title: case_534 mRNA-seq

description:
Yang_SysBio_case_534
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

tag: age

value: m

value: unknown

value: hispanic


title: BMMo_AM_neonates_3

status: Public on Jul 01 2022

type: SRA

city: Zürich

first: Manfred

last: Kopf

address: Otto-Stern-Weg 7

department: Biologie

country: Switzerland

institute: ETH Zürich

description: AM_BMMo_3 [normalized count]

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adapter sequence, then mapped to the GRCm38  mouse reference genome (Version25.06.2015) using the STAR aligner with input parameters: --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --outMultimapperOrder Random --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 100000 --alignMatesGapMax 100000  --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif --alignEndsProtrude 3 ConcordantPair
Read counts were scaled with the use of the trimmed mean of M-values (TMM) method proposed by Robinson and Oshlack (Robinson & Oshlack, 2010).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files, the processed data file includes Gene Identifier, gene name, gene type and normalized count (between-sample-normalization, TMM)

molecule: total RNA

organism: Mus musculus

source_name: lung

extract_protocol:
Cells were isolated from bronchoalveolar lavage and FACS sorted. 50,000 cells were collected and RNA was extracted with an RNeasy Plus Micro Kit (Qiagen) following manufacturer’s instructions.
Smart Seq RNA Stranded sample kit (Takara Bio USA, Inc) was used for library construction

treatment_protocol: WT mice were infected with Influenza virus 5 weeks before cell collection. Csf2ra deficient newborns were injected intranasally with FACS sorted bone marrow monocytes or fetal liver monocytes. Mature alveolar macrophages were collected 8 weeks later.

tag: tissue

value: lung

tag: cell type

value: alveolar macrophages

tag: genotype

tag: treatment

value: transferred into lungs of neonatal Csf2Ra KO mice


title: Ectopic expression of MSI1 in HEK293 cells

city: Barcelona

first: Manuel

last: Irimia

state: Barcelona

address: 88 Dr. Aiguader

department: MELIS

country: Spain

institute: Universitat Pompeu Fabra - Centre for Genomic Regulation

description:
CL_293_L_MSI1_OE
PolyA-selected stranded RNA-seq.

data_processing:
Raw reads were mapped with vast-tools align v2.5.1.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *.cRPKM.txt: Tab-delimited text files with raw read counts and cRPKMs.

molecule: polyA RNA

organism: Homo sapiens

source_name: HEK 293 cells

growth_protocol: Cell lines were cultured at 37°C and 5% CO2 in DMEM (H3BE12-604F/U1, Lonza Group AG [Cultek S.L.U, Madrid, Spain]) supplemented with 10% tetracycline-free FBS (631106, Clontech, [Conda Laboratories, Torrejon de Ardoz, Spain]) and 1% penicillin/streptomycin (15140122, Life Technologies S.A., [Fisher Scientific, Madrid, Spain]).

extract_protocol:
RNeasy Mini kit (QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 1 ug/mL of Doxycycline induction for 24 h.

tag: cell line

value: Ectopic expression of MSI1


title: BM860-RCMD

city: Houston

first: Jia

last: Li

state: Texas

address: 2121 W HOLCOMBE BLVD

department: CEDP

country: USA

institute: Guangzhou Medical University

library_source: genomic

data_processing:
Library strategy: sCMS-IP
For the sCMS-IP data analysis, raw FASTQ files were mapped to the NCBI Human Reference Genome Build GRCh37 (hg19) using BSMAP. The alignment files from BSMAP were transformed to a bigwig file format. The bigwig files were uploaded to the UCSC genome browser for visualization.
For sCMS-IP-seq analysis, raw FASTQ files were mapped to NCBI Human Reference Genome Build GRCh37 (hg19) using BSMAP. Only uniquely mapped non duplicated reads were kept as input for MACS2 to call 5hmC enriched regions (peaks). Differential hydroxymethylation regions (DHMRs) were identified using DESeq2 with default parameters. Bam files were transformed to bigwig format, which can be used to visualize 5hmC signals in the UCSC genome browser.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

molecule: genomic DNA

source_name: bone marrow

extract_protocol:
DNA were purified from bone marrow aspirates in corresponding individual person using Qiagen Dneasy Blood and Tissue kit.
sCMS-IP-seq was performed as described previously with some modifications. Briefly, genomic DNA was combined with unmethylated λ-bacteriophage DNA (NEB) for bisulfite conversion efficiency check and then sheared into median 300-bp size range using a Covaris M220 Focused-ultrasonicator (Covaris). Sheared DNA was bisulfite converted using a EZ DNA methylation-lightning kit (Zymo Research) with suggested protocols to convert 5-hydroxymethylcytosin (5hmC) to cytosine-5-methylenesulfonate (CMS). CMS-containing DNA fragments were then immunoprecipitated using CMS-specific antiserum pre-conjugated with protein A/G dynabeads. Precipitated DNA fragments were purified by the conventional phenol/chloroform/isomyl-alcohol method. Purified enriched fragments were amplified with random primers followed by adaptor ligation. Final amplification was performed with illumina TruSeq indices using a Pico Methyl-Seq Library Prep Kit (Zymo Research) with manufacturer’s protocols. Constructed library size distribution was determined by a Bioanalyzer with an Agilent High Sensitivity DNA Kit (Agilent). Library concentration was measured by a Qubit 4 Fluorometer using a Qubit dsDNA high sensitivity assay kit (Thermo Fisher Scientific). Pooled DNA libraries were sequenced on NextSeq 500 (Illumina) with a NextSeq 500/550 High Output Kit v2 (single-end reads, 75 Cycles) following protocols suggested by the manufacturer (Illumina).

tag: disease state

value: RCMD

value: bone marrow

tag: ip reagent

value: CMS-specific antiserum pre-conjugated with protein A/G dynabeads (Thermofisher scientific; A dynabeads:#88846;G dynabeads:#88848)


title: AM_WT_uninfecte_3

description: AM_WT_3 [normalized count]

value: Naive


title: BM845-RCMD


title: DPN1_333_G_519

city: Stockholm

first: Dan

last: Huang

address: Neo, Department of Biosciences and Nutrition, Huddinge, Stockholm.

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

description: DPN rep1

data_processing:
Bcl files were converted and demultiplexed to fastq using the bcl2fastq program. A hybrid human-mouse genome was created by merging the fasta files of the two organisms (hg38/mm10). Subsequently STAR was used to index the hybrid reference genome and align the fastq files.
The exon annotations of the two organisms were merged and mapped reads were then counted using featureCounts. The entrez gene annotations and reference genome for both human and mouse were obtained from UCSC.
The count table from featureCounts was imported into R/Bioconductor and the gene counts originating from the two organisms were separated to their corresponding organism. Subsequent differential gene expression was performed separately on each organism using the EdgeR package and its general linear models pipeline.
For the gene expression analysis genes that had 1 count per million in 3 or more samples were used and normalized using TMM normalization.
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: NOD/SCID IL2gnull (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ) mice (referred to as NSG mice)

growth_protocol: Cells  were maintained in RPMI 1640 supplemented with 10% FBS. Then 15 X 106 Granta-519 cells in 100ul sterile PBS were injected subcutaneously to NSG mice.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen, Valencia, CA).
RNA libraries for sequencing were prepared using TruSeq Stranded mRNA Sample prep kit with 96 dual indexes (Illumina, CA, USA).

treatment_protocol: When the tumor size in the mice reached 100 mm3, mice were randomly selected into two groups, injected once per day subcutaneously with vehicle or the ESR2 selective agonist DPN (12.5 mmol/kg body weight) dissolved in 100% ethanol and further diluted 1:10 in rapeseed oil.

value: Mantle cell lymphoma

tag: condition

value: Granta-519 cells were grafted to NSG mice

value: DPN


title: case_533 mRNA-seq

city: Aurora

first: Ivana

last: Yang

state: CO

institute: University of Colorado Anschutz Medical Campus

description:
Yang_SysBio_case_533
*** 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

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: center

value: UCSF

tag: dx

value: ipf

value: case

tag: rnaseqid

tag: Sex

tag: race

value: white

tag: ethnicity

value: not hispanic or latino

value: N

tag: raw data disclaimer


title: FliMo_AM_neonates_3

description: AM_FliMo_3 [normalized count]

value: lung


title: case_531 mRNA-seq

description:
Yang_SysBio_case_531
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: m


title: Ectopic expression of empty vector in HEK293 cells

description:
CL_293_L_EmptyV_OE
PolyA-selected stranded RNA-seq.

value: Ectopic expression of empty vector


title: AM_WT_uninfecte_2

description: AM_WT_2 [normalized count]

value: alveolar macrophages


title: AM_WT_uninfecte_1

description: AM_WT_1 [normalized count]


title: case_530 mRNA-seq

description:
Yang_SysBio_case_530
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

source_name: tissue-Biopsy

value: f


title: Ectopic expression of SRRM4 in HEK293 cells

description:
CL_293_L_SRRM4_OE
PolyA-selected stranded RNA-seq.

value: Ectopic expression of SRRM4


title: BM836-RAEB

value: RAEB

value: bone marrow

value: CMS-specific antiserum pre-conjugated with protein A/G dynabeads (Thermofisher scientific; A dynabeads:#88846;G dynabeads:#88848)


title: BM838-RAEB


title: AM_SiglecFlow_WT_Flu_2

description: AM_SiglecFlo_WT_Flu_2 [normalized count]

value: Influenza A Virus infection


title: BM734.pre-RAEB


title: case_528 mRNA-seq

description:
Yang_SysBio_case_528
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: Y


title: case_527 mRNA-seq

description:
Yang_SysBio_case_527
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: UCSF


title: BM740-RA

value: RA


title: annoP5IP_Factor_IP_3

city: Cleveland

first: Sujata

last: Rao

state: OH

address: 2022 E 105th St i building

institute: Cole eye, Cleveland Clinic foundation

data_processing:
Basecalls were performed using bcl2fastq for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using TrimGalore.
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie alignment tool. Visualization was done using IGV.
Peaks were called uing MACS2 for broad regions of enrichement with variable-width peaks found in CHIP-seq.
Motif discover was done using MEME and Cistrome.
Assembly: GRCm38 mouse reference genome (mm10)
Supplementary files format and content: narrowpeak

source_name: P5 retina

extract_protocol:
Isolated retina from postnatal day 3 and postnatal day 5 animals were lysed, sheared with an an Ultrasonicator Model s2 (Covaris).
Chip_SEQ libraries were prepared using the TruSeq ChIP Sample Preparation Kit protocol (Illumina provided). Library quality and quantity was assessed using the Agilent bio-analyzer and libraries were sequenced using an Illumina NovaSEQ4000 (illumina provided reagents and protocols). Sequence Assemly was done using CASAVA 1.8.2.

treatment_protocol: Library input DNA was quantitated using the qubit.

value: P5 retina

value: retina

tag: chip antibody

value: Bmal1 (Abcam, ab#3350)


title: BM842-RAEB


title: annoP5IP_Factor_IP_2


title: annoP3IP_Factor_IP_5

source_name: P3 retina

value: P3 retina


title: control_526 mRNA-seq

description:
Yang_SysBio_control_526
*** 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: age

value: white

value: not hispanic or latino

value: N


title: annoP3IP_Factor_IP_4


title: case_524 mRNA-seq

description:
Yang_SysBio_case_524
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

tag: tissue

value: ipf

value: case

value: m


title: BM55-RAEB

value: RAEB

value: bone marrow

value: CMS-specific antiserum pre-conjugated with protein A/G dynabeads (Thermofisher scientific; A dynabeads:#88846;G dynabeads:#88848)


title: AM_SiglecFhi_WT_Flu_2

description: AM_SiglecFhi_WT_Flu_2 [normalized count]

tag: cell type

value: alveolar macrophages

value: Influenza A Virus infection


title: BM28-CMML

value: CMML


title: AM_SiglecFhi_WT_Flu_1

description: AM_SiglecFhi_WT_Flu_1 [normalized count]

tag: genotype


title: s571_L4_fat

city: Rochester

first: Mrunal

middle: Kishor

last: Dehankar

state: MN

address: 200 First St. SW

department: Computational genomics

institute: Mayo Clinic

data_processing:
Base calling was performed with the Illumina bcl2fastq
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by STAR-2.6.1c aligner
Gene counts were generated using Subread featureCounts (http://subread.sourceforge.net/)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts and FPKM values for each gene per sample

source_name: Fat

extract_protocol:
Brains (cross-sectional brain region encompassing hippocampal and cortical tissue) and inguinal fat depots were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. RNA isolation using miRNeasy (Qiagen cat. # 217004)  was used with 200 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using TruSeq RNA Library Prep Kit v2 (Illumina)

treatment_protocol: Adult mice were treated with either vehilce or CP2 (25 mg/kg/day in 0.1% PEG dissolved in drinking water ad lib) or vehicle-containing water (0.1% PEG) starting at 21 months of age.

value: Fat

tag: strain

value: M

value: wild type

tag: treatment


title: s612_L3_fat


title: BM27-RAEB

tag: disease state


title: case_522 mRNA-seq

description:
Yang_SysBio_case_522
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: UCSF

value: Y


title: AM_SiglecFlow_WT_Flu_1

description: AM_SiglecFlo_WT_Flu_1 [normalized count]


title: s530_L3_fat


title: BM26.pre-RAEB

tag: ip reagent


title: BM734.post-RAEB


title: BM26.post-RAEB


title: control_519 mRNA-seq

description:
Yang_SysBio_control_519
*** 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: white

value: not hispanic or latino


title: control_517 mRNA-seq

description:
Yang_SysBio_control_517
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: m


title: s451_L2_fat

value: F


title: case_516 mRNA-seq

description:
Yang_SysBio_case_516
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

source_name: tissue-Unknown

value: National Jewish

value: ipf

value: case

value: N


title: BM226-CMML

value: CMML

value: bone marrow

value: CMS-specific antiserum pre-conjugated with protein A/G dynabeads (Thermofisher scientific; A dynabeads:#88846;G dynabeads:#88848)


title: control_523 mRNA-seq

description:
Yang_SysBio_control_523
*** 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


title: s664_L1_fat

value: Fat

value: wild type


title: MG_FACS_MIA_PLX_SAL_Rep4

city: Baltimore

first: Lindsay

middle: N

last: Hayes

state: Maryland

address: 600 North Wolfe Street, Meyer 4-136

department: Neuroscience

institute: Johns Hopkins University

data_processing:
Alignment: FASTQ files aligned and assembled with RSEM and STAR: rsem-calculate-expression -p 4 --paired-end --star --star-output-genome-bam --calc-ci --forward-prob 0.5
Counts: Count matrix was assembled using tximport in R  files <- list.files(path = "../1.align/genes.results/")  names(files) <- strtrim(files, 4)  txi.rsem <- tximport(files, type = "rsem", txIn = FALSE, txOut = FALSE)  txi.rsem$length[txi.rsem$length == 0] <- 1  table(txi.rsem$length == 0)  save(txi.rsem, file = "txi.rsem.RData")
Differential expression was performed with DESeq2.
Assembly: GRCm38vM25
Supplementary files format and content: Adult_Rescue_counts.csv: Comma-separated file of raw counts from RSEM output.

source_name: brain striatum

extract_protocol:
Male mice (8-10 wk) were deeply anesthetized with ether, perfused with PBS, and brains extracted. The meninges were removed and then the frontal cortex and striatum were collected into 2 mL tubes with HBSS on ice. The anterior striatum was collected from a coronal slice anterior to 1.7 mm bregma by collecting the tissue surrounding the nucleus accumbens. The next coronal slice was cut at -0.5 bregma and the dorsal and ventral striatum was excised from this slice, excluding the olfactory tubercle, and all striatum pieces were pooled together. The brain pieces were diced with scissors and then homogenized with papain according to the adult neural dissociation kit (Miltenyi). Briefly, the tissue was treated with papain and DNase at 37°C for 30 min with rotation. The homogenates were pipetted gently and filtered with a 70 µm strainer. The cell pellet was resuspended in debris removal solution (300 µL debris removal, 700 µL PBS), overlaid with 300 µL of PBS, centrifuged at 3000xg for 10 min, debris aspirated, washed with PBS, and centrifuged at 1000xg for 10 min. The cells were resuspended in 0.5% BSA in HBSS. For fluorescence-activated cell sorting the cells were stained with CD45-APC, CD11b-BV421, and P2RY12-PE antibodies for 30 min at 4C. The cells were washed with buffer and sorted for live (PI-), CD11b+,CD45-low, P2RY12+ before final collection into RNA lysis buffer. RNA was collected according to the kit instructions (Qiagen, Micro-RNeasy, PicoPure RNA isolation Kits).
RNA samples were converted to double stranded cDNA using the Ovation RNA-Seq System v2.0 kit (Tecan, Männedorf, Switzerland), which utilizes a proprietary strand displacement technology for linear amplification of mRNA without rRNA/tRNA depletion as per the manufacturer’s recommendations. This approach does not retain strand specific information. Quality and quantity of the resulting cDNA were monitored using the Bioanalyzer High Sensitivity kit (Agilent) which yielded a characteristic smear of cDNA molecules ranging in size from 500 to 2000 nucleotides in length. After shearing 500 nanograms of cDNA to an average size of 250 nucleotides with the Covaris S4 (Covaris Inc., Woburn, MA) library construction was completed with the TruSeq Nano kit (Illumina; San Diego, CA) according to the manufacturer’s instructions. mRNA libraries were sequenced on an Illumina Novaseq 6000 instrument using 150bp paired-end dual indexed reads and 1% of PhiX control.

treatment_protocol: Lipopolysaccharide (LPS) was delivered by intraperitoneal injection to mice at a dose of 4500 endotoxin units / gram body weight. Microglia were extracted 18 hours after LPS or saline treatment.

value: brain striatum

value: microglia

tag: group

value: SAL

value: male


title: MG_FACS_MIA_PLX_SAL_Rep3


title: s454_L1_fat

value: F


title: BM223-CMML


title: control_513 mRNA-seq

description:
Yang_SysBio_control_513
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

tag: center

value: control

value: m

value: white

value: not hispanic or latino


title: BM19-RAEB

value: RAEB


title: MG_FACS_MIA_PLX_SAL_Rep2


title: MG_FACS_MIA_PLX_LPS_Rep5

value: LPS


title: s552_L4_fat

value: M

value: Veh


title: MG_FACS_MIA_PLX_LPS_Rep4


title: BM180-CMML

value: CMML

value: bone marrow

value: CMS-specific antiserum pre-conjugated with protein A/G dynabeads (Thermofisher scientific; A dynabeads:#88846;G dynabeads:#88848)


title: MG_FACS_MIA_PLX_LPS_Rep3


title: MG_FACS_MIA_PLX_SAL_Rep1_exclude


title: s551_L4_fat

value: Fat

value: wild type


title: case_512 mRNA-seq

description:
Yang_SysBio_case_512
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: UCSF

tag: dx

value: ipf

value: case

value: Y


title: s562_L2_fat


title: case_514 mRNA-seq

description:
Yang_SysBio_case_514
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

tag: rnaseqid

value: m

value: asian

value: unknown

value: N


title: MG_FACS_MIA_PLX_LPS_Rep2

value: brain striatum

value: microglia

value: LPS

tag: Sex

value: male


title: MG_FACS_MIA_PLX_LPS_Rep6


title: s443_L4_fat

value: F

value: Veh


title: case_511 mRNA-seq

description:
Yang_SysBio_case_511
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: Pittsburgh Lung Donor Core

tag: race

value: white

value: not hispanic or latino


title: case_510 mRNA-seq

description:
Yang_SysBio_case_510
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

tag: ethnicity

value: U


title: BM173-CMML

value: CMML

value: bone marrow

value: CMS-specific antiserum pre-conjugated with protein A/G dynabeads (Thermofisher scientific; A dynabeads:#88846;G dynabeads:#88848)


title: case_508 mRNA-seq

description:
Yang_SysBio_case_508
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: ipf

value: case

value: m

tag: raw data disclaimer


title: BM154-CMML


title: s643_L3_fat

value: Fat

value: wild type


title: MG_FACS_MIA_PLX_LPS_Rep1

value: brain striatum

value: microglia

value: LPS


title: BM179-CMML


title: BM150-CMML


title: case_504 mRNA-seq

description:
Yang_SysBio_case_504
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***


title: MG_FACS_MIA_CON_SAL_Rep4

value: SAL

value: male


title: s463_L3_fat

value: F

value: Veh


title: BM149-CMML


title: BM147-CMML


title: s621_L3_fat

value: M


title: control_503 mRNA-seq

description:
Yang_SysBio_control_503
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: Pittsburgh Lung Donor Core

value: normal

value: control

value: white

value: not hispanic or latino

value: N


title: MG_FACS_MIA_CON_SAL_Rep3


title: s540_L3_fat

value: Fat


title: s553_L2_fat

value: wild type


title: MG_FACS_MIA_CON_SAL_Rep2

value: brain striatum


title: s442_L1_fat


title: BM1257-MDS/MPD

value: MDS/MPD

value: bone marrow

value: CMS-specific antiserum pre-conjugated with protein A/G dynabeads (Thermofisher scientific; A dynabeads:#88846;G dynabeads:#88848)


title: MG_FACS_MIA_CON_SAL_Rep1

value: microglia

value: SAL

value: male


title: MG_FACS_MIA_CON_LPS_Rep6

value: LPS


title: case_506 mRNA-seq

description:
Yang_SysBio_case_506
*** 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: m

value: U


title: BM1256-MDS

value: MDS


title: s530_L6_brain

source_name: Brain

value: Brain

value: M


title: case_500 mRNA-seq

description:
Yang_SysBio_case_500
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: Pittsburgh Lung Donor Core

value: white

value: not hispanic or latino


title: MG_FACS_MIA_CON_LPS_Rep5

value: brain striatum


title: s612_L6_brain

value: wild type


title: control_501 mRNA-seq

description:
Yang_SysBio_control_501
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: normal

value: control

value: N


title: BM1255-MDS

value: bone marrow

value: CMS-specific antiserum pre-conjugated with protein A/G dynabeads (Thermofisher scientific; A dynabeads:#88846;G dynabeads:#88848)


title: case_499 mRNA-seq

description:
Yang_SysBio_case_499
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: ipf


title: s571_L6_brain


title: MG_FACS_MIA_CON_LPS_Rep3

value: microglia

value: LPS

value: male


title: BM1253-MDS

value: MDS


title: MG_FACS_MIA_CON_LPS_Rep4


title: s583_L6_brain

value: Brain

value: M


title: control_498 mRNA-seq

description:
Yang_SysBio_control_498
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: Pittsburgh Lung Donor Core

value: m

value: white

value: Y


title: case_502 mRNA-seq

description:
Yang_SysBio_case_502
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: case

value: not hispanic or latino

value: U


title: MG_FACS_MIA_CON_LPS_Rep1

value: brain striatum


title: case_497 mRNA-seq

description:
Yang_SysBio_case_497
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: f

value: N


title: MG_FACS_MIA_CON_LPS_Rep2


title: BM1251-MDS

value: bone marrow

value: CMS-specific antiserum pre-conjugated with protein A/G dynabeads (Thermofisher scientific; A dynabeads:#88846;G dynabeads:#88848)


title: MG_FACS_CON_PLX_SAL_Rep4

value: microglia

value: SAL


title: s660_L5_brain

value: F

value: wild type


title: control_496 mRNA-seq

description:
Yang_SysBio_control_496
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: normal

value: control


title: s664_L5_brain

value: Brain


title: case_495 mRNA-seq

description:
Yang_SysBio_case_495
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: Pittsburgh Lung Donor Core

value: ipf

value: white


title: s454_L5_brain


title: BM1250-MDS

value: MDS


title: s492_L5_brain


title: BM1254-MDS


title: case_494 mRNA-seq

description:
Yang_SysBio_case_494
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: case

value: m

value: not hispanic or latino

value: Y


title: MG_FACS_CON_PLX_SAL_Rep2

value: brain striatum

value: male


title: control_492 mRNA-seq

description:
Yang_SysBio_control_492
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: f


title: BM1247-MDS

value: bone marrow

value: CMS-specific antiserum pre-conjugated with protein A/G dynabeads (Thermofisher scientific; A dynabeads:#88846;G dynabeads:#88848)


title: BM1252-MDS


title: s491_L4_brain

value: F

value: wild type


title: BM1249-MDS


title: case_493 mRNA-seq

description:
Yang_SysBio_case_493
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung


title: MG_FACS_CON_PLX_LPS_Rep6

value: microglia

value: LPS


title: s581_L2_brain

value: Brain

value: M


title: BM1246-MDS

value: MDS


title: BM1245-MDS


title: MG_FACS_CON_PLX_LPS_Rep5


title: case_489 mRNA-seq

description:
Yang_SysBio_case_489
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: Pittsburgh Lung Donor Core

value: ipf

value: case

value: white

value: U


title: case_491 mRNA-seq

description:
Yang_SysBio_case_491
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: not hispanic or latino

value: N


title: MG_FACS_CON_PLX_LPS_Rep4

value: brain striatum

value: male


title: MG_FACS_CON_PLX_LPS_Rep3


title: s640_L6_brain

value: F

value: Veh


title: s642_L5_brain

value: wild type


title: case_487 mRNA-seq

description:
Yang_SysBio_case_487
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: m

value: Y


title: case_486 mRNA-seq

description:
Yang_SysBio_case_486
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***


title: BM1243-MDS

value: bone marrow

value: CMS-specific antiserum pre-conjugated with protein A/G dynabeads (Thermofisher scientific; A dynabeads:#88846;G dynabeads:#88848)


title: BM1244-MDS

value: MDS


title: MG_FACS_CON_PLX_SAL_Rep1

value: microglia

value: SAL


title: BM1248-MDS


title: s643_L5_brain

value: Brain


title: BM1242-MDS


title: case_484 mRNA-seq

description:
Yang_SysBio_case_484
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: Pittsburgh Lung Donor Core

value: ipf

value: case

value: f

value: white


title: MG_FACS_CON_PLX_LPS_Rep1

value: brain striatum

value: LPS

value: male


title: MG_FACS_CON_PLX_SAL_Rep3


title: case_483 mRNA-seq

description:
Yang_SysBio_case_483
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: not hispanic or latino


title: s631_L4_brain

value: F

value: wild type

value: Veh


title: BM1241-MDS

value: MDS

value: bone marrow

value: CMS-specific antiserum pre-conjugated with protein A/G dynabeads (Thermofisher scientific; A dynabeads:#88846;G dynabeads:#88848)


title: s641_L6_brain

value: Brain


title: s621_L2_brain

value: M


title: BM1240-MDS


title: MG_FACS_CON_CON_SAL_Rep4

value: microglia

value: SAL


title: control_482 mRNA-seq

description:
Yang_SysBio_control_482
*** 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


title: case_481 mRNA-seq

description:
Yang_SysBio_case_481
*** 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: m

value: white


title: s620_L2_brain

value: wild type

value: Veh


title: BM1238-MDS

value: MDS

value: bone marrow

value: CMS-specific antiserum pre-conjugated with protein A/G dynabeads (Thermofisher scientific; A dynabeads:#88846;G dynabeads:#88848)


title: s551_L1_brain

value: Brain

value: M


title: BM1239-MDS


title: MG_FACS_CON_CON_SAL_Rep3

value: brain striatum

value: microglia

value: SAL

value: male


title: MG_FACS_CON_CON_SAL_Rep2


title: MG_FACS_CON_PLX_LPS_Rep2

value: LPS


title: MG_FACS_CON_CON_SAL_Rep1


title: s601_L1_brain


title: MG_FACS_CON_CON_LPS_Rep5


title: case_477 mRNA-seq

description:
Yang_SysBio_case_477
*** 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: not hispanic or latino

value: Y


title: control_478 mRNA-seq

description:
Yang_SysBio_control_478
*** 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: white

value: U


title: MG_FACS_CON_CON_LPS_Rep3_exclude


title: BM1236-MDS

value: MDS

value: bone marrow

value: CMS-specific antiserum pre-conjugated with protein A/G dynabeads (Thermofisher scientific; A dynabeads:#88846;G dynabeads:#88848)


title: MG_FACS_CON_CON_LPS_Rep4

value: brain striatum

value: microglia


title: BM1235-MDS


title: BM1234-MDS


title: case_476 mRNA-seq

description:
Yang_SysBio_case_476
*** 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: N


title: MG_FACS_CON_CON_LPS_Rep2

value: LPS

value: male


title: case_475 mRNA-seq

description:
Yang_SysBio_case_475
*** 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: not hispanic or latino

value: Y


title: BM1232-MDS


title: BM1233-MDS


title: control_474 mRNA-seq

description:
Yang_SysBio_control_474
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: LTRC

value: control

value: asian


title: control_472 mRNA-seq

description:
Yang_SysBio_control_472
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: other

value: f

value: white

value: U


title: case_479 mRNA-seq

description:
Yang_SysBio_case_479
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: ipf


title: BM1230-MDS

value: MDS

value: bone marrow

value: CMS-specific antiserum pre-conjugated with protein A/G dynabeads (Thermofisher scientific; A dynabeads:#88846;G dynabeads:#88848)


title: MG_FACS_CON_CON_LPS_Rep1

value: brain striatum

value: microglia

value: LPS


title: MG_ATAC_CON_LPS_Rep7

data_processing:
Alignment: FASTQ files were trimmed with CUTADAPT ( cutadapt -a CTGTCTCTTATA -A CTGTCTCTTATA --cores=0 --pair-filter=any -m 20 ). Trimmed FASTQ files were aligned and assembled with bowtie2 ( bowtie2 -p 8 --very-sensitive-local -X 2000 -x ${index_path}/mm10 )
Cleanup: Mitochondrial and Duplicates reads were tagged and removed with picard (picard MarkDuplicates VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=false ) and samtools (samtools view -h -q 30 -F 1804 -f 2 ${in_path}/mark.bam | awk '{if(!match($3, /chrM/)){print $0}}' | awk '{if(!match($3, /[_]/)){print $0}}' | samtools view -hb > ${out_path}/clean.bam)
Peaks: Peaks were called with MACS2 ( macs2 callpeak -t ${in_path}/clean.bam -f BAMPE --min-length 100 --max-gap 50 --bdg -g mm --keep-dup all -n SID --outdir ${out_path}/ --tempdir ${tmp_path}/ )
Differential accessibility was performed with DiffBind and permutation tests.
Assembly: mm10 (GRCm38)
Supplementary files format and content: narrowPeak files

extract_protocol:
Male mice (8-10 wk) were deeply anesthetized with ether, perfused with PBS, and brains extracted. The meninges were removed and then the frontal cortex and striatum were collected into 2 mL tubes with HBSS on ice. The anterior striatum was collected from a coronal slice anterior to 1.7 mm bregma by collecting the tissue surrounding the nucleus accumbens. The next coronal slice was cut at -0.5 bregma and the dorsal and ventral striatum was excised from this slice, excluding the olfactory tubercle, and all striatum pieces were pooled together. The brain pieces were diced with scissors and then homogenized with papain according to the adult neural dissociation kit (Miltenyi). Briefly, the tissue was treated with papain and DNase at 37°C for 30 min with rotation. The homogenates were pipetted gently and filtered with a 70 µm strainer. The cell pellet was resuspended in debris removal solution (300 µL debris removal, 700 µL PBS), overlaid with 300 µL of PBS, centrifuged at 3000xg for 10 min, debris aspirated, washed with PBS, and centrifuged at 1000xg for 10 min. The cells were resuspended in 0.5% BSA in HBSS. For fluorescence-activated cell sorting the cells were stained with CD45-APC, CD11b-BV421, and P2RY12-PE antibodies for 30 min at 4C. The cells were washed with buffer and sorted for live (PI-), CD11b+, CD45-low, P2RY12+ before final collection into ATAC collection buffer.
The ATAC libraries were prepared according to Corces et al. 2017. Briefly, cells were pelleted by spinning at 500g for 15 min at 4C and the supernatant carefully removed. 50 ul of cell lysis buffer was added (10 mM Tris-HCl, 10mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween-20, 0.01% Digitonin), pipetted to mix 3-5 times, incubated on ice for 3 min, and washed (10 mM Tris-HCl, 10mM NaCl, 3 mM MgCl2, 0.1% Tween-20). The nuclei were spun to pellet at 500 g for 30 min at 4C and the supernatant carefully removed. Then the Tn5 buffer (1X TD Buffer, 1x PBS, 0.1% Tween-20, 0.01 Digotinin, 1 ul Tn5) was added and incubated at 37°C for 1 hour with 1000 RPM shaking. The DNA was collected using the Qiagen Minelute cleanup kit. The DNA was eluted with 11 ul EB Buffer. For library preparation, 10 ul of prepared DNA was mixed with 1.25 uM indexing primers and 1x NEBNext High-Fidelity PCR Master Mix and amplified (72C 5 min, 98C 30 sec, 5 cycles: 98C 10 sec, 63C 30 sec, 72C 1 min). 5 ul was used for qPCR to test amplification and calculate additional cycles. 6-8 more cycles were run before cleanup with Ampure XP beads. The libraries with quality control checked using a Bioanalyzer then pooled at equal mass for sequencing on a Novaseq6000.

value: CON

value: male

tag: number of_cells

tag: ID


title: control_480 mRNA-seq

description:
Yang_SysBio_control_480
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

tag: tissue

value: lung

tag: age

value: not hispanic or latino


title: case_470 mRNA-seq

description:
Yang_SysBio_case_470
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: Pittsburgh Lung Donor Core

value: case

value: m


title: Prdm16 Null 3

city: Downers Grove

first: Michael

last: Ebeid

state: IL

address: 555 31st St, Anatomy

department: Anatomy

institute: Midwestern University

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: raw counts

source_name: Cochlear duct

extract_protocol:
E14.5 cochlear ducts from both inner ears of one embryo were microdissected in DEPC-treated cold PBS, collected in RNA extraction buffer and homogenized (Bel-Art 650000000). RNA extraction and subsequent removal of genomic DNA were performed using RNAqueous RNA isolation kit (Invitrogen, AM1931) as per the manufacturer protocol. Three littermates per genotype were used.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

tag: genotype


title: s622_L1_brain

value: Brain

tag: strain

value: M

value: wild type

tag: treatment

value: Veh


title: MG_ATAC_CON_LPS_Rep6

tag: cell type


title: BM1229-MDS

tag: disease state

value: MDS

tag: ip reagent


title: MG_ATAC_MIA_SAL_Rep6

tag: group

value: MIA

value: SAL


title: BM1228-MDS

value: bone marrow

value: CMS-specific antiserum pre-conjugated with protein A/G dynabeads (Thermofisher scientific; A dynabeads:#88846;G dynabeads:#88848)


title: case_471 mRNA-seq

description:
Yang_SysBio_case_471
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

tag: center

tag: dx

value: ipf

tag: rnaseqid

value: white

value: N


title: MG_ATAC_CON_LPS_Rep5

value: brain striatum

value: microglia

value: CON

value: LPS

tag: Sex

value: male


title: Prdm16 Null 2


title: control_469 mRNA-seq

description:
Yang_SysBio_control_469
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: LTRC

value: other

value: control

value: m

tag: race

tag: ethnicity

value: not hispanic or latino

value: Y

tag: raw data disclaimer


title: BM1226-MDS

value: MDS

tag: tissue

value: bone marrow


title: BM1227-MDS

value: CMS-specific antiserum pre-conjugated with protein A/G dynabeads (Thermofisher scientific; A dynabeads:#88846;G dynabeads:#88848)


title: Prdm16 Het 3


title: case_467 mRNA-seq

description:
Yang_SysBio_case_467
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: Pittsburgh Lung Donor Core

value: ipf

value: case

tag: age

value: white


title: MG_ATAC_CON_SAL_Rep5

value: brain striatum

value: microglia

value: CON

value: SAL

tag: number of_cells

tag: ID


title: Prdm16 Null 1

tag: developmental stage

tag: genotype


title: BM1224-MDS


title: case_468 mRNA-seq

description:
Yang_SysBio_case_468
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: N


title: BM1223-MDS


title: case_462 mRNA-seq

description:
Yang_SysBio_case_462
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: LTRC

value: White


title: Prdm16 Het 1


title: Prdm16 Het 2


title: BM1210-MDS


title: Prdm16 WT 3

value: wild type


title: case_458 mRNA-seq

description:
Yang_SysBio_case_458
*** 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

value: Y


title: MG_ATAC_MIA_SAL_Rep5

tag: cell type

value: MIA

tag: treatment

value: male


title: Prdm16 WT 2


title: control_460 mRNA-seq

description:
Yang_SysBio_control_460
*** 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: MG_ATAC_MIA_LPS_Rep5

value: brain striatum

value: LPS


title: MG_ATAC_MIA_SAL_Rep4

value: microglia


title: control_457 mRNA-seq

description:
Yang_SysBio_control_457
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: f

value: white


title: Prdm16 WT 1


title: BM1139-MDS

tag: disease state

value: MDS

value: bone marrow

tag: ip reagent

value: CMS-specific antiserum pre-conjugated with protein A/G dynabeads (Thermofisher scientific; A dynabeads:#88846;G dynabeads:#88848)


title: BM1132-MDS


title: MG_ATAC_MIA_LPS_Rep4

tag: group


title: MG_ATAC_MIA_SAL_Rep3

value: SAL


title: Untransfected biological RNA-seq replicate library 2

city: London

first: Kayleigh

last: Bozon

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

description: RNA-seq

data_processing:
Adapter trimming was performed with cutadapt (version 1.9.1) (Martin M, 2011) with parameters "--minimum-length=25 --quality-cutoff=20 -a AGATCGGAAGAGC".
The RSEM package (version 1.3.0) (Li and Dewey, 2011) in conjunction with the STAR alignment algorithm (version 2.5.2a) (Dobin et al., 2013) was used for the mapping and subsequent gene-level counting of the sequenced reads with respect to mm10 RefSeq genes downloaded from the UCSC Table Browser (Karolchik et al., 2004) on 19th February 2016. The parameters used were "--star-output-genome-bam --forward-prob 0".
Differential expression analysis was performed with the DESeq2 package (version 1.12.3) (Love et al., 2014) within the R programming environment (version 3.3.1).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file containing raw counts and TPM values generated by RSEM where gene names are rows and columns represent all RNA-Seq samples generated in the study.

source_name: Trophoblast stem cells

growth_protocol: Trophoblast stem cells were maintained in MEF conditioned medium as described in Tanaka et al. 1998 (Science, 282, 2072-5).

extract_protocol:
Cells were harvested in TRIzol and snap frozen. RNA was extracted using the RNAeasy Plus Micro Kit according to manufacturer instructions.
RNA integrity (RIN) was determined using Caliper LabChip GX (Perkin Elmer, USA). Libraries were generated using the TruSeq Stranded mRNA Library Prep Kit as per manufacturer’s instructions (Illumina, USA) and sequenced as 76bp single-end, stand-specific reads on the Illumina HiSeq 4000 platform (Francis Crick Institute).

treatment_protocol: Cells were incubated with shRNA vectors and jetPRIME transfection reagent for 4 hours; after which the medium was aspirated and fresh medium added and cells cultured for a further 44 hours. Cells were dissociated using TrypLE, clumps removed using cell strainers and pelleted. Transfected (mCherry positive) and untransfected (mCherry negative) resuspended cells were isolated by fluorescent activated cell sorting (FACS).

value: wild-type

tag: timepoint

value: Untransfected, sorted by FACs


title: case_456 mRNA-seq

description:
Yang_SysBio_case_456
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

tag: center

value: UCSF

tag: dx

value: ipf

value: case

tag: rnaseqid

value: m

value: not hispanic or latino

value: Y


title: Untransfected biological RNA-seq replicate library 3

description: RNA-seq


title: case_453 mRNA-seq

description:
Yang_SysBio_case_453
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

tag: Sex

tag: race

tag: ethnicity


title: case_455 mRNA-seq

description:
Yang_SysBio_case_455
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

tag: tissue

tag: age

tag: raw data disclaimer


title: BM1065-CMML

value: CMML


title: MG_ATAC_CON_SAL_Rep4

value: brain striatum

value: microglia

value: CON

value: male

tag: number of_cells

tag: ID


title: MG_ATAC_MIA_SAL_Rep2

tag: cell type

value: MIA


title: BM1073-MDS

value: MDS

value: bone marrow

value: CMS-specific antiserum pre-conjugated with protein A/G dynabeads (Thermofisher scientific; A dynabeads:#88846;G dynabeads:#88848)


title: case_452 mRNA-seq

description:
Yang_SysBio_case_452
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: LTRC

value: white

value: N


title: BM1063-CMML


title: Untransfected biological RNA-seq replicate library 1

description: RNA-seq

tag: genotype

value: wild-type

tag: treatment

value: Untransfected, sorted by FACs


title: BM1166-MDS

tag: disease state

tag: ip reagent


title: case_451 mRNA-seq

description:
Yang_SysBio_case_451
*** 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: m


title: MG_ATAC_CON_LPS_Rep4

value: brain striatum

tag: group

value: LPS


title: Scrambled positive RNA-seq biological replicate library 3

description: RNA-seq

tag: timepoint

value: Transfected with scrambled shRNA (mCherry positive), sorted by FACS


title: MG_ATAC_MIA_LPS_Rep3

value: microglia

value: male


title: MG_ATAC_CON_LPS_Rep3

value: CON


title: Scrambled positive RNA-seq biological replicate library 2

description: RNA-seq


title: 8738_3 RNA-Seq

city: Thousand Oaks

first: Xianglong

last: Zhang

state: CA

address: One Amgen Center Dr.

department: Department of Cardiometabolic Disorders

institute: Amgen Inc.

data_processing:
RNA-Seq data: Cutadapt (Version 1.8.1) was used to trim Illumina TruSeq adapters and low-quality ends from the raw reads. Bowtie2 (Version 2.3.1) was used to align the trimmed reads to the RefSeq transcriptome (GRCh38.p10) and RSEM (Version 1.2.30) was used to quantify gene expression in a strand-specific manner by setting parameter “--forward-prob 0”. DESeq2 (Version 1.12.4) was used to perform differential expression analysis between cell types as well as between patients and controls within each cell type.
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: RNA-Seq data — gene name, transcript id, length, effective_length, expected count, TPM, FPKM

source_name: induced pluripotent stem cell

growth_protocol: Each iPSC line was cultured using mTeSR media (Stemcell Technologies, 85850) in clear plastic BioLite 6-well multidish plates (Thermo Scientific, 130184) coated with Matrigel hESC‐qualified Matrix (BD Biosciences, 356234). The cells were kept at 37° C and 5% CO2; media was changed daily. The cells were passaged every 4 to 5 days once the wells reached ~ 75-100% confluency. For passaging, cells were washed with DPBS (Life Technologies, 14190-144), dissociated with TrypLE Express Enzyme (1X) (ThermoFisher, 12604013) and added to fresh media on a new plate and/or added to freezing media for storage. All lines were grown concurrently to avoid batch effects.

extract_protocol:
RNA were extracted using the All Prep kit (Qiagen, Cat. #80204) once the wells reached ~80-100% confluency (~1 to 3 million cells). mRNA purification was performed using the Dynabeads mRNA Purification Kit (Invitrogen, Cat #61006) for RNA sequencing.
The libraries for all samples at both iPSC and iN stages were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England BioLabs, E7530S)

tag: individual

tag: phenotype

value: wild type

value: induced neuron


title: Scrambled positive RNA-seq biological replicate library 1

description: RNA-seq


title: 726_1 RNA-Seq


title: MG_ATAC_MIA_LPS_Rep2

value: MIA

tag: Sex


title: Scrambled negative RNA-seq biological replicate library 2

description: RNA-seq

value: Non-transfected scrambled shRNA (mCherry negative), sorted by FACS


title: case_450 mRNA-seq

description:
Yang_SysBio_case_450
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

tag: center

value: LTRC

tag: dx

tag: rnaseqid

tag: race

value: asian

value: not hispanic or latino

value: Y


title: control_449 mRNA-seq

description:
Yang_SysBio_control_449
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

tag: tissue

value: lung

value: UCSF

value: normal

value: control

tag: age

value: black

tag: ethnicity

value: unknown

tag: raw data disclaimer


title: 6632_4 RNA-Seq

tag: cell type


title: MG_ATAC_MIA_SAL_Rep1

value: brain striatum

value: microglia

tag: treatment

value: SAL

tag: number of_cells

tag: ID


title: 5401_1 RNA-Seq

value: wild type


title: MG_ATAC_MIA_LPS_Rep1

tag: group

value: LPS

value: male


title: case_448 mRNA-seq

description:
Yang_SysBio_case_448
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

source_name: tissue-Autopsy

value: University of Colorado

value: ipf

value: case

value: f

value: N


title: Scrambled negative RNA-seq biological replicate library 3

description: RNA-seq

tag: genotype

value: wild-type

tag: timepoint

value: Non-transfected scrambled shRNA (mCherry negative), sorted by FACS


title: 14781X16_101_4 RNA-Seq

tag: individual

tag: phenotype

value: induced neuron


title: control_446 mRNA-seq

description:
Yang_SysBio_control_446
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

tag: center

value: Pittsburgh Lung Donor Core

value: normal

value: control

tag: Sex

value: white

value: not hispanic or latino


title: MG_ATAC_CON_LPS_Rep2

value: brain striatum

value: microglia

value: CON


title: 14781X16_101_3 RNA-Seq


title: MG_ATAC_CON_LPS_Rep1

value: LPS

value: male


title: Cdx2 knockdown positive RNA-seq biological replicate library 2

description: RNA-seq

value: Transfected with shRNA targetting Cdx2 (mCherry postive), sorted by FACS


title: case_447 mRNA-seq

description:
Yang_SysBio_case_447
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: UCSF

tag: dx

value: ipf

value: case

tag: rnaseqid

value: m


title: MG_ATAC_CON_SAL_Rep3

tag: tissue

value: SAL


title: case_444 mRNA-seq

description:
Yang_SysBio_case_444
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

tag: age

tag: race

value: Y


title: Scrambled negative RNA-seq biological replicate library 1

description: RNA-seq

value: wild-type

value: Non-transfected scrambled shRNA (mCherry negative), sorted by FACS


title: Cdx2 knockdown positive RNA-seq biological replicate library 3

description: RNA-seq


title: 14765X2_101_2 RNA-Seq

value: induced neuron


title: MG_ATAC_CON_SAL_Rep2


title: case_442 mRNA-seq

description:
Yang_SysBio_case_442
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: unknown

tag: ethnicity

value: N

tag: raw data disclaimer


title: 14765X2_101_1 RNA-Seq

tag: cell type


title: 14758X3_101_8 RNA-Seq


title: case_441 mRNA-seq

description:
Yang_SysBio_case_441
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: white


title: MG_ATAC_CON_SAL_Rep1

value: brain striatum

value: microglia

value: CON

tag: treatment

tag: number of_cells


title: 14756X9_201_2 RNA-Seq


title: Arid1a (f/f) cre+ 0h

city: Beijing

first: ye

last: hu

address: Dongdan

country: China

institute: PUMC

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using hisat2 v2.0.4 with parameters --rna-strandness RF
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were computed by summing the FPKMs of transcripts in each gene group using cuffdiff v2.1.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: BMDM

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: BMDM

value: untreated

value: Arid1a (f/f) cre+


title: BM1237-MDS

tag: disease state

value: MDS

value: bone marrow

tag: ip reagent

value: CMS-specific antiserum pre-conjugated with protein A/G dynabeads (Thermofisher scientific; A dynabeads:#88846;G dynabeads:#88848)


title: MG_SC_MIA_PLX_LPS_Rep5

description:
2012231MP
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting were made using the Cell Ranger software (Cell Ranger Count v6.0.0) with Reference (Mouse (mm10) 2020-A). Doublet detection was calculated with scDblFinder.
Cells were filtered based on nFeature_RNA > 500 & nFeature_RNA < 10000 & nCount_RNA > 600 & nCount_RNA < 150000 & percent.mt < 10 & scDblFinder =='singlet'.
Data was normalized and integrated using Seurat:  NormDat <- lapply(X = FiltDat_v1, FUN = SCTransform, method = "glmGamPoi", vars.to.regress = "percent.mt")  features <- SelectIntegrationFeatures(object.list = NormDat, nfeatures = 3000)  NormDat <- PrepSCTIntegration(object.list = NormDat, anchor.features = features)  NormDat <- lapply(X = NormDat, FUN = RunPCA, features = features)  anchors <- FindIntegrationAnchors(object.list = NormDat, normalization.method = "SCT", anchor.features = features, reduction = "rpca")  FinalDat <- IntegrateData(anchorset = anchors, normalization.method = "SCT")
Assembly: mm10 (GRCm38)
Supplementary files format and content: Tar archives include barcodes.tsv, features.tsv, and matrix.mtx files.

extract_protocol: Male mice (8-10 wk) were deeply anesthetized, perfused with HBSS, brains extracted, and striatum collected into glass tissue homogenizers on ice with homogenization buffer (15 mM HEPES, 5% Trehalose, 500 U/mL DNaseI, 80 U/mL RNasin, in 1x HBSS)44. The brain pieces were homogenized 7-10 times, filtered through a 70 µm strainer, and spun at 2500 RPM for 2 min to collect the cells. Debris and myelin was removed using a debris removal solution (Miltenyi). The cells were incubated with Fc block (eBiosciences 16-0161-81) for 5 min then incubated with antibodies (CD45-APC BD Biosciences 559864, P2RY12-PE Biolegend 848003, and CD11b-BV421 BD Biosciences 562605) for 30 min at 4°C in incubation buffer (0.5% BSA, 2 mM EDTA, 25 mM HEPES, 5% Trehalose, 80 U/mL RNAsin in 1x HBSS), washed well with FACS buffer (0.5% BSA, 2 mM EDTA, 25 mM HEPES, in 1x HBSS), and strained though a 40 µm strainer. Cells were gated on size, singlet, and propidium iodide negative (live cells), before sorting on CD45-APC low, CD11b-BV421, P2RY12 positive using a MoFlo Legacy sorter. Single cells were captured on a 10X Genomics Chromium Platform at a capture target of 6,000 – 10,000 cells. The libraries were pooled and sequenced on a Novaseq6000.

treatment_protocol: Lipopolysaccharide (LPS) was delivered by intraperitoneal injection to mice at a dose of 4500 endotoxin units / gram body weight. Microglia were extracted 18 hours after LPS treatment.

tag: group

value: LPS

value: male

tag: batch

value: D


title: case_439 mRNA-seq

description:
Yang_SysBio_case_439
*** 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: f

value: not hispanic or latino

value: Y


title: Arid1a (f/f) cre- 8h

value: treated with VSV for 8 hours

tag: genotype

value: Arid1a (f/f) cre-


title: MG_SC_MIA_PLX_LPS_Rep4

description:
201112MP
10x Genomics

value: brain striatum

value: microglia


title: case_438 mRNA-seq

description:
Yang_SysBio_case_438
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

tag: center

value: white

value: U


title: Arid1a (f/f) cre- 0h

value: BMDM

value: untreated


title: MG_SC_MIA_PLX_LPS_Rep3

description:
201063MP
10x Genomics

value: LPS

tag: Sex

value: male


title: 14756X9_201_1 RNA-Seq

tag: individual

tag: phenotype

value: induced neuron


title: case_435 mRNA-seq

description:
Yang_SysBio_case_435
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

tag: tissue

value: lung

value: LTRC

tag: dx

tag: rnaseqid

value: N


title: Cdx2 knockdown positive RNA-seq biological replicate library 1

description: RNA-seq

value: wild-type

tag: timepoint

value: Transfected with shRNA targetting Cdx2 (mCherry postive), sorted by FACS


title: MG_SC_MIA_PLX_LPS_Rep2

description:
20961MP
10x Genomics

value: G


title: 14756X16_101_2 RNA-Seq


title: D44_SPL_2

city: La Jolla

first: Ananda

last: Goldrath

address: 9500 Gilman Dr

institute: UCSD

description: 3' Transcriptome sequencing (10X genomics V3)

data_processing:
data were processed by cellranger 2.1.0 with default parameter, using mm10 as reference.
Raw cell-reads were then loaded to R using the cellrangerRkit package. The scRNA-seq dataset was then further filtered based on gene numbers and mitochondria gene counts tototal counts ratio. Only cells with > 400 genes,UMI > 0,and 0.5% ~ 20% of their UMIs mappingto mitochondria genes were kept for downstream analysis.
For the scRNA-seq, the first 16 bp of R1 is the cell barcode and the next 10bp (17-26bp) is the UMI.
Genome_build: mm10
Supplementary_files_format_and_content: CellRanger output of filtered gene matrix with barcodes & features files

growth_protocol: No growth procedure was required.

extract_protocol:
For isolation of CD4+ T cells from spleen, spleens were collected and dissociated to yield a cell suspension prior to lysis of red blood cells.
Single cell libraries were prepared according to the protocol for 10X Genomics for 3’ Gene Expression. Approximately 10,000 sorted CD45.1+ Va2+ CD4+ CD44+ cells were loaded and partitioned into Gel Bead In-Emulsions (GEM). scRNA libraries were sequenced on a HiSeq4000 (Illumina).

treatment_protocol: These details are included in extraction protocol.

value: spleen

tag: cell subtype

value: CD4 T cell


title: control_433 mRNA-seq

description:
Yang_SysBio_control_433
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: UCSF

value: normal

value: control

tag: age

value: m

tag: race

value: black

tag: ethnicity

value: unknown

tag: raw data disclaimer


title: 14756X16_101_1 RNA-Seq

tag: cell type


title: D44_SPL_1


title: Arid1a (f/f) cre+ 8h

value: BMDM

tag: treatment

value: treated with VSV for 8 hours

value: Arid1a (f/f) cre+


title: 14723X10_202_8 RNA-Seq

value: induced neuron


title: MG_SC_MIA_PLX_LPS_Rep6

description:
2012232MP
10x Genomics

value: brain striatum

value: microglia

tag: group

value: LPS

value: male

tag: batch

value: D

tag: number of_cells


title: case_432 mRNA-seq

description:
Yang_SysBio_case_432
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

tag: center

value: ipf

value: case

tag: Sex

value: asian

value: Y


title: 14758X3_101_7 RNA-Seq

tag: individual

tag: phenotype


title: D21_SPL_2

tag: tissue

value: spleen

value: CD4 T cell


title: MG_SC_MIA_PLX_LPS_Rep1

description:
20862MP
10x Genomics

value: G


title: case_431 mRNA-seq

description:
Yang_SysBio_case_431
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: UCSF

tag: dx

tag: rnaseqid

value: m

value: white

value: unknown


title: MG_SC_MIA_CON_LPS_Rep4

description:
201201MC
10x Genomics

value: brain striatum


title: control_440 mRNA-seq

description:
Yang_SysBio_control_440
*** 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: not hispanic or latino

value: N


title: D21_SPL_1

tag: cell subtype


title: case_429 mRNA-seq

description:
Yang_SysBio_case_429
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: ipf

tag: age

value: f


title: MG_SC_MIA_CON_LPS_Rep2

description:
20893MC
10x Genomics

value: microglia

value: LPS

value: male


title: D7_SPL_2

value: spleen

value: CD4 T cell


title: MG_SC_MIA_CON_LPS_Rep3

description:
201141MC
10x Genomics

value: D


title: control_428 mRNA-seq

description:
Yang_SysBio_control_428
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: UCSF

tag: race

value: black


title: iN_726_1 RNA-Seq

source_name: induced neuron

value: wild type

value: induced neuron


title: iN_8738 RNA-Seq


title: control_425 mRNA-seq

description:
Yang_SysBio_control_425
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: normal

value: m

tag: ethnicity

value: unknown

value: Y


title: iN_6632_4 RNA-Seq


title: MG_SC_MIA_CON_LPS_Rep1

description:
20661MC
10x Genomics

value: brain striatum

value: G


title: MG_SC_CON_PLX_LPS_Rep4

description:
201172CP
10x Genomics


title: D7_SPL_1


title: iN_65X2_101_2 RNA-Seq


title: control_421 mRNA-seq

description:
Yang_SysBio_control_421
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: control

value: f

value: not hispanic or latino

tag: raw data disclaimer


title: iN_58X3_101_8 RNA-Seq

tag: cell type


title: MG_SC_CON_PLX_LPS_Rep3

description:
201021CP
10x Genomics

value: microglia

tag: treatment

value: LPS

value: male


title: iN_81X16_101_4 RNA-Seq


title: iN_56X9_201_2 RNA-Seq


title: control_415 mRNA-seq

description:
Yang_SysBio_control_415
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: UCSF

value: N


title: MG_SC_CON_PLX_LPS_Rep2

description:
20921CP
10x Genomics

tag: group


title: MG_SC_CON_CON_LPS_Rep4

description:
WT2CC
10x Genomics

tag: batch

value: D


title: case_414 mRNA-seq

description:
Yang_SysBio_case_414
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: ipf

value: case

value: white


title: MG_SC_CON_PLX_LPS_Rep1

description:
20821CP
10x Genomics

tag: number of_cells


title: case_416 mRNA-seq

description:
Yang_SysBio_case_416
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

tag: center

value: m

value: unknown


title: R2W1_Input-seq

city: shanghai jingan district

first: ZHONGQI

last: CUI

state: shanghai

address: 301 yanchangzhong road

institute: shanghai tenth people hospital

data_processing:
Library strategy: MeRIP-seq
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30.After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
Clean reads of all libraries were aligned to the reference genome (UCSC MM10)  by Hisat2 software (v2.0.4). Methylated sites on RNAs (peaks) were identified by MACS software.
Differentially methylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA  were figured out and choosed by home-made scripts
GO and Pathway enrichment analysis were performed by the differentially methylated protein coding genes
Genome_build: mm10
Supplementary_files_format_and_content: bed format
Supplementary_files_format_and_content: 13 of raw junction read

extract_protocol:
Briefly, fragmented RNA was incubated with anti-m6A polyclonal antibody (Synaptic Systems, 202003) in IPP buffer for 2 hours at 4°C. The mixture was then immunoprecipitated by incubation with protein-A beads (Thermo Fisher) at 4°C for an additional 2 hours. Then, bound RNA was eluted from the beads with N6-methyladenosine (BERRY & ASSOCIATES, PR3732) in IPP buffer and then extracted with Trizol reagent (Thermo Fisher) by following the manufacturer’s instruction.
Purified RNA was used for RNA-seq library generation with NEBNext® Ultra™ RNA Library Prep Kit (NEB). Both the input sample without immunoprecipitation and the m6A IP samples were subjected to 150 bp paired-end sequencing on Illumina HiSeq sequencer.

value: liver tissue

tag: strain

tag: time point

value: 3W reversal


title: case_413 mRNA-seq

description:
Yang_SysBio_case_413
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: LTRC

tag: Sex

value: White

value: Y


title: case_423 mRNA-seq

description:
Yang_SysBio_case_423
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

tag: tissue


title: iN_56X9_201_1 RNA-Seq

tag: individual

tag: phenotype

value: induced neuron


title: R1W2_Input-seq

value: 1W reversal


title: Control1W_Input-seq


title: Control3W_Input-seq


title: R2W2_Input-seq


title: Control6W_Input-seq


title: R1W1_Input-seq


title: iN_56X16_101_2 RNA-Seq


title: control_412 mRNA-seq

description:
Yang_SysBio_control_412
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

tag: dx

value: normal

value: control

tag: rnaseqid

value: black


title: iN_58X3_101_7 RNA-Seq


title: 6W2_Input-seq


title: iN_5401_1 RNA-Seq

value: wild type


title: 6W1_Input-seq


title: case_411 mRNA-seq

description:
Yang_SysBio_case_411
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: UCSF

value: ipf

tag: age

tag: race

value: not hispanic or latino

value: N


title: iN_23X10_202_8 RNA-Seq


title: MG_SC_CON_CON_LPS_Rep1

description:
20651CC
10x Genomics

value: brain striatum

value: microglia

value: LPS

value: male

value: G


title: MG_FACS_MIA_LPS_Rep4

data_processing:
Alignment: FASTQ files aligned and assembled with RSEM and STAR: rsem-calculate-expression -p 4 --paired-end --star --star-output-genome-bam --calc-ci --forward-prob 0.5
Counts: Count matrix was assembled using tximport in R  files <- list.files(path = "../1.align/genes.results/")  names(files) <- strtrim(files, 4)  txi.rsem <- tximport(files, type = "rsem", txIn = FALSE, txOut = FALSE)  txi.rsem$length[txi.rsem$length == 0] <- 1  table(txi.rsem$length == 0)  save(txi.rsem, file = "txi.rsem.RData")
Differential expression was performed with DESeq2.
Assembly: GRCm38vM25
Supplementary files format and content: Adult_FACS_counts.csv: Comma-separated file of raw counts from RSEM output.

extract_protocol:
Male mice (8-10 wk) were deeply anesthetized with ether, perfused with PBS, and brains extracted. The meninges were removed and then the frontal cortex and striatum were collected into 2 mL tubes with HBSS on ice. The anterior striatum was collected from a coronal slice anterior to 1.7 mm bregma by collecting the tissue surrounding the nucleus accumbens. The next coronal slice was cut at -0.5 bregma and the dorsal and ventral striatum was excised from this slice, excluding the olfactory tubercle, and all striatum pieces were pooled together. The brain pieces were diced with scissors and then homogenized with papain according to the adult neural dissociation kit (Miltenyi). Briefly, the tissue was treated with papain and DNase at 37°C for 30 min with rotation. The homogenates were pipetted gently and filtered with a 70 µm strainer. The cell pellet was resuspended in debris removal solution (300 µL debris removal, 700 µL PBS), overlaid with 300 µL of PBS, centrifuged at 3000xg for 10 min, debris aspirated, washed with PBS, and centrifuged at 1000xg for 10 min. The cells were resuspended in 0.5% BSA in HBSS. For fluorescence-activated cell sorting the cells were stained with CD45-APC, CD11b-BV421, and P2RY12-PE antibodies for 30 min at 4C. The cells were washed with buffer and sorted for live (PI-), CD11b+,CD45-low, P2RY12+ before final collection into RNA lysis buffer. RNA was collected according to the kit instructions (Qiagen, Micro-RNeasy, PicoPure RNA isolation Kits).
Bulk cell RNA sequencing libraries were prepared using a modified Smart-Seq2 protocol. 5 ng of purified RNA were mixed with 2.5 mM dNTP mix, 2.5 µM oligo-dT30VN, and 1 U/µL RNasin and incubated at 72°C for 3 min. Then 5.7 µL of the single-cell reverse transcription mix (1x superscript II buffer, 1 M betaine, 5 mM DTT, 100 U superscript II, 10 U RNasin, 1 µM TSO oligo, 6 mM MgCl2) was added to each sample for reverse transcription. The cDNA was amplified with the KAPA HF Ready mix with 9 PCR cycles. The cDNA was cleaned up with AMPure XP beads (Beckman Coulter) at a ratio of 0.7:1, washed with 80% ethanol, and resuspended in 17.5 µL water. The libraries were tagmented for sequencing using the Illumina Nextera XT DNA sample preparation kit. 200-250 pg of cDNA was added to 2.5 µL tagment DNA buffer (Illumina) and 1.25 µL of amplicon tagment mix (Illumina) and incubated at 55°C for 5 min to tagment cDNA. The reaction was neutralized with 1.25 µL of neutralize tagment buffer and incubated at room temperature for 5 min. Then the tagmented DNA was indexed and amplified with 3.75 µL of PCR master mix (Illumina) and 1.25 µL each of i5 and i7 indexing primers (Illumina, diluted 1:5). The samples were indexed with the following PCR cycles: 1 cycle of 72°C for 3 min and 95°C for 30 sec; 12 cycles of 95°C for 10 sec, 55°C for 30 sec, and 72°C for 30sec, and 1 cycle of 72°C for 5 min. The final libraries were purified using AMPure XP beads (Beckman Coulter) at a 0.6:1 ratio, washed with 80% ethanol and resuspended in 12 µL water.

value: MIA

tag: ID


title: MG_SC_CON_CON_LPS_Rep3

description:
WT1CC
10x Genomics

tag: cell type

value: D


title: 3W2_Input-seq

value: liver tissue


title: case_410 mRNA-seq

description:
Yang_SysBio_case_410
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: case

value: m

value: white

tag: ethnicity

tag: raw data disclaimer


title: 3W1_Input-seq


title: control_409 mRNA-seq

description:
Yang_SysBio_control_409
*** 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: MG_FACS_CON_SAL_Rep6

tag: group

value: CON

tag: treatment

value: SAL

tag: batch


title: TS667_g11_MEOX2_ACTseq_rep3

city: Heidelberg

first: Sevin

last: Turcan

address: Im Neuenheimer Feld 460

country: Germany

institute: Heidelberg University Hospital

description: ACT-Seq

data_processing:
The fastq files were trimmed using trimmomatic and aligned to hg19 with bowtie2 using parameters --end-to-end --very-sensitive --no-mixed --no-discordant.
Mitochondrial and blacklisted regions were removed from the aligned bam files using samtools.
Duplicates were removed using Picard tools (MarkDuplicates). Low quality reads (quality score < 2) were removed using samtools.
Peaks were called using MACS version 2.1.2. Differentially bound sites were identified using DiffBind (R statistical package). The reads within peak regions were plotted as a heatmap using deepTools. For visualization, the bam files were normalized to 1x depth using BPM.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files

source_name: Glioblastoma

extract_protocol:
ACT-seq was largely performed according to Carter et al (Carter et al., 2019) as described in detail recently (Liu et al., 2021) on triplicates of TS600 and TS667 NTC and KD2 lines. For CUT&Tag experiments, nuclei isolation was performed according to the published protocol (Narayanan et al. 2020) using a minimum of 105 nuclei. Isolated nuclei were washed and centrifuged at 600 g for 4 minutes. Nuclei were resuspended in 200 ul antibody buffer containing 4 ug MEOX2 antibody or IgG for control and incubated at 4 ºC overnight.
bulk library was prepared using 30 μL of 2 x Kapa, 20 μL of bulk DNA, 5 μL of Index 1 (i5 10 μM) and 5 μL of index 2 (i7 10 μM) and run in a thermal cycler for 17 cycles. Concentrations were measured using Nano Drop. QC was performed using D1000 Tapestation. The samples were sequenced on NextSeq 550 (paired-end 75-bp mid-output).

value: brain

tag: cell line

value: patient-derived GBM tumorsphere

value: MEOX2 sgRNA2


title: case_405 mRNA-seq

description:
Yang_SysBio_case_405
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

tag: center

value: National Jewish

value: ipf

value: f

value: not hispanic or latino

value: Y


title: TS667_g11_MEOX2_ACTseq_rep1

description: ACT-Seq


title: 1W2_Input-seq

value: liver tissue

tag: strain

tag: time point


title: MG_FACS_CON_SAL_Rep5

tag: tissue

value: brain striatum

value: microglia

tag: Sex

value: male


title: TS667_g11_MEOX2_ACTseq_rep2

description: ACT-Seq


title: MG_SC_CON_CON_LPS_Rep2

description:
20942CC
10x Genomics

value: LPS

value: G

tag: number of_cells


title: 1W1_Input-seq


title: MG_FACS_CON_LPS_Rep4


title: TS667_NTC_MEOX2_ACTseq_rep3

description: ACT-Seq

value: non-targeting sgRNA


title: case_397 mRNA-seq

description:
Yang_SysBio_case_397
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: LTRC

tag: dx

value: case

tag: rnaseqid

value: m

value: white


title: TS667_NTC_MEOX2_ACTseq_rep2

description: ACT-Seq

value: brain

value: patient-derived GBM tumorsphere


title: Control3W_MeRip-seq

tag: antibody

value: anti-m6A polyclonal antibody (Synaptic Systems, 202003)


title: MG_FACS_MIA_SAL_Rep6_excluded

value: MIA

value: SAL

tag: ID


title: TS667_NTC_MEOX2_ACTseq_rep1

description: ACT-Seq


title: control_396 mRNA-seq

description:
Yang_SysBio_control_396
*** 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: age

tag: race

value: not hispanic or latino

value: Y


title: MG_FACS_CON_LPS_Rep5

value: brain striatum

tag: cell type

value: microglia

value: CON

value: LPS

value: male


title: case_395 mRNA-seq

description:
Yang_SysBio_case_395
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: Inova Fairfax

value: ipf

value: case

value: m

tag: ethnicity

tag: raw data disclaimer


title: MG_FACS_CON_SAL_Rep4

tag: group

tag: treatment

tag: batch


title: MG_FACS_CON_SAL_Rep3


title: TS667_g11_IgG_ACTseq

description: ACT-Seq

value: brain

tag: cell line

value: patient-derived GBM tumorsphere

value: MEOX2 sgRNA2


title: TS667_NTC_IgG_ACTseq

description: ACT-Seq

value: non-targeting sgRNA


title: control_400 mRNA-seq

description:
Yang_SysBio_control_400
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

tag: center

value: LTRC

value: other

value: control

value: white


title: R2W2_MeRip-seq

tag: tissue

value: liver tissue

tag: strain

tag: time point

value: 3W reversal

value: anti-m6A polyclonal antibody (Synaptic Systems, 202003)


title: MG_FACS_CON_LPS_Rep3

value: brain striatum

value: microglia

value: CON

value: LPS

tag: Sex

value: male


title: control_393 mRNA-seq

description:
Yang_SysBio_control_393
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: Pittsburgh Lung Donor Core

tag: dx

value: normal

tag: rnaseqid

value: m

value: not hispanic or latino

value: Y


title: TS600_g11_MEOX2_ACTseq_rep3

description: ACT-Seq

value: brain

value: patient-derived GBM tumorsphere

value: MEOX2 sgRNA2


title: Control6W_MeRip-seq

value: liver tissue

tag: antibody


title: R2W1_MeRip-seq

value: 3W reversal


title: MG_FACS_MIA_SAL_Rep5

value: MIA

value: SAL

tag: ID


title: case_392 mRNA-seq

description:
Yang_SysBio_case_392
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: Inova Fairfax

value: ipf

value: case

tag: age

tag: race

value: white


title: MG_FACS_MIA_LPS_Rep3

value: brain striatum

tag: cell type

value: microglia

value: LPS

value: male


title: case_394 mRNA-seq

description:
Yang_SysBio_case_394
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: m

tag: ethnicity

value: not hispanic or latino

tag: raw data disclaimer


title: R1W2_MeRip-seq

value: 1W reversal

value: anti-m6A polyclonal antibody (Synaptic Systems, 202003)


title: case_391 mRNA-seq

description:
Yang_SysBio_case_391
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: Y


title: case_390 mRNA-seq

description:
Yang_SysBio_case_390
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: LTRC

value: White


title: TS600_g11_MEOX2_ACTseq_rep1

description: ACT-Seq

value: brain

value: patient-derived GBM tumorsphere

tag: treatment

value: MEOX2 sgRNA2


title: R1W1_MeRip-seq

value: liver tissue


title: case_389 mRNA-seq

description:
Yang_SysBio_case_389
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: ipf

value: case

value: U


title: 6W2_MeRip-seq


title: MG_FACS_CON_SAL_Rep2

value: brain striatum

value: microglia

tag: group

value: CON

value: SAL

tag: batch


title: Control1W_MeRip-seq


title: 6W1_MeRip-seq


title: TS600_NTC_MEOX2_ACTseq_rep2

description: ACT-Seq

tag: cell line

value: non-targeting sgRNA


title: TS600_NTC_MEOX2_ACTseq_rep1

description: ACT-Seq

tag: tissue


title: TS600_NTC_MEOX2_ACTseq_rep3

description: ACT-Seq


title: 3W2_MeRip-seq

tag: strain


title: TS600_g11_MEOX2_ACTseq_rep2

description: ACT-Seq


title: MG_FACS_MIA_LPS_Rep2

value: MIA

value: LPS

value: male


title: TS600_g11_IgG_ACTseq

description: ACT-Seq


title: 3W1_MeRip-seq

tag: time point

value: anti-m6A polyclonal antibody (Synaptic Systems, 202003)


title: MG_FACS_MIA_SAL_Rep2

tag: Sex


title: case_386 mRNA-seq

description:
Yang_SysBio_case_386
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

tag: center

value: LTRC

tag: dx

value: m

value: black

value: not hispanic or latino

value: Y


title: TS600_NTC_IgG_ACTseq

description: ACT Seq

value: brain

value: patient-derived GBM tumorsphere


title: 1W2_MeRip-seq

value: liver tissue

tag: antibody


title: MG_FACS_MIA_SAL_Rep1

value: brain striatum

value: microglia

tag: ID


title: case_387 mRNA-seq

description:
Yang_SysBio_case_387
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: ipf

value: case

tag: rnaseqid

tag: age

value: White


title: GBM_IgG_CUT&Tag

description: CUT&Tag

value: fresh frozen GBM

value: tumor


title: 1W1_MeRip-seq

value: anti-m6A polyclonal antibody (Synaptic Systems, 202003)


title: MG_FACS_CON_SAL_Rep1

tag: cell type

value: CON

value: SAL

value: male


title: MG_FACS_MIA_SAL_Rep4

value: MIA


title: control_382 mRNA-seq

description:
Yang_SysBio_control_382
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: LTRC

value: other

value: control

value: m

tag: race

value: white

tag: ethnicity

value: not hispanic or latino


title: MG_FACS_MIA_LPS_Rep1

value: brain striatum

value: microglia

tag: treatment

value: LPS


title: GBM_MEOX2_CUT&Tag

description: CUT&Tag

value: brain

value: fresh frozen GBM


title: spleen, T. gondii, 14dpi, scRNAseq

city: Philadelphia

first: Christopher

last: Hunter

address: 380 S. University Ave #341

institute: University of Pennsylvania

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger softwareRaw sequence data was aligned and transcripts were counted with Cell Ranger (10X Genomics) using the mus musculus reference genome mm10-3.0.0.
Assembly: mm10_3.0.0
Supplementary files format and content: Tab-separated values files of gene counts per cell

source_name: Spleen

extract_protocol:
Spleen tissue was manually disrupted with a razor blade in a 6cm dish and suspended in 1 mL plain PBS + 5 mM CaCl2 + 10 mg/mL B. Licheniformis protease + 125U/mL DNase / 50 mg tissue, then manually disrupted by pipette every 2 minutes for 45 minutes at 4C. Digested tissue was then mashed through a 70uM filter and washed with 10% FBS RPMI. Cells were pelleted via centrifugation at 300 x g for 5 min @ 4C. The pellet was then ACK lysed at 4C for 5 minutes, followed by washing with 10% RPMI.
Library was performed according to the manufacter’s instructions. Briefly, single cell drop encapsulation, RT-PCR, amplification, and adapter ligation were performed with the 10X Chromium Controller platform with the Chromium Next GEM Single Cell 3’ GEM, Library and Gel Bead Kit v3.1, Chromium Next GEM Chip G Singe Cell Kit, and Single Index Kit T Set A (10X Genomics). Following encapsulation, samples were cleaned-up using Dynabeads (Invitrogen) according to manufacturer’s protocol. RNA and DNA quality was checked on a Tapestation (Agilent). Paired-end sequencing was performed on a NextSeq5000 (Illumina).

treatment_protocol: infection protocol: 8 week old mouse revieved intravenous transfer of 5,000 OT-I and were infected intraperitoneally with 10,000 tachyzoites of the Pru strain. Two weeks post infection the mouse was sacrificed and the spleen isolated for sequencing of splenocytes

tag: infection

value: Toxoplasma gondii, Pru, 14dpi

value: Spleen

value: 8 weeks old


title: MG_FACS_CON_LPS_Rep1

tag: group

value: CON

value: male

tag: batch


title: MG_FACS_MIA_SAL_Rep3

tag: tissue

value: MIA

value: SAL


title: control_388 mRNA-seq

description:
Yang_SysBio_control_388
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: UCSF

value: normal

value: unknown

value: hispanic

value: Y

tag: raw data disclaimer


title: case_379 mRNA-seq

description:
Yang_SysBio_case_379
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: LTRC

value: ipf

value: case

value: m

value: White

value: not hispanic or latino


title: iB-Treg(C) 2

city: Fukuoka

first: Minako

last: Ito

address: 3-1-1 Maidashi, Higashi-ku

country: Japan

institute: Kyushu University

data_processing:
reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Assembly: mm10

source_name: in vitro

growth_protocol: Tregs and glial cells were co-cultured using the method described below. The culture medium was removed from the semi-confluent glial cells culture, and the Treg cells (1.0 × 106/well) were then added and cultured in the presence of 2-mercaptoethanol (×1000 dilution), and stimuation factor, such as anti-CD3 antibody (2 μg/mL), anti-CD28 antibody (2 μg/mL), IL-2 (20 ng/mL), IL-33 (20 ng/mL), serotonin hydrochloride (10 μM), CCL20 (20 ng/mL), and CCL1 (20 ng/mL) for 3–6 days.

extract_protocol:
For total cell RNA sequencing (RNAseq) analysis, hCD2+ T cells were also isolated using the auto-MACS, and total RNA was purified using a MagMAX mirVana Total RNA Isolation Kit (Thermo Fisher).
NEBNext PolyA stranded Ultra II Directional RNA Library Prep

tag: strain

tag: cell line

value: in vitro

value: Treg

value: cuture on astrocytes for 6 days with αCD3, αCD28, IL-2, IL-33, serotonin, mCCL1, mCCL20


title: MG_FACS_CON_LPS_Rep2

value: brain striatum

value: microglia

value: CON

value: LPS

tag: Sex

value: male


title: case_378 mRNA-seq

description:
Yang_SysBio_case_378
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

tag: center

tag: dx

value: N


title: iB-Treg(C) 1


title: iB-Treg(B) 2

value: cuture on astrocytes for 6 days with αCD3, αCD28, IL-2, IL-33, serotonin


title: control_377 mRNA-seq

description:
Yang_SysBio_control_377
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

source_name: tissue-Explant

value: UCSF

value: normal

value: control

value: f

value: black

value: unknown


title: MGE_H3K27ME3_rep2_1

city: Bethesda

first: Timothy

last: Petros

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

institute: NICHD

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

source_name: Medial ganglionic eminence

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

value: Medial ganglionic eminence

tag: genotype

value: wild-type


title: MGE_H3K27ME3_rep1_1


title: control_384 mRNA-seq

description:
Yang_SysBio_control_384
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

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

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

value: LTRC

value: other

tag: rnaseqid

value: white

value: not hispanic or latino

value: Y


title: case_376 mRNA-seq

description:
Yang_SysBio_case_376
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: ipf

value: case

tag: age

value: m

value: White


title: iB-Treg(B) 1

value: in vitro

tag: cell type

value: Treg

value: cuture on astrocytes for 6 days with αCD3, αCD28, IL-2, IL-33, serotonin


title: iB-Treg(A) 2

value: cuture on astrocytes for 6 days with αCD3, αCD28, IL-2


title: LGE_H3K27ME3_rep2_1

source_name: Lateral ganglionic eminence

value: Lateral ganglionic eminence


title: control_380 mRNA-seq

description:
Yang_SysBio_control_380
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: UCSF

value: normal

value: control

value: f

tag: race

value: black

value: unknown

value: N


title: iB-Treg(A) 1


title: LGE_H3K27ME3_rep2_2

value: wild-type


title: Ischmiea-Treg 2

value: Brain

value: 28 days after ischemic stroke onset


title: control_374 mRNA-seq

description:
Yang_SysBio_control_374
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: Pittsburgh Lung Donor Core

value: m

value: white

tag: ethnicity

value: not hispanic or latino


title: LGE_H3K27ME3_rep1_1


title: Ischmiea-Treg 1

value: Treg

tag: treatment


title: control_371 mRNA-seq

description:
Yang_SysBio_control_371
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***


title: case_370 mRNA-seq

description:
Yang_SysBio_case_370
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: Inova Fairfax

value: ipf

value: case

value: Y


title: CTX_H3K27ME3_rep2_2

source_name: Cortex

value: Cortex


title: SP-Treg 2

value: Spleen

value: no treatment


title: CTX_H3K27ME3_rep1_1


title: case_372 mRNA-seq

description:
Yang_SysBio_case_372
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: f


title: CTX_H3K27ME3_rep2_1

value: wild-type


title: case_373 mRNA-seq

description:
Yang_SysBio_case_373
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: N


title: SP-Treg 1


title: case_368 mRNA-seq

description:
Yang_SysBio_case_368
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***


title: CGE_H3K27ME3_rep2_1

source_name: Caudal ganglionic eminence

value: Caudal ganglionic eminence


title: CGE_H3K27ME3_rep1_1


title: control_367 mRNA-seq

description:
Yang_SysBio_control_367
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: LTRC

value: control


title: Tyk2fl6

city: Vienna

first: Robert

last: Eferl

address: Borschkegasse 8a

department: Center for Cancer Research

country: Austria

institute: Medical University Vienna

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

source_name: Colon tumors

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

value: colon

value: AOM/DSS induced CRC


title: Tyk2fl5


title: control_364 mRNA-seq

description:
Yang_SysBio_control_364
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: other

value: m

value: white

value: not hispanic or latino


title: case_375 mRNA-seq

description:
Yang_SysBio_case_375
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

source_name: tissue-Unknown

value: ipf

value: case

value: White

value: U