title: Macrophages, IFNgamma stimulation + polished Ti disc, donor 1

description: Gene expression data from human macrophages stimulated with IFNgamma and cultured for 6 days on polished titanium discs

value: IFN


title: Macrophages, IFNgamma stimulation, donor 1

status: Public on Feb 10 2021

type: RNA

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

description: Gene expression data from human macrophages stimulated with IFNgamma and cultured for 6 days on cell culture plastic

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 7, from SAS. Gene expression profiling was performed using arrays of human Hugene-1_0-type from Affymetrix. A Custom CDF Version 19 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Buffy coat, donor 1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Macrophages were cultured in Macrophage Serum Free Medium at a concentration of 2x10^6 cells/ml, supplemented with 1ng/ml M-CSF, 10^-8M Dexamethasone for 6 days

extract_protocol: RNA was extracted using E.Z.N.A. total RNA Kit I according to manufacturer´s instructions.

treatment_protocol: Macrophages were cultured on cell culture plastic or on polished titanium discs. Additionally they were stimulated at day 0 either with IL-4 (10ng/ml) or with IFNgamma (100ng/ml) or with M2Cocktail(10ng/ml M-CSF + 3ng/ml IL-4 + 10ng/ml IL-10 + 10ng/ml TGFbeta) or left untreated as control.

tag: tissue

value: PBMC derived monocytes

tag: donornr

tag: treatment

tag: titanium

value: ctrl


title: MRC-149C [10-PBDE_CUMULUS]

city: Montreal

first: Thomas

middle: Constantine

last: Nardelli

state: Quebec

address: 3655 Prom. Sir-William-Osler

department: Pharmacology and Therapeutics

country: Canada

institute: McGill University

description: SG11514161_257236311888_S001_GE1_1105_Oct12_2_1.txt

hyb_protocol: After 17 h of hybridization at 65 degees celsius, the microarray slides were washed as per the recommendations for the Agilent hybridization kit.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (SureScan G2600D) using one color scan setting for 8x60k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software Version 11.5.1.1 (Agilent) using default parameters (protocol GE1_1105_Oct12). Scale normalization 75.0 percentile .

source_name: Cumulus Granulosa

label_protocol: Sample input was 100 ng of total RNA to generate fluorescent cRNA using the Agilent's low input Quick Amp labeling kit and 600 ng of Cy3 labeled cDNA was used for the single-color microarray.

extract_protocol: Total RNA was extracted using theRNeasy Plus minikit (Qiagen)

tag: exposure

value: LOW


title: RNA complexed with MS2 - sample 2 (control)

type: SRA

city: Rennes

first: Vincent

last: Cattoir

address: 2 rue Henri Le Guilloux

country: France

institute: CHU de Rennes

library_source: transcriptomic

data_processing:
The reads were mapped against the genomic sequence of S. aureus HG003 strain (Genbank accession no. CP000253) and counted using the CLC Genomics Workbench software v8.1 (Qiagen).
The expression of genes in different RNA-seq samples was compared using the R package DESeq2 R package.
Genome_build: S. aureus HG003 strain (Genbank accession no. CP000253.1).
Supplementary_files_format_and_content: *.txt: Tab-delimited text files generated using the CLC Genomics Workbench software v8.1 (Qiagen).

organism: Staphylococcus aureus

source_name: Bacteria

growth_protocol: Bacterial cells of Staphylococcus aureus HG003 strain were cultured at 37°C to early- and the late-exponential-growth phases in BHI broth.

extract_protocol:
Total RNA was extracted using phenol/chloroform method with followed ethanol precipitation.
The strand-specific library preparation was performed using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® and the samples were sequenced using the Illumina MiSeq instrument.

treatment_protocol: Affinity purification of target RNAs bound to MS2-tagged sRNAs expressed in vivo.

tag: strain

tag: ms2 tag


title: Input_Liver_ChIPSeq

city: Gainesville

first: Danxin

last: Wang

state: FL

address: 1345 Center Drive MSB PG-05B

department: Pharmacotherapy and Translational Research

country: USA

institute: University of Florida

description: Source was from three male and three female European American liver samples, ages ranged from 44 to 73 years old

library_source: genomic

data_processing:
Raw ChIP-Seq reads were processed with Trimmomatic to remove adaptor sequences, bases with quality scores less than 20, and sequences less than 20 bp in length
Raw ChIP-Seq reads were aligned to the hg38 genome assembly using Bowtie2 with the default settings
Homer v4.10 was used to call peaks
Genome_build: hg38
Supplementary_files_format_and_content: bedgraph files were geneated with Homer v4.10

molecule: genomic DNA

source_name: Liver Tissue

extract_protocol: Frozen tissue and cells were provided to Active Motif (Carlsbad, CA, USA) who conducted ChIP and library preparation as a commerical service

tag: tissue/cell type

value: Liver Tissue

tag: chip-antibody


title: MRC-051NF [10-PBDE_CUMULUS]

description: SG11514161_257236311888_S001_GE1_1105_Oct12_1_4.txt

value: HIGH


title: ESR1_Liver_ChIPSeq

description: Source was from three male and three female European American liver samples, ages ranged from 44 to 73 years old.

value: sc-543 (Santa Cruz, Ca, USA)


title: MRC-053NF [10-PBDE_CUMULUS]

description: SG11514161_257236311888_S001_GE1_1105_Oct12_1_2.txt


title: Macrophages, IL-4 stimulation, donor 1

description: Gene expression data from human macrophages stimulated with IL-4 and cultured for 6 days on cell culture plastic


title: Macrophages, IL-4 stimulation + polished Ti disc, donor 1

description: Gene expression data from human macrophages stimulated with IL-4 and cultured for 6 days on polished titanium discs

value: TI


title: Macrophages, without stimulation, donor 1

description: Gene expression data from human unstimulated macrophages cultured for 6 days on cell culture plastic

value: NO


title: Input_Hep_DMSO_ChIPSeq

description: Source was combined sample from one male and one female European American donor, ages 32 and 62, respectively.  Cultured in serum-free William’s E media supplemented with penicillin/streptomycin/fungizone (100 U/100 µg/0.25µg per ml), 100 nM dexamethasone, 2 mM L-glutamine, 15 mM HEPES and ITS (0.55 mg/ml human transferrin, 1 mg/ml bovine insulin and 0.5 µg/ml sodium selenite, from Sigma). Cells were fixated with 2% formaldehyde.

source_name: Primary Hepatocytes

value: Primary hepatocytes

value: DMSO

tag: treatment time

value: 8 hours


title: ESR1_Hep_DMSO_ChIPSeq


title: MRC-008NF [10-PBDE_CUMULUS]

description: SG11514161_257236311887_S001_GE1_1105_Oct12_2_2.txt


title: Macrophages, M2Cocktail stimulation + polished Ti disc, donor 3

description: Gene expression data from human macrophages stimulated with M2Cocktail and cultured for 6 days on polished titanium discs

source_name: Buffy coat, donor 3

value: Cocktail


title: Macrophages, without stimulation + polished Ti disc, donor 1

description: Gene expression data from human unstimulated macrophages cultured for 6 days on polished titanium discs


title: BLISS8_shCTR9_A1

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

institute: University of Wuerzburg

data_processing:
Base calling perfomed using Illumina's FASTQ Generation software v1.0.0
reads were demultiplexed according to sample-barcode with UMI-tools v1.0.1
barcodes used as following: A1: CATCACGC, A2: GTCGTTCC, A3: TGATGATC, A4: ACGACATC, A5: CATCATCC, A6: ACGACCGC
reads were aligned with Bowtie2 v2.3.4.1 to hg19
reads were filtered with bedtools intersect v2.26.0
bedgraph-files were normalized within each replicate to the condition with the lowest amount of AsiSI-induced breaks (BLISS8), or readnormalized between replicates ("BLISS Etoposide")
reads were counted for specific regions using the R package exomeCopy v1.18.0
density plots were generated using the R package metagene2 v3.10
Genome_build: hg19
Supplementary_files_format_and_content: begraph files were generated with bedtools genomecov

growth_protocol: U2OS cells expressing doxycycline-inducible MYC or K562 cells carrying endogenously AID-tagged MYC

extract_protocol:
blunting of DSB, adapter ligation, DNA purification and fragmentation, in vitro transcription, fragmentation
libraries were prepared for sequencing using a modified NEBNext Small RNA library preperation protocol

treatment_protocol: Treated with/without doxycycline for 24 hrs, with or without Etoposide for 3 hrs and with or without IAA for 3.5h

tag: cell line

value: U-2 OS

tag: cell type

value: osteosarcoma cell line

value: Ethanol, stable expression of CTR9-targeting shRNA


title: MRC-113C [10-PBDE_CUMULUS]

description: SG11514161_257236311887_S001_GE1_1105_Oct12_1_2.txt


title: Macrophages, M2Cocktail stimulation, donor 3

description: Gene expression data from human macrophages stimulated with M2Cocktail and cultured for 6 days on cell culture plastic


title: ESR1_Hep_E2Treated_ChIPSeq

value: 17 β-estradiol (1 µM)


title: MRC-039NF [10-PBDE_CUMULUS]

description: SG11514161_257236311887_S001_GE1_1105_Oct12_1_1.txt


title: TE79_Ser2_K1_EtOH_0

description: EtOH treatment

data_processing:
Base calling perfomed using Illumina's FASTQ Generation software v1.0.0
ChIPseq reads were aligned with Bowtie2 to hg19 and to mm10 for the spike-in
human reads were normalized to the number of spike-in reads
metagenes were established with ngs.plot.r v2.41.2
chromosome ideagrams were drawn with RIdeogram v0.2.2
read distribution was determined with betdools intersect v2.26.0, either over specified regions or over the whole genome in 100-nt-bins
Genome_build: hg19, mm10
Supplementary_files_format_and_content: begraph files were generated with bedtools (v2.26.0) genomecov

source_name: osteosarcoma cell line

growth_protocol: cells were grwon in DMEM for 24 h

extract_protocol:
crosslink (5 min), harvest, 10% of NIH 3T3 spike in, lysis of cells, fragment with covaris
libraries were prepared for sequencing using standard NEB protocols

treatment_protocol: treat with EtOH, or 4-OHT (200 nM) for 10 min

tag: chip antibody

value: Anti RNA Pol2 phospho Ser2 (rabbit, abcam, ab5095)


title: MS2_SPI-2

city: Würzburg

first: Tom

last: Gräfenhan

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

department: Core Unit SysMed

description:
MS2-affinity-purified RNA
MS2 only control

data_processing:
Base calling with Illumina NextSeq RTA v2.4.11 (SPI-2 and in vivo, SPI-1 unknown)
FASTQ conversion with bcl2fastq v2.20.0.422 (SPI-2 and in vivo, SPI-1 unknown)
FASTQ quality and adapter trimming using Cutadapt (Martin, 2011). SPI-1: version 1.10/1.12 with parameters -q 20 -m 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT; SPI-2/in vivo: version 1.16/2.5 with parameters --nextseq-trim=20 -m 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
SPI-1/2: read alignment to Salmonella Typhimurium SL1344 genome and MS2-PinT, MS2 and PinT constructs using segemehl version 0.2.0  (parameters for reademption align: -l 12 -P -a 95) (READemption 0.4.3, Förstner et al., 2014); in vivo: read alignment to Salmonella Typhimurium SL1344 and mouse genome as well as MS2-PinT, MS2 and PinT constructs using segemehl version 0.2.0  (parameters for reademption align: -r -l 20 -P -a 90 -S) (READemption 0.4.5, Förstner et al., 2014)
Read quantification via reademption gene_quanti using Salmonella annotations (parameters: -o 1 -t "5UTR,CDS,3UTR,rRNA,tRNA,sRNA,transcript" -a) (READemption 0.4.3/0.4.5, Förstner et al., 2014)
Size factor calculation based on rRNA read counts only via DESeq2 (Love et al., 2014)
Coverage calculation via reademption coverage based on all aligned reads (full-length) (READemption 0.4.5, Förstner et al., 2014)
Extraction of Salmonella raw coverage values (in vivo only) and coverage normalization by rRNA-based size factors
Genome_build: Salmonella Typhimurium SL1344 (GCF_000210855.2) and mouse (GRCm38.p6)
Supplementary_files_format_and_content: wiggle files containing positional read coverage values

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

source_name: Salmonella Typhimurium SL1344 cells

growth_protocol: Salmonella Thyphimurium strain SL1344 was grown from single colonies in SPI-1, SPI-2 conditions. For SPI-1 cells were grown to OD600nm of 2.0, overexpression of the different constructs was induced by the addition of 0.1% arabinose. After two minutes, a volume of 60OD of cell was harvested and chilled on ice for 5 minutes. To grow Salmonella under SPI-2-inducing conditions, 1 ml of Salmonella grown in LB to OD600nm2 was washed 2x in PBS and 1x in synthetic SPI-2 medium (Löber et al., 2006). The resulting pellet was resuspended in 1 mL of SPI-2 medium and diluted 1:50 in fresh, pre-warmed SPI-2 medium (10 mL total culture volume) in 100 mL Erlenmeyer flasks. The culture was grown at 37°C, 220 rpm until it reached an OD600nm of 0.3 (takes approximately 3 h).

extract_protocol:
Eluted RNA was extracted with phenol-chloroform (V/V) and precipitated by the addition of ethanol (2 vol) and ~15μg of glycogen (1μl of Glycoblue 15mg/ml). RNA samples were treated with DNase I (Fermentas) for 45 min at 37°C. DNase I was then removed using phenol- chloroform extraction and RNA was again precipitated.
The RNA samples were first fragmented using ultrasound (4 pulses of 30 s each at 4°C). Then, an oligonucleotide adapter was ligated to the 3' end of the RNA molecules. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase and the 3’ adapter as primer. The first-strand cDNA was purified and the 5' Illumina TruSeq sequencing adapter was ligated to the 3' end of the antisense cDNA. The resulting cDNA was PCR-amplified to about 10-20 ng/μl using a high fidelity DNA polymerase (11 cycles). The TruSeq barcode sequences which are part of the 5' TruSeq sequencing adapter are included in Table 2. The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and was analyzed by capillary electrophoresis. For Illumina NextSeq sequencing, the samples were pooled in approximately equimolar amounts. The cDNA pool in the size range of 200-550 bp was eluted from a preparative agarose gel. The cDNA pool was paired- end sequenced on an Illumina NextSeq 500 system using 2x50 bp read length.
library strategy: MAPS

treatment_protocol: Cells were centrifuged at 10000 g for 10 minutes and the pellets frozen in liquid nitrogen. After thawing on ice, the pellets were resuspended in 600 μl of chilled Buffer A (20 mM Tris pH8.0, 150 mM KCL, 1 mM of MgCl2, 1 mM DTT). A volume of 750 μl of glass beads was added to the cells and lysed using Retsch (10 min, 30 Hz) (adaptors were pre-chilled at -20°C). Next, lysate was cleared by centrifugation 10 min at 16000g at 4°C and the clear lysate was collected into a new tube. The in-vitro infections of iBMMs (M.O.I 50) was carried out following a previously published protocol (Westermann et al., 2016) with slight modifications. Briefly, two days before infection 2 × 105 iBMMs /mL were seeded in 10 ml complete DMEM (T75 flask). A total of 4 flaks of each cell type were infected with each Salmonella strain. Overnight cultures of Salmonella carrying either PinT (pYC55), MS2-PinT (pSS31) or MS2 (pSS32), were diluted 1:100 in fresh LB medium and grown aerobically to an OD600nm of 2. Bacterial cells were harvested by centrifugation (2 min at 12,000 r.p.m., room temperature) and resuspended in DMEM. In iBMMs infection, bacterial cells were opsonized with 10% mouse serum for 20 min, prior to addition to the cells. After 4h of infection, the mammalian cells where washed with ice cold PBS and lysed with a solution of PBS 0.1% Triton. The bacterial cells where separated from the host cells debris by centrifugation at 500g for 5 min. After, the supernatant containing the bacteria was centrifuged again at 10 000 g for 5 min, washed with PBS and frozen. After elution, the purified RNA was sequenced and mapped to the either the Mouse genome and to the Salmonella genome.  While the lysate is being prepared, affinity purification columns were prepared at the 4°C room. ~70 μl of amylose (New England Biolabs #E8021S) were added to 2mL Bio-Spin disposable chromatography columns (BioRad #732-6008). Amylose beads were washed three times with 2ml of Buffer A. 1ml of Buffer A with 250 pmol of MS2-MBP coat protein was added to the closed column followed incubation with rotation. After 5 minutes, the column was open and the MS2-coat protein was to run through the column and collected in a tube. This incubation step was repeated one more time until the lysate was ready. At this point, the solution was allowed to run and the column was washed once with 1ml of Buffer A.  The clear lysate was subjected to affinity chromatography (all the following steps were performed at 4 °C). Lysate was added to the closed column and incubated for 5 minutes with rotation. After the incubation, the lysate run was collected and the incubation step was repeated. Next, the column is washed 8 times with 2ml of Buffer A. Bound RNA was eluted using 300μl of Elution Buffer (Buffer A + 15 mM maltose). This step was repeated one more time.

tag: condition

tag: salmonella genetic background

value: Salmonella Typhimurium SL1344 {delta}pinT, MS2-PinT

tag: ms2/pint expression

value: MS2 expressed from the native pinT locus in the chromosomes (keeps PinT terminator)


title: Macrophages, IFNgamma stimulation, donor 3

description: Gene expression data from human macrophages stimulated with IFNgamma and cultured for 6 days on cell culture plastic

value: PBMC derived monocytes

value: IFN

value: ctrl


title: Macrophages, IFNgamma stimulation + polished Ti disc, donor 3

description: Gene expression data from human macrophages stimulated with IFNgamma and cultured for 6 days on polished titanium discs


title: TE79_NELF_K1_EtOH_0

description: EtOH treatment

value: TH1L (D5G6W) (NELFC)(rabbit, Cell Signaling, 12265S)


title: MRC-039NF [BDE-153 CUMULUS]

source_name: cumulus granulosa cells

value: HIGH


title: TE79_NELF_K1_OHT_10

description: 4-OHT treatment


title: TE79_MYC_K1_OHT_10

description: 4-OHT treatment

value: c-Myc (Y69)(rabbit, abcam, ab32072)


title: Macrophages, without stimulation, donor 3

value: NO


title: Macrophages, IL-4 stimulation, donor 3


title: Macrophages, IL-4 stimulation + polished Ti disc, donor 3

value: TI


title: WT_SPI-2

description:
MS2-affinity-purified RNA
PinT only control

value: Salmonella Typhimurium SL1344 WT

value: PinT expressed from native pinT locus in the chromosome


title: TE79_Input

description: merge of all inputs


title: MS2-PinT_SPI-2

description:
MS2-affinity-purified RNA
signal sample

value: Salmonella Typhimurium SL1344 MS2-PinT

value: MS2-PinT expressed from the native pinT locus in the chromosome


title: MS2_SPI-1_rep1

value: Salmonella Typhimurium SL1344 {delta}pinT pBAD-MS2

value: MS2 expressed from a pBAD promotor in a plasmid


title: TE79_Ser2_K1_OHT_10

description: 4-OHT treatment

value: osteosarcoma cell line

value: Anti RNA Pol2 phospho Ser2 (rabbit, abcam, ab5095)


title: MS2_SPI-1_rep2


title: Macrophages, without stimulation + polished Ti disc, donor 3


title: Macrophages, M2Cocktail stimulation + polished Ti disc, donor 4

source_name: Buffy coat, donor 4

value: Cocktail


title: Macrophages, M2Cocktail stimulation, donor 4

value: PBMC derived monocytes


title: TE79_CDC73_K1_OHT_10

description: 4-OHT treatment

value: Parafibromin (rabbit, bethyl laboratories, A300-171A)


title: MRC-029C [10-PBDE_CUMULUS]

description: SG11514161_257236311887_S001_GE1_1105_Oct12_2_4.txt


title: Macrophages, IFNgamma stimulation, donor 4

value: IFN

value: ctrl


title: TE79_MYC_K1_EtOH_0

description: EtOH treatment


title: TE79_CTR9_K1_EtOH_0

description: EtOH treatment

value: CTR9 (rabbit, bethyl laboratories, A301-395)


title: PinT_SPI-1_rep2

value: Salmonella Typhimurium SL1344 {delta}pinT pBAD-PinT

value: PinT expressed from a pBAD promotor in a plasmid


title: MS2-PinT_SPI-1_rep2

description:
MS2-affinity-purified RNA
signal sample

value: Salmonella Typhimurium SL1344 {delta}pinT pBAD-MS2-PinT

value: MS2-PinT expressed from a pBAD promotor in a plasmid


title: PinT_SPI-1_rep1


title: Macrophages, IFNgamma stimulation + polished Ti disc, donor 4

value: TI


title: leave48tt32 rep3

city: Cerdanyola del Vallès

first: Laura

last: Pérez-Martín

state: Barcelona

address: Cerdanyola del Vallès

department: Biologia animal biologia vegetal i ecologia

country: Spain

institute: Universitat Autònoma de Barcelona

data_processing:
Raw Illumina quality control  read  was performed using FASTQC software.
Each paired set of two fastq files were first processed and  Reads containing adaptor- or vector-derived sequences were removed using Trim Galore!
Cleaned reads together with the transcriptome of Arabidopsis thaliana were used to quantify gene expression at transcript level using the software Salmon. v0.9.1
Design Formula, Construction of the DESeq2 Object and Collapse of Technical Replicates. DESeq R package (1.18.0)
The resulting p-values were adjusted using the Benjamini and Hochberg’s approach [29] for controlling the false discovery rate (FDR). To perform a definitively list of DGEs, genes were filtered by  adj pvalue (adjusted p-value) <0.05 and LFC >1 and LFC <-1.
Genome_build: Arabidopsis thaliana reference transcriptome file used: Arabidopsis_thaliana.TAIR10.cdna.all.fa
Supplementary_files_format_and_content: Matrix table with clean and normalized  gene counts for every gene and every sample

organism: Arabidopsis thaliana

source_name: Leaves

growth_protocol: Selected seeds were surface sterilized by soaking in 70% (v/v) ethanol for 1 min, suspended in 30% (v/v) commercial Clorox bleach and 1 drop of Tween-20 for 5 min and rinsed 5 times in sterile 18 MΩmilli-Q water.Seeds were sown in 0.2 ml tubes containing 0.6 % agar prepared in nutrient solution 1/2 Hoagland, pH 5.9. Seeds were kept at 4 °C for 7 days in the dark to synchronize germination. After 10 days in the growth chamber (12h light/12h dark, 150 µmol cm−2·s−1, 40% humidity and 25 °C) the bottom of the tubes containing seedlings was cut off and the tubes were placed in 150 ml hydroponic content, containing aerated nutrient solution 1/2 Hoagland, pH 5.9. When 15 days old,  the seedlings were separated in different sets and the following  treatments were  applied.

extract_protocol:
Leaf material from plants cultivated under hydroponic conditions was recollected at 3 and 48 hours after initiating the treatments.Leaves were immersed in liquid nitrogen, homogenized to a fine powder, and stored at -80º C. The total RNA of 100 mg of leaf powder for each biological replicate was extracted using the Maxwell® plant RNA kit (Promega Corporation,WI, USA) following the manu-facturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-Seq. Library preparation was perform using Novogene protocol. Sequence reads: 150 bp-Illumina reads, paired-end, unstranded. Number of analyzed reads: 30-47 million pairs.

treatment_protocol: Treatments were applied in  15 day-old plants growing on hydroponics. Control (½ Hoagland solution at pH 5.9), high pH (½ Hoagland solution at pH 8.3), and bicarbonate (½ Hoagland solution at pH 8.3 and 10 mM NaHCO3). Solutions were buffered with different proportions of MES and BTP depending on final pH

value: Leaves

tag: age

value: 15 days

tag: genotype

value: Sensitive

value: Bic pH 8.3

tag: extraction time


title: MS2-PinT_SPI-1_rep1

description:
MS2-affinity-purified RNA
signal sample


title: TE33_Input_CTR9_merged

description: merge of input samples

growth_protocol: cells were grwon in DMEM for 72 h

extract_protocol:
crosslink (10 min), harvest, lysis of cells, fragment with sonifier
libraries were prepared for sequencing using standard NEB protocols

treatment_protocol: treatment with EtOH, or Dox for 48 h

tag: tissue

value: osteosarcoma cell line


title: TE79_CDC73_K1_EtOH_0

description: EtOH treatment


title: leave48tt32 rep2

tag: treatment


title: leave48tt31 rep2


title: TE79_A10_K1_EtOH_0

description: EtOH treatment

value: anti-Pol II (A-10)(mouse, Santa cruz, sc-17798)


title: Macrophages, without stimulation, donor 4

tag: donornr

value: NO

tag: titanium


title: Macrophages, IL-4 stimulation + polished Ti disc, donor 4

value: PBMC derived monocytes


title: TE79_CTR9_K1_OHT_10

description: 4-OHT treatment


title: TE33_CTR9_MYC_shCTR9_E_5

description: MYC transgene, shCTR9 not induced (EtOH)


title: leave48tt31 rep3


title: TE33_CTR9_MYC_shCTR9_D_6

description: MYC transgene, shCTR9 induced (Dox)


title: Macrophages, M2Cocktail stimulation, donor 5

source_name: Buffy coat, donor 5

value: Cocktail


title: Macrophages, without stimulation + polished Ti disc, donor 4


title: leave48tt31 rep1


title: Macrophages, IL-4 stimulation, donor 4


title: leave48at32 rep3

value: Tolerant


title: TE33_CTR9_MYC_shCDC73_E_2

description: MYC transgene, shCDC73 not induced (EtOH)


title: leave48at32 rep2


title: TE79_A10_K1_OHT_10

description: 4-OHT treatment


title: leave48tt32 rep1


title: Macrophages, IFNgamma stimulation + polished Ti disc, donor 5

value: IFN


title: Macrophages, M2Cocktail stimulation + polished Ti disc, donor 5


title: TE33_CTR9_empty_shCDC73_E_1

description: no MYC transgene, shCDC73 not induced (EtOH)

value: CTR9 (rabbit, bethyl laboratories, A301-395)


title: leave48at32 rep1


title: Macrophages, IFNgamma stimulation, donor 5

value: ctrl


title: Macrophages, IL-4 stimulation + polished Ti disc, donor 5

description: Gene expression data from human macrophages stimulated with IL-4 and cultured for 6 days on polished titanium discs


title: TE39_MYC_MYC_shCTR9_E_5

value: c-Myc (Y69)(rabbit, abcam, ab32072)


title: leave48at31 rep2


title: leave48at31 rep3


title: TE39_MYC_MYC_shCTR9_D_6

description: MYC transgene, shCTR9 induced (Dox)


title: Macrophages, IL-4 stimulation, donor 5

description: Gene expression data from human macrophages stimulated with IL-4 and cultured for 6 days on cell culture plastic


title: Macrophages, without stimulation, donor 5

description: Gene expression data from human unstimulated macrophages cultured for 6 days on cell culture plastic


title: TE39_MYC_MYC_shCDC73_E_2


title: leave48at31 rep1


title: Macrophages, without stimulation + polished Ti disc, donor 5


title: TE39_MYC_MYC_shCDC73_D_3

description: MYC transgene, shCDC73 induced (Dox)


title: TE33_CTR9_MYC_shCDC73_D_3

description: MYC transgene, shCDC73 induced (Dox)


title: TE33_CTR9_empty_shCTR9_E_4

description: no Myc transgene, shCTR9 not induced (EtOH)


title: Macrophages, M2Cocktail stimulation + polished Ti disc, donor 6

description: Gene expression data from human macrophages stimulated with M2Cocktail and cultured for 6 days on polished titanium discs

source_name: Buffy coat, donor 6


title: TE39_MYC_empty_shCTR9_E_4


title: Macrophages, M2Cocktail stimulation, donor 6


title: Macrophages, IFNgamma stimulation + polished Ti disc, donor 6


title: leave48tt22 rep1

value: High pH 8.3


title: TE39_Input_MM_merged_MYC

description: merge of input samples


title: leave48tt22 rep2


title: leave48tt22 rep3


title: leave48tt21 rep2


title: TE81_Input_merged_MYC

description: merge of input samples


title: Macrophages, IL-4 stimulation + polished Ti disc, donor 6


title: Macrophages, IFNgamma stimulation, donor 6


title: Macrophages, IL-4 stimulation, donor 6


title: TE81_CDC73_MYC_shCTR9_E_5_MYC

value: Parafibromin (rabbit, bethyl laboratories, A300-171A)


title: Macrophages, without stimulation, donor 6


title: leave48tt21 rep1


title: leave48at22 rep3


title: leave48at22 rep2


title: TE81_CDC73_MYC_shCDC73_E_2_MYC


title: Macrophages, without stimulation + polished Ti disc, donor 6

description: Gene expression data from human unstimulated macrophages cultured for 6 days on polished titanium discs

value: TI


title: Macrophages, M2Cocktail stimulation + polished Ti disc, donor 8

source_name: Buffy coat, donor 8


title: TE39_MYC_empty_shCDC73_E_1


title: Macrophages, M2Cocktail stimulation, donor 8


title: TE81_CDC73_MYC_shCDC73_D_3_MYC

description: MYC transgene, shCDC73 induced (Dox)


title: leave48at21 rep1

value: Leaves


title: TE81_CDC73_empty_shCDC73_E_1_MYC


title: RNA complexed with MS2 - sample 3 (control)

tag: strain

tag: ms2 tag


title: TE41_Ser2_MYC_shCDC73_E_2_MYC

value: Anti RNA Pol2 phospho Ser2 (rabbit, abcam, ab5095)


title: TE81_CDC73_empty_shCTR9_E_4_MYC


title: leave48at21 rep3

value: 15 days


title: leave48at21 rep2


title: leave48tt12 rep3

value: Sensitive

value: Control pH 5.9


title: leave48tt12 rep2


title: Macrophages, IL-4 stimulation + polished Ti disc, donor 8


title: leave48tt12 rep1


title: Macrophages, IFNgamma stimulation, donor 8


title: TE81_CDC73_MYC_shCTR9_D_6_MYC

description: MYC transgene, shCTR9 induced (Dox)

value: osteosarcoma cell line


title: Macrophages, IFNgamma stimulation + polished Ti disc, donor 8


title: TE41_Ser2_MYC_shCDC73_D_3_MYC

description: MYC transgene, shCDC73 induced (Dox)


title: Macrophages, without stimulation, donor 8

value: NO


title: leave48tt11 rep3


title: mixed sample (non-demultiplexed); Male and Female

city: San Francisco

first: Stephanie

middle: A

last: Redmond

state: CA

address: 35 Medical Center Way, 933D Box 0525

department: Neurosurgery

institute: University of California San Francisco

data_processing:
Replicate 1 consists of the ‘G1; mRNA and ‘TGACCAAT’ barcode libraries. Replicate 2 consists of the ‘G2’ mRNA library and the ‘ACAGTGAT’ barcode libraries.
Reads were aligned using CellRanger 3.0.2-v3.2.0 (10x Genomics) using standard parameters
Seurat version 3 was used to analyze data
Low-quality cells were filtered out of the dataset: percentage mitochondrial genes >10%, nCount <5th or >95th percentiles, nFeatures <5th percentile
Cells with more than one detected MULTI-Seq barcode were considered doublets and removed from the analysis.
Genome_build: GRCm38
Supplementary_files_format_and_content: Seurat 3 Data Object rds file of all biological samples and technical replicates
Supplementary_files_format_and_content: CellRanger filtered output: sparse UMI matrix mtx file with features (rows) and cells (columns)
Supplementary_files_format_and_content: Cell Ranger filtered output: cell barcodes in tsv file
Supplementary_files_format_and_content: Cell Ranger filtered output: features/genes in tsv file

organism: Mus musculus

source_name: Micro dissected ventricular-subventricular zone

extract_protocol:
The V-SVZs were microdissected and mechanically dissociated into single cells after papain digestion. Cells from each sample were labeled with a MULTI-Seq barcode and combined together. Myelin was removed using Myelin Removal Beads (130-096-733, Miltenyi Biotec). The cells were incubated with TotalSeq antibodies against mouse VCAM1 and CD24 (Biolegend), washed, filtered and counted.
Genomic mRNA libraries were prepared according to 10x Genomics 3’ version 3 chemistry & Illumina protocols. MULTI-Seq & TotalSeq barcode libraries were prepared according to MULTI-Seq (McGinnis et al. 2019) and Illumina protocols.

value: hGFAP::GFP (FVB/N-Tg(GFAPGFP)14Mes/J, The Jackson Laboratory (003257))

value: Ventricular-subventricular zone (brain)

value: Postnatal day 35 and Postnatal day 29

tag: mixed

value: mixed sample (non-demultiplexed)


title: Macrophages, without stimulation + polished Ti disc, donor 8

value: PBMC derived monocytes


title: TE41_Ser2_empty_shCTR9_E_4_MYC


title: leave48tt11 rep2


title: CUT&Tag BSA condition 3

city: Stockholm

first: Marek

last: Bartosovic

address: Solnavagen 9

country: Sweden

institute: Karolinska Institute

data_processing:
Library strategy: CUT&Tag
Adapters were trimmed using trim galore
Reads were mapped to genome using bowtie2
PCR duplicates were removed using picard
bigwig files were generated using deepTools bamCoverage
Genome_build: mm10

source_name: Oli-neu

growth_protocol: Brain was dissociated using Miltenyi neural tissue dissociation kit P (130-092-628), and primary mouse OPCs extracted using CD140a MicroBead kit (Miltenyi Biotec, 130-101-502); Oli-neu cells were cultured in DMEM medium (Gibco, 41966029) supplemented with 1x N2 supplement (ThermoFisher, 17502001), 1x penicilin/streptomycin/glutamine (Gibco, 10378016), 340ng/ml T3 (Sigma, T6397), 400ng/ml T4 (Sigma, 89430), 10ng/ml bFGF (R&D, 233-FB), 1ng/ml Pdgf-BB (R&D, 520-BB) and 0.5% FBS (Gibco, 10500064)

extract_protocol:
CUT&run was performed according to https://dx.doi.org/10.17504/protocols.io.zcpf2vn ; Cut&tag was performed according to https://dx.doi.org/10.17504/protocols.io.bcuhiwt6 Briefly, fresh nuclei were incubater with primary, secondary antibody, then proteinA-Tn5 fusion and Tn5 was activated by Mg2+. Nuclei were lysed using SDS and proteinase K, DNA extracted using Zymo DNA clean&concentrator-5 kit, and eluted DNA used as input to PCR with sample-specific barcoded primers.
Cut&run libraries were prepared using Kapa hyper prep kiy (Kapa biosystems, 7962363001); CUT&Tag libraries were prepared by tagmentation

value: Cell line

value: WT

tag: antibody

tag: 2nd antibody

value: Guinea pig anti-rabbit (Novus Biologicals, NBP1-72763)

tag: enzyme

value: In house produced pA-Tn5


title: TE41_Ser2_MYC_shCTR9_D_6_MYC

description: MYC transgene, shCTR9 induced (Dox)

tag: cell line

tag: chip antibody


title: TE41_Ser2_MYC_shCTR9_E_5_MYC


title: TE41_Ser2_empty_shCDC73_E_1_MYC


title: leave48at22 rep1

value: Tolerant

value: High pH 8.3


title: CUT&Tag BSA condition 4


title: leave48tt11 rep1

value: Leaves


title: TE41_Input_Ser2_merged_MYC

description: merge of input samples


title: Macrophages, IL-4 stimulation, donor 8

value: ctrl


title: leave48at12 rep3

value: 15 days


title: leave48at12 rep1

value: Control pH 5.9


title: TE41_Input_A10_merged_MYC

description: merge of input samples

value: osteosarcoma cell line


title: CUT&Tag BSA condition 1


title: TE41_A10_MYC_shCTR9_E_5_MYC

value: anti-Pol II (A-10)(mouse, Santa cruz, sc-17798)


title: leave48at12 rep2


title: TE41_A10_MYC_shCTR9_D_6_MYC

description: MYC transgene, shCTR9 induced (Dox)


title: CUT&Run H3K27me3 OPCs

data_processing:
Library strategy: CUT&RUN
Adapters were trimmed using trim galore
Reads were mapped to genome using bowtie2
PCR duplicates were removed using picard
bigwig files were generated using deepTools bamCoverage
Genome_build: mm10

source_name: OPC

value: H3K27me3 (Cell Signaling, 9733T)

value: In house produced pA-MNAse


title: scC&T H3K27me3 cell lines mixture v1.1

description:
cluster_3T3.bw
cluster_mESC_1.bw
cluster_mESC_2.bw
cluster_Oli-neu_1.bw
cluster_Oli-neu_2.bw
fragments.tsv.gz
H3K27me3_cell_lines_seurat_object.Rds
H3K27me3_cell_lines_matrix.h5

data_processing:
Library strategy: CUT&TAG
Fastq files were processed using cellranger-ATAC v1.2.0
Cellranger-ATAC was loaded into seurat object and cell by bin matrix was generated
Cells were filtered based on number of reads and fraction of reads coming from peak reagions called on bulk data
Reduction of dimensionality was done using package Signac's LSI and UMAP
Genome_build: mm10
Supplementary_files_format_and_content: Rds files containing Seurat object that can be loaded into R using `object <- readRDS(path)` function. Seurat object contain multiple assays and UMAP/LSI embeddings used in the paper. BigWig files merged per cluster.

source_name: Cell lines (3T3, mESC, Oli-neu)

growth_protocol: Brain was dissociated using Miltenyi neural tissue dissociation kit P (130-092-628), cleared with Debris removal solution (130-109-398), filtered through 50 um strainer and FACS sorted for GFP+/GFP- on FACS Aria III or FACS Aria Fusion

extract_protocol:
Nuclei were extracted using NP-40 / Digitonin buffer
Single Cell Cut&Tag was performed with 1:50 diluted primary and secondary antibody and 1:100 diluted in house produced proteinA-Tn5
Tagmented nuclei were processed using the 10x scATAC-seq kit according to manufactureres instructions skipping Step 1 "Transposition" and continuing from Step 2.0 "Generation and barcoding".

tag: c&t antibody

value: Cell signaling 9733T

value: Novus Biologicals NBP1-72763

value: In House pA-Tn5; 1:100


title: TE41_A10_MYC_shCDC73_D_3_MYC

description: MYC transgene, shCDC73 induced (Dox)


title: CUT&Run H3K27me3 Oli-neu

value: Cell line


title: TE41_A10_MYC_shCDC73_E_2_MYC


title: leave48at11 rep3


title: scRNA_seq 2

data_processing:
Fastq files were processed using cellranger 3.0.2
Only cells with GFP reads were considered
h5 matrices from cellranger are provided as
Genome_build: mm10
Supplementary_files_format_and_content: raw h5 matrices with counts; csv with cells metadata after filtering

source_name: P21 Brain

extract_protocol: scRNA-seq library was constructed using 10x chromium 3' gene expression kit v3

value: Sox10:Cre RCE+


title: TE41_A10_empty_shCDC73_E_1_MYC


title: leave48at11 rep1


title: scRNA_seq 1


title: leave3tt32 rep3

value: Sensitive

value: Bic pH 8.3


title: leave48at11 rep2

value: Tolerant


title: leave3tt32 rep1


title: scC&T H3K27me3 cell lines mixture v1


title: CUT&Tag BSA condition 2

value: WT

value: Guinea pig anti-rabbit (Novus Biologicals, NBP1-72763)

value: In house produced pA-Tn5


title: TE41_A10_empty_shCTR9_E_4_MYC


title: leave3tt32 rep2

value: Leaves

value: 15 days


title: U2OS_TE84_MYC_W11_E_shCTR9_5

growth_protocol: cells infected with pGIPZ shCDC73 or shCTR9, split and selected with puromycin

extract_protocol:
crosslink (5 min), harvest, spike in with 10% of NIH-3T3 cells, lysis of cells, fragment with covaris
libraries were prepared for sequencing using standard NEB protocols

treatment_protocol: treat with EtOH for 24 h (no MYC induction)

value: osteosarcoma cell line

value: c-Myc (Y69)(rabbit, abcam, ab32072)


title: U2OS_TE84_MYC_W11_E_NTC_1


title: U2OS_TE84_MYC_W11_E_shCDC73_3


title: P17103_1003

description: replicate 2

data_processing:
Fastq files were aligned to the mm10 genome and filtered for duplcate reads using the HiC-Pro pipeline
allValidPairs files from the HiC-Pro pipeline for each replicate were merged together
hicpro2juicebox.sh from HiC-Pro was used on the merged allValidPairs file to generate the .hic file
Genome_build: mm10
Supplementary_files_format_and_content: Juicebox compatible .hic files, contains contact matrices at multiple resolutions

source_name: Mouse brain

growth_protocol: Cells were cultured in OPC proliferation medium (DMEM/Glutamax, 1xN2 supplement, 1x Penicilin-streptomycin, 1x NeuroBrew, 20ng/mL bFGF, 20ng/mL mPDGF-AA)

extract_protocol:
Cells were harvested using TrypLE and fixed with 1% formaldehyde prior to processing for HiChIP
Libraries were prepared as specified in Mumbach et.al. (2016) and with 0.75uL Tn5 enzyme.
Samples were sequenced on a single-lane of an SP flowcell on the NovaSeq6000 with the 2x50bp read setup

value: Abcam Ab177178

value: In-house Tn5


title: P17103_1001

description: replicate 1


title: P17103_1005

description: replicate 3


title: leave3tt31 rep3


title: TE80_Input

description: merge of all inputs

source_name: lymphoblast from bone marrow

growth_protocol: cells were grown in RPMI 1640 + L-Glutamine (4mM).  6h before treatment cells were 0.6 mio/ml diluted.

extract_protocol:
crosslink 5 min), harvest, 10% of NIH 3T3 spike in, lysis of cells, fragment with covaris
libraries were prepared for sequencing using standard NEB protocols

treatment_protocol: treat with DMSO or IAA (100 uM) for 30 min

value: lymphoblast from bone marrow

value: Parafibromin (rabbit, bethyl laboratories, A300-171A)


title: leave3tt31 rep2


title: leave3tt31 rep1


title: U2OS_TE84_Input_W11_E_merged


title: scC&T Olig2 brain P25 GFP pos rep2

description:
Olig2_fragments.tsv.gz
Olig2_non_oligo.bw
Olig2_oligo.bw
Olig2_seurat_object.Rds
Olig2_matrix.h5

value: brain

value: Novus Biologicals NBP1-28667

value: Novus Biologicals NBP1-72763

value: In House pA-Tn5; 1:100


title: leave3at32 rep2

value: Bic pH 8.3


title: TE80_CDC73_D10_IAA_4

description: IAA treatment


title: leave3at32 rep3

value: Tolerant


title: scC&T Rad21 brain P25 GFP pos

description:
Rad21_fragments.tsv.gz
Rad21_Astrocytes.bw
Rad21_mOL.bw
Rad21_OEC.bw
Rad21_seurat_object.Rds
Rad21_matrix.h5

value: Genetex GTX106012


title: scC&T Olig2 brain P25 GFP pos rep1


title: scC&T H3K36me3 brain P25 GFP pos rep2

description:
H3K36me3_fragments.tsv.gz
H3K36me3_Astrocytes.bw
H3K36me3_mOL.bw
H3K36me3_OEC.bw
H3K36me3_OPC.bw
H3K36me3_seurat_object.Rds
H3K36me3_matrix.h5

value: Abcam Ab9050


title: leave3at32 rep1


title: TE80_CDC73_C3_IAA_1

description: IAA treatment


title: scC&T H3K36me3 brain P25 GFP pos rep1


title: TE80_CDC73_D10_DMSO_5

description: DMSO treatment


title: leave3at31 rep3


title: scC&T H3K27ac brain P25 GFP pos rep2

description:
H3K27ac_fragments.tsv.gz
OLIGO_ABC_EP_predictions_H3K4me3_filter.bedpe
OLIGO_ABC_EP_predictions_H3K4me3_Rad21_doublefilter.bedpe
OLIGO_ABC_EP_predictions_unfiltered.bedpe
H3K27ac_Astrocytes.bw
H3K27ac_mOL.bw
H3K27ac_OEC.bw
H3K27ac_OPC.bw
H3K27ac_VLMC.bw
cluster_Astrocytes.bedpe
cluster_mOL.bedpe
cluster_OEC.bedpe
cluster_OPC.bedpe
cluster_VLMC.bedpe
H3K27ac_seurat_object.Rds
H3K27ac_matrix.h5


title: leave3at31 rep2


title: TE80_A10_D10_IAA_4

description: IAA treatment

value: anti-Pol II (A-10)(mouse, Santa cruz, sc-17798)


title: TE80_CDC73_C3_DMSO_2

description: DMSO treatment


title: scC&T H3K27ac brain P25 GFP pos rep1


title: leave3at31 rep1

value: Leaves


title: scC&T H3K27me3 brain P15 GFP neg

description:
H3K27me3_fragments.tsv.gz
H3K27me3_Astrocytes.bw
H3K27me3_Microglia.bw
H3K27me3_mOL.bw
H3K27me3_Neurons_1.bw
H3K27me3_Neurons_3.bw
H3K27me3_OEC.bw
H3K27me3_OPC.bw
H3K27me3_VLMC.bw
H3K27me3_seurat_object.Rds
H3K27me3_matrix.h5

value: Cell signaling 9733T


title: leave3tt22 rep3

value: 15 days

value: Sensitive

value: High pH 8.3


title: TE80_A10_D10_DMSO_5

description: DMSO treatment


title: scC&T H3K27me3 brain P15 GFP pos


title: U2OS H2B_BI8626

description: Treated with Doxycyclin and BI8626

data_processing:
Base calling perfomed using Illumina's FASTQ Generation software v1.0.0
ChIPseq reads were aligned with Bowtie1 to hg19 and to mm10 for the spike-in
Input of different conditions was merged
human reads were normalized to the number of spike-in reads; Experiment H2Bubi_rep1 was readnormalized
metagenes were established with ngs.plot.r v2.63
read distribution was determined with betdools intersect v2.26.0, either over specified regions or over the whole genome in 100-nt-bins
Genome_build: hg19, mm10
Supplementary_files_format_and_content: begraph files were generated with bedtools genomecov

growth_protocol: U2OS cells expressing doxycycline-inducible MYC

extract_protocol:
crosslink (5 min), harvest, spike-in with 10 % NIH-3T3, lysis of cells, fragment with covaris
libraries were prepared for sequencing using standard NEB protocols

treatment_protocol: Treated with/without doxycycline for 24 hrs and with or without BI8626 for 4 hrs

value: osteosarcoma cell line

value: Anti-Histone H2B (Abcam ab1790)


title: scC&T H3K27me3 brain P25 GFP pos rep2


title: leave3tt22 rep2


title: U2OS H2B_DMSO

description: Treated with Doxycyclin and DMSO


title: leave3tt21 rep3


title: U2OS Input_H2B

description: Merge of all Conditions used for H2B- & H2Bubi ChIP


title: U2OS H2Bubi_BI8626

description: Treated with Doxycyclin and BI8626

value: Ubiquityl-Histone H2B (Cell Signlaing 5546S)


title: leave3tt22 rep1


title: leave48tt21 rep3


title: leave3tt21 rep1


title: scC&T H3K27me3 brain P25 GFP pos rep1

value: brain


title: leave3tt21 rep2


title: U2OS H2Bubi_Dox_BI8626_rep1

description: Treated with Doxycyclin and BI8626


title: scC&T H3K4me3 brain P15 GFP neg

description:
H3K4me3_fragments.tsv.gz
H3K4me3_Astrocytes.bw
H3K4me3_Microglia.bw
H3K4me3_mOL.bw
H3K4me3_Neurons_1.bw
H3K4me3_Neurons_2.bw
H3K4me3_Neurons_3.bw
H3K4me3_OEC.bw
H3K4me3_OPC.bw
H3K4me3_VLMC.bw
H3K4me3_seurat_object.Rds
H3K4me3_matrix.h5

value: Diagenode C15410030


title: leave3at22 rep3


title: scC&T H3K4me3 brain P25 GFP pos rep2

value: Novus Biologicals NBP1-72763


title: U2OS H2Bubi_Dox_DMSO_rep1

description: Treated with Doxycyclin and DMSO


title: scC&T H3K4me3 brain P25 GFP pos rep1

value: In House pA-Tn5; 1:100


title: SJMMNORM055351_G1 RNAseq

city: Memphis

first: Chunxu

last: Qu

state: TN

address: 262 Danny Thomas Pl

department: Pathology

institute: St Jude Children's Research Institute

data_processing:
Basecalls performed using bcl2fastq version v2.19.0.316
Sequencing reads was mapped to mouse genome mm9 using STAR (version 2.5.3a) through the standard two-pass mapping pipeline.
Gene expression was quantified using RSEM (v1.3.0) against Ensemble gene annotation (v67)
Genome_build: mm9
Supplementary_files_format_and_content: RSEM-counts.txt, RSEM-FPKM.txt, RSEM-TPM.txt generated using RSEM

source_name: lin- HSPC untransduced

extract_protocol:
Leukemic spleen samples were flow sorted for GFP and RFP double positive expression. Germline samples were from lin- HSPC untransduced. RNA was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols
total stranded RNAseq

tag: primary mouse id

tag: passage

value: Normal

value: control


title: SJMMNORM055350_G1 RNAseq

tag: genotype


title: leave3at22 rep1

tag: age

value: Tolerant

tag: extraction time


title: leave3at21 rep3

tag: tissue

tag: treatment


title: SJMMNORM049654_G1 RNAseq


title: U2OS Input_H2Bubi_rep1

description: Merge of all Conditions used for H2B- & H2Bubi ChIP in repeat 1


title: U2OS H2Bubi_DMSO

description: Treated with Doxycyclin and DMSO


title: U2OS MYC EtOH BI8626

description: Treated with Ethanol and BI8626

value: anti-MYC (ab32072)


title: SJMMNORM049653_G1 RNAseq


title: leave3at21 rep1


title: leave3tt12 rep3

value: Control pH 5.9


title: U2OS MYC Dox DMSO

description: Treated with Doxycyclin and DMSO


title: scC&T H3K4me3 brain P15 GFP pos


title: leave3at21 rep2

value: Leaves


title: SJMMAEL060187_D1 RNAseq

source_name: spleen

value: Secondary

value: NUP98-HOXA9 fusion


title: leave3at22 rep2

value: 15 days


title: leave3tt12 rep2

value: Sensitive


title: leave3tt12 rep1


title: leave3tt11 rep3


title: SJMMAEL060185_D1 RNAseq

value: Primary


title: U2OS MYC EtOH DMSO

description: Treated with Ethanol and DMSO

source_name: osteosarcoma cell line

value: osteosarcoma cell line


title: U2OS CTR9 Dox BI8626

description: Treated with Doxycyclin and BI8626


title: SJMMAEL060184_D1 RNAseq


title: U2OS H2Bubi_EtOH_DMSO_rep1

description: Treated with Ethanol and DMSO

value: Ubiquityl-Histone H2B (Cell Signlaing 5546S)


title: U2OS H2Bubi_EtOH_BI8626_rep1

description: Treated with Ethanol and BI8626


title: U2OS CTR9 Dox DMSO

description: Treated with Doxycyclin and DMSO


title: leave3tt11 rep2


title: SJMMAEL060180_D1 RNAseq

value: Tertiary


title: SJMMNORM049906_G1 RNAseq


title: SJMMAEL060183_G1 RNAseq


title: U2OS CTR9 EtOH DMSO

description: Treated with Ethanol and DMSO


title: SJMMAEL060173_D1 RNAseq


title: leave3at12 rep2


title: leave3at12 rep1


title: SJMMAEL060168_D1 RNAseq


title: U2OS Pol2-pS2 Dox DMSO

description: Treated with Doxycyclin and DMSO

value: anti-Pol II pS2 (ab5095)


title: U2OS Pol2-pS2 Dox BI8626

description: Treated with Doxycyclin and BI8626


title: U2OS Pol2-pS2 EtOH BI8626

description: Treated with Ethanol and BI8626


title: SJMMAEL060167_D1 RNAseq


title: SJMMAEL060171_D1 RNAseq


title: U2OS CTR9 EtOH BI8626

description: Treated with Ethanol and BI8626


title: leave3at11 rep2


title: SJMMAEL058595_D1 RNAseq


title: leave3at11 rep1


title: SJMMAEL060166_D1 RNAseq


title: U2OS Pol2-A10 Dox BI8626

description: Treated with Doxycyclin and BI8626

value: anti-Pol II (sc-17798)


title: leave3at11 rep3


title: leave3tt11 rep1


title: U2OS Pol2-pS2 EtOH DMSO

description: Treated with Ethanol and DMSO


title: PD

data_processing:
Reads were aligned using CellRanger 2.1.0-2.3.0 (AV, AD, PD samples); 3.0.2-v3.2.0 (PV sample) (10x Genomics) using standard parameters
Seurat version 3 was used to analyze data
Low-quality cells were filtered out of the dataset: percentage mitochondrial genes >10%, nCount <5th or >95th percentiles, nFeatures <5th percentile
Genome_build: GRCm38
Supplementary_files_format_and_content: Seurat 3 Data Object rds file of all biological samples and technical replicates
Supplementary_files_format_and_content: CellRanger filtered output: sparse UMI matrix mtx file with features (rows) and cells (columns)
Supplementary_files_format_and_content: Cell Ranger filtered output: cell barcodes in tsv file
Supplementary_files_format_and_content: Cell Ranger filtered output: features/genes in tsv file

molecule: polyA RNA

extract_protocol:
The V-SVZs were microdissected and mechanically dissociated into single nuclei using a tissue douncer. Cell debris were removed using ultacentrifugation on a sucrose cushion. The nuclei were washed, filtered and counted.
Genomic mRNA libraries were prepared according to 10x Genomics 3’ version 2 chemistry & Illumina protocols.

value: CD1-elite (Charles River)

value: Ventricular-subventricular zone (brain)

value: Postnatal day 35


title: PV


title: SJMMAEL058593_D1 RNAseq


title: SJMMAEL058594_D1 RNAseq


title: U2OS Pol2-A10 Dox DMSO

description: Treated with Doxycyclin and DMSO


title: U2OS Pol2-A10 EtOH DMSO

description: Treated with Ethanol and DMSO


title: SJMMAEL058591_D1 RNAseq


title: leave3at12 rep3

value: Tolerant


title: U2OS MYC Dox BI8626

description: Treated with Doxycyclin and BI8626

value: anti-MYC (ab32072)


title: AD


title: U2OS Pol2-A10 EtOH BI8626

description: Treated with Ethanol and BI8626


title: SJMMAEL058590_D1 RNAseq


title: U2OS Input

description: Merge of all Conditions used for anti-Ser2, -CTR9, -Myc ChIP


title: SJMMAEL058587_D1 RNAseq


title: SJMMAEL058588_D1 RNAseq


title: BLISS_U2OS_Etoposide_Rep3_A3

description: Treated with Etoposide and Doxycyclin

data_processing:
Base calling perfomed using Illumina's FASTQ Generation software v1.0.0
reads were demultiplexed according to sample-barcode with UMI-tools v1.0.1
barcodes used as following: A1: CATCACGC, A2: GTCGTTCC, A3: TGATGATC, A5: CATCATCC, A6: ACGACCGC
reads were aligned with Bowtie2 v2.3.4.1 to hg19
reads were filtered with bedtools intersect v2.26.0
bedgraph-files were readnormalized among the three replicates in the BLISS Etoposide experiment
reads were counted for specific regions using the R package exomeCopy v1.18.0
density plots were generated using the R package metagene2 v3.10
Genome_build: hg19
Supplementary_files_format_and_content: begraph files were generated with bedtools genomecov

treatment_protocol: Treated with/without doxycycline for 24 hrs and with or without Etoposide for 3 hrs


title: BLISS_U2OS_Etoposide_Rep3_A2

description: Treated with Etoposide


title: SJMMNORM055350_G1 Methylseq

data_processing:
Basecalls performed using bcl2fastq version v2.19.0.316
Paired end bisulfite sequencing data were trimmed using trimgalore (version 0.4.4) (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove standard Illumina paired-end adaptors.
Trimmed data were aligned to the mouse genome mm9 using Bismark (version 0.14.5) with default settings and deduplicated using a Bismark perl script.
Genome_build: mm9
Supplementary_files_format_and_content: RSEM-counts.txt, RSEM-FPKM.txt, RSEM-TPM.txt generated using RSEM

extract_protocol:
Leukemic spleen samples were flow sorted for GFP and RFP double positive expression. Germline samples were from lin- HSPCs untransduced. DNA extraction was performed using the AllPrep DNA/RNA Mini Kit (Qiagen) as described in the manufacturer’s protocol.
Mouse methylation specific genomic libraries were generated using the SureSelectXT Methyl-Seq kit specific for the Illumina HiSeq instrument (Catalog No. G9651A; Agilent Technologies, Santa Clara, CA), followed by exome enrichment using the SureSelectXT Mouse Methyl-Seq target enrichment bait set (Catalog No. 931052).  The resulting methylation enriched libraries were then sequenced by the Genome Sequencing Facility.

value: lin- HSPC untransduced

value: Normal

value: control


title: SJMMNORM055351_G1 Methylseq


title: SJMMAEL058586_D1 RNAseq

value: Secondary


title: SJMMNORM049906_G1 Methylseq


title: SJMMAEL058584_D1 RNAseq


title: BLISS_U2OS_Etoposide_Rep2_A3

description: Treated with Etoposide and Doxycyclin


title: SJMMAEL058581_D1 RNAseq


title: BLISS_U2OS_Etoposide_Rep2_A2

description: Treated with Etoposide


title: SJMMNORM049654_G1 Methylseq


title: SJMMNORM049653_G1 Methylseq


title: SJMMAEL058579_D1 RNAseq


title: SJMMAEL060187_D1 Methylseq

value: spleen

value: NUP98-HOXA9 fusion


title: SJMMAEL060183_G1 Methylseq


title: BLISS_U2OS_Etoposide_Rep2_A1

description: Treated with Ethanol


title: U2OS Input_A10

description: Merge of all Conditions used for anti-Pol II ChIP


title: BLISS_U2OS_Etoposide_Rep1_A3

description: Treated with Etoposide and Doxycyclin


title: SJMMAEL058578_D1 RNAseq


title: SJMMAEL060180_D1 Methylseq


title: SJMMAEL058576_D1 RNAseq

value: Primary


title: AV


title: BLISS_U2OS_Etoposide_Rep1_A2

description: Treated with Etoposide

value: osteosarcoma cell line


title: BLISS_U2OS_Etoposide_Rep1_A1

description: Treated with Ethanol


title: SJMMAEL060173_D1 Methylseq


title: SJMMAEL058575_D1 RNAseq


title: U2OS, EtOH, pGIPZ, shNTC, Replicate4

data_processing:
Base calling perfomed using Illumina's FASTQ Generation software v1.0.0
RNAseq reads were aligned with bowtie1
reads were counted using the “summarizeOverlaps” function from the R package “GenomicAlignments"
differentially expressed genes were called with edgeR
differential exon usage was determined with DEXseq after mapping with hisat2
gene set enrichment analysis was carried out with GSEA and the MSigDB gene sets Hallmarks, C2, C5
Genome_build: hg19
Supplementary_files_format_and_content: count files were generated with edgeR

extract_protocol:
RNA was isolated using RLT containing beta-mercaptoethanol buffer from Qiagen
RNA libraries were prepared for sequencing using standard NEB protocols

treatment_protocol: treat with EtOH, or Dox for 24 h


title: SJMMAEL060168_D1 Methylseq


title: SJMMAEL058573_D1 RNAseq


title: SJMMAEL060171_D1 Methylseq


title: U2OS, EtOH, pGIPZ, shNTC, Replicate3


title: SJMMAEL060167_D1 Methylseq


title: SJMMAEL058574_D1 RNAseq


title: SJMMAEL058582_D1 RNAseq

value: Dnmt3a;Tet2; Asxl1


title: U2OS, EtOH, pGIPZ, shNTC, Replicate2


title: SJMMAEL058595_D1 Methylseq


title: SJMMAEL060166_D1 Methylseq


title: SJMMAEL058570_D1 RNAseq


title: U2OS, EtOH, pGIPZ, shNTC, Replicate1


title: SJMMAEL058594_D1 Methylseq


title: U2OS, EtOH, pGIPZ shCTR9#5, Replicate4


title: SJMMAEL058593_D1 Methylseq


title: SJMMAEL055370_D1 RNAseq


title: SJMMAEL055369_D1 RNAseq


title: SJMMAEL058591_D1 Methylseq


title: SJMMAEL055367_D1 RNAseq

value: Bcor;Trp53; Asxl1; Ppm1d


title: SJMMAEL055366_D1 RNAseq


title: U2OS, EtOH, pGIPZ shCTR9#5, Replicate2


title: U2OS, EtOH, pGIPZ shCTR9#5, Replicate1


title: SJMMAEL058586_D1 Methylseq


title: SJMMAEL058584_D1 Methylseq


title: SJMMAEL058571_D1 RNAseq


title: SJMMAEL055362_D1 RNAseq

value: Bcor;Trp53; Asxl1; Ezh2; Ppm1d; Tet2


title: U2OS, EtOH, pGIPZ shCTR9#3, Replicate3


title: SJMMAEL058582_D1 Methylseq


title: SJMMAEL058581_D1 Methylseq


title: U2OS, EtOH, pGIPZ shCTR9#3, Replicate1


title: SJMMAEL055357_D1 RNAseq


title: U2OS, EtOH, pGIPZ shCTR9#3, Replicate2


title: BLISS_U2OS_Etoposide_Rep3_A1

description: Treated with Ethanol

extract_protocol:
blunting of DSB, adapter ligation, DNA purification and fragmentation, in vitro transcription, fragmentation
libraries were prepared for sequencing using a modified NEBNext Small RNA library preperation protocol


title: SJMMAEL058579_D1 Methylseq


title: SJMMAEL055371_D1 RNAseq


title: U2OS, EtOH, pGIPZ shCDC73#4, Replicate4


title: SJMMAEL058576_D1 Methylseq


title: U2OS, EtOH, pGIPZ shCTR9#5, Replicate3


title: U2OS, EtOH, pGIPZ shCDC73#4, Replicate3


title: SJMMAEL055355_D1 RNAseq


title: SJMMAEL055356_D1 RNAseq


title: SJMMAEL058574_D1 Methylseq


title: ChIP-seq LAPC4 WCE EtOH rep2

city: Quebec

first: Steve

last: Bilodeau

address: 2260 boul. Henri-Bourassa

institute: Centre de recherche du CHU de Québec-Université Laval

data_processing:
Analysis of raw sequencing reads was performed using the ChIP-Seq pipeline developed at the McGill University and Génome Québec Innovation Centre (version 3.1.5).
Reads were trimmed using Trimmomatic 0.36 with the following parameters: TRAILING=30, MINLEN=50.
High-quality reads were aligned to the human reference genome (hg38) with BWA aligner (version 0.7.12).
PCR duplicates were removed with picard MarkDuplicates (version 2.0.1).
Narrow peaks were called using MACS2 callpeak (version 2.1.1.20160309), supplying the sequenced corresponding input DNA as background control.
Genome_build: hg38
Supplementary_files_format_and_content: List of binding sites in bed format generated with MACS2

source_name: ChIP-seq LAPC4 WCE EtOH

growth_protocol: LAPC4 cells were cultured in DMEM media containing 20% FBS.

extract_protocol:
Cells were crosslinked for 10 min with 1% formaldehyde and quenched with 125 mM glycine for 5 min. Cells were then washed with PBS, pelleted, flash frozen and stored at -80°C. Lysates were clarified from sonicated nuclei and AR- or KLF4-DNA complexes were isolated with antibody.
Libraries were prepared according to NEB’s instructions accompanying the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®. After adapter ligation, DNA was PCR amplified for 12 cycles. The purified DNA was captured on an S4 Flowcell (PE100) for cluster generation. Libraries were sequenced on the Illumina NovaSeq 6000 following the manufacturer’s protocols at the next generation sequencing platform of Centre de Recherche du CHU de Québec (CRCHUQ).

treatment_protocol: 50 million of LAPC4 cells treated for 1h with vehicle (EtOH) or DHT (100 nM).

tag: cell type

value: human prostate cancer cells

value: EtOH


title: ChIP-seq LAPC4 WCE DHT rep2

source_name: ChIP-seq LAPC4 WCE DHT

value: DHT


title: SJMMAEL055354_D1 RNAseq

value: Bcor;Trp53; Asxl1; Ezh2


title: ChIP-seq LAPC4 WCE DHT rep1


title: U2OS, EtOH, pGIPZ shCDC73#4, Replicate1


title: ChIP-seq LAPC4 WCE EtOH rep1


title: U2OS, EtOH, pGIPZ shCDC73#4, Replicate2


title: SJMMAEL055361_D1 RNAseq

value: Bcor;Trp53; Asxl1; Ppm1d; Tet2


title: ChIP-seq LAPC4 AR DHT rep2

source_name: ChIP-seq LAPC4 AR DHT

value: AR (Sigma, EMB Millipore, #06-680)


title: ChIP-seq LAPC4 AR DHT rep1


title: SJMMAEL058571_D1 Methylseq


title: SJMMAEL058570_D1 Methylseq


title: SJMMAEL055352_D1 RNAseq

value: Bcor;Tet2;Trp53; Asxl1; Ppm1d


title: U2OS, EtOH, pGIPZ shCTR9#3, Replicate4


title: ChIP-seq LAPC4 AR EtOH rep2

source_name: ChIP-seq LAPC4 AR EtOH


title: SJMMAEL055353_D1 RNAseq


title: SJMMAEL055371_D1 Methylseq


title: SJMMAEL049909_D1 RNAseq

value: NUP98-KDM5A fusion


title: U2OS, EtOH, pGIPZ shCDC73#3, Replicate3


title: U2OS, EtOH, pGIPZ shCDC73#3, Replicate2


title: U2OS, EtOH, pGIPZ shCDC73#3, Replicate4


title: ChIP-seq LAPC4 AR EtOH rep1


title: SJMMAEL049908_D1 RNAseq


title: SJMMAEL055370_D1 Methylseq


title: SJMMAEL055369_D1 Methylseq


title: U2OS, EtOH, pGIPZ shCDC73#3, Replicate1


title: SJMMAEL058573_D1 Methylseq


title: SJMMAEL049666_D1 RNAseq


title: U2OS, Dox, pGIPZ, shNTC, Replicate3


title: SJMMAEL049665_D1 RNAseq


title: U2OS, Dox, pGIPZ, shNTC, Replicate4


title: ChIP-seq LAPC4 KLF4 DHT rep2

source_name: ChIP-seq LAPC4 KLF4 DHT

value: KLF4 (R&D Systems, AF3640)


title: SJMMAEL055367_D1 Methylseq

value: Secondary


title: ChIP-seq LAPC4 KLF4 DHT rep1


title: SJMMAEL055362_D1 Methylseq

value: spleen


title: SJMMAEL055366_D1 Methylseq


title: ChIP-seq LAPC4 KLF4 EtOH rep2

source_name: ChIP-seq LAPC4 KLF4 EtOH


title: SJMMAEL055361_D1 Methylseq


title: SJMMAEL049664_D1 RNAseq


title: U2OS, Dox, pGIPZ, shNTC, Replicate2


title: U2OS, Dox, pGIPZ, shNTC, Replicate1


title: ChIP-seq LAPC4 KLF4 EtOH rep1


title: SJMMAEL049661_D1 RNAseq


title: SJMMAEL055357_D1 Methylseq


title: Pool 8

type: genomic

city: Cologne

first: Richard

middle: James

last: Acton

state: North Rhine-Westphalia

address: CECAD Cluster of Excellence at the University of Cologne, Joseph-Stelzmann-Straße 26

department: Bioinformatics Core

institute: CECAD

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina EPIC Human Methylation580 BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

label: Cy5 and Cy3

source_name: Pool 8

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA was extracted and purified from blood samples according to standard instructions.

value: Whole blood

tag: Sex

value: Female

tag: mean age


title: Pool 7

source_name: Pool 7


title: U2OS, Dox, pGIPZ shCTR9#5, Replicate4

value: osteosarcoma cell line


title: SJMMAEL049660_D1 RNAseq

value: NTRK1 WT, TP53.R172H


title: SJMMAEL049907_D1 RNAseq

value: Primary


title: Pool 5

source_name: Pool 5


title: U2OS, Dox, pGIPZ shCTR9#5, Replicate1


title: Pool 6

source_name: Pool 6


title: Pool 4

source_name: Pool 4


title: SJMMAEL049662_D1 RNAseq


title: U2OS, Dox, pGIPZ shCTR9#5, Replicate2


title: SJMMAEL055356_D1 Methylseq


title: SJMMAEL055355_D1 Methylseq

value: Dnmt3a;Tet2; Asxl1


title: SJMMAEL049657_D1 RNAseq


title: SJMMAEL055354_D1 Methylseq


title: SJMMAEL049658_D1 RNAseq


title: SJMMAEL049659_D1 RNAseq


title: U2OS, Dox, pGIPZ shCTR9#3, Replicate4


title: Pool 3

source_name: Pool 3


title: U2OS, Dox, pGIPZ shCTR9#3, Replicate3


title: U2OS, Dox, pGIPZ shCTR9#5, Replicate3


title: SJMMAEL055353_D1 Methylseq


title: Pool 2

source_name: Pool 2


title: SJMMAEL049656_D1 RNAseq


title: U2OS, Dox, pGIPZ shCTR9#3, Replicate2


title: Pool 1

source_name: Pool 1

value: Male


title: SJMMAEL049655_D1 RNAseq


title: SJMMAEL055352_D1 Methylseq


title: U2OS, Dox, pGIPZ shCTR9#3, Replicate1


title: DIP4

city: Caen

first: Francois

last: Gravey

state: Normandy

address: Esplanade de la paix

department: Microbiology

institute: Normandy Université

data_processing:
fastqc
STAR alingment
Htseq
EdgeR package
Genome_build: S. lugdunensis reference genome: N920143 NC_017353.1
Supplementary_files_format_and_content: Count tables

organism: Staphylococcus lugdunensis

source_name: Bacteria

growth_protocol: 37°C - Aerobic - Brain Heart Infusion agar

extract_protocol: Direct-zol RNA miniprep kit

treatment_protocol: With or without DIP

value: 2,2′-dipyridyl (DIP)


title: U2OS, Dox, pGIPZ shCDC73#4, Replicate4


title: SJMMAEL049907_D1 Methylseq

source_name: spleen


title: SJMMAEL049665_D1 Methylseq


title: U2OS, Dox, pGIPZ shCDC73#4, Replicate3

source_name: osteosarcoma cell line


title: SJMMAEL049664_D1 Methylseq


title: DIP3


title: BCAS-Cis Ptau mAb-R2

city: Boston

first: Chenxi

last: Qiu

state: MA

address: NRB 858, 77 Avenue Louis Pasteur

institute: Harvard Medical School

data_processing:
Transcripts were mapped to the mouse transcriptome following an established bioinformatics pipeline (https://github.com/indrops/indrops) for inDrop experiments to create a raw gene-cell counts matrix (Klein et al, Cell, 2015)
The file Unique_barocde_sequences.txt contains the barcode sequenes for each cell ID and is available on the series record.
Genome_build: GRCm38.81
Supplementary_files_format_and_content: text files include Gene_vs_Cell raw counts matrix (single cell matrix)

molecule: nuclear RNA

source_name: Brain cortex

extract_protocol:
Cortical tissue was dissected from mice perfused with cold PBS buffer with a transcription inhibitor cocktail at a speed of 6 mL/min for 8 minutes and flash frozen in liquid nitrogen. The frozen tissue was subsequently placed into a tissue dounce for homogenization with homogenization buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 20mM Tricine-KOH pH7.8 with freshly added 1mM DTT, 0.15mM spemine (Sigma), 0.5mM spermidine (Sigma), 0.04% BSA (Sigma) and RNase inhibitors (Promega)). 5% IGEPAL (Sigma) stock solution was added to the homogenization buffer to a final concentration of 0.32% for 20 strokes with tight pestle. The homogenate was visually inspected, passed through 40-µm filter (BD Falcon) and layered onto an OptiPrep (Sigma) gradient, as previously described. The gradient was centrifuged at 10,000g for 18 minutes, and nuclei were collected between the 30% and 40% OptiPrep gradient layers. Single nucleic suspension was visually confirmed under microscope and diluted to 80,000 nuclei/mL for nuclei encapsulation and sequencing library preparation following an inDrop protocol as previously described. Approximately about 1,500 nuclei per mouse cortex were encapsulated and passed the quality controls. The prepared libraries are sequenced on Illumina Nova-seq at Broad Institute Walk-up sequencing facility, at a coverage of about 7 billion reads for ~15,000 droplets (~450,000 reads per nuclei).
Sequencing libraries were prepared following an inDrop protocol as previously described (Klein et al, Cell, 2015)

treatment_protocol: The mice are treated on day 1, 4, 7, 10, 13, 20, 27 after BCAS surgery

tag: strain

value: Brain cortex

value: 3 months


title: U2OS, Dox, pGIPZ shCDC73#4, Replicate2


title: BCAS-Cis Ptau mAb-R1


title: BCAS-IgG-R3


title: SJMMAEL049659_D1 Methylseq


title: SJMMAEL049909_D1 Methylseq


title: BCAS-IgG-R2


title: U2OS, Dox, pGIPZ shCDC73#4, Replicate1


title: BCAS-IgG-R1


title: DIP1


title: SJMMAEL049657_D1 Methylseq


title: BCAS-Cis Ptau mAb-R3


title: BHI3

value: no DIP


title: Sham-R3


title: BHI4


title: SJMMAEL049658_D1 Methylseq


title: U2OS, Dox, pGIPZ shCDC73#3, Replicate3


title: BHI2


title: U2OS, Dox, pGIPZ shCDC73#3, Replicate2


title: DIP2


title: Sham-R2


title: Sham-R1


title: SJMMAEL049655_D1 Methylseq


title: U2OS, Dox, pGIPZ shCDC73#3, Replicate1


title: MMIA03.09.S88.L005.R1.001

status: Public on Feb 09 2021

city: Davis

first: Alexander

middle: Star

last: Nord

address: 1544 Newton Court

department: Center for Neuroscience

institute: University of California Davis

data_processing:
Reads from RNA-seq were aligned to the mouse genome (mm9) using STAR (version 2.4.2a).
Aligned reads mapping to genes were counted at the gene level using subreads featureCounts.
The mm9 knownGene annotation track and aligned reads were used to generate quality control information using the full RSeQC tool suite.
Samples that exhibited strong 3′ _bias using geneBody_coverage.py or poor exon distribution using read_distribution.py were discarded.
Unaligned reads were quality checked by FastQC to ensure high quality datasets.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: dorsal telencephalon/pallium or developing cortex

extract_protocol:
Total RNA was isolated using Ambion RNAqueous total RNA Isolation Kit and assayed using Agilent RNA 6000 Nano Bioanalyzer kit/instrument.
Stranded mRNA libraries were prepared using TruSeq Stranded mRNA kits. 8–12 samples per lane were pooled and sequenced on an Illumina HiSeq 4000 instrument using a single-end 50-bp protocol.

treatment_protocol: Pregnant mice at gestational day E12.5 were injected intraperitoneally (IP) with 30 mg/kg poly(I:C) dsRNA from Sigma Aldrich (St. Louis, MO, cat #P0913) or with vehicle control (sterile 0.9% saline) injected at 5ul per gram of body weight. Pregnancy was determined to be E12.5 by visualizing vaginal seminal plug, noted as embryonic day 0.5 (E0.5) and by an increase in body weight.

value: PolyIC

tag: response to polyic

value: med

tag: sex by xist counts

value: M


title: MMIA03.01.S55.L007.R1.001

value: F

value: dorsal telencephalon/pallium or developing cortex


title: MMIA03.02.S56.L007.R1.001

value: high


title: U2OS, Dox, pGIPZ shCDC73#3, Replicate4


title: MIA.P0.8.S41.L003


title: MIA.P0.6.S49.L006


title: MIA.P0.8.S51.L006


title: MIA.P0.5.S38.L003


title: MIA.P0.5.S48.L006


title: MIA.P0.2.S35.L003


title: MIA.P0.11.S44.L004


title: MMIA04.03.S58.L007.R1.001

value: Saline


title: MIA.P0.7.S40.L003


title: MMIA04.11.S94.L005.R1.001


title: MMIA04.10.S93.L005.R1.001


title: MIA.P0.14.S47.L004


title: SJMMAEL049656_D1 Methylseq

value: spleen

value: Secondary


title: MIA.P0.16.S49.L004


title: MIA.P0.1.S44.L006


title: MIA.P0.13.S46.L004


title: MIA.e17.5.1823.2.S57.L006


title: MIA.P0.1.S34.L003


title: BHI1


title: MIA.e17.5.1823.1.S56.L006


title: MIA.P0.3.S46.L006


title: MIA.P0.10.S43.L004


title: MIA.P0.7.S50.L006


title: MIA.e17.5.1712.1.S54.L005


title: MIA.e17.5.1712.3.S55.L006


title: MIA.e17.5.1641.4.S48.L005


title: MIA.e17.5.1631.2.S53.L005


title: MIA.e17.5.1826.4.S59.L006


title: MIA.e17.5.1641.5.S45.L004


title: MIA.e17.5.1842.11.S61.L006


title: MIA.e17.5.1842.1.S60.L006


title: MIA.e17.5.1631.1.S52.L005


title: MIA.e17.5.1826.3.S58.L006


title: MMIA03.04.S85.L005.R1.001


title: MIA.e14.5.9.S58.L005


title: MMIA03.06.S57.L007.R1.001


title: MMIA03.08.S60.L007.R1.001


title: MIA.e14.5.8.S57.L005


title: MIA.e14.5.3.S2.L001


title: MIA.e14.5.13.S7.L001


title: MIA.e14.5.4.S3.L001


title: MIA.e14.5.14.S15.L002


title: MIA.e14.5.16.S16.L002


title: MIA.e14.5.11.S60.L005


title: MMIA04.08.S92.L005.R1.001


title: MMIA04.04.S59.L007.R1.001


title: MMIA04.07.S64.L007.R1.001


title: MMIA04.05.S87.L005.R1.001


title: MIA.e14.5.6.S55.L005


title: MIA.e14.5.6.S11.L002


title: MIA.e14.5.10.S59.L005


title: MIA.e14.5.7.S56.L005


title: MMIA03.07.S86.L005.R1.001


title: MIA.e14.5.5.S10.L002


title: MIA.e14.5.5.S54.L005


title: MIA.e14.5.3.S52.L005


title: MIA.e14.5.1.S50.L005


title: MIA.e12.5.1819.4.S40.L004


title: MIA.e14.5.2.S51.L005


title: MIA.e12.5.1644.4.S47.L005


title: MIA.e14.5.1.S1.L001


title: MIA.e12.5.1819.2.S39.L004


title: MMIA05.03.S91.L005.R1.001


title: MIA.e12.5.1644.3.S44.L004


title: MIA.e12.5.1623.2.S51.L005


title: MIA.e12.5.1646.4.S49.L005


title: MMIA05.02.S63.L007.R1.001


title: MIA.e12.5.1858.1.S62.L006


title: MIA.e12.5.1623.1.S50.L005


title: MIA.e12.5.1646.3.S42.L004


title: MIA.e12.5.1635.5.S46.L004


title: MIA.e12.5.1635.4.S41.L004


title: WTold Rep 5

city: Philadelphia

first: Ryan

last: Von Kleeck

state: PA

address: 421 Curie Blvd

institute: University of Pennsylvania

description:
WT_24mo_s32
LMNA_rawCounts_18samp.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads were counted against the mouse transcriptome defined in Gencode M23.
Reads were summarized per gene with tximport.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: LMNA_rawCounts_18samp.txt: Raw counts per gene, tab-delimited text.

source_name: Aorta

extract_protocol:
Descending aortas containing the intimal, medial and adventitial layers were isolated from 2- and 24-month male WT and 2-month HGPS mice, and RNA was extracted using the RNeasy Plus Micro kit (Qiagen 74034).
The high-throughput library was prepared using the TruSeq stranded total RNA (ribo-Zero) kit (Illumina 20037135). Paired-end sequencing was performed on a HiSeq4000 Sequencing System (Illumina) and generated 14-30 million reads/sample.

value: wild type

value: descending aorta

value: 748 day

tag: age group

value: old

value: male


title: WTyng Rep 1

description:
WT_02mo_s41
LMNA_rawCounts_18samp.txt

value: 62 day

value: young


title: WTold Rep 4

description:
WT_24mo_s31
LMNA_rawCounts_18samp.txt

value: 762 day


title: WTold Rep 1

description:
WT_24mo_s24
LMNA_rawCounts_18samp.txt

value: 651 day


title: WTyng Rep 3

description:
WT_02mo_s43
LMNA_rawCounts_18samp.txt


title: WTyng Rep 4

description:
WT_02mo_s44
LMNA_rawCounts_18samp.txt


title: WTold Rep 3

description:
WT_24mo_s28
LMNA_rawCounts_18samp.txt

value: 609 day


title: WTyng Rep 6

description:
WT_02mo_s46
LMNA_rawCounts_18samp.txt

value: 95 day


title: LMNAG609G Rep 6

description:
LMNA_02mo_s50
LMNA_rawCounts_18samp.txt

value: 66 day


title: WTyng Rep 5

description:
WT_02mo_s45
LMNA_rawCounts_18samp.txt


title: WTyng Rep 2

description:
WT_02mo_s42
LMNA_rawCounts_18samp.txt


title: WTold Rep 2

description:
WT_24mo_s25
LMNA_rawCounts_18samp.txt


title: LMNAG609G Rep 4

description:
LMNA_02mo_s48
LMNA_rawCounts_18samp.txt


title: LMNAG609G Rep 5

description:
LMNA_02mo_s49
LMNA_rawCounts_18samp.txt

value: 64 day


title: LMNAG609G Rep 1

description:
LMNA_02mo_s19
LMNA_rawCounts_18samp.txt

value: 69 day


title: RNA-seq Utx-/- CD8+ T cells Rep 4

city: Chapel Hill

first: Joshua

last: Starmer

state: NORTH CAROLINA

address: 120 Mason Farm Road

department: Genetics

institute: University of North Carolina at Chapel Hill

data_processing:
Initial processing and basecalling was done using Genome Analyzer Pipeline Software
FASTQ files were trimmed with the TruSeq adapter and an additional 3bp on each end.
RNA-seq alignment to the mm9 genome was performed using Tophat2
RNA-seq reads were counted at mm9 genes using HTseq-count
CUT&RUN aligment to the mm9 genome was performed using Bowtie2
CUT&RUN peaks called with MACS2 and hiddenDomains
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited files with reads per gene (RNA-seq) or peak (CUT&RUN)

source_name: Utx-/- CD8+ T cells

extract_protocol:
RNA was extracted using TRIZOL reagent, followed by mRNA purification
Libraries were generated using KAPA mRNA HyperPrep Kit (KK8580) for RNA-seq or KAPA HyperPrep Kit (KK8504) for CUT&RUN

treatment_protocol: WT or Utx-/- P14+CD8+ T cells were transferred to C57BL/6 recipient mice, CD4+ T cells were depleted prior to LCMV-A22 infection, and donor P14+CD8+ T cells were sorted from spleens at day 21 post-infection (RNA-Seq) or 15 days post-infection (CUT&RUN).

tag: time point

value: 21 days post infection

tag: agent

value: chronic lymphocytic choriomeningitis virus

value: Utx-/- knock-out


title: WTold Rep 6

description:
WT_24mo_s34
LMNA_rawCounts_18samp.txt

value: wild type


title: RNA-seq Utx-/- CD8+ T cells Rep 3


title: RNA-seq Utx-/- CD8+ T cells Rep 1


title: RNA-seq Utx-/- CD8+ T cells Rep 2


title: RNA-seq WT CD8+ T cells Rep 1

source_name: WT CD8+ T cells

value: wild-type


title: RNA-seq WT CD8+ T cells Rep 2


title: LMNAG609G Rep 3

description:
LMNA_02mo_s23
LMNA_rawCounts_18samp.txt

value: descending aorta

value: 75 day


title: MIA.e12.5.1819.5.S43.L004

value: PolyIC

value: high

value: M

value: dorsal telencephalon/pallium or developing cortex


title: LMNAG609G Rep 2

description:
LMNA_02mo_s22
LMNA_rawCounts_18samp.txt

value: 65 day

value: young

value: male


title: mBLM1

city: Beijing

first: xiaoxi

last: lv

address: No Jia2, Nanwei road, Xi Cheng district

country: China

institute: Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College

data_processing:
Solexa pipeline version 1.8, FastQC, Hisat2, and StringTie software used for basecalling.
Read quality was checked for each sample using FastQC v0.10.1.
High-quality reads were then imported into Hisat2 for alignment.
Using StringTie and R software Ballgown to get FPKM value.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file includes FPKMs (log2-transformed with an offset value of 1.0) for each sample.

source_name: mouse lung alveolar epithelial type 2 cells

growth_protocol: AEC2s were isolated from mulitple pbs or bleomycin (1 U/kg) exposed mice.

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to manufacturer’s instructions.
1-2 μg of total RNA was subjected to library synthesis using the KAPA Stranded RNA-Seq Library Prep Kit.

value: lung alveolar epithelial type 2 cells

value: multiple bleomycin


title: mBLM3


title: sham2

value: PBS


title: Con-Ad-2

description: Con-Ad infected AEC2s

data_processing:
Solexa pipeline version 1.8, FastQC, Hisat2, and StringTie software used for basecalling.
Read quality was checked for each sample using FastQC v0.10.1.
High-quality reads were then imported into Hisat2 for alignment.
Using StringTie and R software Ballgown to get FPKM value.

Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file includes FPKMs (log2-transformed with an offset value of 1.0) for each sample.

growth_protocol: The newly isolated AEC2s were cultured on Fibronectin-coated dishes with DMEM containing 10 % FBS.

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to manufacturers instructions.
1-2 g of total RNA was subjected to library synthesis using the KAPA Stranded RNA-Seq Library Prep Kit.

treatment_protocol: The newly isolated AEC2s were infected with Con or Slug adenovirus for 48 hr.

value: Con adenovirus


title: Con-Ad-1

description: Con-Ad infected AEC2s


title: sham1


title: RNA-seq WT CD8+ T cells Rep 3

value: 21 days post infection

value: chronic lymphocytic choriomeningitis virus


title: Con-Ad-3

description: Con-Ad infected AEC2s


title: Slug-Ad-2

description: Slug-Ad infected AEC2s

value: Slug adenovirus


title: Slug-Ad-1

description: Slug-Ad infected AEC2s


title: Slug-Ad-3

description: Slug-Ad infected AEC2s


title: sham3


title: mBLM2


title: Cord Blood_TD125

city: Tokyo

first: Kohei

last: Kashima

address: 7-3-1 Hongo Bunkyo-ku

department: Pediatrics

country: Japan

institute: The University of Tokyo Hospital

hyb_protocol: The resultant cRNAs were fragmented for 30 min at 60°C in dark. The fragmented cRNAs (600 ng) were hybridized on the microarray at 65°C for 17 h.

scan_protocol: After washing, slides were scanned with the Agilent microarray scanner G2505B.

data_processing: Feature extraction software (version 10.7.3.1) was used to calculate signal intensities from the scanned images.

source_name: CBMC

label_protocol: Starting with 100  ng of the isolated RNA for each sample, double stranded cDNA and cyanine 3 labeled cRNA were synthesized using low input quick amp labeling kit, one-color and RNA spike-in kit, one-color (Agilent).

extract_protocol: DNA extracted by Qiagen AllPrep kit.

treatment_protocol: Mononuclear cells were separated by gradient centrifugation using Ficoll-Hypaque from cord blood and postnatal peripheral blood samples within 24 h of the sample collection.

tag: gender

value: female

tag: batch

tag: estimated bcell

tag: estimated cd4t

tag: estimated cd8t

tag: estimated gran

tag: estimated mono

tag: estimated nk

tag: estimated nrbc

tag: gestational age

tag: birthweight sdscore


title: Cord Blood_TD126


title: Cord Blood_TD145


title: Cord Blood_TD141


title: Cord Blood_TD115


title: Cord Blood_TD140


title: Cord Blood_TD146


title: Cord Blood_TD143


title: Cord Blood_TD142


title: Cord Blood_TD107


title: Cord Blood_TD106


title: Cord Blood_TD144


title: Cord Blood_TD147


title: Cord Blood_TD133


title: Cord Blood_TD134


title: Cord Blood_TD132


title: Cord Blood_TD119


title: Cord Blood_TD138


title: Cord Blood_TD099


title: Cord Blood_TD120


title: Cord Blood_TD123


title: Cord Blood_TD139


title: Cord Blood_TD108


title: Cord Blood_TD105


title: Cord Blood_TD112


title: Cord Blood_TD118


title: Cord Blood_TD116


title: Cord Blood_TD124


title: Cord Blood_TD103


title: Cord Blood_TD097


title: Cord Blood_TD114


title: Cord Blood_TD113


title: Cord Blood_TD101


title: Cord Blood_TD085


title: Cord Blood_TD111


title: Cord Blood_TD089


title: Cord Blood_TD104


title: Cord Blood_TD093


title: Cord Blood_TD102


title: Cord Blood_TD100


title: Cord Blood_TD076


title: Cord Blood_TD073


title: Cord Blood_TD075


title: Cord Blood_TD069


title: Cord Blood_TD078


title: Cord Blood_TD109


title: Cord Blood_TD092


title: Cord Blood_TD087


title: Cord Blood_TD086


title: Cord Blood_TD067


title: Cord Blood_TD080


title: Cord Blood_TD072


title: blood_249_female_T0

city: Jouy-en-Josas

first: Marco

last: Moroldo

address: Domaine de Vilvert

department: Animal Genetics

institute: INRA

description: Gene expression T0

hyb_protocol: For each sample, 1.65 μg of Cy3-labeled cRNA (specific activity >9.0 pmol Cy3/μg of cRNA) were fragmented at 60 °C for 30 minutes in a volume of 55 μl containing 25× Agilent Fragmentation Buffer and 10× Agilent Blocking Agent. Subsequently, 55 μl of 2× Agilent Hybridization Buffer were added to the fragmentation mixture and hybridized to the array, in accordance with the recommended protocol. After hybridization, the microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute at 37 °C using GE Wash Buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing using a G2565CA Scanner System (Agilent Technologies) using one color scan settings for 4X44K slides

data_processing: The scanned images were analyzed with the Feature Extraction Software v10.7.3.1 (Agilent Technologies) using default parameters (protocol GE1_107_Sep09).

organism: Equus caballus

source_name: blood, 249, female, T0

label_protocol: Cyanine-3 (Cy3)-labelled cRNAs were prepared from 100 ng of total RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent Technologies). Specific activities and cRNA yields were measured using the NanoDrop ND-1000 (Thermo Scientific, USA).

extract_protocol: Total RNAs were isolated using the Preserved Blood RNA Purification Kit I (Norgen Biotek Corp., Ontario, Canada), according to the manufacturer’s instructions. RNA yield and purity were measured using a NanoDrop 1000 (Thermo Fisher Scientific, Waltham, MA, USA). RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA)

treatment_protocol: Twenty pure-breed or half-breed Arabian horses (7 females, 3 male, and 10 geldings; mean ± SD age: 10 ± 1.69) were selected from the cohort used by Plancade et al, 2019 (PMID: 31270376).Among the 20 horses selected for this study, 16 horses were enrolled for the 160 km category and four for the 120 km category.

tag: tissue

value: blood

tag: individual

tag: Sex

tag: time of sampling


title: blood_238_female_TF

description: Gene expression TF

source_name: blood, 238, female, TF

value: TF


title: blood_238_female_T0

description: Gene expression T0

source_name: blood, 238, female, T0


title: blood_227_male_T0

description: Gene expression T0

source_name: blood, 227, male, T0


title: Cord Blood_TD071


title: blood_226_gelding_TF

description: Gene expression TF

source_name: blood, 226, gelding, TF

value: gelding


title: NSCs, ctrl

city: Singapore

first: Hongyan

last: Wang

state: Singapore

address: 8 College Rd

country: Singapore

institute: Duke-NUS

data_processing:
Library strategy: DamID-seq
Basecalls performed using Illumina's bcl2fastq v2.19.0.316
DamID-seq reads were aligned to the dm6 genome assembly using Bowtie version 2.2.6 with the option --very-fast
peaks were called using MACS version 1.4.2 with the option -g dm
Genome_build: dm6
Supplementary_files_format_and_content: peak file (bed format)

organism: Drosophila melanogaster

source_name: Drosophila NSCs at 24h after larval hatching

growth_protocol: UAS-Dam or UAS-Dam-Pr-set7 was expressed under the control of grh-Gal4 driver. Eggs were collected within a 6h period and raised at 25 °C for 24h till larvae hatched out. Hatched larvae were transferred to 29 °C for 24 hours before dissection.

extract_protocol:
Genomic DNA was extracted and digested by DpnI (targets only methylated GATC sites). After that, methylated DNA was amplified by PCR
The Illumina TruSeq DNA PCR-free library preparation kit were used according to the manufacturer’s protocol. Briefly, DNA was fragmented and end-repaired first. Then an adenine (A) nucleotide was added to the 3ʹ ends of the fragments to prevent self-ligation. After that, index adaptors were ligated and followed by quantifying. normalizing and pooling of libraries. The libraries were sequenced on the illumina MiSeq equipment.

tag: developmental stage

value: 24h after larval hatching

tag: cell type

value: Neural stem cells (NSCs)

tag: genotype

value: UAS-Dam induced by grh-Gal4


title: blood_224_female_TF

description: Gene expression TF

source_name: blood, 224, female, TF


title: NSCs, Gal4 DamPr Set7 replicate

value: UAS-Dam-Pr-set7 (pUASTattB-LT3-NDam-Pr-set7) induced by grh-Gal4


title: blood_218_gelding_T0

description: Gene expression T0

source_name: blood, 218, gelding, T0


title: blood_220_gelding_TF

description: Gene expression TF

source_name: blood, 220, gelding, TF


title: blood_227_male_TF

description: Gene expression TF

source_name: blood, 227, male, TF


title: blood_216_gelding_T0

description: Gene expression T0

source_name: blood, 216, gelding, T0


title: blood_220_gelding_T0

description: Gene expression T0

source_name: blood, 220, gelding, T0


title: NSCs, ctrl_replicate


title: blood_217_female_TF

description: Gene expression TF

source_name: blood, 217, female, TF


title: blood_216_gelding_TF

description: Gene expression TF

source_name: blood, 216, gelding, TF


title: blood_213_gelding_TF

description: Gene expression TF

source_name: blood, 213, gelding, TF


title: blood_226_gelding_T0

description: Gene expression T0

source_name: blood, 226, gelding, T0


title: blood_217_female_T0

description: Gene expression T0

source_name: blood, 217, female, T0


title: blood_218_gelding_TF

description: Gene expression TF

source_name: blood, 218, gelding, TF


title: blood_215_gelding_TF

description: Gene expression TF

source_name: blood, 215, gelding, TF


title: blood_222_female_T0

description: Gene expression T0

source_name: blood, 222, female, T0


title: blood_224_female_T0

description: Gene expression T0

source_name: blood, 224, female, T0


title: Cord Blood_TD088

source_name: CBMC

tag: gender

tag: batch


title: blood_222_female_TF

description: Gene expression TF

source_name: blood, 222, female, TF


title: blood_215_gelding_T0

description: Gene expression T0

source_name: blood, 215, gelding, T0


title: blood_212_gelding_T0

description: Gene expression T0

source_name: blood, 212, gelding, T0


title: PAX-BJ-014-post-methy

first: Wenbo

last: Guo

state: Beijing

address: Haidian

institute: Tsinghua University

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450k Beadchip using standard Illumina protocol.   Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450k Beadchip using standard Illumina protocol.

data_processing: Arrays were imported and quality control. Methylation score of each CpG is represented as AVG_beta value.

label: Cy3 and Cy5

source_name: PDX model of pancreatic cancer patient PAX-BJ-014 after gemcitabine treatment

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified using Qiagen DNeasy Kit according to standard instructions.

tag: patient id

value: patient-derived xenograft


title: blood_211_gelding_TF

description: Gene expression TF

source_name: blood, 211, gelding, TF


title: blood_212_gelding_TF

description: Gene expression TF

source_name: blood, 212, gelding, TF


title: blood_211_gelding_T0

description: Gene expression T0

source_name: blood, 211, gelding, T0


title: PAX-SH-108-post-methy

source_name: PDX model of pancreatic cancer patient PAX-SH-108 after gemcitabine treatment


title: PAX-SH-075-post-methy

source_name: PDX model of pancreatic cancer patient PAX-SH-075 after gemcitabine treatment


title: PAX-BJ-030-post-methy

source_name: PDX model of pancreatic cancer patient PAX-BJ-030 after gemcitabine treatment


title: PAX-SH-116-post-methy

source_name: PDX model of pancreatic cancer patient PAX-SH-116 after gemcitabine treatment


title: blood_206_gelding_TF

description: Gene expression TF

source_name: blood, 206, gelding, TF


title: PAX-BJ-168-post-methy

source_name: PDX model of pancreatic cancer patient PAX-BJ-168 after gemcitabine treatment


title: PAX-SH-095-post-methy

source_name: PDX model of pancreatic cancer patient PAX-SH-095 after gemcitabine treatment


title: PAX-BJ-158-post-methy

source_name: PDX model of pancreatic cancer patient PAX-BJ-158 after gemcitabine treatment


title: PAX-BJ-020-post-methy

source_name: PDX model of pancreatic cancer patient PAX-BJ-020 after gemcitabine treatment


title: PAX-BJ-167-post-methy

source_name: PDX model of pancreatic cancer patient PAX-BJ-167 after gemcitabine treatment


title: blood_205_male_TF

description: Gene expression TF

source_name: blood, 205, male, TF

value: male


title: PAX-BJ-026-post-methy

source_name: PDX model of pancreatic cancer patient PAX-BJ-026 after gemcitabine treatment


title: blood_204_male_T0

description: Gene expression T0

source_name: blood, 204, male, T0


title: blood_203_female_TF

description: Gene expression TF

source_name: blood, 203, female, TF


title: blood_206_gelding_T0

description: Gene expression T0

source_name: blood, 206, gelding, T0


title: blood_204_male_TF

description: Gene expression TF

source_name: blood, 204, male, TF


title: blood_205_male_T0

description: Gene expression T0

source_name: blood, 205, male, T0


title: blood_203_female_T0

description: Gene expression T0

source_name: blood, 203, female, T0


title: blood_202_gelding_TF

description: Gene expression TF

source_name: blood, 202, gelding, TF


title: PAX-SH-128-post-methy

source_name: PDX model of pancreatic cancer patient PAX-SH-128 after gemcitabine treatment


title: PAX-BJ-019-post-methy

source_name: PDX model of pancreatic cancer patient PAX-BJ-019 after gemcitabine treatment


title: PAX-SH-138-post-methy

source_name: PDX model of pancreatic cancer patient PAX-SH-138 after gemcitabine treatment


title: PAX-SH-130-post-methy

source_name: PDX model of pancreatic cancer patient PAX-SH-130 after gemcitabine treatment


title: PAX-SH-115-post-methy

source_name: PDX model of pancreatic cancer patient PAX-SH-115 after gemcitabine treatment


title: PAX-BJ-179-post-methy

source_name: PDX model of pancreatic cancer patient PAX-BJ-179 after gemcitabine treatment


title: PAX-SH-091-post-methy

source_name: PDX model of pancreatic cancer patient PAX-SH-091 after gemcitabine treatment


title: PAX-BJ-008-post-methy

source_name: PDX model of pancreatic cancer patient PAX-BJ-008 after gemcitabine treatment


title: PAX-SH-054-post-methy

source_name: PDX model of pancreatic cancer patient PAX-SH-054 after gemcitabine treatment


title: N574I_rep_4 [GC079657]

city: Leuven

first: Rik

last: Schrijvers

address: Herestraat 49 bus 1023

department: Department of Microbiology, Immunology and Transplantation, Allergy and Clinical Immunology

country: Belgium

institute: KU Leuven

description:
GC079657
mRNA

data_processing:
Single-end reads of 50 bp length were produced with a minimum of 1.5M reads per sample.
Adapters were filtered with ea-utils fastq-mcf (https://github.com/ExpressionAnalysis/ea-utils).
Splice-aware alignment was performed with STAR v2 against the human reference genome hg37 using the default parameters. Reads mapping to multiple loci in the reference genome were discarded.
Resulting BAM alignment files were handled with Samtools v1.5. Quantification of reads per gene was performed with HT-Seq Count v2.7.14.
Differential expression analysis was performed with R-based (The R Foundation for Statistical Computing, Vienna, Austria) Bioconductor package DESeq2.
Genome_build: hg37 (GRCh37)
Supplementary_files_format_and_content: *_plus_differential_expression.csv: Differential expression analysis was performed with R-based (The R Foundation for Statistical Computing, Vienna, Austria) Bioconductor package DESeq2.

source_name: U3A cells

growth_protocol: U3A cells were grown in DMEM 10% serum.

extract_protocol:
Total mRNA was isolated using AurumTM total RNA mini kit (Biorad, REF 7326820).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Each sample was either left unstimulated or stimulated for 4h with IFNγ (1U/µl).

tag: cell line

value: fibrosarcoma

tag: complement

value: STAT1 N574I

tag: ifngamma stimulation

value: yes


title: N574I_rep_4 [GC079652]

description:
GC079652
mRNA

value: no


title: N574I_rep_5 [GC079658]

description:
GC079658
mRNA


title: N574I_rep_1 [GC079654]

description:
GC079654
mRNA


title: PAX-SH-129-post-methy

source_name: PDX model of pancreatic cancer patient PAX-SH-129 after gemcitabine treatment


title: N574I_rep_3 [GC079656]

description:
GC079656
mRNA


title: N574I_rep_2 [GC079655]

description:
GC079655
mRNA


title: blood_202_gelding_T0

description: Gene expression T0

source_name: blood, 202, gelding, T0


title: blood_201_female_TF

description: Gene expression TF

source_name: blood, 201, female, TF


title: N574I_rep_3 [GC079651]

description:
GC079651
mRNA


title: N574I_rep_2 [GC079650]

description:
GC079650
mRNA


title: PAX-BJ-181-post-methy

source_name: PDX model of pancreatic cancer patient PAX-BJ-181 after gemcitabine treatment


title: PAX-BJ-004-post-methy

source_name: PDX model of pancreatic cancer patient PAX-BJ-004 after gemcitabine treatment


title: PROB_2_p14

city: Budapest

first: János

middle: Miklós

last: Réthelyi

address: Balassa utca 6.

country: Hungary

institute: Semmelweis University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for short or low-quality sequence using Trimgalore! With parameters: s -5, -q 20, -l 50, then mapped to hg19 reference genome using hisat2 v.2.1.0
Mapped reads were annotated to genes using featureCounts
After exclusion of all X and Y chromosome genes, differential expression analysis (SZ-HU-PROB compare to SZ-HU-MO and SZ-HU-PROB compare to SZ-HUFA) was performed by using DESeq2 program
Rlog normalization was performed by DESeq2 analysing all the sample
Genome_build: hg19
Supplementary_files_format_and_content: xlsx file containing read counts of genes per sample

source_name: Neuronal progenitor cell

growth_protocol: We used the dentate gyrus differentiation protocol (Yu et al, Stem Cell Reports, 2014)

extract_protocol:
Total RNA was isolated from NPCs using TRIzol™ reagent.
RNA libraries were prepared for sequencing using standard Illumina NextSeq 500 protocols
Sequencing was performed after library preparation on the NextSeq500 platform using 75 bp reads.

treatment_protocol: NO specific treatment was applied.

value: IPSC-derived neural progenitor cells

tag: passage

tag: phenotype

value: schizophrenia


title: PAX-BJ-153-post-methy

source_name: PDX model of pancreatic cancer patient PAX-BJ-153 after gemcitabine treatment


title: PROB_2_p15


title: N574I_rep_1 [GC079649]

description:
GC079649
mRNA


title: PAX-BJ-172-post-methy

source_name: PDX model of pancreatic cancer patient PAX-BJ-172 after gemcitabine treatment


title: PAX-BJ-175-post-methy

source_name: PDX model of pancreatic cancer patient PAX-BJ-175 after gemcitabine treatment


title: PAX-BJ-035-post-methy

source_name: PDX model of pancreatic cancer patient PAX-BJ-035 after gemcitabine treatment


title: T419R_rep_5 [GC079648]

description:
GC079648
mRNA

value: STAT1 T419R


title: T419R_rep_4 [GC079647]

description:
GC079647
mRNA


title: blood_249_female_TF

description: Gene expression TF

source_name: blood, 249, female, TF

value: female


title: T419R_rep_2 [GC079645]

description:
GC079645
mRNA


title: T419R_rep_3 [GC079646]

description:
GC079646
mRNA