title: MGE_H3K4ME3_rep2_2

data_processing:
Reads were aligned to mouse genome (GRCm38/mm10 build) with the Bowtie2 aligner, aligned reads mapping to blacklisted regions were removed, and PCR duplicates were removed with PICARD.
Quality control and reproducibility was assessed using deepTools plotHeatmap/plotProfile and MACS each.
Replicates were merged with samtools merge,deduplicated with PICARD, and peaks called with MACS.
Assembly: mm10
Supplementary files format and content: bed for peaks
Supplementary files format and content: bw for signals
Library strategy: CUT&Tag

extract_protocol:
To recover embryonic tissue, dams were anesthetized with isoflurane and then euthanized by cervical dislocation. Embryos were removed from the uterus and kept in chilled artificial cerebrospinal fluid (ACSF, in mM: 87 NaCl, 26 NaHCO3, 2.5 KCl, 1.25 NaH2PO4, 0.5 CaCl2, 7 MgCl2, 10 glucose, 75 sucrose, saturated with 95% O2, 5% CO2, pH 7.4). Brains were extracted from E12.5 and E14.5 embryos, hemisected, microdissected to obtain the MGE, LGE, CGE and somatosensory cortex, and kept in ACSF. Nuclei isolation followed the 10X Genomics ATAC nuclei isolation protocol with several modifications. All steps were performed on ice. For each brain region, tissue was transferred to a Dounce homogenizer containing 1mL ATAC lysis buffer (10 mM Tris-HCL, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1 Tween-20, 0.1% IGEPAL, 2% BSA). Samples were dounced with 10 strokes pestle A and 10 strokes pestle B. Lysate was strained through a 40 μm filter pre-wetted with ATAC wash buffer (10 mM Tris-HCL, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 2% BSA) and neutralized with 2 mL wash buffer. For CUT&Tag, tissue was homogenized as described above. Nuclei suspensions were centrifuged 500 g for 5 min at 4oC, supernatant removed, and washed once with 1 mL wash buffer, centrifuged 500 g for 5 min and washed a final time with 1 mL 1X CUT&Tag wash buffer (from CUT&Tag IT Assay Kit, Active Motif, #53610). A diluted aliquot of nuclei solution was mixed with Trypan Blue (1:1) and counted on a hemocytometer. Equal numbers of MGE, CGE, LGE and cortex nuclei were pooled and diluted to a final concentration of 1000 nuclei/μL in wash buffer, with 100 μL (~100,000 nuclei) used for each CUT&Tag reaction.
For each CUT&Tag replicate, 100,000 nuclei were resuspended in 1.5 mL 1X Wash Buffer and then processed with the Active Motif CUT&Tag IT Assay Kit (#53610) following manufacturer’s instructions. Anti-H3K4me3 (Active Motif, 39159) antibody was used as a primary antibody. Following library amplification, DNA quantity was determined with a Thermo Qubit and library quality characterized with an Agilent Tapestation. Libraries were balanced for DNA content and pooled before performing a final SPRIselect bead 1x left size selection and paired-end sequenced (50 x 50 bp). Samples were sequenced to a following depths per library: CGE: Replicate 1: 50,541,513; Replicate 2: 25,035,394; CTX: Replicate 1: 18,35,546; Replicate 2: 30,114,008; LGE: Replicate 1: 14,760,336; Replicate 2: 17,211,681; MGE: Replicate 1: 5,518,769; Replicate 2: 14,720,921.

value: Medial ganglionic eminence


title: Tyk2fl4

status: Public on Jul 01 2022

type: SRA

city: Vienna

first: Robert

last: Eferl

address: Borschkegasse 8a

department: Center for Cancer Research

country: Austria

institute: Medical University Vienna

library_source: transcriptomic

data_processing:
Reads in fastq format were aligned to the mouse reference genome version GRCm38 with Gencode mV23 annotations using STAR aligner v2.6.1a in 2-pass mode.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Mus musculus

source_name: Colon tumors

extract_protocol:
Colonic tumors were induced using AOM/DSS. Colons were disected, flushed with PBS and cut open to reveil the colon lumen. Single tumors were removed using disecting tools and homogenized in Trizol. RNA purification was performed using a Quiagen RNeasy Kit ( Cat# 75144). RNAseq libraries were constructed using 1ug of total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

tag: tissue

value: colon

tag: treatment

value: AOM/DSS induced CRC


title: MGE_H3K4ME3_rep2_1

city: Bethesda

first: Timothy

last: Petros

state: Maryland

address: 35 Convent Drive, Bg 35 Room 3B-1002

country: USA

institute: NICHD

library_source: genomic

molecule: genomic DNA

source_name: Medial ganglionic eminence

value: wild-type

tag: strain


title: case_361 mRNA-seq

city: Aurora

first: Ivana

last: Yang

state: CO

institute: University of Colorado Anschutz Medical Campus

description:
Yang_SysBio_case_361
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

data_processing:
For RNA, RNA paired-end reads were aligned at the gene level to Ensembl GrCh38 using Kallisto {Bray, 2016, 27043002}. Genes and transcripts were detected in the mRNA dataset using hg38 Gencode v27 and filter of at least 6 reads in at least 20% of the samples, TMM normalized across all samples, and then inverse normalization transformed on a per-gene basis.
Genome_build: GRCh38
Supplementary_files_format_and_content: For RNA-seq, the gene-level filtered and normalized count file is included as a processed data file

organism: Homo sapiens

source_name: tissue-Explant

extract_protocol:
RNA was isolated from the same sample of lung tissue using the AllPrep kit (Qiagen). Samples with RNA integrity number (RIN) and DNA integrity number (DIN) >5 were used.
mRNA libraries were prepared from 500 ng total RNA with TruSeq stranded mRNA library preparation kits (illumina) and sequenced at the average depth of 80M reads on the Illumina NovaSeq 6000 (illumina).

value: lung

tag: center

value: LTRC

tag: dx

value: ipf

value: case

tag: rnaseqid

tag: age

tag: Sex

value: m

tag: race

value: white

tag: ethnicity

value: not hispanic or latino

value: Y

tag: raw data disclaimer


title: Tyk2fl3


title: CGE_H3K27ME3_rep2_2

data_processing:
Reads were aligned to mouse genome (GRCm38/mm10 build) with the Bowtie2 aligner, aligned reads mapping to blacklisted regions were removed, and PCR duplicates were removed with PICARD.
Quality control and reproducibility was assessed using deepTools plotHeatmap/plotProfile and MACS each.
Replicates were merged with samtools merge,deduplicated with PICARD, and peaks called with MACS.
Merged bam files were converted to normalized for visualization bigWig files using deeptools bamCoverage.
Assembly: mm10
Supplementary files format and content: bed for peaks
Supplementary files format and content: bw for signals
Library strategy: CUT&Tag

source_name: Caudal ganglionic eminence

extract_protocol:
To recover embryonic tissue, dams were anesthetized with isoflurane and then euthanized by cervical dislocation. Embryos were removed from the uterus and kept in chilled artificial cerebrospinal fluid (ACSF, in mM: 87 NaCl, 26 NaHCO3, 2.5 KCl, 1.25 NaH2PO4, 0.5 CaCl2, 7 MgCl2, 10 glucose, 75 sucrose, saturated with 95% O2, 5% CO2, pH 7.4). Brains were extracted from E12.5 and E14.5 embryos, hemisected, microdissected to obtain the MGE, LGE, CGE and somatosensory cortex, and kept in ACSF. Nuclei isolation followed the 10X Genomics ATAC nuclei isolation protocol with several modifications. All steps were performed on ice. For each brain region, tissue was transferred to a Dounce homogenizer containing 1mL ATAC lysis buffer (10 mM Tris-HCL, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1 Tween-20, 0.1% IGEPAL, 2% BSA). Samples were dounced with 10 strokes pestle A and 10 strokes pestle B. Lysate was strained through a 40 μm filter pre-wetted with ATAC wash buffer (10 mM Tris-HCL, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 2% BSA) and neutralized with 2 mL wash buffer. For CUT&Tag, tissue was homogenized as described above. Nuclei suspensions were centrifuged 500 g for 5 min at 4oC, supernatant removed, and washed once with 1 mL wash buffer, centrifuged 500 g for 5 min and washed a final time with 1 mL 1X CUT&Tag wash buffer (from CUT&Tag IT Assay Kit, Active Motif, #53610). A diluted aliquot of nuclei solution was mixed with Trypan Blue (1:1) and counted on a hemocytometer. Equal numbers of MGE, CGE, LGE and cortex nuclei were pooled and diluted to a final concentration of 1000 nuclei/μL in wash buffer, with 100 μL (~100,000 nuclei) used for each CUT&Tag reaction.
For each CUT&Tag replicate, 100,000 nuclei were resuspended in 1.5 mL 1X Wash Buffer and then processed with the Active Motif CUT&Tag IT Assay Kit (#53610) following manufacturer’s instructions. Anti-H3K27me3 (Cell Signaling, 9733T) antibody was used as a primary antibody. Following library amplification, DNA quantity was determined with a Thermo Qubit and library quality characterized with an Agilent Tapestation. Libraries were balanced for DNA content and pooled before performing a final SPRIselect bead 1x left size selection and paired-end sequenced (50 x 50 bp). Samples were sequenced to a following depths per library: CGE: Replicate 1: 13,604,105; Replicate 2: 47,136,470; CTX: Replicate 1: 13,640,572; Replicate 2: 36,097,462; LGE:  Replicate 1: 13,539,124; Replicate 2: 30,498,855; MGE: Replicate 1: 17,214,723; Replicate 2: 16,336,430.

value: Caudal ganglionic eminence


title: control_359 mRNA-seq

description:
Yang_SysBio_control_359
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: control

value: f

value: N


title: Tyk2fl7


title: LGE_H3K4ME3_rep1_1

source_name: Lateral ganglionic eminence

value: Lateral ganglionic eminence


title: control_355 mRNA-seq

description:
Yang_SysBio_control_355
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: other


title: LGE_H3K4ME3_rep2_1


title: CTX_H3K4ME3_rep2_2

source_name: Cortex

value: Cortex


title: MGE_H3K4ME3_rep1_1

value: Medial ganglionic eminence


title: case_360 mRNA-seq

description:
Yang_SysBio_case_360
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: U


title: control_363 mRNA-seq

description:
Yang_SysBio_control_363
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung


title: Tyk2DIEC4

value: colon

value: AOM/DSS induced CRC


title: Tyk2DIEC3


title: Tyk2fl1


title: Tyk2DIEC2


title: CTX_H3K4ME3_rep2_1

value: wild-type


title: CTX_H3K4ME3_rep1_1


title: control_353 mRNA-seq

description:
Yang_SysBio_control_353
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: LTRC


title: control_348 mRNA-seq

description:
Yang_SysBio_control_348
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: m

value: white


title: control_345 mRNA-seq

description:
Yang_SysBio_control_345
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: hispanic

value: Y


title: Tyk2DIEC1


title: Tyk2KO2


title: CGE_H3K4ME3_rep2_1

value: Caudal ganglionic eminence


title: Tyk2fl2


title: Tyk2KO3


title: case_344 mRNA-seq

description:
Yang_SysBio_case_344
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

source_name: tissue-Unknown

value: Inova Fairfax

value: ipf

value: case

value: f

value: not hispanic or latino


title: CGE_H3K4ME3_rep2_2


title: CGE_H3K4ME3_rep1_2


title: Tyk2KO1


title: control_343 mRNA-seq

description:
Yang_SysBio_control_343
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: Pittsburgh Lung Donor Core

value: normal

value: control


title: control_351 mRNA-seq

description:
Yang_SysBio_control_351
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: other

value: U


title: CGE_H3K4ME3_rep1_1

value: wild-type


title: case_342 mRNA-seq

description:
Yang_SysBio_case_342
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: m


title: Tyk2wt3

value: colon

value: AOM/DSS induced CRC


title: Tyk2wt1


title: case_341 mRNA-seq

description:
Yang_SysBio_case_341
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: white

value: N


title: MGE, H3K27AC, rep2

description:
MGE_H3K27AC.bed
MGE_H3K27AC.bw

data_processing:
Reads were aligned to mouse genome (GRCm38/mm10 build) with the Bowtie2 aligner, aligned reads mapping to blacklisted regions were removed, and PCR duplicates were removed with PICARD.
Quality control and reproducibility was assessed using deepTools plotHeatmap/plotProfile and MACS each.
Replicates were merged with samtools merge,deduplicated with PICARD, and peaks called with MACS.
Merged bam files were converted to normalized for visualization bigWig files using deeptools bamCoverage.
Assembly: mm10
Supplementary files format and content: bed for peaks
Supplementary files format and content: bw for signals
Library strategy: CUT&RUN

extract_protocol:
To recover embryonic tissue, dams were anesthetized with isoflurane and then euthanized by cervical dislocation. Embryos were removed from the uterus and kept in chilled artificial cerebrospinal fluid (ACSF, in mM: 87 NaCl, 26 NaHCO3, 2.5 KCl, 1.25 NaH2PO4, 0.5 CaCl2, 7 MgCl2, 10 glucose, 75 sucrose, saturated with 95% O2, 5% CO2, pH 7.4). Brains were extracted from E12.5 and E14.5 embryos, hemisected, microdissected to obtain the MGE, LGE, CGE and somatosensory cortex, and kept in ACSF. Nuclei isolation followed the 10X Genomics ATAC nuclei isolation protocol with several modifications. All steps were performed on ice. For each brain region, tissue was transferred to a Dounce homogenizer containing 1mL ATAC lysis buffer (10 mM Tris-HCL, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1 Tween-20, 0.1% IGEPAL, 2% BSA). Samples were dounced with 10 strokes pestle A and 10 strokes pestle B. Lysate was strained through a 40 μm filter pre-wetted with ATAC wash buffer (10 mM Tris-HCL, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 2% BSA) and neutralized with 2 mL wash buffer. For CUT&RUN, tissue was homogenized as described above. Nuclei suspensions were centrifuged 500 g for 5 min at 4oC, supernatant removed, and washed once with 1 mL wash buffer, centrifuged 500 g for 5 min and washed a final time with 1 mL CUT&RUN 1X wash buffer (1 mL HEPES pH 7.5, 1.5 m 5M NaCl, 12.5 uL 2M spermidine and 47.5 mL dH2O with 1Roche Complete Protease Inhibitor EDTA-Free tablet). Equal numbers of MGE, CGE, LGE and cortex nuclei were pooled and diluted to a final concentration of 1000 nuclei/μL in wash buffer, with 100 μL (~100,000 nuclei) used for each CUT&RUN reaction.
For each CUT&RUN replicate, 100,000 nuclei were resuspended in 1.5 mL 1X Wash buffer. BioMag. Plus Concanavalin A beads (Bangs Laboratories) were washed in in Binding Buffer (20mM HEPES pH 7.5, 10mM KCl, 1mM CaCl2, 1mM MnCl2). Nuclei were resuspended in Wash Buffer, mixed with a slurry of the Concavalin A coated magnetic beads, and rotated for 10 minutes at room temperature. 10 μl of Concavalin A bead slurry was used per 100,000 cells. The beads were resuspended in Wash Buffer containing 2 mM EDTA, 0.1% bovine serum albumin, 0.05% Digitonin, and 1:50 dilution of primary antibody, which was then incubated on a nutating platform for 2 hours at room temperature. The beads were then washed twice in Digitonin Buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1x Roche Complete Protease Inhibitor no EDTA, 0.05% Digitonin and 0.1% bovine serum albumin). Then they were incubated with pA-MN (600 μg/ml, 1:200, either home-made or a gift from S. Henikoff) in Digitonin Buffer for 1 hour at 4.C. Following this incubation, beads were washed twice with Digitonin Buffer and finally resuspended in 150 μl of Digitonin Buffer, and equilibrated to 0.C before adding CaCl2 (2mM). The beads were then incubated for 1 hour at 0.C. After this hou,150 μl of 2X Stop Buffer (200 mM NaCl, 20 mM EDTA, 4 mM EGTA, 50 μg/ml RNase A, 40 μg/ml glycogen), was added. Beads were incubated for 30 minutes at 37.C and then pelleted at 16,000g for 5 minutes at 4.C. Supernatant was transferred, mixed with 3 μL 10% SDS and 1.8U Proteinase K (NEB), and incubated for 1 hour at 50.C, shaking at 900 rpm. 300 μl of 25:24:1 Phenol/Chloroform/Isoamyl Alcohol was added, solutions were vortexed, and transferred to Maxtrack phase-lock tubes (Qiagen). The samples in the phase-lock tubes were centrifuged at 16,000g for 3 minutes at room temperature. 300 μl of Chloroform was added, solutions were mixed by inversion, and centrifuged at 16,000g for 3 minutes at room temperature. Aqueous layers were transferred to new tubes and DNA isolated through Ethanol precipitation. These samples were resuspended in 10mM Tris-HCl pH 8.0 (ThermoFisher). CUT&RUN libraries were prepared following the SMARTer ThruPlex TAKARA Library Prep kit with small modifications. Double stranded DNA (10 μl), TemplatePreparation D Buffer (2 μl), and Template Preparation 569 D Enzyme (1 μl) were combined and added to each sample. End Repair and A-tailing was performed in a Thermocycler with a heated lid (22.C, 25 min; 55.C, 20 min). To each sample, library Synthesis D Buffer (1 μl) and Library Synthesis D Enzyme (1 μl) and library synthesis was performed (22.C, 40 min). Library Amplification D Buffer (25 μl), Library Amplification D Enzyme (1 μl), Nuclease-free water (4 μl), and a unique Illumina-compatible indexed primer (5 μl) were added. Library amplification was performed using the following conditions: 72.C for 3 min; 85.C for 2 min; 98.C for 2 min (denaturation); 4 cycles of 98.C for 20 s, 67.C for 20 s, 72.C for 10 s (addition of indexes); 14 cycles of 98.C for 20 s, 72.C for 10 s (library amplification). Post-PCR clean-up involved  SPRIselect bead 0.6X left/1x right double size selection then washed twice gently in 80% ethanol, and eluted in 10-12 μl 10 mM Tris pH 8.0. 1:50-diluted of primary antibody against H3K27ac (Abcam, ab4729) was used to assess active modifications. Following library amplification, DNA quantity was determined with a Thermo Qubit and library quality characterized with an Agilent Tapestation. Libraries were balanced for DNA content and pooled before performing a final SPRIselect bead 1x left size selection and paired-end sequenced (50 x 50 bp). CGE: Replicate 1: 39,950,806; Replicate 2: 68,704,235; CTX: Replicate 1: 45,279,956; Replicate 2: 73,920,447; LGE: Replicate 1: 46,933,225; Replicate 2: 55,438,848; MGE: Replicate 1: 55,871,849; Replicate 2: 77,034,587.

value: Medial ganglionic eminence


title: LGE, H3K27AC, rep2

description:
LGE_H3K27AC.bed
LGE_H3K27AC.bw

value: Lateral ganglionic eminence


title: BMPGDFD14repeat02

city: New York

first: YUJIE

last: FAN

state: New York

address: 430 E 67th St

institute: Memorial Sloan Kettering Cancer Center; Weill Graduate School of Medical Sciences of Cornell University

data_processing:
ATAC-seq data was processed following the recommendations of the ENCODE consortium (The ENCODE Consortium ATAC-seq Data Standards and Prototype Processing Pipeline https://www.encodeproject.org/atac-seq/).
Reads were aligned to the human reference genome (hg19) with BWA-backtrack (Li and Durbin, 2009).
Post-alignment filtering was done with samtools (Li et al., 2009) and Picard tools (Institute) to remove unmapped reads, improperly paired reads, non-unique reads, and duplicates.
To identify regions of open chromatin represented by enrichments of reads, peaks were called with MACS2 (Liu, 2014). Peaks with an adjusted P < 0.01 were merged, quantified, and normalized using DiffBind v3.2.1(Brown, 2022).
ATAC-seq signal profiles were created with bamCoverage from the deepTools suite (Ramírez et al., 2016)using the following parameters: -bs 10 --normalizeUsing RPGC --effectiveGenomeSize 2776919808 --blackListFileName hg19-blacklist.v2.bed --ignoreForNormalization chrX chrY --ignoreDuplicates --minFragmentLength 40.  Blacklisted regions (Amemiya et al., 2019)were retrieved from https://sites.google.com/site/anshulkundaje/projects/blacklists
Assembly: hg19
Supplementary files format and content: wig files and peak text files

source_name: Neural crest cells

growth_protocol: Neural crest cells are growed as described in coresponding paper

extract_protocol:
Profiling of chromatin was performed by ATAC-Seq as described by Buenrostro, et al  (Buenrostro et al., 2013).
Briefly, 50,000 viably frozen neural crest cells were washed in cold PBS and lysed. The transposition reaction containing TDE1 Tagment DNA Enzyme (Illumina catalog # 20034198) was incubated at 37°C for 30 minutes. The DNA was cleaned with the MinElute PCR Purification Kit (QIAGEN catalog # 28004) and material was amplified for 5 cycles using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs catalog # M0541L). After evaluation by real-time PCR, 7-10 additional PCR cycles were done. The final product was cleaned by aMPure XP beads (Beckman Coulter catalog # A63882) at a 1X ratio, and size selection was performed at a 0.5X ratio. Libraries were sequenced on a HiSeq 4000 in a PE100 run, using the HiSeq 3000/4000 SBS Kit (Illumina).  An average of 42 million paired reads were generated per sample. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position.

tag: cell type

value: hPSC-derived sacral neural crest cells

tag: time point


title: Input DNA [WT_2]

city: Bad Nauheim

first: Mario

last: Looso

address: Ludwigstrasse 43

country: Germany

institute: Max Planck Institute for Heart and Lung Research

data_processing:
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC.
Trimmomatic version 0.36 was employed to trim reads after a quality drop below a mean of Q20 in a window of 5 nucleotides. Only reads between 30 and 150 nucleotides were cleared for further analyses.
Reads were further deduplicated using Picard 2.17.10 to eliminate PCR artefacts.
The Macs2 peak caller version 2.1.0 was employed to accommodate for the range of peak widths typically expected.
To be able to compare peaks in different samples to assess reproducibility, the resulting lists of significant peaks were overlapped and unified to represent identical regions and recounted. A background-correction was performed to correct read counts on various regions (unified peaks, promoters, genes).
Treatment and Input samples were normalized for sequencing depth, before subtracting reads of the Input sample from reads of the respective Treatment sample in windows of 50nt length. All windows with negative values (Input > Treatment) were set to zero. Background-corrected counts for regions were calculated using bigWigAverageOverBed and normalized with DESeq2.
Peaks were annotated with the promoter (TSS +- 5000 nt) of the gene most closely located to the centre of the peak based on reference data from GENCODE v25.
Finally, DESeq2 was used to identify significantly differentially modified peaks based on background-corrected read counts from recounted unified peak regions.
Assembly: mm10 (GRCm38)
Supplementary files format and content: bigWig files; library size normalized counts.

source_name: Lung smooth muscle cells

extract_protocol:
1 million FACS-purified SMCs were crosslinked upon the instruction of Covaris kit (#520154). 20 µg sheared genomic DNA was subjected to immunoprecipitation with 4 µg H3K36me3 antibody according to the established protocol.
0.5-10ng of DNA was used as input for TruSeq ChIP Library Preparation Kit (Illumina) with size selection by SPRI-bead based approach after final PCR with 18 cycles.

value: Lung smooth muscle cells

value: WT

tag: chip antibody


title: case_338 mRNA-seq

description:
Yang_SysBio_case_338
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: Inova Fairfax

value: ipf

value: case

value: not hispanic or latino

value: Y


title: LGE, H3K27AC, rep1

description:
LGE_H3K27AC.bed
LGE_H3K27AC.bw


title: Input DNA [WT_3]


title: BMPGDFD14repeat01


title: MGE, H3K27AC, rep1

description:
MGE_H3K27AC.bed
MGE_H3K27AC.bw


title: H3K36me3 ChIPSeq [WT_3]

value: H3K36me3  (Abcam ab9050)


title: BMPD14repeat01


title: case_336 mRNA-seq

description:
Yang_SysBio_case_336
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: LTRC

value: White


title: BMPD14repeat02


title: CTX, H3K27AC, rep2

description:
CTX_H3K27AC.bed
CTX_H3K27AC.bw

value: Cortex

value: wild-type


title: case_339 mRNA-seq

description:
Yang_SysBio_case_339
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: m

value: white


title: CTX, H3K27AC, rep1

description:
CTX_H3K27AC.bed
CTX_H3K27AC.bw


title: H3K36me3 ChIPSeq [WT_2]


title: control_335 mRNA-seq

description:
Yang_SysBio_control_335
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: UCSF

value: normal

value: control

value: f

value: black

value: unknown


title: control_340 mRNA-seq

description:
Yang_SysBio_control_340
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: Pittsburgh Lung Donor Core

value: N


title: Tyk2wt2

value: colon

value: AOM/DSS induced CRC


title: BMPGDFD7repeat02

value: hPSC-derived sacral neural crest cells


title: CGE, H3K27AC, rep2

description:
CGE_H3K27AC.bed
CGE_H3K27AC.bw

value: Caudal ganglionic eminence


title: Input DNA [Mut_3]

value: Lung smooth muscle cells

value: Tet3 mutant


title: CGE, H3K27AC, rep1

description:
CGE_H3K27AC.bed
CGE_H3K27AC.bw

value: wild-type


title: control_333 mRNA-seq

description:
Yang_SysBio_control_333
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: m

value: Y


title: H3K36me3 ChIPSeq [Mut_3]

value: H3K36me3  (Abcam ab9050)


title: Input DNA [Mut_2]


title: BMPGDFD7repeat01


title: Liver, rep2

data_processing:
Libraries were sequenced with paired-end reads of 51 nucleotides
The make_viewpoints Hicpro script was used to obtain 803 individual Capture-C bigwig files for each replicate of each viewpoint with 2kb-sized bins and excluding 500bp surrounding the DpnII-fragment where probes hybridize.
Averages from replicates were used for visualization
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: Capture-C

source_name: Liver

extract_protocol:
To recover embryonic tissue, dams were anesthetized with isoflurane and then euthanized by cervical dislocation. Embryos were removed from the uterus and kept in chilled artificial cerebrospinal fluid (ACSF, in mM: 87 NaCl, 26 NaHCO3, 2.5 KCl, 1.25 NaH2PO4, 0.5 CaCl2, 7 MgCl2, 10 glucose, 75 sucrose, saturated with 95% O2, 5% CO2, pH 7.4). Brains were extracted from E12.5 embryos, hemisected, microdissected to obtain the MGE, LGE, CGE and somatosensory cortex, and kept in ACSF. To collect whole cells, embryonic MGE, LGE, CGE and cortex tissue was incubated in 1 mg/mL Pronase (Roche #10165921001) in ACSF for 20 minutes at RT. Pronase solution was removed and 2 ml of reconstitution solution (1% fetal bovine serum + DNAse (1:10,000, Roche #47167280001)) in oxygenated ACSF was added. DNAse was not included in the reconsititution solution. Cells were triturated sequentially with fire-polished large, medium and small bore Pasteur pipettes to mechanically dissociate tissue.
After cell dissociation, 1 million cells per region were fixed with 1% formaldehyde (Thermo: 28908) made in 1 ml HBSS media. Fixation was carried out at room temperature on a nutator, for 10 mins, protected from light. To stop fixation, glycine was added at a final concentration of 0.13 M and samples were incubated for 5 mins 595 at room temperature followed by 15 mins on ice. Fixed cells were then washed once with ice-cold PBS. After spinning cells at 2500g 4oC for 5 mins, the pellet was flash frozen in liquid nitrogen and stored at -80oC. To perform Capture-C, pellets were first thawed on ice and then incubated with 1 ml lysis buffer (10 mM Tris-HCL pH8, 10 mM NaCl, 0.2% Igepal CA-630, Roche Complete EDTA-free Sigma #11836170001). After lysis, cells were dounced and washed with cold PBS. Nuclei extracted with this method were then collected by centrifugation and subjected to DpnII digest in 50 μl 0.5% SDS and incubated at 62oC for 10 minutes after which 150 μl of 1.5% Triton-X was added and cells incubated for 15 minutes at 37oC while shaking at 900 rpm. 25 μl of 10X DpnII restriction buffer (NEB) was then added, and cells were incubated for 15 minutes while shaking. After that, 200U of DpnII (NEB R0543M) were added and incubated for 2 hours, then 200U more and incubated overnight. Next morning 200U more were added and incubated for 3h (total 600U of DpnII). DpnII was inactivated at 62oC for 20 minutes. For Hi-C, biotin fill-in was done by incubating cells with a mixture of 4.5 μl dCTP dTTP and dGTP at 3.3 mM, 8 μl klenow polymerase (NEB M0210L) and 37.5 μl Biotin-14-dATP (Thermo 19524016) for 4h at RT while shaking at 900 rpm for 10 seconds every 5 minutes. Ligation was done overnight at 16oC also rotating at 900 rpm for 10 seconds every 5 minutes by adding 120 μl of 10X ligation buffer (NEB), 664 μl water, 100 μl 10% Triton-X, 6 μl BSA 20mg/ml, and 2 μl T4 ligase (NEB cat #M0202M). For Capture-C, biotin fill-in step was skipped and 50 μl more of water was added to the ligation mix. Crosslink removal was done overnight with 50 μl of proteinase K in 300 μl of following buffer (10 mM Tris-HCl pH8.0, 0.5 M NaCl, 1%SDS) while shaking at 1400 rpm at 65oC. Following Sodium Acetate and 100% Ethanol -80oC precipitation, DNA was resuspended in 130 μl 10 mM Tris HCL. Sonication was done using Covaris AFA microtubes 130 with following settings for a fragment size of 200 bp fragments (Duration: 225 secs, peak power-75W, duty factor 25%, Cycles per Burst-1000). Sonications were performed in a Covaris ME220 sonicator. Sonicated material was then size selected using SPRI beads with the following ratios: 0.55X and 1X. Following sonication and size selection, 1 μg of template material was resuspended in 50 μl of 10 mM Tris and used for library prep with 10 μl of End-Repair reaction. 5 μl of 15 mM annealed - Illumina adaptors were ligated to the Capture-C material. Using a total volume of 100 μl, library 635 was amplified by PCR using 6 cycles. For capture, 1 μg of Capture-C library per sample was mixed with mouse COT1 DNA and universal as well as index-specific blocking oligos from SeqCap EZ HE-oligo (Roche). 4.5 μl pool of biotinylated probes (xGen Lockdown Probe Pools from IDT), with each probe at 0.4 fmol/μl targeting the promoters of our loci of interested were added to this mixture and incubated for 3 days at 47oC. Following binding to Streptavidin C1beads, material was washed as recommended by the SeqCap EZ Hybridization and Wash Kits. Following washes material was amplified by PCR using Kapa polymerase and 14 cycles. Material from different samples was then combined and 1 μg of pooled libraries was recaptured in a single reaction and amplified with 8 cycles. Probes were designed using Capsequm (capsequm.molbiol.ox.ac.uk/cgi-bin/CapSequm.cgi) by selecting regions adjacent to the gene promoters of interest.

value: Liver


title: case_332 mRNA-seq

description:
Yang_SysBio_case_332
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: LTRC

value: ipf

value: case

value: White

value: not hispanic or latino


title: BMPD7repeat02


title: Ovaries, poolC

city: Ottawa

first: David

last: Cook

state: ON

address: 501 Smyth Rd

department: Cancer Therapeutics Program

country: Canada

institute: Ottawa Hospital Research Institute

description:
3' RNA
MULTI-seq
cell_metadata.txt
umi_count_matrix.txt
LMOlist.csv

data_processing:
Raw sequencing reads from the gene expression libraries were processed using “CellRanger” v3.0.2. The GRCm38 build of the mouse genome was used. Except for explicitly setting --expect-cells = 25,000, default parameters were used for all samples. MULTI-seq barcode libraries were simply trimmed to 28 bp (v3 kit) using Trimmomatic48 (v0.36) prior to demultiplexing.
Demultiplexing was performed using the deMULTIplex R package (v1.0.2). Only cells positive for a single barcode were kept for further analysis and sample annotations were added to all cells in the data set.
Assembly: mm10
Supplementary files format and content: Cell metadata table: Various metadata (sample ID, cluster, etc) for each cell contained in the UMI count matrix. UMI count matrix: Matrix containing UMI counts for all cells passing quality control filters. LMO list: A list containing MULTI-seq DNA barcodes

source_name: Ovary

extract_protocol:
Ovaries were collected immediately after euthanasia, cleaned from any extraneous remaining tissue (fat, oviduct, etc.) and washed in PBS 3 times. All 3 ovaries from each group were pooled together in 3mL of enzymatic dissociation solution [HBSS with 1.25mg/ml Pronase, 9.2ug/mL Elastase, 100ug/mL DNaseI, 100ug/mL Dispase, 1.5mg/Ml Collagenase A]. Ovaries were further chopped using surgical scissors in dissociation media and incubated for 30 min at 37°C in a rotatory shaker. Single cell suspensions were filtered using a 40 μm cell strainer (which removed all oocytes as well), spun down and resuspended in ACK lysis buffer for 30 sec to remove red blood cells. Cells were washed in sterile PBS (PBS; Corning, #21-031-CV) before preparing for flow sorting. Single-cell suspensions were processed using the 10x Genomics Single Cell 3’ v3 RNA-seq kit by Ottawa Hospital Research Institute Stem Core Laboratories. Gene expression libraries were prepared according to the manufacturer’s protocol. MULTI-seq barcode libraries were retrieved from the samples and libraries were prepared independently. Final libraries were sequenced on the NextSeq 500 platform (Illumina) to reach an approximate depth of 20,000-25,000 reads/cell.
3' scRNA-seq

value: Ovary

value: Aged, Young

value: metformin


title: BMPGDFD3repeat02

value: hPSC-derived sacral neural crest cells


title: H3K36me3 ChIPSeq [Mut_2]

value: Lung smooth muscle cells


title: LGE, rep2

value: Lateral ganglionic eminence


title: control_328 mRNA-seq

description:
Yang_SysBio_control_328
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

source_name: tissue-Biopsy

value: other

value: control

value: f

value: white


title: CTX, rep2

value: Cortex

value: wild-type


title: BMPGDFD3repeat01


title: Ovaries, poolA


title: case_325 mRNA-seq

description:
Yang_SysBio_case_325
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: Inova Fairfax

value: m

value: Y


title: BMPD7repeat01


title: BMPD3repeat02


title: control_331 mRNA-seq

description:
Yang_SysBio_control_331
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: UCSF

value: normal

value: unknown

value: hispanic


title: case_322 mRNA-seq

description:
Yang_SysBio_case_322
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: LTRC

value: ipf

value: case

value: White

value: not hispanic or latino

value: N


title: Liver, rep1

value: Liver


title: CGE, rep2

value: Caudal ganglionic eminence


title: case_334 mRNA-seq

description:
Yang_SysBio_case_334
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: white


title: case_320 mRNA-seq

description:
Yang_SysBio_case_320
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung


title: LGE, rep1

value: Lateral ganglionic eminence

value: wild-type


title: Ovaries, poolB

value: Ovary

value: Aged, Young

value: metformin


title: MGE, rep2

value: Medial ganglionic eminence


title: MGE, rep1


title: 73C5 MDX PLX

city: Vancouver

first: Fabio

last: Rossi

state: BC

address: 2222 Health Sciences Mall

department: School of Biomedical Engineering

institute: University of British Columbia

description: PI- Hoechst+ CD45+ cells from skeletal muscle of a one-year old dystrophic mouse following 10 months of CSF1R inhibition

data_processing:
Demultiplexed FASTQ reads were aligned to the mouse reference genome, mm10 (GRCm38.p5, primary assembly) using the 10X Genomics Cellranger v4.0.0 pipeline. Default and recommended parameters were adopted. The resulting gene-barcode matrices were processed and analyzed in Seurat (Satija Lab, v3.2.0). Further demultiplexing with hashtag oligos (using 0.99 quantile as a threshold for positivity)  was applied to remove cross-sample multiplets.
Low quality cells (< 200 genes/cell and >10% mitocondrial UMIs/cell) were removed prior to principal component analysis, Louvain clustering, and dimensionality reduction with UMAP (30 PCs). Differential gene expression using the Wilcoxon rank sum test was performed on filtered and normalized counts.
Genome_build: mm10 (GRCm38.p5)
Supplementary_files_format_and_content: HDF5 file containing gene count matrices (and HTO if applicable)

molecule: polyA RNA

extract_protocol:
Mice were anesthetized via intraperitoneal injection of 2,2,2-tribromoethyl alcohol (Aldrich T4840-2) and then perfused with warm PBS.  Following removing the fascia, skeletal muscle was harvested and cut into small pieces with scissors which was then followed by enzymatic digestion with a mixture of Collagenase D (Roche; 1.5 U ml-1; # 11088882001) and Dispase II (Roche; 2.4 U ml-1; # 04942078001) for an hour at 37 °C. Samples were vortexed every 20 minutes during incubation. Digested tissues were filtered through a 40-μm cell strainer (FALCON, # 352340), washed with PBS and collected by centrifugation at 545g for 7min.  Cell preparations were blocked with PBS containing 2 mM EDTA and 2% FBS (FACS buffer) + anti-Fcy receptor antibody on ice for 10 minutes and then stained with various antibodies on ice for 15 minutes (Supplementary Table 2). Finally, cells were washed and stained with cell hashing antibodies against mouse CD45 and MHC class I (Biolegend, # 155801, # 155803, # 155805, # 155807) to pool up to four samples for one single-cell analysis run. Cell sorting was performed using a BD FACSAria (Becton Dickinson) equipped with three lasers or BD Influx cell sorter both equipped with four lasers. Cells were sorted twice. To ensure adequate numbers of small cell populations such as TIM4+ after injury, a balanced number of cells were collected from each population and one sample was used for single cell analysis.
Viable cells were delivered into a Chromium Controller (10X Genomics), captured and libraried with the Chromium single cell 3’ reagent kit v2 (10X Genomics) as per the manufacturer's protocol. cDNA libraries were sequenced on Illumina Nextseq 500 using the High Output 75 Cycle kits to a minimum depth of 20,000 mean reads per cell.

treatment_protocol: For CSF1R inhibition, mice were fed with medicated food (AIN-76A Rodent Diet with 200 mg PLX73086 /kg) for least 3 weeks. AIN-76A Rodent Diet was used as the control.

value: Skeletal muscle

value: Hematopoietic cells

value: DMDmdx:PDGFRaEGFP (male)


title: HASH-TIM43hr8hrMQ HTO

description: A balanced number of PI- Hoechst+ CD45+ CD11B+ LY6G/SIGLECF- TIM4+ and PI- Hoechst+ CD45+ CD11B+ LY6G/SIGLECF- TIM4- cells were sorted by FACS. Hash1: 8hr sample #1, Hash2: 8hr sample #2, Hash3 3hr sample #1, Hash4 3hr sample #2

value: Damaged TAs 3 hours and 8 hours post injury

value: Macrophage

value: WT (male)


title: BMPGDF11D1403

data_processing:
The output data (FASTQ files) are mapped to the target genome using the STAR aligner [Dobin2012] that maps reads genomically and resolves reads across splice junctions.
We use the 2 pass mapping method outlined in [Engström2013] in which the reads are mapped twice. The first mapping pass uses a list of known annotated junctions from Ensemble. Novel junctions found in the first pass are then added to the known junctions and a second mapping pass is done (on the second pass the RemoveNoncanoncial flag is used).
After mapping we post process the output SAM files using the PICARD tools to: add read groups, AddOrReplaceReadGroups which in additional sorts the file and coverts it to the compressed BAM format.
We then compute the expression count matrix from the mapped reads using HTSeq (www-huber.embl.de/users/anders/HTSeq)
The raw count matrix generated by HTSeq are then be processed using the R/Bioconductor package DESeq (www-huber.embl.de/users/anders/DESeq) which is used to both normalize the full dataset and analyze differential expression between sample groups.
Assembly: hg19
Supplementary files format and content: Matrix table with normalized gene counts for every gene and every sample

extract_protocol:
Briefly, phase separation in cells lysed in 1mL TRIzol Reagent (ThermoFisher catalog # 15596018) was induced with 200 µL chloroform and RNA was extracted from the aqueous phase using the miRNeasy Mini Kit (Qiagen catalog # 217004) on the QIAcube Connect (Qiagen) according to the manufacturer’s protocol with 350 µL input
500ng of total RNA with RIN values of 9.6-10 underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit, catalog # RS-122-2102), with 8 cycles of PCR

value: hPSC-derived sacral neural crest cells


title: BMPD3repeat01


title: BMPGDF11D1402


title: CTX, rep1

value: Cortex


title: Hashed_18h_MQ HTO

description: PI- Hoechst+ CD45+ CD11B+ LY6G/SIGLECF- F4/80+ cells sorted by FACS. Hash 1 and 2: damaged muscle 18hr after injury, Hash 3 and 4: undamaged muscle. Only undamaged muscle data is shown in the manuscript.

value: Skeletal muscle at steady state and 18hr after injury

value: Myelomonocytic cells


title: control_317 mRNA-seq

description:
Yang_SysBio_control_317
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: LTRC

value: other

value: control

value: m

value: white

value: not hispanic or latino

value: N


title: Cornea neutrophils, IL1a -/- PAO1, 24hr, bio rep 2

city: Irvine

first: Morgan

last: Dragan

state: CA

address: D288 Medical Sciences I

department: Biological Chemistry

institute: UC Irvine

data_processing:
Fastqc v 0.11.9; Trimmomatic-0.39; Star v 2.7.8a
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic NexteraPE-PE adapters.
Trimmed sequence reads were mapped to GrCM38/mm10 using start alignment (parameters: chimSegmentMin 15, chimJunctionOverhangMin 15, outFilterMismatchNmax 3, alignEndsType Local, runThreadN 8,  outFilterMultimapNmax 1, outBAMcompression 10, outBAMsortingThreadN 8, quantMode GeneCounts TranscriptomeSAM, quantTranscriptomeBAMcompression 10, outSAMtype BAM, SortedByCoordinate, alignSJDBoverhangMin 6, alignIntronMax 300000
Read count extraction and normalization were performed using STAR
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: eye

extract_protocol:
RNA was harvested using RNeasy Micro kit (Qiagen)
RNA libraries for RNA-seq were prepared using Clontech SMART-seq v4 ultra low input Library Prep Kit by UCI Genomic core

value: eye

value: neutrophil

value: IL1a -/


title: Parabiosis HTO

description: PI- CD45+ CD11B+ LY6G/SIGLECF- GFP+ cells spiked with a few PI- CD45+ CD11B+ LY6G/SIGLECF- TIM4+ GFP- cells sorted by FACS

value: Damaged TAs 6 hours, 2 days, 4 days, and 8 days after injury

value: Macrophage

value: The WT partner of a GFP/WT female parabiotic pair


title: 73C6 MDX PLX

source_name: PI- Hoechst+ CD45+ cells from skeletal muscle of a one-year old dystrophic mouse following 10 months of CSF1R inhibition

value: Skeletal muscle

value: Hematopoietic cells

value: DMDmdx (male)


title: control_321 mRNA-seq

description:
Yang_SysBio_control_321
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung


title: BMPD1403

value: hPSC-derived sacral neural crest cells


title: Cornea neutrophils, IL1a -/- PAO1, 24hr, bio rep 1


title: hESCD0repeat02

value: hESC

value: no treatment


title: case_315 mRNA-seq

description:
Yang_SysBio_case_315
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: LTRC

value: ipf

value: case

value: m


title: control_327 mRNA-seq

description:
Yang_SysBio_control_327
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: other

value: control

value: white

value: not hispanic or latino

value: Y


title: 73C9 MDX CNTL

description: PI- Hoechst+ CD45+ cells from skeletal muscle of a one-year old dystrophic mouse following 10 months of treatment with the control diet


title: CGE, rep1

value: Caudal ganglionic eminence

value: wild-type


title: hESCD0repeat01


title: control_319 mRNA-seq

description:
Yang_SysBio_control_319
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: U


title: case_318 mRNA-seq

description:
Yang_SysBio_case_318
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***


title: control_314 mRNA-seq

description:
Yang_SysBio_control_314
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***


title: Parabiosis

source_name: PI- CD45+ CD11B+ LY6G/SIGLECF- GFP+ cells spiked with a few PI- CD45+ CD11B+ LY6G/SIGLECF- TIM4+ GFP- cells sorted by FACS

value: Damaged TAs 6 hours, 2 days, 4 days, and 8 days after injury

value: Macrophage

value: The WT partner of a GFP/WT female parabiotic pair


title: Cornea neutrophils, IL1a -/- PAO1, 24hr, bio rep 3

value: eye

value: neutrophil

value: IL1a -/


title: Cornea neutrophils, WT PAO1, 24hr, bio rep 1

value: WT


title: BMPGDF11D703

value: hPSC-derived sacral neural crest cells


title: BMPGDF11D1401


title: control_309 mRNA-seq

description:
Yang_SysBio_control_309
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: UCSF

value: normal

value: m

value: unknown

value: hispanic


title: 73C8 MDX CNTL

source_name: PI- Hoechst+ CD45+ cells from skeletal muscle of a one-year old dystrophic mouse following 10 months of treatment with the control diet

value: Skeletal muscle

value: Hematopoietic cells

value: DMDmdx (male)


title: case_316 mRNA-seq

description:
Yang_SysBio_case_316
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: LTRC

value: ipf

value: case

value: white

value: not hispanic or latino

value: N


title: HASH-TIM43hr8hrMQ

source_name: A balanced number of PI- Hoechst+ CD45+ CD11B+ LY6G/SIGLECF- TIM4+ and PI- Hoechst+ CD45+ CD11B+ LY6G/SIGLECF- TIM4- cells were sorted by FACS. Hash1: 8hr sample #1, Hash2: 8hr sample #2, Hash3 3hr sample #1, Hash4 3hr sample #2

value: Damaged TAs 3 hours and 8 hours post injury

value: Macrophage

value: WT (male)


title: murine adult splenocytes replicate3 BD WTA kit

city: Chiba

first: Shigeyuki

last: Shichino

address: 2641, Yamasaki, Noda-shi

department: Department of Molecular regulation of Inflammatory and Immune Diseases

country: Japan

institute: Tokyo University of Science

data_processing:
Pair-end Fastq files (R1: cell barcode reads, R2: RNA reads) of TAS-Seq and BD WTA kit data were processed as follows. Adapter trimming of sequencing data was performed using cutadapt 3.444. Filtered reads were chunked into 16 parts for parallel processing by using Seqkit 0.15.045. Filtered cell barcode reads were annotated by Python script provided by BD Biosciences with minor modification for compatibility to Python 3.7. Reference RNA sequences were built by concatenating cDNA and ncRNA fasta files of the Ensembl database (build GRCm38 release-101 for mouse data and GRCh38 release-101 for human data)46. Associated cDNA reads were mapped to reference RNA using bowtie2-2.4.247 by the following parameters: -p 2 --very-sensitive-local -N 1 -norc -seed 656565 -reorder. Then, cell barcode information of each read was added to the bowtie2-mapped BAM files by the python script and pysam 0.15.4 (https://github.com/pysam-developers/pysam), and read counts of each gene in each cell barcode were counted using mawk. Resultant count data was converted to a single-cell gene-expression matrix file. The inflection point of the knee-plot (total read count versus the rank of the read count) was detected using DropletUtils package48 in R-4.1.2 (https://cran.r-project.org/). Cells of which total read count was over inflection point were considered as valid cells.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include raw tag-count values for each sample

source_name: spleen

extract_protocol:
Murine lung samples were minced into 0.5 mm2 with a razor blade and digested with Liberase solution [RPMI-1640 (Nacalai Tesque) supplemented with 10% FBS, 10 mM HEPES pH7.2-7.4, 0.25 mg/ml Liberase TM (Roche), and 2 kU/mL DNase I (Merck)] at 37 ºC for 60 minutes. The cell suspension was agitated 20 times with an 18G needle (Terumo, Tokyo, Japan) after 20 minutes incubation, agitated 20 times with 21G needle (Terumo) after 40 minutes incubation, and agitated 10 times with 200 μL pipette tip.Cell suspensions were passed through a 70 μm cell strainer (BD Biosciences), centrifuged at 4ºC for 500 ×g for 5 minutes, and their supernatant was discarded. Cells were resuspended with 25% Percoll PLUS (Cytiva), agitated with an 18G needle five times. After under layered 65% Percoll PLUS, cell suspensions were centrifuged at 20ºC for 1,000 ×g for 20 minutes, and the middle layer was collected. Resultant cell suspensions were diluted thrice with preparation medium [RPMI-1640 supplemented with 5% FBS and 10 mM HEPES], centrifuged 500 ×g at 4ºC for 7 minutes, and their supernatants were discarded. Resultant cells were resuspended with 500 μL of preparation medium. Tumor cells of the subcutaneous model of lewis lung carcinoma were collected as described previously18. Spleen cells were collected as follows. The spleen tissue from eight-week-old B6 mice was mushed on a cell strainer with 5 mL of ACK lysis buffer [155 mM NH4Cl, 10 mM KHCO3, 0.1 mM EDTA, pH 7.3] and incubated for 1 min at 20 ºC. Then, 5 mL of preparation medium were added and centrifuged at 4ºC for 500 × g for 5 min, suspended in 1 mL of ACK lysis buffer, and incubated for 1 min at 20 ºC. The cell suspension was washed twice with 5 mL of preparation medium and subjected to BD Rhapsody analysis. Kidney cells were collected as follows. Murine kidney lung samples were minced into 0.5 mm2 with a razor blade and digested with Liberase solution [RPMI-1640 (Nacalai Tesque) supplemented with 10% FBS, 10 mM HEPES pH7.2-7.4, 0.5 mg/ml Liberase TH (Roche), and 2 kU/mL DNase I (Merck)] at 37 ºC for 60 minutes. The cell suspension was agitated 20 times with an 18G needle (Terumo, Tokyo, Japan) after 20 minutes incubation, agitated 20 times with 21G needle (Terumo) after 40 minutes incubation, and agitated 10 times with 200 μL pipette tip. Cell suspensions were passed through a 70 μm cell strainer (BD Biosciences), centrifuged at 4ºC for 500 ×g for 5 minutes, and their supernatant was discarded. Cells were resuspended with 25% Percoll PLUS (Cytiva), agitated with an 18G needle five times. After under layered 65% Percoll PLUS, cell suspensions were centrifuged at 20ºC for 1,000 ×g for 20 minutes, and the middle layer was collected. Resultant cell suspensions were diluted thrice with preparation medium [RPMI-1640 supplemented with 5% FBS and 10 mM HEPES], centrifuged 500 ×g at 4ºC for 7 minutes, and their supernatants were discarded. Resultant cells were resuspended with 500 μL of preparation medium. Each single-cell suspension cell concentration was counted using Flow-count fluorospheres (Beckman Coulter, Brea, CA, USA) and a Gallios flow cytometer (Beckman Coulter) or a CytoFLEX S flow cytometer (Beckman Coulter).
Single-cell suspensions were subjected to a BD Rhapsody system with BD Rhapsody Targeted & Abseq Reagent kit (BD Biosciences) following the manufacture’s instructions. 20000 cells (for lung and spleen) or 5000 cells (for kidney) were subjected to the BD Rhapsody workflow. After reverse transcription, Exonuclease I treatment of the resultant BD Rhapsody beads was performed at 37ºC for 60 minutes with 1,200 rpm on a Thermomixer C with Thermotop. Resultant beads were immediately chilled on ice; the supernatant was removed and washed with 1 mL of WTA wash buffer [10 mM Tris-HCl (pH 8.0), 50 mM NaCl, 1 mM EDTA, and 0.05% Tween-20], 200 μL of BD Rhapsody lysis buffer (for inactivation of enzyme), once with 1 ml of WTA wash buffer, twice with 500 μL of WTA wash buffer, resuspended with 200 μL of Beads resuspension buffer. During the washing step, beads-containing DNA LoBind tubes (Eppendorf Japan) were replaced twice. Exonuclease I-treated BD Rhapsody beads were subjected to TAS- Seq workflow (for lung, spleen and kidney samples) or BD WTA kit (for spleen samples, BD Biosciences) for cDNA library amplification (Shichino S., bioRxiv, 2021). 150 ng of TAS-Seq amplified cDNA libraries was subjected to fragmentation/end-repair/A-tailing using NEBNext Ultra II FS DNA Library Prep Kit for Illumina. Ligated products were purified by AmPure XP beads and 9 cycles of Barcoding PCR were performed. Resultant products were purified twice by double size selection with 0.5× → 0.3× (final 0.8×) AmPure XP beads and eluted with 30 μL of 10 mM Tris-HCl pH8.0. Size distribution of amplified products was analyzed by MultiNA system with appropriate dilutions. For BD WTA kit library, libraries were barcorded according to the manufacture's instructions. Resultant libraries and barcoded hashtag libraries were quantified using the KAPA Library Quantification Kit. Pooled libraries were sequenced by Illumina Novaseq 6000 sequencer.

value: WT

value: spleen

value: 8 week old


title: BMPD1402

value: hPSC-derived sacral neural crest cells


title: 180B9PLX18hr

description: Following 3 weeks of CSF1R inhibition and 3 days of withdrawal (switch to a regular diet), TAs were damaged. 18 hours after injury, total RNA was extracted from one TA for RNA sequencing.

data_processing:
Illumina base call files were de-multiplexed by bcl2fastq2 on Basespace. Adaptor sequences were trimmed and low-quality reads (< 35 base pairs) were discarded. Additionally, Bowtie was used to remove read pairs that aligned against abundant sequences. Demultiplexed read sequences were then aligned to the mm10 genome reference using STAR aligner. Assembly and differential expression was estimated using Cufflinks. Bowtie, STAR, and Cufflinks are tools built under RNA-Seq Alignment.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with FPKMs for every gene and sample

extract_protocol:
Mice were anesthetized via intraperitoneal injection of 2,2,2-tribromoethyl alcohol (Aldrich T4840-2) and then perfused with warm PBS.  Following removing the fascia, skeletal muscle was harvested and cut into small pieces with scissors which was then followed by enzymatic digestion with a mixture of Collagenase D (Roche; 1.5 U ml-1; # 11088882001) and Dispase II (Roche; 2.4 U ml-1; # 04942078001) for an hour at 37 °C. Samples were vortexed every 20 minutes during incubation. Digested tissues were filtered through a 40-μm cell strainer (FALCON, # 352340), washed with PBS and collected by centrifugation at 545g for 7min.  Cell preparations were blocked with PBS containing 2 mM EDTA and 2% FBS (FACS buffer) + anti-Fcy receptor antibody on ice for 10 minutes and then stained with various antibodies on ice for 15 minutes (Supplementary Table 2). Stained cells were washed for cell sorting. Cell sorting was performed using a BD FACSAria (Becton Dickinson) equipped with three lasers or BD Influx cell sorter both equipped with four lasers.  RNeasy Micro Kit (Qiagen, # 74004) and RNeasy Fibrous Tissue Mini Kit (Qiagen # 74704) were used to isolate RNA from sorted cells and the total TA, respectively.
Sample quality control was performed using the Agilent 2100 Bioanalyzer. Qualifying samples were then prepped following the standard protocol for the NEBnext Ultra ii Stranded mRNA (New England Biolabs). Sequencing was performed on Illumina Nextseq 500 using the High Output 75 Cycle kits to generate paired end reads (43bp × 43bp reads).

value: Damaged TA 18 hours post injury

value: whole musle

value: C57BL/6J (male)


title: 180B8PLX12hr

description: Following 3 weeks of CSF1R inhibition and 3 days of withdrawal (switch toa regular diet), TAs were damaged. 12 hours after injury, total RNA was extracted from one TA for RNA sequencing.

value: Damaged TA 12 hours post injury


title: case_308 mRNA-seq

description:
Yang_SysBio_case_308
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: LTRC

value: f

value: White

value: U


title: Cornea neutrophils, WT PAO1, 24hr, bio rep 2

value: eye

value: neutrophil


title: murine adult splenocytes replicate2 BD WTA kit


title: Hashed_18h_MQ

source_name: PI- Hoechst+ CD45+ CD11B+ LY6G/SIGLECF- F4/80+ cells sorted by FACS. Hash 1 and 2: damaged muscle 18hr after injury, Hash 3 and 4: undamaged muscle. Only undamaged muscle data is shown in the manuscript.

value: Skeletal muscle at steady state and 18hr after injury

value: Myelomonocytic cells


title: 178B7PLX18hr

source_name: Following 3 weeks of CSF1R inhibition and 3 days of withdrawal (switch to a regular diet), TAs were damaged. 18 hours after injury, total RNA was extracted from one TA for RNA sequencing.


title: BMPD703


title: control_311 mRNA-seq

description:
Yang_SysBio_control_311
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

source_name: tissue-Explant

value: UCSF

value: normal

value: control

value: m

value: black

value: unknown

value: N


title: case_306 mRNA-seq

description:
Yang_SysBio_case_306
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: Vanderbilt

value: ipf

value: case

value: white

value: not hispanic or latino

value: Y


title: BMPGDF11D702

value: hPSC-derived sacral neural crest cells


title: case_310 mRNA-seq

description:
Yang_SysBio_case_310
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: LTRC

value: White


title: murine adult kidney replicate1

description: KidneyTASSeq

source_name: kidney

value: WT

value: kidney

value: 8 week old


title: murine adult splenocytes replicate3

value: spleen


title: Cornea neutrophils, WT PAO1, 24hr, bio rep 3

value: eye

value: neutrophil


title: BMPD1401


title: case_305 mRNA-seq

description:
Yang_SysBio_case_305
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: m


title: BMPGDF11D701


title: BMPD702


title: 180B6CNTL18hr

description: Following 3 weeks of treatment with the control diet and 3 days of withdrawal (switch to a regular diet), TAs were damaged. 18 hours after injury, total RNA was extracted from one TA for RNA sequencing.

value: Damaged TA 18 hours post injury

value: whole musle

value: C57BL/6J (male)


title: control_307 mRNA-seq

description:
Yang_SysBio_control_307
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: UCSF

value: normal

value: control

value: f

value: black

value: unknown

value: N


title: BMPGDF11D302

value: hPSC-derived sacral neural crest cells


title: murine adult splenocytes replicate2

value: WT


title: murine adult splenocytes replicate1 BD WTA kit

value: 8 week old


title: 81D4-MDX-CNTL

description: Total RNA extracted from a TA of an 8-month old DMDmdx mouse following 6 months of treatment with the control diet

value: Tibialis Anterior muscle

value: DMDmdx (female)


title: 178B5CNTL18hr

source_name: Following 3 weeks of treatment with the control diet and 3 days of withdrawal (switch to a regular diet), TAs were damaged. 18 hours after injury, total RNA was extracted from one TA for RNA sequencing.


title: murine adult splenocytes replicate1

value: spleen


title: BMPD701


title: 82A1_MDX_CNTL

description: Total RNA extracted from a TA of an 8-month old DMDmdx:PDGFRaEGFP mouse following 6 months of treatment with the control diet

value: DMDmdx:PDGFRaEGFP (female)


title: control_301 mRNA-seq

description:
Yang_SysBio_control_301
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: LTRC

value: other

value: m

value: white

value: not hispanic or latino

value: Y


title: BMPGDF11D303


title: 180B7CNTL12hr

description: Following 3 weeks of treatment with the control diet and 3 days of withdrawal (switch to a regular diet), TAs were damaged. 12 hours after injury, total RNA was extracted from one TA for RNA sequencing.

value: Damaged TA 12 hours post injury

value: whole musle

value: C57BL/6J (male)


title: control_298 mRNA-seq

description:
Yang_SysBio_control_298
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: Pittsburgh Lung Donor Core

value: normal

value: control


title: BMPD302

value: hPSC-derived sacral neural crest cells


title: murine adult lung replicate3

source_name: lung

value: WT

value: 8 week old


title: 82A3_MDX_PLX

description: Total RNA extracted from a TA of an 8-month old DMDmdx mouse following 6 months of CSF1R inhibition

value: Tibialis Anterior muscle

value: DMDmdx (female)


title: murine adult lung replicate2

value: lung


title: murine adult lung replicate1


title: BMPGDF11D301

source_name: Neural crest cells


title: case_300 mRNA-seq

description:
Yang_SysBio_case_300
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: LTRC

value: ipf

value: case


title: case_297 mRNA-seq

description:
Yang_SysBio_case_297
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

source_name: tissue-Unknown

value: m

value: White

value: not hispanic or latino


title: 81A1_MDX_PLX

description: Total RNA extracted from a TA of an 8-month old DMDmdx:PDGFRaEGFP mouse following 6 months of CSF1R inhibition

value: whole musle

value: DMDmdx:PDGFRaEGFP (female)


title: BMPD301


title: 81D1-MDX-PLX

source_name: Total RNA extracted from a TA of an 8-month old DMDmdx mouse following 6 months of CSF1R inhibition


title: D6_15k_para_35

description: PI- CD45+ CD11B+ LY6G/SIGLECF- GFP+ cells sorted by FACS

value: Damaged TAs 6 days post injury

value: Macrophage

value: The WT partner of a WT/GFP  female parabiotic pair


title: BMPD303

value: hPSC-derived sacral neural crest cells


title: DKO - leu-free diet - day 8 - mouse 6

city: Cambridge

first: Andrew

last: Cangelosi

state: MA

address: 455 Main Street

institute: Whitehead Institute for Biomedical Research

data_processing:
Paired-end reads were mapped to the canonical chromosomes of the mouse genome (GRCm38/mm10) using STAR 2.7.1a (default parameters), indexed with all mouse genes from Ensembl 96.
Gene counts were obtained using featureCounts (v 2.0.1, with “-p -s 2”) and the same gene annotations.
Differential expression was assayed using DESeq2 (v1.26.0, with lfcShrink(type="ashr")).
Genome_build: GRCm38/mm10

source_name: Liver

extract_protocol:
Livers were removed, flash frozen in liquid nitrogen, and RNA extracted using Qiagen miRNeasy Mini Kit. NEBNext UltraII directional RNA Library Prep for Illumina was used with 250ng of RNA to construct sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Liver

value: Sesn2 DKO

tag: diet

value: Leucine-free

tag: timepoint

value: 8 days


title: DKO - leu-free diet - day 8 - mouse 5

tag: genotype


title: case_295 mRNA-seq

description:
Yang_SysBio_case_295
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

tag: tissue

value: lung

value: Y


title: hESCD003

value: hESC

tag: treatment

value: no treatment


title: D4_60k_para_31

source_name: PI- CD45+ CD11B+ LY6G/SIGLECF- GFP+ cells sorted by FACS

value: Damaged TAs 4 days post injury


title: control_294 mRNA-seq

description:
Yang_SysBio_control_294
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: Pittsburgh Lung Donor Core

value: normal

value: control

value: m

value: white

value: N


title: case_299 mRNA-seq

description:
Yang_SysBio_case_299
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: LTRC

value: ipf

value: case

value: unknown

value: hispanic


title: hESCD002


title: 81A3_MDX_CNTL

source_name: Total RNA extracted from a TA of an 8-month old DMDmdx:PDGFRaEGFP mouse following 6 months of treatment with the control diet

value: Tibialis Anterior muscle

value: whole musle

value: DMDmdx:PDGFRaEGFP (female)


title: hESCD001

value: hESC


title: control_291 mRNA-seq

description:
Yang_SysBio_control_291
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

source_name: tissue-Biopsy

value: lung

value: other

value: not hispanic or latino


city: Jeddah

first: Antonio

last: Adamo

state: Not in US

address: 4700 KAUST, Thuwal

department: Biological and Environmental Science and Engineering Division, BESE

country: Saudi Arabia

institute: King Abdullah University of Science and Technology, KAUST

description:
H1 hESC (Time point) - KDM1A ChIP (Experiment#3)
Chip-SEQ Novaseq 6000 SP1 Replicate #3

data_processing:
Raw data was quality-checked and trimmed with BBDuk (version December 10, 2015) [Bushnell et al. 2017a] with a minimum read length of 35 bp and a minimum Phred quality score of 20. High-quality reads were then mapped against the human genome (GRCh38) using bowtie2 (version 2.3.4.1) [Langmead B et al 2019]. Read duplicates were removed using Picard MarkDuplicates (version 2.8.1) [http://broadinstitute.github]. Peak calling was performed using MACS2 (version 2.2.4) [Zhang Y et al 2008] using default ‘sharp’ settings, setting the format of the tag file to “BAMPE.” Peak annotation was carried out using the R package ChIPseeker (version 1.26.2) [Yu G et al 2015] with the UCSC knownGene annotation derived from the R package TxDb.Hsapiens.UCSC.hg38.knownGene. Peak annotation was further enriched for active or poised enhancers using H3K4m1 (ENCFF238YJA, ENCFF558IKG, ENCFF694ENI) and H3K27ac (ENCFF045CUG, ENCFF162HPV) ChIP-seq public data (https://www.encodeproject.org/). Thus, distal intergenic peaks overlapping with both   H3K27ac and H3K4me1 peaks were annotated as active enhancers, while distal intergenic peaks overlapping only with H3K4m1 peaks were annotated as poised enhancers.
Excel files including the annotated peak for each ChIP and the narrowPeak files containing the peak locations together with peak summit, p-value, and q-value.
Genome_build: GrCh38 release 91

source_name: Day 0-hESC

growth_protocol: hESCs H1 were grown on Vitronectin-coated plates in presence of E8 medium, dissociated using Accutase and differentiated into cardiomyocytes using the The PSC Cardiomyocyte Differentiation Kit (Thermo Fisher Scientific) according to the Manufacturer ‘s instruction

extract_protocol:
Briefly, about 8×106 hESCs and 5×106 hESC-derived cardiomyocytes were used for each immunoprecipitation. Cells were detached using Accutase, fixed in PBS containing 1% formaldehyde and quenched with 125 mM glycine. Cells were lysed in ChIP lysis buffer (1% SDS, 10 mM EDTA and 50 mM Tris-HCl at pH 8.1) and sonicated (E220evolution Focused-ultrasonicator, Covaris) to generate 250-bp DNA fragments. Soluble chromatin was diluted eightfold in ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl at pH 8.1, and 167 mM NaCl). Chromatin was incubated overnight at 4°C with KDM1A or T7-tag antibodies and recovered using Dynabeads Protein G (Thermo Fisher Scientific). Beads were washed sequentially with buffers at different salt concentrations: low-salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1) and 150 mM NaCl), high-salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1) and 500 mM NaCl), lithium chloride wash buffer (0.25 M lithium chloride, 1% Nonidet P-40, 1% deoxycholate, 1 mM EDTA and 10 mM Tris-HCl (pH 8.1)) and TE buffer. Immunocomplexes were eluted in ChIP elution buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1) and 500 mM NaCl), at 30°C for 20 minutes and cross-linked overnight at 65°C. DNA was purified using QIAquick PCR columns (Qiagen) according to the manufacturer's instructions.
DNA libraries were generated using the MicroPlex Library Preparation Kit v2 (Diagenode) according to the manufacturer's instructions
ChIP-seq sequencing has been performed on Illunima Hiseq 4000 or Novaseq 6000 SP1 with 150 bp paired-edn method

treatment_protocol: hESC-derived cardiomyocytes were cultered on Vitronectin (VTN-N) coated plates in presence of differentiation medium and RNA extraction was performed around 15-18 of differentiation when the monolayer started beating

value: WT hESC

value: KDM1A (Abcam, ab17721, lot )

tag: name in the manuscript

value: H1 hESC (Time point)


title: DKO - leu-free diet - day 8 - mouse 3

value: Liver

value: Sesn2 DKO

value: Leucine-free

value: 8 days


title: DKO - leu-free diet - day 8 - mouse 4


title: DKO - leu-free diet - day 8 - mouse 2


description:
H1 hESC (Time point) - Input (Experiment#3)
Input Novaseq 6000 SP1 Replicate #3


title: case_296 mRNA-seq

description:
Yang_SysBio_case_296
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

tag: center

value: LTRC

value: ipf

value: case

value: f

value: black

value: N


title: Resident_MQs_D

description: CD45+ CD11B+ LY6G- F4/80+ MERTK+ MHCII- GFP- cells sorted by FACS

value: Skeletal muscle at steady state

value: Macrophage

value: Cx3cr1-GFP (male)


title: control_284 mRNA-seq

description:
Yang_SysBio_control_284
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: Pittsburgh Lung Donor Core

tag: dx

value: normal

value: control

value: m

value: white

value: not hispanic or latino


title: case_290 mRNA-seq

description:
Yang_SysBio_case_290
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

tag: rnaseqid

value: hispanic


title: DKO - leu-free diet - day 8 - mouse 1

value: Liver

value: Sesn2 DKO

value: Leucine-free

value: 8 days


description:
H1 hESC (Time point) - KDM1A ChIP (Experiment#1)
Chip-SEQ HiSeq 4000 Replicate #1

value: WT hESC

value: KDM1A (Abcam, ab17721, lot )

value: H1 hESC (Time point)


title: Resident_MQs_C

description: CD45+ CD11B+ LY6G- F4/80+ MERTK+ MHCII- GFP+ cells sorted by FACS

value: Skeletal muscle at steady state

value: Macrophage


title: Resident_MQs_B

description: CD45+ CD11B+ LY6G- F4/80+ MERTK+ MHCII+ GFP+ cells sorted by FACS

value: Cx3cr1-GFP (male)


title: KDM1A KO hESC Rescued with 3XT7-ubKDM1A variant Bulk RNAseq Novaseq 6000 SP1 2353

description:
KDM1A KO hESC Rescued with 3XT7-ubKDM1A variant Bulk RNAseq Novaseq 6000 SP1
Bulk RNAseq Novaseq 6000 SP1

data_processing:
Bulk RNA-Seq data validation, pairing and FastQC quality control was followed by trimming using BBDuk by setting a minimum read length of 35 bp and a minimum Phred-quality score of 25. After trimming quality control, high quality reads were mapped against the reference genome (GrCh38 release 91) using the STAR end-to-end alignment method and gene expression quantification performed with featureCounts. Data normalization was performed with the Trimmed Mean of M-values (TMM) method
The pre-processing of single cell RNA-Seq data that includes the identification of cell barcodes and the steps of UMI detection, extraction and processing was performed using UMI-tools 1.0.1. Read quality control (QC) analyses and filtering of high-quality reads, were executed using FastQC and BBDuk with default options of minimum size 35 bp and minimum quality score 25 to perform adapter and quality trimming. To align the filtered reads to a human genome reference (GrCh38 release 91) STAR 2.7.3a was used, while FeatureCounts 1.6.3 package was used to assign reads to genes.
Genome_build: GrCh38 release 91

source_name: hESC H1

extract_protocol:
For bulk RNA-Seq libraries the RNA has been extracted using the Qiagen RNeasy Mini Kit according to manufacturer’s instructions
Bulk RNA libraries were generated using the human mRNA TruSeq Stranded library preparation KIT from Illumina.
Bulk RNA-Sequencing  was performed using HiSeq4000 and Novaseq 6000 SP1 systems (Illumina) with 150 bp paired-end sequencing method

tag: rna identifier

value: KDM1A KO + ubKDM1A-T7 tag Rescue cell line


title: case_283 mRNA-seq

description:
Yang_SysBio_case_283
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: National Jewish

value: ipf

value: case

tag: age

tag: Sex

value: Y


title: WT - leu-free diet - day 8 - mouse 6

value: WT


title: WT - leu-free diet - day 8 - mouse 5

value: Liver


title: WT - leu-free diet - day 8 - mouse 4


title: control_279 mRNA-seq

description:
Yang_SysBio_control_279
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: LTRC

value: control

value: f

tag: race

value: white

tag: ethnicity

value: not hispanic or latino


title: D2_200k_para_30

description: PI- CD45+ CD11B+ LY6G/SIGLECF- GFP+ cells sorted by FACS

value: Damaged Tibialis Anterior (TA)s 2 days post injury

tag: cell type

value: The WT partner of a WT/GFP  female parabiotic pair


title: KDM1A KO hESC Rescued with 3XT7-ubKDM1A variant Bulk RNAseq Novaseq 6000 SP1 2352


title: D4_50k_para_32

value: Damaged TAs 4 days post injury

value: Macrophage


title: WT - leu-free diet - day 8 - mouse 3

value: Leucine-free

value: 8 days


title: control_276 mRNA-seq

description:
Yang_SysBio_control_276
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: other

value: N

tag: raw data disclaimer


title: KDM1A KO hESC Rescued with 3XT7-ubKDM1A variant Bulk RNAseq Novaseq 6000 SP1 2341

value: KDM1A KO + ubKDM1A-T7 tag Rescue cell line


title: Adult_scRNA_Seq

city: Houston

first: Manuel

middle: Eliezer

last: Cantu Gutierrez

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Briefly, raw sequencing data were handled using the 10x Genomics Cell Ranger software (www.10xgenomics.com). Fastq files were mapped to the mm10 genome, and gene counts were quantified using the Cellranger count function. Subsequently, expression matrices from each experiment were merged and were then imported into Seurat (version 4.0.4) for log  normalization. Cells with a percentage of mitochondrial reads above 10% and with less than 250 features were filtered out. Batch effects were corrected by regressing out the number of mitochondrial read percentage using the vars.to.regress function. Doublet contamination was removed using DoubletFinder (version 2.0.3). Sample integration was achieved using SCTransform (version 0.3.2) before running principal component analysis (PCA) was performed and significant principal components were used for graph-based clustering. UMAP was used for 2-dimensional visualization (https://github.com/lmcinnes/umap). Differential expression of genes per cluster was performed using the Wilcoxon rank sum test (FindMarkers function default). For pseudotemporal analysis, normalized data from endothelial cells were passed from Seurat to Monocle2 (version 2.20.2). The Monocle2 BEAM statistical test was utilized to determine genes changing in a pseudo temporal manner.
Genome build: mm10
Cell barcodes, matrix and features/genes

source_name: Brain

extract_protocol:
Processing of brain tissue at different timepoints for MACS was different for embryonic tissue and postnatal. For embryonic brains (E9.5, E12.5, E16.5), the embryos were harvested in cold Buffer HBSS++ (HBSS plus FBS, penstrep and HEPES). Dissected brain was placed in 250ul of Collagenase (1mg/ml) and placed at 37C for 15 minutes. Tissue was pipetted up and down gently every two minutes, first with a P1000 and then with a P200, very few to no clumps of tissue should be seen at the end of the dissociation. For P8 and adult brain, cortex was dissected, and cells were dissociated using the neural tissue dissociation kit P (Miltenyi # 130-092-628). At this point for both, the cell suspension was pelleted (5min @ 800g), the pellet was washed two times with PBS and then resuspended in 180 uL MACS PEB buffer (phosphate-buffered saline (PBS), pH 7.2, 0.5% bovine serum albumin (BSA), and 2 mM EDTA. The cell suspension was then incubated for 15 minutes with 20 uL of anti-CD31 MicroBeads (Miltenyibiotec, Cat. No. 130-097-418) at 4°C. Cells were then washed with 1 mL of PEB buffer, centrifuged at 300 xg for 5 minutes, and applied to an MS Column (Miltenyi Biotec, Cat. No. 130-042-201) on a magnetic stand. Cells were collected after three consecutive washes with 0.5 mL of PEB. These cells were then pelleted at 300 xg for 10 minutes at 4°C, then resuspended in 1x PBS at a concentration of 50,000 cells per 50 uL in a total of 50 uL with a viability ≥ 90% and then used for downstream applications (see below).
The scRNA-Seq libraries were generated using the 10x Chromium Single Cell 3′ v2 reagent kit, according to the manufacturer’s instructions, and were sequenced on an Illumina Nextseq500.

tag: cell type source

value: Brain cortex

value: Adult


title: KDM1A KO hESC Rescued with 3XT7-ubKDM1A variant Bulk RNAseq Novaseq 6000 SP1 2340


title: WT - leu-free diet - day 8 - mouse 2

value: Liver

value: WT

tag: diet


title: WT - leu-free diet - day 8 - mouse 1

tag: timepoint


title: P8_scRNA_Seq


title: case_275 mRNA-seq

description:
Yang_SysBio_case_275
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: LTRC

value: ipf

value: case

value: m

value: Y


title: E16_5_scRNA_Seq

value: Brain


title: KDM1A KO hESC Rescued with 3XT7-KDM1A+2a variant Bulk RNAseq Novaseq 6000 SP1 2309

description:
KDM1A KO hESC Rescued with 3XT7-KDM1A+2a variant Bulk RNAseq Novaseq 6000 SP1
Bulk RNAseq Novaseq 6000 SP1

value: KDM1A KO + KDM1A+2a-T7 tag Rescue cell line


title: case_274 mRNA-seq

description:
Yang_SysBio_case_274
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: white

value: not hispanic or latino


title: KDM1A KO hESC Rescued with 3XT7-KDM1A+2a variant Bulk RNAseq Novaseq 6000 SP1 2308


title: control_282 mRNA-seq

description:
Yang_SysBio_control_282
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: Pittsburgh Lung Donor Core

value: normal

value: control


title: control_273 mRNA-seq

description:
Yang_SysBio_control_273
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: other

value: f

value: black

value: U


title: Resident_MQs_A

description: CD45+ CD11B+ LY6G- F4/80+ MERTK+ MHCII+ GFP- cells sorted by FACS

value: Skeletal muscle at steady state

value: Macrophage

tag: genotype

value: Cx3cr1-GFP (male)


title: E12_5_scRNA_Seq


title: KDM1A KO hESC Rescued with 3XT7-KDM1A+2a variant Bulk RNAseq Novaseq 6000 SP1 2307


title: case_272 mRNA-seq

description:
Yang_SysBio_case_272
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

tag: tissue

value: LTRC

value: ipf

value: case

value: m

value: White


title: DKO - control diet - day 8 - mouse 4

value: Liver

value: Sesn2 DKO

value: Control

value: 8 days


title: control_271 mRNA-seq

description:
Yang_SysBio_control_271
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: Pittsburgh Lung Donor Core

value: normal

value: control

value: white

value: not hispanic or latino

value: N


title: DKO - control diet - day 8 - mouse 3


title: KDM1A+2a KO hESC derived with CRISPR-Cas9 Bulk RNAseq HiSeq 4000 1151

description:
KDM1A+2a KO hESC derived with CRISPR-Cas9 Bulk RNAseq HiSeq 4000
Bulk RNAseq HiSeq 4000

value: KDM1A+2a KO Clone #1


title: P6_Retina_Input_Rep2_RNA

data_processing:
Reads were first mapped to the mouse genome (mm10) using Salmon (version 1.5.1) (Patro, Duggal et al. 2017). Transcript level quantification was then imported using txtimport (version 1.20.0) (Soneson, Love et al. 2015) and analyzed using DESeq2 (Love, Huber et al. 2014).
Genome build: mm10
sf abundance quantification file: Plain-text, tab-separated file with a single header line (which names all of the columns) that contains Name, Length, EffectiveLength, TPM and NumReads

molecule: nuclear RNA

source_name: Retina

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).
In parallel to our ATAC-seq experiments, all remaining bead-bound EGFP+ nuclei were processed for RNA extraction using the RNEasy Plus Micro kit (Qiagen). Nuclear RNA-seq libraries were constructed with the Stranded RNA-seq Kit with Ribo Erase (cat #  KK8484, Kapa Biosystems) with custom Y-shaped adapters. Paired-end 2 x 75 bp NSQ 500/550 Hi Output KT v2.5 - 75 CYS Cat # 20024906) was performed for RNA-seq libraries on an Illumina Nextseq 500 instrument.

value: Input


title: KDM1A+2a KO hESC derived with CRISPR-Cas9 Bulk RNAseq HiSeq 4000 1282


title: E9_5_scRNA_Seq

value: Brain


title: KDM1A+2a KO hESC derived with CRISPR-Cas9 Bulk RNAseq HiSeq 4000 1276


title: DKO - control diet - day 8 - mouse 2


title: case_270 mRNA-seq

description:
Yang_SysBio_case_270
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

data_processing:
For RNA, RNA paired-end reads were aligned at the gene level to Ensembl GrCh38 using Kallisto {Bray, 2016, 27043002}. Genes and transcripts were detected in the mRNA dataset using hg38 Gencode v27 and filter of at least 6 reads in at least 20% of the samples, TMM normalized across all samples, and then inverse normalization transformed on a per-gene basis.
Genome_build: GRCh38
Supplementary_files_format_and_content: For RNA-seq, the gene-level filtered and normalized count file is included as a processed data file

extract_protocol:
RNA was isolated from the same sample of lung tissue using the AllPrep kit (Qiagen). Samples with RNA integrity number (RIN) and DNA integrity number (DIN) >5 were used.
mRNA libraries were prepared from 500 ng total RNA with TruSeq stranded mRNA library preparation kits (illumina) and sequenced at the average depth of 80M reads on the Illumina NovaSeq 6000 (illumina).

value: LTRC

value: ipf

value: case

value: f


title: DKO - control diet - day 8 - mouse 1

value: Liver

value: Sesn2 DKO


title: KDM1A+2a KO hESC derived with CRISPR-Cas9 Bulk RNAseq HiSeq 4000 1153

value: KDM1A+2a KO Clone #2


title: P6_Retina_Input_Rep1_RNA


title: P6_Retina_Endo_Rep2_RNA

value: Endothelial


title: control_269 mRNA-seq

description:
Yang_SysBio_control_269
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: Pittsburgh Lung Donor Core

value: m


title: case_268 mRNA-seq

description:
Yang_SysBio_case_268
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: black


title: WT - control diet - day 8 - mouse 5

value: WT

value: Control

value: 8 days


title: P6_Retina_Endo_Rep1_RNA


title: DKO - control diet - day 8 - mouse 5


title: KDM1A+2a KO hESC derived with CRISPR-Cas9 Bulk RNAseq HiSeq 4000 1283


title: WT - control diet - day 8 - mouse 4


title: control_267 mRNA-seq

description:
Yang_SysBio_control_267
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: normal

value: control

value: white

value: not hispanic or latino

value: Y


title: case_266 mRNA-seq

description:
Yang_SysBio_case_266
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: LTRC

value: ipf

value: case

value: f

value: White

value: N


title: WT - control diet - day 8 - mouse 2

value: Liver


title: WT - control diet - day 8 - mouse 3


title: KDM1A+2a KO hESC derived with CRISPR-Cas9 Bulk RNAseq HiSeq 4000 1277

value: KDM1A+2a KO Clone #2


title: control_264 mRNA-seq

description:
Yang_SysBio_control_264
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: other

value: m

value: U


title: P6_Lung_Endo_Rep2_RNA

source_name: Lung

value: Endothelial


title: control_262 mRNA-seq

description:
Yang_SysBio_control_262
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: control


title: DKO - leu-free diet - day 1 - mouse 18

value: Sesn2 DKO

value: Leucine-free

value: 24 hours


title: WT - control diet - day 8 - mouse 1

value: WT

value: Control

value: 8 days


title: P6_Lung_Endo_Rep1_RNA


title: case_261 mRNA-seq

description:
Yang_SysBio_case_261
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: LTRC

value: ipf

value: case

value: f

value: white

value: not hispanic or latino


title: P6_Liver_Input_Rep2_RNA

value: Input


title: P6_Liver_Input_Rep1_RNA


title: DKO - leu-free diet - day 1 - mouse 17

value: Liver


title: control_260 mRNA-seq

description:
Yang_SysBio_control_260
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: other

value: Y


title: KDM1A KO hESC derived with CRISPR-Cas9 Bulk RNAseq HiSeq 4000 1297

description:
KDM1A KO hESC derived with CRISPR-Cas9 Bulk RNAseq HiSeq 4000
Bulk RNAseq HiSeq 4000

value: KDM1A KO hESC derived with CRISPR-Cas9

value: KDM1A KO Clone #1


title: KDM1A KO hESC derived with CRISPR-Cas9 Bulk RNAseq HiSeq 4000 1298

value: KDM1A KO Clone #2


title: KDM1A KO hESC derived with CRISPR-Cas9 Bulk RNAseq HiSeq 4000 1657


title: KDM1A KO hESC derived with CRISPR-Cas9 Bulk RNAseq HiSeq 4000 397


title: P6_Liver_Endo_Rep2_RNA

value: Endothelial


title: case_259 mRNA-seq

description:
Yang_SysBio_case_259
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***


title: P6_Lung_Input_Rep2_RNA


title: DKO - leu-free diet - day 1 - mouse 16

value: Sesn2 DKO

value: Leucine-free

value: 24 hours


title: DKO - leu-free diet - day 1 - mouse 15


title: KDM1A KO hESC derived with CRISPR-Cas9 Bulk RNAseq HiSeq 4000 372


title: KDM1A+2a-/- hESC-Derived Cardiomyocytes Bulk RNAseq HiSeq 4000 1334

description:
KDM1A+2a-/- hESC-Derived Cardiomyocytes Bulk RNAseq HiSeq 4000
Bulk RNAseq HiSeq 4000

source_name: Cardiomyocytes

value: KDM1A+2a-/- hESC-Derived Cardiomyocytes

value: KDM1A+2a-/-  Clone #2 -derived cardiomyocytes


title: P6_Lung_Input_Rep1_RNA


title: P6_Liver_Endo_Rep1_RNA


title: P6_Kidney_Input_Rep2_RNA

source_name: Kidney


title: DKO - leu-free diet - day 1 - mouse 14


title: control_253 mRNA-seq

description:
Yang_SysBio_control_253
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

source_name: tissue-Explant

value: LTRC

value: control

value: f

value: black

value: N


title: control_254 mRNA-seq

description:
Yang_SysBio_control_254
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: m

value: white

value: not hispanic or latino


title: KDM1A+2a-/- hESC-Derived Cardiomyocytes Bulk RNAseq HiSeq 4000 892


title: DKO - leu-free diet - day 1 - mouse 13

value: Liver


title: KDM1A+2a-/- hESC-Derived Cardiomyocytes Bulk RNAseq HiSeq 4000 1343

value: KDM1A+2a-/-  Clone #1 -derived cardiomyocytes


title: P6_Kidney_Input_Rep1_RNA

value: Input


title: case_252 mRNA-seq

description:
Yang_SysBio_case_252
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: ipf

value: case

value: Y


title: DKO - leu-free diet - day 1 - mouse 12

value: Sesn2 DKO

value: Leucine-free

value: 24 hours


title: KDM1A+2a-/- hESC-Derived Cardiomyocytes Bulk RNAseq HiSeq 4000 1335

value: KDM1A+2a-/- hESC-Derived Cardiomyocytes

value: KDM1A+2a-/-  Clone #2 -derived cardiomyocytes


title: DKO - leu-free diet - day 1 - mouse 10


title: DKO - leu-free diet - day 1 - mouse 11


title: ubKDM1A-/- hESC-Derived Cardiomyocytes Bulk RNAseq Novaseq 6000 SP1 1069

description:
ubKDM1A-/- hESC-Derived Cardiomyocytes Bulk RNAseq Novaseq 6000 SP1
Bulk RNAseq Novaseq 6000 SP1

value: ubKDM1A-/- hESC-Derived Cardiomyocytes

value: KDM1A-/- Clone #1 -derived cardiomyocytes WT


title: P6_Heart_Input_Rep2_RNA

source_name: Heart


title: P6_Kidney_Endo_Rep1_RNA

value: Endothelial


title: case_247 mRNA-seq

description:
Yang_SysBio_case_247
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: LTRC

value: m

value: White

value: N


title: control_257 mRNA-seq

description:
Yang_SysBio_control_257
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: other

value: control

value: white

value: not hispanic or latino


title: P6_Heart_Input_Rep1_RNA

value: Input


title: P6_Heart_Endo_Rep2_RNA


title: DKO - leu-free diet - day 1 - mouse 9

value: Liver

value: Sesn2 DKO

value: Leucine-free


title: ubKDM1A-/- hESC-Derived Cardiomyocytes Bulk RNAseq Novaseq 6000 SP1 1131


title: case_246 mRNA-seq

description:
Yang_SysBio_case_246
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: ipf

value: case

value: black

value: hispanic


title: DKO - leu-free diet - day 1 - mouse 8

value: 24 hours


title: control_245 mRNA-seq

description:
Yang_SysBio_control_245
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: Pittsburgh Lung Donor Core

value: normal

value: f

value: Y


title: DKO - leu-free diet - day 1 - mouse 7


title: KDM1A+2a-/- hESC-Derived Cardiomyocytes Bulk RNAseq HiSeq 4000 1342

value: KDM1A+2a-/- hESC-Derived Cardiomyocytes

value: KDM1A+2a-/-  Clone #1 -derived cardiomyocytes


title: P6_Brain_Input_Rep2_RNA


title: case_244 mRNA-seq

description:
Yang_SysBio_case_244
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: LTRC

value: m

value: White

value: not hispanic or latino


title: P6_Kidney_Endo_Rep2_RNA

value: Endothelial


title: P6_Heart_Endo_Rep1_RNA


title: islets, SMNDC1_sh3_D3

first: Stefan

last: Kubicek

address: Lazarettgasse 14

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

data_processing:
Illumina HiSeq Control Software (HCS) HD 3.4.0.38 was used for the data acquisition on the sequencing instrument.
On-instrument base-calling performed by the Illumina Real-Time Analysis (RTA) software 2.7.7.
BCL to BAM file conversion and demultiplexing with custom programmes (https://github.com/epigen/picard/) based on Picard tools 2.19.2 (https://broadinstitute.github.io/picard/)
Spliced genome alignments to GRCh38 (UCSC Genome Browser hg38) and Ensembl reference transcriptome e100 (April 2020) with STAR 2.7.5a and options recommended by the ENCODE project (--alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --outFilterMultimapNmax 20 --outFilterType BySJout)
Differential expression modelling with Bioconductor 3.12 package DESeq2 1.30.0, running under R 4.0.
Genome_build: UCSC hg38 based on GRCh38
Supplementary_files_format_and_content: Per gene and sample raw (integer) counts and DESeq2-calculated FPKMs in tab-separated value (TSV) format

source_name: islets, SMNDC1_sh3_D3

extract_protocol:
RNA was isolated using the RNeasy Micro Kit (Qiagen), including DNase treatment, following the manufacturer’s instructions.
Low-input full-length cDNA, was prepared with the Smart-seq2 protocol (Picelli, S. et al, Nat Protoc. 2014 Jan;9(1):171-81. doi:10.1038/nprot.2014.006) and subsequently the Nextera XT DNA library prep kit (Illumina). Library amounts were quantified using the Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the size distribution was assessed using the Experion Automated Electrophoresis System (Bio-Rad). For sequencing, libraries were pooled, diluted and sequenced on Illumina HiSeq 3000/4000 instruments using 75 bp paired-end chemistry.

value: pancreatic human islets

tag: donor

tag: treatment

value: transduced with SMNDC1 shRNA #3


title: DKO - leu-free diet - day 1 - mouse 6

value: Liver

value: Sesn2 DKO

value: Leucine-free