title: Patient DCP31, 10x 3' expression multiflex library from PBMCs collected on D0, 21, 42

city: Los Angeles

first: Linh

middle: My

last: Tran

state: California

department: Medicine - Pulmonary & Critical Care

institute: University of Los Angeles

description:
Library name: DCP31_PBMC_RNA
10X Genomics Chromium Next GEM Single Cell 3' v3.1 Dual Index + 3' CellPlex

data_processing:
For tumor scRNA/TCR-seq, CellRanger 9.0 (10X Genomics) was used to align raw reads to the GRCh38 human and GRCm39 mouse combined reference genome provided by 10X Genomics. For PBMC scRNA-seq, CellRanger 9.0 was used to align raw reads to the GRCh38 human reference genome.
The feature_README.txt provides information for demultiplexing samples
Assembly: Raw reads were aligned and annotated using the 10X reference data, version 2024-A. In brief, raw reads were aligned to the reference human genome GRCh38 (PBMC samples) or combination of GRCh38 and GRCm39 genome (tumor biopsy samples). Transcripts were annotated using GENCODE v44/Ensembl110 for human and GENCODE vM33/Ensembl110 for mouse.
Supplementary files format and content: tab-delimited text files (tsv) and tatrix files (mt) provide raw counts of transcripts for filtered barcodes.
Supplementary files format and content: cvs-delimited text file provide counts associated with specified contig and cell barcode.

source_name: PBMCs

extract_protocol:
For scRNA/TCR-seq of tumor biopsies, single cell dissociated tumor samples were thawed and stained using the Zombie NIR Fixable Viability Kit (Biolegend). The KPL mouse cell line was simultaneously stained with Zombie NIR and mixed with tumor samples at a 2:1 ratio to act as carrier cells. Viable cells were sorted using a FACSAria III flow cytometer (BD Biosciences), centrifuged at 400 x g for 5 minutes, and resuspended in PBS + 5% fetal bovine serum (FBS) at a concentration of ~1500 cells/uL prior to library construction. For scRNA-seq of PBMCs, samples from days 0, 21, 42, and 63 for each patient were tagged using the 10X Genomics CellPlex Kit per manufacturer’s protocols. The cells were pooled and then stained with Zombie NIR prior to flow sorting for viability on a FACSAria III flow cytometer.
For scRNA/TCR-seq, library construction was performed according to the manufacturer’s instructions (10x Genomics) to capture the maximum target cells.

value: PBMCs

tag: subject id

value: female


title: HacaT cell, high glucose+rFGF4, C-FOS, ChIP

status: Public on May 01 2026

type: SRA

city: Wenzhou

first: Zhiming

last: Zhang

address: Chashan Campus of Wenzhou Medical University

country: China

institute: Department of Cardiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China

description: Library name: HacaT, HG, rFGF4, CHIP

library_source: genomic

data_processing:
Sequencing Run: Load the final purified DNA library onto an Illumina NovaSeq X Plus sequencer for sequencing.
Instrument Operation: The sequencing run is completed in approximately 2 days.
Data Processing: After the run, convert the raw sequencing data (.bcl format) into standard Fastq format files for downstream analysis.
Assembly: Homo sapiens GRCh38

molecule: genomic DNA

organism: Homo sapiens

source_name: skin

extract_protocol:
The ChIP assays were performed using the SimpleChIP Plus Enzymatic Chromatin IP Kit (Magnetic Beads) (Cell Signaling Technology, 9005) following the manufacturer's instructions. Briefly, HaCaT cells were cross-linked with 1% formaldehyde at room temperature for 10 minutes and then incubated in 2 ml of 10x glycine for 5 minutes. Cells were harvested in SDS lysis buffer and DNA fragments were digested to 150-900 bp fragments by Micrococcal Nuclease treatment. Then, samples were incubated overnight at 4°C with shaking with c-Fos antibody(Cat#31254S,Cell Signaling Technology) and normal IgG antibody as a control, followed by incubation with Magnetic Beads at 4°C with shaking for 2 hours the next day. After washing, chromatin was eluted from the beads using elution buffer and incubated with 5M NaCl and proteinase K at 65°C for 2 hours.
The ChIP-seq library construction was performed as follows: The ChIP-enriched DNA fragments were first assessed for quality by quantification using a Qubit 4.0 Fluorometer and integrity analysis via agarose gel electrophoresis. Qualified DNA samples (20-100 ng) underwent end repair and dA-tailing (30°C for 20 min, 72°C for 20 min). Sequencing adapters were then ligated using Fast T4 DNA Ligase at 20°C for 15 min. The ligation product was purified with magnetic beads (0.6X ratio) to remove free adapters. The library was then amplified by 7 cycles of PCR (98°C for 10 sec, 60°C for 30 sec, 72°C for 30 sec) using index primers for enrichment, followed by another round of purification with magnetic beads (0.9X ratio).

tag: tissue

value: skin

tag: cell line

value: HacaT

tag: cell type

value: keratinocyte

tag: antibody

tag: treatment

value: high glucose (33mM) + recombinant human FGF4 (100ng/ml) for 48h


title: Patient DCP29, 10x 3' expression multiflex library from PBMCs collected on Day 0, 21, 42, 63

country: USA

description:
Library name: DCP29_PBMC_RNA
10X Genomics Chromium Next GEM Single Cell 3' v3.1 Dual Index + 3' CellPlex

library_source: transcriptomic single cell

molecule: total RNA

tag: Sex


title: 2_2422_Pten_KO_Young

type: RNA

city: La Jolla

first: Kathryn

last: Lande

state: CA

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_2

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

organism: Mus musculus

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

value: Male

tag: genotype

value: PtenKO

tag: age

value: Young


title: Patient DCP30, 10x 3' expression multiflex library from PBMCs collected on Day 0, 21, 42, 63

description:
Library name: DCP30_PBMC_RNA
10X Genomics Chromium Next GEM Single Cell 3' v3.1 Dual Index + 3' CellPlex


title: 86001

city: Indianapolis

first: Helen

last: Masson

address: 893 S Delaware St.

institute: Eli Lilly and Company

description: Library name: Sample 675

library_source: transcriptomic

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

molecule: polyA RNA

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: 85803

description: Library name: Sample 674


title: 85602

description: Library name: Sample 672


title: HacaT cell, low glucose, C-FOS, ChIP

description: Library name: HacaT, LG, CHIP

value: low glucose (25mM)


title: 3_2422_Pten_KO_Young

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_3


title: CFPAC-1 (shKLF4#2)

city: Guangzhou

first: bei

last: Jin

address: Jinsui street

institute: Zhongshan Ophthalmic Center

description: Library name: CFPAC_shKLF4#2_ATAC

data_processing:
RNA-seq：HTSeq v0.6.0 was used to count the reads numbers mapped to each gene. ChIP-seq：Reads were mapped to the reference genome using BWA v0.7.12 and BWA mem v0.7.12. Wiggle files for gene tracks were generated using MACS2, and peaks were visualized in Integrative Genomics Viewer. ChIP-seq reads were first processed to remove adapter sequences using Cutadapt (v2.5) and then aligned to the human genome (hg38) using bowtie2 (v2.3.5.1) with default parameters. Significant H3K27ac enrichment peaks were identified using MACS2 (v2.1.2), generating narrowPeak files. Peaks overlapping blacklist regions were removed based on the ENCODE blacklist database. The remaining peaks were analyzed using the ROSE algorithm to identify active enhancers and super-enhancers. Enhancers were stitched, and super-enhancers were ranked based on input-subtracted H3K27ac signal. Typical enhancers were defined as peaks within 2.5 kb of transcription start sites (TSS), while super-enhancers were distinguished by an inflection point in the rank versus signal curve. ATAC-seq：Library DNA was sequenced in paired-end mode with 150 bp reads on an Illumina HiSeq X Ten platform.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Processed data include gene expression matrices in XLS format containing FPKM values for each gene across samples.Processed data include TDF files representing genome-wide ChIP-seq and ATAC signal tracks for visualization in IGV.

extract_protocol:
RNA-seq：1) For THZ1 treatment, Mel270 cells were incubated in medium containing THZ1 at the indicated.concentrations or DMSO for 6 h, RNA was isolated with Rneasy Micro Kit (Qiagen). 2) For exosomal RNA-Seq, RNA extraceted from HUVEC exosomes was treated with terminator 5’-Phosphate-Dependent Exonuclease (Epicenter, Madsion, WI) to degrade 5’-monophosphate RNA in exosomal RNA, and subsequently treated with 5’ polyphosphatase (Epicenter, Madsion, WI) to convert 5’ppp to 5’p, yielding specifically ligated RNA adaptor P5_RNA to RNAs that originally have 5’ppp. ChIP-seq：EZ-ChIP Kit (EMD Millipore, Burlington, MA) was used for ChIP according to our previous reports⁹. In brief, Mel270 cells (1×10⁷) were crosslinked in 1% formaldehyde for 10 min at room temperature and quenched unreacted formaldehyde with glycine. The cell lysates were sonicated to shear DNA to length of 200–500 bp and centrifuged at 12,000 g at 4 °C for 10 min. Protein G agarose (60 μL) was added to each tube to preclear the chromatin before immunoprecipitated with anti-H3K27ac antibodies (5 μg), anti-ELK-1 antibodies (5 μg), anti-STAT1 antibodies (5 μg) or rabbit IgG (negative Parental) overnight at 4 °C with rotation. The protein-DNA complexes underwent reverse crosslinks overnight. RNase A and Proteinase K were used to digest RNA and protein, respectively. DNA was then purified with spin columns. ATAC-seq: CFPAC-1 (pTSB-Vector or pTSB-KLF4; Scramble, shKLF4#1 or shKLF4#2) cells were digested with 0.25% Trypsin. After washing with PBS, 5 × 10^4 cells were lysed in ice-cold lysis buffer (10 mmol/L Tris-HCl pH 7.5, 10 mmol/L NaCl, 3 mmol/L MgCl2, 0.5% IGEPAL CA-630, and 0.1% Tween-20) for 10 min. After nuclei were collected by centrifuging at 500 g for 5 min, Tn5 transposase reactions (#TD501, Vazyme Biotech, Nanjing, China) were immediately performed at 37°C for 30 min. The transposed DNA fragments were purified with VAHTS DNA Clean Beads (#N411, Vazyme Biotech, Nanjing, China).
RNA-seq：Sequencing libraries were generated using NEBNext® UltraTMRNA Library Prep Kit.for Illumina® (New England Biolabs, Ipswich, MA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. ChIP-seq： Illumina sequencing libraries were generated using TruSeq PE Cluster Kit v3-cBot-HS and sequenced on an Illumina HiSeq platform. ATAC-seq：The purified DNA fragments were amplified using TruePrep Index Kit V2 for Illumina (#TD202, Vazyme Biotech, Nanjing, China) according to the manufacturer’s instructions.

value: Pancreatic Ductal Adenocarcinoma

value: WT

value: CFPAC-1 (shKLF4#2)


title: Patient DCP24, 10x 3' expression multiflex library from PBMCs collected on D0, 21, 42

description:
Library name: DCP24_PBMC_RNA
10X Genomics Chromium Next GEM Single Cell 3' v3.1 Dual Index + 3' CellPlex


title: Patient DCP18, 10x 3' expression multiflex library from PBMCs collected on D0, 21, 42

description:
Library name: DCP18_PBMC_RNA
10X Genomics Chromium Next GEM Single Cell 3' v3.1 Dual Index + 3' CellPlex

value: male


title: Patient DCP25, 10x 3' expression multiflex library from PBMCs collected on Day 0, 21, 42, 63

description:
Library name: DCP25_PBMC_RNA
10X Genomics Chromium Next GEM Single Cell 3' v3.1 Dual Index + 3' CellPlex

value: PBMCs


title: 85601

description: Library name: Sample 671


title: Patient DCP22, 10x 3' expression multiflex library from PBMCs collected on Day 0, 21, 42, 63

description:
Library name: DCP22_PBMC_RNA
10X Genomics Chromium Next GEM Single Cell 3' v3.1 Dual Index + 3' CellPlex

value: female


title: 85603

description: Library name: Sample 673


title: Normal_Rosa26KO_S2197_FOV50

description:
R6271_E1_Liver_exprMat_file.csv
R6271_E1_Liver_fov_positions_file.csv
R6271_E1_Liver_metadata_file.csv
R6271_E1_Liver-polygons.csv
R6271_E1_Liver_tx_file.csv
Slide 1

label: CosMx probes

extract_protocol: FFPE mouse liver sections

tag: pathology

value: Normal


title: 1_2422_Pten_KO_Young

description:
R6272_E5_Liver_exprMat_file.csv
R6272_E5_Liver_fov_positions_file.csv
R6272_E5_Liver_metadata_file.csv
R6272_E5_Liver-polygons.csv
R6272_E5_Liver_tx_file.csv
R6272_E5_Liver_tx_file.csv
Slide 5
E5_1


title: Normal_Rosa26KO_S2197_FOV49


title: Patient DCP17, 10x 3' expression multiflex library from PBMCs collected on Day 0, 21, 42, 63

description:
Library name: DCP17_PBMC_RNA
10X Genomics Chromium Next GEM Single Cell 3' v3.1 Dual Index + 3' CellPlex


title: Patient DCP14, 10x 3' expression multiflex library from PBMCs collected on Day 0, 21, 42, 63

description:
Library name: DCP14_PBMC_RNA
10X Genomics Chromium Next GEM Single Cell 3' v3.1 Dual Index + 3' CellPlex


title: Patient DCP19, 10x 3' expression multiflex library from PBMCs collected on Day 0, 21, 42, 63

description:
Library name: DCP19_PBMC_RNA
10X Genomics Chromium Next GEM Single Cell 3' v3.1 Dual Index + 3' CellPlex


title: Patient DCP10, 10x 3' expression multiflex library from PBMCs collected on Day 0, 21, 42, 63

description:
Library name: DCP10_PBMC_RNA
10X Genomics Chromium Next GEM Single Cell 3' v3.1 Dual Index + 3' CellPlex


title: Patient DCP07, 10x 3' expression multiflex library from PBMCs collected on Day 0, 21, 42, 63

description:
Library name: DCP07_PBMC_RNA
10X Genomics Chromium Next GEM Single Cell 3' v3.1 Dual Index + 3' CellPlex


title: 85503

description: Library name: Sample 670


title: Patient DCP06, 10x 3' expression multiflex library from PBMCs collected on Day 0, 21, 42, 63

description:
Library name: DCP06_PBMC_RNA
10X Genomics Chromium Next GEM Single Cell 3' v3.1 Dual Index + 3' CellPlex


title: Patient DCP27, 10x 3' expression multiflex library from PBMCs collected on D0, 21, 42

description:
Library name: DCP27_PBMC_RNA
10X Genomics Chromium Next GEM Single Cell 3' v3.1 Dual Index + 3' CellPlex


title: Normal_Rosa26KO_S2197_FOV48


title: 85502

description: Library name: Sample 669


title: Normal_Rosa26KO_S2197_FOV47


title: Patient DCP03, 10x 3' expression multiflex library from PBMCs collected on Day 0, 21, 42, 63

description:
Library name: DCP03_PBMC_RNA
10X Genomics Chromium Next GEM Single Cell 3' v3.1 Dual Index + 3' CellPlex


title: Patient DCP09, 10x 3' expression multiflex library from PBMCs collected on D0, 21, 42

description:
Library name: DCP09_PBMC_RNA
10X Genomics Chromium Next GEM Single Cell 3' v3.1 Dual Index + 3' CellPlex


title: 85501

description: Library name: Sample 668


title: Normal_Rosa26KO_S2197_FOV46


title: 85203

description: Library name: Sample 667


title: hVIC,NC1,Day5

city: Hangzhou

first: dilin

last: xu

state: 默认

address: 88 Jiefang Road, Shangcheng District

institute: zhejiang university

data_processing:
Raw data (raw reads) of fastq format were firstly processed using Trimmomatic and the low quality reads were removed to obtain the clean reads.
Assembly: The clean reads were mapped to the human genome (GRCh38) using HISAT2
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: aortic valve

growth_protocol: human valvular interstitial cells were maitained in DMEM supplemented with 10% FBS and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer’s protocol.
Then the libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

value: aortic valve

value: primary valvular interstitial cells

value: interstitial cells

value: control medium


title: Normal_Rosa26KO_S2197_FOV45

value: Male

value: whole liver


title: 85202

description: Library name: Sample 666


title: 85201

description: Library name: Sample 665


title: Patient DCP02, 10x 3' expression multiflex library from PBMCs collected on Day 0, 21, 42, 63

description:
Library name: DCP02_PBMC_RNA
10X Genomics Chromium Next GEM Single Cell 3' v3.1 Dual Index + 3' CellPlex


title: Patient DCP01, 10x 3' expression multiflex library from PBMCs collected on Day 0, 21, 42, 63

description:
Library name: DCP01_PBMC_RNA
10X Genomics Chromium Next GEM Single Cell 3' v3.1 Dual Index + 3' CellPlex


title: Hek293T, CRISPR-cas9, starved for 16.5hrs, rep2

city: Dallas

first: Ram

last: Madabhushi

state: TX

address: 5323 Harry Hines Blvd

department: Psychiatry

institute: UT Southwestern Medical Center

description: Library name: CRISPR_Starved_2

data_processing:
4Cker mapping was performed using Bowtie2 to a reduced genome consisting of all unique x-nt (nucleotide count differs depending on sequencing run and viewpoint specific primers) regions surrounding DpnII sites from the hg38 or mm10 reference genome allowing for zero mismatches.
To define regions with significant interaction with the viewpoint we used either cisAnalysis (cis) or nearBaitAnalysis (nb) of 4Cker inputting three replicates per sample
Mapping with pipe4C was done with the following parameters: normalization to 1 million reads in cis, non-blind fragments only, window size 21, top 2 read counts removed.
Assembly: mm10 and hg38
Supplementary files format and content: Bigwig files
Library strategy: 4C-Seq

growth_protocol: Dissociated primary cortical neurons from E16 Swiss-Webster mice were plated at a density of 0.25 million cells/cm2 in 10 cm culture dishes, 6 well plates, or 24 well plates coated beforehand with poly-D-lysine (0.5 mg/ml) overnight at 37°C, followed by washing twice with dH2O. Neurons were maintained for 13 days in neurobasal media (GIBCO) and supplemented with L-glutamine, penicillin/streptomycin (final of 1%), and B27. Human embryonic kidney cells, HEK293, were maintained in Dulbecco’s modified Eagle’s medium (DMEM, high glucocse) supplemented with 10% fetal bovine serum and 5% penicillin/streptomycin.

extract_protocol:
Approximately 10 million primary cortical neurons (DIV13) or Hek 293T cells were cross-linked in 2% formaldehyde for 10 min at room temperature and quenched with glycine (0.13M final concentration). Cells were incubated for 20 min on ice in lysis buffer (50mM Tris-HCl pH 75, 150mM NaCl, 5mM EDTA, 0.5% NP-40, 1% TX-100, and protease inhibitors).
Nuclei were resuspended in 450uL 1.2x CutSmart buffer and permeabilized with 15uL 10% SDS for 1hr and 75uL 20% Triton X-100. A sample of undigested chromatin was collected to assess chromatin integrity. DNA was digested with 100U NlaIII at 37°C for 3hrs while shaking at 750rpm and then an additional 100U of NlaIII was added and incubated overnight. The extent of chromatin digestion was assessed via gel electrophoresis. NlaIII was deactivated for 20 min at 65°C. Chromatin was diluted to 7mL, supplemented with 10X ligation buffer, and 4000U NEB T4 DNA Ligase for overnight ligation at 16°C while shaking. Ligation efficiency was checked by gel electrophoresis. Crosslinks were reversed and proteins digested with proteinase K (30uL of 10mg/ml) overnight at 65°C. DNA was extracted via phenol:chloroform and precipitated with ethanol. DNA was then digested overnight at 37°C with 50U DpnII supplemented with 10X DpnII Buffer while shaking. Second digestion efficiency was determined via gel electrophoresis. DpnII was deactivated at 65°C for 20 min. DNA circularized in a 7mL reaction, supplemented with 10X ligation buffer, and 4000U NEB T4 DNA Ligase overnight at 16°C with shaking. Indexed Illumina sequencing adapters were introduced to ligation fragments of interest with a two-step PCR strategy using Expand Long Template Polymerase starting with 200ng of 4C library template. Viewpoint-specific primers were used to amplify circular templates with the bait of interest. The first round of amplification with the following thermocycler conditions 94°C  for 2 min; 94°C for 10sec, 58° C for 1 min, 68°C for 3 min, for 16 cycles; and 68°C for 5 min. Five different PCR reactions per sample were pooled and 50uL of the pool was used to perform 0.8 x AMPure XP bead purification. 5uL of purified round 1 PCR product was then used for the second round of amplification conducted with the following cycling conditions 94°C for 2 min; 94°C for 10 sec, 60°C for 1 min, 68°C for 3 min for 20 cycles; and 68°C for 5 min. PCR clean up was doing using Qiagen PCR Purification.  DNA fragment size of final, clean PCR products was assessed via Tapestation (Agilent). Library concentrations for each sample was assessed using fluormetry (dsDNA high sensitivity Qubit assay, Thermo) and RT-qPCR (KAPA Biosystems) library quantification.

treatment_protocol: All ETP treatments were conducted with 10mM final concentration, for at most 1hr. NMDA treatments were with 50mM and lasted for 10 min followed by a recovery in conditional neuron media. Serum starvation of the Hek293 cells was done in 0.5% fetal bovine serum for ~16.5hrs and then serum stimulated in 18% fetal bovine serum.

tag: bait

value: Fos promoter


title: Hek293T, CRISPR-cas9, starved for 16.5hrs, rep3

description: Library name: CRISPR_Starved_3


title: Hek293T, CRISPR-cas9, starved for 16.5hrs, rep1

description: Library name: CRISPR_Starved_1


title: Hek293T, control, starved for 16.5hrs then serum stimulated for 30 min, rep2

description: Library name: Control_StarveStim_2


title: Hek293T, CRISPR-cas9, starved for 16.5hrs then serum stimulated for 30 min, rep2

description: Library name: CRISPR_StarveStim_2


title: Normal_Rosa26KO_S2197_FOV44


title: 85105

description: Library name: Sample 664

value: whole blood


title: Hek293T, CRISPR-cas9, starved for 16.5hrs then serum stimulated for 30 min, rep3

description: Library name: CRISPR_StarveStim_3


title: Hek293T, CRISPR-cas9, starved for 16.5hrs then serum stimulated for 30 min, rep1

description: Library name: CRISPR_StarveStim_1


title: Hek293T, control, starved for 16.5hrs then serum stimulated for 30 min, rep3

description: Library name: Control_StarveStim_3


title: 85103

description: Library name: Sample 663

value: SLE


title: Hek293T, control, starved for 16.5hrs then serum stimulated for 30 min, rep1

description: Library name: Control_StarveStim_1


title: Normal_Rosa26KO_S2197_FOV41


title: Normal_Rosa26KO_S2197_FOV42


title: Hek293T, control, starved for 16.5hrs, rep3

description: Library name: Control_Starved_3


title: Hek293T, control, starved for 16.5hrs, rep1

description: Library name: Control_Starved_1


title: Hek293T, CRISPR-cas9, generation 5, rep3

description: Library name: CRISPR_gen5_3


title: Hek293T, control, starved for 16.5hrs, rep2

description: Library name: Control_Starved_2


title: 84403

description: Library name: Sample 661


title: Abnormal_Stat1KO_S2207_FOV40

value: Abnormal


title: Hek293T, CRISPR-cas9, generation 5, rep2

description: Library name: CRISPR_gen5_2


title: Abnormal_Stat1KO_S2207_FOV39


title: Hek293T, CRISPR-cas9, generation 5, rep1

description: Library name: CRISPR_gen5_1


title: Hek293T, control, generation 5, rep3

description: Library name: Control_gen5_3


title: Normal_Rosa26KO_S2197_FOV43


title: Hek293T, control, generation 5, rep2

description: Library name: Control_gen5_2


title: Abnormal_Stat1KO_S2207_FOV38


title: Hek293T, control, generation 5, rep1

description: Library name: Control_gen5_1


title: Normal_Stat1KO_S2207_FOV36


title: Hek293T, 72hrs post CRISPR-cas9 transfection, rep2

description: Library name: CRISPR_gen1_2


title: Hek293T, control, generation 1, rep3

description: Library name: Control_gen1_3


title: Abnormal_Stat1KO_S2207_FOV35


title: Hek293T, 72hrs post CRISPR-cas9 transfection, rep3

description: Library name: CRISPR_gen1_3


title: 84311

description: Library name: Sample 657


title: Hek293T, control, generation 1, rep2

description: Library name: Control_gen1_2


title: 84317

description: Library name: Sample 659


title: POLR2A pAB, WT, Rep3

city: Evanston

first: vadim

last: backman

state: IL

address: 2170 Campus Drive, Silverman Hall 3627

department: Bioengineering

institute: Northwestern University

data_processing:
RNA-seq reads were preprocessed with FastQC v.0.12.0 and aligned with STAR v.2.6.0using the --quantMode TranscriptomeSAM parameter to human reference genome GRCh38 (Ensembl). Aligned samples were converted to binary alignment map (BAM) files, sorted, and indexed using SAMtools v.1.6. Coverage files were generated as BigWigs for the postive and negative strand using DeepTools v.3.1.1 BamCoverage utility and normalized by either CPM or RPGC. Coverage files were later merged for ease of analysis. Alignment statistics were generated using SAMtools Flagstat utility. Aligned and processed BAMs were then quantified to generate a counts table using the rsem-calculate-expression command from RSEM v.1.3.3 or the htseq-count command from HTSeq v.2.0.2 and the Homo_sapiens.GRCh38.111.gtf (Ensembl) genome annotation. Differential gene expression analysis was performed using DESeq2 v.1.44.0 in R. Intron-centric differential expression analysis was performed using the Intron Differences To Exon or INDEX package (https://github.com/Shians/index) and Superintronic package (https://github.com/sa-lee/superintronic) in R.
Assembly: hg38
Supplementary files format and content: tab delimited file containing raw RSEM counts for each sample replicate
Supplementary files format and content: merged BigWig files containing  RPGC normalized coverage for each sample
Library strategy: Cut&Tag

growth_protocol: HCT116-POLR2A-AID2, HCT116-POLR1A-AID, and HCT116 cells were grown in McCoy’s 5A Modified Medium  supplemented with 10% FBS and penicillin-streptomycin (100 μg/ml) All cells were cultured under recommended conditions at 37°C and 5% CO2. Lines in this study were maintained between passage 5 and 20. Cells were allowed at least 48 hours to re-adhere and recover from trypsin-induced detachment prior to experiments. All experiments  were performed at a confluence between 40–70%.

extract_protocol:
Cut&Tag was generated using CUT&Tag-IT Assay Kit (Active Motif, Carlsbad, CA, USA) with modifications recommended in the manufacturer’s protocol using Active Motif's pAG-Tn5. 100,000-200,000 HCT116 cells were harvested at room temperature per replicate. Three replicates were prepared for each condition.
CUT&Tag-IT Assay Kit (Active Motif, Carlsbad, CA, USA)

value: human collecteral

value: POLR2A AB (Active Motif,  91152)


title: 84306

description: Library name: Sample 655


title: POLR1A pAB, WT, Rep3

value: POLR1A AB (Santa Cruz, sc48385)


title: POLR2A pAB, WT, Rep2


title: Abnormal_Stat1KO_S2207_FOV33


title: POLR1A pAB, WT, Rep2


title: 84318

description: Library name: Sample 660


title: Normal_Stat1KO_S2207_FOV34


title: POLR1A pAB, WT, Rep1


title: Abnormal_Stat1KO_S2207_FOV37


title: POLR2A pAB, WT, Rep1


title: H3K9me3 pAB, WT, Rep3

value: H3K9me3 (Active Motif, 39065)


title: Abnormal_Stat1KO_S2207_FOV31


title: 84228

description: Library name: Sample 652


title: H3K9me3 pAB, WT, Rep2


title: Hek293T, 72hrs post CRISPR-cas9 transfection, rep1

description: Library name: CRISPR_gen1_1

value: WT


title: 84234

description: Library name: Sample 653


title: Abnormal_Stat1KO_S2207_FOV32


title: Normal_Stat1KO_S2207_FOV30


title: Hek293T, control, generation 1, rep1

description: Library name: Control_gen1_1


title: 84224

description: Library name: Sample 651


title: H3K4me3 pAB, WT, Rep1

value: H3K4me3 (Active Motif, 39916)


title: H3K9me3 pAB, WT, Rep1


title: 84217

description: Library name: Sample 650


title: 84216

description: Library name: Sample 649


title: Normal_Stat1KO_S2207_FOV28

value: Normal


title: Normal_Stat1KO_S2207_FOV29


title: Normal_Rosa26KO_S2199_FOV27


title: 84213

description: Library name: Sample 648


title: Normal_Rosa26KO_S2199_FOV26


title: Normal_Rosa26KO_S2199_FOV25


title: 84210

description: Library name: Sample 647


title: AHCCLDP [207723860007_R02C01]

type: genomic

city: Ottawa

first: Hamed

last: Yasavoli Sharahi

state: ON

address: 451 Smyth Rd

country: Canada

institute: University of Ottawa

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Infinium MouseMethylation285 BeadChip (Illumina) using standard Illumina protocol

scan_protocol: Illumina iScan System

data_processing:
Sesame R package
*processed value definition: Average Beta

label: biotin

source_name: Mammary Gland

label_protocol: Standard Illumina Protocol

extract_protocol: Tissue DNA extraction was carried out using the Gentra Puregene Tissue Kit (33g) (Qiagen, Toronto, Canada) according to the manufacturer’s instructions. The extracted DNA was subsequently diluted with DNA rehydration solution, provided with the kit, to a final concentration of 20 ng/µl and stored at -20ºC.

value: Mammary Gland

value: AHCCLDP


title: Control [207723860007_R03C01]

value: Control


title: AHCC [207723860005_R05C02]

value: AHCC


title: LDP [207723860007_R04C01]

value: LDP


title: LDP [207723860005_R04C02]


title: AHCC [207723860007_R01C01]


title: 84209

description: Library name: Sample 646


title: AHCCLDP [207723860005_R06C02]


title: AHCC [207723860005_R01C02]


title: LDP [207723860004_R05C01]


title: Control [207723860004_R04C01]


title: Control [207723860005_R01C01]


title: Normal_Rosa26KO_S2199_FOV24

value: Male

value: whole liver


title: 84206

description: Library name: Sample 645

value: whole blood


title: AHCCLDP [207723860004_R03C01]


title: Control [207723860004_R02C02]


title: Normal_Rosa26KO_S2199_FOV23


title: AHCCLDP [207723860004_R01C02]


title: Normal_Rosa26KO_S2199_FOV22


title: AHCC [207723860004_R02C01]


title: LDP [207723860004_R01C01]


title: 84201

description: Library name: Sample 643

value: SLE


title: IDH-G_single-nucleus_TKU3095

city: Charlestown

first: Masashi

last: Nomura

state: MA

address: 149 13th street

department: Pathology

institute: Massachusetts General Hospital

description:
Library name: IDH-G_single-nucleus_TKU3095
TKU3095_p4_A01

data_processing:
Analysis of single cell DNA methylation data was performed based on the methods detailed in Chaligne et al 2021.
Assembly: GRCh38

extract_protocol:
Nuclear suspension was stained by Vybrant DyeCycle Ruby Stain (Thermo Fisher Scientific) immediately before FACS-sorting. Single-nucleus sorting was performed on a FACS Aria Fusion sorter (Becton Dickinson) using 640nm laser (Ruby, 670/14 filter). After doublet discrimination, intact nuclei were selected with ruby positive and were sorted into 96-well plates containing TCL buffer (Qiagen) with 1% beta-mercaptoethanol. Plates were frozen on dry ice immediately after sorting and stored at -80℃ prior to joint XRBS and Smart-seq2 experiment.
Genomic DNA (gDNA) and mRNA in 96 well plats were separated by oligo-dT primer conjugated to streptavidin-coupled magnetic beads (Dynabeads, Life Technologies). The mRNA was then collected to the side of the well using a magne, and the supernatant, containing the gDNA, was transferred to a fresh plate for XRBS protocol. XRBS (Shareef et al Nat Biotchnol 2021) was done by modifying RRBS protocol used in a previous paper (Chaligne et al Nat Genet 2021). The gDNA was restricted by enzyme Msp. Digested DNA was filled-in and A-tailed at the 3′ sticky ends with Klenow supplemented with dNTP. Custom barcoded methylated adaptors were then ligated with T4 DNA ligase. Pooled genomic DNA was cleaned-up and was then sodium bisulfite-converted. Next, bisulfite-converted DNA was eluted in TE, then Hexamer extension were performed as reported by Shareef et al, with a slight modification. Bisulfite-converted single-stranded DNA was mixed with random hexamer primer. Then, 1.3 μl of Klenow enzyme was added to each reaction. Hexamer base pairing is mediated through a gradual increase in temperature. The product was washed by AMPure XP beads , and was then amplified using primers containing Illumina i7 and i5 index. Library enrichment was by PCR using KAPA HiFi Uracil+ master mix. Enriched libraries were cleaned-up and concentrated using AMPure XP beads. The library was pooled sequenced by a Nextseq2000.


title: 84202

description: Library name: Sample 644


title: 84102

description: Library name: Sample 641


title: Normal_Rosa26KO_S2199_FOV19


title: 84104

description: Library name: Sample 642


title: Normal_Rosa26KO_S2199_FOV21


title: FB visit 3

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

description: Library name: lib92198

data_processing:
Base-calling was performed automatically with Illumina RTA (v. 1.18.66.3).
For each flowcell, libraries were demultiplexed using Cellranger mkfastq (v 6.1.1; All unambiguously demultiplexed reads for each sample were combined for downstream processing.)
Reads were aligned to the genome, collapsed to UMIs, and counts per gene ID were estimated using 10X Cell Ranger count (v. 6.1.1).
Barcodes were called as cells or background using default settings in 10X Cell Ranger (v. 6.1.1).
Assembly: GRCh38
Supplementary files format and content: h5 feature barcode matrix file
Supplementary files format and content: Aggregated TCR contig annotation filesfrom Cell Ranger's vdj pipeline .
Supplementary files format and content: 10X feature reference files for each pool

source_name: PBMC

extract_protocol:
CD8 T cells were sorted from PBMC samples collected from a donor undergoing immune checkpoint inhibitor therapy
Cells were loaded onto a 10X Genomics GemCode Single-Cell Instrument per manufacturer instructions for nanodroplet single-cell capture, cell lysis, mRNA rtPCR, and cDNA barcoding within droplets.

value: CD8 T cells

value: PBMC

value: cemiplimab

tag: diagnosis

value: Head and neck cancer

tag: visit

value: male


title: 82604

description: Library name: Sample 639


title: Normal_Rosa26KO_S2199_FOV18


title: Normal_Rosa26KO_S2199_FOV20


title: FB visit 1

description: Library name: lib92196


title: Pt6_Bx_I1D118_VDJ

city: Seattle

first: Aude

last: Chapuis

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Center

description:
Library name: Sample27
10x Genomics

data_processing:
TCR sequencing reads were processed using Cell Ranger V(D)J pipeline to assemble and annotate TCR sequences.
Assembly: GRCh38 reference genome
Supplementary files format and content: filtered_contig_annotations.csv – assembled TCR contigs with V(D)J gene assignments and CDR3 sequences; includes information on productive paired α/β chains and clonotype assignments
Library strategy: TCR-Seq

source_name: Tumor

extract_protocol:
Cryopreserved PBMCs were thawed and washed in PBS with 0.04% BSA. Tumor biopsies were enzymatically dissociated, washed, and subjected to dead cell removal. Cells were counted and resuspended for single-cell capture.
TCR V(D)J libraries were generated using 10x Genomics Chromium Single Cell V(D)J Reagent Kits according to the manufacturer’s instructions.

tag: patient id

tag: infusion

tag: day

value: Tumor

tag: collection site

value: Pelvic lymph node

tag: treatment group


title: Pt6_Bx_PostIFNg_VDJ

description:
Library name: Sample24
10x Genomics

value: PostIFNg (-1)

tag: tissue


title: Pt6_Bx_PreIFNg_VDJ

description:
Library name: Sample23
10x Genomics

value: PreIFNg (-11)


title: 84101

description: Library name: Sample 640


title: 84307

description: Library name: Sample 656


title: Pt6_Bx_I1D014_VDJ

description:
Library name: Sample25
10x Genomics


title: 82601

description: Library name: Sample 638


title: FB visit 2

description: Library name: lib92197

tag: cell type


title: Pt6_Bx_I1D052_VDJ

description:
Library name: Sample26
10x Genomics


title: Normal_Rosa26KO_S2199_FOV17

value: Normal


title: 82506

description: Library name: Sample 637


title: TCR visit 2

description: Library name: lib92194


title: TCR visit 3

description: Library name: lib92195


title: Abnormal_Stat1KO_S2208_FOV16

value: Abnormal


title: Abnormal_Stat1KO_S2208_FOV15


title: GEX visit 3

description: Library name: lib92192


title: 82505

description: Library name: Sample 636


title: TCR visit 1

description: Library name: lib92193


title: Normal_Stat1KO_S2208_FOV14


title: GEX visit 2

description: Library name: lib92191


title: GEX visit 1

description: Library name: lib92190


title: Abnormal_Stat1KO_S2208_FOV13


title: Abnormal_Stat1KO_S2208_FOV11


title: 82504

description: Library name: Sample 635


title: Abnormal_Stat1KO_S2208_FOV12


title: 82503

description: Library name: Sample 634


title: 82502

description: Library name: Sample 633


title: 84314

description: Library name: Sample 658


title: 82410

description: Library name: Sample 631


title: Abnormal_Stat1KO_S2208_FOV10


title: Normal_Stat1KO_S2208_FOV9


title: Normal_Stat1KO_S2208_FOV8


title: 82405

description: Library name: Sample 630


title: GEX channel 3

description: Library name: Memory_CD3_Well3_S3

data_processing:
Base-calling was performed automatically with Illumina RTA (v. 1.18.66.3).
For each flowcell, libraries were demultiplexed using Cellranger mkfastq (v 6.1.1; All unambiguously demultiplexed reads for each sample were combined for downstream processing.)
Reads were aligned to the genome, collapsed to UMIs, and counts per gene ID were estimated using 10X Cell Ranger count (v. 6.1.1).
Barcodes were called as cells or background using default settings in 10X Cell Ranger (v. 6.1.1).
Assembly: GRCh38
Supplementary files format and content: R Seurat object with cell level gene expression data and metadata. Contains hashtag demultiplexing results.
Supplementary files format and content: Pool-level TCR contig annotation filesfrom Cell Ranger's vdj pipeline .
Supplementary files format and content: 10X feature reference files for each pool

extract_protocol:
T cells were sorted from PBMC samples collected from a donor undergoing immune checkpoint inhibitor therapy
Cells were loaded onto a 10X Genomics GemCode Single-Cell Instrument per manufacturer instructions for nanodroplet single-cell capture, cell lysis, mRNA rtPCR, and cDNA barcoding within droplets.

value: T cells

value: Pembrolizumab

value: Urinary tract cancer

value: female


title: FB channel 3

description: Library name: Memory_CD3_Well3_S9


title: FB channel 2

description: Library name: Memory_CD3_Well2_S8


title: TCR channel 3

description: Library name: Memory_CD3_Well3_S6


title: GEX channel 2

description: Library name: Memory_CD3_Well2_S2


title: GEX channel 1

description: Library name: Memory_CD3_Well1_S1


title: TCR channel 2

description: Library name: Memory_CD3_Well2_S5


title: 82403

description: Library name: Sample 629

value: whole blood


title: TCR channel 1

description: Library name: Memory_CD3_Well1_S4


title: FB channel 1

description: Library name: Memory_CD3_Well1_S7


title: 82412

description: Library name: Sample 632

value: SLE


title: Abnormal_Stat1KO_S2208_FOV7

value: Male

value: whole liver


title: FB pool 3 channel 1

description: Library name: lib111261_FB

data_processing:
Base-calling was performed automatically with Illumina RTA (v. 1.18.66.3).
For each flowcell, libraries were demultiplexed using Cellranger mkfastq (v 6.1.1; All unambiguously demultiplexed reads for each sample were combined for downstream processing.)
Reads were aligned to the genome, collapsed to UMIs, and counts per gene ID were estimated using 10X Cell Ranger count (v. 6.1.1).
Barcodes were called as cells or background using default settings in 10X Cell Ranger (v. 6.1.1).
Assembly: GRCh38
Supplementary files format and content: R Seurat object with cell level gene expression data and metadata. Contains hashtag demultiplexing results.
Supplementary files format and content: 10X Cell ranger TCT contig annotations

extract_protocol:
B and T cells were sorted from PBMC samples collected from patients undergoing checkpoint inhibitor therapy
Cells were loaded onto a 10X Genomics GemCode Single-Cell Instrument per manufacturer instructions for nanodroplet single-cell capture, cell lysis, mRNA rtPCR, and cDNA barcoding within droplets.

value: B and T cells

value: PBMC


title: FB pool 3 channel 2

description: Library name: lib111262_FB


title: FB pool 2 channel 3

description: Library name: lib111260_FB


title: FB pool 2 channel 2

description: Library name: lib111259_FB


title: 82320

description: Library name: Sample 628


title: FB pool 3 channel 3

description: Library name: lib111263_FB


title: FB pool 2 channel 1

description: Library name: lib111258_FB


title: FB pool 1 channel 2

description: Library name: lib111256_FB


title: 84605

description: Library name: Sample 662


title: Abnormal_Stat1KO_S2208_FOV6


title: Normal_Stat1KO_S2208_FOV5


title: FB pool 1 channel 3

description: Library name: lib111257_FB


title: 82319

description: Library name: Sample 627


title: FB pool 1 channel 1

description: Library name: lib111255_FB


title: 82314

description: Library name: Sample 625


title: 82313

description: Library name: Sample 624


title: TCR pool 3 channel 3

description:
Library name: lib111254_TCR
filtered_contig_annotations_pool3.csv

data_processing:
Base-calling was performed automatically with Illumina RTA (v. 1.18.66.3).
For each flowcell, libraries were demultiplexed using Cellranger mkfastq (v 6.1.1; All unambiguously demultiplexed reads for each sample were combined for downstream processing.)
Reads were aligned to the genome, collapsed to UMIs, and counts per gene ID were estimated using 10X Cell Ranger count (v. 6.1.1).
Barcodes were called as cells or background using default settings in 10X Cell Ranger (v. 6.1.1).
Assembly: GRCh38
Supplementary files format and content: R Seurat object with cell level gene expression data and metadata. Contains hashtag demultiplexing results.
Supplementary files format and content: 10X Cell ranger TCT contig annotations
Library strategy: TCR-Seq


title: TCR pool 3 channel 1

description:
Library name: lib111252_TCR
filtered_contig_annotations_pool3.csv


title: Abnormal_Stat1KO_S2208_FOV4


title: TCR pool 3 channel 2

description:
Library name: lib111253_TCR
filtered_contig_annotations_pool3.csv


title: Abnormal_Stat1KO_S2208_FOV2

description:
R6271_E1_Liver_exprMat_file.csv
R6271_E1_Liver_fov_positions_file.csv
R6271_E1_Liver_metadata_file.csv
R6271_E1_Liver-polygons.csv
R6271_E1_Liver_tx_file.csv
Slide 1


title: 82315

description: Library name: Sample 626


title: TCR pool 2 channel 3

description:
Library name: lib111251_TCR
filtered_contig_annotations_pool2.csv


title: TCR pool 2 channel 1

description:
Library name: lib111249_TCR
filtered_contig_annotations_pool2.csv


title: TCR pool 1 channel 3

description:
Library name: lib111248_TCR
filtered_contig_annotations_pool1.csv


title: Normal_Stat1KO_S2208_FOV3


title: TCR pool 2 channel 2

description:
Library name: lib111250_TCR
filtered_contig_annotations_pool2.csv


title: Normal_Stat1KO_S2208_FOV1


title: IDH-G_single-nucleus_Smart-seq2 (TKU3095)

description: Library name: IDH-G_single-nucleus_Smart-seq2

data_processing:
We processed Smart-seq2 data from raw reads to gene expression matrices as previously described in Neftel et al, 2019. We used bcl2fastq to generate demultiplexed FASTQ files, and aligned the resulting paired-end scRNA-seq reads to the reference transcriptome using Bowtie (v0.12.7).
Assembly: GRCh38 for Homo sapiens
Supplementary files format and content: .txt

extract_protocol:
Nuclear suspension was stained by Vybrant DyeCycle Ruby Stain (Thermo Fisher Scientific) immediately before FACS-sorting. Single-nucleus sorting was performed on a FACS Aria Fusion sorter (Becton Dickinson) using 640nm laser (Ruby, 670/14 filter). After doublet discrimination, intact nuclei were selected with ruby positive and were sorted into 96-well plates containing TCL buffer (Qiagen) with 1% beta-mercaptoethanol. Plates were frozen on dry ice immediately after sorting and stored at -80℃ prior to Smart-seq2 and XRBS experiment
Genomic DNA (gDNA) and mRNA in 96 well plats were separated by oligo-dT primer conjugated to streptavidin-coupled magnetic beads (Dynabeads, Life Technologies). The mRNA was then collected to the side of the well using a magnet. The mRNA plates were processed by Smart-seq2 protocol. On 96-well plates, RNA derived from single-nuclei was first purified with Agencourt RNAClean XP beads (Beckman Coulter). Then, Oligo-dT primed reverse transcription was performed using Maxima H Minus reverse transcriptase (Thermo Fisher Scientific) and locked TSO oligonucleotide (Qiagen). This was followed by PCR amplification (22 cycles for snRNA-seq) using KAPA HiFi HotStart ReadyMix (KAPA Biosystems) with subsequent Agencourt AMPure XP bead purification. Libraries were tagmented using the Nextera XT Library Prep kit (Illumina) with custom barcode adapters. Libraries from 768 cells with unique barcodes were pooled and sequenced on Illumina sequencer.


title: TCR pool 1 channel 2

description:
Library name: lib111247_TCR
filtered_contig_annotations_pool1.csv


title: GEX pool 3 channel 3

description: Library name: lib111245_GEX


title: TCR pool 1 channel 1

description:
Library name: lib111246_TCR
filtered_contig_annotations_pool1.csv


title: 82308

description: Library name: Sample 622


title: 82312

description: Library name: Sample 623


title: Patient DCP32, 10x Genomics 5' V(D)J sequencing of tumor biopsy on day D21

description:
Library name: DCP32_D21_Tumor_RNA
10X Genomics Chromium GEM-X Single Cell 5' v3 Dual Index and V(D)J Enrichment Kit

organism:
Homo sapiens
Mus musculus

source_name: human lung tumor tissue + mouse KPL lung cancer cell line

tag: subject id


title: 82302

description: Library name: Sample 621


title: GEX pool 3 channel 2

description: Library name: lib111244_GEX


title: GEX pool 3 channel 1

description: Library name: lib111243_GEX


title: 82301

description: Library name: Sample 620


title: Patient DCP31, 10x Genomics 5' V(D)J sequencing of tumor biopsy on day D42

description:
Library name: DCP31_D42_Tumor_RNA
10X Genomics Chromium GEM-X Single Cell 5' v3 Dual Index and V(D)J Enrichment Kit

value: human lung tumor tissue + mouse KPL lung cancer cell line


title: GEX pool 2 channel 2

description: Library name: lib111241_GEX


title: Patient DCP32, 10x Genomics 5' V(D)J sequencing of tumor biopsy on day D0

description:
Library name: DCP32_D0_Tumor_RNA
10X Genomics Chromium GEM-X Single Cell 5' v3 Dual Index and V(D)J Enrichment Kit


title: 82201

description: Library name: Sample 619


title: Patient DCP31, 10x Genomics 5' V(D)J sequencing of tumor biopsy on day D21

description:
Library name: DCP31_D21_Tumor_RNA
10X Genomics Chromium GEM-X Single Cell 5' v3 Dual Index and V(D)J Enrichment Kit


title: 82120

description: Library name: Sample 618


title: GEX pool 1 channel 3

description: Library name: lib111239_GEX


title: Patient DCP31, 10x Genomics 5' V(D)J sequencing of tumor biopsy on day D0

description:
Library name: DCP31_D0_Tumor_RNA
10X Genomics Chromium GEM-X Single Cell 5' v3 Dual Index and V(D)J Enrichment Kit


title: 82119

description: Library name: Sample 617


title: FB_pool_3

description:
Library name: lib114798_FB
pool690-1_3_featureReference.csv
P690-1_seuratObject_demux.RDS

extract_protocol:
T cells were sorted from PBMC samples collected from donors with Down Syndrome
Cells were loaded onto a 10X Genomics GemCode Single-Cell Instrument per manufacturer instructions for nanodroplet single-cell capture, cell lysis, mRNA rtPCR, and cDNA barcoding within droplets.


title: GEX pool 1 channel 2

description: Library name: lib111238_GEX


title: Patient DCP30, 10x Genomics 5' V(D)J sequencing of tumor biopsy on day D42

description:
Library name: DCP30_D42_Tumor_RNA
10X Genomics Chromium GEM-X Single Cell 5' v3 Dual Index and V(D)J Enrichment Kit

extract_protocol:
For scRNA/TCR-seq of tumor biopsies, single cell dissociated tumor samples were thawed and stained using the Zombie NIR Fixable Viability Kit (Biolegend). The KPL mouse cell line was simultaneously stained with Zombie NIR and mixed with tumor samples at a 2:1 ratio to act as carrier cells. Viable cells were sorted using a FACSAria III flow cytometer (BD Biosciences), centrifuged at 400 x g for 5 minutes, and resuspended in PBS + 5% fetal bovine serum (FBS) at a concentration of ~1500 cells/uL prior to library construction. For scRNA-seq of PBMCs, samples from days 0, 21, 42, and 63 for each patient were tagged using the 10X Genomics CellPlex Kit per manufacturer’s protocols. The cells were pooled and then stained with Zombie NIR prior to flow sorting for viability on a FACSAria III flow cytometer.
For scRNA/TCR-seq, library construction was performed according to the manufacturer’s instructions (10x Genomics) to capture the maximum target cells.


title: 82113

description: Library name: Sample 616


title: GEX pool 2 channel 3

description: Library name: lib111242_GEX


title: GEX_pool_3

description:
Library name: lib114796_GEX
pool690-1_3_featureReference.csv
P690-1_seuratObject_demux.RDS


title: FB_pool_2

description:
Library name: lib114795_FB
pool690-1_2_featureReference.csv
P690-1_seuratObject_demux.RDS


title: GEX_pool_2

description:
Library name: lib114793_GEX
pool690-1_2_featureReference.csv
P690-1_seuratObject_demux.RDS


title: GEX pool 2 channel 1

description: Library name: lib111240_GEX


title: 82110

description: Library name: Sample 614


title: Patient DCP30, 10x Genomics 5' V(D)J sequencing of tumor biopsy on day D0

description:
Library name: DCP30_D0_Tumor_RNA
10X Genomics Chromium GEM-X Single Cell 5' v3 Dual Index and V(D)J Enrichment Kit


title: GEX pool 1 channel 1

description: Library name: lib111237_GEX


title: TCR_pool_2

description:
Library name: lib114794_TCR
pool690-1_2_featureReference.csv
P690-1_seuratObject_demux.RDS
pool690-1_2_filtered_contig_annotations.csv

data_processing:
Base-calling was performed automatically with Illumina RTA (v. 1.18.66.3).
For each flowcell, libraries were demultiplexed using Cellranger mkfastq (v 6.1.1; All unambiguously demultiplexed reads for each sample were combined for downstream processing.)
Reads were aligned to the genome, collapsed to UMIs, and counts per gene ID were estimated using 10X Cell Ranger count (v. 6.1.1).
Barcodes were called as cells or background using default settings in 10X Cell Ranger (v. 6.1.1).
Assembly: GRCh38
Supplementary files format and content: R Seurat object with cell level gene expression data and metadata. Contains hashtag demultiplexing results.
Supplementary files format and content: Pool-level TCR contig annotation filesfrom Cell Ranger's vdj pipeline .
Supplementary files format and content: 10X feature reference files for each pool
Library strategy: TCR-Seq


title: FB_pool_1

description:
Library name: lib114722_FB
pool690-1_1_featureReference.csv
P690-1_seuratObject_demux.RDS


title: TCR_pool_3

description:
Library name: lib114797_TCR
pool690-1_3_featureReference.csv
P690-1_seuratObject_demux.RDS
pool690-1_3_filtered_contig_annotations.csv


title: Patient DCP30, 10x Genomics 5' V(D)J sequencing of tumor biopsy on day D21

description:
Library name: DCP30_D21_Tumor_RNA
10X Genomics Chromium GEM-X Single Cell 5' v3 Dual Index and V(D)J Enrichment Kit

data_processing:
For tumor scRNA/TCR-seq, CellRanger 9.0 (10X Genomics) was used to align raw reads to the GRCh38 human and GRCm39 mouse combined reference genome provided by 10X Genomics. For PBMC scRNA-seq, CellRanger 9.0 was used to align raw reads to the GRCh38 human reference genome.
The feature_README.txt provides information for demultiplexing samples
Assembly: Raw reads were aligned and annotated using the 10X reference data, version 2024-A. In brief, raw reads were aligned to the reference human genome GRCh38 (PBMC samples) or combination of GRCh38 and GRCm39 genome (tumor biopsy samples). Transcripts were annotated using GENCODE v44/Ensembl110 for human and GENCODE vM33/Ensembl110 for mouse.
Supplementary files format and content: tab-delimited text files (tsv) and tatrix files (mt) provide raw counts of transcripts for filtered barcodes.
Supplementary files format and content: cvs-delimited text file provide counts associated with specified contig and cell barcode.


title: Patient DCP29, 10x Genomics 5' V(D)J sequencing of tumor biopsy on day D42

description:
Library name: DCP29_D42_Tumor_RNA
10X Genomics Chromium GEM-X Single Cell 5' v3 Dual Index and V(D)J Enrichment Kit


title: GEX_pool_1

description:
Library name: lib114720_GEX
pool690-1_1_featureReference.csv
P690-1_seuratObject_demux.RDS


title: 82103

description: Library name: Sample 612


title: 82101

description: Library name: Sample 611


title: TCR_pool_1

description:
Library name: lib114721_TCR
pool690-1_1_featureReference.csv
P690-1_seuratObject_demux.RDS
pool690-1_1_filtered_contig_annotations.csv


title: Patient DCP29, 10x Genomics 5' V(D)J sequencing of tumor biopsy on day D21

description:
Library name: DCP29_D21_Tumor_RNA
10X Genomics Chromium GEM-X Single Cell 5' v3 Dual Index and V(D)J Enrichment Kit


title: 82112

description: Library name: Sample 615


title: 82104

description: Library name: Sample 613


title: Patient DCP27, 10x Genomics 5' V(D)J sequencing of tumor biopsy on day D21

description:
Library name: DCP27_D21_Tumor_RNA
10X Genomics Chromium GEM-X Single Cell 5' v3 Dual Index and V(D)J Enrichment Kit


title: Patient DCP27, 10x Genomics 5' V(D)J sequencing of tumor biopsy on day D0

description:
Library name: DCP27_D0_Tumor_RNA
10X Genomics Chromium GEM-X Single Cell 5' v3 Dual Index and V(D)J Enrichment Kit


title: human CD34⁺CD45RA-CD90+ HSCs, HOTSCRAMBL CBE, Day 5, bulk RNA-seq, Repeat 1

city: Boston

first: Peng

last: Lyu

state: Massachusetts

address: 1 Blackfan Street

institute: Boston Children's Hospital

description:
Library name: Sample 10
Column name in featurecounts_output.txt: HOTSCRAMBL_CBE_n1

data_processing:
Featurecount v2.0.6
Assembly: h38
Supplementary files format and content: tab-delimited txt file including raw read counts

source_name: Blood

growth_protocol: Human HSPCs were cultured at 37°C in StemSpan Serum-Free Expansion Medium (SFEM) II supplemented with 1% L-Glutamine (200 mM), 1% Penicillin-Streptomycin (10,000 U/mL), 1× CC100 cytokine cocktail (contains FLT3L. SCF. IL-3 and IL-6), 100 ng/mL TPO and 35 nM UM171 (Stem Cell Technologies)

extract_protocol:
RNA was extract by using Total RNA Purification Micro Kit (Norgen Biotek) with DNase I treatment, and 30 ng RNA was used for generating the sequencing library.
SMART-Seq® mRNA LP Kit (Takara) was used to construction the library according to the manufacturer's instructions.

treatment_protocol: Nucleofection was performed using the Lonza 4D-Nucleofector system with the P3 Primary Cell 4D-Nucleofector (20 µL cuvette) for CD34⁺ HSPCs on day 2 after thawing. CRISPR/Cas9 RNPs and cytosine base editors are delivered to HSPC with guide RNA. Program DZ-100 was used for nucleofection.

value: Blood

tag: cell line

value: primary cell

value: HSC

tag: treatment

value: base editing

tag: batch

value: day 5


title: human CD34⁺CD45RA-CD90+ HSCs, HOTSCRAMBL CBE, Day 5, bulk RNA-seq, Repeat 3

description:
Library name: Sample 12
Column name in featurecounts_output.txt: HOTSCRAMBL_CBE_n3

tag: genotype


title: human CD34⁺CD45RA-CD90+ HSCs, HOTSCRAMBL CBE, Day 5, bulk RNA-seq, Repeat 2

description:
Library name: Sample 11
Column name in featurecounts_output.txt: HOTSCRAMBL_CBE_n2


title: human CD34⁺CD45RA-CD90+ HSCs, AAVS1 CBE, Day 5, bulk RNA-seq, Repeat 3

description:
Library name: Sample 9
Column name in featurecounts_output.txt: AAVS1_CBE_n3

value: WT


title: human CD34⁺CD45RA-CD90+ HSCs, AAVS1CBE, Day 5, bulk RNA-seq, Repeat 2

description:
Library name: Sample 8
Column name in featurecounts_output.txt: AAVS1_CBE_n2


title: 81414

description: Library name: Sample 610


title: human CD34⁺CD45RA-CD90+ HSCs, AAVS1 CBE, Day 5, bulk RNA-seq, Repeat 1

description:
Library name: Sample 7
Column name in featurecounts_output.txt: AAVS1_CBE_n1


title: Patient DCP26, 10x Genomics 5' V(D)J sequencing of tumor biopsy on day D0

description:
Library name: DCP26_D0_Tumor_RNA
10X Genomics Chromium GEM-X Single Cell 5' v3 Dual Index and V(D)J Enrichment Kit

tag: Sex


title: human CD34⁺CD45RA-CD90+ HSCs, HOTSCRAMBL KO, Day 5, bulk RNA-seq, Repeat 2

description:
Library name: Sample 5
Column name in featurecounts_output.txt: HOTSCRAMBL_KO_n2

value: HOTSCRAMBL KO

value: gene knockout


title: human CD34⁺CD45RA-CD90+ HSCs, HOTSCRAMBL KO, Day 5, bulk RNA-seq, Repeat 3

description:
Library name: Sample 6
Column name in featurecounts_output.txt: HOTSCRAMBL_KO_n3


title: human CD34⁺CD45RA-CD90+ HSCs, HOTSCRAMBL KO, Day 5, bulk RNA-seq, Repeat 1

description:
Library name: Sample 4
Column name in featurecounts_output.txt: HOTSCRAMBL_KO_n1


title: human CD34⁺CD45RA-CD90+ HSCs, AAVS1 KO, Day 5, bulk RNA-seq, Repeat 3

description:
Library name: Sample 3
Column name in featurecounts_output.txt: AAVS1_KO_n3


title: 81408

description: Library name: Sample 608


title: 81407

description: Library name: Sample 607


title: Patient DCP25, 10x Genomics 5' V(D)J sequencing of tumor biopsy on day D42

description:
Library name: DCP25_D42_Tumor_RNA
10X Genomics Chromium GEM-X Single Cell 5' v3 Dual Index and V(D)J Enrichment Kit

value: male


title: human CD34⁺CD45RA-CD90+ HSCs, AAVS1 KO, Day 5, bulk RNA-seq, Repeat 2

description:
Library name: Sample 2
Column name in featurecounts_output.txt: AAVS1_KO_n2


title: Patient DCP25, 10x Genomics 5' V(D)J sequencing of tumor biopsy on day D21

description:
Library name: DCP25_D21_Tumor_RNA
10X Genomics Chromium GEM-X Single Cell 5' v3 Dual Index and V(D)J Enrichment Kit


title: human CD34⁺CD45RA-CD90+ HSCs, AAVS1 KO, Day 5, bulk RNA-seq, Repeat 1

description:
Library name: Sample 1
Column name in featurecounts_output.txt: AAVS1_KO_n1


title: 81412

description: Library name: Sample 609


title: 84304

description: Library name: Sample 654


title: 81403

description: Library name: Sample 605


title: LMS spheroid, control, rep2

city: Cincinnati

first: Stacey

middle: C

last: Schutte

state: OH

address: 2901 Woodside Dr.

department: Biomedical Engineering

institute: University of Cincinnati

description:
Library name: C2
column name in LMS_gene_counts: C2

data_processing:
Bioinformatic analysis was performed via BaseSpace Sequence Hub app RNA-Seq Alignment v2.0.2 followed by RNA-Seq Differential Expression version 1.0.1. The analysis used STAR for alignment and Salmon for quantification. RNA-seq Alignment setting is Mark Duplicates unchecked.
Assembly: UCSC hg19
Supplementary files format and content: csv file includes raw counts for each sample

source_name: Vulva

extract_protocol:
Total RNA was isolated using mirVana miRNA Isolation Kit
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep kit

value: Vulva

value: leiomyosarcoma

value: 0 mmHg compression


title: LMS spheroid, compression, rep2

description:
Library name: T2
column name in LMS_gene_counts: T2

value: 7.2 mmHg compression


title: Patient DCP25, 10x Genomics 5' V(D)J sequencing of tumor biopsy on day D0

description:
Library name: DCP25_D0_Tumor_RNA
10X Genomics Chromium GEM-X Single Cell 5' v3 Dual Index and V(D)J Enrichment Kit


title: LMS spheroid, compression, rep3

description:
Library name: T3
column name in LMS_gene_counts: T3


title: LMS spheroid, control, rep3

description:
Library name: C3
column name in LMS_gene_counts: C3


title: Patient DCP24, 10x Genomics 5' V(D)J sequencing of tumor biopsy on day D42

description:
Library name: DCP24_D42_Tumor_RNA
10X Genomics Chromium GEM-X Single Cell 5' v3 Dual Index and V(D)J Enrichment Kit

value: female


title: LMS spheroid, compression, rep1

description:
Library name: T1
column name in LMS_gene_counts: T1


title: 81316

description: Library name: Sample 603

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

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: 81402

description: Library name: Sample 604


title: Patient DCP24, 10x Genomics 5' V(D)J sequencing of tumor biopsy on day D21

description:
Library name: DCP24_D21_Tumor_RNA
10X Genomics Chromium GEM-X Single Cell 5' v3 Dual Index and V(D)J Enrichment Kit

value: human lung tumor tissue + mouse KPL lung cancer cell line


title: 81405

description: Library name: Sample 606


title: Patient DCP24, 10x Genomics 5' V(D)J sequencing on day D0, sample 2

description:
Library name: DCP24_D0-2_Tumor_RNA
10X Genomics Chromium GEM-X Single Cell 5' v3 Dual Index and V(D)J Enrichment Kit


title: LMS spheroid, control, rep1

description:
Library name: C1
column name in LMS_gene_counts: C1


title: Patient DCP24, 10x Genomics 5' V(D)J sequencing on day D0, sample 1

description:
Library name: DCP24_D0-1_Tumor_RNA
10X Genomics Chromium GEM-X Single Cell 5' v3 Dual Index and V(D)J Enrichment Kit


title: A549 cells, control FLuc siRNA, IFN, 12h, rep1

city: Abbotsford

first: Brenna

middle: N

last: Hay

address: 33844 King Rd

institute: University of the Fraser Valley

data_processing:
Sequencing data was de-multiplexed using Illumina’s BCL Convert
Assembly: Sequencing data was de-multiplexed using Illumina’s BCL Convert
Supplementary files format and content: tab-delimited text file includes normalized counts for each Sample

growth_protocol: A549 cells were cultured at 37°C in Dulbecco’s Modified Eagle’s Medium (DMEM, Gibco) supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin.

extract_protocol:
RNA samples were harvested with 500 μL TRI-zol (Invitrogen) and total cellular RNA was extracted according to the Direct-zol RNA Miniprep Kit, including the optional DNase I treatment (Zymo Research, R2052).
Samples were prepared following the standard protocol for the Illumina Stranded mRNA prep (Illumina).

treatment_protocol: A total of 3.0 x 105 A549 cells were seeded into 6-well plates and incubated at 37°C for 24 h. Knockdowns were performed by adding 5 μL Dharmafect 1 (Dharmacon) to 195 μL Opti-MEM (Thermo Fisher) in one tube and 2.5 μL 20 μM target SMARTpool siRNA (Dharmacon) to 197.5 μL Opti-MEM in a second tube, then incubating at room temperature for 5 min. The contents of tubes A and B were combined and incubated at room temperature for 20 min. Media was aspirated from cells and replaced with this transfection mixture and 1.6 mL of antibiotic-free DMEM supplemented with 10% fetal bovine serum, allowing for incubation at 37°C for 48 h. For IFN stimulation, cells were incubated in DMEM supplemented with 10% fetal bovine serum with 1000 units/mL of IFN-B.

value: control Fluc knockdown

value: IFN

tag: time


title: A549 cells, control FLuc siRNA, IFN, 12h, rep3


title: 81315

description: Library name: Sample 602


title: A549 cells, control FLuc siRNA, mock, 12h, rep3

value: mock


title: A549 cells, control FLuc siRNA, IFN, 8h, rep3


title: A549 cells, control FLuc siRNA, IFN, 12h, rep2


title: Patient DCP22, 10x Genomics 5' V(D)J sequencing of tumor biopsy on day D21

description:
Library name: DCP22_D21_Tumor_RNA
10X Genomics Chromium GEM-X Single Cell 5' v3 Dual Index and V(D)J Enrichment Kit


title: 81311

description: Library name: Sample 600


title: Patient DCP22, 10x Genomics 5' V(D)J sequencing of tumor biopsy on day D42

description:
Library name: DCP22_D42_Tumor_RNA
10X Genomics Chromium GEM-X Single Cell 5' v3 Dual Index and V(D)J Enrichment Kit


title: 81314

description: Library name: Sample 601


title: A549 cells, control FLuc siRNA, IFN, 8h, rep2


title: A549 cells, control FLuc siRNA, IFN, 8h, rep1


title: A549 cells, control FLuc siRNA, mock, 12h, rep2


title: 81304

description: Library name: Sample 599


title: Patient DCP22, 10x Genomics 5' V(D)J sequencing of tumor biopsy on day D0

description:
Library name: DCP22_D0_Tumor_RNA
10X Genomics Chromium GEM-X Single Cell 5' v3 Dual Index and V(D)J Enrichment Kit


title: A549 cells, control FLuc siRNA, mock, 8h, rep2


title: 81301

description: Library name: Sample 598


title: A549 cells, control FLuc siRNA, mock, 8h, rep1


title: A549 cells, control FLuc siRNA, mock, 8h, rep3


title: A549 cells, control FLuc siRNA, mock, 12h, rep1


title: Patient DCP21, 10x Genomics 5' V(D)J sequencing of tumor biopsy on day D21

description:
Library name: DCP21_D21_Tumor_RNA
10X Genomics Chromium GEM-X Single Cell 5' v3 Dual Index and V(D)J Enrichment Kit


title: A549 cells, BOP1 siRNA, IFN, 12h, rep3

value: BOP1 knockdown


title: A549 cells, BOP1 siRNA, IFN, 12h, rep1


title: Patient DCP21, 10x Genomics 5' V(D)J sequencing of tumor biopsy on day D0

description:
Library name: DCP21_D0_Tumor_RNA
10X Genomics Chromium GEM-X Single Cell 5' v3 Dual Index and V(D)J Enrichment Kit


title: 81211

description: Library name: Sample 597


title: A549 cells, BOP1 siRNA, IFN, 8h, rep3


title: 81209

description: Library name: Sample 596


title: A549 cells, BOP1 siRNA, IFN, 12h, rep2


title: A549 cells, BOP1 siRNA, IFN, 8h, rep2


title: Patient DCP19, 10x Genomics 5' V(D)J sequencing of tumor biopsy on day D21

description:
Library name: DCP19_D21_Tumor_RNA
10X Genomics Chromium GEM-X Single Cell 5' v3 Dual Index and V(D)J Enrichment Kit


title: Patient DCP19, 10x Genomics 5' V(D)J sequencing of tumor biopsy on day D42

description:
Library name: DCP19_D42_Tumor_RNA
10X Genomics Chromium GEM-X Single Cell 5' v3 Dual Index and V(D)J Enrichment Kit


title: 81207

description: Library name: Sample 595


title: 81203

description: Library name: Sample 593


title: Patient DCP19, 10x Genomics 5' V(D)J sequencing on day D0, sample 2

description:
Library name: DCP19_D0-2_Tumor_RNA
10X Genomics Chromium GEM-X Single Cell 5' v3 Dual Index and V(D)J Enrichment Kit


title: A549 cells, BOP1 siRNA, mock, 12h, rep3


title: A549 cells, BOP1 siRNA, mock, 12h, rep1


title: Patient DCP19, 10x Genomics 5' V(D)J sequencing on day D0, sample 1

description:
Library name: DCP19_D0-1_Tumor_RNA
10X Genomics Chromium GEM-X Single Cell 5' v3 Dual Index and V(D)J Enrichment Kit


title: Patient DCP18, 10x Genomics 5' V(D)J sequencing of tumor biopsy on day D42

description:
Library name: DCP18_D42_Tumor_RNA
10X Genomics Chromium GEM-X Single Cell 5' v3 Dual Index and V(D)J Enrichment Kit


title: A549 cells, BOP1 siRNA, IFN, 8h, rep1


title: 81204

description: Library name: Sample 594


title: A549 cells, BOP1 siRNA, mock, 8h, rep3


title: A549 cells, BOP1 siRNA, mock, 8h, rep2


title: A549 cells, BOP1 siRNA, mock, 8h, rep1


title: 81201

description: Library name: Sample 591


title: Patient DCP17, 10x Genomics 5' V(D)J sequencing of tumor biopsy on day D42

description:
Library name: DCP17_D42_Tumor_RNA
10X Genomics Chromium GEM-X Single Cell 5' v3 Dual Index and V(D)J Enrichment Kit


title: anti-CSF1R only, cell surface protein

first: Julie

last: Boiko

state: Washington

address: 1101 Fairview Ave N

description:
Library name: Sample 3 cell surface protein
10X Genomics

library_source: other

data_processing:
Libraries were sequenced by Illumina Nextseq 2000. Fastq files were generateed using Cell Ranger.
Assembly: Mouse mm10
Supplementary files format and content: Matrix files and tab seperated values files

molecule: protein

source_name: Bone marrow

growth_protocol: Ex vivo samples

extract_protocol:
BM was collected from transplanted mice and sorted using flow cytometry prior to scRNA seq capture. All experimental details are included in supplementary methods in the published manuscript.
Library was constructed according to manufacturer's instructions following the 10X Genomics 5' Next GEM protocol.

treatment_protocol: Mice were treated with immunotherapy post-transplant

value: Bone marrow

value: T cells, CD64+ myeloid cells


title: Lenalidomide + anti-CSF1R, cell surface protein

description:
Library name: Sample 4 cell surface protein
10X Genomics

value: CRBN

value: aCSF1R + lenalidomide


title: Patient DCP18, 10x Genomics 5' V(D)J sequencing of tumor biopsy on day D21

description:
Library name: DCP18_D21_Tumor_RNA
10X Genomics Chromium GEM-X Single Cell 5' v3 Dual Index and V(D)J Enrichment Kit

value: male


title: A549 cells, BOP1 siRNA, mock, 12h, rep2


title: 81103

description: Library name: Sample 589


title: 81104

description: Library name: Sample 590


title: Lenalidomide + anti-CSF1R, gene expression

description:
Library name: Sample 4 gene expression
10X Genomics


title: 81202

description: Library name: Sample 592


title: Control group, cell surface protein

description:
Library name: Sample 1 cell surface protein
10X Genomics

value: WT

value: Isotype


title: Lenalidomide only, cell surface protein

description:
Library name: Sample 2 cell surface protein
10X Genomics

value: Lenalidomide


title: Patient DCP17, 10x Genomics 5' V(D)J sequencing of tumor biopsy on day D0

description:
Library name: DCP17_D0_Tumor_RNA
10X Genomics Chromium GEM-X Single Cell 5' v3 Dual Index and V(D)J Enrichment Kit


title: anti-CSF1R only, gene expression

description:
Library name: Sample 3 gene expression
10X Genomics


title: 81007

description: Library name: Sample 588


title: Patient DCP16, 10x Genomics 5' V(D)J sequencing of tumor biopsy on day D21

description:
Library name: DCP16_D21_Tumor_RNA
10X Genomics Chromium GEM-X Single Cell 5' v3 Dual Index and V(D)J Enrichment Kit


title: Lenalidomide only, gene expression

description:
Library name: Sample 2 gene expression
10X Genomics


title: LP469403A23

type: protein

description: title describes sample ID used in raw data (NPX.csv)

data_processing:
A set of internal controls (incubation, extension and amplification) was used to assess overall assay quality.  Internal plate controls were used to normalize the data and to calculate the limit of detection (LOD) for each assay.
Protein expression levels are given as normalized protein expression (NPX) values, which are arbitrary units used on a log2 scale that were normalized to the plate controls.

source_name: Whole blood

extract_protocol: Baseline SLE serum samples were collected according to the clinical trial protocols. Blood was collected using a tube containing a clotting agent (BD SST 5ml tube). Circulating proteins were assayed using the Olink Explore 3072 panel, a proteomics platform that combines an antibody-based immunoassay with a proximity oligonucleotide extension assay and signal detection with next-generation sequencing on the NovaSeq6000 instrument (Ilumina Inc.).

value: F

tag: disease


title: BBS0500-Z1110042555100719SS

value: healthy controls


title: 81006

description: Library name: Sample 587

value: whole blood


title: Control group, gene expression

description:
Library name: Sample 1 gene expression
10X Genomics


title: Patient DCP14, 10x Genomics 5' V(D)J sequencing of tumor biopsy on day D42

description:
Library name: DCP14_D42_Tumor_RNA
10X Genomics Chromium GEM-X Single Cell 5' v3 Dual Index and V(D)J Enrichment Kit

value: female


title: SP606314B23

value: SLE


title: BBS0050-Z1110040412011221S0

value: M


title: BBS0500-Z1110044374093019SS


title: Patient DCP16, 10x Genomics 5' V(D)J sequencing of tumor biopsy on day D0

description:
Library name: DCP16_D0_Tumor_RNA
10X Genomics Chromium GEM-X Single Cell 5' v3 Dual Index and V(D)J Enrichment Kit

value: human lung tumor tissue + mouse KPL lung cancer cell line


title: BBS0500-Z1888236332071922S0


title: Patient DCP14, 10x Genomics 5' V(D)J sequencing of tumor biopsy on day D21

description:
Library name: DCP14_D21_Tumor_RNA
10X Genomics Chromium GEM-X Single Cell 5' v3 Dual Index and V(D)J Enrichment Kit


title: BBS0500-Z1110044812100319SS


title: BBS0500-Z1110042858100419SS


title: 81003

description: Library name: Sample 586


title: 80807

description: Library name: Sample 585


title: 80802

description: Library name: Sample 584


title: BBS0500-Z1888882695071122S0


title: BBS0500-Z1110032752062722S0


title: BBS0500-Z1110044845062822S0


title: Patient DCP12, 10x Genomics 5' V(D)J sequencing of tumor biopsy on day D0

description:
Library name: DCP12_D0_Tumor_RNA
10X Genomics Chromium GEM-X Single Cell 5' v3 Dual Index and V(D)J Enrichment Kit


title: Patient DCP14, 10x Genomics 5' V(D)J sequencing of tumor biopsy on day D0

description:
Library name: DCP14_D0_Tumor_RNA
10X Genomics Chromium GEM-X Single Cell 5' v3 Dual Index and V(D)J Enrichment Kit


title: 80603

description: Library name: Sample 582


title: Patient DCP12, 10x Genomics 5' V(D)J sequencing of tumor biopsy on day D14

description:
Library name: DCP12_D14_Tumor_RNA
10X Genomics Chromium GEM-X Single Cell 5' v3 Dual Index and V(D)J Enrichment Kit


title: 80801

description: Library name: Sample 583


title: BBS0500-Z1888713165062422S0


title: BBS0500-Z1110044475062322S0


title: BBS0500-Z1888949831062422S0


title: Patient DCP10, 10x Genomics 5' V(D)J sequencing of tumor biopsy on day D42

description:
Library name: DCP10_D42_Tumor_RNA
10X Genomics Chromium GEM-X Single Cell 5' v3 Dual Index and V(D)J Enrichment Kit


title: 80504

description: Library name: Sample 581


title: 80502

description: Library name: Sample 580


title: BBS0500-Z1110046231071822S0


title: S0022527912


title: Patient DCP10, 10x Genomics 5' V(D)J sequencing of tumor biopsy on day D0

description:
Library name: DCP10_D0_Tumor_RNA
10X Genomics Chromium GEM-X Single Cell 5' v3 Dual Index and V(D)J Enrichment Kit


title: 80402

description: Library name: Sample 577


title: BBS0500-Z1888247070062322S0


title: BBS0500-Z1888454783071522S0


title: 80403

description: Library name: Sample 578


title: S0022524187


title: Patient DCP10, 10x Genomics 5' V(D)J sequencing of tumor biopsy on day D21

description:
Library name: DCP10_D21_Tumor_RNA
10X Genomics Chromium GEM-X Single Cell 5' v3 Dual Index and V(D)J Enrichment Kit


title: S0022519315


title: Patient DCP09, 10x Genomics 5' V(D)J sequencing of tumor biopsy on day D21

description:
Library name: DCP09_D21_Tumor_RNA
10X Genomics Chromium GEM-X Single Cell 5' v3 Dual Index and V(D)J Enrichment Kit


title: 80404

description: Library name: Sample 579


title: Patient DCP09, 10x Genomics 5' V(D)J sequencing of tumor biopsy on day D42

description:
Library name: DCP09_D42_Tumor_RNA
10X Genomics Chromium GEM-X Single Cell 5' v3 Dual Index and V(D)J Enrichment Kit


title: BBS0500-Z1110048520071822S0


title: BBS0500-Z1110046189032521RT


title: S0022521599


title: 80401

description: Library name: Sample 576


title: S0022518197


title: BBS0500-Z1110046272031821RT


title: BBS0500-Z1110029953032921RT


title: 80346

description: Library name: Sample 575


title: 80345

description: Library name: Sample 574


title: S0022524854


title: BBS0500-Z1888647920041221RT


title: 80342

description: Library name: Sample 573


title: BBS0500-Z1110044866040121RT


title: BBS0500-Z1888364317071122S0


city: St. Louis

first: India

last: Reiss

state: Missouri

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University in St. Louis

description:
Library name: mnase_GTAC_SR011163_062625_wt_1mo_female
rep1
mnase-seq_wt.bw

data_processing:
Calling Cards FASTQ reads were processed with a custom bash pipeline to generate per-sample insertion files for peak calling. Briefly, reads were first adapter-trimmed and demultiplexed by requiring an exact 5′ match to the OM-piggyBac transposon sequence using cutadapt with zero mismatches/indels and discarding untrimmed reads, then SRT barcodes were extracted with umi_tools extract, followed by an additional exact-match trim of the transposon sequence and trimming of trailing Nextera adapters (cutadapt).  Trimmed reads were aligned to the reference genome with Bowtie2 and converted to BAM; mapped reads were retained, then sorted and indexed. Transposon insertion sites were then computed per read by assigning the insertion point to the alignment start (forward reads) or end (reverse reads), correcting for soft clipping, and encoding the genomic interval immediately preceding the insertion. For piggyBac, reads were optionally filtered to those matching the expected “TTAA” insertion motif.  Finally, unique insertions were aggregated into an insertion table (“qbed” file)  by counting identical insertion sites; these insertion files were then used as input for downstream peak calling.
Differential Calling Cards peak sets were generated using a custom pipeline that (i) defines a unified candidate peak set and (ii) classifies those peaks as condition-enriched (CLN3-specific/WT-specific) or shared. For each condition, peaks were called with PyCallingCards using the MACCs (“cctools”) framework with the parameters  pvalue_cutoffbg=0.05, window_size=800, step_size=400, pvalue_cutoffTTAA=0.005, lam_win_size=1,000,000, pseudocounts=0.4. Peaks from the two TF conditions were then concatenated and collapsed into a nonredundant “union” peak set by sorting and merging intervals with bedtools merge using a 1 kb merge distance (-d 1000).  To call differential peaks, we quantified insertions from the two TF qbed files across the union peak set using pycallingcards.pp.make_Anndata, then tested TF_C1 vs TF_C2 per peak with Fisher’s exact test and ranked peaks by multiple-testing–adjusted p-values. Peaks with adjusted p < 0.05 enriched in TF_C1 were designated CLN3-specific peaks, and peaks enriched in TF_C2 were designated WT-specific peaks (written as separate BED files). Finally, “shared” peaks were defined as the remaining union peaks not assigned to either differential class, implemented with bedtools intersect -v against the condition-specific BED files.
Paired-end MNase-seq FASTQ files were aligned to the mm10 reference genome using Bowtie2 v2.3.5. Alignments were performed in paired-end mode with an expected insert-size range of 110-210 bp (-I 110 -X 210), requiring properly paired reads, and reads were trimmed to 40 bp prior to alignment. SAM files were converted to BAM and unmapped reads were removed, followed by coordinate sorting and indexing. To restrict analyses to canonical chromosomes, BAMs were filtered to chr1-chr19, chrX, chrY, name-sorted, and processed with samtools fixmate.  BAMs were then coordinate-sorted and PCR duplicates were removed with samtools markdup -r.
To generate genome-browser tracks, processed replicate BAMs for each condition were supplied to DANPOS3 for differential analysis using the standard danpos.py. DANPOS3 outputs included pooled per-condition WIG tracks (normalized/smoothed signal) and a differential WIG track (Poisson-based difference). Finally, WIG files were converted to bigWig format using the UCSC wigToBigWig utility. This produced bigWig tracks for each condition’s normalized/smoothed MNase signal and for the DANPOS differential signal.
RNA-seq counts tables produced by GTAC.
Assembly: mm10, hg38
Supplementary files format and content: Calling Cards: qBED, BED. Mnase-seq: bigWig. RNA-seq: counts  csv and metadata csv

source_name: astrocytes

growth_protocol: Hepg2 cells were maintained in DMEM+10% FBS, 1x Penstrep in 6 well plates.

extract_protocol:
For MNase-seq, MNase digestion was performed immediately following astrocyte isolation. Cells were fixed for 10 minutes in 1% formaldehyde and the reaction was quenched for 5 minutes with 2.5 M glycine, added to a final concentration of 0.125 M. The cells were then washed twice in 1x PBS. Nuclei were prepared by adding 100 μl of Nuclei Prep Buffer (Zymo EZ Nucleosome DNA Prep Kit, D5220) per 1 million cells. After centrifugation, the cells were resuspended in 1x Takara MNase Digestion Buffer. Chromatin was digested with 4 units of Takara MNase (2910A) per 1,000,000 cells. The reaction was stopped by adding 5x MN stop buffer from the EZ kit. Subsequently, 4.8 μl of 5 M NaCl and 2 μl of proteinase K were added per 1 million cells, and samples were incubated at 65°C overnight. The following day, DNA was isolated using the EZ kit according to the manufacturer’s instructions. For Calling Cards and RNA-seq, total RNA extraction after MACS was done using the Qiagen RNeasy Plus Mini Kit (Cat no. 74134) according to the manufacturer's protocol. All of the total RNA was used for reverse transcription.
For Calling Cards, First-strand cDNA was generated by oligo(dT) priming with the SMART_dT18VN primer and Maxima H Minus reverse transcriptase in the presence of RNase inhibitor, followed by heat inactivation and RNase H treatment to remove the RNA strand, yielding cDNA for downstream library construction. Self-reporting transposon (SRT) transcripts were then PCR-amplified from cDNA using KAPA HiFi HotStart with a reporter specific primer (tdtomato or puromycin) and SMART reverse primers (cycle number minimized/optimized to avoid over-amplification; typical program uses ~20 cycles with 98°C denaturation, 65°C annealing, and long 72°C extension), and amplicons were size-selected/cleaned with a 0.6× AMPure XP bead cleanup and QC’d by Qubit. Purified SRT PCR products were converted into sequencing-ready libraries by Nextera XT tagmentation (ATM + TD buffer at 55°C), neutralization, and an indexing PCR using a barcoded piggyBac (OM-PB) primer together with a Nextera N7 index primer to enable multiplexing, followed by a final 0.6× bead cleanup and fragment distribution QC prior to pooling and Illumina sequencing. A fraction of the samples were checked for sequencing quality using WashU’s DNA Sequencing Innovation Lab (DSIL)’s spike in program with the Illumina MiSeq or Illumina Miniseq. All samples were then submitted to the the Washington University Genome Technology Access Center (GTAC) to be deeply sequenced with the Illumina NovaSeq X Plus. All sequencing data was combined at the end for each sample. MNase-seq libraries were prepared using the NEBNext Ultra end repair and A-tailing module (NEBNext End Prep, E7442), followed by adapter ligation using the NEBNext Ultra Ligation Module with Quick Ligation (E7445). Libraries were purified using Agencourt AMPure XP beads (Beckman Coulter, A63880). Adapter-ligated DNA was PCR-amplified using Phusion High-Fidelity DNA Polymerase with NEB primers (NEB, E6440S), followed by a second cleanup with Agencourt AMPure XP beads. All samples were then submitted to the the Washington University Genome Technology Access Center (GTAC) to be deeply sequenced with the Illumina NovaSeq X Plus. RNA-seq libraries were prepared in-house from total RNA using the NEBNext UltraExpress® RNA Library Prep Kit (New England Biolabs) according to the manufacturer’s instructions. Indexes used from NEBNext Multiplex Oligos for Illumina® (E6440S).  Final libraries were quantified, pooled, and submitted to the Washington University Genome Technology Access Center (GTAC) for sequencing. GTAC performed sequencing on the Illumina NovaSeq X Plus (paired end reads extending 150 bases) and generated gene-level RNA-seq count tables from the resulting sequencing data using their standard RNA-seq processing workflow; these GTAC-provided count tables were used to assemble the final count matrix for downstream analyses.

treatment_protocol: AAV injections were performed as described in (Yen et al. 2023). Viral titers (viral genomes [vg] per milliliter) were ∼1.0 × 10. Neonatal mice (P0-P1) received intracerebroventricular (ICV) injections of Calling Cards AAVs encoding the piggyBac transposase (unfused or BMAL1 fusion) and donor/self-reporting transposon. AAV stocks were mixed 1:1 immediately prior to injection (6 µL total per pup). Pups were anesthetized by hypothermia on ice (5-8 min; ≤15 min maximum) and injected bilaterally using a Hamilton syringe fitted with a depth guard to ensure a consistent 2 mm insertion depth. Virus was delivered at 1 µL per site at three sites per hemisphere (1 µL/s); after each injection, the needle was held in place for 5 s before withdrawal to minimize backflow. Following injection, pups were placed on a low warming pad for recovery (5-10 min) and returned to the home cage with the dam. For HepG2 cells, calling card constructs (with puro as the marker gene) transfected through neon electroporation (2*10^6 cells/well). Puro selection performed with 3ug/mL puro. Puro selection done over 5 days to allow for cells without insertions to die off, a non-transfected well was used to determine that all cells without insertions had died at that point.

value: astrocytes


title: mnase_ GTAC_SR011163_103025_wt_1mo_male

description:
Library name: mnase_ GTAC_SR011163_103025_wt_1mo_male
rep2
mnase-seq_wt.bw


description:
Library name: mnase_GTAC_SR011163_103025_cln3_1mo_male
rep2
mnase-seq_cln3.bw

value: CLN3delta7/8 (C57BL/6J background)


title: BBS0500-Z1110046264050321RT


description:
Library name: mnase_GTAC_SR011163_062625_cln3_1mo_female
rep1
mnase-seq_cln3.bw


title: BBS0500-Z1888992066033021RT

description: title describes sample ID used in raw data (NPX.csv)


title: BBS1000-Z1110029969032519S7


title: BBS0500-Z1110046622031721RT


title: BBS0500-Z1110044681041221RT


title: 80329

description: Library name: Sample 570


title: BBS0500-Z1110042853032521RT


title: Patient DCP09, 10x Genomics 5' V(D)J sequencing of tumor biopsy on day D0

first: Linh

last: Tran

description:
Library name: DCP09_D0_Tumor_RNA
10X Genomics Chromium GEM-X Single Cell 5' v3 Dual Index and V(D)J Enrichment Kit


title: BBS0500-Z1110046939041221RT


title: 80328

description: Library name: Sample 569


title: BBS0500-Z1110046778042321RT


title: 80334

description: Library name: Sample 571


title: E18.5_RNA_Mutant_Male_1

city: Chcago

first: Gal

last: Finier

address: 225 E. Chciago Ave

department: Peditrics

description: Library name: Sample D3

data_processing:
E145 scRNA: Raw sequencing data was demultiplexed and processed using  CellRanger with a custom reference combining the mm10 transcriptome with the eGFP and tdTomato RNA sequences.
E185 scRNA: Raw sequencing data was demultiplexed and processed using  CellRanger with a custom reference combining the mm10 transcriptome with the eGFP and tdTomato RNA sequences.
E145 scATAC: Raw sequencing data was demultiplexed and processed using the CellRanger ATAC with the mm10 genome.
E185 bulk-RNA: Raw sequencing data was demultiplexed and mapped to mm10 using HISAT2. Normalized gene expression values (fragments per kilobase million; FPKM) were calculated using Cufflinks.
Assembly: mm10
Supplementary files format and content: E145 scRNA: tab-separated values files and matrix files
Supplementary files format and content: E185 scRNA: tab-separated values files and matrix files
Supplementary files format and content: E145 scATAC: tab-separated values files and matrix files
Supplementary files format and content: E185 bulk-RNA: csv files containing FPKM per sample

source_name: kidney

extract_protocol:
E145 scRNA: Single cell suspensions were prepared from mouse embryonic kidneys using a cold-active protease cell dissociation protocol (Adam et al. Development 2017). Foxd1+ progenitors and their derivates were subsequently isolated by fluorescence-activated cell sorting (FACS).
E185 scRNA: Single cell suspensions were prepared from mouse embryonic kidneys using a cold-active protease cell dissociation protocol (Adam et al. Development 2017). Foxd1+ progenitors and their derivates were subsequently isolated by fluorescence-activated cell sorting (FACS).
E145 scATAC: Single cell suspensions were prepared as for scRNA-seq. Nuclei was subsequently isolated using the protocol from 10x Genomics.
E185 bulk-RNA: RNA was extracted using the RNeasy Mini Kit (Qiagen 74104).
E145 scRNA: Libraries were constructed using the 10x Genomics Chromium 3' Kit version 3.
E185 scRNA: Libraries were constructed using the 10x Genomics Chromium 3' Kit version 3.
E145 scATAC: Libraries were constructed using the 10x Genomics Chromium Single Cell ATAC Kit version 2.
E185 bulk-RNA: libraries were constructed using the Illumina Stranded mRNA-seq Library Prep Kit.

value: kidney

value: Foxd1cre +/- Tcf21 f/f

tag: developmental stage

value: Male

value: Mutant


title: E18.5_RNA_Control_Male_2

description: Library name: Sample D2

value: Foxd1cre +/- Tcf21 +/+

value: Control


title: BBS0500-Z1110039290033021RT


title: BBS0500-Z1110035347032221RT


title: BBS0500-Z1888921995032421RT


title: E18.5_RNA_Mutant_Male_2

description: Library name: Sample D4


title: BBS0500-Z1110040764092419SS


title: 80338

description: Library name: Sample 572


title: E18.5_RNA_Control_Male_1

description: Library name: Sample D1


title: E18.5_scRNA_Mutant_Male

description:
Library name: Sample B4
10x Genomics

value: Foxd1cre +/- mTmG +/- Tcf21 f/f


title: E14.5_scATAC_Control_Male

description:
Library name: Sample C1
10x Genomics

value: Foxd1cre +/- mTmG +/- Tcf21 +/+


title: 80324

description: Library name: Sample 567


title: 80327

description: Library name: Sample 568


title: BBS0050-Z1110040414012921S0

value: F


title: BBS0500-Z1110040735042121RT

value: healthy controls


title: E14.5_scATAC_Mutant_Male

description:
Library name: Sample C2
10x Genomics


title: 80323

description: Library name: Sample 566

value: whole blood


title: E18.5_scRNA_Mutant_Female

description:
Library name: Sample B3
10x Genomics

value: Female


title: BBS0500-Z1888849255032621RT


title: E18.5_scRNA_Control_Male

description:
Library name: Sample B2
10x Genomics


title: BBS0500-Z1110048196033121RT


title: 80322

description: Library name: Sample 565

value: SLE


title: BBS0500-Z1110044782031821RT


title: 80320

description: Library name: Sample 564


title: BBS0050-Z1110044658011221S0


title: 80318

description: Library name: Sample 563


title: E18.5_scRNA_Control_Female

description:
Library name: Sample B1
10x Genomics


title: BBS0050-Z1110046733011421S0


title: BBS0050-Z1110046051010821S0


title: BBS0050-Z1888100344010721S0

value: M


title: 80316

description: Library name: Sample 562


title: 80313

description: Library name: Sample 561


title: BBS0050-Z1110042731011321S0


title: E14.5_scRNA_Mutant_Female

description:
Library name: Sample A3
10x Genomics


title: BBS0050-Z1110044358020221S0


title: E14.5_scRNA_Mutant_Male

description:
Library name: Sample A4
10x Genomics