title: ATAC_Brain_Endothelial_P6_2

status: Public on Jul 01 2022

first: Manuel

middle: Eliezer

last: Cantu Gutierrez

address: 1 Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Reads were mapped to the mm10 version of the mouse genome using Bowtie2 with default paired-end settings (Langmead and Salzberg 2012). Mitochondrial reads, reads with a MAPQ < 10, and reads which did not align to the reference genome were removed using Samtools (version 1.13) (Danecek, Bonfield et al. 2021). Duplicated reads were then removed with Picard MarkDuplicates (Institute 2019). Peak calling was carried out with MACS2 (callpeak  --nomodel –broad) (v2.2.7.1)(Zhang, Liu et al. 2008). Diffbind (version 3.2) (Stark R 2011, Ross-Innes, Stark et al. 2012) was used to import peaksets (min.overlap= 0.66) into RStudio Server (version 1.4.1717, https://www.rstudio.com) using R (version 4.1 (Team 4.1). dba.blacklist function was used to filter out peaks that overlap with the ENCODE blacklist. Differentially accessible regions between the endothelium and the input nuclei of each organ were extracted using DESeq2 (version 1.32.0) (Love, Huber et al. 2014) with <p-value 0.5 and >1 fold change difference.
Genome build: mm10
Bigwig, bam and peak files for ATAC data.

source_name: Brain

extract_protocol:
For embryonic analysis, tamoxifen (0.015 mg/kg bodyweight) was administered to pregnant dams by intraperitoneal (i.p.) injection at E10.5 and embryos were collected at E12.5. For postnatal tissues, tamoxifen (0.015 mg/kg bodyweight) was administered by subcutaneous injection at P1 and P3, and tissues were collected at P7. For adult experiments, tamoxifen (0.015 mg/kg bodyweight) was administered by i.p. injection 7 days prior to tissue isolation. In all cases, after gross dissection, GFP expression within the vasculature of each tissue of interest (or embryo) was confirmed by direct immunofluorescence for each sample collected. GFP negative samples were not processed further. Nuclear isolation was performed according to Mo et. al (Mo, Mukamel et al. 2015). Briefly, fresh tissue was harvested on ice in Buffer HB++ composed of 0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH, pH 7.8 with protease inhibitors (Roche/Sigma Cat. #11873580001), 1mM DTT (Sigma D0632), 0.15 mM Spermine (Sigma S1141), 0.5 mM Spermidine (Sigma S2501), and RNAse inhibitors (Promega N2611) and immediately dissected and minced into 1mm-by-1mm portions with curved scissors. Tissue was transferred along 1ml of HB++ in a chilled Eppendorf tube in ice and homogenized using Bio-gen Series PRO200 homogenizer. Short bursts of ~5-8 seconds were done to prevent overheating. Once no large pieces are observed the tissue was transferred to large clearance dounce homogenizer “A” (7ml, Kontes Glass Company) and 4ml of HB++ was added. Tissue was homogenized with 20 strokes and transferred to small clearance homogenizer “B”, 320 ul of IGEPAL CA-630++ was added and dounce with tight pestle 20 more times slowly and avoiding the creation of bubbles  to disrupt cell membranes. Homogenate was then strained using a 40um cell strainer into a 50ml conical tube. 5ml of working solution of 5 volumes of Optiprep solution (Sigma, D1556) and one volume of diluent (150mM KCl, 30mM MgCl2, 120mM Tricine-KOH, pH 7.8 in water) was added and homogenized by inversion and poured into an empty pre-chilled 30mL Corex tube. Once all samples were ready, using a pipette aid, the tip was placed just above the bottom surface of the Corex tube, and sample was slowly underlay with 7.5 mL of the 30% and then 4 mL of the 40% iodixanol++ solutions (diluted with buffer HB). Nuclei were then isolated by density gradient centrifugation with optiprep density gradient medium. Nuclei were collected from the 30-40% interface and then pre-cleared with Protein-G Dynabeads (Life technologies, 10003D). A portion of these nuclei were held back for use as input samples. Next, GFP+ nuclei were immunoprecipitated with an anti-EGFP antibody (ABfinity Rabbit monoclonal anti-GFP antibody; 0.2 mg/mL) for 40 minutes at 4C with gentle agitation, followed by binding to Protein-G Dynabeads (Invitrogen, 10003D) for 20 minutes hours at 4C to enrich for endothelial cell nuclei. Isolated nuclei were filtered using 20 um Celltrics filter (Sysmex #04-004-2326).
Approximately 50,000 bead-bound EGFP+ and 50,000 input nuclei from murine tissues were used as input for ATAC-seq. ATAC-seq libraries for murine endothelial cells were as previously described (Buenrostro, Wu et al. 2015) and libraries were generated using the Nextera DNA Sample Preparation Kit (Illumina, FC-121-1030). The quality of purified DNA libraries was checked by Agilent High Sensitivity DNA kit (Agilent Technologies).

tag: cell type source

value: Endothelial


title: ATAC_Brain_Endothelial_P6_1

type: SRA

city: Houston

state: TX

country: USA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: age


title: Syngeneic islet graft

status: Public on May 25 2022

city: Shenzhen

first: Lisha

last: Mou

state: Guangdong

address: Room 604, Building 1, Yinxingzhijie 1 Qi Guanlan, Longhua District

country: China

institute: Shenzhen Second People's Hospital

library_source: transcriptomic

data_processing:
Sequences obtained from sequencing using the 10x Genomics single-cell RNA sequencing platform were demultiplexed and mapped to the mm10 transcriptome using the Cell Ranger package (10x Genomics). Cells were removed if they were expressing fewer than 200 unique genes, more than 4,500 unique genes, or greater than 15% mitochondrial reads. Genes not detected in at least 3 cells were removed from subsequent analysis.
To analyze the single-cell RNA-seq data, we performed Uniform Manifold Approximation and Projection for Dimension Reduction (UMAP) using the Seurat R Package (version 3.1.5) with the first 75 principal components, after performing principal component analysis (PCA) on the 2000 most variable genes. Identification of significant clusters was performed using the FindClusters() algorithm in the Seurat package with the resolution set as 0.6. Marker genes for each significant clusters were found using the Seurat function FindAllMarkers(). Cell types were determined using a combination of marker genes identified from the literature and the CellMarker web tool (http://biocc.hrbmu.edu.cn/CellMarker/).
All single-cell sequencing data statistical analysis was performed in R (version 4.0.5) using Seurat (3.1.5). Wilcoxon Rank Sum test was applied for comparisons in two groups. Statistical significance was accepted for p < 0.05.
Assembly: mm10
Supplementary files format and content: barcodes.tsv, features.tsv, matrix.mtx files.

molecule: total RNA

source_name: islet graft

extract_protocol:
After dissociation, the concentration of single-cell suspension was adjusted to 700–1,200 cells/μl. Cell viability was determined by trypan blue staining with TC20 automated cell counter (Bio-rad, Hercules, CA). The ratio of viable cells was required to be more than 85%. The input cells were then loaded onto the channel of Single Cell B Chip (v3 chemistry, PN-1000153) and loaded onto a Chromium Controller (10x Genomics, Pleasanton, CA) to generate single-cell GEMs (gel beads in emulsion).
Reverse transcription and library preparation was performed using the Chromium Single Cell 3’ Reagent Kits following the 10x Genomics protocol.
Libraries were sequenced, aiming at a minimum coverage of 50,000 raw reads per cell on an Illumina NovaSeq 6000 by Novogene Bioinformatics Technology Co., Ltd (Tianjing, China).

tag: strain

tag: tissue

value: pancreatic islet

tag: condition

value: C57bl/6 islets to C57bl/6 recipients


title: W3_DG_18

status: Public on Mar 02 2022

type: RNA

city: Canyon

first: Matthew

last: Scott

address: 3201 Russell Long Blvd

institute: Texas A&M University

description:
mRNA count data
AWO22587-0239-W3-DG-18

hyb_protocol: NanoString nCounter PrepStation

scan_protocol: NanoString SPRINT Profiler set to high resolution (550)

data_processing: NanoString nSolver Analysis Software v4.0 was utilized for quality assessment and raw gene count accession. Four housekeeping, six positive spike-in, and eight negative control genes were used for intersample count normalization.

label: Biotin

organism: Bos taurus

source_name: Whole blood

label_protocol: NanoString nCounter mRNA Bovine Custom Panel

extract_protocol: Total RNA was isolated from Tempus Blood Tubes with Tempus Spin RNA Isolation Kit

tag: treatment group

value: Healthy

tag: study

tag: location

value: MO

tag: animal info

tag: vaccinated

tag: dewormed


title: 140_DG_17

description:
mRNA count data
AWO22587-0235-140-DG-17

value: Steer


title: 162_MH_19

description:
mRNA count data
AWO22587-0240-162-MH-19

value: MS

value: Heifer


title: 130_PS_19

description:
mRNA count data
AWO22587-0237-130-PS-19

value: Bull


title: 179_MH_19

description:
mRNA count data
AWO22587-0238-179-MH-19


title: 140_MH_19

description:
mRNA count data
AWO22587-0233-140-MH-19


title: 243_PS_19

description:
mRNA count data
AWO22587-0234-243-PS-19


title: 58_DG_17

description:
mRNA count data
AWO22587-0236-58-DG-17


title: 109_DG_18

description:
mRNA count data
AWO22587-0232-O109-DG-18


title: 132_MH_19

description:
mRNA count data
AWO22587-0230-132-MH-19


title: 131_MH_19

description:
mRNA count data
AWO22587-0231-131-MH-19


title: R1_DG_18

description:
mRNA count data
AWO22587-0228-R1-DG-18


title: Y53_DG_18

description:
mRNA count data
AWO22587-0226-Y53-DG-18


title: 147_MH_19

description:
mRNA count data
AWO22587-0227-147-MH-19


title: 148_DG_17

description:
mRNA count data
AWO22587-0229-148-DG-17


title: 154_MH_19

description:
mRNA count data
AWO22587-0217-154-MH-19


title: 111_VD_17

description:
mRNA count data
AWO22587-0211-111-VD-17


title: 220_PS_19

description:
mRNA count data
AWO22587-0212-220-PS-19


title: 151_MH_19

description:
mRNA count data
AWO22587-0216-151-MH-19


title: 158_MH_19

description:
mRNA count data
AWO22587-0215-158-MH-19


title: 103_DG_18

description:
mRNA count data
AWO22587-0213-O103-DG-18


title: 108_MH_19

description:
mRNA count data
AWO22587-0205-108-MH-19


title: 108_VD_17

description:
mRNA count data
AWO22587-0210-108-VD-17


title: 165_MH_19

description:
mRNA count data
AWO22587-0209-165-MH-19


title: 64_DG_17

description:
mRNA count data
AWO22587-0206-64-DG-17


title: 39_DG_17

description:
mRNA count data
AWO22587-0203-39-DG-17


title: 126_MH_19

description:
mRNA count data
AWO22587-0208-126-MH-19


title: 174_MH_19

description:
mRNA count data
AWO22587-0223-174-MH-19


title: 108_PS_19

description:
mRNA count data
AWO22587-0221-108-PS-19


title: 170_MH_19

description:
mRNA count data
AWO22587-0201-170-MH-19


title: 192_VD_17

description:
mRNA count data
AWO22587-0220-192-VD-17


title: 127_VD_17

description:
mRNA count data
AWO22587-0219-127-VD-17


title: W2_DG_18

description:
mRNA count data
AWO22587-0222-W2-DG-18


title: 284_TA_20

description:
mRNA count data
AWO22587-0200-284-TA-20


title: 110_DG_18

description:
mRNA count data
AWO22587-0207-O110-DG-18


title: 184_VD_17

description:
mRNA count data
AWO22587-0224-184-VD-17


title: 281_TA_20

description:
mRNA count data
AWO22587-0225-281-TA-20


title: 154_PS_19

description:
mRNA count data
AWO22587-0218-154-PS-19


title: 172_VD_17

description:
mRNA count data
AWO22587-0195-172-VD-17


title: 160_MH_19

description:
mRNA count data
AWO22587-0194-160-MH-19


title: 296_PS_19

description:
mRNA count data
AWO22587-0204-296-PS-19


title: 294_PS_19

description:
mRNA count data
AWO22587-0202-294-PS-19


title: 124_VD_17

description:
mRNA count data
AWO22587-0214-124-VD-17


title: Tdt Control rep-2 [RNA-seq]

status: Public on Aug 04 2022

city: Madison

first: Jeffrey

last: Dilworth

email: jdilworth@ohri.ca, fdilworth@wisc.edu

state: WI

address: 1111 Highland Ave - WIMR II 4518

department: Cell and Regenerative Biology

institute: University of Wisconsin - Madison

data_processing:
Sequencing adapters were trimmed using Cutadapt v2.6.
Transcript quantification with Salmon v1.1.0.
Differential expression with DEseq2 v1.28.1.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Table containing differentially expressed genes.
Supplementary_files_format_and_content: Quantified transcripts for all samples.

source_name: Satellite Stem cells

extract_protocol: Muscle satellite stem cells were isolated from indicated muscles by mincing and straining, which were further collected in microfuge tubes by fluorescence activated cell sorting.

treatment_protocol: Cardiotoxin Injections into the tibialis anterior and gastrocnemius muscle of hind limb.

tag: genotype

value: Tdt Control

tag: treatment

value: Cardiotoxin injury

value: Tibialis Anterior and Gastrocnemius muscles

tag: cell type

value: Satellite Stem cells

tag: development stage

value: Adult


title: S.048.J124_S48

status: Public on Aug 29 2022

data_processing:
FastQC v0.11.9 was used for read quality assessment.
Trimmomatic v0.39 was used for read pair trimming and adaptor removal (parameters- SLIDINGWINDOW:4:20 MINLEN:28 LEADING:3 TRAILING:3 ILLUMINACLIP:adaptor.fa:2:30:20:2:TRUE).
Trimmed reads were mapped to the ARS-UCD1.2 bovine genome assembly with HISAT2 v2.2.1 (parameters- -hSbo).
Gene-level transcriptome assembly was performed with StringTie v2.1.7 (parameters-e -G ARSUCD1.2.gff)
Raw gene counts were generated by the Python3 program prepDE.py, provided by the authors of StringTie (parameters- -l 150).
Assembly: ARS-UCD1.2
Supplementary files format and content: Comma-delimited text file of annotated raw gene counts of all samples.

extract_protocol:
Total RNA was isolated from Tempus RNA blood tubes with Tempus Spin RNA Isolation Kit (Applied Biosystems), based on manufacturer’s instruction.
Sequencing libraries were constructed with the TruSeq Stranded mRNA Library Prep Kit (Illumina), following manufacturer’s instruction.

value: Whole blood

tag: timepoint

tag: pasture location

tag: age at_sampling

tag: vaccination

value: N


title: 125_MH_19

description:
mRNA count data
AWO22587-0196-125-MH-19


title: 107_DG_18

description:
mRNA count data
AWO22587-0187-O107-DG-18


title: 12_DG_17

description:
mRNA count data
AWO22587-0188-12-DG-17


title: 155_MH_19

description:
mRNA count data
AWO22587-0193-155-MH-19


title: S.028.J023_S28

value: Y


title: 105_MH_19

description:
mRNA count data
AWO22587-0190-105-MH-19


title: 196_VD_17

description:
mRNA count data
AWO22587-0199-196-VD-17


title: 173_DG_17

description:
mRNA count data
AWO22587-0198-173-DG-17


title: 106_VD_17

description:
mRNA count data
AWO22587-0197-106-VD-17


title: 176_VD_17

description:
mRNA count data
AWO22587-0189-176-VD-17


title: 161_VD_17

description:
mRNA count data
AWO22587-0191-161-VD-17


title: 143_PS_19

description:
mRNA count data
AWO22587-0183-143-PS-19


title: 142_MH_19

description:
mRNA count data
AWO22587-0192-142-MH-19


title: 173_MH_19

description:
mRNA count data
AWO22587-0179-173-MH-19


title: 130_MH_19

description:
mRNA count data
AWO22587-0186-130-MH-19


title: 241_PS_19

description:
mRNA count data
AWO22587-0184-241-PS-19


title: 76_DG_17

description:
mRNA count data
AWO22587-0177-76-DG-17


title: 166_VD_17

description:
mRNA count data
AWO22587-0182-166-VD-17


title: 267_TA_20

description:
mRNA count data
AWO22587-0172-267-TA-20


title: 148_MH_19

description:
mRNA count data
AWO22587-0178-148-MH-19


title: 225_PS_19

description:
mRNA count data
AWO22587-0173-225-PS-19


title: 231_TA_20

description:
mRNA count data
AWO22587-0185-231-TA-20


title: 252_TA_20

description:
mRNA count data
AWO22587-0171-252-TA-20


title: 237_TA_20

description:
mRNA count data
AWO22587-0181-237-TA-20


title: Y55_DG_18

description:
mRNA count data
AWO22587-0180-Y55-DG-18


title: 166_MH_19

description:
mRNA count data
AWO22587-0170-166-MH-19


title: 161_DG_17

description:
mRNA count data
AWO22587-0175-161-DG-17


title: 233_PS_19

description:
mRNA count data
AWO22587-0166-233-PS-19


title: 212_TA_20

description:
mRNA count data
AWO22587-0174-212-TA-20


title: 262_TA_20

description:
mRNA count data
AWO22587-0165-262-TA-20


title: 297_PS_19

description:
mRNA count data
AWO22587-0176-297-PS-19


title: 225_TA_20

description:
mRNA count data
AWO22587-0163-225-TA-20


title: 167_MH_19

description:
mRNA count data
AWO22587-0161-167-MH-19


title: 138_MH_19

description:
mRNA count data
AWO22587-0162-138-MH-19


title: 188_PS_19

description:
mRNA count data
AWO22587-0169-188-PS-19


title: 131_VD_17

description:
mRNA count data
AWO22587-0156-131-VD-17


title: 250_TA_20

description:
mRNA count data
AWO22587-0168-250-TA-20


title: 163_VD_17

description:
mRNA count data
AWO22587-0152-163-VD-17


title: 150_VD_17

description:
mRNA count data
AWO22587-0150-150-VD-17


title: 279_TA_20

description:
mRNA count data
AWO22587-0167-279-TA-20


title: R9_DG_18

description:
mRNA count data
AWO22587-0164-R9-DG-18


title: 242_PS_19

description:
mRNA count data
AWO22587-0160-242-PS-19


title: 183_VD_17

description:
mRNA count data
AWO22587-0153-183-VD-17


title: 34_DG_17

description:
mRNA count data
AWO22587-0158-34-DG-17


title: 257_TA_20

description:
mRNA count data
AWO22587-0149-257-TA-20


title: 159_MH_19

description:
mRNA count data
AWO22587-0147-159-MH-19


title: 124_MH_19

description:
mRNA count data
AWO22587-0143-124-MH-19


title: 112_PS_19

description:
mRNA count data
AWO22587-0157-112-PS-19


title: 238_PS_19

description:
mRNA count data
AWO22587-0146-238-PS-19


title: 136_MH_19

description:
mRNA count data
AWO22587-0155-136-MH-19


title: 133_MH_19

description:
mRNA count data
AWO22587-0138-133-MH-19


title: 146_VD_17

description:
mRNA count data
AWO22587-0154-146-VD-17


title: 136_PS_19

description:
mRNA count data
AWO22587-0145-136-PS-19


title: 264_TA_20

description:
mRNA count data
AWO22587-0148-264-TA-20


title: 159_VD_17

description:
mRNA count data
AWO22587-0151-159-VD-17


title: 163_MH_19

description:
mRNA count data
AWO22587-0136-163-MH-19


title: 135_VD_17

description:
mRNA count data
AWO22587-0137-135-VD-17


title: 189_VD_17

description:
mRNA count data
AWO22587-0140-189-VD-17


title: 234_TA_20

description:
mRNA count data
AWO22587-0159-234-TA-20


title: 227_TA_20

description:
mRNA count data
AWO22587-0139-227-TA-20


title: 129_MH_19

description:
mRNA count data
AWO22587-0142-129-MH-19


title: 267_PS_19

description:
mRNA count data
AWO22587-0144-267-PS-19


title: 211_TA_20

description:
mRNA count data
AWO22587-0127-211-TA-20


title: 201_PS_19

description:
mRNA count data
AWO22587-0141-201-PS-19


title: 103_VD_17

description:
mRNA count data
AWO22587-0128-103-VD-17


title: W1_DG_18

description:
mRNA count data
AWO22587-0134-W1-DG-18


title: 175_VD_17

description:
mRNA count data
AWO22587-0126-175-VD-17


title: R7_DG_18

description:
mRNA count data
AWO22587-0132-R7-DG-18


title: 198_VD_17

description:
mRNA count data
AWO22587-0131-198-VD-17


title: 204_TA_20

description:
mRNA count data
AWO22587-0130-204-TA-20


title: 221_TA_20

description:
mRNA count data
AWO22587-0129-221-TA-20


title: 109_DG_17

description:
mRNA count data
AWO22587-0123-109-DG-17


title: Y58_DG_18

description:
mRNA count data
AWO22587-0135-Y58-DG-18


title: 188_VD_17

description:
mRNA count data
AWO22587-0116-188-VD-17


title: 183_PS_19

description:
mRNA count data
AWO22587-0133-183-PS-19


title: 282_TA_20

description:
mRNA count data
AWO22587-0124-282-TA-20


title: 193_PS_19

description:
mRNA count data
AWO22587-0125-193-PS-19


title: 36_DG_17

description:
mRNA count data
AWO22587-0117-36-DG-17


title: 169_MH_19

description:
mRNA count data
AWO22587-0121-169-MH-19


title: 217_TA_20

description:
mRNA count data
AWO22587-0122-217-TA-20


title: 193_VD_17

description:
mRNA count data
AWO22587-0120-193-VD-17


title: 118_MH_19

description:
mRNA count data
AWO22587-0119-118-MH-19


title: 118_VD_17

description:
mRNA count data
AWO22587-0110-118-VD-17


title: 272_TA_20

description:
mRNA count data
AWO22587-0111-272-TA-20


title: R10_DG_18

description:
mRNA count data
AWO22587-0118-R10-DG-18


title: 215_TA_20

description:
mRNA count data
AWO22587-0101-215-TA-20


title: 161_MH_19

description:
mRNA count data
AWO22587-0115-161-MH-19


title: 171_VD_17

description:
mRNA count data
AWO22587-0098-171-VD-17


title: 274_TA_20

description:
mRNA count data
AWO22587-0104-274-TA-20


title: R5_DG_18

description:
mRNA count data
AWO22587-0102-R5-DG-18


title: 143_MH_19

description:
mRNA count data
AWO22587-0103-143-MH-19


title: 160_DG_17

description:
mRNA count data
AWO22587-0113-160-DG-17


title: 52_DG_17

description:
mRNA count data
AWO22587-0097-52-DG-17


title: 278_TA_20

description:
mRNA count data
AWO22587-0112-278-TA-20


title: 206_TA_20

description:
mRNA count data
AWO22587-0105-206-TA-20


title: 77_DG_17

description:
mRNA count data
AWO22587-0107-77-DG-17


title: 180_MH_19

description:
mRNA count data
AWO22587-0114-180-MH-19


title: W8_DG_18

description:
mRNA count data
AWO22587-0100-W8-DG-18


title: 145_MH_19

description:
mRNA count data
AWO22587-0109-145-MH-19


title: 102_MH_19

description:
mRNA count data
AWO22587-0108-102-MH-19


title: 197_VD_17

description:
mRNA count data
AWO22587-0099-197-VD-17


title: 168_MH_19

description:
mRNA count data
AWO22587-0093-168-MH-19


title: 144_MH_19

description:
mRNA count data
AWO22587-0089-144-MH-19


title: 249_TA_20

description:
mRNA count data
AWO22587-0095-249-TA-20


title: 120_VD_17

description:
mRNA count data
AWO22587-0096-120-VD-17


title: 153_MH_19

description:
mRNA count data
AWO22587-0094-153-MH-19


title: 101_PS_19

description:
mRNA count data
AWO22587-0084-101-PS-19


title: 134_DG_17

description:
mRNA count data
AWO22587-0091-134-DG-17


title: 245_TA_20

description:
mRNA count data
AWO22587-0090-245-TA-20


title: 137_MH_19

description:
mRNA count data
AWO22587-0088-137-MH-19


title: 105_DG_18

description:
mRNA count data
AWO22587-0092-105-DG-18


title: 171_PS_19

description:
mRNA count data
AWO22587-0086-171-PS-19


title: 255_TA_20

description:
mRNA count data
AWO22587-0087-255-TA-20


title: 146_DG_17

description:
mRNA count data
AWO22587-0073-146-DG-17


title: Y59_DG_18

description:
mRNA count data
AWO22587-0080-Y59-DG-18


title: 112_VD_17

description:
mRNA count data
AWO22587-0082-112-VD-17


title: 190_VD_17

description:
mRNA count data
AWO22587-0074-190-VD-17


title: 88_DG_17

description:
mRNA count data
AWO22587-0085-88-DG-17


title: 223_TA_20

description:
mRNA count data
AWO22587-0081-223-TA-20


title: 116_MH_19

description:
mRNA count data
AWO22587-0075-116-MH-19


title: W4_DG_18

description:
mRNA count data
AWO22587-0083-W4-DG-18


title: Y51_DG_18

description:
mRNA count data
AWO22587-0072-Y51-DG-18


title: 110_PS_19

description:
mRNA count data
AWO22587-0066-110-PS-19


title: 126_VD_17

description:
mRNA count data
AWO22587-0076-126-VD-17


title: Y52_DG_18

description:
mRNA count data
AWO22587-0078-Y52-DG-18


title: 246_TA_20

description:
mRNA count data
AWO22587-0070-246-TA-20


title: 164_VD_17

description:
mRNA count data
AWO22587-0077-164-VD-17


title: 260_PS_19

description:
mRNA count data
AWO22587-0064-260-PS-19


title: 140_VD_17

description:
mRNA count data
AWO22587-0079-140-VD-17


title: 107_VD_17

description:
mRNA count data
AWO22587-0071-107-VD-17


title: 109_MH_19

description:
mRNA count data
AWO22587-0059-109-MH-19


title: 121_MH_19

description:
mRNA count data
AWO22587-0069-121-MH-19


title: 119_MH_19

description:
mRNA count data
AWO22587-0067-119-MH-19


title: 275_TA_20

description:
mRNA count data
AWO22587-0106-275-TA-20


title: 110_VD_17

description:
mRNA count data
AWO22587-0068-110-VD-17


title: 162_PS_19

description:
mRNA count data
AWO22587-0060-162-PS-19


title: 281_PS_19

description:
mRNA count data
AWO22587-0063-281-PS-19


title: 68_DG_17

description:
mRNA count data
AWO22587-0061-68-DG-17


title: R8_DG_18

description:
mRNA count data
AWO22587-0062-R8-DG-18


title: 263_PS_19

description:
mRNA count data
AWO22587-0057-263-PS-19


title: 265_PS_19

description:
mRNA count data
AWO22587-0051-265-PS-19


title: 182_VD_17

description:
mRNA count data
AWO22587-0065-182-VD-17


title: 190_PS_19

description:
mRNA count data
AWO22587-0056-190-PS-19


title: Y60_DG_18

description:
mRNA count data
AWO22587-0053-Y60-DG-18


title: 178_MH_19

description:
mRNA count data
AWO22587-0055-178-MH-19


title: 107_PS_19

description:
mRNA count data
AWO22587-0052-107-PS-19


title: 273_PS_19

description:
mRNA count data
AWO22587-0058-273-PS-19


title: 270_TA_20

description:
mRNA count data
AWO22587-0049-270-TA-20


title: 209_TA_20

description:
mRNA count data
AWO22587-0054-209-TA-20


title: 147_VD_17

description:
mRNA count data
AWO22587-0050-147-VD-17


title: 230_PS_19

description:
mRNA count data
AWO22587-0046-230-PS-19


title: 127_MH_19

description:
mRNA count data
AWO22587-0047-127-MH-19


title: 150_MH_19

description:
mRNA count data
AWO22587-0041-150-MH-19


title: 172_MH_19

description:
mRNA count data
AWO22587-0048-172-MH-19


title: 189_PS_19

description:
mRNA count data
AWO22587-0045-189-PS-19


title: 165_VD_17

description:
mRNA count data
AWO22587-0036-165-VD-17


title: 128_VD_17

description:
mRNA count data
AWO22587-0043-128-VD-17


title: 174_PS_19

description:
mRNA count data
AWO22587-0039-174-PS-19


title: 19_DG_17

description:
mRNA count data
AWO22587-0034-19-DG-17


title: 202_TA_20

description:
mRNA count data
AWO22587-0035-202-TA-20


title: W6_DG_18

description:
mRNA count data
AWO22587-0042-W6-DG-18


title: 152_PS_19

description:
mRNA count data
AWO22587-0040-152-PS-19


title: 106_MH_19

description:
mRNA count data
AWO22587-0044-106-MH-19


title: 180_VD_17

description:
mRNA count data
AWO22587-0032-180-VD-17


title: 276_TA_20

description:
mRNA count data
AWO22587-0038-276-TA-20


title: 138_VD_17

description:
mRNA count data
AWO22587-0037-138-VD-17


title: 273_TA_20

description:
mRNA count data
AWO22587-0031-273-TA-20


title: 146_MH_19

description:
mRNA count data
AWO22587-0030-146-MH-19


title: 261_TA_20

description:
mRNA count data
AWO22587-0029-261-TA-20


title: 114_MH_19

description:
mRNA count data
AWO22587-0025-114-MH-19


title: 134_MH_19

description:
mRNA count data
AWO22587-0033-134-MH-19


title: 205_TA_20

description:
mRNA count data
AWO22587-0024-205-TA-20


title: 232_PS_19

description:
mRNA count data
AWO22587-0027-232-PS-19


title: 121_VD_17

description:
mRNA count data
AWO22587-0026-121-VD-17


title: 278_PS_19

description:
mRNA count data
AWO22587-0022-278-PS-19


title: 178_VD_17

description:
mRNA count data
AWO22587-0023-178-VD-17


title: 129_VD_17

description:
mRNA count data
AWO22587-0020-129-VD-17


title: 143_VD_17

description:
mRNA count data
AWO22587-0017-143-VD-17


title: 292_PS_19

description:
mRNA count data
AWO22587-0019-292-PS-19


title: 154_VD_17

description:
mRNA count data
AWO22587-0018-154-VD-17


title: 152_VD_17

description:
mRNA count data
AWO22587-0021-152-VD-17


title: 107_MH_19

description:
mRNA count data
AWO22587-0028-107-MH-19


title: 266_TA_20

description:
mRNA count data
AWO22587-0009-266-TA-20


title: 70_DG_17

description:
mRNA count data
AWO22587-0010-70-DG-17


title: 195_PS_19

description:
mRNA count data
AWO22587-0014-195-PS-19


title: 136_VD_17

description:
mRNA count data
AWO22587-0011-136-VD-17


title: 101_MH_19

description:
mRNA count data
AWO22587-0016-101-MH-19


title: 244_TA_20

description:
mRNA count data
AWO22587-0012-244-TA-20


title: GM12878_HiCAR_rep3

status: Public on Feb 28 2022

first: Jianhong

last: Ou

state: Wisconsin

address: 330 N Orchard Street

institute: Morgridge Institute For Research

data_processing:
Reads were aligned to hg38 reference genome using bwa mem with flags -SP.
Alignments were parsed and paired end tags (PET) were generated using the pairtools
PET with low mapping quality (MAPQ < 10) were filtered out.
Uniquely mapped PET were then flipped as side1 with the lower genomic coordinate and aggregated into contact matrices in the cooler  format using the cooler tools
MAPS is used to call the significant chromatin interaction fro HiCAR library.
Genome_build: hg38
Supplementary_files_format_and_content: Chromatin interactions  identified by MAPS, provided in BEDPE formate.

organism: Homo sapiens

growth_protocol: WA01 were cultured in Matrigel (corning, 354230) coated plates with Stabilized feeder-free maintenance medium mTeSRTM Plus (STEMCELL, #05825). mTeSRTM Plus was changed every other day.  GM12878 cells were grown in suspension using RPMI 1640 with 15% FBS in T-75 flasks, cells were maintained between 200,000-800,000 cells/ml.

extract_protocol:
For crosslinking, cells were washed once by PBS, then treated by accutase (biolegend, #423201) for 10mins at 37°C. After removing the accutase, cells were resuspended by DMEM. Formaldehyde was added to the final concentration of 1%, incubated at room temperature for 10mins. Glycine was added to the final concentration of 0.2M, incubated at room temperature for 10 mins to quench formaldehyde.
HiCAR libraries were constructed following the method in the HiCAR manuascript.

treatment_protocol: For NPC induction, the transgenic WA01 were seeded onto Matrigel coated 24-well plates at 200k-400k cells per well. And cultured in STEMdiff™ SMADi Neural Induction media (Stemcell Catalog # 08581). Media was changed every day. Cells were harvested at the end of day 3.  For ME induction, the transgenic WA01 were seeded onto Matrigel coated at a density of around 1x104 cells/cm2 and cultured in differentiation media (E8 with 5ng/ml BMP4 and 25ng/ml Activin A). Media was changed every day. Cells were harvested at the end of day2.

tag: cell line


title: 111_PS_19

description:
mRNA count data
AWO22587-0015-111-PS-19


title: 72_VD_15

description:
mRNA count data
AWO22587-0007-72-VD-15


title: 55_VD_15

description:
mRNA count data
AWO22587-0004-55-VD-15


title: 207_TA_20

description:
mRNA count data
AWO22587-0013-207-TA-20


title: 6_VD_15

description:
mRNA count data
AWO22587-0005-6-VD-15


title: 101_VD_17

description:
mRNA count data
AWO22587-0008-101-VD-17


title: 68_VD_15

description:
mRNA count data
AWO22587-0006-68-VD-15


title: 40_VD_15

description:
mRNA count data
AWO22587-0003-40-VD-15


title: GM12878_HiCAR_rep4


title: 20_VD_15

description:
mRNA count data
AWO22587-0002-20-VD-15


title: GM12878_HiCAR_rep2

data_processing:
reads were aligned to hg38 reference genome using bwa mem with flags -SP.
Alignments were parsed and paired end tags (PET) were generated using the pairtools
PET with low mapping quality (MAPQ < 10) were filtered out. PET with the same coordinate on the genome or mapped to the same digestion fragment were removed.
Uniquely mapped PET were then flipped as side1 with the lower genomic coordinate and aggregated into contact matrices in the cooler  format using the cooler tools
MPAS is used to call the significant chromatin interaction.
Genome_build: hg38, mm10
Supplementary_files_format_and_content: Chromatin interactions  called by MAPS, provided in BEDPE formate. Raw_count for RNA-seq libraries generated by feature counts.

growth_protocol: WA01 were cultured in Matrigel (corning, 354230) coated plates with Stabilized feeder-free maintenance medium mTeSRTM Plus (STEMCELL, #05825). mTeSRTM Plus was changed every other day.  GM12878 cells were grown in suspension using RPMI 1640 with 15% FBS in T-75 flasks, cells were maintained between 200,000-800,000 cells/ml. mESCs  were cultured in KnockOut™ Serum Replacement with Leukemia Inhibitory Factor (LIF)

extract_protocol:
For crosslinking, cells were washed once by PBS, then treated by accutase (biolegend, #423201) for 10mins at 37°C. After removing the accutase, cells were resuspended by DMEM. Formaldehyde was added to the final concentration of 1%, incubated at room temperature for 10mins. Glycine was added to the final concentration of 0.2M, incubated at room temperature for 10 mins to quench formaldehyde.
HiCAR libraries were constructed following the method in the HiCAR manuascript. RNA libaraies were constructed following the SMART-seq2 protocol.
HiCAR


title: GM12878_HiCAR_rep1


title: 15_VD_15

description:
mRNA count data
AWO22587-0001-15-VD-15


title: hicar_rep1

data_processing:
Library strategy: HiCAR-seq
reads were aligned to hg38 reference genome using bwa mem with flags -SP.
Alignments were parsed and paired end tags (PET) were generated using the pairtools
PET with low mapping quality (MAPQ < 10) were filtered out. PET with the same coordinate on the genome or mapped to the same digestion fragment were removed.
Uniquely mapped PET were then flipped as side1 with the lower genomic coordinate and aggregated into contact matrices in the cooler  format using the cooler tools
MPAS is used to call the significant chromatin interaction.
Genome_build: hg38
Supplementary_files_format_and_content: Chromatin interactions  called by MAPS, provided in BEDPE formate. Raw_count for RNA-seq libraries generated by feature counts.

source_name: H1 hESC

growth_protocol: WA01 were cultured in Matrigel (corning, 354230) coated plates with Stabilized feeder-free maintenance medium mTeSRTM Plus (STEMCELL, #05825). mTeSRTM Plus was changed every other day.

extract_protocol:
For crosslinking, cells were washed once by PBS, then treated by accutase (biolegend, #423201) for 10mins at 37°C. After removing the accutase, cells were resuspended by DMEM. Formaldehyde was added to the final concentration of 1%, incubated at room temperature for 10mins. Glycine was added to the final concentration of 0.2M, incubated at room temperature for 10 mins to quench formaldehyde.
HiCAR libraries were constructed following the method in the HiCAR manuscript. RNA libraries were constructed following the SMART-seq2 protocol.

value: H1 hESC


title: CEN_Homo_Kidney_RNAseq_rep3

status: Public on Feb 25 2022

data_processing:
RNA-Seq reads were trimmed by Trim Galore (0.6.4, with -q 15) and then mapped with TopHat (v 2.1.1, with parameters --b2-very-sensitive --no-coverage-search and supplying the UCSC danRer10 refSeq gene annotation).
Gene-level read counts were obtained using the htseq-count (v1.6.1) by the reads with MAPQ greater than 30.
Genome_build: danRer10
Supplementary_files_format_and_content: raw counts of sequencing reads for the features of interest for RNAseq

organism: Danio rerio

source_name: Kidney

growth_protocol: Embryos are raised in 28℃ egg water until 5 dpf and then transferred to the aquarium system. Adult male fish between 4~12 month old were used in this study.

extract_protocol:
Whole kidney were snap freezed. Total RNA was extracted using TRI reagent (T9424, Sigma-Aldrich) and treated with DNase1 to degrade genomic DNA.  Samples were purified with Quick-RNA Miniprep kit (R1054, Zymo Research).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: animals were incubated in 0.5~0.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction.

tag: strain

value: EK

tag: tissue

value: Kidney

value: CEN homozygous knockout

value: cardiomyocyte ablation


title: hicar_rep3


title: CEN_Homo_Kidney_RNAseq_rep1


title: hicar_rep2


title: CEN_WT_Kidney_RNAseq_rep2

value: Wild type


title: cebpd_WT_Kidney_RNAseq_rep3


title: CEN_Homo_Kidney_RNAseq_rep2


title: cebpd_Homo_Kidney_RNAseq_rep2

value: cebpd homozygous knockout


title: CEN_WT_Kidney_RNAseq_rep3


title: cebpd_Homo_Kidney_RNAseq_rep3


title: CEN_WT_Kidney_RNAseq_rep1


title: Homo_Brain_RNAseq_rep1

data_processing:
RNA-Seq reads were trimmed by Trim Galore (0.6.4, with -q 15) and then mapped with TopHat (v 2.1.1, with parameters --b2-very-sensitive --no-coverage-search and supplying the UCSC danRer10 refSeq gene annotation).
Gene-level read counts were obtained using the htseq-count (v1.6.1) by the reads with MAPQ greater than 30.
ATAC-Seq reads were trimmed by Trim Galore (0.4.1, with -q 15) and then mapped with bowtie2(2.2.5, with parameters --very-sensitive) to zebrafish genome (UCSC danRer10 refSeq annotation).
The mapped reads were filtered by MAPQ greater than 30 by samtools (v 1.5) and duplicated reads were removed by picard (v 1.91). Bigwig files were generated by kentUtils.
Genome_build: danRer10
Supplementary_files_format_and_content: raw counts of sequencing reads for the features of interest for RNAseq; bigwig files were generated using kentUtils by converting the output of macs2 bedgraph

extract_protocol:
Brain and whole kidney were snap freezed. Total RNA was extracted using TRI reagent (T9424, Sigma-Aldrich) and treated with DNase1 to degrade genomic DNA.  Samples were purified with Quick-RNA Miniprep kit (R1054, Zymo Research). Brain and WKM nuclei were isolated through douncer homogenization or vigorous pipette respectively. 100,000 cells/nuclei were used for library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols; ATAC library preparation was performed as described in (Buenrostro et al., 2013).

treatment_protocol: animals were incubated in 0.5~0.7uM tamoxifen for 17 h and then released from tamoxifen treatment. Tissues were collected at 7day post incubation for RNA extraction and nuclei isolation.

value: Brain


title: Homo_Brain_RNAseq_rep2


title: Homo_Brain_RNAseq_rep3


title: WT_Brain_RNAseq_rep3


title: cebpd_WT_Kidney_RNAseq_rep2


title: cebpd_Homo_Kidney_RNAseq_rep1


title: WKM_RNAseq_uninjured_rep1

source_name: Whole kidney marrow

value: Whole kidney marrow

value: uninjured


title: WT_Brain_RNAseq_rep1


title: WKM_ATACseq_uninjured_rep1


title: WT_Brain_RNAseq_rep2


title: WKM_ATACseq_regeneration_rep3


title: WKM_ATACseq_uninjured_rep2


title: WKM_RNAseq_regeneration_rep2


title: cebpd_WT_Kidney_RNAseq_rep1


title: WKM_RNAseq_uninjured_rep2


title: Brain_RNAseq_regeneration_rep2


title: WKM_ATACseq_regeneration_rep1


title: WKM_ATACseq_uninjured_rep3


title: WKM_RNAseq_regeneration_rep1


title: WKM_ATACseq_regeneration_rep2


title: Brain_RNAseq_uninjured_rep1


title: Brain_RNAseq_uninjured_rep2


title: Brain_ATACseq_uninjured_rep2


title: Brain_RNAseq_regeneration_rep1


title: Brain_ATACseq_uninjured_rep1


title: Brain_ATACseq_regeneration_rep1


title: Brain_ATACseq_regeneration_rep2


title: 295-2019_S57

status: Public on Dec 13 2021

description: Sex: S

data_processing:
Illumina RTA v3 software was used for basecalling.
Read quality was assessed in FastQC v0.11.9
Read trimming was performed with Trimmomatic v0.39 with parameters for a 4-base pair sliding window and removing read segments below a minimum base quality score of 20 and a read length of less than 36 bases
Read mapping and indexing was performed with HISAT2 v2.1.1, using the bovine whole genome assembly ARS-UCD1.2; parameters -p 8 --dta -x GCF_002263795.1_ARS-UCD1.2_genomic
Read assembly and quantification was performed with StringTie v2.1.2 with parameters -p 8 -G ref_ARS-UCD1.2, followed by ./stringtie --merge -p 8 -G ref_ARS-UCD1.2, and /stringtie -e -p 8 -G stringtie_merge.gtf -o. A read count matrix was generated with prepDE.py with parameters python2.7 ./prepDE.py  -l 150 -i mergelist.txt. Differential expression analysis was performed with edgeR v3.30.3.
Genome_build: GCF_002263795.1
Supplementary_files_format_and_content: tab-delimited text file of gene counts for each sample

molecule: polyA RNA

extract_protocol:
RNA purification and extraction was performed with the Tempus Spin RNA Isolation kit (Applied Biosystems), per product instructions. RNA concentration and quality was measured with an Agilent 2100 (Agilent).
Library construction was performed with the TruSeq RNA Sample Library Kit (Illumina). 150bp paired-end sequencing was performed with an Illumina Novaseq 6000 (v1.7; S4 reagent kit v1.5) in one lane (~50M reads/sample).

treatment_protocol: All blood samples were collected in Tempus blood tubes (Applied Biosystem). Samples were stored per product recommendation.

tag: arrival weight (lbs)

tag: times treated

tag: disease severity cohort

value: Healthy


title: 248-2019_S48

description: Sex: S

value: Treated Once


title: 287-2019_S56

description: Sex: S


title: 285-2019_S55

description: Sex: S


title: 272-2019_S53

description: Sex: S


title: 255-2019_S51

description: Sex: S


title: 252-2019_S49

description: Sex: S

value: Treated Twice or Died


title: 212-2019_S46

description: Sex: S


title: 210-2019_S44

description: Sex: S


title: 266-2019_S52

description: Sex: S


title: 274-2019_S54

description: Sex: S


title: 254-2019_S50

description: Sex: S


title: 205-2019_S43

description: Sex: S


title: 211-2019_S45

description: Sex: S


title: 197-2019_S42

description: Sex: S


title: 194-2019_S41

description: Sex: S


title: 246-2019_S47

description: Sex: S


title: 199-2017_S33

description: Sex: B


title: 195-2017_S32

description: Sex: B


title: 181-2017_S29

description: Sex: B


title: 167-2017_S25

description: Sex: B


title: 168-2017_S26

description: Sex: S


title: 177-2017_S28

description: Sex: B


title: 175-2019_S40

description: Sex: S


title: 187-2017_S31

description: Sex: B


title: 169-2017_S27

description: Sex: B


title: 160-2017_S23

description: Sex: B


title: 158-2017_S22

description: Sex: B


title: 166-2019_S39

description: Sex: S


title: 123-2017_S15

description: Sex: B


title: 133-2017_S18

description: Sex: B


title: 156-2017_S21

description: Sex: B


title: 125-2017_S16

description: Sex: B


title: 130-2017_S17

description: Sex: B


title: 155-2017_S20

description: Sex: B


title: 155-2019_S38

description: Sex: S


title: 119-2017_S14

description: Sex: B


title: 109-2017_S12

description: Sex: B


title: 113-2019_S34

description: Sex: S


title: 118-2019_S35

description: Sex: S


title: 115-2017_S13

description: Sex: S


title: 139-2017_S19

description: Sex: S


title: 105-2017_S11

description: Sex: B


title: 185-2017_S30

description: Sex: B


title: Nelfb-WT_rep1

status: Public on Mar 18 2021

data_processing:
Reads aligned with STAR 2.6.0a
featureCounts -s2 v1.6.1 was used for summarization of counts
DESeq2 v1.26.0 was used for Differential expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: FeatureCount Table

source_name: Muscle satellite cells

growth_protocol: Myoblasts were harvested from muscle 5-days post injury and immediately purified by FACS (TdTomato+, Alpha-integrin 7+). Myoblasts were kept on ice when possible.

extract_protocol:
Total RNA was isolated using a total RNA isolation kit (ThermoFisher cat. No. 12183020) on FACS-purified myoblasts (TdT+, AI7+) derived from regenerating skeletal muscle 5 days post-injury.
Total RNA (approx. 430 ng per sample) underwent rRNA depletion with a Ribo-Zero Magnetic Gold Kit (Human/Mouse/Rat) (Illumina cat. No. MRZG12324). RNA library preparation proceeded with a KAPA stranded RNA-seq kit (roche 07962169001-KAPA KK8401). Fragmentation/1st strand / 2nd strand end-repair and A-tailing steps proceeded, followed with ligation to  Illumina TruSeq LT Indexes (Illumina FC-121-2001 / FC-121-2002) followed by 8 cycles of PCR enrichment.

treatment_protocol: Mice were induced with tamoxifen, then skeletal muscle damage induced with an acute intramuscular cardiotoxin injection.

value: Skeletal Muscle

value: Myogenic progenitor (TdT+, ITGA7+)

tag: developmental stage

value: Adult

value: WT


title: 104-2017_S10

description: Sex: B

value: Whole blood


title: Uninjured RNAseq rep1

status: Public on Apr 14 2021

data_processing:
Sequenced reads were trimmed for adaptor sequence TrimGalore (v.0.6.4), then mapped to danRer10 whole genome using STAR (v2.6.1d) with default setting
Read counts for each gene provied in the reference s3://ngi-igenomes/igenomes//Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.gtf were prepared by subread::featureCounts (v1.6.4)
Genome_build: danRer10
Supplementary_files_format_and_content: text file with raw reads counts by featureCounts v1.6.4

source_name: adult heart ventricles

growth_protocol: Adult zebrafish were raised using standard practice.

extract_protocol:
toRNA was extracted using Trizol and standard purification measures
Libraries were constrcuted using the Illumina Tru-Seq mRNA cloning kit

treatment_protocol: Fish were incubated overnight in 5uM tamoxifen (18 hrs).

tag: creer

value: negative


title: Nelfb-KO_rep3

value: Nelfb-KO


title: Nelfb-WT_rep3


title: Nelfb-WT_rep2


title: KO2-S5

data_processing:
Library strategy: CUT&Tag
Nextera adapters were trimmed from sequenced reads with Cutadapt 2.6 (Python 3.7.4);
Trimmed sequences were aligned to mm10 using Bowtie2 version 2.3.4.1 with the following parameters: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700;
Trimmed sequences were aligned to spike-in DNA (Amp - pBluescript II SK(+)) using Bowtie2 version 2.3.4.1 with the following parameters: --very-sensitive ;
Duplicates, non-uniquely aligned reads were filtered from BAMs using Samtools v1.10 (htslib 1.10). Retained mapped and properly paired reads.
Spike-in normalized genome coverage was calculated using bamCoverage v3.3.2 (Deeptools v3.3.2)
Genome_build: mm10

source_name: Muscle Satellite cells

growth_protocol: Myoblasts were cultured in vitro on Matrigel-coated tissue culture sterile dish during progenitor expansion and 4-hydroxy-tamoxifen induction. Myoblasts were maintianed at low confluence throughout in vitro culturing, to avoid cell-cell contacts.

extract_protocol:
Whole cells were bound to concanavalin A beads and permeablized with 0.1% digitonin for faclitating antibody binding. Protein-A tagged Tn5 was added for targeted Clevage and Tagmentation.
Libraries were prepared as recommended in the CUT & Tag protocol by using 21 µl DNA of purified DNA and 2 µl each of uniquely barcoded i5 and i7 universal primers. Libraries were amplified using NEBNext® High-Fidelity 2X PCR Master Mix  (M0541L). Conditions for PCR amplifcation were followed as recommended in the protocol.

treatment_protocol: Ex vivo knockout was induced using 4-hydroxy-tamoxifen, supplemented in growth medium for 72 hours.

value: NELF-BscKO (KO)

value: Myoblasts from Satellite cells

tag: antibody

value: Phospho-Rpb1 CTD (Ser5) (D9N5I) Rabbit mAb #13523 (Cell Sig.Tech Sampler Kit Cat # 54020)


title: 7dpt Nrg1 RNAseq rep2

value: positive


title: Uninjured RNAseq rep2


title: 162-2017_S24

description: Sex: S


title: Wt1-IgG

tag: genotype

value: Wildtype (WT)


title: Nelfb-KO_rep1


title: KO1-IgG


title: Nelfb-KO_rep2


title: KO2-IgG


title: Wt1-S5


title: ED-Ko1-nE

data_processing:
Library strategy: CUT&Tag
Nextera adapters were trimmed from sequenced reads with Cutadapt 2.6 (Python 3.7.4);
Trimmed sequences were aligned to mm10 using Bowtie2 version 2.3.4.1 with the following parameters: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700;
Trimmed sequences were aligned to spike-in DNA (U00096.3) using Bowtie2 version 2.3.4.1 with the following parameters: --end-to-end --very-sensitive --no-overlap --no-dovetail --no-mixed --no-discordant --phred33 -I 10 -X 700;
Duplicates, non-uniquely aligned reads were filtered from BAMs using Samtools v1.10 (htslib 1.10). Retained mapped and properly paired reads.
Spike-in normalized genome coverage was calculated using bamCoverage v3.3.2 (Deeptools v3.3.2)
Genome_build: mm10
Supplementary_files_format_and_content: Normalized genome coverage bigWig for every sample

value: NelfE(Proteintech, Cat#10705-1-AP) + NelfE(F-9) (Santacruz, Cat#SC - 377052) (Mixed 1:1 (Concentration)


title: EC-Wt3-nE


title: KO1-S5


title: Wt2-IgG


title: EI-K4me3-Wt

value: H3K4me3(EMD Millipore Cat No. 07-473)


title: 134-2019_S37

description: Sex: S

value: Healthy


title: EF-Ko3-nE


title: EE-Ko2-nE


title: 7dpt Nrg1 RNAseq rep1


title: DR-JF-Ott_KO1

data_processing:
Reads aligned with STAR 2.6.0a
featureCounts -s2 v1.6.1 was used for summarization of counts
DESeq2 v1.26.0 was used for Differential expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: tabluar format with DESeq2 output

source_name: FACS-sorted myogenic progenitor cells from hindlimb skeletal muscle

growth_protocol: Hindlimb skeletal muscle was damaged with cardiotoxin, and provided a 48-hour in vivo recovery period. Skeletal muscle was isolated, mechanically and enzymatically digested, and myogenic progenitor cells FACS-sorted based on TdTomato expression (endogenous expression to all Pax7-expressing adult tissues), and Alpha-Integrin 7 expression. Purified myogenic progenitors  immediately  underwent RNA extraction. At all steps, myogenic progenitors were stored on ice.

extract_protocol:
Total RNA was isolated using a total RNA isolation kit (ThermoFisher cat. No. 12183020) on FACS-purified myogenic progenitor cells (TdT+, AI7+) at the specified timepoint
Total RNA (approx. 350 ng per sample) underwent rRNA depletion with a Ribo-Zero Magnetic Gold Kit (Human/Mouse/Rat) (Illumina cat. No. MRZG12324). RNA library preparation proceeded with a KAPA stranded RNA-seq kit (roche 07962169001-KAPA KK8401). Fragmentation/1st strand / 2nd strand end-repair and A-tailing steps proceeded, followed with ligation to  Illumina TruSeq LT Indexes (Illumina FC-121-2001 / FC-121-2002) followed by 8 cycles of PCR enrichment.

treatment_protocol: Skeletal muscle from the hindlimbs was damaged in vivo with cardiotoxin

value: Skeletal muscle (hindlimbs)

value: Myogenic progenitor cells

tag: treatment

value: Cardiotoxin


title: DR-JF-Ott_KO3

tag: cell type


title: Wt2-S5


title: DR-JF-Ott_WT2


title: 121-2019_S36

description: Sex: S


title: DR-JF-Ott_WT3


title: Nelfb-WT_A

data_processing:
cellranger mkfastq  v2.1.1; performed on 10X Cell ranger pipeline
cellranger count v2.1.1
Genome_build: mm10
Supplementary_files_format_and_content: .mtx, .tsv: Processed contains single-cell gene expression matrix

growth_protocol: Myoblasts were harvested from muscle 72h post injury and immediately purified by FACS (TdTomato+, Alpha-integrin 7+). Myoblasts were kept on ice when possible.

extract_protocol:
Myoblasts were prepared for single-cell RNA-sequencing using a 10 X genomics Chromium Single Cell 3' Reagent kit (cat. No. pn-1000075), according to the manufacturer protocol
Sequencing library were constructed using the 10 X genomics Chromium Single cell 3'v2.2 and 3'v3 Reagent kit (cat. No. pn-1000075), according to the manufacturer protocol

treatment_protocol: Mice were induced with tamoxifen, then skeletal muscle damage through acute intramuscular cardiotoxin injection.

tag: tissue type

value: Skeletal Muscle

value: Myogenic progenitor (TdT+, ITGA7+)


title: Nelfb-WT_1

value: WT


title: DR-JF-Ott_WT1


title: EB-Wt2-nE


title: EJ-K4me3-Ko


title: Nelfb-KO_3


title: Nelfb-WT_B


title: DR-JF-Ott_KO2


title: EA-Wt1-nE


title: Ctrl-Pan-PolII

data_processing:
Mapping: Satellite cells/Myoblasts
PeakCalling: Uniquely mapped reads were used for peak calling using MACS2
Visualization: Mapped reads were converted to bigWigs with RPKM normalization
Peak calls were converted to bigBed files
Genome_build: MM10
Supplementary_files_format_and_content: narrowPeak [peak information, location]

source_name: Satellite cells/Myoblasts

growth_protocol: Satellite cells isolated from mice muscle tissue were cultured in F10 media with 20% BGS and bFGF (2.5 ng/ml)

extract_protocol:
Cells were fixed with 1% formaldehyde for 20 min and quenched for 10 min in 125 mM glycine. Cells were sonicated in 1% SDS containing sonication buffer for extracting sonicated chromatin
Library was constructed using KAPA HyperPrep Kit (Roche 07962363001-KAPA KK8504 ). End Repair/A-tailing step then ligation of IDT for Illumina TruSeq UD Indexes (Illumina-20022370) followed by dual SPRI size selection Left  1.0 - 0.52 Right and 11 cycles of PCR enrichment.

treatment_protocol: Satellite cells were treated with 4-OHT for 72 hrs for CreERT2 activation. Before proceeding for experiment cells were cultured in 4-OHT free media for 24 hrs

tag: chip antibody

value: Pan-PolII (Millipore Cat.No.05-623)

value: Satellite cells


title: Ctrl-PolII-S5

value: PolII-S5 (Abcam Cat.No.ab5131)


title: high Erk activity; rep3

status: Public on Sep 23 2020

data_processing:
Reads were trimmed by Trim Galore (0.4.1, with -q 15 --paired) and then mapped with TopHat (v 2.1.1, with parameters --b2-very-sensitive --no-coverage-search and supplying the UCSC danRer10 refSeq annotation).
Gene-level read counts were obtained using the featureCounts (v1.6.1) by the reads with MAPQ greater than 30
Genome_build: danRer10
Supplementary_files_format_and_content: raw counts of sequencing reads for the features of interest for RNAseq

source_name: high Erk activity

growth_protocol: Scale regeneration was induced by plucking about 50 scales, in three rows, from each side of osx:H2A-mCherry osx:Venus-hGeminin fish. At 4 days post plucking (dpp), all regenerating scales were plucked  and collected in PBS on ice. About 3-5 fish were used per sample. Tissue was pelleted by centrifugation (5 min at 600g) and resuspended in 600 µl of 13U/ml Liberase (DH-Research Grade - Sigma #5401054001) in HBSS (Gibso #14025-092) and incubated at 37 C for 1 h. Every 15 min, 500 µl of supernatant was removed, quenched with 65µl sheep serum (Sigma S2263) on ice, and 500 µl of fresh Liberase was added to the primary tube. All collected supernatant was filtered using 50 µl filters (Corning #431750), pelleted (5 min at 600 g) and resuspended in 1 ml DMEM + 1% BSA (UltraPure - Invitrogen AM2616).  Before sorting, 1 µg/ml DAPI (Sigma D9542) was added to the tube.

extract_protocol:
RNA was extracted using TriReagent followed by RNAeasy microKit (Qiagen #74004)
Library preparation was performed by BGI Genomics (Low Input Library Preparation – BT01)

treatment_protocol: Cells were analyzed and sorted using a SH800S Sony Cell Sorter using a 100 µm disposable chip. Initially, events were gated using Forward versus Side Scatter Areas (488 nm laser). Then, single cells were enriched by gating Forward Scatter Height versus Forward Scatter Area (488 nm excitation laser). Live cells were enriched by selecting a population with low DAPI emission (405 nm excitation laser). Finally, H2A-mCherry+ Venus-hGeminin- and H2A-mCherry+ Venus-hGeminin+ were sorted by gating Venus-hGeminin (488 nm excitation laser) versus mCherry (561 nm excitation laser). Cells were collected in PBS or TriReagent (Sigma T9424)

tag: fluorescence

value: osx:H2A-mCherry+ osx:Venus-hGeminin+

value: osteoblasts of regenerating zebrafish scales


title: high Erk activity; rep2


title: Nelfb-KO_B

value: Nelfb-KO


title: high Erk activity; rep1


title: Ventricles, uninj_p53_pos.rep3

status: Public on Sep 21 2020

data_processing:
RNA-Seq reads were trimmed by Trim Galore (0.6.4, with -q 15) and then mapped with TopHat (v 2.1.1, with parameters --b2-very-sensitive --no-coverage-search and supplying the UCSC danRer10 refSeq gene annotation).
Gene-level read counts were obtained using the htseq-count (v1.6.1) by the reads with MAPQ greater than 30.
Genome_build: danRer10
Supplementary_files_format_and_content: raw counts of sequencing reads for the features of interest

source_name: Ventricles of uninjured Tg(tpWT) zebrafish

growth_protocol: Fish were grown at 28 degrees.  Male and female animals between 6 and 12 months and of ~2 cm in length were used.

extract_protocol:
Zebrafish ventricles were collected and placed in cold PBS while still pumping to help decrease intra-ventricular blood. Atrium and outflow tract were removed and ventricles (5 per sample) were homogenized in Trizol using a Tissue Lyser II (QIAGEN). RNA was extracted using the standard Trizol protocol, genomic DNA removed using RNA clean and Concentrator Kit (Zymo Research) and processed for libraries preparation.
Libraries were constructed by single-end 50-bp sequencing, with 30 M reads/sample was performed at BGI. RNA-Seq reads were trimmed by Trim Galore (0.6.4, with -q 15) and then mapped with TopHat (v 2.1.1, with parameters --b2-very-sensitive --no-coverage-search and supplying the UCSC danRer10 refSeq gene annotation). Gene-level read counts were obtained using the htseq-count (v1.6.1) by the reads with MAPQ greater than 30. DESeq2 (v 1.26.0) was employed for differential expression analysis.

treatment_protocol: Fish were treated ~ 17 hours  with 0.5 μM tamoxifen to ablate cardiomyocytes. Control fish were equally treated.

value: EK /AB strain

value: ~ 17 hours treatment with 0.5 μM tamoxifen

value: Ventricles


title: low Erk activity; rep1

source_name: low Erk activity

value: osx:H2A-mCherry+ osx:Venus-hGeminin-


title: Ventricles, uninj_p53_pos.rep1


title: Ventricles, uninj_p53_neg.rep1

source_name: Ventricles of uninjured Tg(tp53M214K) zebrafish


title: Ventricles, inj_p53_pos.rep1

source_name: Ventricles of  Tg(Cmlc2:CreER; β-actin2:loxp-mCherry-STOP-loxp-DTA) zebrafish 7 days after tamoxifen-induced genetic ablation of cardiomyocytes


title: low Erk activity; rep3


title: low Erk activity; rep2


title: Ventricles, uninj_p53_pos.rep2


title: Ventricles, inj_p53_pos.rep3


title: ex0063_SCC034_72

status: Public on Aug 21 2020

city: Oxford

first: chao

last: jiang

address: Botnar Research Centre

department: NDORMS

country: United Kingdom

institute: University of Oxford

data_processing:
basecalling with bcl2fastq v2.17.1.14
QC with fastQC v0.11.3
mapping with hisat 2.0.5
quantification with featureCounts 1.5.0
differential gene expression with deseq2 1.16.1
Genome_build: hg38
Supplementary_files_format_and_content: txt file generated from featureCounts

source_name: BM-MSC

growth_protocol: 50,000 cells were seeded in 6-well plates in maintenance medium: MesenPRO-RS™ (Thermo Fisher Scientific, Massachusetts, USA)

extract_protocol:
total RNA was isolated using TRIzol with the Direct-zol RNA kit (ZymoResearch, USA)
RNA-seq library preparation was carried out using the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, USA)

treatment_protocol: After 3 days, medium was replaced with osteogenic differentiation medium: DMEM high glucose supplemented with 10% FBS, 1x non-essential amino acids (NEAA), 2mM L-glutamine, 0.28mM ascorbic (Sigma-Aldrich, USA) acid, 10 mM β glycerophosphate, and 10 nM dexamethasone

tag: gender

value: M

tag: age

tag: hours after osteogenic media added

tag: passage


title: Ventricles, uninj_p53_neg.rep3

tag: strain

tag: tissue


title: Ventricles, inj_p53_neg.rep2

source_name: Ventricles of  Tg(Cmlc2:CreER; β-actin2:loxp-mCherry-STOP-loxp-DTA; tp53M214K) zebrafish 7 days after tamoxifen-induced genetic ablation of cardiomyocytes


title: Ventricles, inj_p53_neg.rep1


title: Ventricles, inj_p53_pos.rep2


title: ex0063_SCC034_168


title: ex0063_SCC034_12


title: ex0063_SCC034_504


title: Ventricles, inj_p53_neg.rep3


title: ex0063_SCC034_336


title: ex0063_SCC034_16


title: Ventricles, uninj_p53_neg.rep2


title: ex0063_SCC034_48


title: ex0063_SCC034_120


title: ex0063_SCC034_24


title: ex0063_SCC034_96


title: ex0063_SCC034_2


title: ex0063_SCC034_4


title: ex0063_SCC034_1


title: ex0063_SCC034_0.5


title: ex0072_0208_24

value: F


title: ex0072_0208_1


title: ex0072_0208_72


title: ex0072_0208_6


title: ex0072_1309_72


title: ex0063_SCC034_8


title: ex0063_SCC034_0


title: ex0072_1309_6


title: ex0004_28386_504


title: ex0072_0208_0


title: ex0072_1309_1


title: ex0072_0208_2


title: ex0072_1309_24


title: ex0072_0208_168


title: ex0004_28386_72


title: ex0004_28386_336


title: ex0072_1309_0


title: ex0004_28386_24


title: ex0004_28386_8


title: ex0004_28386_2


title: ex0004_28386_12


title: ex0004_28386_16


title: ex0004_28386_168


title: ex0004_28386_6


title: ex0004_28386_0


title: ex0072_1309_2


title: RNAseq; LEN deletion; 0dpa; uninjured; batch 3; rep1

status: Public on Jul 19 2020

source_name: whole fin

growth_protocol: D. rerio from the outbred Ekkwill (EK) strain ranging from 4 to 12 months were used for whole fin library preparations, Tg(tph1b:mCherry-NTR;ubi:switch) fish were used for fibroblast library preparation (Tornini et al 2016). Water temperature was maintained at 27.5°C, and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2-phenoxyethanol (Sigma-Aldrich) in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.

extract_protocol:
For RNA-seq, biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa, 1 dpa, or 4 dpa time points via razor blade (VWR) from 15 fish aged between 3-12 months. Fin tissue was collected in Tri-Reagent (Sigma) and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit-5 (Zymo).
RNA-seq libraries were prepared using a Stranded mRNA-seq Kit (KAPA).

treatment_protocol: For fibroblast libraries, triplicate Tg(tph1b:creER;ubi:switch) caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen (Sigma-Aldritch) (Tornini et al., 2016). Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool.

tag: date

value: 0 dpa

value: whole fin


title: RNAseq; whole fin; 2dpa; injured; batch 3; rep1

value: 2 dpa


title: ex0004_28386_0.5


title: ex0004_28386_1


title: ATACseq; Fibroblast; 4dpa; injured; batch 3; rep3

source_name: ATACseq; Fibroblast; 4dpi; injured

growth_protocol: D. rerio from the outbred Ekkwill (EK) strain ranging from 4 to 12 months were used for whole fin library preparations, Tg(tph1b:mCherry-NTR;ubi:switch) fish were used for fibroblast library preparation (Tornini et al 2016), and homozygous evx1 knockout fish were used for evx1 libraries (Schulte et al 2011). Water temperature was maintained at 27.5°C, and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2-phenoxyethanol (Sigma-Aldrich) in fish water. Work with D. rerio was performed in accordance with Duke University guidelines.

extract_protocol:
For RNA-seq, biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa, 1 dpa, or 4 dpa time points via razor blade (VWR) from 15 fish aged between 3-12 months. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri-Reagent (Sigma) and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit-5 (Zymo).
For ATAC-seq libraries, biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa, 1 dpa, or 4 dpa time points via razor blade (VWR) from 15 fish aged 3-12 months. Homozygous Evx1 knockout fish (screened visually by jointless phenotype) (Borday et al., 2001) were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH (Roche) in Hank’s Balanced Salt Solution (Gibco) stirring at 37°C for 2 hours, collected in 15 minute increments, then strained through a 70 μm nylon cell strainer (Corning). Samples were quantitated for 100K live cells using the Countess Automated Cell Counter (Thermo Fisher Scientific).Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B-C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter.
RNA-seq libraries were prepared using a Stranded mRNA-seq Kit (KAPA).
ATAC-seq library preparation was performed as detailed in (Buenrostro et al., 2013).

tag: time

value: 4 dpa

value: fibroblast

value: wild type


title: RNAseq; LEN deletion; 2dpa; injured; batch 3; rep1


title: ATACseq; Fibroblast; 4dpa; injured; batch 3; rep2


title: ATACseq; whole fin; 1dpa; injured; batch 2; rep3

source_name: ATACseq; whole fin; 1dpi; injured


title: ATACseq; whole fin; 0dpa; uninjured; batch 2; rep3

source_name: ATACseq; whole fin; 0dpi; uninjured


title: ATACseq; whole fin; 0dpa; uninjured; batch 2; rep2


title: RNAseq; whole fin; 0dpa; uninjured; batch 3; rep1


title: ATACseq; whole fin; 1dpa; injured; batch 2; rep2


title: ATACseq; Fibroblast; 0dpa; uninjured; batch 3; rep1

source_name: ATACseq; Fibroblast; 0dpi; uninjured


title: ATACseq; whole fin; 0dpa; uninjured; batch 1; rep3


title: ex0072_1309_168


title: ATACseq; Fibroblast; 0dpa; uninjured; batch 3; rep2


title: ATACseq; whole fin; 0dpa; uninjured; batch 1; rep1


title: ATACseq; Fibroblast; 0dpa; uninjured; batch 3; rep3


title: ATACseq; whole fin; 0dpa; uninjured; batch 2; rep1


title: ATACseq; Fibroblast; 4dpa; injured; batch 3; rep1


title: ATACseq; whole fin; 1dpa; injured; batch 2; rep1


title: ATACseq; whole fin; 4dpa; injured; batch 1; rep3

source_name: ATACseq; whole fin; 4dpi; injured


title: ATACseq; whole fin; 4dpa; injured; batch 1; rep1


title: ATACseq; whole fin; 0dpa; uninjured; batch 1; rep2


title: RNAseq; Fibroblast; 0dpa; uninjured; batch 3; rep2

source_name: RNAseq; Fibroblast; 0dpi; uninjured


title: RNAseq; Fibroblast; 4dpa; injured; batch 3; rep1

source_name: RNAseq; Fibroblast; 4dpi; injured


title: RNAseq; Fibroblast; 0dpa; uninjured; batch 3; rep1


title: RNAseq; whole fin; 1dpa; injured; batch 2; rep2

source_name: RNAseq; whole fin; 1dpi; injured

value: 1 dpa


title: RNAseq; whole fin; 1dpa; injured; batch 2; rep1


title: ATACseq; whole fin; 4dpa; injured; batch 1; rep2


title: RNAseq; Fibroblast; 4dpa; injured; batch 3; rep2


title: RNAseq; whole fin; 1dpa; injured; batch 2; rep3


title: RNAseq; whole fin; 0dpa; uninjured; batch 2; rep3

source_name: RNAseq; whole fin; 0dpi; uninjured


title: RNAseq; whole fin; 0dpa; uninjured; batch 1; rep2


title: RNAseq; whole fin; 4dpa; injured; batch 1; rep2

source_name: RNAseq; whole fin; 4dpi; injured


title: RNAseq; whole fin; 0dpa; uninjured; batch 1; rep1


title: RNAseq; whole fin; 4dpa; injured; batch 1; rep1


title: RNAseq; whole fin; 0dpa; uninjured; batch 2; rep2


title: TCF4-wt-3

status: Public on Jul 01 2020

city: Amsterdam

first: Marten

middle: Piet

last: Smidt

state: NH

address: Sciencepark 904

department: SILS

country: Netherlands

institute: UVA

data_processing:
adapter trimming and quality filtering
aligments (tophat 1.0.14/Bowtie 2.1.0)
mRNAseq readcounting (Htseq-count 0.6.1p1)
differential expression analysis WT vs Mut
Deseq 1.10.1 (R) for selection of differential expressed genes (137)
Genome_build: Mus musculus (GRCm38p4 Fasta and GFT format)
Supplementary_files_format_and_content: txt file, DESeq significant differential genes

source_name: Cortical dissected material E14.5

extract_protocol:
Dissected cortical material dfrom E14.5 mouse embryo’s, total RNA extraction (trizol)
RNAseq library construction from Total RNA samples (1-6) (Illumina “preparing samples for sequencing of mRNA” Rev. A ,September 2008)

treatment_protocol: WT vs KO

tag: sample type

value: neuronal material

tag: genotype/variation


title: TCF4-ko-3


title: TCF4-wt-1


title: TCF4-wt-2


title: TCF4-ko-2


title: BRD 6 [S_85]

status: Public on Jan 14 2020

data_processing:
Illumina RTA v2 software was used for base calling.
Read quality was assessed in FastQC v0.11.8
Read trimming was performed with Trimmomatic v0.38 with parameters ILLUMINACLIP:TruSeq2-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Read mapping and indexing was performed with HISAT2 v2.1.0, using the bovine whole genome assembly ARS-UCD1.2; parameters -p 8 --dta -x GCF_002263795.1_ARS-UCD1.2_genomic
Read assembly and quantification was performed with StringTie v1.3.4 with parameters -p 8 -G ref_ARS-UCD1.2_top_level, followed by ./stringtie --merge -p 8 -G ref_ARS-UCD1.2_top_level, and /stringtie -e -p 8 -G stringtie_merge.gtf -o. A read count matrix was generated with prepDE.py with parameters python2.7 ./prepDE.py -i mergelist.txt. Differential expression analysis was performed with edgeR v3.24.3 and DESeq2 v1.22.2.
Genome_build: GCF_002263795.1
Supplementary_files_format_and_content: tab-delimited text file of gene counts for each sample

source_name: BRD_whole blood

extract_protocol:
RNA purification and extraction was performed with the Tempus Spin RNA Isolation kit (Applied Biosystems), per product instructions. RNA concentration and quality was measured with an Agilent 2100 (Agilent).
Paired end libraries were prepared using the TruSeq stranded mRNA kit. All samples were generated in 2 x 150 base pair lengths, in 2 lanes, at 80 million reads per sample.

tag: arrival weight (lbs.)

tag: disease status

value: bovine respiratory disease (BRD)

value: whole blood


title: TCF4-ko-1


title: Healthy 6 [S_72]

source_name: healthy_whole blood

value: healthy


title: BRD 4 [S_75]


title: Healthy 3 [S_12]


title: Healthy 1 [S_5]


title: BRD 5 [S_76]


title: Healthy 2 [S_6]


title: RNAseq; whole fin; 0dpa; uninjured; batch 2; rep1

tag: genotype


title: BRD 2 [S_51]


title: BRD 1 [S_33]


title: Healthy 5 [S_55]


title: Healthy 4 [S_28]


title: BRD 3 [S_52]


title: D2 Foxp1CTL + ControlAAV #1 (WPRE)

status: Public on Feb 20 2024

city: Los Angeles

first: Genevieve

last: Konopka

state: CA

address: 650 Charles Young Drive South, 73-214 CHS

department: Neurobiology

institute: UCLA David Geffen School of Medicine

library_source: transcriptomic single cell

data_processing:
cellranger mkfastq
cellranger count
cellbender
doubletfinder
harmony
seurat
Assembly: mm10 (GRCm38p6)
Supplementary files format and content: matrix.mtx.gz' has raw counts for all samples
Supplementary files format and content: barcodes.tsv' has list of barcodes for all samples matching with raw counts
Supplementary files format and content: features.tsv' has list of genes matching to raw counts
Supplementary files format and content: meta.tsv' has all meta information including assigned celltypes

source_name: Dorsal Striatum

extract_protocol:
We sacrificed P18 mice by rapid decapitation and quickly dissected the brain and transferred it into ice-cold nACSF that contained (mM): 125 NaCl, 25 NaHCO3, 10 Dextrose, 3 KCl, 1.25 NaH2PO4, 2 CaCl2.2H2O, 2 MgCl2 with 7.3-7.4 pH and 300-305 mOsm osmolality. We placed the brain onto an ice-cold 1.0 mm stainless steel brain matrix (Stoelting, Cat#51386) and obtained three 1.0 mm thick striatal sections which were then transferred into a petri-dish containing cold nACSF. Using forceps and under a dissection microscope, striatum was dissected out from these slices, flash frozen in liquid N2, and stored at -80°C. The striatal tissue was collected from P18 mice of required genotypes at different time points and stored. Protocol for isolating nuclei was adapted and modified from our previously published work6. Briefly, tissue was homogenized 20 times with pestle A, followed by 20 times with pestle B, in a glass Dounce tissue grinder (Sigma, Cat#D8938) in 2 ml ice-cold EZ Nuclei Lysis Buffer (Sigma, Cat #NUC-101). Homogenized samples were transferred into 15 ml tube with an additional 2 ml ice-cold EZ Nuclei Lysis Buffer, incubated on ice for 3 min and centrifuged at 500 X g for 5 min at 4°C. The supernatant was discarded, and nuclei pellet was resuspended in 3 ml ice-cold Nuclei Suspension Buffer (NSB; 1X PBS, 0.01% Ultrapure BSA, and 0.1% RNase inhibitor) and again centrifuged at 500 X g for 5 min at 4°C. The supernatant was then discarded, and nuclei pellet was resuspended in 300-400 µl NSB, and filtered through 40 µm size Flowmi cell strainer (Bel-Art Products, Cat# H13680-0040). An aliquot of the filtered nuclei suspension was mixed with Trypan Blue and transferred into a disposable cell counting chamber nuclei to visualize and count the healthy nuclei under a light microscope to determine desired nuclei concentration (targeting 700-1,200 nuclei/µl).
Libraries from a total of 9 mice (3 mice/genotype) were prepared using the Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1 (10X Genomics, Cat#1000121) targeting 10,000 nuclei per sample as per the manufacturer’s instructions. All mice were injected either with ControlAAV or Foxp1AAV in their striatum at P1 age where only a fraction of neurons was infected that were identified based on the presence of AAV transcripts. However, the proportion of AAV transcripts is exceptionally small in the pool of total transcripts that are captured by snRNA-seq experiment and therefore we used a modified approach 12 where we amplified the viral transcript specific sequences and prepared separate libraries. Briefly, we used 5% of the total cleaned up cDNA (amplified from the GEMs that were generated from each sample for the targeted 10,000 nuclei) and amplified the viral transcripts with reverse primer 10X_Enrich_R – 5’CTACACGACGCTCTTCCG3’ and forward primers 10X_WPRE_F1 – 5’ACGAGTCGGATCTCCCTTT3’ (for ControlAAV infected mice) and 10X_mCherry_F1 – 5’GCATGGACGAGCTGTACA3’ (for Foxp1AAV infected mice) for 25 cycles using Phusion High-Fidelity PCR Master Mix with HF Buffer (NEB, Cat# M0531S). We used different forward primers for ControlAAV and Foxp1AAV infected mice since ControlAAV vector has a WPRE sequence at the 3’end whereas we had to remove WPRE sequence from the AAVFoxp1 vector to accommodate Foxp1 and mCherry into the vector and thus have the mCherry sequence at 3’end of Foxp1AAV vector. The amplified PCR product was run on an agarose gel, where a ~250 bp product was excised from the gel and eluted using QIAquick Gel Extraction Kit (Qiagen, Cat#28706) in 20 µl elution buffer (NEB). 5% of this first round amplified product was used to perform a second round of amplification using the reverse primer, i. e. 10X_WPRE_F1 and forward primers 10X_WPRE_F2 – 5’GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTACGAGTCGGATCTCCCTTT3’ (for AAVControl infected mice) and 10X_mCherry_F2 –5’GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGTACAAGTAGACCCAGCTT3’ (for AAVFoxp1 infected mice) for 20 cycles using the same Phusion polymerase. Once again, this amplified PCR product was loaded on an agarose gel where similar size product (~250 bp) was excised and eluted in 30 µl elution buffer. The eluted PCR products were once again cleaned up using SPRIselect Reagent and subjected to sample-index PCR amplification according to the manufacturer’s instructions (10X Genomics) to generate cDNA libraries. Finally, both (total and AAV_transcript) libraries were subjected to quality control using 4200 TapeStation System (Agilent, Cat# G2991BA) and quantified using Qubit 2.0 Fluorometer (Invitrogen). For each sample, 5 nM of the total libraries and 0.5 nM of the AAV transcript libraries (10% of the total library) were pooled and sequenced on a NovaSeq 6000 (Illumina) platform on S4 flow cell.

value: Dorsal Striatum

value: D2 Foxp1CTL


title: D1_E02_RNAseq

status: Public on May 31 2025

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

institute: The Babraham Institute

description: 2i_release_NMTSeq_RNAseq_filtered_normalized.txt

data_processing:
All sequencing was carried out on HiSeq instrument. RNA-seq libraries were pooled as 96-plex or 192-plex pools and sequenced using 75-bp paired-end reads.
scRNA-seq alignments were performed using Hisat 2 as described previously (Clark et al. Nature Communications, 2018).
Genome_build: GRCm38
Supplementary_files_format_and_content: Comma-delimited file with Ensembl Gene IDs, quantified values show number of reads per gene per sample

growth_protocol: E14 mESC were cultured in 2i+LIF media consisting out of N2B27 medium, composed out of DMEM/F12 (Life Technologies, 12634010) and Neurobasal (Life Technologies, 21103049) in a volume/volume (v/v) ratio 1:1, 0.1 mM 2-mercaptoethanol, 2 mM L-Glutamine, 1:200 v/v N2 (Life Technologies, 17502048) and 1:100 v/v B27 supplement (Life Technologies, 17504044), supplemented with 3 µM CHIR99021, 1 µM PD0325901 and 20 ng/ml of leukemia inhibitory factor (LIF)  (all Department of Biochemistry, University of Cambridge). mESCs were cultured on tissue culture plastic pre-coated with 0.1 % gelatine in H2O. Cultures were passaged when approaching confluence (every 2 days). All cells were cultured in a humidified incubator at 37 °C in 5 % CO2 and 20 % O2. mESCs were subject to routine mycoplasma testing using the MycoAlert testing kit (Lonza) and tested negative. For induction for 2i-relase experiment, the cell been rinsed with PBS before the culture media was changed to serum + LIF medium consisting of DMEM (Life Technologies, 10566-016), containing 15% Fetal Bovine Serum (FBS) (Gibco, 10270106), 1x non-essential amino acids (NEAA) (Life Technologies, 11140050), 0.1 mM 2-mercaptoethanol (Life Technologies, 31350-010), 2 mM L-Glutamine (Life Technologies, 25030-024), supplemented with 20 ng/ml of LIF (Department of Biochemistry, University of Cambridge).

extract_protocol:
0h, 24h, and 48h after induction of 2i-release  the cells been dissociated into single cells using accutase before flow sorting  (BD Influx) into 96-well plate containing 2.5μl of methylase reaction buffer (1 × M.CviPI Reaction buffer (NEB), 2 U M.CviPI (NEB), 160 μM S-adenosylmethionine (NEB), 1 U μl−1 RNasein (Promega), 0.1% IGEPAL CA-630 (Sigma)). Samples were incubated for 15 min at 37 °C to methylate accessible chromatin before the reaction was stopped with the addition of RLT plus buffer (Qiagen) and samples frozen down and stored at −80 °C before processing.
All downstream library preparation steps been performed as previously described by Clark et al. (Clark et al. Nature Communications, 2018).

tag: cell type

value: embryonic stem cell