title: WT hESC-Derived Cardiomyocytes Bulk RNAseq Novaseq 6000 SP1 890

description:
WT hESC-Derived Cardiomyocytes Bulk RNAseq Novaseq 6000 SP1
Bulk RNAseq Novaseq 6000 SP1

value: WT hESC-Derived Cardiomyocytes

tag: name in the manuscript

value: H1-derived cardiomyocytes WT


title: control_250 mRNA-seq

status: Public on Jul 01 2022

type: SRA

city: Aurora

first: Ivana

last: Yang

state: CO

country: USA

institute: University of Colorado Anschutz Medical Campus

description:
Yang_SysBio_control_250
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

library_source: transcriptomic

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

molecule: total RNA

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).

tag: tissue

value: lung

tag: center

value: LTRC

tag: dx

value: other

value: control

tag: rnaseqid

tag: age

tag: Sex

value: f

tag: race

value: white

tag: ethnicity

value: not hispanic or latino

value: Y

tag: raw data disclaimer


title: control_241 mRNA-seq

description:
Yang_SysBio_control_241
*** 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: m

value: N


title: KDM1A+2a-/- hESC-Derived Cardiomyocytes Bulk RNAseq HiSeq 4000 1345

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

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: Cardiomyocytes

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:
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

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

tag: cell type

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

tag: rna identifier

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


title: DKO - leu-free diet - day 1 - mouse 5

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

organism: Mus musculus

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

tag: genotype

value: Sesn2 DKO

tag: diet

value: Leucine-free

tag: timepoint

value: 24 hours


title: case_242 mRNA-seq

description:
Yang_SysBio_case_242
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

source_name: tissue-Unknown

value: lung

value: LTRC

value: ipf

value: case

value: White

value: hispanic


title: islets, Empty_Vector_D3

city: Vienna

first: Stefan

last: Kubicek

address: Lazarettgasse 14

country: Austria

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, Empty_Vector_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 control empty vector


title: P6_Brain_Input_Rep1_RNA

city: Houston

first: Manuel

middle: Eliezer

last: Cantu Gutierrez

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

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: Brain

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

tag: cell type source

value: Input


title: P6_Brain_Endo_Rep2_RNA

value: Endothelial


title: case_240 mRNA-seq

description:
Yang_SysBio_case_240
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

tag: tissue

value: m

value: not hispanic or latino

value: U


title: islets, SMNDC1_sh1_D3

source_name: islets, SMNDC1_sh1_D3

value: transduced with SMNDC1 shRNA #1


title: control_239 mRNA-seq

description:
Yang_SysBio_control_239
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

tag: center

value: Pittsburgh Lung Donor Core

value: normal

value: control

value: f

value: white

value: N


title: DKO - leu-free diet - day 1 - mouse 3

value: Liver

value: Sesn2 DKO

value: Leucine-free

value: 24 hours


title: islets, SMNDC1_sh1_D5

source_name: islets, SMNDC1_sh1_D5

value: pancreatic human islets


title: control_235 mRNA-seq

description:
Yang_SysBio_control_235
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

tag: dx


title: WT hESC-Derived Cardiomyocytes Bulk RNAseq Novaseq 6000 SP1 1341

value: WT hESC-Derived Cardiomyocytes

tag: name in the manuscript

value: H1-derived cardiomyocytes WT


title: DKO - leu-free diet - day 1 - mouse 2


title: P6_Brain_Endo_Rep1_RNA

value: Endothelial

tag: age


title: islets, Empty_Vector_2_D5

source_name: islets, Empty_Vector_2_D5

value: transduced with control empty vector


title: islets, Empty_Vector_1_D5

source_name: islets, Empty_Vector_1_D5


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


title: case_234 mRNA-seq

description:
Yang_SysBio_case_234
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: LTRC

value: ipf

value: case

tag: rnaseqid

tag: Sex

value: m

value: White

value: not hispanic or latino

value: Y


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

value: Liver

value: WT


title: case_233 mRNA-seq

description:
Yang_SysBio_case_233
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

tag: race

tag: ethnicity


title: DKO - leu-free diet - day 1 - mouse 4

value: Sesn2 DKO

value: Leucine-free


title: E12_Trunk_Input_Rep1_RNA

source_name: Trunk

value: Input


title: HBEC_1075_rep2_IL13

city: San Francisco

first: David

last: Erle

state: CA

address: 555 Mission Bay Blvd

institute: UCSF

library_source: genomic

data_processing:
Library strategy: CUT&Tag
alignment with STAR
peak calling with MACS2
IDR to find reproducible peaks between samples
Genome_build: hg38
Supplementary_files_format_and_content: wig file, average count of reads per million between 2 replicates

molecule: genomic DNA

source_name: HBECs

growth_protocol: Three donors of HBECs were seeded on HPC-coated Transwells and cultured at ALI for 23 d.

extract_protocol:
After removal of accumulated mucus with 10 mM DTT in PBS, cells were trypsinized with 0.25% trypsin-EDTA for 10 min at 37 °C and neutralized.
Preparation of sequencing libraries for CUT&Tag against KLF5 was conducted using a Hyperactive pA-Tn5 In-Situ ChIP Library Prep Kit for Illumina (Vazyme Biotech Co., Nanjing, China) with slight modifications to the manufacturer’s protocol. The following antibodies were used in the protocol: anti-KLF5 (ab137676, rabbit IgG; Abcam) and normal rabbit IgG as negative control (NI01; Sigma-Aldrich). No secondary antibody was used. Starting cell amount was 500,000 cells, and primary antibody incubation was done overnight. Post-amplification, magnetic bead-based clean-up (HighPrep PCR Clean-up System; MAGBIO Genomics, Gaithersburg, MD) were conducted twice for each clean-up step. We have used a small amount of the tagmented and pre-amplified library to set the final number of cycles needed for final library amplification. The Ct for which the library had reached 1/3 of its max Rn was set independently for each sample.

treatment_protocol: Cells were left unstimulated or treated with IL-13 (10 ng/mL) for last 7 d of culture.

tag: cell type

value: ALI-cultured HBECs d 23

tag: chip antibody


title: E12_Trunk_Endo_Rep1_RNA


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

tag: genotype

value: 24 hours


title: case_230 mRNA-seq

description:
Yang_SysBio_case_230
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: f

tag: raw data disclaimer


title: E12_Brain_Input_Rep1_RNA


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

tag: diet

tag: timepoint


title: control_228 mRNA-seq

description:
Yang_SysBio_control_228
*** 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: white

value: N


title: E12_Trunk_Endo_Rep2_RNA

value: Endothelial


title: HBEC_1430_rep2_IL13

tag: treatment


title: control_226 mRNA-seq

description:
Yang_SysBio_control_226
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: LTRC

value: other

value: m

value: not hispanic or latino


title: case_229 mRNA-seq

description:
Yang_SysBio_case_229
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: ipf

value: case

value: White

value: Y


title: HBEC_1332_rep2_IL13

value: ALI-cultured HBECs d 23


title: E12_Brain_Endo_Rep2_RNA

tag: cell type source


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

tag: tissue

value: Liver

value: WT

value: Leucine-free

value: 24 hours


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


title: E12_Brain_Endo_Rep1_RNA


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


title: Adult_Retina_Input_Rep2_RNA

source_name: Retina

value: Input

value: Adult


title: HBEC_1430_rep1_IL13


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


title: Adult_Retina_Input_Rep1_RNA


title: HBEC_1332_rep1_IL13


title: case_225 mRNA-seq

description:
Yang_SysBio_case_225
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

tag: center

value: f

value: white


title: control_224 mRNA-seq

description:
Yang_SysBio_control_224
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: LTRC

tag: dx

value: other

value: control

value: U


title: HBEC_1430_rep2_UT

value: Untreated


title: case_219 mRNA-seq

description:
Yang_SysBio_case_219
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: ipf

value: case

value: m

value: not hispanic or latino


title: WT - leu-free diet - day 1 - mouse 4

value: Liver

value: WT


title: WT - leu-free diet - day 1 - mouse 5

value: Leucine-free

value: 24 hours


title: HBEC_1332_rep2_UT

value: ALI-cultured HBECs d 23


title: Adult_Retina_Endo_Rep2_RNA

value: Endothelial

value: Adult


title: control_220 mRNA-seq

description:
Yang_SysBio_control_220
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: white

value: Y


title: Adult_Retina_Endo_Rep1_RNA


title: HBEC_1075_rep1_UT


title: Adult_Lung_Input_Rep2_RNA

source_name: Lung

value: Input


title: HBEC_1430_rep1_UT


title: control_215 mRNA-seq

description:
Yang_SysBio_control_215
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: LTRC

value: other

value: control

value: f

value: U


title: HBEC_1075_rep1_IL13


title: WT - leu-free diet - day 1 - mouse 3


title: Adult_Lung_Input_Rep1_RNA


title: control_217 mRNA-seq

description:
Yang_SysBio_control_217
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: m

value: not hispanic or latino


title: HBEC_1075_rep2_UT

value: Untreated


title: WT - leu-free diet - day 1 - mouse 2

value: Liver

value: WT

value: Leucine-free


title: Adult_Lung_Endo_Rep2_RNA

value: Endothelial


title: Adult_Liver_Input_Rep1_RNA

value: Adult


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

value: 24 hours


title: case_214 mRNA-seq

description:
Yang_SysBio_case_214
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: ipf

value: case

value: asian


title: Adult_Lung_Endo_Rep1_RNA


title: HBEC_1332_rep1_UT

value: ALI-cultured HBECs d 23


title: Adult_Liver_Endo_Rep2_RNA


title: L0512_MEOX2_rep3

city: Heidelberg

first: Sevin

last: Turcan

address: Im Neuenheimer Feld 460

country: Germany

institute: Heidelberg University Hospital

description: MEOX2 overexpression

data_processing:
The RNAseq data were analysed with the DKFZ/ODCF RNAseq workflow (https://github.com/DKFZ-ODCF/RNAseqWorkflow,v1.2.22-6).
FASTQ reads for individual samples were aligned by a 2 pass alignment using the STAR aligner v2.5.2b. Reads were aligned to a STAR index generated from the 1000 genomes assembly, gencode 19 gene models. Duplicate marking of the resultant main alignment file was done with sambamba v0.6.5. BAM indexes were generated using sambamba. Quality control analysis was performed using the samtools flagstat command (samtools v1.6), and the rnaseqc tool.
Featurecounts was used to perform gene specific read counting over exon features based on the gencode 19 gene models. Strand unspecific counting was used.
Genome_build: hg19 (1KGRef_PhiX)
Supplementary_files_format_and_content: tab-delimited text file of raw feature counts for each sample

source_name: Glioblastoma

extract_protocol:
RNA was isolated using an RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol.
RNA-Seq libraries were prepared using an Illumina RNA-Seq Preparation Kit and sequenced (Illumina HiSeq 4000, single-end 50-bp).

value: brain

value: MEOX2 overexpression


title: DKO - control diet - day 1 - mouse 5

value: Sesn2 DKO

value: Control


title: DKO - control diet - day 1 - mouse 7


title: case_211 mRNA-seq

description:
Yang_SysBio_case_211
*** 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

value: Y


title: DKO - control diet - day 1 - mouse 6

value: Liver


title: L0512_MEOX2_rep2

description: MEOX2 overexpression


title: L0512_empty_vector_rep2

description: overexpression control

value: empty vector


title: case_207 mRNA-seq

description:
Yang_SysBio_case_207
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: f

value: multiple-unspecified

value: N


title: case_210 mRNA-seq

description:
Yang_SysBio_case_210
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: ipf

value: case

value: U


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

value: 24 hours


title: L0512_MEOX2_rep1

description: MEOX2 overexpression

value: brain

value: MEOX2 overexpression


title: control_213 mRNA-seq

description:
Yang_SysBio_control_213
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: LTRC

value: other

value: control


title: Adult_Liver_Input_Rep2_RNA

value: Input

value: Adult


title: Adult_Kidney_Input_Rep2_RNA

source_name: Kidney


title: Adult_Liver_Endo_Rep1_RNA

value: Endothelial


title: L0512_empty_vector_rep1

description: overexpression control

value: empty vector


title: case_202 mRNA-seq

description:
Yang_SysBio_case_202
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: m

value: white

value: not hispanic or latino

value: Y


title: L0125_MEOX2_rep3

description: MEOX2 overexpression


title: control_203 mRNA-seq

description:
Yang_SysBio_control_203
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: f


title: Adult_Kidney_Input_Rep1_RNA


title: DKO - control diet - day 1 - mouse 3

value: Liver

value: Sesn2 DKO

value: Control


title: case_201 mRNA-seq

description:
Yang_SysBio_case_201
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

source_name: tissue-Biopsy

value: ipf

value: case


title: DKO - control diet - day 1 - mouse 2

value: 24 hours


title: Adult_Kidney_Endo_Rep2_RNA


title: L0125_MEOX2_rep2

description: MEOX2 overexpression

value: brain

value: MEOX2 overexpression


title: Adult_Kidney_Endo_Rep1_RNA

value: Adult


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


title: DKO - control diet - day 1 - mouse 4


title: L0125_empty_vector_rep3

description: overexpression control


title: case_197 mRNA-seq

description:
Yang_SysBio_case_197
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: LTRC


title: WT - control diet - day 1 - mouse 7

value: WT


title: WT - control diet - day 1 - mouse 5


title: Adult_Heart_Input_Rep2_RNA

source_name: Heart

value: Input


title: WT - control diet - day 1 - mouse 6


title: control_196 mRNA-seq

description:
Yang_SysBio_control_196
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

source_name: tissue-Explant

value: other

value: control

value: m

value: white


title: Adult_Heart_Input_Rep1_RNA


title: L0125_empty_vector_rep2

description: overexpression control

value: empty vector


title: Adult_Heart_Endo_Rep2_RNA

value: Endothelial


title: L0125_empty_vector_rep1

description: overexpression control


title: WT - control diet - day 1 - mouse 4

source_name: Liver

value: Liver


title: control_195 mRNA-seq

description:
Yang_SysBio_control_195
*** 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: not hispanic or latino

value: N


title: control_198 mRNA-seq

description:
Yang_SysBio_control_198
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***


title: Adult_Heart_Endo_Rep1_RNA

value: Adult


title: control_200 mRNA-seq

description:
Yang_SysBio_control_200
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: LTRC

value: Y


title: case_194 mRNA-seq

description:
Yang_SysBio_case_194
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: ipf

value: case


title: IHA_MEOX2_rep3

description: MEOX2 overexpression

source_name: Astrocytes

value: brain

value: immortalized human astrocytes

value: MEOX2 overexpression


title: WT - control diet - day 1 - mouse 2

value: WT

value: Control

value: 24 hours


title: IHA_MEOX2_rep2

description: MEOX2 overexpression


title: case_193 mRNA-seq

description:
Yang_SysBio_case_193
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: m

value: white


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

value: Liver


title: Adult_Brain_Input_Rep1_RNA

value: Input


title: Adult_Brain_Endo_Rep2_RNA

value: Endothelial


title: control_192 mRNA-seq

description:
Yang_SysBio_control_192
*** 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: f

value: not hispanic or latino


title: IHA_MEOX2_rep1

description: MEOX2 overexpression

value: brain


title: IHA_empty_vector_rep3

description: overexpression control

value: immortalized human astrocytes

value: empty vector


title: Day 4 – TSA 500nM rep. 3

city: Gainesville

first: Thomas

last: Schmittgen

state: FL - FLORIDA

address: 2033 Mowry Road

department: Pharmacy

institute: Univ of Florida

data_processing:
Quality control of sequences were performed using Trime Glore 0.5.0
low quality and adapter trimmed using Trim Glore 0.5.0
Read were aligned using Hisat2 (v 2.2.1) againes indexed mouse genome (Mus_musculus.GRCm39)
Read were quatified using featureCounts from subread package 2.0.0
Genome_build: GRCm39
Supplementary_files_format_and_content: Transcript read counts, rowes are transcript values, columns are samples

source_name: pancreatic acinar cells

growth_protocol: The acinar clusters were collected from fresh islet-depleted cell fractions containing digested acinar clusters from KC mouse pancreas.

extract_protocol:
Total RNA was extracted from Trizol lysate using Qiagen miRNesay Mini Kit
The preparation was performed using the reagents provided in the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760S, New England Biolabs,USA), in conjunction with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) and the NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs, NEB #6440s)

treatment_protocol: Five hundred nM of TSA or LLL12B treatments vs untreated controls of three-dimensional (3-D) culture of acinar cells on Matrigel

tag: agent

value: TSA 500nM


title: IHA_empty_vector_rep2

description: overexpression control


title: Adult_Brain_Endo_Rep1_RNA

source_name: Brain

tag: age

value: Adult


title: WT - control diet - day 1 - mouse 3

value: WT

value: Control

value: 24 hours


title: ATAC_Trunk_Input_E12_1

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

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


title: case_189 mRNA-seq

description:
Yang_SysBio_case_189
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: LTRC

value: ipf

value: case

tag: rnaseqid

value: white

value: Y


title: Day 4 – TSA 500nM rep. 2


title: ATAC_Trunk_Endothelial_E12_4

value: Endothelial


title: Day 4 – TSA 500nM rep. 1


title: IHA_empty_vector_rep1

description: overexpression control


title: TS667_MEOX2_KD2_rep2

description: MEOX2 knockdown 2

value: MEOX2 sgRNA2


title: Day 4 – LLL12B 500nM rep. 3

value: LLL12B 500nM


title: control_188 mRNA-seq

description:
Yang_SysBio_control_188
*** 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

tag: Sex

value: f

value: not hispanic or latino

value: N


title: Day 4 – LLL12B 500nM rep. 2


title: ATAC_Trunk_Endothelial_E12_3


title: control_186 mRNA-seq

description:
Yang_SysBio_control_186
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: m

tag: race


title: case_185 mRNA-seq

description:
Yang_SysBio_case_185
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

tag: ethnicity


title: TS667_MEOX2_KD1_rep2

description: MEOX2 knockdown1

value: brain

tag: cell type

value: MEOX2 sgRNA1


title: ATAC_Trunk_Endothelial_E12_2


title: Day 4 – LLL12B 500nM rep. 1


title: TS667_MEOX2_KD2_rep1

description: MEOX2 knockdown 2


title: case_183 mRNA-seq

description:
Yang_SysBio_case_183
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: LTRC


title: TS667_NTC_rep2

description: CRISPR-Cas9 control

value: non-targeting sgRNA


title: Day 4 – Control rep. 2

value: Control


title: case_190 mRNA-seq

description:
Yang_SysBio_case_190
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: ipf

value: case

value: white

value: U


title: control_177 mRNA-seq

description:
Yang_SysBio_control_177
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: Pittsburgh Lung Donor Core


title: ATAC_Trunk_Endothelial_E12_1

value: Endothelial


title: case_181 mRNA-seq

description:
Yang_SysBio_case_181
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

source_name: tissue-Unknown

value: White

value: Y


title: case_176 mRNA-seq

description:
Yang_SysBio_case_176
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: black

value: not hispanic or latino


title: ATAC_Retina_Input_P6_2

value: Input


title: control_182 mRNA-seq

description:
Yang_SysBio_control_182
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: normal

value: control

value: f

value: N


title: ATAC_Retina_Input_Adult_2

value: Adult


title: TS667_NTC_rep1

description: CRISPR-Cas9 control

value: brain

value: non-targeting sgRNA


title: Day 4 – Control rep. 3

value: Control


title: Day 4 – Control rep. 1


title: case_175 mRNA-seq

description:
Yang_SysBio_case_175
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: LTRC

value: ipf

value: case

value: m


title: S4_2Y_10X_RNA_28052020, S4-2Y

first: Samar

middle: Hayat Khan

last: Tareen

address: Babraham Hall, Babraham

country: United Kingdom

institute: Babraham Institute

data_processing:
Initial QC and counts generated via Cell Ranger v4.0
Data imported into Seurat v4.0.2 in R v4.0.5 and filtered to retain cell with <10% mitochondrial expression in total expression
Filtered data normalised via SCT v0.3.2 and filtered to remove multiplets via scDblFinder v1.4.0
Data projected in UMAP, clusters produced via Louvain algorithm, and cell types identified by known markers
Microglia, Oligodendrocytes and Astrocytes separated into subsets and analysed for differential expression using negative binomial tests
Pathway analysis performed using GAGE v2.44.0 and Pathview v1.34.0
Genome_build: Mus_musculus.GRCm38.101
Supplementary_files_format_and_content: Processed files are .RData files containing the respective seurat objects for the full data, the microglia, the oligodendrocytes and the astrocyte subsets

source_name: Sorted brain glia

growth_protocol: Mice 4 months of age or 24 months of age, at take-down

extract_protocol:
Cell sorting was performed using a Sony MA900 with a 100μm nozzle, with a panel including CD11b, CD45, CX3CR1, eBioscience™ Fixable Viability Dye eFluor™ 780, O4, ACSA-2 and PDGFRα for sorting glial cells.
Library preparations for the scRNA-seq was performed using 10X Genomics Chromium Single Cell 3’ Kit, v3 (10X Genomics)

treatment_protocol: Intravenous injection of PHP.GFAP-IL2 or PHP.GFAP-GFP, two months prior to take-down

tag: strain

value: glia

value: 2 years


title: ATAC_Retina_Input_P6_1


title: TS600_MEOX2_KD2_rep2

description: MEOX2 knockdown 2

value: MEOX2 sgRNA2


title: ATAC_Retina_Endothelial_P6_3

value: Endothelial


title: TS600_MEOX2_KD2_rep1

description: MEOX2 knockdown 2


title: ATAC_Retina_Input_Adult_1

value: Input


title: TS600_MEOX2_KD1_rep2

description: MEOX2 knockdown1

value: MEOX2 sgRNA1


title: TS600_MEOX2_KD1_rep1

description: MEOX2 knockdown1


title: TS667_MEOX2_KD1_rep1

description: MEOX2 knockdown1


title: S3_2Y_10X_RNA_28052020, S3-2Y


title: S2_2Y_10X_RNA_28052020, S2-2Y


title: ATAC_Retina_Endothelial_P6_2


title: TS600_NTC_rep1

description: CRISPR-Cas9 control


title: S6_2Y_10X_RNA_28052020, S6-2Y


title: control_170 mRNA-seq

description:
Yang_SysBio_control_170
*** 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: TS600_NTC_rep2

description: CRISPR-Cas9 control

value: brain

value: non-targeting sgRNA


title: ATAC_Retina_Input_P6_3


title: control_169 mRNA-seq

description:
Yang_SysBio_control_169
*** 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: f

value: N


title: ATAC_Retina_Endothelial_Adult_2

value: Adult


title: S1_2Y_10X_RNA_28052020, S1-2Y

value: glia

value: 2 years


title: case_168 mRNA-seq

description:
Yang_SysBio_case_168
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: ipf

value: case

value: m


title: ATAC_Retina_Endothelial_P6_1

value: Endothelial


title: S5_2Y_10X_RNA_28052020, S5-2Y


title: control_162 mRNA-seq

description:
Yang_SysBio_control_162
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: control

value: white


title: control_172 mRNA-seq

description:
Yang_SysBio_control_172
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: not hispanic or latino

value: Y


title: ATAC_Retina_Endothelial_Adult_1


title: UN259

city: Shanghai

first: Weili

last: Zhao

address: 197 Rui Jin Er Road

country: China

institute: Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
Read pairs were aligned  by Burrows–Wheeler Aligner version 0.7.13-r1126. Samtools version 1.3 was used to generate chromosomal coordinate-sorted bam files and to remove PCR duplications.
Transcript counts table files were generated by the HTSeq.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Lymphoma

extract_protocol:
Biopsy before treatment, flash frozen, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq RNA Sample Prep Kit)

treatment_protocol: Before treatment

tag: subtype

value: GCB

tag: disease state

value: DLBCL


title: S6_10X_4mos_03082020

value: 4 months


title: S4_10X_4mos_03082020


title: ATAC_Lung_Input_P6_2

value: Input


title: S5_10X_4mos_03082020


title: ATAC_Lung_Input_P6_3


title: UN210


title: UN193


title: S3_10X_4mos_03082020


title: case_161 mRNA-seq

description:
Yang_SysBio_case_161
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: LTRC

value: f

tag: raw data disclaimer


title: UN352


title: control_159 mRNA-seq

description:
Yang_SysBio_control_159
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: other

value: N


title: ATAC_Lung_Input_P6_1


title: S2_10X_4mos_03082020

value: glia


title: UN309


title: S1_10X_4mos_03082020


title: case_163 mRNA-seq

description:
Yang_SysBio_case_163
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: ipf

value: case


title: control_157 mRNA-seq

description:
Yang_SysBio_control_157
*** 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: m


title: multiplexed PDX tumor cells - PDX_tr1, PDX_tr2, PDX_1, PDX_2

city: Seattle

first: James

middle: H.

last: Park

state: WA

address: 1736 Belmont ave, Apt 105

institute: Institute for Systems Biology

data_processing:
reads aligned to human genome GRCh38
filter out cells < mimnum num of cells, filter genes < minium count per cell per in minimum number of cells
filter out cells < maximum % of mitochondrial genes
for hashtag-oligo-labeled samples, demultiplexing perofrmed using Seurat platform v3.2.2
Genome_build: GRCh38
Supplementary_files_format_and_content: h5 matrix file containing both barcode and feature information for each sample
Supplementary_files_format_and_content: tab separated values files for features and barcodes identified in single-cell RNA-seq (10X Genomics)
Supplementary_files_format_and_content: comma separated values files include gene coutns for genes and single-cells that passed QC for each sample

source_name: patient-derived xenograft

extract_protocol:
Single-nucleus RNA sequencing was performed using the 10X Chromium v2 system.
Library preparation was performed using 10x manufacturer instructions on an Illumina NovaSeq 6000.

value: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ

value: XRT/TMZ and untreated

value: patient-derived xenograft


title: circBNC2-KO-L-02 cell

city: guangzhou

first: peng

last: wang

address: 1838 North Guangzhou Avenue

institute: Southern Medical University

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5)software
The transcript abundances for each sample was estimated with StringTie（1.3.1c）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)
The mRNA reads were aligned to reference genome using STAR(2.5.2b)detecting backesplicec junction reads with CIRCexplore2 (2.2.6)
Genome_build: hg19
Supplementary_files_format_and_content: FPKM

source_name: L-02 cells

growth_protocol: Cells were cultured in 1640 supplemented with 10% Fetal Bovine Serum

extract_protocol:
Total RNA was extracted with TRIZol reagent. The total RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
Total RNA of each sample was used to prepare the RNA sequencing library 1)RNA fragment；2)Random primed first strand cDNA synthesis；3)dUTP based second strand cDNA synthesis;4)Adaptor ligation and PCR amplification.

treatment_protocol: Cas9 overexpressed Cells were infected with lentivirus carrying either empty vector or sgRNAs targeting BNC2 introns

tag: cell line

value: hepatocytes

value: sgRNA targeting BNC2 introns

tag: overexpression

value: Cas9 overexpression


title: ATAC_Lung_Input_Adult_1

tag: cell type source

value: Input

value: Adult


title: WT

tag: treatment

value: Empty vector


title: circBNC2-KO-HK2 Rep2

description: tubular epithelial cell line

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5)software
The transcript abundances for each sample was estimated with StringTie（1.3.1c）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)
The mRNA reads were aligned to reference genome using STAR(2.5.2b)detecting backesplicec junction reads with CIRCexplore2 (2.2.6)
Genome_build: hg19
Supplementary_files_format_and_content: The Fastq format file contains the sequence of reads and the sequencing quality of base.

source_name: HK2 cells

growth_protocol: Cells were cultured in DMEM/F12 supplemented with 10% Fetal Bovine Serum

tag: sgrna


title: ATAC_Lung_Endothelial_P6_2

value: Endothelial


title: control_154 mRNA-seq

description:
Yang_SysBio_control_154
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

tag: tissue

value: lung

tag: center

tag: dx

value: control

value: white

value: not hispanic or latino

value: Y


title: case_153 mRNA-seq

description:
Yang_SysBio_case_153
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: National Jewish

value: ipf

value: case

tag: rnaseqid

tag: age

value: multiple-unspecified

value: hispanic

value: N


title: control_147 mRNA-seq

description:
Yang_SysBio_control_147
*** 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

tag: Sex

value: m

tag: race


title: control_145 mRNA-seq

description:
Yang_SysBio_control_145
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: f

tag: ethnicity


title: ATAC_Lung_Endothelial_Adult_2

value: Adult


title: circBNC2-KO-HK2 Rep1

description: tubular epithelial cell line

value: sgRNA targeting BNC2 introns

value: Cas9 overexpression


title: WT-HK2 Rep2

description: tubular epithelial cell line

value: Empty vector


title: control_133 mRNA-seq

description:
Yang_SysBio_control_133
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: control

value: white


title: ATAC_Lung_Input_Adult_2

value: Input


title: control_137 mRNA-seq

description:
Yang_SysBio_control_137
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: not hispanic or latino

value: Y


title: ATAC_Lung_Endothelial_Adult_1

value: Endothelial


title: ATAC_Liver_Input_P6_4


title: UN261

value: GCB

value: DLBCL


title: case_132 mRNA-seq

description:
Yang_SysBio_case_132
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: UCSF

value: ipf

value: case


title: case_131 mRNA-seq

description:
Yang_SysBio_case_131
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: m

value: N


title: ATAC_Liver_Input_P6_3


title: ATAC_Lung_Endothelial_P6_1


title: ATAC_Liver_Input_Adult_2

value: Adult


title: case_130 mRNA-seq

description:
Yang_SysBio_case_130
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***


title: Monocytes - C53

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

data_processing:
Sequencing, data quality, reads repartition (e.g., for potential ribosomal contamination), and insert size estimation were performed using FastQC, Picard-Tools, Samtools and rseqc
Reads were mapped using STAR_2.4.0
Count on FAST DB gene annotations (GenoSplice) and normalization using Deseq
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file includes deseq normalized expression values for each gene and for each sample. Annotations from Human FAST DB v2018_1 were also provide

molecule: polyA RNA

source_name: Blood

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from peripheral blood (EDTA tubes) of patients P1 and P2 and healthy individuals provided from the Etablissement Francais du Sang using Pancoll density gradient tubes (PANbiotech). Following isolation, monocytes were selected from PBMCs by adherence for 1 hour and cultured for 24h at 37°C in 5% CO2 in the presence of RPMI 1640 supplemented with glutamine, 10% pooled human serum, 100 U/ml Penicillin and 100 mg/ml Streptomycin (PS).

extract_protocol:
RNeasy Mini Kit (Qiagen)
TruSeq Stranded mRNA kit (Illumina). The purification of PolyA containing mRNA molecules was performed using poly-T oligo attached magnetic beads from 1µg total RNA. Fragmentation using divalent cations under elevated temperature to obtain approximately 300bp pieces, double strand cDNA synthesis and Illumina adapters’ ligation and cDNA library amplification by PCR for sequencing. Sequencing is then carried out on paired-end 75 bp of Illumina HiSeq4000

treatment_protocol: no treatment

value: Blood

tag: cell type

value: Monocytes

value: Healthy individual


title: Monocytes - C52


title: ATAC_Liver_Input_Adult_1


title: Monocytes - HRF145

value: Patient 2 - Cytokine storm


title: ATAC_Liver_Endothelial_P6_2


title: L0125_MEOX2_rep1

description: MEOX2 overexpression

value: brain

value: MEOX2 overexpression


title: case_129 mRNA-seq

description:
Yang_SysBio_case_129
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: unknown

value: hispanic


title: Monocytes - HRF144

value: Patient 1 - Cytokine storm


title: ATAC_Liver_Endothelial_P6_1

value: Endothelial


title: control_128 mRNA-seq

description:
Yang_SysBio_control_128
*** 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: f

value: white

value: not hispanic or latino


title: case_127 mRNA-seq

description:
Yang_SysBio_case_127
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: UCSF

value: ipf

value: case

value: Y


title: ATAC_Liver_Endothelial_Adult_2

value: Adult


title: case_126 mRNA-seq

description:
Yang_SysBio_case_126
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: m

value: N


title: ATAC_Liver_Endothelial_Adult_1


title: WT-HK2 Rep1

description: tubular epithelial cell line

value: Empty vector

value: Cas9 overexpression


title: control_125 mRNA-seq

description:
Yang_SysBio_control_125
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung


title: UC3_VDJ

city: Oxford

first: Alison

last: Simmons

address: John Radcliffe Hospital/Headley Way

department: The MRC Weatherall Institute of Molecular Medicine

institute: University of Oxford

description:
TCR RNA
Sample34

data_processing:
Basecalling was performed using Illumina Casava software
Samples were demultiplexed using Illumina bcl2fasq software
Sequenced reads were processed, aligned and counts summarised using Cellranger pipeline
VDJ library sequenced reads were processed, aligned and clonotypes assembled using Cellranger pipeline
Genome_build: hg38
Supplementary_files_format_and_content: Compressed matrix files with raw UMI counts per sample
Supplementary_files_format_and_content: Tab-delimited text file with assembled TCR clonotypes per sample

source_name: Colon

extract_protocol:
Colonic biopsies stored in Cryostore DS10 (Sigma Aldrich) were processedall at the same time to avoid  batch effects. Biopsies were incubated in media with Collagenase and then  passed through 70-µm. Cell counts and viability were confirmed with a Countess II automated cell counter.
Chromium Single Cell 5′ scRNA-seq and VDJ Library & Gel Bead Kit
Paired-end

value: CD8+ T Cell

tag: disease

value: Ulcerative Colitis


title: UC2_VDJ

description:
TCR RNA
Sample33


title: case_124 mRNA-seq

description:
Yang_SysBio_case_124
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***


title: HC3_VDJ

description:
TCR RNA
Sample23

value: Healthy Control


title: UC1_VDJ

description:
TCR RNA
Sample24


title: ATAC_Kidney_Input_P6_3

value: Input


title: ATAC_Kidney_Input_P6_2


title: ATAC_Kidney_Input_P6_1


title: Adult_Brain_Input_Rep2_RNA


title: HC1_VDJ

description:
TCR RNA
Sample21


title: case_123 mRNA-seq

description:
Yang_SysBio_case_123
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***


title: control_122 mRNA-seq

description:
Yang_SysBio_control_122
*** 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: f


title: HC2_VDJ

description:
TCR RNA
Sample22


title: ATAC_Kidney_Endothelial_P6_2

value: Endothelial


title: UC3

description:
mRNA
Sample34


title: ATAC_Kidney_Endothelial_P6_1


title: case_120 mRNA-seq

description:
Yang_SysBio_case_120
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: UCSF

value: ipf

value: case

value: white

value: not hispanic or latino


title: UC2

description:
mRNA
Sample33


title: case_121 mRNA-seq

description:
Yang_SysBio_case_121
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: m

value: N


title: ATAC_Kidney_Input_Adult_2

value: Adult


title: ATAC_Kidney_Input_Adult_1


title: UC1

description:
mRNA
Sample24

value: CD8+ T Cell


title: ATAC_Kidney_Endothelial_Adult_2


title: control_119 mRNA-seq

description:
Yang_SysBio_control_119
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: black

value: unknown

value: U


title: HC2

description:
mRNA
Sample22

value: Healthy Control


title: case_118 mRNA-seq

description:
Yang_SysBio_case_118
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: Y


title: control_116 mRNA-seq

description:
Yang_SysBio_control_116
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: National Jewish

value: normal

value: control

value: f


title: HC1

description:
mRNA
Sample21


title: WT_Thapsigargin_3

city: South San Francisco

first: Mengshu

last: Xu

address: 561 Eccles Ave

institute: RAPT Therapeutics

data_processing:
FastQC
Kallisto Quant pseudoalignment transcript quatification against the mm10 transcriptome
Merge transcript-level TPM signals into gene-level TPMs
Genome_build: mm10
Supplementary_files_format_and_content: TPM matrix

source_name: MEF cells

growth_protocol: MEFs were grown in RPMI 1640 medium with 10% fetal bovine serum and 1% penicillin-streptomycin under standard conditions

extract_protocol:
Total RNA was extracted using standard Trizol Chloroform extraction followed by precipitation in isopropanol with glycogen as carrier
cDNA libraries were prepared with standard Illumina Stranded TruSeq protocols

treatment_protocol: Cells were treated to amino acid starvation (RPMI 1640 SILAC -Lys -Arg) or Thapsigargin (200nM) treatment for 6 hours to activate the GCN2 and PERK pathways, respectively

value: MEF

tag: genotype

value: WT

value: Thapsigargin

tag: technical replicate


title: case_117 mRNA-seq

description:
Yang_SysBio_case_117
*** 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

value: ipf

value: case

value: m

value: white

value: not hispanic or latino

tag: raw data disclaimer


title: WT_no_treat_3

tag: cell line

value: no treat


title: WT_Thapsigargin_1


title: ATAC_Heart_Input_Adult_1

tag: cell type source

value: Input

value: Adult


title: H1_+BMP4(4HRS)_REP2

city: Ioannina

first: Carol

last: Murphy

address: University Campus of Ioannina, Building E5

country: Greece

institute: Institute of Molecular Biology and Biotechnology of the Foundation for Research and Technology Hellas

description: RNAseq BMP4_1HR_4HRS Up_Down Transcripts

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using tophat v2.0.9 with parameters -p 8 -q 2
Reads Per Kilobase of exon per Megabase of library size (RPKM) and differential expression were calculated against ensemble gene annotations using cuffdiff program with default options and masking repeats.
Genome_build: hg19
Supplementary_files_format_and_content: Differential expression

source_name: Wild-Type H1 Cells

growth_protocol: Matrigel adapted H1 cells (WiCell, Lot Number WB 0113) were cultured in mTeSR without select factors (Stem Cell Technologies - 05896) supplemented with 100ng/mL bFGF (ImmunoTools – 11343627), 0,5ng/mL Activin A (by Dr Marko Hyvönen, Cambridge University), 1mM LiCl (Sigma – 62476), 1mM G AminoButyric Acid (Sigma A5835) and 0.1mM Pipecolic Acid (Sigma – P2519) on matrigel (Corning – 354277) coated 6-well dishes (Sarstedt – 83.3920).

extract_protocol:
Cells were washed twice with ice-cold PBS and total RNA was harvested using the Macherey Nagel RNA extraction kit (119-22402).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Hi cells were induced with 50ng/mL recombinant BMP4 (Gibco, PHC9531) for 1 or 4hrs respectively.

value: Human Embryonic Stem Cell Line (Wicell)

tag: passage number

tag: treatment

value: BMP4 4 hours


title: ATAC_Heart_Input_E12_1


title: ATAC_Heart_Input_P6_1


title: H1_+BMP4(4HRS)_REP3


title: H1_+BMP4(4HRS)_REP1


title: control_110 mRNA-seq

description:
Yang_SysBio_control_110
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

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).

tag: tissue

value: lung

value: Pittsburgh Lung Donor Core

value: Y


title: HC3

description:
mRNA
Sample23

value: CD8+ T Cell

value: Healthy Control


title: ATAC_Heart_Endothelial_P6_2

value: Endothelial


title: H1_+BMP4(1HR)_REP3

value: BMP4 1 hour


title: case_109 mRNA-seq

description:
Yang_SysBio_case_109
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

tag: center

value: UCSF

value: ipf


title: H1_+BMP4(1HR)_REP2


title: ATAC_Heart_Endothelial_P6_1


title: WT_no_treat_2

value: MEF

value: WT


title: ATAC_Heart_Input_P6_2


title: ATAC_Kidney_Endothelial_Adult_1

source_name: Kidney


title: WT_DMSO_3

value: DMSO


title: case_107 mRNA-seq

description:
Yang_SysBio_case_107
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

tag: dx

value: case

value: f

value: white

value: not hispanic or latino

value: N


title: control_113 mRNA-seq

description:
Yang_SysBio_control_113
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: National Jewish

value: normal

value: control

tag: rnaseqid

value: m

value: multiple-unspecified

value: hispanic


title: H1_WT_REP3

value: Human Embryonic Stem Cell Line (Wicell)

value: untreated


title: WT_Thapsigargin_2

value: MEF

value: Thapsigargin


title: case_111 mRNA-seq

description:
Yang_SysBio_case_111
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: UCSF

value: ipf

tag: age

value: Y


title: WT_DMSO_2

value: WT

value: DMSO


title: H1_+BMP4(1HR)_REP1

value: BMP4 1 hour


title: ATAC_Heart_Endothelial_E12_3

source_name: Heart

value: Endothelial


title: H1_WT_REP2


title: case_106 mRNA-seq

description:
Yang_SysBio_case_106
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

source_name: tissue-Explant

value: lung

value: case

tag: Sex

value: white

value: N


title: H1_WT_REP1


title: case_105 mRNA-seq

description:
Yang_SysBio_case_105
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: m

tag: race

value: unknown


title: ATAC_Heart_Endothelial_E12_2


title: case_103 mRNA-seq

description:
Yang_SysBio_case_103
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

tag: ethnicity

value: not hispanic or latino


title: WT_AAS_3

value: AAS


title: control_108 mRNA-seq

description:
Yang_SysBio_control_108
*** 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: WT_AAS_2

value: MEF


title: case_102 mRNA-seq

description:
Yang_SysBio_case_102
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: UCSF

value: ipf

value: Y


title: WT_DMSO_1

value: WT

value: DMSO


title: gemin3_WT_3

city: Bethesda

first: zelin

last: chen

state: MD

address: 50 South Dr.

department: NHGRI

institute: NIH

data_processing:
Reads are trimmed using Trimmomatic v0.36
Trimmed reads are aligned using STAR 2.5.4a (mRNA) or "hisat2 2.2.1.0 --no-softclip --no-spliced-alignment  --rna-strandness R --new-summary" (miRNA)
abundance is measured by RSEM ("rsem-calculate-expression --paired-end --forward-prob 0.0 --alignments -p 16 --seed 987347 --calc-ci --calc-pme --estimate-rspd --time --no-bam-output" for mRNA-Seq, "rsem-calculate-expression --forward-prob 1.0 --alignments -p 16 --seed 987347 --calc-ci --calc-pme --estimate-rspd --time --no-bam-output --fragment-length-mean 22 --fragment-length-sd 10 --seed-length 15" for miRNA-Seq)
Genome_build: danRer10/Ensembl release 91 for mRNA-Seq, miRBase mature miRNA for microRNA-Seq
Supplementary_files_format_and_content: RSEM output, gene abundance

organism: Danio rerio

source_name: Wildtype siblings of gemin3 mutants, repeat 3

extract_protocol:
Embryos were placed in Qiazol, and RNA was extracted by using Qiagen miRNeasy Mini Kit.
Prepare one paired end index library from each total RNA sample, pool 24 libraries, load  pool on NovaSeq6000_S4, run as indexed 150 base paired end reads
embryos were placed in Qiazol, and RNA was extracted by using Qiagen miRNeasy Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

tag: genotype/variation

value: Wildtype siblings of gemin3 mutants

tag: Stage

value: 7 dpf

value: whole fish embryos


title: gemin3_hom_3

source_name: Homozygous gemin3 mutants, repeat 3

value: Homozygous gemin3 mutants


title: ATAC_Heart_Endothelial_E12_4

value: Endothelial


title: ATAC_Heart_Endothelial_Adult_2

value: Adult


title: control_101 mRNA-seq

first: Ivana

last: Yang

institute: University of Colorado Anschutz Medical Campus

description:
Yang_SysBio_control_101
*** 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: WT_AAS_1

tag: genotype

value: AAS

tag: technical replicate


title: gemin3_WT_2

source_name: Wildtype siblings of gemin3 mutants, repeat 2


title: ATAC_Heart_Endothelial_Adult_1


title: PERK_del_Thapsigargin_3

tag: cell line

value: MEF

value: PERK delete

value: Thapsigargin


title: control_100 mRNA-seq

description:
Yang_SysBio_control_100
*** 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: f

value: N

tag: raw data disclaimer


title: ATAC_Brain_Input_P6_3

source_name: Brain

tag: cell type source

value: Input


title: PERK_del_Thapsigargin_2

tag: treatment


title: gemin3_hom_2

source_name: Homozygous gemin3 mutants, repeat 2

value: Homozygous gemin3 mutants

value: 7 dpf

tag: tissue

value: whole fish embryos


title: ATAC_Brain_Input_P6_2


title: gemin3_WT_1

source_name: Wildtype siblings of gemin3 mutants, repeat 1

value: Wildtype siblings of gemin3 mutants


title: PERK_del_Thapsigargin_1


title: ATAC_Heart_Endothelial_E12_1

value: Endothelial


title: case_99 mRNA-seq

description:
Yang_SysBio_case_99
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

tag: center

value: UCSF

value: ipf

value: case

value: m

value: unknown

value: hispanic

value: Y


title: case_97 mRNA-seq

description:
Yang_SysBio_case_97
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

tag: dx

value: white

value: not hispanic or latino


title: ATAC_Brain_Input_P6_1


title: gemin3_hom_1

source_name: Homozygous gemin3 mutants, repeat 1


title: case_96 mRNA-seq

description:
Yang_SysBio_case_96
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

tag: rnaseqid

value: asian


title: PERK_del_no_treat_3

value: MEF

value: PERK delete

value: no treat


title: ATAC_Brain_Input_E12_2

value: Input

tag: age


title: PERK_del_no_treat_1


title: case_95 mRNA-seq

description:
Yang_SysBio_case_95
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

tag: Sex


title: PERK_del_no_treat_2


title: ATAC_Brain_Input_Adult_1

value: Adult


title: ATAC_Brain_Endothelial_P6_3

value: Endothelial


title: WT_no_treat_1

value: WT


title: control_94 mRNA-seq

description:
Yang_SysBio_control_94
*** 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

tag: race

value: N


title: 3_1_w_o_control

city: Würzburg

first: Jakob

middle: Jeremias

last: Jung

state: Bayern

address: Josef-Schneider-Str. 2/Bau D15

department: Institute of Molecular Infection Biology (IMIB)

institute: University of Würzburg

data_processing:
reads obtained from RNA sequencing were trimmed, filtered and mapped against the respective reference genome. The reference genome consisted of the the Salmonella enterica subsp. enterica serovar Typhimurium SL1344 (FQ312003.1) reference genome and three plasmids: pSLT_SL1344 (HE654724.1), pCol1B9_SL1344 (HE654725.1), and pRSF1010_SL1344 (HE654726.1) (Kröger et al. 2012).
Bases with a Phred quality score of <10 were trimmed and adapters were removed using BBDuk.
Next, the trimmed reads were mapped against the reference genome using BBMap (v38.84)
Alignmentts were then assigned to genomic features, including both CDSs and annotated sRNAs (Kröger et al. 2012; Hör et al. 2020) using the featureCounts method of the Subread (2.0.1) package (Liao, Smyth, and Shi 2014).
Assembly: Salmonella enterica subsp. enterica serovar Typhimurium
Supplementary files format and content: CSV format, describes the raw read counts of mRNAs and sRNAs after mapping them to the salmonella genome.

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: Salmonella treated with water

growth_protocol: The strain was streaked on Luria-Bertani plates and cultured in non-cation adjusted Mueller-Hinton Broth, with aeration at 37°C and 220 rpm shaking.

extract_protocol:
Total RNA was purified from bacterial pellets using the miRNeasy Mini kit (Qiagen) according to the protocol #3 described in Popella et al. (REF). Briefly, cells were resuspended in 0.5 mg/mL lysozyme (Roth) in TE buffer (pH 8.0) and incubated for 5 min. Afterwards, RLT buffer supplemented with β-mercaptoethanol, and ethanol were added according to the manufacturer’s instructions. After sample loading, column wash-steps were performed according to the manual. RNA concentration was measured with a NanoDrop spectrophotometer.
Briefly, samples were treated with DNase (XXX) and quality was checked on a bioanalyzer (RNA chip XXX). Then, RNA was subjected to cDNA library preparation using the Corall kit (Lexogen) and including the depletion of ribosomal RNA (RiboCop-META kit, Lexogen) according to the manufacturer’s instructions. Afterwards, library samples were pooled in equimolar amounts and quality was verified using a bioanalyzer (DNA chip XXX). The cDNA pools were sequenced using the NextSeq 500 system (HighOutput flow cell, 400 M, 1x 75 cycle single-end; Illumina).

treatment_protocol: Bacterial overnight cultures were diluted 1:100 in fresh MHB and grown to an OD600 of 0.5. Subsequently, obtained cultures were again diluted 1:100 in fresh MHB to adjust a cell concentration of approximately 106 cfu/mL. After transferring 1.9 mL of the bacterial solution into 5 mL low-binding tubes (LABsolute), 100 µL of 20x PPNA stock solutions were added to reach a final concentration of 5 µM for all KFF-conjugated PNAs. In parallel, an equal amount of cells was treated with the respective volume of sterile nuclease-free water, which was used as solvent for the test compounds, and served as negative control. After incubating the samples for 15 min at 37 °C, RNAprotect Bacteria (Qiagen) was added according to the manufacturer’s instructions. Following a 10-min incubation, cells were pelleted at 4 °C and 21,100 xg for 20 min. The supernatant was discarded and pellets were either directly used or stored at – 20 °C (< 1 day) for subsequent bacterial RNA isolation.

tag: strain

value: 15 min exposure to water

value: water control


title: 2_2_JVpna35

source_name: Salmonella treated with mm7 acpP PNA

value: 15 min exposure to 5 uM PNA


title: case_93 mRNA-seq

city: Aurora

description:
Yang_SysBio_case_93
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: UCSF

value: ipf

value: case

value: f

value: white

tag: ethnicity

value: not hispanic or latino


title: 2_2_w_o_control


title: PERK_del_DMSO_3

value: MEF

value: PERK delete

value: DMSO


title: ATAC_Brain_Endothelial_P6_1

value: Endothelial


title: PERK_del_DMSO_1


title: ATAC_Brain_Endothelial_P6_2


title: case_91 mRNA-seq

description:
Yang_SysBio_case_91
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: Y


title: PERK_del_DMSO_2


title: control_92 mRNA-seq

description:
Yang_SysBio_control_92
*** 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


title: 2_2_JVpna29

source_name: Salmonella treated with mm1 acpP PNA

value: 15 min exposure to 5 uM PNA


title: 3_2_w_o_control

value: 15 min exposure to water

value: water control


title: PERK_del_AAS_2

value: AAS


title: 2_1_Jvpna37

source_name: Salmonella treated with mm9 acpP PNA


title: 2_1_w_o_control


title: control_89 mRNA-seq

description:
Yang_SysBio_control_89
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: N


title: PERK_del_AAS_1


title: ATAC_Brain_Endothelial_E12_1


title: PERK_del_AAS_3


title: ATAC_Brain_Endothelial_Adult_2

value: Adult


title: case_88 mRNA-seq

description:
Yang_SysBio_case_88
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: UCSF

value: ipf

value: case

value: white

value: not hispanic or latino


title: 2_1_Jvpna36

source_name: Salmonella treated with mm8 acpP PNA


title: ATAC_Brain_Endothelial_E12_3

value: Endothelial


title: GCN2_del_Thapsigargin_3

source_name: MEF cells

value: MEF

value: GCN2 delete

value: Thapsigargin


title: control_87 mRNA-seq

description:
Yang_SysBio_control_87
*** 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: ATAC_Brain_Endothelial_Adult_1


title: 2_1_Jvpna33

source_name: Salmonella treated with mm5 acpP PNA

value: 15 min exposure to 5 uM PNA


title: case_86 mRNA-seq

description:
Yang_SysBio_case_86
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: m

value: Y


title: myoblast12

city: Chicago

first: Pei

last: Zhu

state: IL

address: 1111 S Laflin Street, Apt314

department: Department of Biochemistry and Molecular Genetics

institute: university of illinois at chicago

data_processing:
Basecalls performed using bcl2fastq
RNA-seq reads were aligned to the mm10 genome assembly using STAR
The mean read insert sizes and their standard deviations were calculated using Picard tools
Reads were counted on the exons of MM10 genes using htseq
The isoform expression level from RNAseq data was quantified using rsem followed by imported into DESeq2 with tximport.
Genome_build: mm10
Supplementary_files_format_and_content: TAB-delimited text, DESeq2 output containing normalized expression values.

source_name: Primary myoblasts

growth_protocol: Primary myoblasts were cultured in Ham's F-10 / 20% FBS / 1x PS / 2.5 ng/ml bFGF.

extract_protocol:
Total RNA from  primary myoblasts was estracted using the Direct-zolTM RNA MicroPrep Kit (Zymo Research) and quantified using QubitTM RNA BR Assay kit (ThermoFisher Scientific).
cDNA libraries were constructed from 1 ug of total RNA using the TruSeq Stranded Total RNA Library Prep kit (#20020596, Illumina).

treatment_protocol: 6 hours placement in 21% O2 (normoxia) versus 1% O2 (hypoxia) 37 ℃ incubator

value: skeletal muscle

value: young adult (~8-week-old)

value: 6 hour in hypoxia


title: GCN2_del_Thapsigargin_2


title: case_90 mRNA-seq

description:
Yang_SysBio_case_90
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: UCSF

value: ipf

value: case

value: f

value: unknown

value: hispanic


title: GCN2_del_Thapsigargin_1

value: MEF

value: GCN2 delete

value: Thapsigargin


title: myoblast10


title: control_85 mRNA-seq

description:
Yang_SysBio_control_85
*** 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: white

value: not hispanic or latino

value: N


title: 2_1_Jvpna31

source_name: Salmonella treated with mm3 acpP PNA

value: 15 min exposure to 5 uM PNA


title: ATAC_Brain_Endothelial_E12_2

value: Endothelial


title: GCN2_del_no_treat_3

value: no treat


title: 2_1_Jvpna32

source_name: Salmonella treated with mm4 acpP PNA


title: 2_1_Jvpna22

source_name: Salmonella treated with scrambled PNA

value: acpP-scrambled


title: case_84 mRNA-seq

description:
Yang_SysBio_case_84
*** 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: ipf

value: case

value: m

value: Y


title: control_80 mRNA-seq

description:
Yang_SysBio_control_80
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: control

value: U


title: 2_1_Jvpna30

source_name: Salmonella treated with mm2 acpP PNA


title: 2_1_Jvpna34

source_name: Salmonella treated with mm6 acpP PNA


title: GCN2_del_no_treat_2

value: MEF

value: GCN2 delete


title: myoblast8

value: skeletal muscle

value: young adult (~8-week-old)

value: wild-type

value: 6 hour in hypoxia


title: myoblast9


title: case_83 mRNA-seq

description:
Yang_SysBio_case_83
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: white

value: not hispanic or latino


title: GCN2_del_no_treat_1

value: no treat


title: case_79 mRNA-seq

description:
Yang_SysBio_case_79
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: UCSF

value: unknown

value: hispanic

value: N


title: myoblast11


title: case_81 mRNA-seq

description:
Yang_SysBio_case_81
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: ipf

value: case

value: f


title: 1_2_JVpna35

value: 15 min exposure to 5 uM PNA


title: 2_1_Jvpna21

source_name: Salmonella treated with acpP PNA

value: acpP


title: GCN2_del_DMSO_1

value: MEF

value: GCN2 delete

value: DMSO


title: myoblast6

value: skeletal muscle

value: young adult (~8-week-old)

value: 6 hour in normoxia


title: GCN2_del_DMSO_3


title: myoblast7

value: wild-type

value: 6 hour in hypoxia


title: GCN2_del_DMSO_2


title: myoblast4


title: case_77 mRNA-seq

description:
Yang_SysBio_case_77
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: UCSF

value: m

value: white

value: not hispanic or latino


title: GCN2_del_AAS_3

value: AAS


title: 1_1_w_o_control

value: 15 min exposure to water

value: water control


title: myoblast5


title: 1_2_JVpna29

value: 15 min exposure to 5 uM PNA


title: myoblast3


title: case_78 mRNA-seq

description:
Yang_SysBio_case_78
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: ipf

value: case

value: f

value: N


title: GCN2_del_AAS_2

value: MEF

value: GCN2 delete


title: 1_1_Jvpna37


title: control_76 mRNA-seq

description:
Yang_SysBio_control_76
*** 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: Y


title: 1_1_Jvpna36


title: GCN2_del_AAS_1


title: islets, SMNDC1_sh3_D4

first: Stefan

last: Kubicek

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_D4

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

value: transduced with SMNDC1 shRNA #3


title: myoblast2

value: skeletal muscle

value: young adult (~8-week-old)

value: wild-type

value: 6 hour in normoxia


title: case_75 mRNA-seq

description:
Yang_SysBio_case_75
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: UCSF

value: other

value: unknown


title: 1_1_Jvpna34

value: 15 min exposure to 5 uM PNA


title: control_74 mRNA-seq

description:
Yang_SysBio_control_74
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: f

value: white

value: not hispanic or latino

value: N


title: WT_KY37

first: Brittney

last: Lozzi

department: Cell & Gene Therapy

institute: Baylor College of Medicine

data_processing:
Quality control was performed on fastq files using fastQC. Paired end reads were mapped to the mouse genome (mm10) using STAR (v2.5.0a).
Reads Per Million (RPM) were calculated using GenomicAlignments (v1.16.0) and DESeq2 (v1.20.0) was used for read count normalization and differential gene expression.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each variant

source_name: Cortex

extract_protocol:
Bulk tissue was dissociated with QIAshredder column. RNA was isolated using trizol and chloroform and purified using the RNeasy Mini Kit (QIAGEN).
Illumina sequencing libraries were constructed from 500-900ng of total RNA using the TruSeq Stranded mRNA Library preperation kit (Illumina)

tag: disease state

value: wild type

value: Cortex

tag: egfr variant

value: WT

value: post-natal day 70


title: islets, SMNDC1_sh1_D4

source_name: islets, SMNDC1_sh1_D4

value: pancreatic human islets

value: transduced with SMNDC1 shRNA #1


title: case_73 mRNA-seq

description:
Yang_SysBio_case_73
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: ipf

value: case


title: T263P_KY29

source_name: Cortical Brain Tumor

value: Glioblastoma


title: WT_KY35


title: 1_2_w_o_control

source_name: Salmonella treated with water

value: 15 min exposure to water

value: water control


title: 1_1_Jvpna33


title: islets, Empty_Vector_D4

source_name: islets, Empty_Vector_D4

value: transduced with control empty vector


title: control_72 mRNA-seq

description:
Yang_SysBio_control_72
*** 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: m

value: Y


title: T263P_KY27

value: Cortex


title: 1_1_Jvpna32

value: 15 min exposure to 5 uM PNA


title: case_71 mRNA-seq

description:
Yang_SysBio_case_71
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: UCSF

value: white

value: not hispanic or latino


title: T263P_KY24

value: post-natal day 70


title: 1_1_Jvpna31


title: 1_1_Jvpna30


title: Exosome, Xantho-granulomatous cholecystitis, 800306

first: Qiang

last: Cai

address: 197 Ruijin No.2 Road

department: Department of General Surgery

institute: Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine

data_processing:
For lncRNA and mRNA, paired-end reads were aligned to the human reference genome hg19 with HISAT2. HTSeq v0.6.0 was used to count the reads numbers mapped to each gene. For circRNA, the purified library products were evaluated using the Agilent 2200 TapeStation and Qubit®2.0(Life Technologies, USA) and then sequenced on HiSeq 3000 with 2 X 150 bp mode.
For lncRNA and mRNA, the whole samples expression levels were presented as RPKM (expected number of Reads PerKilobase of transcript sequence per Million base pairs sequenced), which is the recommended and most common method to estimate the level of gene expression. For circRNA, raw reads were treated with Trimmomatic tools(V0.36) to remove adapters. Following reads quality control: Scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below 15, drop reads which are less than 35% of initiation read length. Then reads quality was inspected using the FastQC software then output statistical result.
For lncRNA and mRNA, the statistically significant DE genes were obtained by an adjusted P-value threshold of <0.05 and |log2(fold change)| > 1 using the DEGseq software. For circRNA, two algorithms, CIRI2 and CIRCexplorer2 were used to detect circRNAs. Reads were mapped to human reference genome GRCh37/ hg19 (http://genome.ucsc.edu/) by BWA-MEM or Tophat, respectively. CIRI2 detects the paired chiastic clipping (PCC) signals from the mapping information of reads by local alignment with BWA-MEM and combines with systematic filtering steps to remove potential false positives.CIRCexplorer2 uses TopHat and TopHat-Fusion alignment output to detect circRNAs.
For lncRNA and mRNA, tab-delimited text files for each Sample. A hierarchical clustering analysis was performed using the R language package gplots according to the RPKM values of differential genes in different groups. And colors represent different clustering information, such as the similar expression pattern in the same group, including similar functions or participating in the same biological process. For circRNA, tab-delimited text files for each Sample. Back-spliced junction reads identified in CIRI2 were combined and scaled to RPM (Reads Per Million mapped reads, bwamem mapping) to quantify every circRNAs.
Genome_build: hg19
Supplementary_files_format_and_content: mRNA_exp.txt, ncRNA_exp.txt, merge_circRNA.txt

source_name: serum exosome

extract_protocol:
The exosome samples were lysed using TRIzol (Invitrogen) and the RNA content was extracted according to the manufacturer’s instruction. Total RNA samples (2 μg) were treated with the Epicenter Ribo-Zero rRNA Removal Kit (Illumina) and RNase R (Epicenter) to remove ribosomal and linear RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Xantho-granulomatous cholecystitis

tag: gender

value: female

value: no treatment

value: serum exosome


title: Exosome, Xantho-granulomatous cholecystitis, 782875

value: male


title: case_69 mRNA-seq

description:
Yang_SysBio_case_69
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: ipf

value: case

value: unknown

value: hispanic


title: 1_1_Jvpna22

value: acpP-scrambled


title: Exosome, Xantho-granulomatous cholecystitis, 772652


title: control_68 mRNA-seq

description:
Yang_SysBio_control_68
*** 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: f

value: Y


title: Exosome, Xantho-granulomatous cholecystitis, 757028


title: R222C_KY31

value: Glioblastoma

value: Cortex

value: post-natal day 70


title: 1_1_Jvpna21

value: 15 min exposure to 5 uM PNA

value: acpP


title: case_67 mRNA-seq

description:
Yang_SysBio_case_67
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: UCSF

value: m

value: white

value: not hispanic or latino

value: N


title: R222C_KY26


title: R222C_KY32


title: Exosome, gallbladder cancer, 735872

value: gallbladder cancer

value: male

value: without any anticancer treatment

value: serum exosome


title: R108K_KY34


title: R108K_KY28


title: Exosome, gallbladder cancer, 733612

value: female


title: control_66 mRNA-seq

description:
Yang_SysBio_control_66
*** 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: case_65 mRNA-seq

description:
Yang_SysBio_case_65
*** 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: DAM20.LPS.P11

city: New York

first: Jordan

last: Marrocco

state: NY

address: 1230 York Ave

institute: The Rockefeller University

data_processing:
Illumina NovaSeq 6000
Quality control was performed on the reads.
Reads were aligned to the rn6 genome from the BSgenome.Rnorvegicus.UCSC.rn6.
The read counts were analyzed using the R/Bioconductor framework (www.R-project.org).
Differentially expressed gene (DEG) expression analysis was conducted using the DESeq2 package.
Assembly: rn6
Supplementary files format and content: DESeq2 files contain logFC (p<0.05) between Saline and LPS animals on P10 and on P11 along with rLog counts.

organism: Rattus norvegicus

source_name: Milk

growth_protocol: Sprague-Dawley rats were maintained at 20°C on a 12 h light/dark cycle (0700-1900 light) with ad libitum access to food and water.

extract_protocol:
2 and 24 hours after receieving either injection, dams were lightly anesthetized with isoflurane in O2, followed by the administration of 0.2 mL of oxytocin (20 USP/mL i.p). Distilled water was used to moisten the teats and milk obtained by gently squeezing its base to manually expel the sample for collection. A microhematocrit tube was used to collect ~20 ul of sample, and samples were stored at -80C until processing. For RNA isolation, milk was spun at 1,000 g to separate the fat layer from the whey. This fat layer was then mixed with an equal volume of PBS and spun again at 3,000 rpm to clean the fat of debris. The miRNeasy Mini Kit (QIAGEN, Cat. #217004) was used to isolate total RNA following the manufacturer’s directions. A NanoDrop 2000 spectrophotometer was used to quantify isolated RNA samples, which were then stored at -80C prior to sequencing.
A total of at least 190ng of RNA per replicate was prepared for sequencing by The New York Genomic Center using the Tru-Seq Stranded mRNA library preparation kit (Illumina, USA). Five biological replicates were used per experimental group. cDNA libraries were sequenced on an Illumina NovaSeq 6000 in two lanes to obtain 100-bp single-end reads at an approximate sequencing depth of 50 million reads per sample.

treatment_protocol: Rat mothers were injected with either lipolysaccharide or pyrogen-free saline on postnatal day 10.

value: Sprague-Dawley

tag: genotype

value: Wild Type

value: Milk

tag: agent

value: LPS


title: Exosome, Xantho-granulomatous cholecystitis, 808934

value: Xantho-granulomatous cholecystitis

value: no treatment


title: Exosome, gallbladder cancer, 732877

value: gallbladder cancer


title: control_62 mRNA-seq

description:
Yang_SysBio_control_62
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: National Jewish

value: m

value: white

value: not hispanic or latino

value: N

tag: raw data disclaimer


title: DAM18.LPS.P11


title: Exosome, gallbladder cancer, 729427

value: male

tag: treatment

value: without any anticancer treatment

value: serum exosome


title: R108K_KY8

address: 1 Baylor Plaza

value: Glioblastoma

tag: tissue

value: Cortex

value: post-natal day 70


title: case_70 mRNA-seq

description:
Yang_SysBio_case_70
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

tag: center

value: UCSF

value: ipf

value: case

value: Y


title: Exosome, gallbladder cancer, 724836

value: gallbladder cancer

value: female


title: control_60 mRNA-seq

description:
Yang_SysBio_control_60
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: National Jewish

tag: dx

value: normal

value: control

value: m


title: DAM23.LPS.P11

value: Sprague-Dawley

value: Wild Type

value: Milk

value: LPS


title: R108K_KY7

value: Glioblastoma

value: Cortex


title: case_58 mRNA-seq

description:
Yang_SysBio_case_58
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

tag: rnaseqid

value: f

value: white

value: not hispanic or latino