title: Male,pDC,CpG1018,6h , 2

city: New York

first: David

last: Oliver

state: New York

address: 535 E 70th St

department: Research

institute: Hospital for Special Surgery

description: countMatrix.tsv

data_processing:
RNA-seq: Sequencing quality was measured with fastp (Chen et al., 2018). Reads were then mapped reads in genes counted against the human genome (hg38) with STAR aligner and Gencode v21(Dobin et al., 2013; Frankish et al., 2019). Differential gene expression analysis was performed in R(Team, 2020) using the edgeR package (Robinson et al., 2010).
ATAC-seq:  fastq files were processed and analyzed according to ENCODE best practices. Briefly, reads were checked for quality and adapters trimmed using fastp. Reads passing QC were aligned to the latest release of the human genome (hg38) with the Bowtie2 aligner(Langmead and Salzberg, 2012). Reads aligning in proper pairs to a single location in the genome were further filtered to exclude PCR duplicates using Samtools(Li et al., 2009). High quality, de-duplicated reads were used to call peaks with Macs2 (Zhang et al., 2008). Peaks which were observed in at least two replicates were used for differential peak analysis with edgeR (Robinson et al., 2010). Analysis of differentially accessible motifs was performed using chromVAR (Schep et al., 2017).  Signal tracks and other visualizations were performed in R using the HSSRscripts package developed by the HSS Genomics Research center (https://gitlab.com/hssgenomics/hssrscripts).
Assembly: human genome (hg38)
Supplementary files format and content: countMatrix.tsv: Tab delimited file of read counts per gene
Supplementary files format and content: edgeR_total_peaks_2020-12-11.xlsx: excel file with peak locations, annotation, and normalized read counts

source_name: blood

extract_protocol:
RNAseq: Total RNA was isolated using RNeasy Plus Mini kit.
ATACseq: See construction protocol
RNAseq: Single-end reads were obtained on an Illumina HiSeq 2500 in the Weill Cornell Epigenomics Core Facility at the depth of 21-37 million fragments per sample.
ATACseq: library preparation was performed as previously described (Corces et al., 2017). Briefly, 1 x 105 purified pDCs cells were cultured in 96 U-bottom well and left unstimulated or cultured with CpG (0.25μM), CXCL4 (10μg/ml) or CpG+CXCL4 (CXCL4 at 10μg/ml, CpG at 0.25μM) for 6h. Cells were harvested for the ATAC-Seq library construction immediately.

value: blood

value: pDC

value: Healthy Donor

tag: Sex

value: Male


title: Male,pDC,CpG1018,6h , 1

status: Public on May 24 2022

type: SRA

country: USA

description: countMatrix.tsv

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

tag: tissue

tag: cell type

tag: genotype

tag: treatment


title: Male,pDC,CXCL4+CpG1018,6h , 2

description: countMatrix.tsv


title: Male,pDC,CXCL4+CpG1018,6h , 1

description: countMatrix.tsv


title: Male,pDC,Untreated,6h, 2

description: countMatrix.tsv

value: Untreated


title: Male,pDC,CXCL4,6h, 1

description: countMatrix.tsv


title: Male,pDC,Untreated,6h, 1

description: countMatrix.tsv


title: Male,pDC,CXCL4,6h, 2

description: countMatrix.tsv


title: Female,pDC,CpG1018,6h

description: countMatrix.tsv

value: Female


title: Female,pDC,Untreated,6h

description: countMatrix.tsv


title: Female,pDC,CXCL4+CpG1018,6h

description: countMatrix.tsv


title: ATAC-Seq Th17_24h_LNANT_replicate1_LANE1

status: Public on May 25 2022

city: Turku

first: Riitta

last: Lahesmaa

address: Tykistökatu 6A

department: Turku Bioscience

country: Finland

institute: University of Turku

library_source: genomic

data_processing:
ATAC-seq reads were aligned to the hg38 genome assembly with Bowtie2 (v. 2.3.3.1)
Reads with mapping quality value < 30 were filtered out using samtools (v. 1.9) and duplicate reads were removed using Picard tool's (v. 2.20.2) MarkDuplicates function.
Peaks were called using MACS2 (v. 2.2.6) with the following settings: -g hs -q 0.05
Genome_build: hg38
Supplementary_files_format_and_content: narrowPeak files generated with MACS2

molecule: genomic DNA

source_name: cord blood

growth_protocol: Ficoll (GE Healthcare, cat# 17-1440-03) was used to isolate PBMCs from human umbilical cord blood samples from Turku University Central Hospital, which was followed by CD4+ T cells were isolation (Invitrogen (cat# 11331D).  CD4+ T cells were activated using a plate coated anti-CD3 antibody (Beckman Coulter, cat# IM-1304) (3750 ng/well in a six-well culture plate), and anti-CD28 antibody (Beckman Coulter, cat# IM1376) was added in the medium in a concentration of 1 μg/mL. X-vivo 20 serum-free medium (Lonza, Bazel, Switzerland) containing 0.5 million cells/mL complemented with L-glutamine (2 mM, Sigma-Aldrich) and antibiotics (50 U/mL penicillin and 50 μg/mL streptomycin; Sigma-Aldrich) was used for the cultures. Cells were plated at a density of 2 million cells per well and cultured at 37° C in 5% CO2. For Th17 polarization of CD4+ cells, IL-6 (20 ng/mL; Roche, cat# 11138600 001), IL-1β (10 ng/mL, R&D Systems, cat# 201 LB) and TGFβ (10 ng/mL, R&D Systems, cat# 240) were used as the cytokine cocktail along with neutralizing antibodies against IFNγ (1 μg/mL, R&D Systems, cat# MAB-285) and IL4 (1 μg/mL, R&D Systems, cat# MAB204). Nonpolarizing control (Th0) cells were activated with anti-CD3 and anti-CD28 antibodies in the presence of the neutralizing antibodies without differentiating cytokines.

extract_protocol:
MIAT deficient and sufficient cells were differentiated under Th17 conditions for 72 h in three biological replicates. Nuclei were isolated as described earlier (Buenrostro et al., 2013, 2015) except that the cells were lysed by Digitonin (Promega, cat no. G9441) to avoid mitochondrial DNA contamination.
Nextera DNA library preparation kit with i7 and i5 indices (15028212) and AMPURE-XP beads (B46053, Beckman Coulter) were used to prepare and purify the libraries, following the manufacturer’s instructions.
18 samples pooled into one pool and sequenced on 2 lanes with 2x50 bp read length. Sequencing was performed at the Finnish Functional Genomics Centre using the NovaSeq 6000 S1 Next-Generation Sequencing platform.

treatment_protocol: For LNA transfections, 4 million cells mixed with 150 pmols of LNA, prepared in 100 μL volume of OptiMEM (Gibco by Life Technologies, cat # 31985-047), were used to transfect the cells using the Amaxa Nucleofector II system (Lonza). After transfection, cells were first rested at 37° C for 48 h in RPMI 1640 (Sigma-Aldrich) medium supplemented with 10% FCS, 50 U/mL penicillin, 50 μg/mL streptomycin, and 2 mM L-glutamine and then activated and cultured as described above. The following LNAs (provided by QIAGEN) were used:  LNA-NC (non-targeting control): 5´-AACACGTCTATACGC -3´;  LNA-1: 5'-ACTTTGGCATTCTAGG-3´;  LNA-4: 5'-AGGCTGGTAGGCTATG-3´.

value: In vitro differentiated Th17 cells

value: Nucleofected cells differentiated for 24 hour in Th17 media


title: UniversalHumanReference_3

city: Cambridge

first: Ioana

last: Olan

state: Cambridgeshire

address: Robinson Way

department: Cancer Research UK Cambridge Institute

country: United Kingdom

institute: University of Cambridge

description: RNA-seq

data_processing:
Reads were quality checked with FastQC (Babraham Institute), aligned with STAR (Dobin et al. 2013) against the hg19 human genome build and GENCODE19 transcriptome.
Uniquely mapping reads were summarised into counts against the GENCODE19 gene reference using featureCounts from subread (Liao, Smyth and Shi 2013).
Raw counts were summed across resequenced samples and used for differential expression analysis using edgeR (Robinson, McCarthy and Smyth 2010).
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

source_name: human

extract_protocol:
Qiagen RNEasy plus kit according to manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: UniversalHumanReference

tag: batch


title: SampleHuman_Brain_Reference_RNA_2

description: RNA-seq

source_name: Brain


title: UniversalHumanReference_1

description: RNA-seq


title: Female,pDC,CXCL4,6h

description: countMatrix.tsv


title: UniversalHumanReference_2

description: RNA-seq


title: Sample4_2_Ras_N1ICD_3

description: RNA-seq

source_name: LSEC

value: liver sinusoidal endothelial cells (LSEC)

value: RAS


title: CTRL1: iB cells Tcrd-GDL ctl 1 atac

city: Heidelberg

first: Elisa

last: Donato

address: Im Neuenheimer Feld 280

department: Division of Stem Cells and Cancer

country: Germany

institute: Deutsches Krebsforschungszentrum  (DKFZ) - German Cancer Research Center

description: ATAC-seq

data_processing:
Adapter trimming was performed using TrimGalore version 0.4.3
Reads alignment was performed using bowtie 2 version 2.3.2
peak calling was performed using macs2 version 2.1.1
Genome_build: mm10
Supplementary_files_format_and_content: Excel file containing list of called peaks

organism: Mus musculus

source_name: spleen

extract_protocol:
ATAC-seq: NUCLEI ISOLATION KIT NUCLEI EZ PREP from Sigma (NUC101-1KT)
ATAC seq: Libraries were prepared according to Illumina's instructions accompanying the kit: DNA tagmentation using TDE1 Tagment DNA Enzyme, TD Tagment DNA Buffer (Illumina cat#15027865, 15027866).

treatment_protocol: In vivo: mice were treated i.p. with two injections of 15 ng DTx per gram body weight separated by 48 hours. Mice were analyzed eight days after the first injection

tag: strain

value: Tcrd-GDL

value: immature B cells (B220+CD93+)

value: untreated


title: Sample4_2_Ras_N1ICD_2

description: RNA-seq


title: SampleHuman_Brain_Reference_RNA_3

description: RNA-seq


title: Sample4_2_Ras_N1ICD_1

description: RNA-seq


title: Sample4_2_N1ICD_2

description: RNA-seq


title: SampleHuman_Brain_Reference_RNA_1

description: RNA-seq


title: Sample4_1_Ras_N1ICD_3

description: RNA-seq


title: Sample4_2_Ras_3

description: RNA-seq


title: Sample4_2_Ras_1

description: RNA-seq


title: Sample4_2_N1ICD_1

description: RNA-seq


title: Sample4_2_Ras_2

description: RNA-seq


title: Sample4_1_Ras_3

description: RNA-seq


title: Sample4_1_Ras_2

description: RNA-seq


title: Sample4_1_Ras_N1ICD_1

description: RNA-seq


title: Sample4_1_Ras_1

description: RNA-seq


title: Sample4_2_Grow_3

description: RNA-seq


title: Sample4_1_N1ICD_1

description: RNA-seq


title: Sample4_1_Grow_3

description: RNA-seq


title: Sample4_1_Grow_2

description: RNA-seq


title: Sample4_2_Grow_1

description: RNA-seq


title: Sample4_1_Ras_N1ICD_2

description: RNA-seq


title: Sample4_2_Grow_2

description: RNA-seq


title: Sample4_1_N1ICD_3

description: RNA-seq


title: Sample3_2_Grow_2

description: RNA-seq


title: Sample4_2_N1ICD_3

description: RNA-seq


title: Sample3_2_N1ICD_1

description: RNA-seq


title: Sample3_2_Ras_3

description: RNA-seq


title: Sample3_2_Ras_N1ICD_2

description: RNA-seq


title: Sample4_1_N1ICD_2

description: RNA-seq


title: Sample4_1_Grow_1

description: RNA-seq


title: Sample3_1_Ras_3

description: RNA-seq


title: Sample3_1_Ras_2

description: RNA-seq


title: Sample3_1_Ras_N1ICD_1

description: RNA-seq


title: Sample3_1_Grow_3

description: RNA-seq


title: Sample3_2_Ras_N1ICD_1

description: RNA-seq


title: Sample3_2_Ras_N1ICD_3

description: RNA-seq


title: Sample3_1_N1ICD_3

description: RNA-seq


title: Sample3_2_N1ICD_3

description: RNA-seq


title: Sample3_2_Ras_1

description: RNA-seq


title: Sample3_2_Ras_2

description: RNA-seq


title: Sample2_2_Ras_3

description: RNA-seq


title: Sample2_2_Ras_N1ICD_1

description: RNA-seq


title: Sample3_2_N1ICD_2

description: RNA-seq


title: Sample3_1_N1ICD_1

description: RNA-seq


title: Sample2_2_N1ICD_1

description: RNA-seq


title: Sample2_2_Grow_3

description: RNA-seq


title: Sample3_2_Grow_3

description: RNA-seq


title: Sample3_2_Grow_1

description: RNA-seq


title: Sample3_1_Ras_N1ICD_3

description: RNA-seq


title: Sample3_1_Ras_N1ICD_2

description: RNA-seq


title: Sample2_2_Grow_2

description: RNA-seq


title: Sample2_1_Ras_3

description: RNA-seq


title: Sample2_1_Ras_N1ICD_1

description: RNA-seq


title: Sample3_1_N1ICD_2

description: RNA-seq


title: Sample2_2_N1ICD_2

description: RNA-seq


title: Sample2_1_N1ICD_2

description: RNA-seq


title: Sample3_1_Grow_2

description: RNA-seq


title: Sample3_1_Grow_1

description: RNA-seq


title: Sample2_2_Ras_N1ICD_3

description: RNA-seq


title: Sample2_1_N1ICD_1

description: RNA-seq


title: Sample2_1_Grow_1

description: RNA-seq


title: Sample3_1_Ras_1

description: RNA-seq


title: Sample1_1_Ras_N1ICD_3

description: RNA-seq


title: Sample2_2_Grow_1

description: RNA-seq


title: Sample2_2_N1ICD_3

description: RNA-seq


title: Sample2_2_Ras_1

description: RNA-seq


title: Sample2_1_Ras_N1ICD_3

description: RNA-seq


title: Sample2_2_Ras_2

description: RNA-seq


title: Sample2_1_Ras_2

description: RNA-seq


title: Sample2_1_Ras_N1ICD_2

description: RNA-seq


title: Sample1_1_Ras_2

description: RNA-seq


title: Sample1_1_N1ICD_1

description: RNA-seq


title: Sample2_2_Ras_N1ICD_2

description: RNA-seq


title: Sample1_1_N1ICD_2

description: RNA-seq


title: Sample1_1_N1ICD_3

description: RNA-seq


title: Sample2_1_Ras_1

description: RNA-seq


title: Sample1_1_Grow_3

description: RNA-seq


title: Sample1_1_Ras_N1ICD_1

description: RNA-seq


title: Sample2_1_N1ICD_3

description: RNA-seq


title: Sample2_1_Grow_3

description: RNA-seq


title: Sample2_1_Grow_2

description: RNA-seq


title: Alcohol placenta CTCF rep4

city: College Station

first: MICHAEL

middle: C.

last: GOLDING

state: Texas

address: 4466 TAMU

department: Physiology

institute: Texas A&M UNiversity

data_processing:
Adaptors and low-quality ChIP-seq reads were trimmed, using Trimmomatic v0.38, discarding reads left with < 20 bp
Reads were aligned to the UCSC mm10 genome using BWA version 0.7.17. Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing MACS v2.1.1 with the significance cut-off q-value <=0.1
bigwig files were generated for visualization using the Wig/BedGraph-to-bigWig converter (Galaxy Version 1.1.1)
Differentially enriched regions were identified using MACS2 bdgdiff
Assembly: mm10
Supplementary files format and content: bigWig files of H3K4me3 ChIP in sperm
Supplementary files format and content: bed or .csv files for peaks common/unique to treatment group (H3K4me3 in sperm) or different between treatments (CTCF placenta ChIP)

source_name: Placenta

extract_protocol:
H3K4me3 enriched DNA was pulled down from MNase-digested sperm DNA (protocol from Hisano et al., 2013). CTCF ChIP was carried out on GD14.5 placenta as described in Veazey et al., 2015
Libraries generated using 10ng of DNA were subjected to 150 bp paired-end (sperm) or 50 bp single-end (placenta) sequencing, obtaining ~50 million reads per sample

value: Placenta

value: Paternal Alcohol


title: Alcohol placenta CTCF rep3


title: Sample1_1_Ras_N1ICD_2

description: RNA-seq


title: Sample1_1_Ras_3

description: RNA-seq


title: Alcohol placenta CTCF rep2


title: Control placenta CTCF rep3

value: Control


title: Alcohol placenta Input


title: Control placenta CTCF rep1


title: Sample1_1_Grow_1

description: RNA-seq


title: Sample1_1_Ras_1

description: RNA-seq


title: Sample1_1_Grow_2

description: RNA-seq


title: Alcohol placenta CTCF rep5


title: Alcohol sperm H3K4me3 rep4

source_name: Spermatozoa

value: Spermatozoa

value: Alcohol


title: Control sperm H3K4me3 rep3


title: Alcohol sperm H3K4me3 rep3


title: RNA-seq_Untrained_Rep3_mH2A1_shRNA

city: Mississauga

first: Iva

middle: Toronto

last: Zovkic

state: Ontario

address: 3359 Mississauga Road North, CCT Building Room 4071

country: Canada

institute: University of Toronto Mississauga

description:
macroH2A1_KD_RNA-seq
Y24_N_S12

data_processing:
Brains were collected from home cage controls or from mice who underwent fear conditioning 1 hour and 6 hour before
RNA was extracted using Qiagen Rneasy mini kit
Library prep was conducted by Princess Margaret Genomics Centre using NEBNext Ultra II library prep kit
Adapters: IlluminaTruSeq LT
Reads were aligned using STAR
Reads were count using featureCounts
Differential expression anaslysi was done using DEseq2
Genome_build: UCSC mm10

source_name: mouse hippocampus area CA1

extract_protocol:
Brains were flash frozen and dissection of hippocampi was carried out on ice. RNA was extracted using Qiagen Rneasy mini kit
Library prep was conducted by Princess Margaret Genomics Centre using NEBNext Ultra II library prep kit

treatment_protocol: mice were left in their home cage or subjected to Fear conditioning, 3 shocks, 0.5 mA and euthanized 1h or 6 h after

tag: gender

value: male

tag: mouse id

value: Mouse 41

tag: condition

value: Home cage control


title: Control placenta CTCF rep2


title: Control placenta Input


title: Alcohol placenta CTCF rep1


title: Alcohol sperm H3K4me3 rep2


title: RNA-seq_Fear_conditioned_Rep1_mH2A1_shRNA

description:
macroH2A1_KD_RNA-seq
Y19_1h_S9

value: Mouse 38

value: 1 hour after fear conditioning


title: Control sperm H3K4me3 rep2


title: Sorted Neurog3+ Cells

city: San Francisco

first: Zachary

last: Knight

state: CA

address: 1550 Fourth St

institute: UCSF

data_processing:
Illumina HiSeq 4000 was used for sequencing of sample 1; Illumina HiSeq 2500 was used for sequencing of sample 2.
For sample 1: De-multiplexing alignment to the mm10 transcriptome and unique molecular identifier (UMI)-collapsing were performed using Cell Ranger version 2.0.1, available from 10X Genomics with default parameters. A gene-barcode matrix was generated. 0.3 billion reads over 7701 cells were captured, with 39.5 thousand mean reads per cell and 1.8 thousand median genes per cell.
For samples 2-5: Raw fastq reads were trimmed by trim_galore (v0.6.7) to remove residual sequencing adapter sequences and low-quality reads. Next, reads were mapped to the Mus musculus reference transcriptome (GRCm39.cdna.all.release-105) and quantified by Salmon (v1.6.0). The Bioconductor package `tximeta`(1.12.4) was then used to convert transcript-level abundance to gene-level counts and package `DESeq2`(v1.34.0) was used to perform count normalization and differential expression analysis. Note that only the most minimal filtering rule was applied: genes that have no counts or only a single count across all samples were removed. before running `DESeq2`. Normalized counts for all genes were then combined with the metadata file to generate the csv file for GEO deposition.
Assembly: mm10
Supplementary files format and content: For sample 1: matrix.mtx file generated by Cell Ranger v2.0.1, including all cells in Sample 1
Supplementary files format and content: For samples 2-5:  CCK_normalized_counts_long_GEO . A csv file containing normalized counts for all genes identified in experiments in Samples 2-5

source_name: Intestinal epithelial cells

extract_protocol:
Sample 1 was extracted using the GemCode Single Cell Platform (10X Genomics, Pleasanton) ; Samples 2-5 were extracted using Ovation RNA-Seq System V2
Sample 1 was prepared using the GemCode Library Kits (10X Genomics, Pleasanton) ; Samples 2-5 were prepared using the Ovation Ultralow DR Multiplex system

value: Small intestine epithelium

value: Neurog3+ intestinal epithelial cells

value: Neurog3-Cre; R26-LSL-tdTomato


title: RNA-seq_Fear_conditioned_Rep2_Scrambled_shRNA

description:
Scrambled_KD_Control_RNA-seq
SCR20_1h_S4

value: Mouse 33


title: RNA-seq_Untrained_Rep1_Scrambled_shRNA

description:
Scrambled_KD_Control_RNA-seq
SCR13_N_S1

value: Mouse 30


title: Control sperm H3K4me3 rep1


title: RNA-seq_Fear_conditioned_Rep3_mH2A1_shRNA

description:
macroH2A1_KD_RNA-seq
Y23_1h_S11

value: Mouse 40


title: Alcohol sperm H3K4me3 rep1


title: JVF_LSK_1

first: Richard

last: Koche

institute: Memorial Sloan Kettering Cancer Center

description:
Table_RNAseq_bulk_LSK_rawCounts.txt
mJAK2_LSK_1

data_processing:
RNA-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to mouse genome assembly mm9 using STAR (v2.4) with default parameters.
Read count tables were created using HTSeq v0.6.1.
Normalization and differential expression analysis was performed with DESeq2.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file with un-normalized read counts over all genes.

source_name: hemopoietic tissue

extract_protocol:
MEPs and LSKs were sorted by flow and RNA was harvested using Trizol reagent. 1.9-2ng total RNA with RNA integrity numbers ranging from 6.7 to 10 underwent amplification using the SMART-Seq v4 Ultra Low Input RNA Kit (Clonetech catalog # 63488).
9.3-10ng of amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit (Kapa Biosystems KK8504)
bulk RNA-seq

value: Lin-Sca+c-Kit+ cells

value: hemopoietic tissue


title: RNA-seq_Untrained_Rep2_mH2A1_shRNA

description:
macroH2A1_KD_RNA-seq
Y14_N_S8

value: Mouse 37


title: RNA-seq_Untrained_Rep1_mH2A1_shRNA

description:
macroH2A1_KD_RNA-seq
Y13_N_S7

value: Mouse 36


title: JVFP-/-_LSK_3

description:
Table_RNAseq_bulk_LSK_rawCounts.txt
mJAK2p53--_LSK_3


title: RNA-seq_Fear_conditioned_Rep2_mH2A1_shRNA

description:
macroH2A1_KD_RNA-seq
Y20_1h_S10

value: Mouse 39


title: JVFP-/-_LSK_1

description:
Table_RNAseq_bulk_LSK_rawCounts.txt
mJAK2p53--_LSK_1


title: JVFPR172H/-_LSK_1

description:
Table_RNAseq_bulk_LSK_rawCounts.txt
mJAK2p53172-_LSK_rep1


title: JVF_LSK_2

description:
Table_RNAseq_bulk_LSK_rawCounts.txt
mJAK2_LSK_2


title: JVFPR172H/+_LSK_2

description:
Table_RNAseq_bulk_LSK_rawCounts.txt
mJAK2p53_172_LSK_rep2


title: JVFP-/-_LSK_2

description:
Table_RNAseq_bulk_LSK_rawCounts.txt
mJAK2p53--_LSK_2


title: WT_LSK_3

description:
Table_RNAseq_bulk_LSK_rawCounts.txt
mWT_LSK_3

value: wild type


title: RNA-seq_Untrained_Rep3_Scrambled_shRNA

description:
Scrambled_KD_Control_RNA-seq
SCR24_N_S6

value: male

value: Mouse 35


title: JVFPR172H/+_LSK_1

description:
Table_RNAseq_bulk_LSK_rawCounts.txt
mJAK2p53_172_LSK_rep1


title: RNA-seq_Untrained_Rep2_Scrambled_shRNA

description:
Scrambled_KD_Control_RNA-seq
SCR14_N_S2

value: Mouse 31

value: Home cage control


title: JVFP-/-_MEP_1

description:
Table_RNAseq_bulk_MEP_rawCounts.txt
mJAK2p53--_MEP_7

value: Megakaryocyte-erythroid progenitor cell


title: JVFP-/-_MEP_3

description:
Table_RNAseq_bulk_MEP_rawCounts.txt
mJAK2p53--_MEP_9


title: RNA-seq_Fear_conditioned_Rep3_Scrambled_shRNA

description:
Scrambled_KD_Control_RNA-seq
SCR23_1h_S5

value: Mouse 34

value: 1 hour after fear conditioning


title: JVFP+/-_MEP_3

description:
Table_RNAseq_bulk_MEP_rawCounts.txt
mJAK2p53P-_MEP_3


title: JVF_LSK_3

description:
Table_RNAseq_bulk_LSK_rawCounts.txt
mJAK2_LSK_3


title: JVFP+/-_MEP_2

description:
Table_RNAseq_bulk_MEP_rawCounts.txt
mJAK2p53P-_MEP_2


title: WT_LSK_1

description:
Table_RNAseq_bulk_LSK_rawCounts.txt
mWT_LSK_1


title: WT_LSK_2

description:
Table_RNAseq_bulk_LSK_rawCounts.txt
mWT_LSK_2


title: JVFP+/-_LSK_2

description:
Table_RNAseq_bulk_LSK_rawCounts.txt
mJAK2p53P-_LSK_2


title: JVFP+/-_LSK_1

description:
Table_RNAseq_bulk_LSK_rawCounts.txt
mJAK2p53P-_LSK_1


title: WT_MEP_1

description:
Table_RNAseq_bulk_MEP_rawCounts.txt
mWT_MEP_1


title: RNA-seq_Fear_conditioned_Rep1_Scrambled_shRNA

description:
Scrambled_KD_Control_RNA-seq
SCR19_1h_S3

value: Mouse 32


title: JVFPR172H/-_LSK_2

description:
Table_RNAseq_bulk_LSK_rawCounts.txt
mJAK2p53172-_LSK_rep2


title: JVFPR172H/+_MEP_1

description:
Table_RNAseq_bulk_MEP_rawCounts.txt
mJAK2p53_172_MEP_rep1


title: JVFPR172H/+_MEP_2

description:
Table_RNAseq_bulk_MEP_rawCounts.txt
mJAK2p53_172_MEP_rep2


title: JVFPR172H/+_LSK_3

description:
Table_RNAseq_bulk_LSK_rawCounts.txt
mJAK2p53_172_LSK_rep3


title: JVFP-/-_MEP_2

description:
Table_RNAseq_bulk_MEP_rawCounts.txt
mJAK2p53--_MEP_8


title: JVFP+/-_MEP_1

description:
Table_RNAseq_bulk_MEP_rawCounts.txt
mJAK2p53P-_MEP_1


title: JVF_MEP_1

description:
Table_RNAseq_bulk_MEP_rawCounts.txt
mJAK2_MEP_1


title: JVF_MEP_3

description:
Table_RNAseq_bulk_MEP_rawCounts.txt
mJAK2_MEP_3


title: JVFP-/-_AML_MEP_1

description:
Table_RNAseq_bulk_leukemic_MEP_rawCounts.txt
mJAK2p53--_MEP_1


title: JVFPR172H/-_MEP_2

description:
Table_RNAseq_bulk_MEP_rawCounts.txt
mJAK2p53172-_MEP_rep2


title: WT_MEP_3

description:
Table_RNAseq_bulk_MEP_rawCounts.txt
mWT_MEP_3


title: WT_MEP_2

description:
Table_RNAseq_bulk_MEP_rawCounts.txt
mWT_MEP_2


title: JVFPR172H/-_AML_MEP_3

description:
Table_RNAseq_bulk_leukemic_MEP_rawCounts.txt
mJAK2p53172-_AML_MEP_rep3


title: JVFPR172H/-_MEP_1

description:
Table_RNAseq_bulk_MEP_rawCounts.txt
mJAK2p53172-_MEP_rep1


title: JVFP-/-_AML_MEP_2

description:
Table_RNAseq_bulk_leukemic_MEP_rawCounts.txt
mJAK2p53--_MEP_2


title: JVF_MEP_2

description:
Table_RNAseq_bulk_MEP_rawCounts.txt
mJAK2_MEP_2


title: JVFP-/-_AML_MEP_3

description:
Table_RNAseq_bulk_leukemic_MEP_rawCounts.txt
mJAK2p53--_MEP_3


title: JVFPR172H/-_MEP_3

description:
Table_RNAseq_bulk_MEP_rawCounts.txt
mJAK2p53172-_MEP_rep3


title: Trim28 WT Ovary Mouse 1 Gonad 2

city: Geneva

first: Chris

last: Rands

address: 1, rue Michel-Servet

country: Switzerland

institute: University of Geneva

data_processing:
Bcl2fastq was used to generate fastq reads split by lane
Cellranger v3 count to generate count matrixes
Genome_build: mm10
Supplementary_files_format_and_content: .h5 files with filtered count matrixes output by cellranger

source_name: WT Ovary

extract_protocol:
Testes or ovaries from eight weeks mice were collected and enzymatically dissociated with a modified protocol from Gaysinskaya et al. 2014, Cytometry for testes and enzymatically dissociated in PBS (10010-015; Gibco) supplemented with 0.25 mg/mL collagenase (C0130;Sigma-Aldrich) and 0.0005% trypsin-EDTA (25300-054; Gibco) for ovaries
Single-cell RNA-Seq libraries were prepared using the Chromium Single Cell 3′ v2 Reagent Kit (10X Genomics) according to manufacturer’s protocol

value: Ovary

tag: knockout

value: Wildtype

tag: gonad


title: Trim28 WT Testis Mouse 1 Gonad 1

source_name: WT Testis

value: Testis


title: JVFPR172H/-_AML_MEP_2

description:
Table_RNAseq_bulk_leukemic_MEP_rawCounts.txt
mJAK2p53172-_AML_MEP_rep2


title: Trim28 WT Ovary Mouse 2 Gonad 1


title: Trim28 WT Ovary Mouse 1 Gonad 1


title: Trim28 KO Ovary Mouse 2 Gonad 1

source_name: KO Ovary


title: JVFPR172H/+_MEP_3

description:
Table_RNAseq_bulk_MEP_rawCounts.txt
mJAK2p53_172_MEP_rep3


title: Trim28 KO Ovary Mouse 1 Gonad 1


title: JVFPR172H/-_AML_MEP_1

description:
Table_RNAseq_bulk_leukemic_MEP_rawCounts.txt
mJAK2p53172-_AML_MEP_rep1


title: INPUT_PHD

city: Montpellier

first: Francis

last: Poulat

address: 141 rue de la Cardonille

department: Genetic and Development

country: France

institute: IGH CNRS-UM UMR9002

description: Tissus were collected from 8 weeks old mouse and frozen. Before fixation, pool of ovary or testes were crushed in powder in nitrogen. Tissue powders were fixed using formaldehyde. Chromatin preparation, and immunoprecipitation were performed using Low cell ChIPseq kit (Active motif). Chromatin shearing was performed using qSonica Sonicator Sequencing libraries were prepared using Next Gen DNA Library Kit and Next Gen Indexing kit (Active Motif). And analysed using Bioanalyser (Agilent)

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome mm10 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
BAM files were sorted using SAMtools v0.1.19.
The tool rmDupByMids.pl provided by Active Motif was then used to remove duplicated reads.
For peak calling data were analyzed using the Encode ChIP-seq pipeline v1.3.6. Peak caller: spp v1.15.5. Peaks were annotated relative to genomic features using Homer v4.11.0 (annotations were extracted from a gtf file downloaded from Ensembl v92).
Genome_build: mm10
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b).

source_name: ovary

extract_protocol:
Dissected ovaries were snap-frozen and stored at −80◦C. Frozen ovaries were crushed in liquid nitrogen using a mini-liquid nitrogen cooled mortar (Bel-Art ref H37260-0100). Powdered tissue samples were immediately fixed in PBS/1% formaldehyde at room temperature for 20 min. Chromatin shearing was performed using qSonica Sonicator.  Chromatin immunoprecipitation (IP) with homemade rabbit anti SUMO1 and anti SUMO2 were performed on 20µg of chromatin using Low cell ChIPseq kit (Active motif, ref 10489). For each genotype, two independent ChIPseq libraries were prepared. For Each library three independent immunoprecipitation were pooled, each IP prepared from ovaries of two different animals.
Libraries were prepared using Next Gen DNA Library Kit which contains molecular identifiers (MIDs) used to remove PCR duplicates, and Next Gen Indexing kit (Active motif, ref 104895).

tag: antibody

value: input


title: INPUT_WT


title: PHD_SUMO2_2


title: PHD_SUMO1_2


title: PHD_SUMO1_1


title: INPUT_KO


title: KO_SUMO2_2


title: KO_SUMO1_2


title: KO_SUMO1_1


title: KO_SUMO2_1


title: WT_SUMO2_1


title: WT_SUMO1_2


title: input

description: Ovaries were collected from 8 weeks old mouse and frozen. Before fixation, pool of ovary were crushed in powder in nitrogen.  Tissue powders were fixed using formaldehyde. Chromatin preparation, and immunoprecipitation were performed using ChIP-IT High sensitivity kit (Active motif). Chromatin shearing was performed using qSonica Sonicator  Sequencing libraries were prepared using Next Gen DNA Library Kit  and Next Gen  Indexing kit (Active Motif).  And analysed using Bioanalyser (Agilent)

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome mm10 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
BAM files were sorted using SAMtools v0.1.19.
The tool rmDupByMids.pl provided by Active Motif were then used to remove duplicated reads.
Peaks were called using MACS2 with default parameters except for “-g mm -f BAM –broad –broad-cuto 0.1 –keep-dup all”.
Genome_build: mm10
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b).

extract_protocol:
Dissected ovaries from 8 weeks old female mice were snap-frozen and stored at −80◦C. Frozen ovaries were crushed in liquid nitrogen using a mini-liquid nitrogen cooled mortar (Bel-Art ref H37260-0100). Powdered tissue samples were immediately fixed in PBS/1% formaldehyde at room temperature for 20 min. Chromatin shearing was performed using qSonica Sonicator.  Chromatin immunoprecipitation (IP) with homemade rabbit anti TRIM28 and anti FOXL2 were performed on 20µg of chromatin using Low cell ChIPseq kit (Active motif, ref 10489). Each ChIPseq libraries were prepared from a pool of three independent IPs, each IP prepared with ovaries of two different animals.
Next Gen DNA Library Kit which contains molecular identifiers (MIDs) used to remove PCR duplicates from sequencing data and Next Gen Indexing kit (Active motif, ref 104895).


title: Trim28 KO Ovary Mouse 1 Gonad 2


title: ChIPseq_FOXL2


title: WT_SUMO1_1


title: Sample_cKO_2

description: Ovaries were collected from 7 months old mice and frozen (3 mice for wild and KO respectively). Total RNA where then extracted using TRIZOL

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads were mapped onto the mm10 assembly of Mus musculus genome using STAR  version 2.5.3a.
Gene expression quantification was performed from uniquely aligned reads using htseq-count  version 0.6.1p1, with annotations from Ensembl version 92 and “union” mode
Comparison between WT and KO samples was performed using the Wald test for differential expression proposed by Love et al. 2014 and implemented in the Bioconductor package DESeq2 version 1.16.1
Genome_build: mm10
Supplementary_files_format_and_content: S18268_alldata.xlsx

extract_protocol:
Ovaries were collected from 7 months old mice and frozen (3 mice for control and KO respectively). Total RNA where then extracted using TRIZOL reagent.
RNA-Seq libraries were generated from 600 ng of total RNA using TruSeq Stranded mRNA LT Sample Preparation Kit (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

value: Trim28 cKO


title: Sample_cKO_3


title: Sample_cKO_1


title: ChIP_Untrained_6hr_Rep4_macroH2A1_input

description: Input

data_processing:
Brains were collected from home cage controls or from mice who underwent fear conditioning 1 hour and 6 hour before
ChIP was conducted on Mnase digested tissue from area CA1 with antibodies against macroH2A1 (abcam cag#37264 for 30 min ChIP and ; Thermo Fisher cat# Ma5-24696 for 1h and 6h ChIP) or macroH2A2 (Abcam cat#3173)
Library prep was conducted by Genome Quebec using NEBNext Ultra II library prep kit
Adapters: IlluminaTruSeq LT
Reads were aligned using Bowtie 2.
Peaks were identified using epic2
Differential analysis for macroH2A1 and macroH2A2 binding was assessed with DiffBind (v.2.10.0)
Genome_build: UCSC mm10
Supplementary_files_format_and_content: bed

extract_protocol: Brains were collected from home cage controls or from mice who underwent fear conditioning 30 min before  ChIP was conducted on Mnase digested tissue from area CA1 with antibodies against macroH2A1 (abcam cag#37264) or macroH2A2 (Abcam cat#3173)  Library prep was conducted by Genome Quebec using NEBNext Ultra II library prep kit  Adapters: IlluminaTruSeq LT

value: Male

value: Mouse 38

value: Input


title: PHD_SUMO2_1


title: ChIP_Untrained_6hr_Rep3_macroH2A1_input

description: Input

value: Mouse 37


title: Sample_Control_1

value: control


title: WT_SUMO2_2


title: ChIP_Untrained_6hr_Rep2_macroH2A1_input

description: Input

value: Mouse 36


title: Sample_Control_2


title: ChIP_Untrained_6hr_Rep5_macroH2A1_input

description: Input

value: Mouse 39


title: ChIP_Untrained_6hr_Rep4_macroH2A1

description: macroH2A1 ChIP

value: Home cage control

value: macroH2A1 ChIP


title: ChIP_Fear_conditioned_6hr_Rep4_macroH2A1_input

description: Input

value: Mouse 33

value: 6 hour after fear conditioning


title: ChIP_Untrained_6hr_Rep3_macroH2A1

description: macroH2A1 ChIP


title: ChIP_Fear_conditioned_6hr_Rep5_macroH2A1_input

description: Input

value: Mouse 34


title: ChIP_Untrained_6hr_Rep2_macroH2A1

description: macroH2A1 ChIP


title: ChIPseq_TRIM28


title: Sample_Control_3


title: ChIP_Fear_conditioned_6hr_Rep5_macroH2A1

description: macroH2A1 ChIP


title: ChIP_Fear_conditioned_6hr_Rep2_macroH2A1_input

description: Input

value: Mouse 31


title: ChIP_Fear_conditioned_6hr_Rep3_macroH2A1_input

description: Input

value: Mouse 32


title: ChIP_Fear_conditioned_6hr_Rep1_macroH2A1_input

description: Input

value: Mouse 30


title: ChIP_Fear_conditioned_6hr_Rep3_macroH2A1

description: macroH2A1 ChIP


title: ChIP_Fear_conditioned_6hr_Rep4_macroH2A1

description: macroH2A1 ChIP


title: ChIP_Untrained_1hr_Rep2_macroH2A2

description: macroH2A2 ChIP

value: Mouse 28

value: macroH2A2 ChIP


title: ChIP_Fear_conditioned_1hr_Rep2_macroH2A2_input

description: Input

value: Male

value: Mouse 25

value: 1 hour after fear conditioning


title: ChIP_Fear_conditioned_6hr_Rep1_macroH2A1

description: macroH2A1 ChIP


title: ChIP_Fear_conditioned_6hr_Rep2_macroH2A1

description: macroH2A1 ChIP


title: ChIP_Untrained_6hr_Rep1_macroH2A1_input

description: Input

value: Mouse 35

value: Input


title: ChIP_Fear_conditioned_1hr_Rep1_macroH2A2_input

description: Input

value: Mouse 24


title: ChIP_Untrained_1hr_Rep2_macroH2A2_input

description: Input


title: ChIP_Fear_conditioned_1hr_Rep3_macroH2A2

description: macroH2A2 ChIP

value: Mouse 26


title: ChIP_Fear_conditioned_1hr_Rep2_macroH2A2

description: macroH2A2 ChIP


title: ChIP_Untrained_1hr_Rep3_macroH2A2

description: macroH2A2 ChIP

value: Mouse 29

value: Home cage control


title: ChIP_Untrained_1hr_Rep1_macroH2A1_input

description: Input

value: Mouse 22


title: ChIP_Fear_conditioned_1hr_Rep2_macroH2A1_input

description: Input

value: Mouse 21


title: ChIP_Fear_conditioned_1hr_Rep3_macroH2A2_input

description: Input


title: ChIP_Untrained_6hr_Rep1_macroH2A1

description: macroH2A1 ChIP

value: macroH2A1 ChIP


title: ChIP_Untrained_6hr_Rep5_macroH2A1

description: macroH2A1 ChIP

value: Mouse 39


title: ChIP_Untrained_1hr_Rep1_macroH2A2

description: macroH2A2 ChIP

value: Mouse 27


title: ChIP_Fear_conditioned_1hr_Rep1_macroH2A2

description: macroH2A2 ChIP


title: ChIP_Untrained_1hr_Rep1_macroH2A1

description: macroH2A2 ChIP


title: ChIP_Untrained_1hr_Rep2_macroH2A1_input

description: Input

value: Mouse 23


title: ChIP_Untrained_1hr_Rep3_macroH2A2_input

description: Input


title: ChIP_Fear_conditioned_1hr_Rep2_macroH2A1

description: macroH2A1 ChIP


title: ChIP_Fear_conditioned_1hr_Rep1_macroH2A1_input

description: Input

value: Mouse 20


title: RNA_Rep3_shH2afy2

description:
FastQ file-paired end
mH2A2_KD_RNA_seq_Raw_Counts.csv

data_processing:
reads were aligned using STAR; featureCounts was used to get the read counts
Differential analysis was done using DEseq2 (v1.22.2)
Genome_build: UCSC mm10

extract_protocol:
Brains were collected from home cage controls or from mice who underwent fear conditioning 1h before
RNA was extracted using Qiagen Rneasy mini kit
Library prep was conducted by Genome Quebec using NEBNext Ultra II library prep kit
NEB Next
adaptors were trimmed with Trim Galore (v0.4.5) running Cutadapt (v2.6)

value: C57BL/6J Male

value: Mouse 16

value: H2afy2 knockdown


title: RNA_Rep2_shH2afy2

value: Mouse 15


title: ChIP_Untrained_1hr_Rep1_macroH2A2_input

description: Input

value: Male


title: RNA_Rep3_shH2afy

description:
FastQ file-paired end
mH2A1_KD_RNA_seq_Raw_Counts.csv

value: Mouse 13

value: H2afy knockdown


title: ChIP_Untrained_1hr_Rep2_macroH2A1

description: macroH2A2 ChIP

value: macroH2A2 ChIP


title: RNA_Rep3_shScramble

description:
FastQ file-paired end
Scramble_KD_RNA_seq_Raw_Counts.csv

value: Mouse 19

value: Scramble control


title: ChIP_Fear_conditioned_1hr_Rep1_macroH2A1

description: macroH2A1 ChIP

value: 1 hour after fear conditioning


title: RNA_Rep2_shScramble

value: Mouse 18


title: RNA_Rep1_shScramble

value: Mouse 17


title: RNA_Rep2_shH2afy

value: Mouse 12


title: RNA_Control_Rep2

description:
Aligned RNAseq file + index file
Fear conditioning_RNA_seq_Raw_Counts.csv

value: Mouse 7

value: Home cage control


title: RNA_Rep1_shH2afy

value: Mouse 11


title: ChIP_Fear conditioned_Rep2_macroH2A1

description:
macroH2A1 ChIP
Fear conditioned_Rep2_mH2A1.bed

data_processing:
Reads were aligned using Bowtie 2.
Peaks were identified using epic2
Differential analysis for macroH2A1 and macroH2A2 binding was assessed with DiffBind (v.2.10.0)
Genome_build: UCSC mm10

extract_protocol:
Brains were collected from home cage controls or from mice who underwent fear conditioning 30 min before
ChIP was conducted on Mnase digested tissue from area CA1 with antibodies against macroH2A1 (abcam cag#37264) or macroH2A2 (Abcam cat#3173)
Library prep was conducted by Genome Quebec using NEBNext Ultra II library prep kit
Adapters: IlluminaTruSeq LT

value: C57BL/6J Male

value: Mouse 5

value: 30 min after fear conditioning


title: RNA_Rep1_shH2afy2

value: Mouse 14

value: H2afy2 knockdown


title: ChIP_Fear conditioned_Rep1_macroH2A2

description:
macroH2A2 ChIP
Fear conditioned_Rep1_mH2A2.bed

value: Mouse 4


title: ChIP_Control_Rep3_input

description: Input

value: Mouse 3


title: ChIP_Fear conditioned_Rep1_input

description: Input


title: ChIP_Control_Rep2_input

description: Input

value: Mouse 2


title: RNA_Fear conditioned_Rep1

value: Mouse 9

value: 1h after fear conditioning


title: RNA_Fear conditioned_Rep2

value: Mouse 10


title: RNA_Control_Rep1

value: Mouse 6


title: ChIP_Control_Rep2_macroH2A2

description:
macroH2A2 ChIP
Control_Rep2_mH2A2.bed


title: ChIP_Control_Rep3_macroH2A2

description:
macroH2A2 ChIP
Control_Rep3_mH2A2.bed


title: ChIP_Fear conditioned_Rep2_input

description: Input


title: ChIP_Fear conditioned_Rep1_macroH2A1

description:
macroH2A1 ChIP
Fear conditioned_Rep1_mH2A1.bed


title: ChIP_Fear conditioned_Rep2_macroH2A2

description:
macroH2A2 ChIP
Fear conditioned_Rep2_mH2A2.bed


title: ChIP_Control_Rep3_macroH2A1

description:
macroH2A1 ChIP
Control_Rep3_mH2A1.bed


title: ChIP_Control_Rep1_macroH2A2

description:
macroH2A2 ChIP
Control_Rep1_mH2A2.bed

value: Mouse 1


title: ChIP_Control_Rep2_macroH2A1

description:
macroH2A1 ChIP
Control_Rep2_mH2A1.bed


title: ChIP_Control_Rep1_input

description: Input


title: RNA_Control_Rep3

value: Mouse 8


title: 53623BCG, Matched Group 41, M.tb-uninfected, CMV-infected

city: Oxford

first: Shuailin

last: Li

address: Old Road Campus Research Building

institute: University of Oxford

data_processing:
Quality control checks on raw sequence data were performed using fastqc. Reads were aligned to the genome using HISAT2. Sequences were quantified as gene counts using the featureCounts tool.
Assembly: HISAT2
Supplementary files format and content: txt.gz, include raw read counts

source_name: PBMC

extract_protocol:
Qiagen RNeasy kit following the manufacturer’s instructions (including optional DNase digestion) and RNA was eluted twice, 30 µl per elution.
Purification of mRNA, generation of double stranded cDNA and library construction were performed using NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760L) with adapters and barcode tags (dual indexing). The concentrations used to generate the multiplex pool were determined by Picogreen.

tag: cell line

value: PBMC

value: BCG


title: 53652BCG, Matched Group 21, M.tb-uninfected, CMV-uninfected


title: 53644US, Matched Group 19, M.tb-uninfected, CMV-infected

value: US


title: 53749US, Matched Group 41, M.tb-uninfected, CMV-uninfected


title: 53618BCG, Matched Group 6, M.tb-uninfected, CMV-uninfected


title: 53574BCG, Matched Group 41, M.tb-uninfected, CMV-infected


title: 53618US, Matched Group 6, M.tb-uninfected, CMV-uninfected


title: 53570BCG, Matched Group 25, M.tb-infected, CMV-unknown


title: 53564US, Matched Group 25, M.tb-uninfected, CMV-uninfected


title: 53749BCG, Matched Group 41, M.tb-uninfected, CMV-uninfected


title: 53685BCG, Matched Group 21, M.tb-uninfected, CMV-unknown


title: 53669US, Matched Group 25, M.tb-uninfected, CMV-infected


title: 53574US, Matched Group 41, M.tb-uninfected, CMV-infected


title: 53652US, Matched Group 21, M.tb-uninfected, CMV-uninfected


title: 53623US, Matched Group 41, M.tb-uninfected, CMV-infected


title: 53575US, Matched Group 37, M.tb-uninfected, CMV-uninfected


title: ChIP_Control_Rep1_macroH2A1

description:
macroH2A1 ChIP
Control_Rep1_mH2A1.bed

value: C57BL/6J Male

value: Home cage control


title: 53669BCG, Matched Group 25, M.tb-uninfected, CMV-infected


title: 53685US, Matched Group 21, M.tb-uninfected, CMV-unknown


title: 53526US, Matched Group 6, M.tb-uninfected, CMV-uninfected


title: 53644BCG, Matched Group 19, M.tb-uninfected, CMV-infected


title: 53484BCG, Matched Group 40, M.tb-uninfected, CMV-uninfected


title: 53528BCG, Matched Group 21, M.tb-uninfected, CMV-infected


title: 53526BCG, Matched Group 6, M.tb-uninfected, CMV-uninfected


title: 53575BCG, Matched Group 37, M.tb-uninfected, CMV-uninfected


title: 53484US, Matched Group 40, M.tb-uninfected, CMV-uninfected


title: 53458BCG, Matched Group 21, M.tb-infected, CMV-infected


title: 53455BCG, Matched Group 19, M.tb-uninfected, CMV-uninfected


title: 53403BCG, Matched Group 40, M.tb-infected, CMV-unknown


title: 53564BCG, Matched Group 25, M.tb-uninfected, CMV-uninfected


title: 53385BCG, Matched Group 40, M.tb-uninfected, CMV-infected


title: 53455US, Matched Group 19, M.tb-uninfected, CMV-uninfected


title: 53458US, Matched Group 21, M.tb-infected, CMV-infected


title: 53385US, Matched Group 40, M.tb-uninfected, CMV-infected


title: 53528US, Matched Group 21, M.tb-uninfected, CMV-infected


title: 53378BCG, Matched Group 25, M.tb-uninfected, CMV-infected


title: 53376US, Matched Group 19, M.tb-uninfected, CMV-infected


title: 53248US, Matched Group 40, M.tb-uninfected, CMV-infected


title: 53154US, Matched Group 30, M.tb-uninfected, CMV-uninfected


title: 53165BCG, Matched Group 6, M.tb-uninfected, CMV-uninfected


title: 53378US, Matched Group 25, M.tb-uninfected, CMV-infected


title: 53248BCG, Matched Group 40, M.tb-uninfected, CMV-infected


title: 52997US, Matched Group 24, M.tb-uninfected, CMV-infected


title: 52926US, Matched Group 23, M.tb-uninfected, CMV-unknown


title: 52926BCG, Matched Group 23, M.tb-uninfected, CMV-unknown


title: 52997BCG, Matched Group 24, M.tb-uninfected, CMV-infected


title: 52921US, Matched Group 12, M.tb-uninfected, CMV-infected


title: 52921BCG, Matched Group 12, M.tb-uninfected, CMV-infected


title: 53376BCG, Matched Group 19, M.tb-uninfected, CMV-infected


title: 53238BCG, Matched Group 30, M.tb-uninfected, CMV-uninfected


title: 53238US, Matched Group 30, M.tb-uninfected, CMV-uninfected


title: 53165US, Matched Group 6, M.tb-uninfected, CMV-uninfected


title: 52885US, Matched Group 23, M.tb-uninfected, CMV-infected


title: 52852US, Matched Group 23, M.tb-infected, CMV-infected


title: 52852BCG, Matched Group 23, M.tb-infected, CMV-infected


title: 52830BCG, Matched Group 30, M.tb-uninfected, CMV-infected


title: 52885BCG, Matched Group 23, M.tb-uninfected, CMV-infected


title: 52766US, Matched Group 27, M.tb-uninfected, CMV-infected


title: 52830US, Matched Group 30, M.tb-uninfected, CMV-infected


title: 52738US, Matched Group 29, M.tb-uninfected, CMV-infected


title: 53154BCG, Matched Group 30, M.tb-uninfected, CMV-uninfected


title: 52738BCG, Matched Group 29, M.tb-uninfected, CMV-infected


title: 52676BCG, Matched Group 28, M.tb-uninfected, CMV-uninfected


title: 52655BCG, Matched Group 28, M.tb-uninfected, CMV-infected


title: 52676US, Matched Group 28, M.tb-uninfected, CMV-uninfected


title: 52655US, Matched Group 28, M.tb-uninfected, CMV-infected


title: 52646BCG, Matched Group 2, M.tb-uninfected, CMV-unknown


title: 52659US, Matched Group 30, M.tb-infected, CMV-infected


title: 52610US, Matched Group 5, M.tb-uninfected, CMV-infected


title: 52605BCG, Matched Group 12, M.tb-uninfected, CMV-infected


title: 52563BCG, Matched Group 29, M.tb-uninfected, CMV-infected


title: 52602US, Matched Group 24, M.tb-uninfected, CMV-uninfected


title: 52646US, Matched Group 2, M.tb-uninfected, CMV-unknown


title: 52605US, Matched Group 12, M.tb-uninfected, CMV-infected


title: 52563US, Matched Group 29, M.tb-uninfected, CMV-infected


title: 52604BCG, Matched Group 24, M.tb-infected, CMV-unknown


title: 52604US, Matched Group 24, M.tb-infected, CMV-unknown


title: 52541US, Matched Group 23, M.tb-uninfected, CMV-uninfected


title: 52766BCG, Matched Group 27, M.tb-uninfected, CMV-infected


title: 52541BCG, Matched Group 23, M.tb-uninfected, CMV-uninfected


title: 52417BCG, Matched Group 7, M.tb-uninfected, CMV-infected


title: 53570US, Matched Group 25, M.tb-infected, CMV-unknown


title: 52408US, Matched Group 5, M.tb-infected, CMV-uninfected


title: 52408BCG, Matched Group 5, M.tb-infected, CMV-uninfected


title: 52393BCG, Matched Group 37, M.tb-uninfected, CMV-uninfected


title: 52377US, Matched Group 29, M.tb-uninfected, CMV-uninfected


title: 52377BCG, Matched Group 29, M.tb-uninfected, CMV-uninfected


title: 52659BCG, Matched Group 30, M.tb-infected, CMV-infected


title: 52393US, Matched Group 37, M.tb-uninfected, CMV-uninfected


title: 52610BCG, Matched Group 5, M.tb-uninfected, CMV-infected


title: 52365BCG, Matched Group 27, M.tb-infected, CMV-uninfected


title: 52602BCG, Matched Group 24, M.tb-uninfected, CMV-uninfected


title: 52365US, Matched Group 27, M.tb-infected, CMV-uninfected


title: 52287US, Matched Group 27, M.tb-uninfected, CMV-uninfected


title: 52288BCG, Matched Group 27, M.tb-uninfected, CMV-infected


title: 52281US, Matched Group 37, M.tb-uninfected, CMV-uninfected


title: 52303BCG, Matched Group 4, M.tb-uninfected, CMV-uninfected


title: 52303US, Matched Group 4, M.tb-uninfected, CMV-uninfected


title: 52260BCG, Matched Group 7, M.tb-infected, CMV-infected


title: 52222US, Matched Group 24, M.tb-uninfected, CMV-infected


title: 52119US, Matched Group 7, M.tb-uninfected, CMV-infected


title: 52260US, Matched Group 7, M.tb-infected, CMV-infected


title: 52281BCG, Matched Group 37, M.tb-uninfected, CMV-uninfected


title: 52167BCG, Matched Group 22, M.tb-uninfected, CMV-infected


title: 52131BCG, Matched Group 22, M.tb-uninfected, CMV-infected


title: 52222BCG, Matched Group 24, M.tb-uninfected, CMV-infected


title: 52131US, Matched Group 22, M.tb-uninfected, CMV-infected


title: 52071BCG, Matched Group 28, M.tb-uninfected, CMV-uninfected


title: 52119BCG, Matched Group 7, M.tb-uninfected, CMV-infected


title: 51987US, Matched Group 22, M.tb-infected, CMV-infected


title: 52071US, Matched Group 28, M.tb-uninfected, CMV-uninfected


title: 51892BCG, Matched Group 4, M.tb-uninfected, CMV-infected


title: 51890US, Matched Group 34, M.tb-uninfected, CMV-infected


title: 52417US, Matched Group 7, M.tb-uninfected, CMV-infected


title: 52105US, Matched Group 37, M.tb-infected, CMV-infected


title: 51892US, Matched Group 4, M.tb-uninfected, CMV-infected


title: 52105BCG, Matched Group 37, M.tb-infected, CMV-infected


title: 51890BCG, Matched Group 34, M.tb-uninfected, CMV-infected


title: 51849BCG, Matched Group 7, M.tb-uninfected, CMV-uninfected


title: 51987BCG, Matched Group 22, M.tb-infected, CMV-infected


title: 52287BCG, Matched Group 27, M.tb-uninfected, CMV-uninfected


title: 51857US, Matched Group 34, M.tb-uninfected, CMV-infected


title: 51741US, Matched Group 5, M.tb-uninfected, CMV-infected


title: 51857BCG, Matched Group 34, M.tb-uninfected, CMV-infected


title: 51741BCG, Matched Group 5, M.tb-uninfected, CMV-infected


title: 51849US, Matched Group 7, M.tb-uninfected, CMV-uninfected


title: 51633BCG, Matched Group 12, M.tb-uninfected, CMV-uninfected


title: 51602US, Matched Group 15, M.tb-uninfected, CMV-uninfected


title: 51444US, Matched Group 22, M.tb-uninfected, CMV-uninfected


title: 51516BCG, Matched Group 2, M.tb-uninfected, CMV-unknown


title: 51470BCG, Matched Group 2, M.tb-uninfected, CMV-infected


title: 51516US, Matched Group 2, M.tb-uninfected, CMV-unknown


title: 51248US, Matched Group 26, M.tb-uninfected, CMV-infected


title: 51268BCG, Matched Group 9, M.tb-uninfected, CMV-unknown


title: 51248BCG, Matched Group 26, M.tb-uninfected, CMV-infected


title: 51470US, Matched Group 2, M.tb-uninfected, CMV-infected


title: 51602BCG, Matched Group 15, M.tb-uninfected, CMV-uninfected


title: 51713BCG, Matched Group 36, M.tb-infected, CMV-unknown


title: 51713US, Matched Group 36, M.tb-infected, CMV-unknown


title: 51633US, Matched Group 12, M.tb-uninfected, CMV-uninfected


title: 51183US, Matched Group 35, M.tb-uninfected, CMV-unknown


title: 51332US, Matched Group 4, M.tb-uninfected, CMV-uninfected


title: 51332BCG, Matched Group 4, M.tb-uninfected, CMV-uninfected


title: 51444BCG, Matched Group 22, M.tb-uninfected, CMV-uninfected


title: 51349US, Matched Group 36, M.tb-uninfected, CMV-uninfected


title: 51349BCG, Matched Group 36, M.tb-uninfected, CMV-uninfected


title: 51137BCG, Matched Group 18, M.tb-infected, CMV-uninfected


title: 51268US, Matched Group 9, M.tb-uninfected, CMV-unknown


title: 51173BCG, Matched Group 9, M.tb-uninfected, CMV-uninfected


title: 51133US, Matched Group 18, M.tb-uninfected, CMV-uninfected


title: 51133BCG, Matched Group 18, M.tb-uninfected, CMV-uninfected


title: 51173US, Matched Group 9, M.tb-uninfected, CMV-uninfected


title: 51181BCG, Matched Group 36, M.tb-uninfected, CMV-infected


title: 51183BCG, Matched Group 35, M.tb-uninfected, CMV-unknown


title: 51106US, Matched Group 10, M.tb-uninfected, CMV-uninfected


title: 51120BCG, Matched Group 17, M.tb-uninfected, CMV-infected


title: 51106BCG, Matched Group 10, M.tb-uninfected, CMV-uninfected


title: 51120US, Matched Group 17, M.tb-uninfected, CMV-infected


title: 51007US, Matched Group 8, M.tb-uninfected, CMV-uninfected


title: 51017US, Matched Group 8, M.tb-uninfected, CMV-infected


title: 50987BCG, Matched Group 8, M.tb-infected, CMV-infected


title: 51017BCG, Matched Group 8, M.tb-uninfected, CMV-infected


title: 50972BCG, Matched Group 26, M.tb-uninfected, CMV-infected


title: 50983BCG, Matched Group 2, M.tb-infected, CMV-uninfected


title: 50983US, Matched Group 2, M.tb-infected, CMV-uninfected


title: 51137US, Matched Group 18, M.tb-infected, CMV-uninfected


title: 50972US, Matched Group 26, M.tb-uninfected, CMV-infected


title: 50892US, Matched Group 38, M.tb-uninfected, CMV-infected


title: 50987US, Matched Group 8, M.tb-infected, CMV-infected


title: 50902BCG, Matched Group 14, M.tb-uninfected, CMV-uninfected


title: 51007BCG, Matched Group 8, M.tb-uninfected, CMV-uninfected


title: 50915US, Matched Group 10, M.tb-uninfected, CMV-infected


title: 50915BCG, Matched Group 10, M.tb-uninfected, CMV-infected


title: 50902US, Matched Group 14, M.tb-uninfected, CMV-uninfected


title: 50892BCG, Matched Group 38, M.tb-uninfected, CMV-infected


title: 50810BCG, Matched Group 36, M.tb-uninfected, CMV-uninfected


title: 50762US, Matched Group 38, M.tb-uninfected, CMV-uninfected


title: 50779US, Matched Group 9, M.tb-infected, CMV-infected


title: 50752US, Matched Group 8, M.tb-uninfected, CMV-infected


title: 50810US, Matched Group 36, M.tb-uninfected, CMV-uninfected


title: 50853BCG, Matched Group 26, M.tb-uninfected, CMV-infected


title: 50853US, Matched Group 26, M.tb-uninfected, CMV-infected


title: 50779BCG, Matched Group 9, M.tb-infected, CMV-infected


title: 50732US, Matched Group 17, M.tb-uninfected, CMV-uninfected


title: 50715BCG, Matched Group 15, M.tb-uninfected, CMV-unknown


title: 50715US, Matched Group 15, M.tb-uninfected, CMV-unknown


title: 50619US, Matched Group 11, M.tb-uninfected, CMV-infected


title: 50601US, Matched Group 10, M.tb-infected, CMV-infected


title: 50732BCG, Matched Group 17, M.tb-uninfected, CMV-uninfected


title: 50752BCG, Matched Group 8, M.tb-uninfected, CMV-infected


title: 50762BCG, Matched Group 38, M.tb-uninfected, CMV-uninfected


title: 50619BCG, Matched Group 11, M.tb-uninfected, CMV-infected


title: 50569US, Matched Group 16, M.tb-uninfected, CMV-infected


title: 50596US, Matched Group 35, M.tb-uninfected, CMV-uninfected


title: 50596BCG, Matched Group 35, M.tb-uninfected, CMV-uninfected


title: 50583BCG, Matched Group 14, M.tb-uninfected, CMV-uninfected


title: 50713BCG, Matched Group 9, M.tb-uninfected, CMV-infected


title: 50520US, Matched Group 17, M.tb-uninfected, CMV-uninfected


title: 50517US, Matched Group 15, M.tb-uninfected, CMV-uninfected


title: 50583US, Matched Group 14, M.tb-uninfected, CMV-uninfected


title: 50514US, Matched Group 14, M.tb-uninfected, CMV-infected


title: 50517BCG, Matched Group 15, M.tb-uninfected, CMV-uninfected


title: 50713US, Matched Group 9, M.tb-uninfected, CMV-infected


title: 50514BCG, Matched Group 14, M.tb-uninfected, CMV-infected


title: 50510US, Matched Group 34, M.tb-uninfected, CMV-infected


title: 50508US, Matched Group 18, M.tb-uninfected, CMV-infected


title: 50601BCG, Matched Group 10, M.tb-infected, CMV-infected


title: 50508BCG, Matched Group 18, M.tb-uninfected, CMV-infected


title: 50498US, Matched Group 18, M.tb-uninfected, CMV-infected


title: 50478US, Matched Group 14, M.tb-infected, CMV-infected


title: 50478BCG, Matched Group 14, M.tb-infected, CMV-infected


title: 50520BCG, Matched Group 17, M.tb-uninfected, CMV-uninfected


title: Scrambled_Control_3

city: Corvallis

first: Andrey

last: Morgun

state: OR

address: Pharmacy Building, 1601 SW Jefferson Way

department: Pharmaceutical Sciences

institute: Oregon State University

description: lane4-s131-index-CACTAA-Scrambled_Control-M7-RAW_S131_L004_R1_001.fastq.gz

data_processing:
Sequences were processed to remove the adapter, polyA and low-quality bases by BBTools (https://jgi.doe.gov/data-and-tools/bbtools/) using bbduk parameters of k=13, ktrim=r, forcetrimleft=12, useshortkmers=t, mink=5, qtrim=r, trimq=15, minlength=20.
Reads were aligned to mouse genome and transcriptome (ENSEMBL NCBIM37) using Tophat (v2.1.1) 70 with default parameters.
Number of reads per million for mouse genes were counted using HTSeq (v 0.6.0) 71
Assembly: ENSEMBL NCBIM37
Supplementary files format and content: CSV files includes relativized counts per million values for each Sample.

growth_protocol: RAW Cells were grown in DMEM (high glucose) media (Thermofisher, MA) supplemented with 10% FBS in 5% CO2 at 37°C. Cells were than seeded in a 24 well plate with 250,000 cells per well in 500 ul complete media for 24 hours.

extract_protocol:
RNA was extracted using an OMNI Bead Ruptor and 2.8 mm ceramic beads (OMNI International) followed by Qiashredder and an RNeasy kit. Total RNA was quantified using Quant-iT RNA Assay Kit (Thermo Fisher Scientific). Complementary DNA was prepared using qScript reverse transcription kit (QuantaBio).
RNA libraries were prepared with the QuantSeq 3’mRNA-Seq Library Prep Kit (Lexogen) for the Apollo 324 NGS Library Prep System and sequenced using Illumina NextSeq.

treatment_protocol: 100,000 RAW cells per well in 500 ul complete medium were seeded in 24 well plate for 24 hours. After 24 h, medium was replaced with fresh medium and cells were treated with siRNAs or scrambled control for 24 h. The final concentration of each siRNA was 20 pmol. After 24 h of siRNA transfection, 5% CFS or its control was added to respective wells and incubated for 24 h, followed by collection of cell lysates in RLT buffer.

value: monocyte/macrophage-like cells; transformed cell line derived from BALB/c mice


title: Myd88_siRNA_Osci_2

description: lane4-s130-index-TCGAGG-Myd88_siRNA_Osci-M6-RAW_S130_L004_R1_001.fastq.gz

value: Myd88 siRNA + O. valericigenes


title: Scrambled_Control_2

description: lane4-s134-index-AATGAA-Scrambled_Control-M10-RAW_S134_L004_R1_001.fastq.gz


title: Scrambled_Osci_3

description: lane4-s135-index-ACAACG-Scrambled_Osci-M11-RAW_S135_L004_R1_001.fastq.gz

value: Oscillibacter valericigenes


title: Myd88_siRNA_Osci_4

description: lane4-s136-index-ATATCC-Myd88_siRNA_Osci-M12-RAW_S136_L004_R1_001.fastq.gz


title: Myd88_siRNA_Osci_1

description: lane4-s133-index-CGCCTG-Myd88_siRNA_Osci-M9-RAW_S133_L004_R1_001.fastq.gz


title: 50477BCG, Matched Group 35, M.tb-infected, CMV-uninfected


title: Scrambled_Osci_4

description: lane4-s132-index-GGTATA-Scrambled_Osci-M8-RAW_S132_L004_R1_001.fastq.gz


title: 50477US, Matched Group 35, M.tb-infected, CMV-uninfected


title: Scrambled_Control_4

description: lane4-s128-index-AATAGC-Scrambled_Control-M4-RAW_S128_L004_R1_001.fastq.gz


title: 50510BCG, Matched Group 34, M.tb-uninfected, CMV-infected


title: 50459BCG, Matched Group 17, M.tb-infected, CMV-infected


title: Myd88_siRNA_Osci_3

description: lane4-s127-index-GCATGG-Myd88_siRNA_Osci-M3-RAW_S127_L004_R1_001.fastq.gz


title: Scrambled_Osci_2

description: lane4-s126-index-CTCCAT-Scrambled_Osci-M2-RAW_S126_L004_R1_001.fastq.gz


title: 50452BCG, Matched Group 11, M.tb-uninfected, CMV-infected


title: 50459US, Matched Group 17, M.tb-infected, CMV-infected


title: 50451US, Matched Group 43, M.tb-uninfected, CMV-uninfected


title: 50498BCG, Matched Group 18, M.tb-uninfected, CMV-infected


title: 50451BCG, Matched Group 43, M.tb-uninfected, CMV-uninfected


title: 50452US, Matched Group 11, M.tb-uninfected, CMV-infected


title: Scrambled_Control_1

description: lane4-s125-index-TAGGCT-Scrambled_Control-M1-RAW_S125_L004_R1_001.fastq.gz


title: Scrambled_Osci_1

description: lane4-s129-index-GTGCCA-Scrambled_Osci-M5-RAW_S129_L004_R1_001.fastq.gz


title: 50445US, Matched Group 1, M.tb-uninfected, CMV-uninfected


title: KO29

city: Pittsburgh

first: Dhivyaa

last: Rajasundaram

state: PA

address: 4401 Penn Avenue

department: Pediatrics

institute: University of Pittsburgh

data_processing:
Quality control fo the data was assessed using FastqQC, and aligned using the STAR aligner. This was followed by read counting using featureCounts.
Assembly: mm10

source_name: Liver tissue

extract_protocol:
RNA was isolated from aliquots of liver tissue (10 mg) procured from euthanized mice (male myeloid cell conditional FoxO1-knockout and male wild-type littermates, n=4 per group) after 25 weeks of NASH diet feeding, using the RNeasy Micro Kit (QIAGEN). RNA purity was first checked on 1% agarose gel and was then validated, using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
Aliquots of liver RNA (1 µg) were used for the preparation of sequencing libraries from each sample, using NEBNext UltraTM RNA Library Prep Kit for Illumina (New England Biolabs, USA). Briefly, mRNA was purified from total RNA, using poly-T oligo-attached magnetic beads. Fragmentation was carried out, using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X) (New England Biolabs, USA). Random hexamer primer and M-MuLV Reverse Transcriptase (RNase H) were used for the first strand cDNA synthesis. Second strand cDNA synthesis was performed, using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of the 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. To select cDNA fragments of 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then USER Enzyme (New England Biolabs, USA) was used with size selected and adaptor-ligated cDNA at 37 °C for 15 min, followed by 5-min incubation at 95 °C. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. RNA-Seq was conducted at the Novogene (Novogene, CA, USA).

tag: stain

value: Myeloid FoxO1 Knockout

tag: age

value: 31 weeks old


title: 50404US, Matched Group 10, M.tb-uninfected, CMV-infected


title: KO26


title: WT23

value: Wild Type


title: WT24


title: WT25


title: 50404BCG, Matched Group 10, M.tb-uninfected, CMV-infected


title: WT22


title: 50392US, Matched Group 16, M.tb-uninfected, CMV-infected


title: KO28


title: 50378US, Matched Group 31, M.tb-uninfected, CMV-infected


title: NSCs, even, rep3

city: Planegg-Martinsried

first: Marius

middle: Frederik

last: Schneider

state: Bayern

address: Großhaderner Str. 9

department: molecular biology

institute: Biomedical center munich - LMU

data_processing:
Library strategy: ChIRP-seq
alignment against mm10 using bowtie2 ( Langmead & Salzberg, 2012)
Filtering of  Bam Files using samtools (Li, et al., 2009).
Peak calling of ChIP DNA samples using MACS 14 (Feng, et al., 2011).
merging of even and odd  samples using deeptools (Ramirez, et al., 2016) and bedtools (Quinlan & Hall, 2010) .
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph files

source_name: NSCs, even

growth_protocol: Neural stem cells (NSC) were isolated from embryonic cortices E15-16 and cultivated as monolayer cultures on poly (D) lysine-coated dishes in DMEM F12 supplemented with 1x B27, 5% FCS, 40 ng/ml FGF2. Differentiation was initiated in Neurobasal medium supplemented with 1x GlutMax, 1x B27 five days post-seeding.

extract_protocol:
ChIRP purified DNA was recovered from beads by Rnase A and RNase H treatment. Eluted DNA was treated with Proteinase K, extracted with Chloroform:Phenol: Isoamyl alcohol 25:24:1, and precipitated in 66% EtOH and 300 mM NaOAC.
purified DNA was end-repaired, A-tailed, and ligated with sequencing adaptors.
ChIP DNA

treatment_protocol: NSCs from 8 x 15cm dishes were harvested seven days post-seeding by trypsinization and 2x washed with 100 ml PBS.  Cells were crosslinked in 100ml 1% Glutaraldehyde for 10min at RT.  Crosslinking reaction was quenched with 125mM Glycine for 5min.  Cells were pelleted at 1000g for 5min.  ChIRP experiment was done according to standard protocol (Chu, et al., 2011).  Crosslinked cells were washed two times in PBS and lysed in 2ml ChIRP-lysis buffer (50mM Tris-HCl pH 7.0, 10mM EDTA, 1% SDS,1mM PMSF, 1x protease inhibitor, SuperaseIn 100U/ml). Chromatin shearing was conducted on Bioruptor for 4h (10sec, 15sec off).  This procedure typically yielded 150-600 bp sheared chromatin.  Sheared chromatin was diluted with 4 ml ChIRP-hybridization buffer (50 mM Tris-HCl pH 7.0, 750 mM NaCl, 15% (m/v) formamide, 1 mM EDTA, 1% SDS ,1 mM PMSF, 1x protease inhibitor, SuperaseIn 100 U/ml) and divided into to pools. Hybridization reaction was performed with two independent probes sets.  100pmol odd-biotinylated probe set containing all probes labeled with odd numbers was added to the first pool, and 100pmol of the even-biotinylated probe set containing all even labeled probes was added to the second pool.  Probes were hybridized 37°C under continuous rotation.  After 4 h hybridization, 100µl of preequilibrated magnetic streptavidin beads were added.  Captured RNA-chromatin complexes were coupled to beads for 30min at 37°C under continuous rotation.  Afterward, beads were washed 5x in 1ml ChIRP-wash buffer (300 mM NaCl, 30 mM tri-sodium-citrate, 0.1% SDS, 1 mM PMSF) for  5min at 37°C.

tag: developmental stage

value: embryonic cortices

value: embryonic neural stem cells (NSC) isolated from cortex

tag: lncrna

tag: probe set

value: even probe set

tag: fraction

value: ChIP DNA

tag: sample type

value: ChIRP-seq


title: NSCs, input, rep3

source_name: NSCs, input

tag: tissue

tag: cell type

value: input


title: NSCs, odd, rep3

source_name: NSCs, odd

tag: strain

value: odd probe set


title: 50378BCG, Matched Group 31, M.tb-uninfected, CMV-infected

value: PBMC

tag: genotype

value: BCG

tag: treatment


title: 50376BCG, Matched Group 11, M.tb-uninfected, CMV-infected


title: 50376US, Matched Group 11, M.tb-uninfected, CMV-infected

value: US


title: 50360US, Matched Group 39, M.tb-uninfected, CMV-infected


title: NSCs, even, rep2


title: KO27


title: NSCs, odd, rep1


title: NSCs, odd, rep2


title: NSCs, input, rep2


title: 50392BCG, Matched Group 16, M.tb-uninfected, CMV-infected


title: 50311US, Matched Group 31, M.tb-uninfected, CMV-infected


title: 50323US, Matched Group 38, M.tb-uninfected, CMV-infected


title: 50323BCG, Matched Group 38, M.tb-uninfected, CMV-infected


title: 50294BCG, Matched Group 33, M.tb-uninfected, CMV-uninfected


title: NSCs, D7, RUSKD, rep2

data_processing:
alignment of RNA sequencing reads against mm10 using Star  (Dobin, et al., 2012)
calculation of tpm values using rsem (Li & Dewey, 2011)
statistical evaluation of transcriptome profiles using DESeq (Love, et al., 2014)
Genome_build: mm10, GRCm38.99  transcriptable
Supplementary_files_format_and_content: DeSeq matrix & tpm estimation

source_name: NSCs, D7, RUSKD

extract_protocol:
RNA was extracted from cells using Trizol  and precipitated with 50% Isopropanol.
Isolated RNA was polyA-enriched and reverse-transcribed. After 2nd strand synthesis of cDNA, DNA was fragmented, end-repaired, A-tailed, and ligated with sequencing adaptors.

treatment_protocol: NSC were lentivirally transduced with a scramble or a RUS targeting shRNA.

value: RUS shRNA

value: RUS KD

tag: time

value: Day 7


title: NSCs, D7, RUSKD, rep1


title: 50311BCG, Matched Group 31, M.tb-uninfected, CMV-infected


title: NSCs, D7, RUSKD, rep3


title: 50569BCG, Matched Group 16, M.tb-uninfected, CMV-infected


title: 50292US, Matched Group 39, M.tb-uninfected, CMV-infected


title: NSCs, even, rep1


title: 50279BCG, Matched Group 42, M.tb-uninfected, CMV-uninfected


title: NSCs, input, rep1


title: 50292BCG, Matched Group 39, M.tb-uninfected, CMV-infected


title: NSCs, D7, ctrl, rep3

source_name: NSCs, D7, ctrl

value: scr shRNA

value: control


title: NSCs, D7, ctrl, rep4


title: NSCs, D7, ctrl, rep1


title: NSCs, D7, ctrl, rep2


title: NSCs, D5, RUSKD, rep4

source_name: NSCs, D5, RUSKD

value: Day 5


title: 50276BCG, Matched Group 32, M.tb-uninfected, CMV-infected


title: 50276US, Matched Group 32, M.tb-uninfected, CMV-infected


title: 50360BCG, Matched Group 39, M.tb-uninfected, CMV-infected


title: NSCs, D5, RUSKD, rep3


title: NSCs, D7, RUSKD, rep4


title: 50264US, Matched Group 33, M.tb-uninfected, CMV-uninfected


title: 50264BCG, Matched Group 33, M.tb-uninfected, CMV-uninfected


title: NSCs, D5, ctrl, rep4

source_name: NSCs, D5, ctrl


title: NSCs, D5, RUSKD, rep2


title: 50248US, Matched Group 38, M.tb-infected, CMV-uninfected


title: NSCs, D5, ctrl, rep3


title: NSCs, D5, RUSKD, rep1


title: 50278US, Matched Group 34, M.tb-infected, CMV-infected


title: 50278BCG, Matched Group 34, M.tb-infected, CMV-infected


title: 50248BCG, Matched Group 38, M.tb-infected, CMV-uninfected


title: 50243BCG, Matched Group 39, M.tb-uninfected, CMV-infected


title: 50241BCG, Matched Group 43, M.tb-uninfected, CMV-unknown


title: NSCs, D5, ctrl, rep2


title: NSCs, D5, ctrl, rep1


title: 50243US, Matched Group 39, M.tb-uninfected, CMV-infected


title: 50241US, Matched Group 43, M.tb-uninfected, CMV-unknown


title: Chow_liver [s103593-001-005]

city: Rijswijk

first: Eveline

last: Gart

state: Zuid-Holland

address: Van vredenburchweg 659

country: Netherlands

institute: TNO

data_processing:
Quality filtering and adapter-trimming of the Illumina Nextseq 500 V2 fastq files was performed by TRIMMOMATIC software
Trimmed Fastq files were merged (in case of Paired-end reads) and aligned to the reference genome using the STAR 2.5 algorithm with default settings (https://github.com/alexdobin/STAR).
Based on the mapped read locations and the gene annotation, Htseq-count 0.6.1p1 was used to count the read mapping frequency/gene (transcript region) resulting in count.files.
Genome_build: Mus_musculus.GRCm38.gencode.vM19
Supplementary_files_format_and_content: The count files contain the # reads mapped per gene (not normalised per sample). These counts serve as input for the statistical analysis using DEseq2 package.

growth_protocol: Male Ldlr-/-.Leiden mice were bred and housed in  the American Association for Accreditation of Laboratory Animal Care (AAALAC)-accredited animal facility at TNO (Leiden, the Netherlands). They were group-housed (four to five mice per cage) in Macrolon cages in clean-conventional animal rooms (relative humidity 50–60%, temperature ~21C, light cycle 07:00 to 19:00) with ad libitum access to food and water. To induce obesity, mice were fed a HFD (D12451, Research Diets Inc., New Brunswick, USA; containing 20 kcal% protein, 35 kcal% carbohydrate, 45 kcal% mainly from lard fat) for 8 weeks, as reported previously (REF will be added prior to submission). Mice on standard rodent chow (Sniff-R/M-V1530, Uden, the Netherlands) were used as a reference.

extract_protocol:
Mice were terminated in week 28 by gradual-fill CO2 asphyxiation. At sacrifice, livers and other organs were isolated and immediately snap-frozen in liquid N2.
Next Generation Sequencing was performed at Genome Scan (Leiden, the Netherlands). For this, strand-specific cDNA libraries were generated from RNA using oligo-dT magnetic beads, mRNA fragmentation, NEBNext Ultra Directional RNA Library Prep Kit from Illumina, NEB #E7420S/L resulting in 300–500 bp amplified libraries/sample. Libraries were multiplexed, clustered, and sequenced on a Nextseq 500 V2 system for Illumina, (New England Biolabs, Inc. Ipswich, MA, USA), with a single-end, 75 bp sequencing protocol, 13-26 million reads per sample and indexing.
Clustering and DNA sequencing using the NovaSeq6000 v1.5 was performed according to manufacturer's protocols. A concentration of 1.1 nM of DNA was used yielding paired end reads (2x 150bp). NovaSeq control software NCS v1.7 was used. Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA3.4.4 and Bcl2fastq v2.20.

treatment_protocol: After a run-in of 8 weeks on HFD, obese hyperinsulinemic mice were treated with 2-fucosyllactose (2’-FL) by oral gavage twice daily (750 mg/kg/day) until week 28, and compared with vehicle control mice receiving saline (n=15/group).

tag: treatmentperiod

value: Chow-Diet

tag: mousenr

value: liver


title: 51181US, Matched Group 36, M.tb-uninfected, CMV-infected


title: 50205US, Matched Group 16, M.tb-infected, CMV-infected


title: 50205BCG, Matched Group 16, M.tb-infected, CMV-infected


title: Chow_liver [s103593-001-004]


title: Chow_liver [s103593-001-002]


title: Chow_liver [s103593-001-003]


title: 50201US, Matched Group 33, M.tb-uninfected, CMV-unknown


title: 50201BCG, Matched Group 33, M.tb-uninfected, CMV-unknown


title: Chow_liver [s103819-001-040]


title: Chow_liver [s103819-001-039]


title: 50192US, Matched Group 43, M.tb-uninfected, CMV-infected


title: Chow_liver [s103819-001-037]


title: 50132US, Matched Group 3, M.tb-uninfected, CMV-uninfected


title: 50167BCG, Matched Group 13, M.tb-uninfected, CMV-infected


title: Chow_liver [s103593-001-006]


title: 50167US, Matched Group 13, M.tb-uninfected, CMV-infected


title: HFD_AHS_liver [s103819-001-035]


title: HFD_AHS_liver [s103819-001-036]


title: HFD_AHS_liver [s103819-001-034]


title: 50132BCG, Matched Group 3, M.tb-uninfected, CMV-uninfected


title: 50123BCG, Matched Group 3, M.tb-uninfected, CMV-infected


title: 50120BCG, Matched Group 42, M.tb-uninfected, CMV-infected


title: 50123US, Matched Group 3, M.tb-uninfected, CMV-infected


title: HFD_AHS_liver [s103819-001-033]


title: HFD_AHS_liver [s103819-001-030]


title: 50092US, Matched Group 31, M.tb-uninfected, CMV-infected


title: HFD_AHS_liver [s103819-001-028]


title: HFD_AHS_liver [s103819-001-027]


title: 50120US, Matched Group 42, M.tb-uninfected, CMV-infected


title: HFD_AHS_liver [s103819-001-029]


title: HFD_AHS_liver [s103819-001-026]


title: 50087BCG, Matched Group 35, M.tb-uninfected, CMV-unknown


title: HFD_AHS_liver [s103819-001-025]


title: 50192BCG, Matched Group 43, M.tb-uninfected, CMV-infected


title: HFD_AHS_liver [s103819-001-024]


title: 50033US, Matched Group 11, M.tb-infected, CMV-infected


title: 50033BCG, Matched Group 11, M.tb-infected, CMV-infected


title: 50012US, Matched Group 32, M.tb-uninfected, CMV-uninfected


title: HFD_AHS_liver [s103819-001-023]


title: HFD_AHS_liver [s103819-001-021]


title: 50012BCG, Matched Group 32, M.tb-uninfected, CMV-uninfected


title: HFD_AHS_liver [s103819-001-020]


title: 20058US, Matched Group 13, M.tb-uninfected, CMV-unknown


title: 20058BCG, Matched Group 13, M.tb-uninfected, CMV-unknown


title: HFD_AHS_liver [s103819-001-022]


title: 20032BCG, Matched Group 32, M.tb-uninfected, CMV-unknown


title: 50092BCG, Matched Group 31, M.tb-uninfected, CMV-infected


title: 50087US, Matched Group 35, M.tb-uninfected, CMV-unknown


title: HFD_AHS_liver [s103819-001-019]


title: HFD_veh_liver [s103819-001-018]

value: HFD(High Fat Diet)+vehicle


title: 20018US, Matched Group 20, M.tb-uninfected, CMV-infected


title: HFD_veh_liver [s103819-001-014]


title: HFD_veh_liver [s103819-001-015]


title: 20016US, Matched Group 3, M.tb-uninfected, CMV-unknown


title: HFD_veh_liver [s103819-001-013]


title: 10583US, Matched Group 33, M.tb-infected, CMV-unknown


title: 10583BCG, Matched Group 33, M.tb-infected, CMV-unknown


title: HFD_veh_liver [s103819-001-011]


title: 10426US, Matched Group 43, M.tb-infected, CMV-unknown


title: HFD_veh_liver [s103819-001-010]


title: HFD_veh_liver [s103819-001-008]


title: HFD_veh_liver [s103819-001-017]


title: 10341US, Matched Group 13, M.tb-infected, CMV-unknown


title: HFD_veh_liver [s103819-001-016]


title: 10260US, Matched Group 3, M.tb-infected, CMV-unknown


title: 20018BCG, Matched Group 20, M.tb-uninfected, CMV-infected


title: 10341BCG, Matched Group 13, M.tb-infected, CMV-unknown


title: 10426BCG, Matched Group 43, M.tb-infected, CMV-unknown


title: HFD_veh_liver [s103819-001-005]


title: HFD_veh_liver [s103819-001-006]


title: 20016BCG, Matched Group 3, M.tb-uninfected, CMV-unknown


title: 10174US, Matched Group 20, M.tb-infected, CMV-infected

value: US (media)


title: 10260BCG, Matched Group 3, M.tb-infected, CMV-unknown


title: HFD_veh_liver [s103819-001-004]


title: Zip8 knockout sample 2

city: Los Angeles

first: DIANHUA

last: JIANG

address: 8700 BEVERLY BLVD

institute: CEDARS SINAI

data_processing:
Cell Ranger (10x Genomics) was used to process raw data and  Seurat was used for downstream analysis.
Genome_build: NOT PROVIDED
Supplementary_files_format_and_content: barcode.tsv, features.tsv, and matrix.mtx

source_name: Lung CD45- cells_Zip8 KO

extract_protocol: mRNAs from sorted single cells were  reverse transcribed and amplified as previously described. Library preparation and sequencing were performed as described previously. Sequencing libraries for cDNA from single cells were prepared as per the Single Cell 3′ v2 Reagent Kits User Guide (10x Genomics, Pleasanton, CA, USA). Cellular suspensions were loaded on a Chromium Controller instrument (10x Genomics) to generate single-cell Gel Bead-In-EMulsions (GEMs). GEM-reverse transcription (RT) was performed in a Veriti 96-well thermal cycler (Thermo Fisher Scientific, Waltham, MA, USA). GEMs were collected and the cDNA was amplified and purified with SPRIselect Reagent Kit (Beckman Coulter, Brea, CA, USA). Indexed sequencing libraries were constructed using Chromium Single-Cell 3′ Library Kit for enzymatic fragmentation, end-repair, A-tailing, adapter ligation, ligation cleanup, sample index PCR, and PCR cleanup. The barcoded sequencing libraries were quantified by quantitative PCR using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems, Roche Holding AG, Basel, Switzerland). Sequencing libraries were loaded on a NextSeq500 (Illumina, San Diego, CA, USA) with a custom sequencing setting (Read 1: 26 bp, Read 2: 91 bp, Index 1: 8 bp) to obtain a sequencing depth of ~200K reads per cell.

tag: mouse lung cells

value: Lung CD45- cells

tag: genotype/variation

value: Zip8 knockout


title: 10174BCG, Matched Group 20, M.tb-infected, CMV-infected

tag: cell line


title: HFD_veh_liver [s103819-001-002]


title: HFD_veh_liver [s103819-001-009]


title: pDC,Untreated,6h,Donor1

data_processing:
RNA-seq: Sequencing quality was measured with fastp (Chen et al., 2018). Reads were then mapped reads in genes counted against the human genome (hg38) with STAR aligner and Gencode v21(Dobin et al., 2013; Frankish et al., 2019). Differential gene expression analysis was performed in R(Team, 2020) using the edgeR package (Robinson et al., 2010).
ATAC-seq:  fastq files were processed and analyzed according to ENCODE best practices. Briefly, reads were checked for quality and adapters trimmed using fastp. Reads passing QC were aligned to the latest release of the human genome (hg38) with the Bowtie2 aligner(Langmead and Salzberg, 2012). Reads aligning in proper pairs to a single location in the genome were further filtered to exclude PCR duplicates using Samtools(Li et al., 2009). High quality, de-duplicated reads were used to call peaks with Macs2 (Zhang et al., 2008). Peaks which were observed in at least two replicates were used for differential peak analysis with edgeR (Robinson et al., 2010). Analysis of differentially accessible motifs was performed using chromVAR (Schep et al., 2017).  Signal tracks and other visualizations were performed in R using the HSSRscripts package developed by the HSS Genomics Research center (https://gitlab.com/hssgenomics/hssrscripts).
Assembly: human genome (hg38)
Supplementary files format and content: countMatrix.tsv: Tab delimited file of read counts per gene
Supplementary files format and content: edgeR_total_peaks_2020-12-11.xlsx: excel file with peak locations, annotation, and normalized read counts

source_name: blood

extract_protocol:
RNAseq: Total RNA was isolated using RNeasy Plus Mini kit.
ATACseq: See construction protocol
RNAseq: Single-end reads were obtained on an Illumina HiSeq 2500 in the Weill Cornell Epigenomics Core Facility at the depth of 21-37 million fragments per sample.
ATACseq: library preparation was performed as previously described (Corces et al., 2017). Briefly, 1 x 105 purified pDCs cells were cultured in 96 U-bottom well and left unstimulated or cultured with CpG (0.25μM), CXCL4 (10μg/ml) or CpG+CXCL4 (CXCL4 at 10μg/ml, CpG at 0.25μM) for 6h. Cells were harvested for the ATAC-Seq library construction immediately.

value: blood

value: pDC

value: Healthy Donor

value: Untreated


title: pDC,CXCL4+CpG1018,6h,Donor3


title: Control sample 4

source_name: Lung CD45- cells_control


title: HFD_veh_liver [s103819-001-001]


title: pDC,Untreated,6h,Donor3


title: pDC,CXCL4+CpG1018,6h,Donor2


title: Control sample 3


title: pDC,Untreated,6h,Donor2


title: Control sample 2


title: HFD_veh_liver [s103819-001-007]


title: Young mice day 14 sample 2

description:
YD14-2
Read 1: 26 bp, Read 2: 91 bp, Index 1: 8 bp

data_processing:
Raw scRNA-seq data was aligned to mouse genome mm10 with Cell Ranger (10x Genomics). Downstream quality control, normalization and visualization were done with Seurat package. For quality control, the output expression matrix from Cell Ranger was done based on number of genes detected in each cell, number of transcripts detected in each cell and percentage of mitochondrial genes. The expression matrix was then normalized and visualized with UMAP.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: csv, h5

source_name: Lung Lin-Epcam+ cells

extract_protocol: mRNAs from sorted single cells were reverse transcribed and amplified as previously described. Library preparation and sequencing were performed as described previously. Sequencing libraries for cDNA from single cells were prepared as per the Single Cell 3′ v2 Reagent Kits User Guide (10x Genomics, Pleasanton, CA, USA). Cellular suspensions were loaded on a Chromium Controller instrument (10x Genomics) to generate single-cell Gel Bead-In-EMulsions (GEMs). GEM-reverse transcription (RT) was performed in a Veriti 96-well thermal cycler (Thermo Fisher Scientific, Waltham, MA, USA). GEMs were collected and the cDNA was amplified and purified with SPRIselect Reagent Kit (Beckman Coulter, Brea, CA, USA). Indexed sequencing libraries were constructed using Chromium Single-Cell 3′ Library Kit for enzymatic fragmentation, end-repair, A-tailing, adapter ligation, ligation cleanup, sample index PCR, and PCR cleanup. The barcoded sequencing libraries were quantified by quantitative PCR using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems, Roche Holding AG, Basel, Switzerland). Sequencing libraries were loaded on a NextSeq500 (Illumina, San Diego, CA, USA) with a custom sequencing setting (26bp for Read 1 and 98bp for Read 2) to obtain a sequencing depth of ~200K reads per cell.

tag: age

value: Young

value: Bleomycin

tag: time point

value: Day 14

value: Lung Lin-Epcam+ cells

tag: assay

value: scRNA-sequencing


title: pDC,CXCL4+CpG1018,6h,Donor1


title: pDC,CpG1018,6h,Donor3


title: pDC,CXCL4,6h,Donor3


title: Young mice day 14 sample 1

description:
YD14-1
Read 1: 26 bp, Read 2: 91 bp, Index 1: 8 bp


title: Control sample 1

value: control


title: Zip8 knockout sample 1


title: Young mice day 14 sample 3

description:
YD14-3
Read 1: 26 bp, Read 2: 91 bp, Index 1: 8 bp


title: pDC,CpG1018,6h,Donor2


title: pDC,CXCL4,6h,Donor2


title: pDC,CXCL4,6h,Donor1


title: Young mice day 4 sample 2

description:
YD4-2
Read 1: 26 bp, Read 2: 91 bp, Index 1: 8 bp

value: Day 4


title: Young mice day 0 sample 2

description:
YD0-2
Read 1: 26 bp, Read 2: 91 bp, Index 1: 8 bp

value: Day 0


title: 30H

city: Memphis

first: Jason

last: Chiang

state: Tennessee

address: 262 Danny Thomas Pl

department: Pathology

institute: St. Jude Children's Research Hospital

data_processing:
The RNA-seq data were subjected to both adaptor and quality trimming and then aligned to the human reference genome (build hg19) with STAR (v2.7.0a).
The read counts of gene expression data were preprocessed, normalized, and filtered to remove genes with very low expression values (bottom 5%) in more than 90% samples using edgeR (v3.34.0).
NetBID (v2.0.3) and SJARACNe-based network reconstruction were then used to infer drivers (transcription factors or signalling factors) from the transcriptomics data by calculating the activity of drivers and gene sets in Ubuntu (v18.04) with Python (v3.6.1).
Differentially expressed genes and differentially activated drivers were then queried against MSigDB (v7.4).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include raw counts for each sample
Supplementary_files_format_and_content: tab-delimited text file include log2-transformed normalized counts for each sample

source_name: Brain

extract_protocol:
Microdissection of high-grade and low-grade areas was accomplished by laying unstained sections upon a printout of a marked H&E-section and scraping the area of interest with sterile razor blades or 30-gauge needles under a stereomicroscope with 40× magnification. Total RNA was prepared from the microdissected sections following the instructions of a PureLink FFPE Total RNA Isolation Kit.
The Illumina Total Stranded RNA protocol was applied.

value: brain

tag: tumor stage

value: tumor

tag: area

value: high grade


title: Young mice day 0 sample 1

description:
YD0-1
Read 1: 26 bp, Read 2: 91 bp, Index 1: 8 bp


title: 27H


title: Young mice day 4 sample 4

description:
YD4-4
Read 1: 26 bp, Read 2: 91 bp, Index 1: 8 bp


title: 27L

value: low grade


title: 50445BCG, Matched Group 1, M.tb-uninfected, CMV-uninfected

value: PBMC

value: BCG


title: pDC,CpG1018,6h,Donor1

first: David

last: Oliver

institute: Hospital for Special Surgery

value: blood

value: pDC


title: 33H


title: Young mice day 4 sample 1

description:
YD4-1
Read 1: 26 bp, Read 2: 91 bp, Index 1: 8 bp


title: 26L


title: Old mice day14 sample 3

description:
OD14-3
Read 1: 26 bp, Read 2: 91 bp, Index 1: 8 bp

value: Old


title: 30L


title: Young mice day 0 sample 3

description:
YD0-3
Read 1: 26 bp, Read 2: 91 bp, Index 1: 8 bp

value: Young


title: 33L


title: Young mice day 4 sample 3

description:
YD4-3
Read 1: 26 bp, Read 2: 91 bp, Index 1: 8 bp

value: Bleomycin


title: Old mice day 4 sample 2

description:
OD4-2
Read 1: 26 bp, Read 2: 91 bp, Index 1: 8 bp


title: Old mice day 4 sample 1

description:
OD4-1
Read 1: 26 bp, Read 2: 91 bp, Index 1: 8 bp


title: Old mice day14 sample 1

description:
OD14-1
Read 1: 26 bp, Read 2: 91 bp, Index 1: 8 bp

value: Day 14


title: 26H


title: Old mice day 4 sample 4

description:
OD4-4
Read 1: 26 bp, Read 2: 91 bp, Index 1: 8 bp

value: Lung Lin-Epcam+ cells


title: 25L


title: 24L


title: 23H


title: 25H


title: 23L


title: 22H


title: 24H


title: Old mice day 0 sample 2

description:
OD0-2
Read 1: 26 bp, Read 2: 91 bp, Index 1: 8 bp

value: scRNA-sequencing


title: 20L


title: 22L


title: Old mice day14 sample 2

description:
OD14-2
Read 1: 26 bp, Read 2: 91 bp, Index 1: 8 bp


title: CFLKO_KO_Refeed_rep3

city: NEW YORK

first: Domenico

last: Accili

state: NY

address: 1150 ST NICHOLAS AVENUE, RM238

department: Medicine

institute: Columbia University

data_processing:
Sequenced reads from the RNA-seq experiment were aligned to mouse genome mm10 using HISAT2
Cufflinks was used for transcript assembly
Gene expression levels were expressed as fragments per kilobase of exon per million mapped sequence reads and Cuffdiff was used for statistical comparison
Genome_build: mm10
Supplementary_files_format_and_content: tab-deliminated text files including FPKM values for each sample
Supplementary_files_format_and_content: tab-deliminated text files with gene expression comparisons between WT control vs. liver-specific FoxO1 for each condition

source_name: liver tissue

extract_protocol:
Isolated liver tissues were snap frozened in liquid nitrogen, and RNA was harvested using Trizol reagent.
Libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina)

treatment_protocol: For acute liver-specific FoxO1 knockout mice were generated by injection of 1×1011 purified viral particles (AAV8.TBG.eGFP or AAV8.TBG.Cre) per mouse via tail vein.

value: liver


title: 20H


title: Old mice day 4 sample 3

description:
OD4-3
Read 1: 26 bp, Read 2: 91 bp, Index 1: 8 bp

value: Day 4


title: CFLKO_WT_Refeed_rep3


title: CFLKO_KO_Refeed_rep2


title: CFLKO_KO_Refeed_rep1


title: CFLKO_WT_Refeed_rep1


title: 12L


title: 11H


title: CFLKO_WT_Refeed_rep2


title: 12H


title: CFLKO_KO_Fast_rep3


title: Old mice day 0 sample 1

description:
OD0-1
Read 1: 26 bp, Read 2: 91 bp, Index 1: 8 bp

value: Day 0


title: CFLKO_KO_Fast_rep2


title: CFLKO_KO_Fast_rep1


title: 7L

value: brain


title: 7H

value: tumor


title: CFLKO_WT_Fast_rep2


title: Old mice day 0 sample 3

description:
OD0-3
Read 1: 26 bp, Read 2: 91 bp, Index 1: 8 bp


title: CFLKO_WT_Fast_rep3


title: Untreated Control HBE Donor 1328 H3K27ac ChIP [D24_UT_K27ac_repHBE1328]

first: Walter

last: Eckalbar

address: 513 Parnassus Ave MSB-813

institute: University of California, San Francisco

data_processing:
aligned with STAR_2.5.2b,  --readFilesCommand gzcat      --outFileNamePrefix Alignments/D28_IFN_K27ac_repHBE1243out/   --outSAMtype BAM   SortedByCoordinate      --outFilterType BySJout   --outFilterMultimapNmax 1   --outFil  terMismatchNmax 999 --outFilterMismatchNoverLmax 0.04   --clip3pAdapterSeq GATCGGAAGAGCACACGTCTGAACTCCAGTCAC  --alignIntronMin 20  --alignIntronMax 1  --alignMatesGapMax 10   --alignSJDBoverhangMin 1   --quantMode GeneCounts
Coverage graphs were created with bedtools v2.29.0
Peaking calling with MACS2 (2.2.6a2)
IDR to find reproducible peaks between samples (2.0.3)
Htseq count (0.11.0) to count reads over reproducable peak regions
Genome_build: GRCh38
Supplementary_files_format_and_content: Experiment-wide Gene by sample counts tables

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

extract_protocol:
After removal of accumulated mucus with 10 mM DTT in PBS, cells were trypsinized with 0.25% trypsin-EDTA for 10 min at 37 °C and neutralized. . Cells were manually counted using a hemocytometer, and equal numbers of cells from each donor were pooled. Each pool included four samples (one from each donor and each representing a different cytokine stimulation).
Manufactures instructions where follow to carry out a ChIP using Diagenoid Low Cell ChIP kit, NGS libraries where created from the purified DNA using Rubicon DNA-seq kit.

treatment_protocol: Cells were cultured at ALI for 23 d without cytokine or with IFN-a (10 ng/mL for the final 1 d), IL-13 (10 ng/mL for the final 7 d), IL-17 (10 ng/mL for the final 7 d), or the combination of IFN-a and IL-13.

value: ALI-cultured HBECs d 23

tag: donor id

value: Donor 1328

value: Untreated Control

tag: chip antibody

value: H3K27ac (Abcam, ab4729)


title: AFLKO_CRE_Refeed_rep3

tag: tissue


title: CFLKO_WT_Fast_rep1

tag: strain


title: Untreated Control HBE Donor 1333 H3K27ac ChIP [D24_UT_K27ac_repHBE1333]

tag: cell type

value: Donor 1333


title: Untreated Control HBE Donor 1326 H3K27ac ChIP [D24_UT_K27ac_repHBE1326]

value: Donor 1326

tag: treatment


title: AFLKO_CRE_Fast_rep3

tag: genotype


title: Untreated Control HBE Donor 1333 Input [D24_UT_Input_repHBE1333]

source_name: Untreated Control HBE Donor 1333 Input


title: 11L

value: low grade


title: AFLKO_GFP_Refeed_rep3


title: Untreated Control HBE Donor 1326 Input [D24_UT_Input_repHBE1326]

source_name: Untreated Control HBE Donor 1326 Input


title: Untreated Control HBE Donor 1605 Input [D24_UT_Input_T]

source_name: Untreated Control HBE Donor 1605 Input

value: Donor 1605


title: Untreated Control HBE Donor 1243 Input [D24_UT_Input_repHBE1243]

source_name: Untreated Control HBE Donor 1243 Input

value: Donor 1243


title: Untreated Control HBE Donor 1243 H3K27ac ChIP [D24_UT_K27ac_repHBE1243]


title: AFLKO_GFP_Refeed_rep2


title: HFD_AHS_liver [s103819-001-032]

tag: treatmentperiod


title: AFLKO_CRE_Refeed_rep2


title: AFLKO_GFP_Fast_rep3


title: IFN Alpha Treatment HBE Donor 1328 H3K27ac ChIP [D24_IFN_K27ac_repHBE1328]

value: IFN Alpha Treatment


title: AFLKO_GFP_Fast_rep2


title: AFLKO_CRE_Fast_rep2


title: IFN Alpha Treatment HBE Donor 1333 H3K27ac ChIP [D24_IFN_K27ac_repHBE1333]


title: AFLKO_CRE_Refeed_rep1


title: AFLKO_GFP_Refeed_rep1


title: Untreated Control HBE Donor 1328 Input [D24_UT_Input_repHBE1328]

source_name: Untreated Control HBE Donor 1328 Input


title: IL13 Plus IFN Alpha Treatment HBE Donor 1328 H3K27ac ChIP [D24_CO_K27ac_repHBE1328]

value: IL13 Plus IFN Alpha Treatment


title: Pooled_input_vehicle

data_processing:
Reads were aligned to mouse genome mm10 using Bowtie2
The reads used in subsequent analysis passed Illumina’s purity filter, aligned with no more than 2 mismatches, and mapped uniquely to the genome. Duplicate reads were removed with Picard tools. The tags were extended at their 3′-ends to 200-bp.
Peak calling was performed by MACS 2.1.0
Genome_build: mm10
Supplementary_files_format_and_content: tdf files were generated using igvtools

extract_protocol:
Lysates were clarified from sonicatd nuclei and GFP- or histone-DNA complexes were isolated with antibody
ChIP-seq libraries were constructed using KAPA Hyper Prep Kit (KAPA Biosystems) according to the manufacturer’s instructions. ChIP-seq libraries were quantified by Tapestation (Agilent) and sequenced on an Illumina NEXTseq (Illumina, San Diego, CA, USA) with 75-base single-end mode.

treatment_protocol: Samples were treated by vehicle or S961 for 48hours

value: Combined samples 1 and 2


title: AFLKO_CRE_Fast_rep1

value: liver


title: D24_UT_K27ac_T


title: IL13 Plus IFN Alpha Treatment HBE Donor 1243 H3K27ac ChIP [D24_CO_K27ac_repHBE1243]


title: H3K27ac_Vehicle_Fast

value: H3K27ac (Active motif, 39133)

value: 4-h-fasted Vehicle control (Normal saline)


title: IL17 Treatment HBE Donor 1326 H3K27ac ChIP [D24_17_K27ac_repHBE1326]

value: IL17 Treatment


title: FoxO1_Vehicle_Refeed

value: GFP (Abcam, ab290)

value: 4-h-fasted / 1-h-refeed Vehicle control (Normal saline)


title: IL17 Treatment HBE Donor 1328 H3K27ac ChIP [D24_17_K27ac_repHBE1328]

value: ALI-cultured HBECs d 23

value: Donor 1328


title: FoxO1_S961_Refeed

value: 4-h-fasted / 1-h-refeed S961 treated


title: IFN Alpha Treatment HBE Donor 1243 H3K27ac ChIP [D24_IFN_K27ac_repHBE1243]

value: H3K27ac (Abcam, ab4729)


title: IL13 Plus IFN Alpha Treatment HBE Donor 1333 H3K27ac ChIP [D24_CO_K27ac_repHBE1333]

value: Donor 1333


title: AFLKO_GFP_Fast_rep1


title: FoxO1_S961_Fast

value: 4-h-fasted S961 treated


title: IFN Alpha Treatment HBE Donor 1326 H3K27ac ChIP [D24_IFN_K27ac_repHBE1326]

value: Donor 1326