city: Jeddah

first: Antonio

last: Adamo

state: Not in US

address: 4700 KAUST, Thuwal

department: Biological and Environmental Science and Engineering Division, BESE

country: Saudi Arabia

institute: King Abdullah University of Science and Technology, KAUST

description:
KDM1A KO rescued with Flag-ubKDM1A  Chip-SEQ HiSeq 4000 Replicate #2
Chip-SEQ HiSeq 4000 Replicate #2

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

source_name: Cardiomyocytes

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

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

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

tag: cell type

value: KDM1A KO rescued with Flag-ubKDM1A

tag: chip antibody

value: KDM1A (Abcam, ab17721, lot )

tag: name in the manuscript

value: KDM1A KO+ubKDM1A


status: Public on Jul 01 2022

type: SRA

description:
KDM1A KO rescued with Flag-ubKDM1A  Input HiSeq 4000 Replicate #2
Input HiSeq 4000 Replicate #2

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens


title: Drp1WT CDM-4 [A4_S4]

city: Kansas City

first: Hong-Min

last: Ni

state: KS

address: 3901 Rainbow Blvd, MS-1018

department: Pharmacology, Toxicology and Therapeutics

country: USA

institute: University of Kansas Medical Center

library_source: transcriptomic

data_processing:
Raw reads weredemultiplexed into Fastq format allowing up to one mismatch.
Reads were aligned to mouse reference genome (GRCm38.90) , using HISAT v.2.1.0.13.
TPM values were generated using HTSeq (version v0.6.0).
Pairwise differential expression analysis was performed using R package edgeR between the WT and L-DRP1 KO group in control and EtOH conditions.
Assembly: GRCm38.90
Supplementary files format and content: normalized_counts

molecule: total RNA

organism: Mus musculus

source_name: Liver

extract_protocol:
Livers were removed and snap frozen in liquid nitrogen. Total RNA was extracted using Trizol reagent and the quality was checked with Qubit quantification and TapeStation gel analysis
RNA libraries were prepared with standard Illumina protocol
RNA-Seq was sequenced as 75bp single reads on Illumina NextSeq 550 machine

treatment_protocol: Liver-specific DRP1 KO mice and paired WT mice were subjected to Gao-Binge alcohol model.

tag: strain

tag: tissue

value: Liver

tag: genotype

value: WT

tag: treatment

value: Control

tag: age


title: H4

city: Hong Kong

first: Qiuyu

last: JING

state: Hong Kong

address: Room 6202C, Academic Building, The Hong Kong University of Science and Technology

department: Division of Life Science

country: Hong Kong

data_processing:
library strategy: metagenomics DNA sequencing library
Illumina Casava1.7 software used for basecalling.
Raw reads were first trimmed to 2x75bp using Cutadapt (version 1.18) and rarefied to 30M to ensure equal library size except for non-template controls due to its low input. Duplicates were then removed using PRINSEQ (version 0.20.4) in a paired-end mode with entropy-based strategy. The threshold of entropy was set as 20. Adapters and bases with quality lower than 20 were then trimmed using BBMap (version 35.74). Reads shorter than 25bp were discarded.
Quality-controlled reads were mapped to human reference GRCh38 downloaded from NCBI RefSeq database using Bowtie2 (version 2.2.6) in a very-sensitive mode. Duplicates were marked and removed using Picard Tools (version 2.18.7). Then both mapped and unmapped reads were extracted using SAMtools (version 1.3.1) for analysis of human fragments and microbial compositions respectively.
Mapped human bam files were firstly sorted using SAMtools (version 1.3.1) and then converted to bed files using BEDtools (version 2.15.0). Human autosome reference was segmented into 1-megabase non-overlap bins using BEDtools. Ratio of fragments of different length overlapped with each bin were calculated using custom script.
Genome_build: GRCh38
Supplementary_files_format_and_content: text file containg the number of fragments with different length within 1M bins across autosomes

source_name: Blood

extract_protocol:
cfDNA was extracted from plasma using QIAamp circulating nucleic acid kit (QIAGEN)
single-strand DNA library preparation with custom sequencing primers

treatment_protocol: Plasma was separated from blood by centrifugation

tag: group

value: Healthy

tag: 28-day mortality

value: Survivors

tag: time point

value: Blood

tag: molecule type

value: cell-free DNA


title: u1T2

institute: The Hong Kong University of Science and Technology

value: Non-sepsis

value: Non-survivors


title: H3


description:
KDM1A KO rescued with Flag-ubKDM1A  Chip-SEQ HiSeq 4000 Replicate #1
Chip-SEQ HiSeq 4000 Replicate #1


title: u1T1


title: H2


title: H1


title: CpG-HCQ (D8)

city: hefei

first: li

last: zhou

state: anhui

address: NO.17 lujiang road

department: the first affiliated hospitail of USTC

country: China

institute: University of Science and Technology of China

data_processing:
Sequencing data were filtered using SOAPnuke (v1.5.2) by removing reads that (1) contained sequencing adapters; (2) had a low-quality base ratio (base quality ≤ 5) over 20%; and (3) had an unknown (‘N’) base ratio over 5%. Clean reads were stored in FASTQ format, mapped to the reference genome using HISAT2 (v2.0.4), and aligned to the reference coding gene set using Bowtie2 (v2.2.5).
Gene expression was calculated using RSEM (v1.2.12) and a heatmap was drawn using pheatmap (v1.0.8).
Differential expression analysis was performed using DESeq2 (v1.4.5) with a Q-value ≤ 0.05.
Differentially expressed genes were subjected to GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analyses using Phyper based on the hypergeometric test.
The statistical significance of terms and pathways were corrected using Bonferroni’s correction with a Q value threshold of ≤ 0.05).
Assembly: NOT PROVIDED
Supplementary files format and content: abundance measurements

growth_protocol: THP-1 cells (5 × 10e5 cells) were cultured in 1 mL RPMI 1640  containing 10% FBS, 100 U/mL penicillin, 100 μg/mL streptomycin , and 2 mmol/L GlutaMAX at 37 °C with 5% CO2 for 24 h.

extract_protocol:
Total RNA was extracted from THP-1 cells using TRIzol reagent (Invitrogen) and a chain-specific library was constructed by removing ribosomal RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 3 μM CpG-c (ODN-2395)  was added to produce macrophage. Human RBCs (1 × 10e7 cells) were added to the system to perform haemophagocytosis for 3 h. Hydroxychloroquine  (10 mg/μL) was administered to inhibit phagocytosis for 3 h.

tag: cell line

tag: trearment

value: CpG-HCQ


title: Drp1WT CDM-1 [A1_S1]


title: Drp1WT CDM-2 [A2_S2]


description:
KDM1A KO rescued with Flag-ubKDM1A  Input HiSeq 4000 Replicate #1
Input HiSeq 4000 Replicate #1


title: CDK19_S3h.3

city: Columbia

first: Mengqian

last: Chen

state: SC

address: CLS710, 715 Sumter Street

department: College of Pharmacy

institute: University of South Carolina

description: 293-dKO-19 (dKO re-expressing CDK19) cells, treated with 1μM Senexin B for 3 hrs, biological replicate-#3

data_processing:
Indexed sequences were sorted by Illumina BaseSpace FASTQ generation | version: 1.0.0
Reads were mapped to the hg38 reference genome using STAR | version 2.4 with default parameters (generation of sam files)
Convert .sam files to .bam files using samtools | version: 1.2 with parameters -bh -F 3840 -q 255
Read counts over annotated genes were obtained using featureCount (subreads | version: 1.4.6) with parameters -p -T 10
Genome_build: GRCh38.77
Supplementary_files_format_and_content: tab-delimited text files include gene counts for each sample

source_name: 293-dKO-19 (dKO re-expressing CDK19)_1μM Senexin B for 3 hrs

growth_protocol: HEK293 cells and its derivatives (8KO, 19KO, dKO, dKO-V, dKO-8 and dKO-19) were grown in DMEM (High-glucose) media with 10% FBS, 1% penicillin-streptomycin and 2 mM L-glutamine. The cells were plated in 12-well plate at the density of 3x10^5 cells per well 24 hours prior to treatment.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) and RNA quality was validated on RNA-1000 chip using Bioanalyzer (Agilent)
Sequencing libraries were generated using the Illumina TruSeq Stranded mRNA prep kit (RS-122-2101/RS-122-2102)

treatment_protocol: Cells were treated with Vehicle control (0.1% DMSO) or 1μM Senexin B for different period of time (3hrs, 5hrs, 24hrs, 3 days and 5 days)

tag: cell line background

value: HEK293 (ATCC)

tag: genotype/variation

value: 293-dKO-19 (dKO re-expressing CDK19)

value: 1μM Senexin B for 3 hours


title: Drp1WT CDM-3 [A3_S3]


description:
KDM1A KO rescued with Flag-KDM1A+2a Input HiSeq 4000 Replicate #1
Input HiSeq 4000 Replicate #1

value: KDM1A KO rescued with Flag-KDM1A+2a

value: KDM1A KO+KDM1A+2a


description:
KDM1A KO rescued with Flag-KDM1A+2a Chip-SEQ HiSeq 4000 Replicate #1
Chip-SEQ HiSeq 4000 Replicate #1

value: KDM1A (Abcam, ab17721, lot )


title: CpG-HCQ (B8)


title: CDK19_S3h.2

description: 293-dKO-19 (dKO re-expressing CDK19) cells, treated with 1μM Senexin B for 3 hrs, biological replicate-#2


title: 3A_carotid atherosclerotic plaque tissue 4

type: RNA

city: Shanghai

first: Qu

last: LeFeng

address: Huangpu District Fengyang Road

department: Department of Vascular and Endovascular Surgery

institute: Second Affiliated Hospital of Naval Medical University

description: lncRNA expression data from carotid atherosclerotic plaque tissue

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: carotid atherosclerotic plaque tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: 30 min egg collections of OreR and yw flies at 25C were aged at room temperature (RT) according to the different temporal classes T0-T4.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Embryos were dechorionated with 50% bleach, put on a cover slip and covered with Halocarbon oil 27 (Sigma). Embryos of the appropriate stage were manually selected under the dissecting scope. Selected embryos were transferred to a basket, rinsed with PBS with 0,7% NaCl, 0,04% triton-X100 and placed on ice in the Trizol solution (GibcoBRL).

tag: Sex

value: Male

value: carotid atherosclerotic plaque tissue


title: 5_endovascular tissue 2

description: lncRNA expression data from endovascular tissue

source_name: endovascular tissue

value: endovascular tissue


title: 2_endovascular tissue 1


title: 5D_carotid atherosclerotic plaque tissue 3


title: 6_endovascular tissue 3


title: 1N_endovascular tissue 4


description:
H1 Day 18-20 (Time Point)- KDM1A ChIP (Experiment#3)
Chip-SEQ HiSeq 4000 Replicate #3

source_name: Day 18-20 cardiomyocytes

tag: cell type

value: WT cardiomyocytes Day 18-20

value: H1 day 18-20 (Time point)


title: 231-siBTF3

city: Jinan

first: Jing

last: Hu

address: Wenhua xi road

department: Department of Pathology

institute: Shandong University

description: This sample is of Vcap transfected with lentivirus of shBTF3.

hyb_protocol: 1.5 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifμgation.

scan_protocol: After being washed in an ozone-free environment, image capture was performed with Ageilent DNA Microarray Scanner and uploaded into Agilent Feature Extraction (v11.0.0.1), and Cy3 label intensities determined.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the Agilent GeneSpring GX software package, version 12.1 .

label_protocol: cDNA samples were amplified, Cy3-labeled with Agilent Quick Amp labeling kit following manufacturer’s protocol.

growth_protocol: Cells were maintained in L-15 medium supplemented with 10% fetal bovine serum (FBS) and 100 U/mL penicillin and streptomycin. Cell cultures were held in a humid, 37℃ and 5% CO2 cell culture incubator.

extract_protocol: Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: MDA-MB-231 cells transfected with siRNA are referred as 231-NC and 231-siBTF3.

value: breast cancer cell line MDA-MB-231


title: 4D_carotid atherosclerotic plaque tissue 2


title: 231-NC

description: This sample is of Vcap transfected with lentivirus of negtive control.


title: CpG (D5)

value: CpG


title: 3D_carotid atherosclerotic plaque tissue 1


description:
H1 Day 18-20 (Time Point)- Input (Experiment#3)
Input HiSeq 4000 Replicate #3

tag: chip antibody


title: CDK19_S3h.1

description: 293-dKO-19 (dKO re-expressing CDK19) cells, treated with 1μM Senexin B for 3 hrs, biological replicate-#1


title: CpG (C5)


title: CpG-HCQ (C8)


title: CpG (B5)


description:
H1 Day 18-20 (Time Point)- KDM1A ChIP (Experiment#2)
Chip-SEQ HiSeq 4000 Replicate #2

tag: name in the manuscript


title: CDK19_C3h.3

description: 293-dKO-19 (dKO re-expressing CDK19) cells, treated with vehicle control for 3 hrs, biological replicate-#3

source_name: 293-dKO-19 (dKO re-expressing CDK19)_vehicle control for 3 hrs

value: 0.1% DMSO (vehicle control) for 3 hours


title: CDK19_C3h.2

description: 293-dKO-19 (dKO re-expressing CDK19) cells, treated with vehicle control for 3 hrs, biological replicate-#2


title: PBS (D2)

value: PBS


title: CDK19_C3h.1

description: 293-dKO-19 (dKO re-expressing CDK19) cells, treated with vehicle control for 3 hrs, biological replicate-#1


description:
H1 Day 18-20 (Time Point)- Input (Experiment#2)
Input HiSeq 4000 Replicate #2


description:
H1 Day 18-20 (Time Point)- KDM1A ChIP (Experiment#1)
Chip-SEQ HiSeq 4000 Replicate #1


title: PBS (C2)


title: PC3-NC

description: This sample is of PC3 transfected with siRNA of negtive control.

growth_protocol: Cells were maintained in RPMI1640 medium supplemented with 10% fetal bovine serum (FBS) and 100 U/mL penicillin and streptomycin. Cell cultures were held in a humid, 37℃ and 5% CO2 cell culture incubator.

treatment_protocol: PC3 cells transfected with siRNA are referred as PC3-NC and PC3-siLASP1.

value: prostate cancer cell line PC3

tag: sirna

value: NC


title: PC3-siLASP1

description: This sample is of PC3 transfected with siRNA targeting LASP1.


title: CDK8_S3h.1

description: 293-dKO-8 (dKO re-expressing CDK8) cells, treated with 1μM Senexin B for 3 hrs, biological replicate-#1

source_name: 293-dKO-8 (dKO re-expressing CDK8)_1μM Senexin B for 3 hrs

value: HEK293 (ATCC)

value: 293-dKO-8 (dKO re-expressing CDK8)


description:
H1 Day 18-20 (Time Point)- Input (Experiment#1)
Input HiSeq 4000 Replicate #1


title: CDK8_C3h.3

description: 293-dKO-8 (dKO re-expressing CDK8) cells, treated with vehicle control for 3 hrs, biological replicate-#3

source_name: 293-dKO-8 (dKO re-expressing CDK8)_vehicle control for 3 hrs


title: PBS (B2)


description:
H1 Day 4 (Time Point)- Input (Experiment#1)
Input HiSeq 4000 Replicate #1

source_name: Day 4- cardiac mesoderm

value: WT Cardiac Mesoderm Day 4

value: H1 Day 4 (Time point)


title: liver tissue, KO, drinking alcohol for 15 days, 1

city: nanjing

state: Jiangsu

address: Longmian Avenue

department: Basic Medicine College

institute: nanjing medical university

data_processing:
SOAPnuke (v1.5.2)
Removing reads containing sequencing adapter
Removing reads containing low-quality base ratio
The clean reads were mapped to the mouse genome (Mus_musculus.GRCm38) using HISAT2(v2.0.4)
Expression level of gene was calculated by StringTie (v2.1.4)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: liver

growth_protocol: all mice were housed under a SPF condition (12-h light/dark cycle)

extract_protocol:
Total RNAs were isolated using Trizol Reagent from tissue samples.
RNA libraries were prepared for sequencing using standard BGIseq protocols

treatment_protocol: all mice drank alcohol for 15 days

tag: tissue

value: liver

value: KO


title: liver tissue, WT, drinking alcohol for 15 days, 2

tag: genotype

value: WT


description:
H1 Day 2 (Time Point)- Input (Experiment#2)
Input HiSeq 4000 Replicate #2

source_name: Day 2-mesoderm

value: WT Mesoderm Day 2

value: H1 Day 2 (Time point)


title: Heads from 24 hpf larvae WT for the eMIC domain of srrm3.

city: Barcelona

first: Manuel

last: Irimia

state: Barcelona

address: 88 Dr. Aiguader

department: MELIS

country: Spain

institute: Universitat Pompeu Fabra - Centre for Genomic Regulation

data_processing:
Raw reads were mapped with vast-tools align v2.5.1
Assembly: danRer10
Supplementary files format and content: Files with raw read counts to each zebrafish gene in Ensembl v80 and cRPKMs.

molecule: polyA RNA

organism: Danio rerio

source_name: Larval heads

growth_protocol: Zebrafish were grown at 28°C 14 h light/10 h dark cycle.

extract_protocol:
24 hpf WT fish heads were removed and pulled for RNA extraction using RNA RNeasy Mini kit (QIAGEN). Larvae eyes were removed and from twenty to sixty eyes per genotype were pulled for RNA extraction using RNA RNeasy Micro kit (QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols


title: liver tissue, KO, drinking alcohol for 15 days, 2


title: Eyes from 72 hpf larvae WT for the eMIC domain of srrm3.

source_name: Larval eyes


description:
H1 Day 2 (Time Point)- Input (Experiment#1)
Input HiSeq 4000 Replicate #1


title: CDK8_S3h.2

description: 293-dKO-8 (dKO re-expressing CDK8) cells, treated with 1μM Senexin B for 3 hrs, biological replicate-#2

tag: treatment

value: 1μM Senexin B for 3 hours


title: CDK8_C3h.1

description: 293-dKO-8 (dKO re-expressing CDK8) cells, treated with vehicle control for 3 hrs, biological replicate-#1


title: CDK8_S3h.3

description: 293-dKO-8 (dKO re-expressing CDK8) cells, treated with 1μM Senexin B for 3 hrs, biological replicate-#3


title: Vec_S3h.2

description: 293-dKO-V (dKO expressing empty lentiviral vector) cells, treated with 1μM Senexin B for 3 hrs, biological replicate-#2

source_name: 293-dKO-V (dKO expressing empty lentiviral vector)_1μM Senexin B for 3 hrs


title: CDK8_C3h.2

description: 293-dKO-8 (dKO re-expressing CDK8) cells, treated with vehicle control for 3 hrs, biological replicate-#2


description:
H1 Day 2 (Time Point)- KDM1A ChIP (Experiment#1)
Chip-SEQ HiSeq 4000 Replicate #1

value: KDM1A (Abcam, ab17721, lot )


title: Vec_S3h.3

description: 293-dKO-V (dKO expressing empty lentiviral vector) cells, treated with 1μM Senexin B for 3 hrs, biological replicate-#3


description:
H1 Day 4 (Time Point)- KDM1A ChIP (Experiment#1)
Chip-SEQ HiSeq 4000 Replicate #1


title: Vec_C3h.3

description: 293-dKO-V (dKO expressing empty lentiviral vector) cells, treated with vehicle control for 3 hrs, biological replicate-#3

source_name: 293-dKO-V (dKO expressing empty lentiviral vector)_vehicle control for 3 hrs


description:
H1 hESC (Time point) - KDM1A ChIP (Experiment#2)
Chip-SEQ Novaseq 6000 SP1 Replicate #2

source_name: Day 0-hESC

value: WT hESC

value: H1 hESC (Time point)


description:
H1 hESC (Time point) - Input (Experiment#1)
Input HiSeq 4000 Replicate #1


title: Eyes from 60 hpf larvae WT for the eMIC domain of srrm3.


title: Vec_S3h.1

description: 293-dKO-V (dKO expressing empty lentiviral vector) cells, treated with 1μM Senexin B for 3 hrs, biological replicate-#1


title: Eyes from 60 hpf larvae mutated for the eMIC domain of srrm3.

value: srrm3 mutant


description:
H1 Day 2 (Time Point)- KDM1A ChIP (Experiment#2)
Chip-SEQ HiSeq 4000 Replicate #2


title: Eyes from 72 hpf larvae mutated for the eMIC domain of srrm3.


description:
H1 hESC (Time point) - Input (Experiment#2)
Input Novaseq 6000 SP1 Replicate #2


title: liver tissue, WT, drinking alcohol for 15 days, 1


title: Eyes from 48 hpf larvae WT for the eMIC domain of srrm3.


title: Vec_C3h.2

description: 293-dKO-V (dKO expressing empty lentiviral vector) cells, treated with vehicle control for 3 hrs, biological replicate-#2

value: 0.1% DMSO (vehicle control) for 3 hours


title: KDM1A KO hESC Rescued with 3XT7-KDM1A+2a variant Bulk RNAseq Novaseq 6000 SP1 2310

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

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

source_name: hESC H1

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

tag: rna identifier

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


title: KDM1A KO hESC Rescued with 3XT7-ubKDM1A variant Bulk RNAseq Novaseq 6000 SP1 2354

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

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


title: Vec_C3h.1

description: 293-dKO-V (dKO expressing empty lentiviral vector) cells, treated with vehicle control for 3 hrs, biological replicate-#1

value: HEK293 (ATCC)


title: 19KO_S3h.2

description: 293-19KO (CDK19 single knockout) cells, treated with 1μM Senexin B for 3 hrs, biological replicate-#2

source_name: 293-19KO (CDK19 single knockout)_1μM Senexin B for 3 hrs

value: 293-19KO (CDK19 single knockout)


title: 19KO_S3h.3

description: 293-19KO (CDK19 single knockout) cells, treated with 1μM Senexin B for 3 hrs, biological replicate-#3


title: WT  Bulk RNAseq Novaseq 6000 SP1 2893

description:
WT  Bulk RNAseq Novaseq 6000 SP1
Bulk RNAseq Novaseq 6000 SP1

value: H1 WT


title: 19KO_S3h.1

description: 293-19KO (CDK19 single knockout) cells, treated with 1μM Senexin B for 3 hrs, biological replicate-#1


title: WT  Bulk RNAseq Novaseq 6000 SP1 2895


title: Retina from WT adult fish, replicate 2

description:
Retina_Adult_b
PolyA-selected stranded RNA-seq.

data_processing:
Raw reads were mapped with vast-tools align v2.5.1.
Genome_build: danRer10
Supplementary_files_format_and_content: *.cRPKM.txt: Tab-delimited text files with raw read counts and cRPKMs.

source_name: Adult retina

extract_protocol:
Adult fish retinae were removed and five retinae per genotype were pulled for RNA extraction using RNA RNeasy Mini kit (QIAGEN). Larvae eyes were removed and twenty eyes per genotype were pulled for RNA extraction using RNA RNeasy Mini kit (QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: developmental stage

value: Adult

value: Retina


title: Retina from WT adult fish, replicate 1

description:
Retina_Adult_a
PolyA-selected stranded RNA-seq.


title: 19KO_C3h.2

description: 293-19KO (CDK19 single knockout) cells, treated with vehicle control for 3 hrs, biological replicate-#2

source_name: 293-19KO (CDK19 single knockout)_vehicle control for 3 hrs


title: Eyes from 5 dpf larvae WT for the eMIC domain of srrm3

description:
Eyes_5dpf_srrm3_17A_WT_a
PolyA-selected stranded RNA-seq.

value: 5 dpf larvae

value: Eye


title: WT  Bulk RNAseq Novaseq 6000 SP1 2881

value: WT


title: WT  Bulk RNAseq Novaseq 6000 SP1 2882


title: 19KO_C3h.3

description: 293-19KO (CDK19 single knockout) cells, treated with vehicle control for 3 hrs, biological replicate-#3


title: Eyes from 5 dpf larvae mutated for the eMIC domain of srrm3

description:
Eyes_5dpf_srrm3_17A_KO_a
PolyA-selected stranded RNA-seq.


title: X1516-RT biological replicate 3

city: Birmingham

first: Christopher

middle: Douglas.

last: Willey

state: Alabama

address: 619 19th St S, HSROC 2232C

department: Radiation Oncology

institute: The University of Alabama at Birmingham

data_processing:
First, preliminary contamination QC was performed with FastQ Screen (v0.11.2 with dependencies to Bowtie2 v2.3.3 and SAMtools v1.6), and the results were aggregated with MultiQC
Following the contamination QC, the following steps were executed in the Snakemake workflow system (v.5.2.2): quality and control of the reads were assessed using FastQC, and trimming of the bases with quality scores of less than 20 and Illumina adapters were performed with Trim_Galore! (v0.4.5) in paired-end mode.
The files were quasi-mapped and quantified to the human transcriptome (GENCODE, release 31) with Salmon (v.0.12.0, with --gencode and -k 31 flags for index generation and -l ISR, --gcBias and --validateMappings flags)
Further, the tx2gene table (https://gitlab.rc.uab.edu/gbm-pdx/deseq2-rnaseq/-/blob/master/tx2gene.csv), which is used in tximport was generated with bioconductor-genomicfeatures package (1.32.3, R version: r-base=3.4.1).
Finally, the following reports were summarized with MultiQC
Samples that contained high levels of cross-species contamination were removed from the analysis. Downstream analysis was conducted by using tximport, DESeq2 and biomaRt
Assembly: Ensembl GRCh37 version 97
Supplementary files format and content: normalized expression tab delimited table from DESeq2

source_name: orthotopic PDX

growth_protocol: 300,000 human tumor cells were injected intracranially into athymic nude mice and allowed to grow until animals became moribund

extract_protocol:
RNA isolated using Norgen Animal Tissue RNA Purification Kit (Cat 25700) standard protocol
stranded total RNA seq library prep using standard Illumina protocols

tag: individual

value: recurrent tumors

tag: radiation sensitivity

value: resistant

tag: temozolomide sensitivity

tag: patient gender

value: Female


title: X1516-RT biological replicate 2


title: ubKDM1A-/- hESC-Derived Cardiomyocytes Bulk RNAseq Novaseq 6000 SP1 1368

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

source_name: Cardiomyocytes

value: ubKDM1A-/- hESC-Derived Cardiomyocytes

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


title: WT  Bulk RNAseq Novaseq 6000 SP1 2880


title: rnpc3_WT_1 [miRNA-seq]

city: Bethesda

first: zelin

last: chen

state: MD

address: 50 South Dr.

department: NHGRI

institute: NIH

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

source_name: Wildtype siblings of rnpc3 mutants, repeat 1

extract_protocol:
Embryos were placed in Qiazol, and RNA was extracted by using Qiagen miRNeasy Mini Kit.
Prepare one paired end index library from each total RNA sample, pool all libraries, load  pool on HiSeq 2500, run as indexed 50 base single end reads.
embryos were placed in Qiazol, and RNA was extracted by using Qiagen miRNeasy Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: Wildtype siblings of rnpc3 mutants

tag: Stage

value: 7 dpf

value: whole fish embryos


title: 19KO_C3h.1

description: 293-19KO (CDK19 single knockout) cells, treated with vehicle control for 3 hrs, biological replicate-#1

tag: cell line background

tag: genotype/variation

value: 0.1% DMSO (vehicle control) for 3 hours


title: X1516 biological replicate 3

value: primary tumors

value: sensitive


title: X1516-RT biological replicate 1


title: smn1_WT_1 [miRNA-seq]

source_name: Wildtype siblings of smn1 mutants, repeat 1

value: Wildtype siblings of smn1 mutants


title: 8KO_S3h.3

description: 293-8KO (CDK8 single knockout) cells, treated with 1μM Senexin B for 3 hrs, biological replicate-#3

source_name: 293-8KO (CDK8 single knockout)_1μM Senexin B for 3 hrs

value: HEK293 (ATCC)

value: 293-8KO (CDK8 single knockout)

value: 1μM Senexin B for 3 hours


title: Eyes from 48 hpf larvae mutated for the eMIC domain of srrm3.

value: srrm3 mutant


title: X1516 biological replicate 2


title: WT  Bulk RNAseq Novaseq 6000 SP1 2894

tag: cell type

value: WT

value: H1 WT


title: gemin5_WT_1 [miRNA-seq]

source_name: Wildtype siblings of germin5 mutants, repeat 1

value: Wildtype siblings of germin5 mutants


title: 8KO_S3h.2

description: 293-8KO (CDK8 single knockout) cells, treated with 1μM Senexin B for 3 hrs, biological replicate-#2


title: X1516 biological replicate 1

value: resistant

value: Female


title: ubKDM1A-/- hESC-Derived Cardiomyocytes Bulk RNAseq Novaseq 6000 SP1 1563

value: ubKDM1A-/- hESC-Derived Cardiomyocytes

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


title: ubKDM1A-/- hESC-Derived Cardiomyocytes Bulk RNAseq Novaseq 6000 SP1 1557


title: WT hESC-Derived Cardiomyocytes Bulk RNAseq Novaseq 6000 SP1 1127

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

value: WT hESC-Derived Cardiomyocytes

value: H1-derived cardiomyocytes WT


title: X1465-RT biological replicate 3

value: recurrent tumors


title: 8KO_S3h.1

description: 293-8KO (CDK8 single knockout) cells, treated with 1μM Senexin B for 3 hrs, biological replicate-#1


title: smn1_hom_2 [miRNA-seq]

source_name: Homozygous smn1 mutants, repeat 2

value: Homozygous smn1 mutants

value: 7 dpf

value: whole fish embryos


title: 8KO_C3h.2

description: 293-8KO (CDK8 single knockout) cells, treated with vehicle control for 3 hrs, biological replicate-#2

source_name: 293-8KO (CDK8 single knockout)_vehicle control for 3 hrs

value: HEK293 (ATCC)

value: 0.1% DMSO (vehicle control) for 3 hours


title: WT hESC-Derived Cardiomyocytes Bulk RNAseq Novaseq 6000 SP1 1346


title: 8KO_C3h.3

description: 293-8KO (CDK8 single knockout) cells, treated with vehicle control for 3 hrs, biological replicate-#3

value: 293-8KO (CDK8 single knockout)


title: 8KO_C3h.1

description: 293-8KO (CDK8 single knockout) cells, treated with vehicle control for 3 hrs, biological replicate-#1


title: gemin5_hom_3 [miRNA-seq]

source_name: Homozygous gemin5 mutants, repeat 3

value: Homozygous gemin5 mutants


title: X1465-RT biological replicate 2

value: sensitive


title: smn1_hom_3 [miRNA-seq]

source_name: Homozygous smn1 mutants, repeat 3


title: smn1_hom_1 [miRNA-seq]

source_name: Homozygous smn1 mutants, repeat 1


title: WT hESC-Derived Cardiomyocytes Bulk RNAseq Novaseq 6000 SP1 1344


title: WT hESC-Derived Cardiomyocytes Bulk RNAseq Novaseq 6000 SP1 1254


title: dKO_S15d.2

description: 293-dKO (CDK8/19 double knockout) cells, treated with 1μM Senexin B for 15 days, biological replicate-#2

source_name: 293-dKO (CDK8/19 double knockout)_1μM Senexin B for 15 days

value: 293-dKO (CDK8/19 double knockout)

value: 1μM Senexin B for 15 days


title: X1465 biological replicate 3

value: primary tumors


title: WT hESC-Derived Cardiomyocytes Bulk RNAseq Novaseq 6000 SP1 1068


title: gemin5_hom_1 [miRNA-seq]

source_name: Homozygous gemin5 mutants, repeat 1


title: X1465 biological replicate 1

value: Female


title: gemin6_hom_3 [miRNA-seq]

source_name: Homozygous gemin6 mutants, repeat 3

value: Homozygous gemin6 mutants


title: dKO_S15d.1

description: 293-dKO (CDK8/19 double knockout) cells, treated with 1μM Senexin B for 15 days, biological replicate-#1


title: gemin6_hom_2 [miRNA-seq]

source_name: Homozygous gemin6 mutants, repeat 2


title: dKO_C15d.3

description: 293-dKO (CDK8/19 double knockout) cells, treated with vehicle control for 15 days, biological replicate-#3

source_name: 293-dKO (CDK8/19 double knockout)_vehicle control for 15 days

value: 0.1% DMSO (vehicle control) for 15 days


title: tumor biopsy  - recurrent GBM

city: Seattle

first: James

middle: H.

last: Park

state: WA

address: 1736 Belmont ave, Apt 105

institute: Institute for Systems Biology

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

molecule: nuclear RNA

source_name: recurrent tumor biopsy

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

value: recurrent tumor biopsy


title: X1153-RT biological replicate 3

source_name: orthotopic PDX

value: resistant


title: gemin6_hom_1 [miRNA-seq]

source_name: Homozygous gemin6 mutants, repeat 1


title: tumor biopsy - primary GBM

source_name: primary tumor biopsy

value: primary tumor biopsy


title: dKO_C15d.2

description: 293-dKO (CDK8/19 double knockout) cells, treated with vehicle control for 15 days, biological replicate-#2


title: HMVC244 - 24h rep 3

first: Anthony

middle: Robert

last: Soltis

address: 4301 Jones Bridge Road

department: Anatomy, Physiology and Genetics

institute: Uniformed Services University

data_processing:
Raw sequencing data were demuxed using bcl2fastq2 conversion software.
Raw paired-end sequencing reads were aligned to the human reference genome (hg38) using MapSplice version 2.2.2.
Gene read counts against GENCODE v28 basic gene models were calculated by HTSeq version 0.9.1 with parameters: -m intersection-nonempty -i gene_id -s reverse
Gene read count normalization and differential expression analysis was performed with DESeq2 version 1.16.1.
Genome_build: hg38
Supplementary_files_format_and_content: raw_gene_counts.txt - tab-delimited text file of gene raw counts for all samples
Supplementary_files_format_and_content: normalized gene counts .txt - tab-delimited text file of normalized gene counts for all samples (DESeq2 size factor method)

source_name: human lung microvascular endothelial cells

growth_protocol: Cells were grown in complete media, 37 deg C, 5% CO2

extract_protocol:
RNA was isolated using a Qiagen RNeasy Mini Kit
Sequencing libraries were generated using the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA). Samples were sequenced using a NovaSeq 6000 instrument (Illumina, San Diego, CA).

treatment_protocol: Cells were treated with 10 Gy X-irradiation (1.15 Gy/minute)

value: lung

tag: 10 gy x-irradiation


title: X1153-RT biological replicate 1

value: recurrent tumors


title: X1465-RT biological replicate 1


title: dKO_C15d.1

description: 293-dKO (CDK8/19 double knockout) cells, treated with vehicle control for 15 days, biological replicate-#1


title: dKO_S15d.3

description: 293-dKO (CDK8/19 double knockout) cells, treated with 1μM Senexin B for 15 days, biological replicate-#3


title: gemin5_hom_2 [miRNA-seq]

source_name: Homozygous gemin5 mutants, repeat 2

value: 7 dpf

value: whole fish embryos


title: HMVC243 - 24h rep 2

value: human lung microvascular endothelial cells


title: gemin4_hom_3 [miRNA-seq]

source_name: Homozygous gemin4 mutants, repeat 3

value: Homozygous gemin4 mutants


title: X1153 biological replicate 3


title: X1153 biological replicate 2


title: gemin4_hom_1 [miRNA-seq]

source_name: Homozygous gemin4 mutants, repeat 1


title: HMVC805 - 8h rep 3


title: HMVC241 - 24h rep 1


title: dKO_S3h.2

description: 293-dKO (CDK8/19 double knockout) cells, treated with 1μM Senexin B for 3 hrs, biological replicate-#2

source_name: 293-dKO (CDK8/19 double knockout)_1μM Senexin B for 3 hrs

value: HEK293 (ATCC)

value: 1μM Senexin B for 3 hours


title: dKO_S3h.1

description: 293-dKO (CDK8/19 double knockout) cells, treated with 1μM Senexin B for 3 hrs, biological replicate-#1

value: 293-dKO (CDK8/19 double knockout)


title: X1153 biological replicate 1

value: sensitive


title: X1153-RT biological replicate 2


title: dKO_C3h.3

description: 293-dKO (CDK8/19 double knockout) cells, treated with vehicle control for 3 hrs, biological replicate-#3

source_name: 293-dKO (CDK8/19 double knockout)_vehicle control for 3 hrs

value: 0.1% DMSO (vehicle control) for 3 hours


title: gemin7_WT_3

source_name: Wildtype siblings of gemin7 mutants, repeat 3

extract_protocol:
Embryos were placed in Qiazol, and RNA was extracted by using Qiagen miRNeasy Mini Kit.
Prepare one paired end index library from each total RNA sample, pool libraries, load  pool on HiSeq 2500, run as indexed 125 base paired end reads
embryos were placed in Qiazol, and RNA was extracted by using Qiagen miRNeasy Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Wildtype siblings of gemin7 mutants


title: gemin6_WT_2

source_name: Wildtype siblings of gemin6 mutants, repeat 2

value: Wildtype siblings of gemin6 mutants


title: HMVC801 - 8h rep1


title: X1066-RT biological replicate 3

value: Female


title: gemin4_hom_2 [miRNA-seq]

source_name: Homozygous gemin4 mutants, repeat 2


title: gemin4_WT_1

source_name: Wildtype siblings of gemin4 mutants, repeat 1

value: Wildtype siblings of gemin4 mutants


title: X1066-RT biological replicate 2

value: resistant


title: dKO_C3h.2

description: 293-dKO (CDK8/19 double knockout) cells, treated with vehicle control for 3 hrs, biological replicate-#2


title: HMVC603 - 6h rep 3


title: dKO_C3h.1

description: 293-dKO (CDK8/19 double knockout) cells, treated with vehicle control for 3 hrs, biological replicate-#1


title: dKO_S3h.3

description: 293-dKO (CDK8/19 double knockout) cells, treated with 1μM Senexin B for 3 hrs, biological replicate-#3


title: HMVC602 - 6h rep 2


title: X1066 biological replicate 3

value: primary tumors


title: HMVC601 - 6h rep 1

value: lung


title: gemin7_hom_2

source_name: Homozygous gemin7 mutants, repeat 2

value: Homozygous gemin7 mutants


title: gemin7_hom_3

source_name: Homozygous gemin7 mutants, repeat 3

value: 7 dpf


title: gemin7_hom_1

source_name: Homozygous gemin7 mutants, repeat 1

value: whole fish embryos


title: X1066 biological replicate 1


title: WT_S15d.2

description: Parental HEK293 (WT) cells, treated with 1μM Senexin B for 15 days, biological replicate-#2

source_name: Parental HEK293 (WT)_1μM Senexin B for 15 days

value: Parental HEK293 (WT)

value: 1μM Senexin B for 15 days


title: WT_S15d.3

description: Parental HEK293 (WT) cells, treated with 1μM Senexin B for 15 days, biological replicate-#3

value: HEK293 (ATCC)


title: HMVC803 - 8h rep 2

value: human lung microvascular endothelial cells


title: JX39P-RT biological replicate 3

source_name: orthotopic PDX

value: recurrent tumors

value: Male


title: HMVC406 - 4h rep 3


title: X1066 biological replicate 2

value: sensitive


title: gemin6_hom_3

source_name: Homozygous gemin6 mutants, repeat 3

value: Homozygous gemin6 mutants


title: WT_S15d.1

description: Parental HEK293 (WT) cells, treated with 1μM Senexin B for 15 days, biological replicate-#1


title: HMVC405 - 4h rep 2


title: JX39P-RT biological replicate 2


title: gemin6_hom_2

source_name: Homozygous gemin6 mutants, repeat 2


title: JX39P-RT biological replicate 1


title: HMVC403 - 4h rep 1

source_name: human lung microvascular endothelial cells


title: WT_C15d.3

description: Parental HEK293 (WT) cells, treated with vehicle control for 15 days, biological replicate-#3

source_name: Parental HEK293 (WT)_vehicle control for 15 days

value: 0.1% DMSO (vehicle control) for 15 days


title: HMVC205 - 2h rep 3


title: gemin4_hom_3

source_name: Homozygous gemin4 mutants, repeat 3

value: Homozygous gemin4 mutants


title: JX39P biological replicate 3


title: WT_C15d.1

description: Parental HEK293 (WT) cells, treated with vehicle control for 15 days, biological replicate-#1


title: WT_C15d.2

description: Parental HEK293 (WT) cells, treated with vehicle control for 15 days, biological replicate-#2


title: WT_S3d.3

description: Parental HEK293 (WT) cells, treated with 1μM Senexin B for 3 days, biological replicate-#3

source_name: Parental HEK293 (WT)_1μM Senexin B for 3 days

value: 1μM Senexin B for 3 days


title: HMVC203 - 2h rep 1


title: gemin4_hom_2


title: HMVC204 - 2h rep 2


title: JX14T-RT biological replicate 3

value: resistant


title: HMVCC03 - control rep 3


title: WT_S3d.2

description: Parental HEK293 (WT) cells, treated with 1μM Senexin B for 3 days, biological replicate-#2


title: WT_S3d.1

description: Parental HEK293 (WT) cells, treated with 1μM Senexin B for 3 days, biological replicate-#1


title: JX14T-RT biological replicate 2


title: gemin2_hom_2

source_name: Homozygous gemin2 mutants, repeat 2

value: Homozygous gemin2 mutants


title: HMVCC02 - control rep 2

value: lung


title: WT_C3d.3

description: Parental HEK293 (WT) cells, treated with vehicle control for 3 days, biological replicate-#3

source_name: Parental HEK293 (WT)_vehicle control for 3 days

value: 0.1% DMSO (vehicle control) for 3 days


title: gemin2_hom_3

source_name: Homozygous gemin2 mutants, repeat 3

value: 7 dpf


title: gemin4_hom_1

source_name: Homozygous gemin4 mutants, repeat 1

value: whole fish embryos


title: JX39P biological replicate 2

value: primary tumors


title: gemin6_hom_1

source_name: Homozygous gemin6 mutants, repeat 1


title: WT_C3d.2

description: Parental HEK293 (WT) cells, treated with vehicle control for 3 days, biological replicate-#2

value: Parental HEK293 (WT)


title: HMVCC01 - control rep 1


title: smn1_hom_3

source_name: Homozygous smn1 mutants, repeat 3

value: Homozygous smn1 mutants


title: gemin2_hom_1

source_name: Homozygous gemin2 mutants, repeat 1


title: control_740 mRNA-seq

city: Aurora

first: Ivana

last: Yang

state: CO

institute: University of Colorado Anschutz Medical Campus

description:
Yang_SysBio_control_740
*** 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: University of Colorado

tag: dx

value: normal

value: control

tag: rnaseqid

tag: age

tag: Sex

value: f

tag: race

value: unknown

tag: ethnicity

value: Y

tag: raw data disclaimer


title: WT_C3d.1

description: Parental HEK293 (WT) cells, treated with vehicle control for 3 days, biological replicate-#1

value: HEK293 (ATCC)

tag: treatment


title: control_739 mRNA-seq

description:
Yang_SysBio_control_739
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

tag: tissue


title: JX39P biological replicate 1

tag: individual

tag: radiation sensitivity

value: sensitive

tag: temozolomide sensitivity

tag: patient gender

value: Male


title: smn1_WT_3

source_name: Wildtype siblings of smn1 mutants, repeat 3

tag: strain background

tag: genotype/variation

value: Wildtype siblings of smn1 mutants

tag: Stage


title: case_691 mRNA-seq

description:
Yang_SysBio_case_691
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

tag: center

value: UCSF

value: ipf

value: case

value: m

value: white

value: not hispanic or latino


title: WT_S24h.3

description: Parental HEK293 (WT) cells, treated with 1μM Senexin B for 24 hrs, biological replicate-#3

source_name: Parental HEK293 (WT)_1μM Senexin B for 24 hrs

tag: cell line background

value: Parental HEK293 (WT)

value: 1μM Senexin B for 24 hours


title: control_676 mRNA-seq

description:
Yang_SysBio_control_676
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: Pittsburgh Lung Donor Core

tag: dx

value: normal

value: control

tag: rnaseqid

value: N


title: WT_S24h.2

description: Parental HEK293 (WT) cells, treated with 1μM Senexin B for 24 hrs, biological replicate-#2

value: HEK293 (ATCC)


title: JX14T biological replicate 2

source_name: orthotopic PDX

value: primary tumors

value: sensitive

value: resistant


title: JX14T biological replicate 1

value: Male


title: smn1_WT_2

source_name: Wildtype siblings of smn1 mutants, repeat 2

value: Wildtype siblings of smn1 mutants

value: 7 dpf

value: whole fish embryos


title: control_674 mRNA-seq

description:
Yang_SysBio_control_674
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

tag: age

tag: Sex

value: m


title: JX14P-RT biological replicate 3

value: recurrent tumors


title: JX14T-RT biological replicate 1


title: WT_C24h.3

description: Parental HEK293 (WT) cells, treated with vehicle control for 24 hrs, biological replicate-#3

source_name: Parental HEK293 (WT)_vehicle control for 24 hrs

value: Parental HEK293 (WT)

value: 0.1% DMSO (vehicle control) for 24 hours


title: JX14T biological replicate 3


title: WT_C24h.2

description: Parental HEK293 (WT) cells, treated with vehicle control for 24 hrs, biological replicate-#2


title: smn1_WT_1

source_name: Wildtype siblings of smn1 mutants, repeat 1


title: JX14P-RT biological replicate 1


title: JX14P biological replicate 3


title: JX14P biological replicate 2


title: smn1_hom_1

source_name: Homozygous smn1 mutants, repeat 1

value: Homozygous smn1 mutants


title: control_671 mRNA-seq

description:
Yang_SysBio_control_671
*** 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: f

tag: race

value: white

tag: ethnicity

value: not hispanic or latino


title: gemin5_hom_3

source_name: Homozygous gemin5 mutants, repeat 3

value: Homozygous gemin5 mutants


title: WT_C24h.1

description: Parental HEK293 (WT) cells, treated with vehicle control for 24 hrs, biological replicate-#1

value: HEK293 (ATCC)

tag: treatment


title: control_646 mRNA-seq

description:
Yang_SysBio_control_646
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

tag: tissue

value: control

value: N

tag: raw data disclaimer


title: control_641 mRNA-seq

description:
Yang_SysBio_control_641
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: National Jewish

value: unknown


title: gemin5_WT_3

source_name: Wildtype siblings of gemin5 mutants, repeat 3

value: Wildtype siblings of gemin5 mutants

value: 7 dpf

value: whole fish embryos


title: WT_S5h.3

description: Parental HEK293 (WT) cells, treated with 1μM Senexin B for 5 hrs, biological replicate-#3

source_name: Parental HEK293 (WT)_1μM Senexin B for 5 hrs

value: Parental HEK293 (WT)

value: 1μM Senexin B for 5 hours


title: control_639 mRNA-seq

description:
Yang_SysBio_control_639
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: Y


title: gemin5_hom_2

source_name: Homozygous gemin5 mutants, repeat 2


title: WT_S5h.2

description: Parental HEK293 (WT) cells, treated with 1μM Senexin B for 5 hrs, biological replicate-#2


title: WT_S24h.1

description: Parental HEK293 (WT) cells, treated with 1μM Senexin B for 24 hrs, biological replicate-#1

value: 1μM Senexin B for 24 hours


title: smn1_hom_2

source_name: Homozygous smn1 mutants, repeat 2

value: Homozygous smn1 mutants


title: JX14P-RT biological replicate 2

tag: individual

value: recurrent tumors

tag: radiation sensitivity

value: resistant

value: sensitive

value: Male


title: case_637 mRNA-seq

description:
Yang_SysBio_case_637
*** 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: m

value: white

value: U


title: JX12T-RT biological replicate 2

tag: temozolomide sensitivity

tag: patient gender


title: gemin5_WT_2

source_name: Wildtype siblings of gemin5 mutants, repeat 2

tag: strain background

tag: genotype/variation

value: Wildtype siblings of gemin5 mutants

value: 7 dpf


title: case_635 mRNA-seq

description:
Yang_SysBio_case_635
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

tag: center

value: National Jewish

value: multiple-unspecified

value: hispanic


title: gemin5_hom_1

source_name: Homozygous gemin5 mutants, repeat 1

value: Homozygous gemin5 mutants

tag: Stage

value: whole fish embryos


title: WT_C5h.3

description: Parental HEK293 (WT) cells, treated with vehicle control for 5 hrs, biological replicate-#3

source_name: Parental HEK293 (WT)_vehicle control for 5 hrs

tag: cell line background

value: HEK293 (ATCC)

value: Parental HEK293 (WT)

value: 0.1% DMSO (vehicle control) for 5 hours


title: WT_S5h.1

description: Parental HEK293 (WT) cells, treated with 1μM Senexin B for 5 hrs, biological replicate-#1

value: 1μM Senexin B for 5 hours


title: JX12T-RT biological replicate 1

value: recurrent tumors

value: resistant

value: sensitive

value: Male


title: case_634 mRNA-seq

description:
Yang_SysBio_case_634
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

source_name: tissue-Autopsy

value: lung

tag: dx

value: ipf

value: case

tag: rnaseqid

value: f

value: white

value: not hispanic or latino

value: Y


title: JX12T biological replicate 3

value: primary tumors


title: WT_C5h.2

description: Parental HEK293 (WT) cells, treated with vehicle control for 5 hrs, biological replicate-#2


title: WT_C5h.1

description: Parental HEK293 (WT) cells, treated with vehicle control for 5 hrs, biological replicate-#1


title: case_624 mRNA-seq

description:
Yang_SysBio_case_624
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: National Jewish

tag: age

tag: Sex

value: m


title: case_629 mRNA-seq

description:
Yang_SysBio_case_629
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

source_name: tissue-Biopsy

tag: race

tag: ethnicity


title: JX12T biological replicate 2

tag: tissue


title: JX12T biological replicate 1


title: JX12T-RT biological replicate 3


title: Sample5_zic_ras_tert_TR_rep2

city: Trieste

first: Silvano

last: Piazza

address: localita' Padriciano 99

country: Italy

institute: ICGEB

description: Adult brain tumor induced by RAS and expressing telomerase

data_processing:
Basecalls performed using CASAVA (Illumina Inc.)
The reads were mapped to the reference genome (ENSEMBL GRCz11) using STAR (Dobin et al., 2013), version 2.5.3a
HTSeq-count (version 0.9.1) was used to generate gene counts.
Differential gene expression analysis was performed using DESeq2 (version 1.22.2)
Genome_build: Zebrafish (Danio rerio) GRCz11 from ENSEMBL database.
Supplementary_files_format_and_content: tab-delimited text files include COUNTS values for each Sample

source_name: Adult brain tumor

growth_protocol: Brain tumors were induced in developing zebrafish through the Gal4/UAS system, using the zic:Gal4 driver line and the injection of a UAS:HRASV12G plasmid

extract_protocol:
RNA extracts were collected from tumors developing in adult zebrafish. Total RNA was isolated  TRIzol reagent (Thermo Fisher Scientific) following manufacturer’s instructions, subjected to DNase-I (Thermo Fisher Scientific) treatment and subsequently purified using phenol-chloroform
Libraries were constructed using Lexogen Quant Seq 3' mRNA Seq library prep kit (Fwd).

treatment_protocol: One of the two groups of samples overexpress also telomerase through the Gal4/UAS system

tag: treatment

value: zic UAS:tert;UAS:TR inj ras


title: Sample6_zic_ras_tert_TR_rep3


title: WT_S3h.3

description: Parental HEK293 (WT) cells, treated with 1μM Senexin B for 3 hrs, biological replicate-#3

source_name: Parental HEK293 (WT)_1μM Senexin B for 3 hrs

value: HEK293 (ATCC)

value: Parental HEK293 (WT)

value: 1μM Senexin B for 3 hours


title: WT_S3h.2

description: Parental HEK293 (WT) cells, treated with 1μM Senexin B for 3 hrs, biological replicate-#2


title: control_620 mRNA-seq

description:
Yang_SysBio_control_620
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

source_name: tissue-Explant

value: LTRC

value: other

value: control

tag: raw data disclaimer


title: Sample4_zic_ras_tert_TR_rep1


title: control_621 mRNA-seq

description:
Yang_SysBio_control_621
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung


title: Sample3_zic_ras_rep3

description: Adult brain tumor induced by RAS and developing ALT

value: zic inj ras


title: EC, No TNF, T=72hrs (I18-1266-23)

city: Rotterdam

first: Rutger

middle: Wubbe Willem

last: Brouwer

address: Wytemaweg 80

department: Center for Biomics

country: Netherlands

institute: Erasmus MC

data_processing:
Adapter trimming with adapter trim
Alignment with HISAT2
Alignment sort with samtools
Alignment merge with samtools
Gene count with HTseq-count
Assembly: GRCh38
Supplementary files format and content: tab-delimited files from HTseq-count

source_name: blood vessel

extract_protocol:
Trizol extraction
Illumina Truseq stranded mRNA with polyA selection

treatment_protocol: Endothelial cells or pericytes exposed to medium (=No TNF) or 1 µg/ml HuTNF for 12, 24 or 72 hours

value: blood vessel

tag: cell line

value: HUVEC

tag: cell type

value: Endothelial cell

tag: genotype

value: wt

value: ctrl

tag: time


title: WT_S3h.1

description: Parental HEK293 (WT) cells, treated with 1μM Senexin B for 3 hrs, biological replicate-#1

tag: genotype/variation


title: Sample2_zic_ras_rep2


title: WT_C3h.3

description: Parental HEK293 (WT) cells, treated with vehicle control for 3 hrs, biological replicate-#3

source_name: Parental HEK293 (WT)_vehicle control for 3 hrs

value: 0.1% DMSO (vehicle control) for 3 hours


title: control_617 mRNA-seq

description:
Yang_SysBio_control_617
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

tag: center

value: white

value: not hispanic or latino

value: Y


title: control_616 mRNA-seq

description:
Yang_SysBio_control_616
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: m

value: black


title: EC, No TNF, T=72hrs (I18-1266-21)


title: Sample1_zic_ras_rep1


title: WT_C3h.2

description: Parental HEK293 (WT) cells, treated with vehicle control for 3 hrs, biological replicate-#2

value: HEK293 (ATCC)

value: Parental HEK293 (WT)


title: control_613 mRNA-seq

description:
Yang_SysBio_control_613
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: LTRC

value: other


title: gemin5_WT_1

source_name: Wildtype siblings of gemin5 mutants, repeat 1

tag: strain background

value: Wildtype siblings of gemin5 mutants

tag: Stage

value: 7 dpf

value: whole fish embryos


title: EC, TNF, T=24hrs (I18-1266-20)

value: blood vessel

value: HUVEC

value: TNF


title: WT_C3h.1

description: Parental HEK293 (WT) cells, treated with vehicle control for 3 hrs, biological replicate-#1

tag: cell line background


title: EC, TNF, T=72hrs (I18-1266-24)

value: Endothelial cell

value: wt


title: control_612 mRNA-seq

description:
Yang_SysBio_control_612
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

tag: dx

value: control

tag: rnaseqid

value: white

value: N


title: control_611 mRNA-seq

description:
Yang_SysBio_control_611
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

tag: age

tag: Sex

value: m

value: not hispanic or latino

value: Y


title: Hepatic CD45+ from Trem2-/- transplanted mice, scRNAseq

city: Vienna

first: Christoph

middle: J

last: Binder

address: Lazarettgasse 14

department: Laboratory Medicine

country: Austria

institute: Medical University of Vienna

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (10X Genomics)
Assembly: mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: liver

extract_protocol:
livers were collected and rinsed in ice-cold PBS prior to dissociation. Tissue was subsequently digested using the Mouse Liver Dissociation kit according to manufacturer’s instructions using the GentleMacs Tissue Dissociator (both Miltenyi Biotech, Germany). Live 7AAD- CD45+ cells from 4 mice per group were sorted on a BD FACS Aria II and pooled in equal proportions and immediately processed according to manufacturer’s instructions
Library was performed according to the manufacter’s instructions (Chromium Next GEM single cell 5’ v2 protocol, 10x Genomics).

value: liver

value: male

value: live CD45+ cells

value: bone marrow chimeric Trem2-/-

value: 4w MCD diet (NASH)


title: Hepatic CD45+ from Trem2+/+ transplanted mice, scRNAseq

description: 10X Genomics

value: bone-marrow chimeric Trem2+/+


title: EC, TNF, T=24hrs (I18-1266-18)

value: blood vessel

value: HUVEC


title: control_610 mRNA-seq

description:
Yang_SysBio_control_610
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: LTRC

value: other

tag: race

tag: ethnicity


title: HES1 over-expressing osteoclasts, Day 4_biol rep 3

city: Farmington

first: Ernesto

last: Canalis

state: CT

address: 263 Farmington Avenue

department: Orthopaedic Surgery

institute: UConn Health

data_processing:
Raw reads were trimmed with Sickle (Version 1.33), with a quality threshold of 30 and length threshold of 45, following that the trimmed reads were mapped to Mus Musculus genome (GRCm38 ensembl release 97) with HISAT2 (version 2.1.0).
The resulting SAM files then converted into BAM format using samtools (version 1.9), and the PCR duplicates were removed using PICARD (http://broadinstitute.github.io/picard/).
The counts were generated against the features with htseq-count.
The differential expression of genes between conditions was evaluated using DESeq2.
Covariates were introduced in the DESeq2 analysis to increase the accuracy of results, and genes showing less than 10 counts across the compared samples were excluded from the analysis.
Genes with a false discovery rate (FDR) < 0.05 were considered significant and used in the downstream analysis.
Assembly: Mus Musculus genome (GRCm38 ensembl release 97)
Supplementary files format and content: COUNTS File (*.counts) and counts

source_name: Osteoclasts

growth_protocol: BMMs were cultured with alpha Minimum Essential Medium including 10% fetal bovine serum in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was extracted from osteoclasts with the RNeasy Mini kit (Qiagen, Valencia, CA)
Total RNA samples were prepared for mRNA-Sequencing using the Illumina TruSeq Stranded mRNA Sample Preparation kit following the manufacturer’s protocol (Illumina, San Diego, CA).
Libraries were validated for length and adapter dimer removal using the Agilent TapeStation 4200 D1000 High Sensitivity assay (Agilent Technologies), and then they were quantified and normalized using the dsDNA High Sensitivity Assay for Qubit 3.0 (Thermo Fisher Scientific).
Sample libraries were prepared for Illumina sequencing by denaturing and diluting the libraries per manufacturer’s protocol (Illumina).
All samples were pooled into one sequencing pool, equally normalized, and run as one sample pool across the Illumina NextSeq 500 using version 2.5 chemistry.
Target read depth was achieved for each sample with paired end 75bp reads.

treatment_protocol: Osteoclasts differentiation was induced by treatment with 30ng/ml of M-CSF and 10 ng/ml of RANKL for 4 days.

value: Osteoclasts

value: Male

tag: treatment

value: M-CSF and RANKL

value: Day 4


title: 293.IS_Rep2

source_name: HEK293 cells, treated with 10ng/mL IFN-γ (with presence of 1µM Senexin B) for 5 hours, biological replicate-#2

growth_protocol: HEK293 cells were grown in DMEM (High-glucose) media with 10% FBS, 1% penicillin-streptomycin and 2 mM L-glutamine. The cells were plated in 12-well plate at the density of 3x10^5 cells per well 24 hours prior to treatment.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) and RNA quality was validated on RNA-1000 chip using Bioanalyzer (Agilent)
Sequencing libraries were generated using the Illumina TruSeq Stranded mRNA prep kit (RS-122-2101/RS-122-2102)

treatment_protocol: HEK293 cells were treated with Vehicle control (293.C), 1μM Senexin B (293.S), 10ng/mL IFN-γ (293.I) or Senexin B/IFN-γ combination (293.IS) for 5 hours.

value: HEK293 (ATCC)


title: 293.IS_Rep3

source_name: HEK293 cells, treated with 10ng/mL IFN-γ (with presence of 1µM Senexin B) for 5 hours, biological replicate-#3


title: EC, No TNF, T=24hrs (I18-1266-17)

tag: tissue

value: Endothelial cell

value: wt

value: ctrl


title: control_608 mRNA-seq

description:
Yang_SysBio_control_608
*** 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: white

value: not hispanic or latino

value: U

tag: raw data disclaimer


title: EC, TNF, T=72hrs (I18-1266-22)

value: blood vessel

tag: cell line

value: HUVEC

tag: cell type

value: TNF


title: HES1 over-expressing osteoclasts, Day 4_biol rep 2

value: Osteoclasts

tag: genotype

tag: time


title: 293.IS_Rep1

source_name: HEK293 cells, treated with 10ng/mL IFN-γ (with presence of 1µM Senexin B) for 5 hours, biological replicate-#1


title: 293.I_Rep3

source_name: HEK293 cells, treated with 10ng/mL IFN-γ for 5 hours, biological replicate-#3

value: treated with 10ng/mL IFN-γ for 5 hours


title: EC, TNF, T=12hrs (I18-1266-16)


title: control_605 mRNA-seq

description:
Yang_SysBio_control_605
*** 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: N


title: control_601 mRNA-seq

description:
Yang_SysBio_control_601
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: m

value: Y


title: 293.I_Rep1

source_name: HEK293 cells, treated with 10ng/mL IFN-γ for 5 hours, biological replicate-#1

value: HEK293 (ATCC)


title: 293.I_Rep2

source_name: HEK293 cells, treated with 10ng/mL IFN-γ for 5 hours, biological replicate-#2


title: Wild type osteoclasts, Day 4_biol rep 2

value: Wild type

value: Male

value: M-CSF and RANKL

value: Day 4


title: EC, TNF, T=12hrs (I18-1266-14)

value: Endothelial cell

value: wt


title: control_606 mRNA-seq

description:
Yang_SysBio_control_606
*** 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: white

value: not hispanic or latino


title: Wild type osteoclasts, Day 4_biol rep 1

value: Osteoclasts


title: EC, No TNF, T=24hrs (I18-1266-19)

value: blood vessel

value: HUVEC

value: ctrl


title: EC, No TNF, T=12hrs (I18-1266-15)


title: PC, TNF, T=72hrs (I18-1266-12)

value: hPL-PC

value: Pericyte

value: TNF


title: Wild type osteoclasts, Day 4_biol rep 3

value: Wild type

value: Male


title: 293.S_Rep3

source_name: HEK293 cells, treated with 1μM Senexin B for 5 hours, biological replicate-#3

value: HEK293 (ATCC)

value: treated with 1uM Senexin B for 5 hours


title: 293.S_Rep2

source_name: HEK293 cells, treated with 1μM Senexin B for 5 hours, biological replicate-#2


title: MNV

city: New York

first: Ken

last: Cadwell

state: NY

address: 430 East 29th Street Suite 424

institute: NYU Langone School of Medicine

data_processing:
Sequencing performed on NovaSeq 6000 platform. Basecalling was done by Illumina's RTA3 software
The Cell Ranger Single Cell Software Suite, version 1.3 was used to perform sample de-multiplexing, barcode and UMI processing, and single-cell 3′ gene counting
Assembly: mm10
Supplementary files format and content: matrix.mtx files are the output of Cell Ranger software, they contain the matrix of sequenced cells and their gene expression
Supplementary files format and content: barcodes.tsv files contain the barcode indices for individual cells
Supplementary files format and content: genes.tsv files contain the feature indices for the matrix files
Supplementary files format and content: counts.raw and counts.normalized contain feature counts for MNV and Naïve oonditions

source_name: Intestinal intraepithelial lymphocytes

growth_protocol: Cells were isolated ex-vivo as described in manuscript

extract_protocol:
Small intestine (Peyer’s patches removed) was cut longitudinally and rinsed in HBSS. The tissue was washed in HBSS containing HEPES, sodium pyruvate, 5 mM EDTA, and 1 mM DTT for 15 min to obtain the IEL fraction. The IEL was filtered and fractionated on a Percoll gradient (40% and 80%). The cells at the interphase of the gradient were collected and washed with complete RPMI.
Sorted IEL suspensions were loaded on a 10x Genomics Chromium instrument to generate 10,000 single-cell gel beads in emulsion (GEMs). Single-cell RNA-Seq libraries were prepared using Single Cell 3’ Reagent Kits v3.1: Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1, PN-1000121; Chromium Next GEM Chip G Single Cell Kit, PN-1000120 and Single Index Kit T Set A PN-1000213 (10x Genomics)

treatment_protocol: Cells were prepared using 10x genomics single cell protocol

tag: strain

value: Intestinal intraepithelial lymphocytes

tag: agent

value: day 10 post MNV-CR6 infection


title: 293.S_Rep1

data_processing:
Indexed sequences were sorted by Illumina BaseSpace FASTQ generation | version: 1.0.0
Reads were mapped to the hg38 reference genome using STAR | version 2.4 with default parameters (generation of sam files)
Convert .sam files to .bam files using samtools | version: 1.2 with parameters -bh -F 3840 -q 255
Read counts over annotated genes were obtained using featureCount (subreads | version: 1.4.6) with parameters -p -T 10
Genome_build: GRCh38.77
Supplementary_files_format_and_content: tab-delimited text files include gene counts for each sample

source_name: HEK293 cells, treated with 1μM Senexin B for 5 hours, biological replicate-#1


title: PC, No TNF, T=72hrs (I18-1266-11)

value: wt


title: HES1 over-expressing osteoclasts, Day 4_biol rep 1

value: M-CSF and RANKL

value: Day 4


title: Naïve

value: naïve (non-infected)


title: EC, No TNF, T=12hrs (I18-1266-13)

value: Endothelial cell


title: control_597 mRNA-seq

description:
Yang_SysBio_control_597
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: LTRC

value: other

value: control

value: m

value: white

value: not hispanic or latino

value: Y


title: PC, TNF, T=72hrs (I18-1266-10)

value: blood vessel

value: hPL-PC

value: Pericyte

value: TNF


title: 293.C_Rep3

source_name: HEK293 cells, treated with vehicle control for 5 hrs, biological replicate-#3

value: HEK293 (ATCC)

value: treated with 0.1% DMSO (vehicle control) for 5 hours


title: PC, No TNF, T=72hrs (I18-1266-09)

value: wt

value: ctrl


title: case_592 mRNA-seq

description:
Yang_SysBio_case_592
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

source_name: tissue-Explant

value: ipf

value: case

value: N


title: 2217_B_BCR_TCR

city: Aarhus

first: Lin

last: Lin

address: Høegh-Guldbergs Gade 10

department: Department of Biomedicine

country: Denmark

institute: Aarhus University

data_processing:
The raw sequencing dData were processed on the Seven Bridges Genomics platform using the BD Rhapsody Targeted Analysis Pipeline. "reference.zip" were used as reference, including immune panel and abseq information.
Supplementary files format and content: expression of immune panel and abseq in one matrix; and VDJ information in another matrix

source_name: spleen

extract_protocol:
For single-cell mRNA and repertoire sequencing, total splenocytes were purified from spleens of two no-bridge chimeras as indicated under Tissue Harvest and Preparation, followed by negative selection with biotinylated Ter-119, anti-biotin microbeads and magnetic separation. For one bridge chimera, the spleen was split in half, and one half was subjected to the same total splenocyte purification whereas the other half was used for purification of GC B cells using a PNA microbead kit (130-110-479, Miltenyi Biotec) according to the manufacturer’s instructions, and the two fractions were mixed to generate a GC B cell enriched splenocyte sample.
From each sample, 1*10^6 cells were added 100 µl of AbSeq staining mix containing a cocktail of 20 Abseq antibodies, and incubated for 60 minutes. Cells were washed three times with 2 ml BD staining buffer (250 g for 8 minutes centrifugation) and for each sample, 20,000 cells were loaded onto a BD Rhapsody cartridge and processed on the Rhapsody Express module following the manufacturer’s instructions. Each sample was subsequently split into two (A and B) to be able to verify technical reproducibility, and each subsample was used for generation of 4 libraries: (1) single-cell targeted library using the Mouse Immune Response Panel (Catalog No. 633753, BD) containing primer pairs targeting 397 genes commonly found in mouse immune cells and a BD Rhapsody Panel supplement (Part number 633742, BD) containing an additional 45 target genes, for a total of 442 targets; (2) Abseq library; (3) BCR V(D)J library; and (4) TCR V(D)J library.

value: spleen

value: bridge' chimeras


title: 2217_B_immune_panel


title: 293.C_Rep2

source_name: HEK293 cells, treated with vehicle control for 5 hrs, biological replicate-#2


title: 2217_A_BCR_TCR


title: control_586 mRNA-seq

description:
Yang_SysBio_control_586
*** 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: f


title: control_590 mRNA-seq

description:
Yang_SysBio_control_590
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: m

value: white

value: not hispanic or latino


title: PC, TNF, T=24hrs (I18-1266-08)

source_name: blood vessel

value: blood vessel

value: hPL-PC

value: Pericyte

value: TNF


title: control_599 mRNA-seq

description:
Yang_SysBio_control_599
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: Y


title: control_582 mRNA-seq

description:
Yang_SysBio_control_582
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***


title: 2217_A_immune_panel


title: control_594 mRNA-seq

description:
Yang_SysBio_control_594
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: unknown


title: PC, No TNF, T=24hrs (I18-1266-07)

value: wt

value: ctrl


title: PC, TNF, T=24hrs (I18-1266-06)


title: 1760_B_BCR_TCR

value: spleen

value: no bridge' chimeras


title: control_580 mRNA-seq

description:
Yang_SysBio_control_580
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: LTRC

value: N


title: BM7264-Healthy

city: Houston

first: Jia

last: Li

state: Texas

address: 2121 W HOLCOMBE BLVD

department: CEDP

institute: Guangzhou Medical University

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

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: Healthy donor

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: control_579 mRNA-seq

description:
Yang_SysBio_control_579
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

tag: dx

value: other

value: control

tag: rnaseqid

value: f

value: white

value: not hispanic or latino


title: BM7021-Healthy


title: 1760_B_immune_panel


title: BM7012-Healthy


title: BM7263-Healthy


title: 1760_A_BCR_TCR


title: 1760_A_immune_panel


title: BM7007-Healthy


title: control_575 mRNA-seq

description:
Yang_SysBio_control_575
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

tag: age

tag: Sex

value: Y


title: control_576 mRNA-seq

description:
Yang_SysBio_control_576
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

tag: race

tag: ethnicity


title: PC, No TNF, T=12hrs (I18-1266-03)

tag: tissue

value: blood vessel

value: hPL-PC

value: Pericyte

tag: treatment


title: PC, TNF, T=12hrs (I18-1266-02)

tag: cell line

value: wt

value: TNF


title: PC, TNF, T=12hrs (I18-1266-04)

tag: cell type


title: 1027_B_BCR_TCR

value: spleen

tag: genotype

value: no bridge' chimeras


title: PC, No TNF, T=24hrs (I18-1266-05)

value: ctrl

tag: time


title: 293.C_Rep1

institute: University of South Carolina

source_name: HEK293 cells, treated with vehicle control for 5 hrs, biological replicate-#1

value: HEK293 (ATCC)

value: treated with 0.1% DMSO (vehicle control) for 5 hours


title: BM6804-Healthy

value: Healthy donor

value: bone marrow

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


title: control_574 mRNA-seq

description:
Yang_SysBio_control_574
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

tag: center

value: LTRC

value: other

value: control

value: f

value: black

tag: raw data disclaimer


title: BM6724-Healthy


title: control_570 mRNA-seq

description:
Yang_SysBio_control_570
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: white

value: not hispanic or latino

value: Y


title: PC, No TNF, T=12hrs (I18-1266-01)

value: blood vessel

value: hPL-PC

value: Pericyte

value: wt


title: V8_350_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: vehicle rep8

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: vehicle


title: V7_344_G_519

description: vehicle rep7


title: case_555 mRNA-seq

description:
Yang_SysBio_case_555
*** 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: m

value: White


title: input-Input

tag: disease state

value: Input

value: bone marrow


title: 1027_A_BCR_TCR

value: spleen

value: no bridge' chimeras


title: 1027_A_immune_panel


title: case_547 mRNA-seq

description:
Yang_SysBio_case_547
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: UCSF

value: white

value: not hispanic or latino


title: BME8-MDS/MPD

value: MDS/MPD

tag: ip reagent

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


title: V4_338_G_519

description: vehicle rep4

value: Mantle cell lymphoma


title: V6_342_G_519

description: vehicle rep6

value: Granta-519 cells were grafted to NSG mice


title: BME44-MDS

value: MDS


title: case_545 mRNA-seq

description:
Yang_SysBio_case_545
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

tag: dx

value: ipf

value: Y


title: V3_336_G_519

description: vehicle rep3

value: vehicle


title: case_546 mRNA-seq

description:
Yang_SysBio_case_546
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: case

tag: rnaseqid

value: m


title: V1_331_G_519

description: vehicle rep1


title: case_543 mRNA-seq

description:
Yang_SysBio_case_543
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

tag: age

value: unknown

value: hispanic

value: N


title: V2_334_G_519

description: vehicle rep2


title: Lung_mf_mo_flu_d7

city: Zürich

first: Manfred

last: Kopf

address: Otto-Stern-Weg 7

department: Biologie

country: Switzerland

institute: ETH Zürich

description: 10x Genomics

data_processing:
Single cell gene expression data were pre-processed with a standard Cell Ranger v6.0.2 (10x Genomics) pipeline, aligning reads to the mm39 mouse reference transcriptome (Release_M26-2021-04-20).
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).
Supplementary files format and content: Tab-separated file containing barcode information, batch and clusters identifier of the combined dataset (annotation.tsv).

source_name: Lung

extract_protocol:
Cells were FACS sorted and viability was proved. 10,000 cells per sample were loaded in to the 10X Chromium controller and library preparation was performed according to the manufacturer’s indications (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 protocol).
10,000 cells per sample were loaded in to the 10X Chromium controller and library preparation was performed according to the manufacturer’s indications (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 protocol)

treatment_protocol: WT mice were infected at different timepoints to be analyzed on one same day. From every timepoint lungs from 3 mice were pooled in one sample.

value: Lung

value: Monocytes and macrophages

value: Influenza A infected


title: BME43-MDS

value: bone marrow


title: LNSC scRNA-seq

city: BALTIMORE

first: yang

last: song

address: 670 W. Baltimore St.

institute: UNIVERSITY OF MARYLAND IN BALTIMORE

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lymph nodes

extract_protocol:
After enzymatic digestion of the lymph nodes (LNs)from  C57BL/6 mice, CD45- cells were purified with the CD45 negative selection beads and were stained with anti-mouse CD45 before sorting for viable CD45- cells.
C57BL/6 mouse lymph node stromal cells were isolated for scRNA-seq, more than 2x104 cells were run on the 10X Chromium Controller (10X Genomics) to partition single cells with uniquely barcoded beads and processed for sequencing library preparation using the Chromium Single Cell 3’ Reagent Kit. cDNA libraries were sequenced on a NovaSeq 6000 sequencing system.

value: lymph nodes

value: stromal cells

tag: strain

value: naive


title: BME1-AML

value: AML

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


title: DPN7_349_G_519

description: DPN rep7

value: Mantle cell lymphoma

value: Granta-519 cells were grafted to NSG mice

value: DPN


title: case_542 mRNA-seq

description:
Yang_SysBio_case_542
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: UCSF

value: ipf

value: case

tag: Sex

tag: race

value: white

value: not hispanic or latino

value: Y


title: Lung_mf_mo_naive

description: 10x Genomics

tag: tissue

value: Lung

value: Monocytes and macrophages

value: Naive


title: BME21-RAEB

value: RAEB

value: bone marrow


title: Lung_mf_mo_flu_d14

description: 10x Genomics

tag: treatment

value: Influenza A infected


title: control_541 mRNA-seq

description:
Yang_SysBio_control_541
*** 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

tag: ethnicity


title: BME18-AML

value: AML

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


title: DPN6_346_G_519

description: DPN rep6

tag: cell type

value: Mantle cell lymphoma

tag: cell line

value: Granta-519 cells were grafted to NSG mice

value: DPN


title: 1027_B_immune_panel

value: spleen

tag: genotype

value: no bridge' chimeras


title: BME7-AML


title: AM_WT_2

description: AM_WT_2 [normalized count]

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)

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.

value: lung

value: alveolar macrophages


title: control_540 mRNA-seq

description:
Yang_SysBio_control_540
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

tag: center

value: m

value: white

value: not hispanic or latino

value: N


title: BME17-CMLPh-

value: CMLPh-

value: bone marrow


title: Lung_mf_mo_flu_d30

description: 10x Genomics

value: Lung

value: Monocytes and macrophages

value: Influenza A infected


title: AM_WT_3

description: AM_WT_3 [normalized count]

value: Naive


title: control_544 mRNA-seq

description:
Yang_SysBio_control_544
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: Pittsburgh Lung Donor Core

value: normal

value: control

value: f

value: Y

tag: raw data disclaimer


title: case_539 mRNA-seq

description:
Yang_SysBio_case_539
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: UCSF

value: ipf

value: case


title: BME16-RAEB

value: RAEB

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


title: DPN5_345_G_519

description: DPN rep5

value: Mantle cell lymphoma

tag: condition

value: Granta-519 cells were grafted to NSG mice

value: DPN


title: control_538 mRNA-seq

description:
Yang_SysBio_control_538
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: m

value: white

value: not hispanic or latino

value: N


title: DPN4_343_G_519

description: DPN rep4


title: BME13-RARS

tag: disease state

value: RARS

value: bone marrow


title: case_537 mRNA-seq

description:
Yang_SysBio_case_537
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***


title: BME14-AML

value: AML

tag: ip reagent


title: FliMo_AM_neonates_2

description: AM_FliMo_2 [normalized count]

value: alveolar macrophages

value: transferred into lungs of neonatal Csf2Ra KO mice


title: DPN3_339_G_519

description: DPN rep3


title: DPN2_337_G_519

description: DPN rep2


title: AM_WT_1

description: AM_WT_1 [normalized count]

value: lung

value: Naive


title: case_536 mRNA-seq

description:
Yang_SysBio_case_536
*** 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

value: f

value: Y


title: FliMo_AM_neonates_1

description: AM_FliMo_1 [normalized count]


title: control_532 mRNA-seq

description:
Yang_SysBio_control_532
*** 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: rnaseqid


title: BME11-RAEB

value: RAEB

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


title: BMMo_AM_neonates_1

description: AM_BMMo_1 [normalized count]


title: Ectopic expression of SRRM3 in HEK293 cells

institute: Universitat Pompeu Fabra - Centre for Genomic Regulation

description:
CL_293_L_SRRM3_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.

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.

value: Ectopic expression of SRRM3


title: BMMo_AM_neonates_2

description: AM_BMMo_2 [normalized count]