yuhangtang Road

department: Institute of genetics

institute: Zhejiang University

data_processing:
Illumina sequencing reads were aligned to the zebrafish mRNA reference genome (GRCz11) using the 10x Genomics CellRanger pipeline (version 6.1.2) and cellranger-arc (version 2.0.0) with default parameters.
Assembly: GRCz11
Supplementary files format and content: tar archivr or  gzip compressed  files included filtered_gene_bc_matrices and ATAC fragments  after running CellRanger or cellranger-arc pipeline.
Library strategy: scMultiome ATAC

organism: Danio rerio

source_name: zebrafish cells

growth_protocol: Explants were cultured in a Petri dish coated with 1.5% agarose filled with Dulbecco's Modified Eagle Medium

extract_protocol: Libraries were prepared using Chromium Controller and Chromium Single Cell 3’Library & Gel Bead Kit v3 (10x Genomics, PN-1000075) and Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle (10x Genomics, 4 rxns PN-1000285) according to the manufacturer’s protocol for 10000 cells recovery.

treatment_protocol: 10pg of ndr2 mRNA was injected to one cell of embryonic animal pole at 128 cell stage. All embryos were incubated in 0.3x Danieau buffer until 1k stage, then, were transferred to Dulbecco's Modified Eagle Medium. Animal pole explants corresponding roughly to half of the blastula were incubated to 6hpf (corresponding to embryonic developmental stage).

tag: strain

value: AB

value: embryonic cells


title: SUM159PT_Clone321_rep1


title: LAC

city: San Diego

first: Nathan

middle: E.

last: Lewis

address: 9500 Gilman Dr.

department: Pediatrics

institute: University of California, San Diego

data_processing:
The BCR sequence data were processed using the Immcantation toolbox (v4.0.0) with default parameter values. Initial germline V(D)J gene annotation was performed using IgBLAST with IMGT germline sequence databases.The IgBLAST database was further used to assign V(D)J gene annotations to the BCR FASTA files for each sample using the Change-O package. The derived matrix contains sequence alignment information for each sample with both light and heavy chain sequences, and individualized genotypes were inferred using the TIgGER package and used to finalize V(D)J annotations.
The clonal groups were identified by the R package – scRepertoire (11) based on paired heavy and light chains. To determine clonal groups, we first used the filtered contig annotation obtained from the results performed using the Cell Ranger Single-Cell Software Suites (http://software.10xgenomics.com/single-cell/overview/welcome). Then, for the cells with high quality paired heavy and light chains were sequenced, clones were assigned based on strict definition of clonotype using the CTstrict() function that considers clonally related two sequences with identical V gene usage and > 85% normalized Levenshtein distance of the nucleotide sequence. The clonotype changes between samples were visualized by the compareClonotypes() function with the clones called by amino acid sequence of the CDR3 region.
Supplementary_files_format_and_content: clonotypes.csv, consensus.fasta, and filtered_contig_annotations.csv.gz

source_name: LAC

growth_protocol: S. aureus Becker and S. aureus Becker IsdB/HarA deletion mutant were gifts from Dr. Secore (Merck). Overnight S. aureus cultures were diluted 1:200 in Todd Hewitt broth (THB) and grown to an optical density of 0.8. Unless otherwise stated, 6-8 weeks old female mice were administered 2x107 LAC (USA 300) i.p. for each S. aureus challenge. Spleen and kidneys were harvested 24 hr after the last infection, homogenized in phosphate-buffered saline (PBS) and plated on THB agar plates for CFU enumeration. Other S. aureus inoculums were: 5x107 LAC i.p. for the LD90 infection, 2x107 SA113 i.p., 4x107 Newman or Becker (WT or IsdB/HarA mutant) i.p., 4x107 LAC s.c., and 1x106 LAC i.v.

extract_protocol:
Opsonophagocytosis killing assay (OPK) was performed. Mouse neutrophils were isolated from bone marrow by MojoSort™ Mouse Neutrophil Isolation Kit (BioLegend). Overnight culture of S. aureus LAC was sub-cultured 1:200 in THB and grown to an optical density of 0.6. S. aureus was washed, resuspended in PBS, and incubated with mouse sera at 37°C for 20 min, then added to 105 mouse neutrophils a multiplicity of infection (MOI) of 1:0.5 in the presence of 2% normal mouse serum. Following incubation at 37°C for 1 hr with agitation at 200 rpm, samples were plated on THB agar plates for CFU enumeration.
Splenocytes from IsdB immunized or LAC-experienced mice were incubated with phycoerythrin (PE)–labeled IsdB and allophycocyanin-conjugated anti-mouse CD45R/B220. IsdB+ B220+ cells were sorted by FACSAria II (BD) and subjected to single-cell preparation by using a Single Cell 5’ Library and Gel Bead kit and Chromium Single Cell A Chip kit, the cell suspension was loaded onto a Chromium single cell controller to generate single-cell gel beads in the emulsion (GEMs) according to the manufacturer’s protocol (10X Genomics). scRNA-seq libraries were constructed using a Chromium Single Cell V(D)J Enrichment Kit, Mouse B Cell following instructions provided by the manufacturer (10X Genomics). The libraries were sequenced using an Illumina Novaseq6000 sequencer with a paired-end 150-bp (PE150) reading strategy (performed by Institute for Genomic Medicine, UCSD).

treatment_protocol: Mice were immunized i.p. three times with IsdB (75μg, 50μg and 50μg) plus aluminum hydroxide (alum, InvivoGen) (450 μg per dose) or with aluminum hydroxide alone at 7-day intervals. Mouse sera were screened for reactivity to IsdB by ELISA. IsdB-specific antibodies were purified from human or mouse sera using immobilized IsdB agarose columns (NHS-activated agarose, ThermoFisher Scientific).

value: Spleen and kidneys

tag: isdb vaccinated

value: No IsdB vaccinated (given adjuvant alone)

tag: lac infection

value: LAC-infected mice


title: SUM159PT_Clone266_rep1


title: 2-m/o mouse liver, baseline, rep1

value: aging


title: SUM159PT_Clone266_rep3


title: iPSC-CM not infected, replicate 3

value: iPSC-CM


title: LAC/IsdB

source_name: LAC/IsdB

value: vaccinated with IsdB


title: SUM159PT_WT_rep3

value: Claudinlow Breast Cancer

value: control


title: SUM159PT_WT_rep2


title: iPSC-CM infected after 24 hours T. cruzi infection, replicate 1

value: cardiomyocyte derived from iPSC

value: T. cruzi infection


title: N/IsdB

source_name: N/IsdB

value: Naïve mice


title: SUM159PT_WT_rep1

value: WT


title: iPSC-CM not infected, replicate 1


title: zebrafish Nodal explants constructed from lft1 mutants

data_processing:
Illumina sequencing reads were aligned to the zebrafish mRNA reference genome (GRCz11) using the 10x Genomics CellRanger pipeline (version 6.1.2) and cellranger-arc (version 2.0.0) with default parameters.
Assembly: GRCz11
Supplementary files format and content: tar archivr or  gzip compressed  files included filtered_gene_bc_matrices and ATAC fragments  after running CellRanger or cellranger-arc pipeline.

value: lft1 mutant


title: zebrafish Nodal explants constructed from ndr1 morphants


title: iPSC-CM not infected, replicate 2


title: zebrafish_embryo_multiomics_expression

data_processing:
Illumina sequencing reads were aligned to the zebrafish mRNA reference genome (GRCz11) using the 10x Genomics CellRanger pipeline (version 6.1.2) and cellranger-arc (version 2.0.0) with default parameters.
Assembly: GRCz11
Supplementary files format and content: tar archivr or  gzip compressed  files included filtered_gene_bc_matrices and ATAC fragments  after running CellRanger or cellranger-arc pipeline.
Library strategy: scMultiome GEX

molecule: nuclear RNA


title: WT_3m_RNA_rep2

status: Public on Jan 27 2023

city: Tianjin

first: Jiayuan

last: Chen

state: State...

address: Heping

institute: Tianjin Medical University

data_processing:
Sequence reads were aligned to the mm10 reference genome sequence using STAR (2.7.4a).
The aligned reads were sorted using samtools (1.12).
Read counts per gene were obtained from mapped reads using FeatureCount (1.6.0).
Differentially expressed genes were identified by DESeq2 (1.26.0) algorithms.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include raw count values for each sample.

source_name: primary cholangiocytes

extract_protocol:
Total RNAs were extracted from primary cholangiocytes using TRIzol (Invitrogen, 15596018) according to the manufacturer’s instructions.
For RNA samples from WT or PLD mice 3 months after tamoxifen induction, libraries were constructed and sequenced on the BGISEQ-500 platform.

treatment_protocol: In brief, the livers of WT or PLD mice were perfused through inferior cava vein with 50 mL solution A (140 mM NaCl, 5.4 mM KCl, 0.8 mM Na2HPO4, 25 mM HEPES, 0.5 mM EGTA, 1 mM MgCl2, pH 7.4) at 37°C, followed by 30 mL solution B (140 mM NaCl, 5.4 mM KCl, 0.8 mM Na2HPO4, 25 mM HEPES, 5mM CaCl2, 0.5mg/mL collagenase II (Worthington, LS004176), pH 7.4) at 37°C. Through mechanical dissociation, shaking and microdissection, the adherent parenchymal cells were removed leaving an intact biliary tree. The biliary tree was finely minced, and digested in digestion solution [RPMI medium containing 0.32 mg/mL collagenase XI (Sigma C7657), 0.4 mg/mL hyaluronidase (Sigma H3506) and 40 U/mL DNase I (Sigma D4513)] with shaking for 60 min at 37°C. Single-cell suspension was collected using a 70-μm cell strainer (Corning, 352350) and then washed three times with RPMI medium. Cholangiocytes were then purified by immunomagnetic isolation. Briefly, Cholangiocytes cell suspensions were incubated with anti-EpCAM antibody (DSHB, G8.8) with rotation for 45 min at 4°C. Dynabeads Protein G (Thermo Fisher Scientific, 10004D) were added into the cell suspensions and continued the rotation for another 45 min at 4°C. After washing three times with PBS, cholangiocytes were collected using a magnetic separator. The purity of cholangiocytes was assessed by staining for cytokeratin-19 (CK19).

value: primary cholangiocytes


title: WT_3m_RNA_rep1


title: PLD_3m_RNA_rep2

value: PLD


title: PLD_3m_RNA_rep1


title: MGH66_persister5

city: Cambridge

first: Peijun

last: Ma

address: 415 Main Street

department: Infectious Disease and Microbiome program

institute: The Broad Institute of MIT and Harvard

data_processing:
bcl2fastq2-v2.20.0 was used to generate fastq files
Sequencing reads were trimed and sorted using fastp-0.20.0
Alignment was using BWA
Pilon was used for mutation detection of the WGS data
Supplementary files format and content: text files containing mutations detected by pilon.
Supplementary files format and content: Excel spreadsheet summarizing mutations from 6 persister strains and the ancestor strain.

organism: Klebsiella pneumoniae

growth_protocol: 37ºC, regular laboratory condition

extract_protocol:
gDNA was extracted using Qiagen DNeasy Blood & Tissue
Library was contructed using Illumina Nextera XT

tag: method

value: Nextera XT

value: Persister derived from MGH66

value: untreated


title: MGH66_ancestor


title: MGH66_persister4


title: PLD_3m_RNA_rep3


title: MGH66_persister6


title: MGH66_persister3


title: MGH66_persister2