title: B cell, Cxxc1-ChIP

city: Kanagawa

first: Kazuki

last: Okuyama

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

department: IMS

institute: RIKEN Yokohama

description: Library name: B cell, Cxxc1-ChIP

data_processing:
Adapter sequences were trimmed from the reads by Cutadapt (v4.0)
Mapping to the mm10 genome using bowtie2 (v2.5.0)
Removing reads with low mapping quality (MAPQ<30) , mitochondrial reads, and improperly paired reads using Filter BAM (v2.5.2)
Removing PCR duplicates by MarkDuplicates (v2.18.2.3)
Peak calling using MACS2 callpeak (v2.2.7.1) with default settings
Generate BigWig files from BedGraph using Convert BedGraph to BigWig (v1.0.1)
Assembly: mm10
Supplementary files format and content: bigwig files

source_name: Spleen

extract_protocol:
Freshly isolated cells were cross-linked with 1 mg/ml disuccinimidyl glutarate and 1% formaldehyde. Nuclei were isolated from the cells and lysed in Lysis Buffer by sonication. The lysate was incubated with rabbit anti-Cxxc1 or anti-Bcl11a antibodies pre-bound to Dynabeads® protein G overnight at 4 oC. Chromatin DNA was reverse-crosslinked and eluted. Samples were treated with RNase A and Proteinase K, and precipitated chromatin DNA was purified by use of ChIP DNA Clean & ConcentratorTM (ZYMO Research, CA).
Library preparation were done using NEBNext Ultra II DNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina (New England BioLabs). Sequencing was performed by Immugen with HiSeq X Ten.

value: Spleen

value: Splenic B cells

value: wild-type


title: HCASMC, siCtrl, Replicate 2

status: Public on May 01 2026

type: SRA

city: New Haven

first: Kathleen

last: Martin

state: CT

address: 300 George Street

country: USA

institute: Yale School of Medicine

description: Library name: Sample 12

library_source: transcriptomic

data_processing:
Primary analysis - sample de-multiplexing and alignment to the human genome - is performed using Illumina's CASAVA 1.8.2 software suite. Partek flow was used for RNA-seq analysis and pathway analysis employed Ingenuity pathway analysis tools.
Assembly: hg19
Supplementary files format and content: txt (expression matrix)

molecule: polyA RNA

organism: Homo sapiens

source_name: Smooth muscle

extract_protocol:
The RNA was extracted from human coronary artery smooth muscle cells (hCASMCs) using the RNA extraction kit from Qiagen.
Total RNA quality was determined by estimating the A260/A280 and A260/A230 ratios by nanodrop. RNA integrity was determined by running an Agilent Bioanalyzer gel, which measures the ratio of the ribosomal peaks. mRNA is purified from approximately 500 ng of total RNA with oligo-dT beads and sheared by incubation at 94°C. Following first-strand synthesis with random primers, second strand synthesis is performed with dUTP for generating strand-specific sequencing libraries. The cDNA library is then end-repaired, and A-tailed, adapters are ligated, and second-strand digestion is performed by Uracil-DNA-Glycosylase. Indexed libraries that meet appropriate cut-offs for both are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the Lab Chip GX or Agilent Bioanalyzer. Samples with a yield of ≥0.5 ng/ul are used for sequencing. Samples are sequenced using 75 bp single end sequencing on an Illumina Hi-Seq 2500 according to Illumina protocols. Signal intensities are converted to individual base calls during a run using the system's Real Time Analysis (RTA) software.

tag: tissue

value: Smooth muscle

tag: cell line

value: Human Coronary Artery Smooth Muscle Cells (HCASMC)

tag: cell type

value: Smooth muscle cells

tag: genotype

value: WT


title: Neuro Sphere RIP - WT Input Repl. 2

city: Heidelberg

first: Ana

last: Martin-Villalba

address: Im Neuenheimer Feld 280

department: Molecular Neurobiology

country: Germany

institute: German Cancer Research Center

description:
immunoprecipitation (IP) input fraction
cpeb4_rip_counts.csv
Sample 8

data_processing:
mapping with bowtie2 to the mm10 genome (local mode, paired)
compressing SAM to BAM (samtools)
sorting the BAM files by region (samtools)
Hash tag oligos (HTOs) very counted by regular expression using custom R scripts for every possible cell barcode.
genes counted with 10X Genomics cellranger for Sample 1 & 2, with custom R scripts for Samples 3 to 4 and with Bioconductor R assays(summarizeOverlaps(mm10_gns, reads,mode="Union")) for samples 7 to 14
immunoprecipitation samples were mapped with bowtie2 (end-to-end alignment)
Genome_build: Mus Musculus (mm 10)
Supplementary_files_format_and_content: gene count tables

organism: Mus musculus

source_name: Neuro Sphere

growth_protocol: Neural stem cells were isolated from the sub-ventricular zone of adult mice

extract_protocol:
10X genomics, oligo(dT) capturing (Hash tag oligos conjugated to anti-MHC1 and anti-CD45; HTO_1: 155803 TotalSeq™-A0302 anti-mouse Hashtag 2 Antibody BioLegend, HTO_2: 155805 TotalSeq™-A0303 anti-mouse Hashtag 3 Antibody BioLegend, HTO_3: 155807 TotalSeq™-A0304 anti-mouse Hashtag 4 Antibody BioLegend)
10X Genomics library preparation

treatment_protocol: cultured NSC were treated either with BMP4 for 3 days or EGF

value: Neuro Sphere

tag: nsc isolation

value: cultured

tag: treatment

value: no treatment

value: wildtype

tag: sequenced molecule

value: mRNA


title: B cell, Bcl11a-ChIP

country: Japan

description: Library name: B cell, Bcl11a-ChIP

library_source: genomic

molecule: genomic DNA


title: Bcl11b m/m, P0, Cxxc1-ChIP

description: Library name: Bcl11b m/m, P0, Cxxc1-ChIP

source_name: Thymus

value: Thymus

value: Total thymocytes

value: Bcl11b m/m


title: Neuro Sphere RIP - WT IgG Repl. 1

description:
immunoprecipitation (IP) IgG fraction
cpeb4_rip_counts.csv
Sample 9


title: HCASMC, siCtrl, Replicate 1

description: Library name: Sample 11


title: WT_WaveNeg_rep1.3

city: Cold Spring Harbor

first: Lucas

last: Cheadle

state: NY

address: 1 Bungtown Rd

department: Neuroscience

institute: Cold Spring Harbor Laboratory

data_processing:
BCL files were downloaded from Illumina BaseSpace platform after sequencing on an Illumina Next-Seq 500
BCL files were converted into FastQ format.
Files were filtered and demultiplexed using .yaml files specifying the indices used for each sample, .yaml file are provided in this upload.
Raw counts files were generated for each sample then used as input for downstream analyses in R.
Putative doublets were identified and removed using Doublet Finder in R.
QC was performed, data were normalized, and cells were clustered using Seurat version 3 in R.
Differential gene expression analysis was performed using Monocle version 2 in R.
Assembly: Custom transcriptome was built from Ensemble GRCm38 genome and GRCm38.84 annotation using Bowtie 1.1.1.
Supplementary files format and content: Counts tables (.tsv) files for each sample are provided. These files can be fed directly into Seurat for re-analysis.

molecule: total RNA

extract_protocol:
Single-nuclear RNA-sequencing was performed using the inDrops strategy on nuclei from anterior and posterior V1 micro-dissected from Beta2fl/fl; Pax6α-Cre mice and Beta2fl/fl; Cre-negative controls
Library was constructed by single-cell core facility at Harvard Medical School

tag: strain

value: Beta2fl/fl; Cre-negative

tag: age

value: Postnatal day 7


title: WT_WaveNeg_rep2.1


title: WT_WaveNeg_rep1.4


title: HCASMC, siSUV39H1, Rep4

description: Library name: Sample 8

value: SUV39H1 knockdown


title: WT_WaveNeg_rep1.2


title: Neuro Sphere RIP - WT Input Repl. 1

description:
immunoprecipitation (IP) input fraction
cpeb4_rip_counts.csv
Sample 7


title: WT_WaveNeg_rep1.1


title: WT_WavePos_rep3.4


title: HCASMC, siSUV39H1, Rep3

description: Library name: Sample 7


title: Bcl11b +/+. P0, Cxxc1-ChIP

description: Library name: Bcl11b +/+, P0, Cxxc1-ChIP


title: Germ-free RNA-seq sample 2

city: Ithica

first: Praveen

last: Sethupathy

address: Cornell University College of Veterinary Medicine, Box 17

institute: Cornell University

description:
RNA
RNA_normalized_counts.csv
GF271

data_processing:
For single cell, sequencing was demultiplexed, aligned to the genome, and quality checked using 10X Genomics Cell Ranger software.
For RNA-seq, sequencing was aligned using STAR and quantified using Salmon. Normalization was accomplished by DESeq2.
For small RNA-seq, sequencing was processed using miRquant2.0.
Genome_build: mm10
Supplementary_files_format_and_content: For single cell, processed data contains barcodes, gene list, and counts matrix. For RNA-seq, processed data is a DESeq2 normalized counts matrix. For small RNA-seq, processed data is in Reads Per Million MiRs Mapped (RPMMM) or as DESeq2 results.

source_name: Sox9-EGFP Low sorted intestine crypt cells from germ-free mice - RNA-seq sample 2

extract_protocol: Clonetech SMARTer Ultra Low Input library preparation kit combined with Nextera XT DNA sample preparation kit

value: small intestine


title: HCASMC, siSUV39H1, Rep2

description: Library name: Sample 6


title: Germ-free RNA-seq sample 3

description:
RNA
RNA_normalized_counts.csv
GF305

source_name: Sox9-EGFP Low sorted intestine crypt cells from germ-free mice - RNA-seq sample 3


title: Germ-free RNA-seq sample 4

description:
RNA
RNA_normalized_counts.csv
GF315

source_name: Sox9-EGFP Low sorted intestine crypt cells from germ-free mice - RNA-seq sample 4


title: WT_WavePos_rep3.3


title: RNA-seq, Wt, DP thymocytes, rep.2

description: Library name: Wt, DP, rep.2

data_processing:
Adapter sequences were trimmed from the reads by Cutadapt (v4.0)
Mapping to the mm10 genome using HISAT2 (v2.2.1)
Mapping reads on each gene were counted using featureCounts (v2.0.8)
Differential gene expression analysis was conduncted edgeR (v3.36.0)
Assembly: mm10
Supplementary files format and content: tabular file including normalized counts of each transcript

extract_protocol:
Total RNA was extracted from FACS-purified DP thymocytes using TRIzol reagent (Thermo Fisher Scientific). RNA integrity number was evaluated using an Agilent 2100 Bioanalyzer with the RNA 6000 Pico Kit (Agiletn), and samples with RNA integrity number > 8 were used for library preparation.
RNA-seq libraries were constructed from 10 ng of total RNA using the SMART-seq Standard Kit (Takara).

value: CD24+TCRb-CD4+CD8a+ thymocytes

value: Cxxc1 +/+ :Lck-cre


title: HCASMC, siSUV39H1, Rep1

description: Library name: Sample 5

value: Smooth muscle

value: Human Coronary Artery Smooth Muscle Cells (HCASMC)


title: WT_WavePos_rep3.2


title: RNA-seq, KO, DP thymocytes, rep.2

description: Library name: KO, DP, rep.2

value: Cxxc1 F/F :Lck-cre


title: RNA-seq, Wt, DP thymocytes, rep.1

description: Library name: Wt, DP, rep.1


title: WT_WavePos_rep3.1


title: Conventionalized RNA-seq sample 4

description:
RNA
RNA_normalized_counts.csv
CD314

source_name: Sox9-EGFP Low sorted intestine crypt cells from conventionalized - RNA-seq sample 4


title: HCASMC, siCtrl, Rep3

description: Library name: Sample 3

value: Smooth muscle cells

value: WT


title: RNA-seq, KO, DP thymocytes, rep.1

description: Library name: KO, DP, rep.1


title: Germ-free RNA-seq sample 1

description:
RNA
RNA_normalized_counts.csv
GF244

source_name: Sox9-EGFP Low sorted intestine crypt cells from germ-free mice - RNA-seq sample 1


title: Conventionalized RNA-seq sample 3

description:
RNA
RNA_normalized_counts.csv
CD304

source_name: Sox9-EGFP Low sorted intestine crypt cells from conventionalized - RNA-seq sample 3


title: HCASMC, siCtrl, Rep4

description: Library name: Sample 4


title: Bcl11b-KO, Cxxc1-ChIP

description: Library name: KO, Cxxc1-ChIP

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

extract_protocol:
Freshly isolated thymocytes cross-linked with 1 mg/ml disuccinimidyl glutarate and 1% formaldehyde. Nuclei were isolated from the cells and lysed in Lysis Buffer by sonication. The lysate was incubated with rabbit anti-Cxxc1 antibody (abcam, EPR19199) pre-bound to Dynabeads® protein G overnight at 4 oC. Chromatin DNA was reverse-crosslinked and eluted. Samples were treated with RNase A and Proteinase K, and precipitated chromatin DNA was purified by use of ChIP DNA Clean & ConcentratorTM (ZYMO Research, CA).
Library preparation were done using NEBNext Ultra II DNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina (New England BioLabs). Sequencing was performed by Immugen with HiSeq X Ten.

value: Bcl11b F/F :Cd4-cre

value: abcam, EPR19199


title: Wt, Cxxc1-ChIP

description: Library name: Wt, Cxxc1-ChIP

value: wild-type


title: WT_WavePos_rep2.3


title: HCASMC, siCtrl, Rep1

description: Library name: Sample 1


title: Total Input

description: Library name: Input

value: Thymus


title: Conventionalized RNA-seq sample 1

description:
RNA
RNA_normalized_counts.csv
CD246

source_name: Sox9-EGFP Low sorted intestine crypt cells from conventionalized - RNA-seq sample 1


title: HCASMC, siCtrl, Rep2

description: Library name: Sample 2


title: Conventionalized RNA-seq sample 2

description:
RNA
RNA_normalized_counts.csv
CD270

source_name: Sox9-EGFP Low sorted intestine crypt cells from conventionalized - RNA-seq sample 2


title: WT_WavePos_rep2.2


title: WT_WavePos_rep2.1


title: Sox9-eGFP low RNA-seq high fat sample 4

description:
RNA
RNA_normalized_counts.csv
BC244

source_name: Sox9-EGFP Low sorted intestine crypt cells from high fat diet - RNA-seq sample 4


title: WT_WavePos_rep2.4


title: ATAC-seq, KO, DP thymocytes, rep.2

description: Library name: KO, DP, rep.2

data_processing:
Adapter sequences were trimmed from the reads by Cutadapt (v4.0)
Mapping to the mm10 genome using bowtie2 (v2.5.0) with the "very sensitive end-to-end" preset
Removing reads with low mapping quality (MAPQ<30) , mitochondrial reads, and improperly paired reads using Filter BAM (v2.5.2)
Removing PCR duplicates by MarkDuplicates (v2.18.2.3)
Peak calling using MACS2 callpeak (v2.2.7.1) with the following parameters: --nomodel, --extension size 200, and --shift -100
Generate BigWig files from BedGraph using Convert BedGraph to BigWig (v1.0.1)
Assembly: mm10
Supplementary files format and content: BigWig files

extract_protocol:
Fifty thousand target thymocyte populations were purified by FACS sorting.
Transpositon and  library preparation were performed using ATAC-Seq Kit (Active Motif) according to the manufacturer's protocol. DNA fragments of 150-500 bp were enriched by size selection using SPRIselect beads (Beckman Coulter).


title: ATAC-seq, KO, DP thymocytes, rep.3

description: Library name: KO, DP, rep.3


title: ATAC-seq, KO, DP thymocytes, rep.1

description: Library name: KO, DP, rep.1


title: Sox9-eGFP low RNA-seq sample 4

description:
RNA
RNA_normalized_counts.csv
BC243

source_name: Sox9-EGFP Low sorted intestine crypt cells from chow diet - RNA-seq sample 4


title: WT_WavePos_rep1.4


title: Sox9-eGFP low RNA-seq high fat diet sample 3

description:
RNA
RNA_normalized_counts.csv
BC242

source_name: Sox9-EGFP Low sorted intestine crypt cells from high fat diet - RNA-seq sample 3


title: WT_WavePos_rep1.3


title: Sox9-eGFP low RNA-seq sample 3

description:
RNA
RNA_normalized_counts.csv
BC241

source_name: Sox9-EGFP Low sorted intestine crypt cells from chow diet - RNA-seq sample 3


title: ATAC-seq, KO, DN thymocytes, rep.2

description: Library name: KO, DN, rep.2

value: CD24+TCRb-CD4-CD8a- thymocytes


title: ATAC-seq, KO, DN thymocytes, rep.3

description: Library name: KO, DN, rep.3


title: WT_WavePos_rep1.2


title: Sox9-eGFP low RNA-seq sample 2

description:
RNA
RNA_normalized_counts.csv
BC183

source_name: Sox9-EGFP Low sorted intestine crypt cells from chow diet - RNA-seq sample 2


title: ATAC-seq, KO, DN thymocytes, rep.1

description: Library name: KO, DN, rep.1


title: WT_WavePos_rep1.1


title: 375-KO sample, set2

description:
single cell RNA
KO_s2

source_name: Separated single intestinal cells from 12 month old 375-KO mice - set2

extract_protocol: Libraries were prepped according to 10X Genomics Chromium library preparation

value: single intestinal cells

value: miR-375 knockout


title: ATAC-seq, Wt, DP thymocytes, rep.3

description: Library name: Wt, DP, rep.3


title: ATAC-seq, Wt, DP thymocytes, rep.2

description: Library name: Wt, DP, rep.2


title: Wildtype sample, set2

description:
single cell RNA
WT_s2

source_name: Separated single intestinal cells from 12 month old WT mice - set2


title: 375-KO sample, set1

description:
single cell RNA
KO_s1

source_name: Separated single intestinal cells from 12 month old 375-KO mice - set1


title: Sox9-eGFP low RNA-seq sample 1

description:
RNA
RNA_normalized_counts.csv
BC180

source_name: Sox9-EGFP Low sorted intestine crypt cells from chow diet - RNA-seq sample 1


title: Sox9-eGFP low RNA-seq high fat diet sample 1

description:
RNA
RNA_normalized_counts.csv
BC181

source_name: Sox9-EGFP Low sorted intestine crypt cells from high fat diet - RNA-seq sample 1


title: Wildtype sample, set1

description:
single cell RNA
WT_s1

source_name: Separated single intestinal cells from 12 month old WT mice - set1


title: Patient 09 extrahepathic cholangiocarcinoma

city: Montpellier

first: Simon

last: Cabello-Aguilar

address: Avenue du doyen Gaston Giraud

country: France

institute: CHU Montpellier

description: Library name: L09

data_processing:
Raw counts matrix were obtained using the DRAGEN RNA pipeline (v4.2.7, Illumina).
Assembly: hg19
Supplementary files format and content: tab-delimited text file containing the raw counts

source_name: bile duct

extract_protocol:
Total RNA were extracted using Maxwell® RSC FFPE RNA kit (Promega), following the manufacturer’s instructions. Concentrations were measured using Qubit RNA HS assays (Thermo Fisher Scientific).
RNA sequencing was performed using the RNA Prep with Enrichment, (L) Tagmentation in combination with the RNA Pan-cancer panel (1,362 genes, Illumina) according to the manufacturer’s recommendations. Libraries were sequenced on a NextSeq 500 instrument (2×150 cycles, Illumina).

value: bile duct


title: Sox9-eGFP low RNA-seq high fat diet sample 2

description:
RNA
RNA_normalized_counts.csv
BC182

source_name: Sox9-EGFP Low sorted intestine crypt cells from high fat diet - RNA-seq sample 2


title: ATAC-seq, Wt, DN thymocytes, rep.3

description: Library name: Wt, DN, rep.3

source_name: Thymus


title: Patient 02 intrahepathic cholangiocarcinoma

description: Library name: L02


title: Patient 04 intrahepathic cholangiocarcinoma

description: Library name: L04


title: ATAC-seq, Wt, DP thymocytes, rep.1

description: Library name: Wt, DP, rep.1


title: B cell progenitor and precursor populations, WT-Aged_VDJ

city: Los Angeles

first: Yu-Sheng

last: Lin

state: California

address: 611 Charles E. Young Drive East

department: MIMG

institute: University of California, Los Angeles

data_processing:
Library strategy: VDJ-seq
I1 read: contains the sample index.
R1 read: contains the cell barcode (first 16 nt) and UMI (next 10 nt).
R2 read: contains the RNA sequence.
For the gene expression(GEX) libraries, Novaseq 6000 S2 pair-ended sequencing(2x50) was used and the resulting bcl2 files were demultiplexed and processed by cellranger mkfastq program. Fastq outputs from gene expression libraries were then processed by cellranger count program to determine the gene expression counts based on the high-quality reads mapped to mm10 reference genome.
For the VDH(Immune profiling) libraries, NextSeq 500 High Output pair-ended sequencing(2x150) was used and the resulting bcl2 files were demultiplexed and processed by cellranger mkfastq program to generate the fastq outputs. Fastq outputs from VDJ libraries were then processed by cellranger vdj program to filter low-quality reads and assemble the contigs in immunoglobulin genes.
Genome_build: mm10
Supplementary_files_format_and_content: For the gene expression(GEX) library, the processed data contains the matrix files which were indexed based on the cell barcode and feature lists from the outputs of cellranger count program. The GEX processed data are in tsv and mtx formats compressed to gz files. For the VDJ(Immune profiling) library, the processed data include the mapped contig for immunoglobulin genes and the resulting clonotypes from the outputs of cellranger vdj program. The VDJ(immune profiling) processed data are in csv format.

source_name: Mouse B lymphoid progenitor and precursor populations

growth_protocol: The sample were prepared directly from primary cells isolated from mouse bone marrow without further growth.

extract_protocol:
CD3e-CD8a-CD11b-F4/80-Gr-1-CD49b-B220+IgM-IgD- populations were sorted from pooled, purified, and enriched mouse bone marrow cells from two mice per group . The sorted cells from different genotypes were then subjected to 10X Genomics Single-cell immune-profiling with Chromium Single Cell V(D)J Enrichment Kit workflows for single-cell gene expression and immune profiling library construction.
Library construction is based on the standard protocol in 10X genomics Chromium Single Cell V(D)J Reagent Kits.

treatment_protocol: The sample were prepared directly from primary cells isolated from mouse bone marrow without further treatment.

value: 100 weeks old


title: Patient 01 intrahepathic cholangiocarcinoma

description: Library name: L01


title: Healthy Lung, Visium D1

city: Lexington

first: Jinpeng

last: Liu

state: Kentucky

address: 800 Rose St

institute: Markey Cancer Center

description: Fresh frozen spatial transcriptome sequencing

data_processing:
Visium libraries from  patient samples were mapped to GRCh38 human references (GRCh38-2020-A) with Space Ranger (v1.3.0, 10x Genomics).
Assembly: GRCh38
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: filtered_feature_bc_matrix.h5: gene expresion count data in H5 format
Library strategy: Visium Spatial Transcriptomics

source_name: Healthy Lung

growth_protocol: Formalin-fixed paraffin-embedded tissue

extract_protocol:
10x Genomics (CG000409)
10x Genomics (Visium FFPE Reagent Kit )

treatment_protocol: No treatment

value: Healthy Lung


title: ATAC-seq, Wt, DN thymocytes, rep.2

description: Library name: Wt, DN, rep.2


title: Sarcoid Lung, Visium C1

source_name: Sarcoid Lung

value: Sarcoid Lung


title: ATAC-seq, Wt, DN thymocytes, rep.1

description: Library name: Wt, DN, rep.1

value: Cxxc1 +/+ :Lck-cre


title: B cell progenitor and precursor populations, IkBKO-Young_VDJ

value: 12 weeks old

value: nfkbie-/-nfkbib-/-nfkbia+/-

value: B lymphoid progenitor and precursor populations


title: B cell progenitor and precursor populations, WT-Young_VDJ


title: ATAC_rep13

status: Public on Apr 02 2025

city: Boston

first: Alexis

last: Caulier

state: Massachusetts

address: 1 Blackfan street

department: Oncology/Hematology

institute: Boston Children's Hospital

description: demultiplexed with BCL Convert

data_processing:
Files were demultiplexed with BCL convert then aligned with Cellranger with GRCh38 genome
Assembly: GRCh38
Supplementary files format and content: h5 matrix, gene expression counts stored in $`Gene Expression`
Supplementary files format and content: h5 matrix, peak counts stored in $`Peaks`
Supplementary files format and content: h5 matrix, CROPseq counts
Supplementary files format and content: atac_fragments.tsv.gz and atac_fragments.tsv.gz.tbi.gz, atac fragment files
Supplementary files format and content: atac_peak_annotation.tsv.gz, peak annotations
Library strategy: 10x ATAC + GEX Multiome

source_name: Hematopoietic cells

growth_protocol: Erythroid media

extract_protocol: Chromium Single Cell Multiome ATAC + Gene Expression

value: Hematopoietic cells

value: erythroid cells


title: Sarcoid Lung, Visium A1


title: ATAC_rep9

description: demultiplexed with BCL Convert


title: ATAC_rep12

description: demultiplexed with BCL Convert


title: ATAC_rep16

description: demultiplexed with BCL Convert


title: ATAC_rep10

description: demultiplexed with BCL Convert


title: ATAC_rep14

description: demultiplexed with BCL Convert


title: ATAC_rep7

description: demultiplexed with BCL Convert


title: Immune cells extracted from mouse HCC treated with vehicle, anti-CD40 agonist, or cabozantinib

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

description: BD Rhapsody™ Single-Cell Analysis System with multiplex

library_source: transcriptomic single cell

data_processing:
FASTQ files were processed to demultiplex and gene expression quantification using the Seven Bridges Genomics cloud server with the BD Rhapsody WTA Analysis Pipeline.
Assembly: GRCm38
Supplementary files format and content: .st: read count, UMI count, RSEC corrected count for cell-gene pairs
Supplementary files format and content: *.csv: UMI count per cell matrices with recursive substation error correction (RSEC)

source_name: hepatocellular carcinoma

growth_protocol: BNL-MEA tumor-bearing Balb/c mice treated with vehicle, anti-CD40 agonist, or cabozantinib

extract_protocol:
The single-cell suspension was stained with antibodies against CD45 and fluorescein diacetate for FACS sorting.
Sample multiplexing and library construction was performed according to the manufacter's instructions (BD Rhapsody WTA kit).

value: hepatocellular carcinoma


title: ATAC_rep6

description: demultiplexed with BCL Convert


title: ATAC_rep5

description: demultiplexed with BCL Convert


title: MCF10A, UT

status: Public on Oct 30 2025

city: Boulder

first: Brianna

last: Fernandez

state: CO

address: 3415 Colorado Avenue

department: Biochemistry

institute: University of Colorado Boulder

description:
Library name: Sample 1
10x Genomics

data_processing:
scRNA-seq data were processed and analyzed using the Seurat (v5.1.0) package in R (v4.4.1). Raw sequencing reads were pre-processed using CellRanger (v7.1.0) and aligned to the Human (GRCh38) 2020-A reference genome. Gene-cell count matrices were generated, and low-quality cells were filtered out based on the number of detected genes, unique molecular identifiers (UMIs), and mitochondrial gene percentage. Cells with fewer than 3,500 genes were excluded to remove low-quality cells. Cells with greater than 15% mitochondrial gene expression were also removed. Data were log-normalized using Seurat’s NormalizeData() function with a scale factor of 10,000.
Assembly: Human (GRCh38) 2020-A
Supplementary files format and content: matrix files for counts, features, and barcodes.
Supplementary files format and content: merged_filtered_etop.h5ad: This file contains a .h5ad format file of the merged and filtered seurat object with all treatments combined and metadata annotated (i.e., sample, dose, cluster ID, UMAP dimensions, etc.)
Supplementary files format and content: merged_filtered_etop.rds: This file contains a .rds format file of the merged and filtered seurat object with all treatments combined and metadata annotated (i.e., sample, dose, cluster ID, UMAP dimensions, etc.)

extract_protocol:
Single-cell suspensions were prepared following the 10x Genomics “Cell Preparation for Single Cell Protocols” guide with a viability of >95%. Single-cell encapsulation, barcoding, cDNA amplification, library preparation, and sequencing were performed by the University of Colorado Anschutz Genomics Shared Resource facility. Cells were encapsulated into droplets using the Chromium Controller, where reverse transcription occurred within individual gel beads-in-emulsion (GEMs).
Single-cell RNA sequencing (scRNA-seq) libraries were generated using the 10x Genomics Chromium platform with the 3' mRNA capture kit. Single-cell suspensions were prepared following the 10x Genomics “Cell Preparation for Single Cell Protocols” guide with a viability of >95%. Single-cell encapsulation, barcoding, cDNA amplification, library preparation, and sequencing were performed by the University of Colorado Anschutz Genomics Shared Resource facility. Cells were encapsulated into droplets using the Chromium Controller, where reverse transcription occurred within individual gel beads-in-emulsion (GEMs). Following barcoding and cDNA amplification, sequencing libraries were constructed according to the manufacturer’s protocol. Libraries were sequenced on an Illumina NovaSeqX to a depth of 81,810 reads per cell for untreated, 74,214 reads per cell for 2.5µM, 81,254 reads per cell for 10µM, and 76,973 reads per cell for 25µM.

treatment_protocol: MCF10A cells were split 1:10 (from a confluent plate) into a plastic 10cm culture plate before being treated with 2.5, 10, or 25μM etoposide the following day for 24 h. Cells were then washed twice with PBS before being returned to full-growth media. Full-growth media was refreshed every 3d during the drug recovery period.

value: normal human breast epithelial cell

value: Untreated


title: ATAC_rep8

description: demultiplexed with BCL Convert


title: ATAC_rep4

description: demultiplexed with BCL Convert


title: ATAC_rep3

description: demultiplexed with BCL Convert


title: ATAC_rep2

description: demultiplexed with BCL Convert


title: Right kidney, Unilateral nephrectomised, 72h, rep5, RNAseq

status: Public on Jul 18 2024

city: Adelaide

first: Jonathan

last: Gleadle

state: SA

address: Renal Unit, FMC

country: Australia

institute: Flinders University

description:
RNASeq-17
RNASeq-17

data_processing:
RNA-seq raw data in FASTQ format from individual libraries were uploaded to Deep Thought High Performance Compute Server, hosted by Flinders University for processing. FastQC (v0.11.8) was used for checking the quality of the FASTQ file. After inspection of data quality, low quality bases and Illumina Truseq adapters were then removed using AdapterRemoval version 2.3.2 with parameters --trimns --minquality 30 --minlength 50.  Quantification of transcript expression in RNA-seq data was conducted using Salmon version 1.5.0 using parameters -libType A --seqBias --numBootstraps 50 –validate Mappings. First, a decoy-aware transcriptome index was built using transcript sequences and primary assembly genome sequences from GENCODE Mouse Release M27. RNA-seq reads were then pseudoaligned to the transcriptome index and output was generated in a sub-directory containing a simple TSV format file listing the name of each transcript, its length, effective length, and its abundance in terms of Transcripts Per Million (TPM) as well as estimated number of reads originating from each transcript. After the quantification, transcript counts from Salmon output were imported into R statistical software environment version 4.10 (R Core Team, 2020)  and the bootstrap samples were used to estimate the mapping uncertainty for each transcript. Transcripts were then associated with gene IDs for gene-level summarization for downstream analysis.
GRCm39
csv files; meta data and information for each samples.
csv files; raw gene-level counts from summarisation of transcript with the same gene id for each samples.

source_name: cross sectional sample

extract_protocol:
Kidney cross-section were freshly harvested at various timepoints after sham surgery or nephrectomy and tissue samples were flash frozen in liquid nitrogen. Samples were stored at -80°C until extraction. Prior to extraction the frozen kidney samples were immersed overnight at -20°C in RNAlater -ICE (Thermo Fisher AM7030) as per the manufacturer’s instructions to transition the tissue to a state that was more amenable to pestle homogenisation. Total RNA was isolated from the kidney samples using the mirVana isolation kit (AM1561) as per the manufacturer’s instructions except that Trizol reagent was used instead of phenol. RNA was eluted in 35µl of elution buffer. The LabChip GX Nucleic Acid Analyser (Perkin Elmer) and the Qubit RNA HS (Thermo Fisher Q32852) were used according to the manufacturer’s instructions to quantify the RNA.
Library preparation was performed using the Illumina TruSeq Stranded mRNA library preparation kit. Briefly, poly-A containing mRNA molecules were purified, fragmented, and converted to strand specific cDNA. This was followed by second strand cDNA synthesis, adapter ligation and PCR amplification. Resulting libraries were quality controlled using the Qubit 2.0 (Thermo Fisher Scientific) for quantitation and the LabChip GX Touch 24 (Perkin Elmer) for quality assessment. Individual libraries were combined into a final equimolar pool and then sequenced using 150bp paired end runs on the NovaSeq  system (Illumina).

value: Right kidney

value: cross sectional sample

value: Unilateral nephrectomy

tag: time post_surgery

tag: gender

value: Male

tag: mouse id

tag: batch

value: 8-12 weeks

tag: library kit

tag: bp size


title: Right kidney, Sham operated, 24h, rep2, snRNAseq

description:
Sham77
Sham77

data_processing:
Raw sequencing data were processed using the Alevin-fry pipeline with the mouse reference genome (mm10) splice reference and index for pseudo-alignment and gene quantification was carried out using Alevin-fry's quant mode. The resulting gene expression matrix was imported into Seurat for single-cell RNA sequencing data analysis. Seurat was used for quality control, filtering out low-quality cells and potential doublets. The filtered data were then SCTransform normalized and to regress out percentage of mitochondria and ribosomal transcript per cell. Principal component analysis (PCA) was performed on the variable genes, followed by unsupervised clustering using the Louvain algorithm. Harmony was used to remove the influence of batch effects11 and Uniform Manifold Approximation and Projection (UMAP) was employed for dimensionality reduction and visualization of the clusters. Differential gene expression analysis was performed on individual clusters using Seurat's FindMarkers function. The results were used to identify marker genes and characterize the cell types present in the kidney tissue.
mm10
csv files; meta data and information for each nucleus labelled by sample name followed by cell barcode.
csv files; raw gene counts from Alevin-fry pipeline output for each nucleus labelled by sample name followed by cell barcode.

extract_protocol:
Nuclei were isolated from a section of the kidney as per published protocol (Leiz et al., 2021). Briefly, kidney section was minced and homogenized in EZ lysis buffer. The homogenate was filtered through a 40 µm cell strainer and centrifuged to pellet the nuclei. The nuclei pellet was resuspended and layered onto a sucrose gradient and centrifuged to separate and remove any other cellular components and debris. The purified nuclei were resuspended in an appropriate volume of resuspension buffer. Single nuclei were then sorted based on DAPI fluorescence using a flow cytometer. The sorted nuclei were counted using a CellDrop FL Automated Cell Counter (DeNovix) to determine the concentration. The single nuclei suspension was loaded onto a Chromium Controller (10x Genomics) for single nuclei encapsulation, barcoding and cDNA synthesis.
Library preparation using the Chromium Single Cell 3' Reagent Kit v3 (10x Genomics) following the manufacturer's instructions. The prepared libraries were sequenced on an MGI FCL sequencer.

value: Sham operation

value: 10x Genomics Chromium Next GEM v3.1, Library & Gel Bead Kit


title: Right kidney, Unilateral nephrectomised, 72h, rep6, RNAseq

description:
RNASeq-18
RNASeq-18

value: Illumina TruSeq Stranded mRNA library preparation kit


title: Right kidney, Unilateral nephrectomised, 24h, rep1, snRNAseq

description:
Unx70
Unx70


title: ATAC_rep1

description: demultiplexed with BCL Convert


title: Right kidney, Unilateral nephrectomised, 72h, rep3, RNAseq

description:
RNASeq-15
RNASeq-15


title: Right kidney, Unilateral nephrectomised, 72h, rep4, RNAseq

description:
RNASeq-16
RNASeq-16


title: Right kidney, Sham operated, 24h, rep1, snRNAseq

description:
Sham71
Sham71


title: Right kidney, Unilateral nephrectomised, 72h, rep1, RNAseq

description:
RNASeq-13
RNASeq-13


title: Right kidney, Unilateral nephrectomised, 48h, rep1, RNAseq

description:
RNASeq-1
RNASeq-1


title: Right kidney, Unilateral nephrectomised, 48h, rep6, RNAseq

description:
RNASeq-6
RNASeq-6


title: Right kidney, Unilateral nephrectomised, 48h, rep4, RNAseq

description:
RNASeq-4
RNASeq-4


title: Right kidney, Unilateral nephrectomised, 48h, rep3, RNAseq

description:
RNASeq-3
RNASeq-3


title: Right kidney, Unilateral nephrectomised, 24h, rep2, RNAseq

description:
RNASeq-30
RNASeq-30


title: Right kidney, Unilateral nephrectomised, 48h, rep2, RNAseq

description:
RNASeq-2
RNASeq-2


title: Right kidney, Unilateral nephrectomised, 24h, rep4, RNAseq

description:
RNASeq-32
RNASeq-32


title: Right kidney, Unilateral nephrectomised, 24h, rep5, RNAseq

description:
RNASeq-33
RNASeq-33


title: Right kidney, Sham operated, 72h, rep6, RNAseq

description:
RNASeq-24
RNASeq-24


title: Right kidney, Unilateral nephrectomised, 48h, rep5, RNAseq

description:
RNASeq-5
RNASeq-5


title: Right kidney, Unilateral nephrectomised, 72h, rep2, RNAseq

description:
RNASeq-14
RNASeq-14


title: Right kidney, Unilateral nephrectomised, 24h, rep1, RNAseq

description:
RNASeq-29
RNASeq-29


title: Right kidney, Unilateral nephrectomised, 24h, rep2, snRNAseq

description:
Unx78
Unx78


title: Right kidney, Unilateral nephrectomised, 24h, rep6, RNAseq

description:
RNASeq-34
RNASeq-34


title: Right kidney, Unilateral nephrectomised, 24h, rep3, RNAseq

description:
RNASeq-31
RNASeq-31


title: Right kidney, Sham operated, 72h, rep4, RNAseq

description:
RNASeq-22
RNASeq-22


title: Right kidney, Sham operated, 72h, rep3, RNAseq

description:
RNASeq-21
RNASeq-21


title: Right kidney, Sham operated, 48h, rep6, RNAseq

description:
RNASeq-12
RNASeq-12


title: Right kidney, Sham operated, 72h, rep1, RNAseq

description:
RNASeq-19
RNASeq-19


title: Right kidney, Sham operated, 72h, rep5, RNAseq

description:
RNASeq-23
RNASeq-23


title: Right kidney, Sham operated, 72h, rep2, RNAseq

description:
RNASeq-20
RNASeq-20


title: Right kidney, Sham operated, 48h, rep3, RNAseq

description:
RNASeq-9
RNASeq-9


title: Right kidney, Sham operated, 48h, rep5, RNAseq

description:
RNASeq-11
RNASeq-11


title: Right kidney, Sham operated, 48h, rep2, RNAseq

description:
RNASeq-8
RNASeq-8


title: Right kidney, Sham operated, 24h, rep6, RNAseq

description:
RNASeq-40
RNASeq-40


title: Right kidney, Sham operated, 48h, rep1, RNAseq

description:
RNASeq-7
RNASeq-7


title: Right kidney, Sham operated, 48h, rep4, RNAseq

description:
RNASeq-10
RNASeq-10


title: Right kidney, Sham operated, 24h, rep2, RNAseq

description:
RNASeq-36
RNASeq-36


title: Right kidney, Sham operated, 24h, rep5, RNAseq

description:
RNASeq-39
RNASeq-39


title: Right kidney, Sham operated, 24h, rep3, RNAseq

description:
RNASeq-37
RNASeq-37


title: Right kidney, Sham operated, 24h, rep4, RNAseq

description:
RNASeq-38
RNASeq-38


title: Right kidney, Sham operated, 24h, rep1, RNAseq

description:
RNASeq-35
RNASeq-35


title: Nasal swab, COVID19+, Patient 10

status: Public on Dec 11 2023

description: MM-C_10 column in coverage_all_samples_hsa_un_COVID_al.txt

data_processing:
FastQC (Andrews, 2010) was used to quality check the smRNAseq sequencing reads.
Cutadapt version 2.3 (Martin, 2011) was used to trim reads with adaptors (AAGATCGGAAGAGCACACGTCT), remove low quality reads and remove reads with a length less than 18bp.
The cleaned reads were first aligned to the Homo sapiens genome (GRCh38, Gencode) using Bowtie2 with the following parameters: -q -D 20 -R 3 -N 0 -L 18 -i S,1,0.50.
The unaligned reads were then aligned to SARS-CoV-2 genome (NC_045512.2, NCBI) using Bowtie2 with the following parameters: -q -D 20 -R 3 -N 0 -L 18 -i S,1,0.50.
The whole read coverage was visualised as a circos plot using the Circlize package in R (Gu et al., 2014) with mapped reads divided into different bins and distribution calculated at each position to produce smooth and uniform coverage.
The alignment process was repeated with 18 to 26 nucleotides size selected reads using awk command. The size distribution of SARS CoV-2 mapped reads and the overrepresented smRNAseq patient reads were determined.
Assembly: hg39, SARS-CoV-2
Supplementary files format and content: bigwig files; BAM files generated from unalignment to human followed alignment to COVID-19. It was then filtered for 18-26 nt and normalized to CPM with a bin size of 1 into bigwig format for visualisation. Patient 6 has not alignment to COVID-19.
Supplementary files format and content: txt files; BAM files generated from unalignment to human followed alignment to COVID-19. Coverage for individual genes for each patients were calculated and then normalize for CIRCOS plot

organism:
Homo sapiens
Severe acute respiratory syndrome coronavirus 2

source_name: Nasopharyngeal swab

extract_protocol:
RNA was isolated from 0.5 mL of viral transport fluid using 1.5 mL of Trizol LS (Thermo Fisher Scientific) and chloroform as per the manufacturer’s recommendations. RNA was precipitated with isopropanol supplemented with 20 µg of glycogen (Thermo Fisher Scientific) as a carrier. RNA pellets were washed with 75% ethanol and resuspended in 30 µL 0.1mM nuclease-free EDTA (Thermo Fisher Scientific). RNA concentration was determined using a NanoDrop 8000 Spectrophotometer (Thermo Fisher Scientific) and Qubit Fluorometer (Thermo Fisher Scientific), and LabChip GX Touch 24 (Perkin Elmer) for quality assessment.
Libraries were prepared from nasopharyngeal RNA from SARS-CoV-2 positive patients using the NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (New England Biolabs) as per the manufacturer’s protocol. PCR amplification was performed using 15 cycles and size selection was performed using AMPureXP beads (Beckman Coulter) according to the manufacturer’s protocol. Libraries were QC checked for quality and quantitation of RNA on the Lab Chip (Perkin Elmer). Pooled libraries were sequenced on the Illumina NextSeq 500 1 x 75 cycle High Output kit.

value: Nasopharyngeal swab

tag: disease

value: COVID19 positive

tag: diagnostic ct


title: Nasal swab, COVID19+, Patient 1

description: MM-C_01 column in coverage_all_samples_hsa_un_COVID_al.txt

tag: tissue


title: Nasal swab, COVID19+, Patient 9

description: MM-C_09 column in coverage_all_samples_hsa_un_COVID_al.txt


title: Nasal swab, COVID19+, Patient 8

description: MM-C_08 column in coverage_all_samples_hsa_un_COVID_al.txt


title: Nasal swab, COVID19+, Patient 3

description: MM-C_03 column in coverage_all_samples_hsa_un_COVID_al.txt


title: Nasal swab, COVID19+, Patient 7

description: MM-C_07 column in coverage_all_samples_hsa_un_COVID_al.txt


title: Nasal swab, COVID19+, Patient 6

description: MM-C_06 column in coverage_all_samples_hsa_un_COVID_al.txt


title: Nasal swab, COVID19+, Patient 2

description: MM-C_02 column in coverage_all_samples_hsa_un_COVID_al.txt


title: H23R

status: Public on May 26 2023

city: Madrid

first: Carlos

last: Rodríguez Antolín

address: Paseo castellana 261

department: Genetics

country: Spain

institute: Hospital Universitario La Paz

data_processing:
The trimmed reads (length >= 15 nt and adapters removal) were aligned to the human pre-miRNA in miRBase 21 using novoalign software. For miRNA alignment, the maximum mismatch was 1. Reads with counts less than 2 were discarded when calculating the miRNA expression.
Assembly: miRBase 21
Supplementary files format and content: Tab-delimited text files include annotations and read counts (number of transcripts per million, TPM) of all mature miRNA variants (miRBase21) in each sample

source_name: Lung cancer resistant cell line

growth_protocol: All cell lines were maintained in RPMI or DMEM supplemented with 10% exosome-depleted FBS, according to manufacturer’cifications. FBS was depleted of bovine exosomes by ultracentrifugation at 100,000 x g 16 h at 4 C.

extract_protocol:
RNA was extracted using miRCURY RNA Isolation Kit - Cell and Plant (Exiqon, Denmark)
Total RNA of each sample was sequentially ligated to 3’ and 5’ small RNA adapters. cDNA was then synthesized and amplified using Illumina’s proprietary RT primers and amplification primers. Subsequently, ~130-150 bp PCR amplified fragments were extracted and purified from the PAGE gel. Sequencing was performed on Illumina HiSeq 2000 using Truseq Rapid SBS Kits, according to the manufacturer's instructions.

treatment_protocol: The Cisplatin (CDDP) resistant variants H23R and A2780R were established by exposing cells to increasing doses of  cisplatin,and selected after a final exposure to 0.2 and 0.5 µ respectively, showing approximately four times more drug resistance than the matched parental cell line (4.07 and 3.89 resistant index; P<0.001 and P<0.002). The CDDP sensitive and resistant ovarian cancer cell lines 41M and 41MR were kindly provided by Dr. Kelland (UK) and maintained in DMEM supplemented with 10% exosome-depleted FBS, showing a similar CDDP resistant-index of 4.8; P<0.001.

tag: biological source

value: Lung

tag: cell line

tag: chemoterapy drug

value: cisplatin

tag: phenotype

value: Resistant


title: H23S

source_name: Lung cancer sensitive cell line

value: Sensitive


title: A2780R

source_name: Ovarian cancer resistant cell line

value: Ovary


title: 41MS

source_name: Ovarian cancer sensitive cell line


title: A2780S


title: 41MR


title: Jurkat GFP-luc Donor 60

status: Public on Mar 29 2023

description:
Karyotype: This is a pseudodiploid human cell line. The modal chromosome number is 46, occurring in 74% with polyploidy at 5.3%. The karyotype is 46,XY,-2,-18,del(2) (p21p23),del(18) (p11.2). Most cells had normal X and Y chromosomes. Genes expressed: interleukin-2 (interleukin 2, IL-2); CD6
21ID00922_RNA1046

data_processing:
Trimmomatic was used to eliminate the remnants from the adaptors and discard those low quality sequences
Reads were mapped (STAR) and quantified on the transcriptome using RSEM
Assembly: GRCh37
Supplementary files format and content: Tab-delimited text files include RSEM expected counts for each sample and gene

source_name: Peripheral blood

growth_protocol: RPMI 10%FBS

extract_protocol:
Sorted Jurkat-GFP cells that remained after overnight exposition to NKG2D-CAR T cells were washed in PBS and pelleted in RLT lysis buffer supplemented with 1:1000 β-mercaptoethanol. RNA isolation and sequencing was carried out as our group previously reported (Fernández A et al. Cancers, 2021).
Poly(A)+ mRNA fraction was isolated from total RNA and cDNA libraries were obtained following Illumina ́s recommendations. Poly(A)+ RNA was isolated on poly-T oligo-attached magnetic beads and chemically fragmented prior to reverse transcription and cDNA generation. The cDNA fragments then go through an end repair process, the addition of a single ‘A’ base to the 3’ end and then ligation of the adapters. Finally, the products are purified and enriched with PCR to create the indexed final double stranded cDNA library.

treatment_protocol: Jurkat GFP-luc cells were  co-cultured with NKG2D-CAR T cells or left untreated for 16h, sorted and used to perform transcriptome analysis

value: Peripheral blood

value: Jurkat

tag: cell type

value: T lymphoblasts

tag: karyotype

value: pseudodiploid

tag: treatment

value: Treated with NKG2D CAR T cells


title: Jurkat GFP-luc Donor 51

description:
Karyotype: This is a pseudodiploid human cell line. The modal chromosome number is 46, occurring in 74% with polyploidy at 5.3%. The karyotype is 46,XY,-2,-18,del(2) (p21p23),del(18) (p11.2). Most cells had normal X and Y chromosomes. Genes expressed: interleukin-2 (interleukin 2, IL-2); CD5
21ID00921_RNA1045


title: P394T_S37S44

status: Public on Apr 10 2020

description: rsem-all.genes.results.txt

data_processing:
TRIMMOMATIC (v.036) was used to eliminate the remnants from the adaptors and discard those low quality sequences
Reads were mapped and quantified on the transcriptome using RSEM (version 1.3.0)
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited text files include RSEM expected counts for each sample and gene

source_name: Lung Tumor Sample

extract_protocol:
DNA (500 ng) from the resistant and the sensitive (used as reference) subtypes of each cell line were double-digested with RsaI and AluI for 2h at 37ºC
Poly(A)+ mRNA fraction was isolated from total RNA and cDNA libraries were obtained following Illumina ́s recommendations. Poly(A)+ RNA was isolated on poly-T oligo-attached magnetic beads and chemically fragmented prior to reverse transcription and cDNA generation. The cDNA fragments then go through an end repair process, the addition of a single ‘A’ base to the 3’ end and then ligation of the adapters. Finally, the products are purified and enriched with PCR to create the indexed final double stranded cDNA library.

tag: dkk1 level

value: upregulated

tag: condition

value: Tumor


title: Jurkat GFP-luc biol rep 2

description:
Karyotype: This is a pseudodiploid human cell line. The modal chromosome number is 46, occurring in 74% with polyploidy at 5.3%. The karyotype is 46,XY,-2,-18,del(2) (p21p23),del(18) (p11.2). Most cells had normal X and Y chromosomes. Genes expressed: interleukin-2 (interleukin 2, IL-2); CD4
21ID00920_RNA1044B

value: Untreated


title: P385N_S35S42

description: rsem-all.genes.results.txt

source_name: Lung Normal Sample

value: Normal


title: P416N_S38S45

description: rsem-all.genes.results.txt


title: Nasal swab, COVID19+, Patient 5

description: MM-C_05 column in coverage_all_samples_hsa_un_COVID_al.txt


title: Jurkat GFP-luc biol rep 1

description:
Karyotype: This is a pseudodiploid human cell line. The modal chromosome number is 46, occurring in 74% with polyploidy at 5.3%. The karyotype is 46,XY,-2,-18,del(2) (p21p23),del(18) (p11.2). Most cells had normal X and Y chromosomes. Genes expressed: interleukin-2 (interleukin 2, IL-2); CD3
21ID00919_RNA1044A


title: P325T_S33S40

description: rsem-all.genes.results.txt


title: P378T_S34S41

description: rsem-all.genes.results.txt


title: P298N_S28S35

description: rsem-all.genes.results.txt


title: P316T_S31S38

description: rsem-all.genes.results.txt

value: downregulated


title: Jurkat GFP-luc Donor 63

description:
Karyotype: This is a pseudodiploid human cell line. The modal chromosome number is 46, occurring in 74% with polyploidy at 5.3%. The karyotype is 46,XY,-2,-18,del(2) (p21p23),del(18) (p11.2). Most cells had normal X and Y chromosomes. Genes expressed: interleukin-2 (interleukin 2, IL-2); CD7
21ID00923_RNA1047


title: P300T_S29S36

description: rsem-all.genes.results.txt


title: P313T_S30S37

description: rsem-all.genes.results.txt


title: P286T_S25S32

description: rsem-all.genes.results.txt


title: P386N_S36S43

description: rsem-all.genes.results.txt


title: P296T_S27S34

description: rsem-all.genes.results.txt


title: P292T_S26S33

description: rsem-all.genes.results.txt


title: P323N_S32S39

description: rsem-all.genes.results.txt


title: OVCAR3-Sensitive

status: Public on Jun 14 2018

description: DNA methylation profiling data by bisulfite conversion from sensitive cisplatin OVCAR3 ovarian cancer cell line

data_processing:
The mapping was carried out using GEM 1.242 to a converted reference sequence (Homo sapiens, GRCh37). The reference file contains two copies of the hsapiens GRCh37 reference, one with all C's changes to T's and one with all G's changed to A's. In addition the file also contains two copies of the NCBI viral genome dataset (rel 53, http://www.ncbi.nlm.nih.gov/genomes/GenomesHome.cgi?taxid=10239), modified in the same way as for the human genome. Before mapping, the original sequence data was then modified so that any C's in the first read of a pair were converted to T's, and any G's on the second read of a pair were converted to A's. The mapping was then performed, and the original sequence was replaced in the output mapping.
Read Filtering: Read pairs were selected where a single paired mapping existed with the correct read pair orientation and with a fragment size within the central 95% of the read size distribution.
Calling of methylation levels and genotypes was performed by the program bscall using the default settings.
Filtering of homozygous CpG sites and homozygous cytosines was performed using a maximum coverage cutoff of 250 reads per position.
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited text file include methylation probability estimation for each CpG

source_name: Sensitive cisplatin OVCAR3 ovarian cancer cell line

growth_protocol: Following the culture recommendations from ATCC and ECACC

extract_protocol:
DNA was extracted using conventional techniques of digestion with proteinase K followed by phenol/chloroform extraction.
Genomic DNA (2 μg) was spiked with unmethylated λ DNA (Promega) at a concentration of 5 ng of λ DNA per 1 μg of genomic DNA. The short-insert paired-end library was prepared using the TruSeq™DNA Sample Preparation Kit v2 (Illumina Inc.) following manufacturer’s guidelines with minor modifications. In brief: The DNA was sheared with a Covaris E220 (Covaris) to 50–500 bp and size-selected to 150-300 bp fragments using AMPure XP beads (Agencourt Bioscience Corp.). DNA fragments were end-repaired, adenylated and ligated to Illumina specific indexed paired-end adaptors. After adaptor ligation, the DNA was treated with sodium bisulfite using the EpiTect Bisulfite kit (Qiagen) following the manufacturer's instructions for formalin-fixed and paraffin-embedded (FFPE) tissue samples with two rounds of conversions. After bisulfite conversion the adaptor-ligated DNA was amplified with 7 cycles of PCR using the PfuTurboCx Hotstart DNA polymerase (Stratagene). The library was quality controlled using BioAnalyzer 7500 assay (Agilent).

treatment_protocol: Cisplatin resistant variant was established from the parental sensitive cell line treated with increasing doses of cisplatin.

value: Ovarian


title: OVCAR3-Resistant

description: DNA methylation profiling data by bisulfite conversion from resistant cisplatin OVCAR3 ovarian cancer cell line

source_name: Resistant cisplatin OVCAR3 ovarian cancer cell line


title: H460-Resistant

description: DNA methylation profiling data by bisulfite conversion from resistant cisplatin H460 lung cancer cell line

source_name: Resistant cisplatin H460 lung cancer cell line


title: H460-Sensitive

description: DNA methylation profiling data by bisulfite conversion from sensitive cisplatin H460 lung cancer cell line

source_name: Sensitive cisplatin H460 lung cancer cell line


title: H23-Resistant-Rep1

type: RNA

description: LncRNA and mRNA expression profiling data from resistant cisplatin H23 lung cancer cell line

hyb_protocol: The labeled cRNAs were hybridized onto the Human LncRNA Array v3.0 (8 x 60K, Arraystar).

scan_protocol: After washing, slides were scanned with the Agilent DNA Microarray Scanner (G2505C). Data was extracted using Agilent Feature Extraction software (version 11.0.1.1).

data_processing: Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 1 out of 16 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

source_name: Resistant cisplatin H23 lung cancer cell line

label_protocol: Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar).

extract_protocol: Total RNA from S and R cells was extracted by the guanidine thiocyanate method using TRIzol reagent (Invitrogen) and followed by a DNAse treatment (Qiagen). RNA integrity and concentration were assessed by Nanodrop ND-1000 and 2100 Bioanalyzer (Agilent Technologies). mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre).

treatment_protocol: Cisplatin resistant variant was established from the parental sensitive cell line treated with increasing doses of cisplatine. There are two independent biological replicates per cell line.

tag: replicate


title: OVCAR3-Sensitive-Rep2

description: LncRNA and mRNA expression profiling data from sensitive cisplatin OVCAR3 ovarian cancer cell line


title: H23-Resistant-Rep2


title: H460-Sensitive-Rep2

description: LncRNA and mRNA expression profiling data from sensitive cisplatin H460 lung cancer cell line


title: H23-Sensitive-Rep2

description: LncRNA and mRNA expression profiling data from sensitive cisplatin H23 lung cancer cell line

source_name: Sensitive cisplatin H23 lung cancer cell line


title: H460-Sensitive-Rep1


title: OVCAR3-Resistant-Rep1

description: LncRNA and mRNA expression profiling data from resistant cisplatin OVCAR3 ovarian cancer cell line


title: A2780-Resistant-Rep1

description: LncRNA and mRNA expression profiling data from resistant cisplatin A2780 ovarian cancer cell line

source_name: Resistant cisplatin A2780 ovarian cancer cell line


title: A2780-Sensitive-Rep2

description: LncRNA and mRNA expression profiling data from sensitive cisplatin A2780 ovarian cancer cell line

source_name: Sensitive cisplatin A2780 ovarian cancer cell line


title: A2780-Resistant-Rep2


title: A2780-Sensitive-Rep1


title: H23-Sensitive

description: DNA methylation profiling data by bisulfite conversion from sensitive cisplatin H23 lung cancer cell line


title: OVCAR3-Sensitive-Rep1


title: OVCAR3-Resistant-Rep2


title: H460-Resistant-Rep1

description: LncRNA and mRNA expression profiling data from resistant cisplatin H460 lung cancer cell line


title: A2780-Sensitive

description: DNA methylation profiling data by bisulfite conversion from sensitive cisplatin A2780 ovarian cancer cell line


title: A2780-Resistant

description: DNA methylation profiling data by bisulfite conversion from resistant cisplatin A2780 ovarian cancer cell line


title: H23-Resistant

description: DNA methylation profiling data by bisulfite conversion from resistant cisplatin H23 lung cancer cell line


title: A2780_R_1

status: Public on Oct 05 2017

description: miRNA expression resistant cisplatin A2780 ovarian cancer cell line

hyb_protocol: 100 ng of Cy3 labelled RNA were hybridized onto Human miRNA Microarray v2, 8x15K (G4470B) for 20 hours at 55ºC in a hybridization oven (G2545A, Agilent Technologies) set to 15 rpm in a final concentration of 1X GE Blocking Agent and 1X Hi-RPM Hybridization Buffer, according to manufacturer's instructions (miRNA Microarray System Protocol, Agilent Technologies). Arrays were washed according to manufacturer's instructions (miRNA Microarray System Protocol, Agilent Technologies). Arrays were dried out using a centrifuge at 1000 rpm for 2 min.

scan_protocol: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2565BA, Agilent Technologies) using the default settings for miRNA Microarray (miRNA Microarray System Protocol, Agilent Technologies).

data_processing: Image (.tiff file) provided by the scanner was analyzed using Feature Extraction software version 10 (Agilent Technologies). Data from the arrays were normalized based on the VSN method. After normalization, were considered for further analysis only those probes present in at least one sample for microRNA microarrays and at least 50% of all the samples for mRNA microarray; both experiments with average expression over the 20th percentile of all average expressions and that change across the experiment (i.e. with coefficient of variation (CV)>5 % across all samples)

source_name: Resistant cisplatin A2780 lung cancer cell line

label_protocol: miRNA Labeling Kit (Agilent Technologies) was used to label RNA. Basically, 100 ng of total RNA were dephosphorylated and Cyanine 3-pCp molecule was ligated to the 3´ end of each RNA molecule by using T4 RNA ligase.

extract_protocol: Total RNA was extracted by the guanidine thiocyanate method using TRIZOL reagent (Invitrogen, CA) and purified with miRNeasy mini kit (Quiagen, CA), combined with DNAsa treatment as recommended by Agilent

treatment_protocol: Cisplatin resistant variant was established from the parental sensitive cell line treated with increasing doses of cisplatine. Resistant variants were treated with epigenetic reactivation drugs 5Aza-2deoxycytidine (5Aza-dC) and Trichostatin A (TSA) (Sigma-Aldrich, Spain)


title: A2780_S_1

description: miRNA expression rene expression sensitive cisplatin A2780 ovarian cancer cell line

source_name: Sensitive cisplatin A2780 lung cancer cell line


title: OVCAR3_S_1

description: miRNA expression sensitive cisplatin OVCAR3 ovarian cancer cell line

source_name: Sensitive cisplatin OVCAR3 lung cancer cell line


title: OVCAR3_RT_2

description: miRNA expression resistant under epimiRNAtic reactivation treatment OVCAR3 ovarian cancer cell line

source_name: Resistant under epigenetic reactivation treatment OVCAR3 lung cancer cell line


title: OVCAR3_S_2


title: A2780_RT_1

description: miRNA expression resistant under epimiRNAtic reactivation treatment A2780 ovarian cancer cell line

source_name: Resistant under epigenetic reactivation treatment A2780 lung cancer cell line


title: H460_RT_2

description: miRNA expression resistant under epimiRNAtic reactivation treatment H460 lung cancer cell line

source_name: Resistant under epigenetic reactivation treatment H460 lung cancer cell line


title: A2780_S_2

description: miRNA expression sensitive cisplatin A2780 ovarian cancer cell line


title: A2780_RT_2

value: Resistant under epigenetic reactivation treatment


title: A2780_R_2


title: H23-Sensitive-Rep1

value: Lung


title: Sarcoid Lung, Visium B1

description: Fresh frozen spatial transcriptome sequencing

source_name: Sarcoid Lung

value: Sarcoid Lung


title: H460-Resistant-Rep2

value: cisplatin

value: Resistant


title: H460_S_2

description: miRNA expression sensitive cisplatin H460 lung cancer cell line

value: Sensitive


title: OVCAR3_R_2

description: miRNA expression resistant cisplatin OVCAR3 ovarian cancer cell line

source_name: Resistant cisplatin OVCAR3 lung cancer cell line


title: OVCAR3_R_1


title: H460_R_2

description: miRNA expression resistant cisplatin H460 lung cancer cell line


title: H23_RT_2

description: miRNA expression resistant under epimiRNAtic reactivation treatment H23 lung cancer cell line

source_name: Resistant under epigenetic reactivation treatment H23 lung cancer cell line


title: H23_R_2

description: miRNA expression resistant cisplatin H23 lung cancer cell line


title: H460_RT_1

description: miRNA expression resistant under epimiRNAtic reactivation treatment H2460 lung cancer cell line

source_name: Resistant under epigenetic reactivation treatment H2460 lung cancer cell line


title: H460_S_1


title: H23_RT_1


title: H23_S_2

description: miRNA expression sensitive cisplatin H23 lung cancer cell line


title: H23_R_1


title: H460_R_1


title: H23_S_1


title: OVCAR3 Resistant vs Sensitive

type: genomic

description: Microarray data from resistant and sensitive cisplatin OVCAR3 ovarian cancer cell line

hyb_protocol: After probe denaturation and pre-annealing with Cot-1 DNA, hybridization was performed at 65ºC with rotation for 24 h.

scan_protocol: After two washing steps, the microarray was then scanned by the Agilent Microarray Scanner and analyzed with Feature Extraction software (v9.1 Agilent Technologies) and Agilent Cytogenomic 3.0.1.1.

data_processing: The analysis and visualization of the microarray data was performed using Agilent Cytogenomic 3.0.1.1.

source_name: Resistan phenotype

label_protocol: After heat inactivation of the enzymes at 65ºC for 20 min, each digested sample was labeled by random priming (Genomic DNA Enzymatic Labeling Kit Agilent) for 2 h using Cy5-dUTP for patient DNAs and Cy3-dUTP for reference DNAs. Labeled products were column purified (Microcon Ym-30 filters, Millipore Corporation).

growth_protocol: Growth protocols were the standard indicated  from the ATCC (Manassas, USA) and ECACC (Sigma-Aldrich, Spain) cells were  cultured as recommended

extract_protocol: DNA (500 ng) from the resistant and the sensitive (used as reference) subtypes of each cell line were double-digested with RsaI and AluI for 2h at 37ºC

treatment_protocol: Cisplatin resistant variant was established from the parental sensitive cell line treated with increasing doses of cisplatine. (Farma Ferrer, Spain)

value: Cisplatin

source_name: Sensitive phenotype


title: OVCAR3_RT_1

description: Gene expression resistant under epigenetic reactivation treatment OVCAR3 ovarian cancer cell line

hyb_protocol: Samples were hybridized to Whole Human Genome Microarray 4 x 44K (G4112F, Agilent Technologies). 1.65 ug of Cy3 labelled aRNA were hybridized for 17 hours at 65ºC in a hybridization oven  (G2545A, Agilent) set to 10 rpm in a final concentration of 1X GEx Hybridization Buffer HI-RPM, according to manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis, Agilent Technologies). Arrays were washed according to manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis, Agilent Technologies). Arrays were dried out using a centrifuge.

scan_protocol: Arrays were scanned at 5 um resolution on an Agilent DNA Microarray Scanner (G2565BA, Agilent Technologies) using the default settings for 4x44k format one-color arrays.

data_processing: Images provided by the scanner were analyzed using Feature Extraction software (Agilent Technologies). Data from the arrays were normalized based on the VSN method. After normalization, were considered for further analysis only those probes present in at least one sample for microRNA microarrays and at least 50% of all the samples for mRNA microarray; both experiments with average expression over the 20th percentile of all average expressions and that change across the experiment (i.e. with coefficient of variation (CV)>5 % across all samples)

label_protocol: One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent Technologies, Palo Alto, CA, USA) was used to amplify and label RNA. Briefly, 1 ug of total RNA was reverse transcribed using T7 promoter Primer and MMLV-RT. Then cDNA was converted to aRNA using T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3-labeled CTP


title: OVCAR3_RT_2


title: A2780_R_1

description: Gene expression resistant cisplatin A2780 ovarian cancer cell line


title: A2780_S_2

description: Gene expression sensitive cisplatin A2780 ovarian cancer cell line


title: A2780_RT_1

description: Gene expression resistant under epigenetic reactivation treatment A2780 ovarian cancer cell line


title: A2780_RT_2


title: OVCAR3_S_1

description: Gene expression sensitive cisplatin OVCAR3 ovarian cancer cell line


title: OVCAR3_S_2


title: OVCAR3_R_1

description: Gene expression resistant cisplatin OVCAR3 ovarian cancer cell line


title: H460_RT_2

description: Gene expression resistant under epigenetic reactivation treatment H460 lung cancer cell line


title: H460_R_2

description: Gene expression resistant cisplatin H460 lung cancer cell line

source_name: Resistant cisplatin H460 lung cancer cell line


title: H460_S_2

description: Gene expression sensitive cisplatin H460 lung cancer cell line

source_name: Sensitive cisplatin H460 lung cancer cell line


title: H460_RT_1

description: Gene expression resistant under epigenetic reactivation treatment H2460 lung cancer cell line


title: A2780 Resistant vs Sensitive

description: Microarray data from resistant and sensitive cisplatin A2780 ovarian cancer cell line


title: A2780_S_1

description: Gene expression rene expression sensitive cisplatin A2780 ovarian cancer cell line


title: A2780_R_2


title: OVCAR3_R_2


title: H23_R_1

description: Gene expression resistant cisplatin H23 lung cancer cell line

source_name: Resistant cisplatin H23 lung cancer cell line


title: H23_RT_1

description: Gene expression resistant under epigenetic reactivation treatment H23 lung cancer cell line


title: H460_R_1


title: H23_RT_2


title: H23_S_2

description: Gene expression sensitive cisplatin H23 lung cancer cell line

source_name: Sensitive cisplatin H23 lung cancer cell line


title: H460_S_1


title: H23_S_1


title: H23 Resistant vs Sensitive

description: Microarray data from resistant and sensitive cisplatin H23 lung cancer cell line


title: H460 Resistant vs Sensitive

description: Microarray data from resistant and sensitive cisplatin H460 lung cancer cell line


title: OVCAR3_RT_1

description: miRNA expression resistant under epimiRNAtic reactivation treatment OVCAR3 ovarian cancer cell line


title: H23_R_2


title: 38_1_Young_Veh

city: La Jolla

first: Kathryn

last: Lande

state: CA

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute

description:
R6274_E9_Liver_exprMat_file.csv
R6274_E9_Liver_fov_positions_file.csv
R6274_E9_Liver_metadata_file.csv
R6274_E9_Liver-polygons.csv
R6274_E9_Liver_tx_file.csv
R6274_E9_Liver_tx_file.csv
Slide 9
E9_38

hyb_protocol: RNA ISH probes (Mouse Universal Cell Characterization Panel, 1000-plex) were denatured at 95°C for 2 min and then placed on ice before preparing the ISH probe mix (1nM ISH probes, 1x Buffer R, 0.2 U/μL SUPERaseIn™ in DEPC H2O). 150 μL ISH probe mix was pipetted into the incubation frame of each slide, then incubation frame covers were applied to help move the hybridization solution across the tissue. Hybridization was performed at 37°C overnight (16-18 h) in a hybridization chamber to prevent evaporation. Following overnight hybridization, incubation frame covers were removed, and samples were washed twice with 50% formamide (VWR) in 2x SSC at 37°C for 25 min, rinsed twice with 2X SSC for 2 min at RT, then blocked with 200 μL Blocking Buffer (BSB) containing DAPI at 1:40 dilution for 15 min at RT. Samples were then incubated with a fluorophore-conjugated antibody cocktail against CD298/B2M, PanCK, CD45, and CD68 proteins at RT for 1 hr. After antibody staining, the samples were washed three times with 1x PBS for 5 min each at RT, then flow cells were assembled on the slide using the Flow Cell Assembly Tool and Kit (BSB).

scan_protocol: Target RNA readout on SMI instrument was performed following published protocols (He et al, 2022). Briefly, assembled flow cells were loaded onto the SMI instrument and samples were washed with Reporter Wash Buffer to rinse the samples and remove any air bubbles from the flow cell. Once loaded and washed, the entire flow cell was scanned, and field of views (FOVs) were placed on each slide for RNA readout. Prior to assay initiation, a 5-channel Z-stack image (4 antibodies and DAPI) was collected for each FOV. These images were used to perform single cell segmentation. Assay cycling was then initiated. The first RNA readout cycle was initiated by flowing 100 µL of Reporter Pool 1 into the flow cell and incubating for 15 min. After incubation, 1 mL of Reporter Wash Buffer was flowed across the flow cell to wash out any unbound reporter probes. The Reporter Wash Buffer was then replaced with Imaging Buffer. Eight Z-stack images (0.8 μm step size) of each FOV were acquired and then fluorophores on the reporter probes were UV-cleaved and washed out with Strip Wash Buffer. This fluidic and imaging procedure was then repeated for the remaining 15 reporter pools, and the 16 cycles of reporter hybridization-imaging was repeated 7 additional times to increase RNA detection sensitivity. Raw image processing and feature extraction were performed using an in-house SMI data processing pipeline (He et al, 2022) which includes registration, feature detection, and localization. First, 3D rigid image registration was made using fiducials embedded in the samples matched with the fixed image reference established at the beginning of SMI run to correct for any shift. Next, RNA image analysis algorithm was used to identify reporter signature locations in X, Y, and Z axes along with an assigned confidence. The reporter signature locations and the associated features were collated into a single list. Lastly, the XYZ location information of individual target transcripts were extracted and recorded in a table by a secondary analysis algorithm, as described in He et al, 2022.

data_processing: The 5-channel Z-stack images of immunostaining + DAPI were used for drawing cell boundaries on the samples. A cell segmentation pipeline using a machine learning algorithm (Stringer et al, Pachitariu and Stringer) was used to accurately assign transcripts to cell locations and subcellular compartments. The transcript profile of individual cells was generated by combining target transcript location and cell segmentation boundaries. Raw files were read into Seurat and SCTransform normalized.

label: SMI imaging barcodes

source_name: whole liver

label_protocol: To prepare samples, the protocol provided in CosMx® SMI Manual Slide Preparation for RNA Assays (Manual MAN-10184-06) was followed. Briefly, slides were baked vertically at 60°C overnight prior to commencing deparaffinization, heat-induced epitope retrieval (HIER), and proteinase digestion. To deparaffinize tissue, slides were put through two 5 min incubations with xylene, followed by two 2 min washes with 100% ethanol. HIER was then carried out at 100°C for 15 min in Target Retrieval Buffer (BSB) and proteinase digestion was performed at 40°C for 30 min with digestion buffer (3 ug/mL Proteinase K in 1x PBS). The samples were then rinsed with fresh DEPC-treated water twice and incubated with 0.001% fiducials (BSB) for 5 min at RT. Fiducials were diluted in 2x saline sodium citrate, 0.001% Tween 20 (2x SSC-T) prior to use. Excess fiducials were removed by rinsing with 1x PBS, followed by fixation with 10% NBF for 1 min at RT. Fixed samples were rinsed with Tris-glycine buffer (0.1M glycine, 0.1M Tris-base in DEPC H2O) twice for 5 min each at RT and then once with 1X PBS for 5 min. Next, samples were blocked using 100 mM N-succinimidyl acetate (NHS-acetate, ThermoFisher) in NHS-acetate buffer (0.1M NaP, 0.1% Tween pH 8 in DEPC H2O). Blocking lasted 15 min at RT. Prepared samples were rinsed twice with 2x saline sodium citrate (SSC) for 5 min each before proceeding to the in-situ hybridization step.

extract_protocol: FFPE mouse liver sections.

value: whole liver

tag: biological replicate

tag: Sex

value: Female

tag: genotype

value: Vehicle

tag: age

value: Young

value: Veh


title: 64201

city: Indianapolis

first: Helen

last: Masson

address: 893 S Delaware St.

institute: Eli Lilly and Company

description: Library name: Sample 414

data_processing:
Data was processed using nf-core/rnaseq v3.14.0 of the nf-core collection of workflows, utilizing reproducible software environments from the Bioconda and Biocontainers projects. The pipeline was executed with Nextflow v23.10.1. Resulting count data was pre-processed using the edgeR packagein R, which included filtering out lowly-expressed genes using edgeR filterByExpr (min.count = 10) and performing quantile-normalized voom transformation.
Assembly: GRCh38
Supplementary files format and content: txt file includes normalized gene counts for each sample

source_name: whole blood

extract_protocol:
Whole blood RNA was extracted from PAXgene blood RNA tubes. Briefly, frozen tubes were thawed at room temperature and centrifuged according to the manufacturer’s protocol. The resulting pellet was then washed with nuclease free water, resuspended in sterile PBS, and split in half. RNA was extracted from one half of the suspension using the QIAsymphony PAXgene Blood RNA Kit (Qiagen). The other half of the suspension was used for DNA extraction. RNA concentration and integrity were assessed using the Ribogreen Assay (Thermo) and a Fragment Analyzer (Agilent), respectively.
Polyadenylated RNA was enriched using NEBNext Magnetic Oligo(dT)25 Beads and prepared into RNA-seq libraries using the NEBNext mRNA Library Prep Reagent Set for Illumina (New England BioLabs, Ipswich, MA, USA). Unique dual-index barcodes were incorporated as specified per manufacturer’s protocol. Library concentration was measured using the Quant-iT PicoGreen dsDNA Reagent (Thermo), and library size distribution and quality were checked using a DNA chip on Caliper Gx Touch (Revity). Library quantification was further refined by qPCR using the KAPA Library Quantificaiton Kit (Roche). Paired-end sequencing (2 x 100 bp, 100 million reads per sample) was carried out on an Illumina NovaSeq 6000 platform (Illumina) following manufacturer’s recommended protocols.

value: whole blood

value: SLE


title: v8601 Pairname L29 Pair time4wk_sep

first: Mary

middle: Ann

last: Allen

state: Co

address: UCB 596  JSCBB

department: BioFrontiers

institute: University of Colorado

description:
Library name: v8601
tpm_all_samples.csv
normcounts_Deseq2_qualitysamples_remove6weeks.csv

data_processing:
Data was mapped to the vole genome  (Microtus_ochrogaster.MicOch1.0.dna.toplevel.fa, Microtus_ochrogaster.MicOch1.0.115.gtf) and reads were counted per gene via the nfcores RNA-seq nextflow pipeline (version 3.17.0). Microtus_ochrogaster.MicOch1.0.dna.toplevel.fa, Microtus_ochrogaster.MicOch1.0.115.gtf
The dds created by the nfcores RNA-seq pipeline was read into R, and expression was normalized via both tpm and deseq2. The normlaized counts from deseq where used to look at correlation of gene expression between paired voles and previously paired voles.
Assembly: Microtus_ochrogaster.MicOch1.0.dna.toplevel.fa
Supplementary files format and content: tpm caulcated from the raw data
Supplementary files format and content: deseq2 normliazed counts for the data used in the publication

organism: Microtus ochrogaster

source_name: BRAIN nucleus accumbens

growth_protocol: Voles were bred in the University of Colorado animal facilities under standardized husbandry protocols.

extract_protocol:
Brain tissue was frozen at -80C and later the nucleus accumbens was dissected from each brain separately.
RNA purity, quantity and integrity was determined with NanoDrop (ThermoFisher Scientific) and TapeStation 4200 (Agilent) analysis prior to RNA-seq library preparation.  The Universal Plus mRNA-Seq library preparation kit with NuQuant was used (Tecan) with an input of 200ng of total RNA to generate RNA-Seq libraries.  Paired-end sequencing reads of 150bp was generated on NovaSeq X (Illumina) sequencer at a target depth of 80 million paired-end reads per sample.  Raw sequencing reads were de-multiplexed using bcl2fastq.

treatment_protocol: Voles were mated to a partner. Some of the voles were then separated at 2 weeks from there partner and then sacrificed. Other voles were kept with there partner for 2 weeks or 6 weeks.

value: BRAIN nucleus accumbens

tag: pair

tag: gender

value: female

tag: cohort batch