title: 977SATB2

city: Ann Arbor

first: Kelly

last: Bakulski

state: MI

address: 1415 Washington Heights

department: Department of Epidemiology

institute: University of Michigan

data_processing:
initial QC with fastQC 0.11.5 and multiQC 0.9
alignment to Oar_rambouillet_v1.0 genome using STAR 2.6.0c
post alignment QC with QoRTs 1.3.6
quantification of reads mapping to gene exons with featureCounts in Subread package 1.6.1
Genome_build: Oar_rambouillet_v1.0
Supplementary_files_format_and_content: comma-separated values file of gene counts with lanes collapsed for all samples

organism: Ovis aries

source_name: subcutaneous adipose tissue

growth_protocol: Female lambs were weaned at ∼8 weeks of age and provided with a maintenance diet consisting of 0.64 kg of corn, 0.64 kg hay per day, and 0.014 kg of supplement (36% crude protein) to prevent the development of obesity.

extract_protocol:
Both subcutaneous and visceral adipose tissue were collected during the second breeding season at ~21 months of age. Before collection, estrus was synchronized with two injections of prostaglandin F2α (PGF2α, 10 mg, i.m.; Lutalyse, Pfizer Animal Health, Florham Park, NJ) administered 11 days apart. Tissues were harvested 24 hours after the second PGF2α injection during the follicular phase to maintain comparable steroid environment. All animals were euthanized by barbiturate overdose (Fatal Plus; Vortech Pharmaceuticals, Dearborn, MI). Visceral adipose from the mesenteric fat surrounding the ventral sac of the rumen and subcutaneous adipose from the sternal region were obtained. Tissues were flash-frozen and stored at -80 °C until processed.
Libraries were prepared with SMARTer universal low input RNA kit (Takara, Mountain View, CA) following ribosome depletion

treatment_protocol: Pregnant sheep were randomly assigned to control and BPA groups. Control mothers received only the vehicle (corn oil) and BPA animals received 0.5 mg/kg /day of BPA dissolved in corn oil. Both treatments were administered daily through subcutaneous injections from days 30 through 90 of gestation (term: ∼147 days).

value: BPA

value: SAT


title: 922SATB2

status: Public on Apr 30 2020

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

tag: treatment


title: 071117_CD14p16p_TB40_41M

city: Charlestown

first: Pritha

last: Sen

state: Massachusetts

address: 149 13th street

institute: Massachusetts General Hospital

description:
Bulk RNA-seq for primary human monocytes infected with CMV
RNA.raw.cnt.table.txt
071117_CD14p16p_TB40_41M

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference genome hg19 using STAR
Transcript abundance was calculated using Htseq
Single-cell libraries were aligned to hg19 reference genome and UMI count files were generated using the Illumina BaseSpace SureCell application
Genome_build: hg19

organism: Homo sapiens

extract_protocol:
Desired monocyte populations for sorted by flow cytometry and RNA was harvested using Qiagen RNeasy micro kit and on column Dnase digestion was performed. RNA quantity and quality was analyzed on Agilent Bioanalyzer.
Lexogen QuantSeq Kit was used for the construction of bulk sequencing libraries. SureCell WTA 3' Library Prep Kit was used for the construction of single-cell sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: THP-1 cells were stimulated with PMA at 100 ng/ml for 48 hours prior to infection with TB40/E-5. Human peripheral blood mononuclear cells (PBMC) were isolated from CMV IgG negative immunocompetent donors and cultured ex vivo in donor autologous serum and infected with TB40/E-5.

value: CMV

tag: gender

value: M

tag: immune status

value: immunocompetent

tag: virus strain


title: 071117_CD14p16p_mock_41M

description:
Bulk RNA-seq for primary human monocytes infected with CMV
RNA.raw.cnt.table.txt
071117_CD14p16p_mock_41M

value: mock


title: 010318_CD14p16p_mock_52M

description:
Bulk RNA-seq for primary human monocytes infected with CMV
RNA.raw.cnt.table.txt
010318_CD14p16p_mock_52M


title: 071717_CD14p16p_TB40_27F

description:
Bulk RNA-seq for primary human monocytes infected with CMV
RNA.raw.cnt.table.txt
071717_CD14p16p_TB40_27F

value: F


title: siC_1_LPS [siRNA]

city: Philadelphia

first: Hoang

last: Nguyen

state: PA

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania Perelman School of Medicine

data_processing:
#genome alignment single read: STAR --genomeDir ~/STAR_mm10_GENOME_DIR  --runThreadN 20 --readFilesIn $i --outFileNamePrefix ${i/.fastq.gz/}_ --outFilterMultimapNmax 1 --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --outSAMstrandField intronMotif
#genome alignment paired-end read: STAR --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --runThreadN 20 --sjdbGTFfile ~/mm10/mm10_genes.gtf  --genomeDir ~/STAR_mm10_GENOME_DIR_150 --readFilesIn $f1 $f2 --outFileNamePrefix $out --outSAMstrandField intronMotif
#counting reads: featureCounts -t exon -g gene_id -a ~/mm10/mm10_genes.gtf -T 20
#DGE with edgeR
Genome_build: mm10
Supplementary_files_format_and_content: featureCounts read counts for all samples

organism: Mus musculus

source_name: bone marrow-derived macrophages

growth_protocol: Control and MHD3KO mice were euthanized, and bone marrow were extracted for hindlimb femurs. Bone marrow cells were cultured for 7 days in DMEM supplemented with 10% FBS and 30% L929 media for 7 days on petri dishes to allow macrophage differentiation.

extract_protocol:
After treatment, cells were immediately lysed in trizol and RNA purified with RNeasy RNA isolation kit according to the manufacturers instructions.  Illumina Truseq Stranded RNA Total RNA library prep kit was used with 1ug RNA of total RNA for construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After 7 days of differeniation, BMDM were replated, rested overnight before treated with BSA control, LPS(5ng/ml for 4 hours), IL4 (100ng/ml for 24hours). For rescue macrophages, retrovirus expressing Y298F or WT HDAC3 were added to BMDM 4 days post harvest from femurs. For siRNA experiments, siRNA were addded 24 hours after replating of the macrophages on the 7th day post harvest.

tag: strain

tag: age

value: 8 weeks

tag: genotype

value: control

tag: agent


title: 010318_CD14p16p_TB40_52M

description:
Bulk RNA-seq for primary human monocytes infected with CMV
RNA.raw.cnt.table.txt
010318_CD14p16p_TB40_52M


title: 941SATB2


title: siC_1_veh [siRNA]


title: siC_2_veh [siRNA]


title: 928SATC

value: Control


title: siC_3_veh [siRNA]


title: siC_3_LPS [siRNA]


title: 122917_CD14p16p_TB40_44M

description:
Bulk RNA-seq for primary human monocytes infected with CMV
RNA.raw.cnt.table.txt
122917_CD14p16p_TB40_44M


title: 924SATC


title: siC_2_LPS [siRNA]


title: 902SATC


title: 122917_CD14p16p_mock_44M

description:
Bulk RNA-seq for primary human monocytes infected with CMV
RNA.raw.cnt.table.txt
122917_CD14p16p_mock_44M


title: 984VATB2

source_name: visceral adipose tissue

value: VAT


title: 112917_32M_CD14p16p_TB40

description:
Bulk RNA-seq for primary human monocytes infected with CMV
RNA.raw.cnt.table.txt
112917_32M_CD14p16p_TB40


title: 918SATB2


title: 931SATC


title: 112917_32M_CD14p16p_mock

description:
Bulk RNA-seq for primary human monocytes infected with CMV
RNA.raw.cnt.table.txt
112917_32M_CD14p16p_mock


title: 112917_31F_CD14p16p_TB40

description:
Bulk RNA-seq for primary human monocytes infected with CMV
RNA.raw.cnt.table.txt
112917_31F_CD14p16p_TB40


title: C4KO_TAC_1week_3

type: RNA

first: Robert

last: Kitchen

state: MA

institute: MGH / HMS

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Samples were assayed with Agilent's MoGene-2.0-st-v1 platform (Affymetrix) for mRNA expression. Raw microarray expression files in the form of .cel were normalized by the robust multichip algorithm (RMA) using the oligo v1.40 package in R. Normalized, log2 transformed microarray expression values were used for differential expression between the C4KO and F/F Ctr hearts using the LIMMA package in R.

label: biotin

label_protocol: standard Affymetrix protocol

extract_protocol: RNA was isolated from frozen heart using Trizol (Qiagen), phase separation followed by column purification was carried out using an RNA isolation kit from Trizol according to manufacturer's instructions.

treatment_protocol: Mice underwent transverse aortic constriction (TAC), one week post-surgery, mice were anaestethized and hearts were harvested and stored at -80°C.

value: male

tag: genotype/variation

value: CITED4 knockout

tag: treatment/time point

value: post-TAC, 1 week

tag: tissue

value: heart


title: 112917_31F_CD14p16p_mock

description:
Bulk RNA-seq for primary human monocytes infected with CMV
RNA.raw.cnt.table.txt
112917_31F_CD14p16p_mock


title: C4KO_TAC_1week_4


title: C4KO_TAC_1week_1


title: 121517_56M_CD14p16p_TB40

description:
Bulk RNA-seq for primary human monocytes infected with CMV
RNA.raw.cnt.table.txt
121517_56M_CD14p16p_TB40


title: 121517_56M_CD14p16p_mock

description:
Bulk RNA-seq for primary human monocytes infected with CMV
RNA.raw.cnt.table.txt
121517_56M_CD14p16p_mock


title: F/FCtr_TAC_1week_4

value: floxed control


title: 928VATC


title: 977VATB2


title: 918VATB2


title: F/FCtr_TAC_1week_3


title: 910VATB2


title: 924VATC


title: 121517_26F_CD14p16p_TB40

description:
Bulk RNA-seq for primary human monocytes infected with CMV
RNA.raw.cnt.table.txt
121517_26F_CD14p16p_TB40


title: C4KO_TAC_1week_2


title: 121517_26F_CD14p16p_mock

description:
Bulk RNA-seq for primary human monocytes infected with CMV
RNA.raw.cnt.table.txt
121517_26F_CD14p16p_mock


title: 908VATC


title: F/FCtr_TAC_1week_1


title: 902VATC


title: 122917_44M_TB40_CD14p16n

description:
Bulk RNA-seq for primary human monocytes infected with CMV
RNA.raw.cnt.table.txt
122917_44M_TB40_CD14p16n

value: CMV 16-


title: shRNF8+DHT-3

city: Shenyang

first: Tingting

last: Zhou

state: Liaoning

address: No.77 Puhe Road, Shenyang North New Area

department: Institute of Translational Medicine

country: China

institute: China Medical University

data_processing:
Basecalls performed using CASAVA version 1.8
RNA-seq reads were mapped to human genome by hisat2 software.
Cuffdiff2 software was used to perform differentially expressed gene analysis.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

source_name: CWR22Rv1 Cell

extract_protocol:
RNA extraction protocol
library construction protocol

tag: cell line


title: shRNF8+DHT-1


title: shRNF8+vehicle-2


title: shRNF8+vehicle-3


title: 121517_56M_mock_CD14p16n

description:
Bulk RNA-seq for primary human monocytes infected with CMV
RNA.raw.cnt.table.txt
121517_56M_mock_CD14p16n

value: mock 16-


title: 122917_44M_mock_CD14p16n

description:
Bulk RNA-seq for primary human monocytes infected with CMV
RNA.raw.cnt.table.txt
122917_44M_mock_CD14p16n


title: 121517_56M_TB40_CD14p16n

description:
Bulk RNA-seq for primary human monocytes infected with CMV
RNA.raw.cnt.table.txt
121517_56M_TB40_CD14p16n


title: shRNF8+vehicle-1


title: 121517_26F_mock_CD14p16n

description:
Bulk RNA-seq for primary human monocytes infected with CMV
RNA.raw.cnt.table.txt
121517_26F_mock_CD14p16n


title: 121517_26F_TB40_CD14p16n

description:
Bulk RNA-seq for primary human monocytes infected with CMV
RNA.raw.cnt.table.txt
121517_26F_TB40_CD14p16n


title: F/FCtr_TAC_1week_2


title: 112917_31F_TB40_CD14p16n

description:
Bulk RNA-seq for primary human monocytes infected with CMV
RNA.raw.cnt.table.txt
112917_31F_TB40_CD14p16n


title: 112917_32M_TB40_CD14p16n

description:
Bulk RNA-seq for primary human monocytes infected with CMV
RNA.raw.cnt.table.txt
112917_32M_TB40_CD14p16n


title: MCF7_CDK7

city: Cambridge

first: Richard

middle: A

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

library_source: genomic

data_processing:
Aligned using /usr/local/bin/bowtie with configuration -p 4 --best -k 2 -m 2 --sam -l 40
Genome_build: hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1

molecule: genomic DNA

source_name: Breast Cancer

growth_protocol: MCF7 cells were grown in phenol red- free high-glucose Dulbecco's Modified Eagle's Media (DMEM; Invitrogen) containing 5% charcoal-dextran treated FBS (Sigma) for 48 hours for the estrogen deprived condition then crosslinked and frozen.

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
sonication

treatment_protocol: For the estrogen stimulated condition, after 48 hours of estrogen deprivation, the cells were treated with 20nM estrogen for 24 hours then crosslinked and frozen. For the hexanediol treated condition, cells were treated with 1.5% hexanediol for 30 minutes after the 24 hours of estrogen stimulation.

tag: cell type

tag: chip antibody

tag: chip antibody vendor

value: Bethyl

tag: chip antibody cat.#

tag: chip antibody lot#


title: 3-hESC_Wt_D0_3_S79

city: Oslo

first: Adnan

last: Hashim

state: Oslo

address: NCMM - Forskningsparken, House 1, 3rd Floor - Gaustadalléen 21

department: NCMM (Centre for Molecular Medicine Norway)

country: Norway

institute: UiO (University of Oslo)

data_processing:
Raw reads were aligned to the human genome (hg19), and splice junctions were mapped using TopHat v2.1.0 with default parameters
Gene based read counts were obtained using featureCount v1.5.0-p1
To perform normalization and statistical evaluation with negative binomial model between conditions on the count data, we used DESeq2 v1.10.1 Biconductor package
Genes were considered differentially expressed when showing an absolute log2 fold change (treatment/control) ≥ 1.5 with adjusted p-value (padj) ≤0.05.
Genome_build: hg19
Supplementary_files_format_and_content: txt files contain gene counts that can be used as input of DESEQ2

source_name: human Embryonic Stem cells

growth_protocol: Day 11 NPC (NPC D11) were differentiated from human embryonic stem cells in N2/B27 media supplemented with dual SMAD inhibitors. NPC D21 are obtained with further differentiation of NPC D11 for 10 more days in N2/B27 media supplemented with dual SMAD inhibitors.

extract_protocol:
Cells are lysed with Trizol reagent (Qiagen) and RNA is extracted with chloroform. Extracted RNA was further cleaned with RNAeasy kit (Qiagen) and on-column DNA digestion according to the manufacturer’s instructions.
Strand-specific Tru-Seq RNA-Seq library preparation

treatment_protocol: Until appearance of neural rosettes dual SMAD inhibitors were added everyday of differentiation protocol. When neural rosettes appear, dual SMAD inhibitors were withdrawn and N2/B27 media is supplemented with basic FGF for 3-4 days.

value: human Embryonic Stem cells

tag: differentiation time

value: 0 days

value: Wild Type


title: 8-OPA1hetneuron7weeks-3_S9

source_name: neurons

value: ES cell derived neurons

value: 7 weeks


title: shRNF8+DHT-2


title: 6_50M_CD14pos16neg_GFP

description:
Bulk RNA-seq for primary human monocytes infected with CMV
RNA.raw.cnt.table.txt
6_50M_CD14pos16neg_GFP

tag: treatment

tag: gender

value: M

value: immunocompetent


title: Huh7_Ribo_rep2

city: Guangzhou

first: Jian-Hua

last: Yang

address: No. 135, Xingang Xi Road

department: School of Life Sciences

institute: Sun Yat-sen University

data_processing:
Library strategy: ribosome profiling
Raw reads were aligned to UCSC hg19 reference genome by STAR with parameters provided by RiboCode manual.
Transcripts annotation files were prepared as gff3 format.
The length range of the RPF reads and  the P-site location was selected through interpretation of the metaplots drawing the distance between 5' end and start codon.
Translated ORFs were detected using RiboCode with parameters:  "-l no -g"
Genome_build: hg19
Supplementary_files_format_and_content: bed files recording the ORFs detected by RiboCode

growth_protocol: HuH-7 cells were cultured in DMEM medium (GIBCO) supplemented with  10% foetal bovine serum plus antibiotics.Cells were maintained in a 5% CO2 atmosphere at 37℃.

extract_protocol:
The cell medium was discarded and HuH-7 cells were washed twice with ice-cold PBS containing 100 µg/mL cycloheximide,which was added to inhibit the translational elongation of ribosomes. The 26-30-nt RPFs were isolated to generate ribosome profiling sequencing libraries.
The ribosome profiling assay was performed as described in the Nature Method’s protocol and the Ribo-seq libraries were prepared according to Illumina’s instructions

value: wild type


title: genomic DNA from PBMC TB299

type: genomic

city: Hsinchu

first: Tingwen

last: Chen

address: No. 75, Boat Street, East District

country: Taiwan

institute: National Yang Ming Chiao Tung University

description: PBMC sample from TB patients

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: PBMC TB299

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from PBMC samples using Qiagen DNeasy Kit according to standard instructions

tag: disease state

value: TB


title: genomic DNA from PBMC TB300

description: PBMC sample from follow up TB patients

source_name: PBMC TB300


title: 112917_32M_mock_CD14p16n

description:
Bulk RNA-seq for primary human monocytes infected with CMV
RNA.raw.cnt.table.txt
112917_32M_mock_CD14p16n

tag: immune status

tag: virus strain


title: Huh7_Ribo_rep1

tag: genotype


title: 8_41M_CD14pos16neg_GFP

description:
Bulk RNA-seq for primary human monocytes infected with CMV
RNA.raw.cnt.table.txt
8_41M_CD14pos16neg_GFP


title: 6-Ctrlneuron7weeks-3_S5


title: genomic DNA from PBMC TB263-2

description: PBMC sample from follow up TB patients

source_name: PBMC TB263-2

tag: age


title: 3_27F_CD14pos16neg_mock

description:
Bulk RNA-seq for primary human monocytes infected with CMV
RNA.raw.cnt.table.txt
3_27F_CD14pos16neg_mock

value: F


title: Glc_Sta_Rep3

city: Baltimore

first: Jeffrey

middle: G.

last: Gardner

state: MD

address: 1000 Hilltop Circle

department: Department of Biological Sciences

institute: University of Maryland - Baltimore County

description:
Standard extraction protocols
GlcNAc_Sta_vs_Glu_Sta.xls

data_processing:
RNA sequencing was performed using an Illumina HiSeq2500 (50bp single-end reads; >10 million reads per sample) by GeneWiz.
The FASTQ files were uploaded to the GALAXY web-based platform for analysis. Aligments of the reads against the C. japonicus genome was perfomed using the HISAT2 and the Transcript quantification was performed with HTSeq.
These counts were then used to generate the differential expression analyses using DESeq2.
Genome_build: GCA_000019225.1
Supplementary_files_format_and_content: Excel Sheet (The following parameters were calculated: base mean, log2 (fold change), standard error of the log2(fold change), and a Benjamini-Hochberg adjusted p-value).

organism: Cellvibrio japonicus

growth_protocol: MOPS defined medium

extract_protocol:
Standard extraction protocols
Standard Illumina protocols

treatment_protocol: 95%EtOH:5%Phenol to stop cellular metabolism

value: WT

tag: carbon source

value: Glucose(Glc)

tag: growth phase

value: Stationary


title: 5-Ctrlneuron7weeks-2_S3


title: genomic DNA from PBMC TB262

description: PBMC sample from TB patients

source_name: PBMC TB262


title: genomic DNA from PBMC TB221

description: PBMC sample from TB patients

source_name: PBMC TB221


title: genomic DNA from PBMC TB221-2

description: PBMC sample from follow up TB patients

source_name: PBMC TB221-2


title: genomic DNA from PBMC TB275-2

description: PBMC sample from follow up TB patients

source_name: PBMC TB275-2


title: 7_41M_CD14pos16neg_mock

description:
Bulk RNA-seq for primary human monocytes infected with CMV
RNA.raw.cnt.table.txt
7_41M_CD14pos16neg_mock


title: genomic DNA from PBMC TB275

description: PBMC sample from TB patients

source_name: PBMC TB275


title: THP-GFPhigh_S8

description:
Bulk RNA-seq for THP-1 infected with CMV
RNA.raw.cnt.table.txt
THP-GFPhigh_S8

value: CMV

tag: culture conditions

value: 100 ng/ml PMA-stimulated

tag: passage

value: passage 3


title: genomic DNA from PBMC TB172

description: PBMC sample from TB patients

source_name: PBMC TB172


title: Glc_Sta_Rep1


title: 5_50M_CD14pos16neg_mock

description:
Bulk RNA-seq for primary human monocytes infected with CMV
RNA.raw.cnt.table.txt
5_50M_CD14pos16neg_mock

value: mock 16-


title: Glc_Sta_Rep2


title: THP-mock_S7

description:
Bulk RNA-seq for THP-1 infected with CMV
RNA.raw.cnt.table.txt
THP-mock_S7

value: mock


title: THP-GFPhigh_S4

description:
Bulk RNA-seq for THP-1 infected with CMV
RNA.raw.cnt.table.txt
THP-GFPhigh_S4


title: 1_33F_CD14pos16neg_mock

description:
Bulk RNA-seq for primary human monocytes infected with CMV
RNA.raw.cnt.table.txt
1_33F_CD14pos16neg_mock


title: THP-GFPhigh_S6

description:
Bulk RNA-seq for THP-1 infected with CMV
RNA.raw.cnt.table.txt
THP-GFPhigh_S6


title: Glc_Exp_Rep3

description:
Standard extraction protocols
GlcNAc_Exp_vs_Glc_Exp.xls

value: Exponential


title: THP-mock_S3

description:
Bulk RNA-seq for THP-1 infected with CMV
RNA.raw.cnt.table.txt
THP-mock_S3


title: PW_Res3

city: Harbin

first: Anshan

last: Shan

state: Heilongjiang

address: NO.600 Changjiang Street

department: Institute of Animal Nutrition

institute: Northeast Agricultural University

description: replicate 3

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: Sus_scrofa.Sscrofa10.2.88
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Sus scrofa

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Hiseq 4000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 28 days

tag: tissue

value: Jejunum


title: Glc_Exp_Rep2


title: GlcNAc_Sta_Rep2

description:
Standard extraction protocols
GlcNAc_Sta_vs_Glu_Sta.xls
CRB_Sta_vs_ GlcNAc_Sta.xls
Chitin_Sta_vs_GlcNAc_Sta.xls
GlcNAc_Exp_vrs_GlcNAc_Sta.xls

value: N-acetylglucosamine (GlcNAc)


title: THP-mock_S1

description:
Bulk RNA-seq for THP-1 infected with CMV
RNA.raw.cnt.table.txt
THP-mock_S1


title: GlcNAc_Sta_Rep1


title: PW_Res2

description: replicate 2


title: genomic DNA from PBMC TB238

description: PBMC sample from TB patients

source_name: PBMC TB238


title: THP-mock_S5

description:
Bulk RNA-seq for THP-1 infected with CMV
RNA.raw.cnt.table.txt
THP-mock_S5


title: DKS14_K_OD1

city: PACIFICA

first: Hiten

last: Madhani

state: CA

institute: UCSF

description:
Affinity purified DNA
processed data file:

data_processing:
Illumina adaptor removed from read 3' ends using Cutadapt
Reads were aligned to the  genome with bowtie v 1.1.2
Analysis performed using custom scripts from bedgraph files normalized to wild type (untagged)
Genome_build: C. neoformans CNA3
Supplementary_files_format_and_content: .bedgraph: Signal of ChIP-seq of the sample normalized to the untagged (wild type, K1) sample and smoothed to a 50bp window

organism: Cryptococcus neoformans

source_name: yeast

growth_protocol: Samples were inoculated at less than an OD600 of 0.01 from starter cultures in YPAD or YNB at 30°C until reaching OD600 of 1.0, 5.0, or 10.0. An aliquot of the culture as it grew in optical density was taken and harvested by centrifugation at 2000xg for 5 minutes.

extract_protocol:
ChIP DNA was extracted by bead beater with 0.5mm zirconia beads.  ChIP DNA was isolated by antibodies directed to our proteins of interest (10 mg anti-FLAG M2).  DNA was then isolated by incubation with SDS/proteinase K followed by column purification (Macherey-Nagel Nucleospin Gel Cleanup Columns).
library preparation as described in Homer et al. 2016

tag: strain

tag: optical density (od600)

tag: media

value: YNB

tag: antibody

value: anti-FLAG

tag: protocol

value: ChIP-seq


title: Glc_Exp_Rep1


title: GlcNAc_Sta_Rep3


title: GlcNAc_Exp_Rep3

description:
Standard extraction protocols
GlcNAc_Exp_vs_Glc_Exp.xls
CRB_Exp_vs_GlcNAc_Exp.xls
Chitin_Exp_vs_GlcNAc_Exp.xls
GlcNAc_Exp_vrs_GlcNAc_Sta.xls


title: genomic DNA from PBMC TB263

description: PBMC sample from TB patients

source_name: PBMC TB263

value: TB


title: genomic DNA from PBMC TB240

description: PBMC sample from TB patients

source_name: PBMC TB240


title: THP-GFPhigh_S2

description:
Bulk RNA-seq for THP-1 infected with CMV
RNA.raw.cnt.table.txt
THP-GFPhigh_S2

tag: treatment


title: genomic DNA from PBMC TB251

description: PBMC sample from TB patients

source_name: PBMC TB251


title: PW_Res1

description: replicate 1


title: genomic DNA from PBMC TB214

description: PBMC sample from TB patients

source_name: PBMC TB214


title: genomic DNA from PBMC TB173

description: PBMC sample from TB patients

source_name: PBMC TB173


title: PW_Con2

description: replicate 2


title: GlcNAc_Exp_Rep2


title: PW_Con3

description: replicate 3


title: achi_Sta_Rep3

description:
Standard extraction protocols
CRB_Sta_vs_Chitin_Sta.xls
Chitin_Sta_vs_GlcNAc_Sta.xls

value: Chitin(achi)


title: achi_Sta_Rep2

value: WT


title: PW_Con1

description: replicate 1


title: achi_Sta_Rep1


title: CRB_Sta_Rep3

description:
Standard extraction protocols
CRB_Sta_vs_ Glc_Sta.xls
CRB_Sta_vs_ GlcNAc_Sta.xls
CRB_Sta_vs_Chitin_Sta.xls
CRB_Exp_vs_CRB_Sta.xls

value: crab shell (CRB)


title: CRB_Sta_Rep2

value: Stationary


title: CRB_Sta_Rep1


title: achi_Exp_Rep3

description:
Standard extraction protocols
CRB_Exp_vs_Chitin_Exp.xls
Chitin_Exp_vs_GlcNAc_Exp.xls


title: W_Res3

description: replicate 3

value: 21 days


title: W_Res2

description: replicate 2


title: achi_Exp_Rep2


title: GlcNAc_Exp_Rep1


title: W_Res1

description: replicate 1


title: achi_Exp_Rep1


title: HCC10T

city: Beijing

first: Yiming

last: Lu

address: Taiping Road

institute: State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine

description:
HCC.scRNAseq.S71915.count.txt.gz
HCC.scRNAseq.S71915.normalized.txt.gz

data_processing:
Cell Ranger’s mkfastq function was used to demultiplex raw base call files from the sequencer, into sample-specific fastq files. Afterward, fastq files for each sample were processed with Cell Ranger’s count function, which was used to align reads to human genome (build hg38) and quantify gene expression levels in single cells.
Genome_build: hg38
Supplementary_files_format_and_content: HCC.scRNAseq.S71915.count.txt.gz: Tab-delimited text file includes single cell gene expression measured in raw counts; HCC.scRNAseq.S71915.normalized.txt.gz: HCC.scRNAseq.S71915.count.txt.gz: Tab-delimited text file includes normalized and log-transformed single cell gene expression.

source_name: Single cells in primary tumor tissue of HCC patient

extract_protocol:
Following surgical resection, fresh tissue samples of primary tumors, adjacent non-tumor livers, portal vein tumor thrombuses and metastatic lymph node were immediately transferred to pre-cooled MACS Tissue Storage Solution (Miltenyi Biotec) and were shipped at 4°C. For each sample, ~1g tissue was used for dissociation, the remaining tissue, if any, was fixed in formalin for 48 hours and embedded in paraffin for further immunohistochemistry analysis. For dissociation, the tissue was minced using surgical scalpels and further disintegrated using the Liver Dissociation Kit (Miltenyi Biotec) and the gentleMACS Dissociator (Miltenyi Biotech) according to manufacturer’s instructions. The resulting single-cell suspension was filtered sequentially through sterile 70-mm and 40-mm cell strainers. The cell suspension was stained for viability with 25 mM cisplatin (Enzo Life Sciences) in a 1-min pulse before quenching with 10% FBS. The single-cell suspensions were then used for subsequent droplet-based scRNA-seq.
Single-cell suspensions were converted to barcoded scRNA-seq libraries by using the Chromium Single Cell 3’ Library, Gel Bead & Multiplex Kit and Chip Kit (10x Genomics), aiming for an estimated 5,000 cells per library and following the manufacturer’s instructions. Samples were processed using kits pertaining to V2 barcoding chemistry of 10x Genomics. Single samples are always processed in a single well of a PCR plate, allowing all cells from a sample to be treated with the same master mix and in the same reaction vessel. For each patient, all samples (NTL, PT, PVTT and MLN) were processed in parallel in the same thermal cycler. The generated scRNA-seq libraries were sequenced on an Illumina NovaSeq sequencer. The Cell Ranger software (version 2.2.0) was used to perform sample demultiplexing, barcode processing and single-cell 3’ counting.

tag: patient

value: primary tumor

tag: tumor

value: Hepatocellular carcinoma (HCC)


title: HCC10N

source_name: Single cells in non-tumor liver tissue of HCC patient

value: adjacent non-tumor liver


title: HCC10L

source_name: Single cells in metastatic lymph node tissue of HCC patient

value: metastatic lymph node


title: W_Con3

description: replicate 3


title: W_Con1

description: replicate 1


title: 61M_TB40_5_23_18_S1_4

description:
Single-cell RNA-seq on primary human monocytes infected with CMV
61M_TB40_5_23_18_S1.pfcell.umiCounts.csv

value: CMV

tag: gender

value: M

tag: immune status

value: immunocompetent


title: CRB_Exp_Rep3

description:
Standard extraction protocols
CRB_Exp_vs_ Glc_Exp.xls
CRB_Exp_vs_GlcNAc_Exp.xls
CRB_Exp_vs_Chitin_Exp.xls
CRB_Exp_vs_CRB_Sta.xls

tag: genotype

value: Exponential


title: CRB_Exp_Rep1


title: W_Con2

description: replicate 2

tag: age

value: Jejunum


title: HCC09T


title: DKS13_K_OD1

value: wild type

value: YNB

value: anti-FLAG


title: HCC09N


title: 61M_TB40_5_23_18_S1_3

tag: virus strain


title: BRHM04_5LD_YNB

description:
processed data file:
WT_v_L5_YNB_DE_sig_changed.csv

data_processing:
A10 trimmed with CutAdapt
Genome alignment with STAR
differential expression analysis with DEseq2
Genome_build: C. neoformans CNA3
Supplementary_files_format_and_content: "sig_changed.csv": contains output from DEseq2 for genes determined as significantly changed between that sample and wild type

extract_protocol: RNA was extracted as described in Burke et al. 2019.

value: Quant-seq


title: 61M_TB40_5_23_18_S1_2


title: HCC08T


title: BRHM04_5LC_YNB


title: HCC08P

source_name: Single cells in portal vein tumor thrombus (PVTT) tissue of HCC patient

value: portal vein tumor thrombus (PVTT)


title: 7-OPA1hetneuron7weeks-2_S7

source_name: neurons

tag: cell type

value: ES cell derived neurons

tag: differentiation time

value: 7 weeks


title: 61M_TB40_5_23_18_S1_1


title: CRB_Exp_Rep2

value: WT

tag: carbon source

value: crab shell (CRB)

tag: growth phase


title: HCC08N

tag: tissue

value: Hepatocellular carcinoma (HCC)


title: BRHM04_5WC_YNB

description: processed data file:

tag: strain

tag: optical density (od600)


title: 61M_mock_5_23_18_S1_4

description:
Single-cell RNA-seq on primary human monocytes infected with CMV
61M_mock_5_23_18_S1.pfcell.umiCounts.csv

value: mock


title: 61M_mock_5_23_18_S1_3


title: HCC07T

value: primary tumor


title: BRHM04_5NB_YNB

description:
processed data file:
WT_v_N5_YNB_DE_sig_changed.csv

tag: media

tag: antibody


title: 61M_mock_5_23_18_S1_1

tag: treatment


title: 61M_mock_5_23_18_S1_2


title: BRHM04_5NA_YNB

tag: protocol


title: HCC07P

tag: patient

tag: tumor


title: BRHM04_5CB_YNB

description:
processed data file:
WT_v_C5_YNB_DE_sig_changed.csv


title: HCC07N

value: adjacent non-tumor liver


title: BRHM04_5CA_YNB


title: BRHM04_5WD_YNB

description: processed data file:


title: HCC06N


title: BRHM04_5QA_YNB

description:
processed data file:
WT_v_Q5_YNB_DE_sig_changed.csv


title: HCC05T


title: 44MTB40_CD14T_S1_1

description:
Single-cell RNA-seq on primary human monocytes infected with CMV
44MTB40_CD14T_S1.pfcell.umiCounts.csv

value: CMV

tag: gender

value: M

tag: immune status


title: 44MTB40_CD14T_S1_3

value: immunocompetent


title: 44MTB40_CD14T_S1_4


title: 44MTB40_CD14T_S1_2


title: AD_APP_ND1_Dif3

city: Lund

first: Jeovanis

last: Gil Valdés

state: Skane

address: Sölvegatan 19, BMC D13

department: Department of Biomedical Engineering

country: Sweden

institute: Lund University

description: GeneChip data generated with Affymetrix GeneChip Command Console (AGCC) and Expression Console (EC)

hyb_protocol: 5,5 µg fragmented and labeled ss cDNA were hybridized to Affymetrix Clariom D human arrays for 16 h at 45° C and 60 rpm in a GeneChip hybridization oven 640. Hybridized arrays were washed and stained in an Affymetrix Fluidics Station FS450.

scan_protocol: The fluorescent signals were measured with an Affymetrix GeneChip Scanner 3000 7G. Fluidics and scan functions were controlled by the Affymetrix GeneChip Command Console v4.3.3 software.

data_processing: Probe set signals in log2 scale were calculated by using the GCCN-SST-RMA algorithm with the Affymetrix GeneChip Expression Console v1.4 Software. The output matrix was processed in Perseus framework.

source_name: iPSC-derived neurons

label_protocol: 200 ng of total RNA was used to generate double-stranded cDNA. 15 µg of subsequently synthesized cRNA was purified and reverse transcribed into sense-strand (ss) cDNA, whereat unnatural dUTP residues were incorporated. Purified ss cDNA was fragmented using a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) followed by a terminal labeling with biotin.

growth_protocol: Spheroids aged 30 DIV were dissociated into single cells and plated in NDM on poly-ornithine/laminin coated surfaces. Two hours later the cells were transduced with either the eGFP or ND1-expressing Moloney murine leukemia-derived retroviral vectors (pCMMP-IRES2eGFP-WPRE or pCMMP-NeuroD1-IRES2eGFP-WPRE) at a multiplicity of infection (MOI) of 5, in proliferation medium supplemented by protamine-sulfate (4 mg/ ml, Sigma-Aldrich)

extract_protocol: Total RNA was extracted from FACS-sorted neurons according to the “Purification of total RNA from animal and human tissue” protocol of the RNeasy Micro Kit (QIAGEN, Hilden, Germany). Total RNA was eluted in 14 μl of nuclease free water. Purity and integrity of the RNA was assessed on the Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip reagent set (Agilent, Palo Alto, CA, USA).

value: iPSC-derived neurons

value: female

tag: disease state

value: APP mutation

tag: transfection


title: AD_APP_ND1_Dif2

tag: cell type


title: Healthy_GFP_Dif2

value: Healthy

value: GFP


title: BRHM04_5WB_YNB

description: processed data file:

tag: genotype

value: wild type

value: YNB

value: Quant-seq


title: Healthy_ND1_Dif3


title: Healthy_GFP_Dif3


title: HCC04T


title: HCC06T


title: 44MMOZK_CD14_S1_3

description:
Single-cell RNA-seq on primary human monocytes infected with CMV
44MMOZK_CD14_S1.pfcell.umiCounts.csv

tag: virus strain


title: BRHM04_5WA_YNB

description: processed data file:


title: AD_APP_ND1_Dif1


title: HCC05N


title: AD_APP_GFP_Dif3


title: AD_APP_GFP_Dif2


title: AD_APP_GFP_Dif1


title: HCC04N


title: BRHM03_1LD_YNB

description:
processed data file:
WT_v_L1_YNB_DE_sig_changed.csv


title: Healthy_ND1_Dif2


title: 44MMOZK_CD14_S1_2


title: Healthy_ND1_Dif1


title: HCC03N


title: 44MMOZK_CD14_S1_4


title: BRHM04_5QB_YNB


title: BRHM03_1WC_YNB

description: processed data file:


title: Healthy_GFP_Dif1


title: HCC02T


title: 31FT840_CD14T_S1_3

description:
Single-cell RNA-seq on primary human monocytes infected with CMV
31FT840_CD14T_S1.pfcell.umiCounts.csv

value: F


title: HCC01T


title: 31FT840_CD14T_S1_4


title: 31FT840_CD14T_S1_2


title: 31FT840_CD14T_S1_1


title: 44MMOZK_CD14_S1_1


title: HCC03T


title: BRHM03_1CB_YNB

description:
processed data file:
WT_v_C1_YNB_DE_sig_changed.csv


title: BRHM03_1NA_YNB

description:
processed data file:
WT_v_N1_YNB_DE_sig_changed.csv


title: 26F_TB40_5_23_18_S1_4

description:
Single-cell RNA-seq on primary human monocytes infected with CMV
26F_TB40_5_23_18_S1.pfcell.umiCounts.csv


title: BRHM03_1WD_YNB

description: processed data file:


title: BRHM03_1QB_YNB

description:
processed data file:
WT_v_Q1_YNB_DE_sig_changed.csv


title: 26F_TB40_5_23_18_S1_2


title: Culture-aged TMSC_1

city: Cheongju

first: Da Hyeon

last: Choi

address: Major in Microbiology, School of Biological Sciences, College of Natural Sciences

country: South Korea

institute: Chungbuk National University

description: Gene expression data from Tonsil-dervied MSC, passage number is 20 - 25.

hyb_protocol: Approximately 5.5 µg of labeled cDNA was hybridized to the Affymetrix GeneChip, Human Clariom D array, at 45°C for 16 h.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip fluidics station 450 and scanned on a GCS3000 scanner (Thermo Fisher Scientific).

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC).

source_name: Tonsil derived MSC from 1 donor passage 20 - 25

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT terminal labeling kit.

growth_protocol: The cells were cultured in DMEM-HG supplemented with 10% fetal bovine serum (FBS), 1% antibiotics/antimycotics (A/A) and penicillin/streptomycin (P/S) at 37°C in a humidified 5% CO2 incubator. The cells were allowed to adhere to the culture plates for 24 h, and the adherent mononuclear cells were taken as TMSCs.

extract_protocol: Trizol extraction of total RNA was performed according to Thermo Fisher Scientific.

treatment_protocol: After reaching 80% confluence, TMSCs were subcultured onto individual dishes and serially cultured to passages 20 to 25 to induce senescence. Maximum passage number was determined by the proliferative capacity. TMSCs used for the current study were between passages 5 and 25. The growth medium was changed every 3 d. In vitro-cultured TMSCs were divided into two groups as follows: control TMSCs (passages 5 – 8) and culture-aged TMSCs (passages 20 – 25).

tag: passages

value: Culture-aged TMSC cells (passage number:20 - 25)

value: tonsil-derived mesenchymal stem cells


title: 26F_TB40_5_23_18_S1_3


title: Control TMSC_1

description: Gene expression data from Tonsil-dervied MSC, passage number is 5 - 8.

source_name: Tonsil derived MSC from 1 donor passage 5 - 8

value: Control TMSC cells (passage number:5 - 8)


title: 26F_TB40_5_23_18_S1_1

value: mock


title: 26F_5_23_18_3

description:
Single-cell RNA-seq on primary human monocytes infected with CMV
26F_5_23_18_S1.pfcell.umiCounts.csv


title: BRHM03_1WA_YNB

description: processed data file:


title: Control TMSC_2


title: BRHM03_1NB_YNB


title: BRHM02_Q10B

description:
processed data file:
W10_v_Q10_YPAD_DE_sig_changed.csv

value: YPAD


title: 26F_5_23_18_2


title: BRHM02_Q10A


title: BRHM03_1CA_YNB


title: BRHM03_1QA_YNB


title: BRHM02_W10B

description: processed data file:


title: BRHM02_W10A

description: processed data file:


title: BRHM04_5CB_YPAD

description:
processed data file:
WT_v_C5_YPAD_DE_sig_changed.csv


title: BRHM03_1WB_YNB

description: processed data file:


title: BRHM04_5CA_YPAD


title: BRHM04_5WB_YPAD

description: processed data file:


title: 26F_5_23_18_4


title: HPP4_3

city: Utrecht

first: Maria

middle: Belen

last: Rabaglino

address: Yalelaan 7

department: Population Health Science

country: Netherlands

institute: Utrecht University

data_processing:
Quality of the reads in the resulting FASTQC files was checked with FastQC (v. 0.11.2)
Adapters and quality trimmer and filtering were performed using the Trimmomatic software  (V. 0.32)
The remaning sequence reads were aligned to the bovine reference genome (Bos taurus UMD3.1) iusing the Rsubread package for R.
The numbers of mapped reads for each gene official symbol were counted to determine gene expression levels.
Genes with low expression counts (less than 1 CPM) in 3 or more samples, were filtered out before normalization by TMM.
Genome_build: bosTau8
Supplementary_files_format_and_content: tab delimited text file containing raw read counts for each sample.

organism: Bos taurus

source_name: Endometrial biopsy

extract_protocol:
RNA was extracted from the endometrial tissue samples by using Trizol (Invitrogen, Carlsbad, USA) following the manufacturer’s direction, resuspended and stored at -80°C until use.  For the RNA sequencing procedure, an aliquot of RNA per sample (2 μg of total RNA) was DNase treated by using the Turbo RNase-free DNase kit (Ambion, Foster City, USA). The RNA concentration was determined with a Nanodrop spectrophotometer (ND-1000, ThermoFisher, Wilmington, USA) and the integrity of RNA (RIN number) was measured by using an Agilent Bioanalyzer 2100 model.
For RNA library construction, one μg of purified RNA was re-suspended in 50 μl of water. Next, mRNA was purified through hybridization with oligo-dT and chemically fragmented. Double strand cDNA was synthesized, followed by end-repair, adaptor ligation and enrichment (amplification) of the libraries according to the TruSeq Stranded mRNA protocol (Illumina Technologies, CA, USA). Quality of each cDNA library was assessed on a 2100 Bioanalyzer (Agilent Technologies) by using the DNA 1000 Kit. The average size per double strand DNA fragments was 260 bp. Libraries were quantified by qPCR (Light Cycler 480 Roche) by using the Qiagen Library Quantification Kit, according to the manufacturer´s protocol, and normalized to a concentration of 3 nM. One equimolar pool containing the 12 samples was prepared from the libraries to generate the clusters in the sequencing cell. Sequencing was performed on a Hiseq 1500 system (Illumina Inc. CA, USA) generating paired-end 2x150bp reads.

tag: progesterone concentration at day 4 of the estrous cycle

value: High (>2.5 ng/ml)


title: SO_3

value: Very high (>20 ng/ml)


title: SO_2


title: HPP4_2


title: HPP4_1


title: BRHM04_5WA_YPAD

description: processed data file:

tag: strain


title: Hereford, Liver_Do, WGBS

city: Beltsville

first: George

middle: E.

last: Liu

state: Maryland (MD)

address: 10300 Baltimore Ave Bldg 306

institute: USDA-ARS

description: WGBS; 150bp paired-end

data_processing:
Programs FastQC (0.11.5) and Trim Galore (0.4.5) were used to generate sequence quality reports and to trim/filter the sequences, respectively.
The cleaned data for each sample were merged and aligned to the reference genome (Bos taurus ARS-UCD1.2) using bowtie2 under the Bismark software (0.19.0)
The methylcytosine information was extracted using the bismark_methylation_extractor after deduplicating the duplication reads.
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: The data files contain the methylatin information for the CG detected. The column names are: chrmosome, position,strand, coverage for methylated cytosine, coverage for unmethylated cytosine, CG type, three bases near the cytosine.

source_name: Liver

extract_protocol:
Genomic DNA was isolated according to the QIAamp DNA Mini Kit protocol (QIAGEN, Valencia, CA, USA).
The qualified genomic DNA from somatic tissues and sperm were used to construct libraries. Briefly, 3 μg of genomic DNA spiked with unmethylated lambda DNA were fragmented into 200-300 bp using a Covaris S220 (Covaris, Inc., Woburn, MA, USA), followed by teriminal repairing and A-ligation. Different cytosine methylated barcodes were ligated to sonicated DNA for different samples. The DNA bisufite conversion was performed using the EZ DNA Methylation Gold Kit (Zymo Research, Irvine, CA, USA). Then single-stranded DNA fragments were amplified using the KAPA HiFi HotStart Uracil + ReadyMix (2 X) (Kapa Biosystems, Wilmington, MA, USA). The library concentration was quantified using a Qubit 2.0 fluorometer (Life Technologies, Carlsbad, CA, USA) and qPCR (iCycler, BioRad Laboratories, Hercules, CA, USA), and the insert size was checked using the Agilent 2100.

tag: tissue

value: Ileum

tag: Sex

value: M

tag: breed

value: Hereford


title: Hereford, Jejun_Dt, WGBS

description: WGBS; 150bp paired-end

source_name: Jejunum

value: Blood


title: Hereford, Kidney_Dt, WGBS

description: WGBS; 150bp paired-end

source_name: Kidney

value: Heart


title: BRHM02_5NB

description:
processed data file:
W52_v_N52_YPAD_DE_sig_changed.csv

source_name: yeast

tag: optical density (od600)

tag: media

tag: antibody


title: Hereford, Jejun_Do, WGBS

description: WGBS; 150bp paired-end


title: Hereford, Heart_Dt, WGBS

description: WGBS; 150bp paired-end

source_name: Heart

value: Adipose


title: 26F_5_23_18_1

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference genome hg19 using STAR
Transcript abundance was calculated using Htseq
Single-cell libraries were aligned to hg19 reference genome and UMI count files were generated using the Illumina BaseSpace SureCell application
Genome_build: hg19

extract_protocol:
Desired monocyte populations for sorted by flow cytometry and RNA was harvested using Qiagen RNeasy micro kit and on column Dnase digestion was performed. RNA quantity and quality was analyzed on Agilent Bioanalyzer.
Lexogen QuantSeq Kit was used for the construction of bulk sequencing libraries. SureCell WTA 3' Library Prep Kit was used for the construction of single-cell sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols

tag: treatment

value: immunocompetent


title: ANE_3

value: Very low (<0.25 ng/ml)


title: BRHM02_5NA2

tag: protocol

value: Quant-seq


title: Hereford, Adipose_Dt, WGBS

description: WGBS; 150bp paired-end

source_name: Adipose

value: F


title: SO_1


title: BRHM02_5LB

description:
processed data file:
W5_v_L5_YPAD_DE_sig_changed.csv


title: ANE_1


title: ANE_2


title: Holstein, Placenta_1_WGBS

description: WGBS; 150bp paired-end

source_name: Placenta

value: Placenta

value: Holstein


title: Holstein, Uterus_1_WGBS

description: WGBS; 150bp paired-end

source_name: Uterus

value: Uterus


title: LPP4_2

value: Low (<1.4 mg/dl)


title: LPP4_3


title: BRHM02_5QA

description:
processed data file:
W5_v_Q5_YPAD_DE_sig_changed.csv

value: YPAD


title: BRHM02_5QB


title: Holstein, Spleen_1_WGBS

description: WGBS; 150bp paired-end

source_name: Spleen

value: Spleen


title: Holstein, Rumen_2_WGBS

description: WGBS; 150bp paired-end

source_name: Rumen

value: Rumen


title: BRHM02_5WA

description: processed data file:

value: wild type


title: BRHM04_1CB_YPAD

description:
processed data file:
WT_v_C1_YPAD_DE_sig_changed.csv


title: Holstein, Ovary_1_WGBS

description: WGBS; 150bp paired-end

source_name: Ovary

value: Ovary


title: Holstein, Lung_2_WGBS

description: WGBS; 150bp paired-end

source_name: Lung

value: Lung


title: Holstein, Rumen_1_WGBS

description: WGBS; 150bp paired-end


title: BRHM04_1CA_YPAD


title: Holstein, Lung_1_WGBS

description: WGBS; 150bp paired-end


title: Culture-aged TMSC_2

value: Culture-aged TMSC cells (passage number:20 - 25)

value: tonsil-derived mesenchymal stem cells


title: BRHM04_1WB_YPAD

description: processed data file:


title: Holstein, Placenta_2_WGBS

description: WGBS; 150bp paired-end


title: BRHM02_5LA


title: BRHM04_1WA_YPAD

description: processed data file:


title: Holstein, Liver_1_WGBS

description: WGBS; 150bp paired-end

value: Liver


title: Holstein, Ldorsi_2_WGBS

description: WGBS; 150bp paired-end

source_name: Ldorsi

value: Ldorsi


title: Ad_ORF3_3

city: shanghai

first: Xie

last: qin

address: Minchi first road, pujiang town, minhang district, Shanghai

institute: LC sciences

data_processing:
Cutadapt was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC .
We used Bowtie2 and Hisat2 to map reads to the genome of species. Remaining reads (unmapped reads) were still mapped to genome using tophat-fusion .
CIRCExplorer2 and CIRI was used to denovo assemble the mapped reads to circular RNAs at first; Then, back splicing reads were identified in unmapped reads by tophat-fusion.
All samples were generated unique circular RNAs. The differentially expressed circRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package–edgeR.
Genome_build: Homo_sapiens.GRCh38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: HepG2 cells of Homo sapiens

extract_protocol:
Total RNA was isolated and purified using Trizol reagent (Invitrogen, Carlsbad, CA, USA) .
RNA libraries were prepared for sequencing using Illumina and the Ribo-Zero™ rRNA Removal protocols

tag: infected with

value: high titer adenovirus ADV4-ORF3

tag: cell line


title: BRHM02_1NA

description:
processed data file:
W1_v_N1_YPAD_DE_sig_changed.csv

value: Quant-seq


title: BRHM02_1NB


title: BRHM02_L1B

description:
processed data file:
W1_v_L1_YPAD_DE_sig_changed.csv


title: LPP4_1


title: Ad_ORF3_1


title: BRHM02_L1A


title: Holstein, Ldorsi_1_WGBS

description: WGBS; 150bp paired-end

value: F


title: Holstein, Kidney_1_WGBS

description: WGBS; 150bp paired-end

value: Kidney


title: Holstein, Ileum_1_WGBS

description: WGBS; 150bp paired-end

source_name: Ileum

value: Ileum

value: Holstein


title: BRHM02_5WB

description: processed data file:


title: Ad_ORF3_2


title: Holstein, Heart_1_WGBS

description: WGBS; 150bp paired-end

value: Heart


title: Ad_GFP_1

value: high titer adenovirus ADV4-NC


title: BRHM02_W1B

description: processed data file:

value: YPAD


title: BRHM02_Q1B

description:
processed data file:
W1_v_Q1_YPAD_DE_sig_changed.csv


title: BRHM02_Q1A


title: Holstein, Blood_2_WGBS

description: WGBS; 150bp paired-end

source_name: Blood

value: Blood


title: Ad_GFP_3


title: rnhPrnhC deletion

city: Ann Arbor

first: Taylor

last: Nye

address: 1105 N University Ave

department: MCDB

institute: University of Michigan

description: Bacillus subtilis NCIB 3610

data_processing:
Read alignment performed using bwa (v 0.7.8-r455)
Sorting of bam files and removal of PCR duplicates performed using Picard tools
Sorting and filtering for QV > 30 with samtools (v 0.1.18)
Genome_build: CP020102.1
Supplementary_files_format_and_content: Genome coverage at each position was calculated using genomeCoverageBed from bedtools (v2.29.1). The coverage at each position for each replicate is indicated as well as the average coverage at each position in the .csv file for the B. subtilis chromosome and plasmid pBS32.

organism: Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10

source_name: double

extract_protocol:
MasterPure Gram Positive DNA Purification Kit
UM Advanced Genomics Core

value: rnhPrnhC deletion


title: Holstein, Adipose_2_WGBS

description: WGBS; 150bp paired-end

value: Adipose


title: BRHM02_W1A

description: processed data file:

value: wild type


title: wild type

description: Bacillus subtilis NCIB 3610

source_name: WT


title: Holstein, Adipose_1_WGBS

description: WGBS; 150bp paired-end


title: Ad_GFP_2


title: Holstein, Blood_1_WGBS

description: WGBS; 150bp paired-end


title: SDCGFP_col_rep1_RNAseq

status: Public on Apr 29 2020

first: Qikun

state: Beijing

address: Haidian District, 5 Yiheyuan Rd., Zonghekeyan BLDG, Rm 502

department: School of Advanced Agricultural Sciences

institute: Peking University

description: RNAseq data

data_processing:
Reads were quality filtered using trim_galore (Babraham Bioinformatics, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with the following parameters: --fastqc --phred64 --stringency 3, and all other parameters default.
The filtered reads were aligned to Arabidopsis TAIR10 reference genome using STAR with the following parameters: --alignSoftClipAtReferenceEnds No –outFilterType BySJout –outFilterMismatchNmax 999 –outSAMtype BAM SortedByCoordinate –outFilterIntronMotifs RemoveNoncanonical.
A java program MarkDuplicates.jar from the picard-tools suite was used to remove PCR duplicates from the resulting BAM files.
We then obtained read counts of all genes and TEs according to Araport11 annotation file in the .gtf format using htseq-count v.0.6.1.p1, with the following parameters: --format=bam --stranded=reverse --idattr=gene_id --mode=union.
We then loaded the count data for all samples into DESeq2. To identify differentially regulated genes, a cut-off value of >1.5 fold change, and adjusted p-value >0.05 were applied. All other parameters were of default value.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text files include gene ID and read sequencing depth normalized read counts generated for DEseq2.

organism: Arabidopsis thaliana

source_name: young seedling

growth_protocol: All plant materials used in this study were 8-day old whole seedlings grown on 1/2 MS media supplemented with 1% sucrose under long-day condition (16h light/ 8h dark).

extract_protocol:
Total RNA was isolated using TRI-zol and the Direct-zol RNA MiniPrep Kit (ZYMO Research) following the manufacturing instructions.
Around 1 μg of total RNA was used as input for RNA-seq library preparation following the standard protocol of TruSeq Stranded mRNA Library Prep Kit (illumina).

treatment_protocol: For light treatment experiments, both wild-type and med12 mutant plants were grown under long-day light condition for 7 days, followed by a 24-hour complete dark treatment. After the dark treatment, plants were brought to light for 15 minutes prior to sample collection. whereas the control plants were collected in dark without light treatment

tag: day post germination

tag: genetic background

value: wild type carrying SDC:GFP transgene


title: morc1/med13_rep4_RNAseq

description: RNAseq data

value: morc1/med13 mutant carrying SDC:GFP transgene


title: morc1/med13_rep1_RNAseq

description: RNAseq data


title: morc1/med13_rep3_RNAseq

description: RNAseq data


title: morc1/med13_rep2_RNAseq

description: RNAseq data


title: morc1/med12_rep3_RNAseq

description: RNAseq data

value: morc1/med12 mutant carrying SDC:GFP transgene


title: morc1/med12_rep1_RNAseq

description: RNAseq data


title: SDCGFP_col_rep2_RNAseq

description: RNAseq data


title: morc1_rep7_control_for_morc1/med12_RNAseq

description: RNAseq data

value: morc1 mutant carrying SDC:GFP transgene


title: morc1_rep6_control_for_morc1/med12_RNAseq

description: RNAseq data


title: morc1_rep5_control_for_morc1/med12_RNAseq

description: RNAseq data


title: morc1_rep4_control_for_morc1/med13_RNAseq

description: RNAseq data


title: POLST1 control

city: Srinagar

first: Shaida

last: Andrabi

state: Kashmir

address: Srinagar

department: Biochemistry

country: India

institute: University of Kashmir

description: Control cells (#1) with no doxycycline, therefore no induction of PyST expression.

hyb_protocol: strandard affymetrix protocol

scan_protocol: Pixel size 1.56, Filter 570, Scanner ID 50205750, No. of scans 1, Scanner Type M10

data_processing: R/Bioconductor software was used to analyze the data. The expression robust multiarray average (RMA) method in the Limma package in the R/Bioconductor package was used to normalize the gene expression cell files (.CEL).

source_name: U2OS_control_no DOX

label_protocol: Whole genone Affymetrix Human Genome U133 Plus 2.0 (HG-U133_Plus_2) chips were used for these experiments. 3 technical replicates were used for control (-DOX) and Small T expressing cells (+Dox).

growth_protocol: Cells were grown in DMEM/10% FCS, 37C, 5% CO2 in incubator until they were 80% confluent and had rounded up morphology induced by small T expression in +DOX cells.

extract_protocol: Trizol extraction followed by purification with RNA isolation using QIAgen RNEasy extraction/purification kit was used to obtain high quality RNA  (A260/A280 ratio: 1.7).

treatment_protocol: Cell lines were treated with Doxycycline (2μg/ml) in POLST expressing cells (+DOX) to induce the expression of Polyoma Small T antigen

value: Human Bone Osteosarcoma Epithelial Cell line

tag: genotype/variation

value: control

value: no doxycycline


title: POLST3 control

description: Control cells (#3) with no doxycycline, therefore no induction of PyST expression.


title: morc1/med12_rep2_RNAseq

description: RNAseq data


title: Fld_C_rep1

city: Rosario

first: Juan

middle: José

last: Pierella Karlusich

state: Santa Fe

address: Esmeralda y Ocampo - Predio CONICET

country: Argentina

institute: Instituto de Biología Molecular y Celular de Rosario (IBR)

description: Gene expression under control conditions in Stpfld252 potato leaves

hyb_protocol: Sample labeling, and hybridization were performed as described in the one-color microarray-based gene expression analysis protocol including the one-color RNA spike-in Kit according to the manufacturer's instructions (v5.0.1, Agilent Technologies).

scan_protocol: Slides were scanned with an Agilent microarray scanner (G2505B) at high resolution.

data_processing: Data were extracted using feature extraction software (v9.5.3, Agilent Technologie) using a standard protocol. Data processing and statistical analysis were carried out with the Bioconductor library limma (Ritchie et al. 2015 Nucl Acids Res 43: e47). Background correction and normalization were performed using the normexp and quantile methods, respectively. Probes with intensities lower than 10% compared to intensities of the negative controls were omitted for subsequent analysis.

organism: Solanum tuberosum

source_name: Stpfld252 potato leaves with normal watering regime, replicate 1

growth_protocol: Tuber slices of similar sizes corresponding to the two lines under study (Stpfld252 and their wild type siblings) were planted in 3-L soil pots and grown under chamber conditions (400 μmol photons m-2 s-1, with a 16-h photoperiod at 25/22°C and a relative humidity of 80%) during 4 weeks,  and watered twice a week.

extract_protocol: Young fully expanded leaves belonging to the fifth node were collected after three days of water withdrawal in the treated group. Leaf material from 10 different plants of each genotype and treatment were frozen in liquid nitrogen and ground with Mixer Mill MM 400 (Retsch). Two pools of biological samples, each from two independent experiments per genotype and condition were used for the microarray analysis. Leaf RNA was extracted as described by Logemann et al. (1987). RNA quantity and quality were determined with a NanoDrop spectrophotometer (Thermo Scientific, Wilmington, DE, United States) and by visual inspection after electrophoresis, respectively. One microgram of RNA from each sample was treated with RQ1 DNase (Promega, Madison, WI, United States) according to the manufacturer’s instructions, and used as template to generate cDNA with M-MLV Reverse Transcriptase (Promega, Madison, WI) and oligo (dT)12−18.

treatment_protocol: Plants were subjected to drought by water withdrawal during 3 days, while control conditions continue the watering regime

value: leaves

tag: genotype

value: control conditions


title: SDCGFP_col_rep4_RNAseq

description: RNAseq data


title: SDCGFP_col_rep3_RNAseq

description: RNAseq data


title: POLST2+Dox Experimental

description: Polyoma Small T expressing U2OS cells( #2); Doxycycline was added to induce expression of small T antigen for about 20 hrs

value: expressing inducible Polyoma Small T (PyST)

value: Doxycycline 2ug/ml


title: WT_C_rep1

description: Gene expression under control conditions in wild-type potato leaves

source_name: WT potato leaves with normal watering regime, replicate 1

label_protocol: Sample labeling, and hybridization were performed as described in the one-color microarray-based gene expression analysis protocol including the one-color RNA spike-in Kit according to the manufacturer's instructions (v5.0.1, Agilent Technologies).


title: WT_D_rep1

description: Gene expression after 3 days of water withdrawal in wild-type potato leaves

source_name: WT potato leaves after 3 days of water withdrawal, replicate 1

value: drought (3 days of water withdrawal)


title: POLST3+Dox Experimental

description: Polyoma Small T expressing U2OS cells( #3); Doxycycline was added to induce expression of small T antigen for about 20 hrs


title: Fld_D_rep1

description: Gene expression after 3 days of water withdrawal in Stpld252 potato leaves

source_name: Stpfld252 potato leaves after 3 days of water withdrawal, replicate 1


title: WT_C_rep2

source_name: WT potato leaves with normal watering regime, replicate 2


title: Fld_D_rep2

description: Gene expression after 3 days of water withdrawal in Stpfld252 potato leaves

source_name: Stpfld252 potato leaves after 3 days of water withdrawal, replicate 2


title: Fld_C_rep2

source_name: Stpfld252 potato leaves with normal watering regime, replicate 2


title: BRHM03_1LC_YNB

description:
processed data file:
WT_v_L1_YNB_DE_sig_changed.csv

source_name: yeast

value: YNB

value: Quant-seq


title: POLST1+Dox Experimental

description: Polyoma Small T expressing U2OS cells( #1); Doxycycline was added to induce expression of small T antigen for about 20 hrs


title: POLST2 control

description: Control cells (#2) with no doxycycline, therefore no induction of PyST expression.


title: morc1_rep1_control_for_morc1/med13_RNAseq

description: RNAseq data


title: WT_D_rep2

source_name: WT potato leaves after 3 days of water withdrawal, replicate 2


title: med13_rep4_RNAseq

description: RNAseq data

value: med13 mutant


title: med13_rep2_RNAseq

description: RNAseq data


title: med13_rep1_RNAseq

description: RNAseq data


title: morc1_rep3_control_for_morc1/med13_RNAseq

description: RNAseq data


title: med12_rep3_RNAseq

description: RNAseq data

value: med12 mutant


title: med12_rep1_RNAseq

description: RNAseq data


title: med13_rep3_RNAseq

description: RNAseq data


title: med12_rep2_RNAseq

description: RNAseq data


title: med12_light_rep1_RNAseq

description: RNAseq data


title: med12_light_rep2_RNAseq

description: RNAseq data


title: med12_dark_rep3_RNAseq

description: RNAseq data


title: ddc/med13_rep4_RNAseq

description: RNAseq data

value: drm1/drm2/cmt3/med13 mutant carrying SDC:GFP transgene


title: med12_dark_rep2_RNAseq

description: RNAseq data


title: ddc/med13_rep2_RNAseq

description: RNAseq data


title: ddc/med13_rep3_RNAseq

description: RNAseq data


title: med12_rep4_RNAseq

description: RNAseq data


title: ddc_rep4_RNAseq

description: RNAseq data

value: drm1/drm2/cmt3 mutant carrying SDC:GFP transgene


title: ddc/med13_rep1_RNAseq

description: RNAseq data


title: ddc_rep3_RNAseq

description: RNAseq data


title: col_rep3_RNAseq

description: RNAseq data

value: wild type


title: ddc_rep2_RNAseq

description: RNAseq data


title: col_rep2_RNAseq

description: RNAseq data


title: col_light_rep2_RNAseq

description: RNAseq data


title: col_rep1_RNAseq

description: RNAseq data


title: col_light_rep3_RNAseq

description: RNAseq data


title: col_light_rep1_RNAseq

description: RNAseq data


title: col_dark_rep1_RNAseq

description: RNAseq data


title: col_dark_rep3_RNAseq

description: RNAseq data


title: SDCGFP_col_H3K36me3_ChIPseq

description: ChIPseq data

data_processing:
Reads were quality filtered using trim_galore (Babraham Bioinformatics, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with the following parameters: --fastqc --phred64 --stringency 3 and all other parameters default.
The filtered reads were aligned to Arabidopsis TAIR10 reference genome using STAR with the following parameters: --alignSoftClipAtReferenceEnds No –outFilterType BySJout –outFilterMismatchNmax 999 –outSAMtype BAM SortedByCoordinate –outFilterIntronMotifs RemoveNoncanonical.
A java program MarkDuplicates.jar from the picard-tools suite (“Picard Toolkit.” 2019. Broad Institute, GitHub Repository. http://broadinstitute.github.io/picard/) was used to remove PCR duplicates from the resulting BAM files.
To defind ChIP-seq peaks, BAM files were loaded into macs2 (v2.1.2) callpeak function with the following parameters: -f BAM -nomodel -g 1.3e8 -B -q 0.01. Peaks obtained from the above procedures were further filtered using the cut-off value -log10q-value >30.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigwig

extract_protocol:
ChIP-seq was done using method described in Johnson, L.M. et al. Nature 507, 124-128 (2014).
ChIP-seq libraries were prepared using the Ovation Ultralow System V2 (NuGEN #0344).

value: wild type carrying SDC:GFP transgene

value: anti-H3K36me3 (abcam #9050)


title: SDCGFP_col_H3PanAc_ChIPseq

description: ChIPseq data

value: anti-H3PanAc active motif #39139)


title: SDCGFP_col_input_ChIPseq

description: ChIPseq data


title: SDCGFP_col_H3K27me3_ChIPseq

description: ChIPseq data

value: anti-H3K27me3 (Millipore 07-449)


title: EV_2

city: Kanazawa

first: Isao

last: Kobayashi

state: Ishikawa

address: Kakumamachi

country: Japan

institute: Kanazawa University

data_processing:
Illumina RTA software was used for base-calling.
Sequence reads were mapped to the zebrafish reference genome (GRCz11) using HiSAT2 (version 2.1.0).
Reads per million (RPM) were calculated using the Subread (ver. 1.6.4).
Genome_build: GRCz11
Supplementary_files_format_and_content: Reads per million (RPM) values for each sample.

organism: Danio rerio

extract_protocol:
Total RNAs were extracted from sorted cells using RNeasy Mini Kit (QIAGEN).
Cells were directly sorted in a lysis buffer containing 1 μg/mL of polyinosinic-polycytidylic acid, and total RNA was extracted using RNeasy Mini Kit. Reverse transcription (RT) was performed using Super Script III (Thermo Fisher Scientific) and an RT primer, which contains oligo-dT, T7 promoter, and PCR target region sequences. After digestion of remaining RT primers by exonuclease I (Takara), a poly-A tail was added to the 3’ ends of the first-strand cDNAs using terminal transferase (Sigma). The second-strand DNA was then synthesized using MightyAmp DNA polymerase (Thermo Fisher Scientific) and a tagging primer, which contains oligo-dT and PCR target region sequences. PCR amplification was performed using a suppression primer, which allow to amplify small-size DNA that contains complementary sequences at both ends of the template DNA. The amplified double-strand cDNA was purified using QIAquick PCR Purification Kit (Qiagen). Library preparation was performed using Nextera XT DNA Library Preparation Kit (illumina).

tag: age

value: adult

value: Sorted from the fractured sclae

tag: cell type

tag: molecule type

value: Amplified RNA


title: SDCGFP_col_H3K9me2_ChIPseq

description: ChIPseq data

value: anti-H3K9me2 (abcam #1220)


title: morc1_input_rep1_ChIPseq

description: ChIPseq data

value: morc1 mutant carrying SDC:GFP transgene


title: SDCGFP_col_H3K4me3_ChIPseq

description: ChIPseq data

value: anti-H3K4m3 (Millipore 04-745)


title: morc1_H3PanAc_rep2_ChIPseq

description: ChIPseq data


title: EV_1

tag: tissue


title: col_rep4_RNAseq

description: RNAseq data


title: morc1_H3PanAc_rep1_ChIPseq

description: ChIPseq data


title: mOC_2

source_name: mature osteoclasts

value: mature osteoclasts


title: mOC_1


title: morc1_H3K36me3_rep1_ChIPseq

description: ChIPseq data


title: pOC_2

source_name: osteoclast precursors

value: osteoclast precursors


title: pOC_1


title: morc1_H3K4me3_rep1_ChIPseq

description: ChIPseq data


title: morc1_H3K27me3_rep2_ChIPseq

description: ChIPseq data


title: morc1_H3K27me3_rep1_ChIPseq

description: ChIPseq data


title: morc1_H3K9me2_rep1_ChIPseq

description: ChIPseq data


title: OB_2

source_name: osteoblasts

value: osteoblasts


title: OB_1


title: morc1_H3K4me3_rep2_ChIPseq

description: ChIPseq data


title: morc1_H3_rep2_ChIPseq

description: ChIPseq data

value: anti-H3 (abcam #1791)


title: MED12-FLAG_rep2_input_ChIPseq

description: ChIPseq data

value: med12 mutant carrying MED12 transgene


title: DMSO-3

city: Philadelphia

first: Kathrin

last: Bernt

address: 3501 Civic Center Boulevard,

institute: Children's Hospital of philadelphia

data_processing:
kallisto to get read counts
DEseq2 to normalize and detect DE genes
Genome_build: hg38

growth_protocol: Molm cells were gown in RPMI supplemented with 10% FBS and 1% PenStrep under standard culture conditions. Cells were plated in 1ml at 50,000 cells/ml

extract_protocol:
mRNA was isolated from cells three days after sort using qiagen RNeasy kit
Library prep was performed using Illumina HiSeq, 2x150bp configuration. ~350M raw paired-end reads per lane


title: DMSO-4


title: Combo-3


title: iDOT1L-4


title: iEZH2-4


title: MED12-FLAG_rep1_input_ChIPseq

description: ChIPseq data


title: Combo-4


title: iDOT1L-3


title: morc1_H3_rep1_ChIPseq

description: ChIPseq data


title: MED12-FLAG_rep2_ChIPseq

description: ChIPseq data


title: iEZH2-3


title: MED12-FLAG_rep1_ChIPseq

description: ChIPseq data


title: Combo-2


title: MED12-FLAG_light_rep1_ChIPseq

description: ChIPseq data

value: light


title: iEZH2-2


title: MED12-FLAG_light_rep2_ChIPseq

description: ChIPseq data


title: morc1_H3K9me2_rep2_ChIPseq

description: ChIPseq data


title: iDOT1L-2


title: med12_dark_rep1_RNAseq

description: RNAseq data

value: med12 mutant


title: DMSO-2


title: MED12-FLAG_light_rep1_input_ChIPseq

description: ChIPseq data


title: Combo-1


title: MED12-FLAG_Dark_rep1_ChIPseq

description: ChIPseq data

value: dark


title: MED12-FLAG_dark_rep2_ChIPseq

description: ChIPseq data


title: iEZH2-1


title: MED12-FLAG_dark_rep1_input_ChIPseq

description: ChIPseq data


title: ddc_input_rep1_ChIPseq

description: ChIPseq data

value: drm1/drm2/cmt3 mutant carrying SDC:GFP transgene


title: iDOT1L-1


title: MED12-FLAG_col_control_ChIPseq

description: ChIPseq data

value: wild type

value: control


title: ddc_H3PanAc_rep2_ChIPseq

description: ChIPseq data

value: anti-H3PanAc active motif #39139)


title: ddc_H3PanAc_rep1_ChIPseq

description: ChIPseq data


title: DMSO-1


title: col_dark_rep2_RNAseq

description: RNAseq data


title: SKMEL5 Palbociclib replicate 2

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

data_processing:
HiSeq2000 using v3 chemistry. Software: Control v2.2.58, RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
RNAseq reads were aligned to the human transcriptome prepared with the hg38 primary assembly and the Ensembl version 95 annotation using STAR version 2.5.3a (Dobin et al., 2013). Gene expression was summarized with RSEM version 1.3.0 (Li and Dewey, 2011) and samtools version 1.3 (Li et al., 2009).
Genome_build: hg38 with ensembl 95 annotation
Supplementary_files_format_and_content: text files with ensemble gene IDs and 6 columns of either integer count data or log2 tpm (with +1 offset prior to log transformation)

source_name: SKMEL5 cells

growth_protocol: SKMEL5 cells were obtained from ATCC and maintained in DMEM medium (Corning) supplemented with 10% FBS (Gibco) and 1% penicillin/streptomycin (Gibco). Cells were maintained at 37C, 5% CO2 and tested for mycoplasma contamination prior to RNA isolation.

extract_protocol:
At the time of harvest, cells were washed with ice-cold 1X PBS over ice and lysed in TRIzol reagent (Thermo Fischer Scientific). Total RNA was isolated from each sample using Direct-zol RNA miniprep kit (Zymo Research) according to manufacturer’s instructions.
RNA were confirmed for quality using the Agilent Fragment Analyzer and 300ng of material was polyA selected using NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490) modified to include two rounds of polyA binding and 10 minute incubations. cDNA was generated using the NEB Ultra II directional kit (E7760) following manufacturers protocol using 12 cycles of PCR and an 0.9X SPRI clean. The resulting libraries were quality assessed using the Fragment Analyzer and quantified by qPCR prior to be sequenced on the Illumina HiSeq2000. The 50nt single-end reads with a depth of at least 10 million reads per sample were sequenced for all conditions.

treatment_protocol: SKMEL5 cells treated with DMSO or 100 nM Palbociclib (Selleckchem, PD-0332991) for 72h.

value: 100 nM Palbociclib


title: SKMEL5 Palbociclib replicate 3


title: SKMEL5 Palbociclib replicate 1


title: ddc_H3K36me3_rep2_ChIPseq

description: ChIPseq data

value: anti-H3K36me3 (abcam #9050)


title: SKMEL5 DMSO replicate 3

value: DMSO


title: ddc_H3K36me3_rep1_ChIPseq

description: ChIPseq data


title: morc1_rep2_control_for_morc1/med13_RNAseq

description: RNAseq data

value: morc1 mutant carrying SDC:GFP transgene


title: SKMEL5 DMSO replicate 2


title: SKMEL5 DMSO replicate 1


title: siBmal1_rep3

city: Genoa

first: benedetto

last: grimaldi

address: via Morego 30

department: Molecular Medicine

country: Italy

institute: Fondazione Istituto Italiano di Tecnologia

data_processing:
Read filtering with fastx toolkit 0.0.13.2: fastq_masker -Q33 -q 20 -r N -v
alignment with tophat version 2.0.8: tophat -r 170 -p 8 --no-novel-juncs --no-novel-indels --library-type fr-unstranded --transcriptome-index transcriptome_index reffile fastq_file_R1 fastq_file_R2
Removing duplicate reads: samtools rmdup -sS bamfile
Quantifying read counts over features with featureCounts v. 1.4.5-p1: featureCounts -T 2 -p -P -a gtffile
Idendifying Differentially Expressed Genes (DEG) using DESeq2 R Bioconductor package
Genome_build: hg19
Supplementary_files_format_and_content: excel file containing differential expression results (DESeq2) and RPKMs

source_name: mammary gland/breast; derived from metastatic site: pleural effusion

growth_protocol: Human breast cancer MDA-MB-231  cell line (previously obtained from American Type Culture Collection (ATCC)) was grown in DMEM medium (Sigma, catalog#D8537) supplemented with 4 mM L-glutamine (EuroClone, catalog#ECB3000D), 10% fetal bovine serum (FBS) (Sigma, catalog#10001432) and 1X penicillin:streptomycin solution (Sigma, catalog#P4333).

extract_protocol:
Fourty-eight hours post-transfection, RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were reverse transfected with 30 nM MISSION® siRNA  targeting Human BMAL1 (Sigma-Aldrich, HA10491373(4), SASI_Hs01_00010171)  or with 30nM MISSION® siRNA  targeting Human MAX (Sigma-Aldrich, HA10491369(70), SASI_Hs02_00333726a) using DharmaFect 1 Transfection reagent  (Dharmacon, catalog#T-2001-03) according with the manufacturer's protocol. Cells transfected with MISSION® siRNA Universal Negative Control #1 (Sigma, catalog#SIC001) were used as a control.

tag: culture properties

value: adherent

tag: disease

value: adenocarcinoma

tag: reverse transfected with sirna sequences against


title: ddc_H3K27me3_rep2_ChIPseq

description: ChIPseq data

value: anti-H3K27me3 (Millipore 07-449)


title: ddc_H3K9me2_rep2_ChIPseq

description: ChIPseq data

value: anti-H3K9me2 (abcam #1220)


title: siBmal1_rep2


title: ddc_H3K9me2_rep1_ChIPseq

description: ChIPseq data


title: siBmal1_rep1


title: ddc_H3K4me3_rep1_ChIPseq

description: ChIPseq data

value: anti-H3K4m3 (Millipore 04-745)


title: siMAX_rep3

value: MYC


title: ddc_H3K4me3_rep2_ChIPseq

description: ChIPseq data


title: siMAX_rep2


title: siMAX_rep1


title: ddc_H3_rep2_ChIPseq

description: ChIPseq data

value: anti-H3 (abcam #1791)


title: ddc_H3_rep1_ChIPseq

description: ChIPseq data


title: CTRL_rep3

value: non-coding control


title: col_input_ChIPseq

description: ChIPseq data


title: CTRL_rep2


title: col_H3PanAc_ChIPseq

description: ChIPseq data


title: Max_ChIP

data_processing:
Read filtering with fastx toolkit version 0.0.13.2: fastq_masker -Q33 -q 20 -r -N -v
Alignment to hg19 with bwa version 0.6.2; bwa aln -t 16 reffile fastqfile| bwa samse -n 1 reffile - fastqfile | samtools view -q 1 -ut reffile - |samtools sort - bamfile
Transcription factors (Max, Bmal1) peak calling with MACS version 2.0.9; macs2 -t samplebam -c inputbam  --mfold=7,30 -g hs -p 0.00001 --mfold=7,30 --nomodel --shiftsize 150
the input alignment file was randomly downsampled to the size of the ChIP sample alignment file
Genome_build: hg19
Supplementary_files_format_and_content: *_peaks.txt files: bed files from MACS2 peak caller of transcription factor's ChIP-Seq

extract_protocol:
Cells were lysed with 0.5% SDS buffer containing protease inhibitors cocktail (SIGMA, catalog# P8340), scraped and centrifuged at 1150 g for 10 min at 4⁰C. Pellets were resuspended in 4 ml of ice-cold IP Buffer composed by a 2:1 micture of SDS buffer (100 mM NaCl, 50mM Tris-Cl, pH8.1 EDTA, pH 8.0, 0.5% SDS) and Triton Dilution Buffer (100 mM Tris-Cl, pH 8.6, 100 mM NaCl, 5mM EDTA, pH 8.0, 5% Triton X-100) containing protease inhibitor cocktail. Samples were sonicated with Branson Digital Sonifier (Danbury, USA) in 30s bursts followed by 30s of cooling on ice for a total sonication time of six minutes per sample. Chromatin was pre-cleared for 1 h at 4 ⁰C with Sepharose protein G beads (Life technologies, catalog# 101242) and subsequently precipitated overnight at 4 ⁰C with 4 µg of either anti-BMAL1 (Protein Tech, catalog# 14268-1-AP) or 4 µg of anti-MAX (Bethyl Lab, catalog#A302-866A). DNA protein complexes were recovered with Sepharose protein G beads for 3 h and washed twice sequentially with Mixed Micelle Wash Buffer (150 mM NaCl, 20 mM Tris-Cl, pH 8, 5 mM EDTA, 5% w/v sucrose, 1% Triton X-100, 0.2% SDS),  LiCl/Detergent buffer (0.5% Na-deoxycholate, 1 mM EDTA, 250 mM LiCl, 0.5% (v/v) NP-40, 10 mM Tris-Cl, pH 8.0), Buffer 500 (0.1% (w/v) deoxycholic acid, 1 mM EDTA, 50 mM HEPES, pH 7.5, 500 mM NaCl, 1% (v/v) Triton X-100) and TE buffer (10mM Tris-Cl, 1mM EDTA, pH 8.0). Beads were further supended in TE-S buffer (TE buffer, 2% SDS) and treated with RNAse A for 30 min at 37 ⁰C. Cross-linking was reverted by overnight incubation at 65 ⁰C in TE-S containing 0.4 mg/ml proteinase K. In parallel, inputs were treated in the same way. Immunoprecipitated and input DNA was purified using PCR purification kit (QIAGEN, catalog#28106) using 60 µl of  buffer T (10mM Tris-Cl, pH 8.0).
Input and immunoprecipitated DNA (1–10 ng) were blunt-ended and phosphorylated, and a single 'A' nucleotide was added to the 3' ends of the fragments in preparation for ligation to an adapter that has a single-base 'T' overhang.  The ligation products were purified and accurately size-selected by agencourt AMPure XP beads. Purified DNA was PCR-amplified to enrich for fragments that have adapters on both ends.  All steps were on automation instrument, Biomek FX by Beckman Coulter.  The final purified product was then quantitated prior to cluster generation on bioanalyzer 2100.  Libraries with distinct adapter indexes were multiplexed (1/5 libraries per lane) and after cluster generation on FlowCell were sequenced for 50 bases in the single read mode on a HiSeq 2000 sequencer.

treatment_protocol: 80% confluent cells were crosslinked for 10 min with 1% formaldehyde (Sigma, catalog#F8775), neutralized with 125 mM glycine at pH 2.5 for 5 min and washed twice in PBS.

value: Max


title: ddc_H3K27me3_rep1_ChIPseq

description: ChIPseq data

value: drm1/drm2/cmt3 mutant carrying SDC:GFP transgene


title: col_H3K9me2_ChIPseq

description: ChIPseq data

value: wild type


title: col_H3K36me3_ChIPseq

description: ChIPseq data


title: Bmal1_ChIP


title: input_ChIP


title: col_H3K4me3_ChIPseq

description: ChIPseq data


title: col_H3K27me3_ChIPseq

description: ChIPseq data


title: col_H3_ChIPseq

description: ChIPseq data


title: med12_light_rep3_RNAseq

description: RNAseq data

value: med12 mutant


title: control1

city: Huai'an

first: Jie

last: Zhang

state: Jiangsu

address: Huaihai South Road

department: Department of Respiratory Diseases

institute: the Affiliated Huai’an Hospital of Xuzhou Medical University

data_processing:
The quality control of the raw reads was implemented using the fastp (version: 0.19.4) software. Clean reads from the samples were obtained and aligned with the rat reference genome (Rnor_6.0, Ensembl) using the HISAT2 (version: 2.1.0) software using the default parameters.
The read count was obtained based on rat genome annotation information in Ensembl using the featureCounts software (version: 1.6.0), followed by normalization using the Reads Per Kilobase per Million mapped reads (RPKM) method.
The annotation information of "protein_coding" was reserved as mRNA. Meanwhile, the annotation information such as "antisense", "sense_intronic", "lincRNA", or "processed_transcript" was reserved as lncRNA.
Genome_build: Rnor_6.0, Ensembl
Supplementary_files_format_and_content: raw and normalized count

organism: Rattus norvegicus

source_name: dorsal root ganglion nerve cells (DRGs)

growth_protocol: DRG cells were plated on PLL-coated coverslips (37℃, 2 h), after digestion with 0.05% trypsin (Sigma, T8003-100 mg), and then mixed with DMEM complete medium to terminate the digestion procedure. All cells were seeded in a 24-well PLL-coated slide (1×10^4 cells/well) and incubated overnight, followed by fixation with 4% paraformaldehyde for 30 min at room temperature.

extract_protocol: DRG cells were digested with 0.05% trypsin, resuspended in 500 μL DMEM medium and diluted with DMEM and high-glucose (45 mmol/L) medium. After 48 h, all cells were digested, centrifuged and washed with PBS, followed by Trizol (RNAiso Plus, TaKaRa, 9109) treatment. Samples were stored at −80℃. There were 3 duplicates in the control group (control1, control2, and control3) and DM group (DM1, DM2, and DM3).

treatment_protocol: All rats selected for the study were anesthetized with intramuscular injection of sodium pentobarbital (50 mg/kg). All anesthetized rats were sacrificed with cervical dislocation method (external force dislocated the cervical vertebra of the rats and disconnected the spinal cord from the cerebrospinal cord), followed by disinfection by immersion in 75% alcohol. Briefly, the spinous process and lamina from lumbar 5 (L5) to sacral vertebra 3 (S3) of all rats were cut off. DRG was obtained via spinal nerve trunk removal

value: dorsal root ganglia


title: control2


title: DM3


title: DM2


title: DM1


title: ddc_rep1_RNAseq

description: RNAseq data

source_name: young seedling


title: CTRL_rep1


title: control3


title: HX D55 GFP+ HX11

city: Los Angeles

first: Haibin

last: Xi

address: 615 Charles E Young Dr South, BSRB 257

department: MIMG

institute: UCLA

description: PAX7-GFP reporter cells derived from H9 human pluripotent stem cells were used for differentiation

data_processing:
The raw sequencing reads were processed using the Drop-seq_tools-1.13 pipeline from the McCaroll lab (https://github.com/broadinstitute/Drop-seq/releases/tag/v1.13), following the general guidelines from the Drop-seq Alignment Cookbook v1.2 (https://github.com/broadinstitute/Drop-seq/files/2425535/Drop-seqAlignmentCookbookv1.2Jan2016.pdf) (Macosko et al., Cell, 2015). Briefly, the first 20 bp from Read1 were filtered by read quality and used to index the corresponding Read2 fragments. The first 75 bp from the indexed Read2 were trimmed off sequencing adapters and polyA sequences, followed by read quality filtration and further removal of reads fewer than 30 nucleotides of length. Processed reads from Read2 were aligned to the human reference genome (hg19) using Bowtie2 (v2.2.9 with the ‘--very-sensitive’ mode) (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml). Aligned reads were tagged to gene exons using Bedtools Intersect (v2.26.0) (https://github.com/arq5x/bedtools2).
After read alignment, knee plots of cell-to-read fraction were generated to estimate the number of cell barcodes representing true cells. Digital gene expression matrices (DGEs) were then generated by counting gene transcripts for the number of cell barcodes selected based on the infliction points in the knee plots. To correct for any bead synthesis errors/read errors leading to false barcodes, transcript barcodes (unique molecular identifiers; UMIs) or cell barcodes were merged when they were within 1 Hamming or 2 Levenshtein distances, respectively. Barcodes containing < 2500 reads were excluded from the DGEs.
Downstream computational analyses of scRNA-seq data were mainly performed using the R package Seurat v2.3.3 (https://github.com/satijalab/seurat/releases/tag/v2.3.3) (Butler et al., Nat Biotechnol, 2018) by largely following the standard guidelines from the Satija lab (https://satijalab.org/seurat/). Seurat objects were generated with DGEs constructed as described above. Violin plots of number of expressed genes and unique transcripts (nGene and nUMI, respectively) of each cell were generated and outliers with too high or too low nGene/nUMI were removed to exclude potential cell doublets/aggregates or low quality cells/cell debris, respectively, based on each object/sample.
After the cell filtration step, retained cell barcodes were intersected with the original DGE files for each sample to generate the processed data files for downstream single cell analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files (.tsv) containing filtered cells/barcodes as columns and unique transcript count (nUMI) for each gene in each cell/barcode as rows.

molecule: polyA RNA

source_name: myogenic culture

growth_protocol: The parental H9 human pluripotent stem cells and engineered PAX7-GFP reporter cells were maintained on Matrigel-coated tissue culture plates in mTeSR1 medium. Cells were fed with fresh medium every day and passaged with 0.5 mM of EDTA every 4-6 days. Myogenic differentiations were carried out according to published protocols: HX protocol (Xi et al., Cell Rep, 2017), JC protocol (Chal et al., Nat Biotechnol, 2015) and MS protocol (Shelton et al., Stem Cell Rep, 2014).

extract_protocol:
Prepared single cell solutions were subjected to single cell capture and droplet formation following instructions in the online Drop-seq protocol v.3.1 (http://mccarrolllab.org/download/905/) and those published in the original Drop-seq paper (Macosko et al., Cell, 2015). Single cells were lysed in oil droplets and polyA-tailed mRNAs were captured by beads coated with barcoded oligonucleotides containing polyT tracks.
After cells were captured and lysed in oil-bead droplets, reverse transcription and library construction were performed according to instructions in the online Drop-seq protocol v.3.1 (http://mccarrolllab.org/download/905/) and those published in the original Drop-seq paper (Macosko et al., Cell, 2015). In brief, after droplets breakdown, cDNAs were made using Thermo Fisher Scientific Maxima H Minus Reverse Transcriptase and amplified using Roche HiFi HotStart ReadyMix. PCR products were made into sequencing-ready libraries with Illumina Nextera XT DNA Library Preparation Kit.

value: H9 human pluripotent stem cell (hPSC)

tag: differentiation protocol

value: HX protocol (Xi et al., Cell Rep, 2017)

tag: differentiation length

value: 55 days

tag: sorting/enrichment strategy

value: live and PAX7-GFP+


title: HX D41 GFP+ HX9

value: 41 days


title: SKM_ERS_mouse #8

city: Lille

first: Jérôme

last: Eeckhoute

address: Bâtiment J&K, Faculté de Médecine de Lille-Pôle Recherche, Boulevard du Professeur Leclerc

country: France

institute: CNRS

description: Transcriptomic gastrocnemius - ER stress

hyb_protocol: Affymetrix GeneChip Hybridization Oven 640 for 16h at 45°C and 60 rpm on MoGene-2_0-st Chip. GeneChips were washed and stained in the Affymetrix Fluidics.

scan_protocol: Affymetrix GeneChip Scanner 7G and Affymetrix GeneChip Command Console software (AGCC).

data_processing: RMA and Quantile Normalization with median polish using Partek. The data obtained are log2-transformed.

source_name: mix C57Bl6/J-SV129 female mouse

label_protocol: RNA were processed using Affymetrix GeneChip® WT PLUS Reagent Kit.

growth_protocol: Female mice (mix C57Bl6/J-SV129) were housed in a temperature-controlled room (22–24°C) with a 12h dark-light cycle. Animal studies were performed in compliance with European Community specifications regarding the use of laboratory animals and approved by the Nord-Pas de Calais Ethical Committee for animal use.

extract_protocol: RNA was extracted using Trizol and reverse transcribed using the High Capacity cDNA Reverse Transcription kit (Applied Biosystems, USA). Total RNA was checked for quantity and quality using the Agilent 2100 Bioanalyzer (Agilent Biotechnologies).

treatment_protocol: Intramuscular injection 24h before euthanasia: In the same animal, one gastrocnemius received tunicamycin solution (30µg/30µL) , the other the control saline solution.

value: WT

tag: treatment

value: tunicamycin


title: HX D20 GFP+ HX5

value: 20 days


title: SKM_Control_mouse #7

description: Transcriptomic gastrocnemius - control

value: saline control


title: Adt Yr34 AP20

source_name: quadriceps muscle

tag: developmental age

value: adult year 34

value: quadriceps muscle

value: live and CD235a-/CD31-/CD45-


title: Juv Yr7 AP11

source_name: gastrocnemius muscle

value: juvenile year 7

value: gastrocnemius muscle


title: SKM_ERS_mouse #6


title: SKM_Control_mouse #8

description: Transcriptomic gastrocnemius - control


title: HX D27 GFP+ HX7

value: 27 days


title: SKM_Control_mouse #9

description: Transcriptomic gastrocnemius - control


title: SKM_ERS_mouse #7


title: SKM_ERS_mouse #5


title: SKM_Control_mouse #4

description: Transcriptomic gastrocnemius - control


title: SKM_Control_mouse #5

description: Transcriptomic gastrocnemius - control


title: SKM_ERS_mouse #3


title: SKM_Control_mouse #3

description: Transcriptomic gastrocnemius - control


title: SDCGFP_col_H3_ChIPseq

description: ChIPseq data

value: wild type carrying SDC:GFP transgene

tag: antibody

value: anti-H3 (abcam #1791)


title: SKM_ERS_mouse #9


title: Infected_Donor4_AMK_Infected

city: Paris

first: Alexandre

last: Giraud-Gatineau

address: 25-28 rue du docteur roux

department: Microbiology

institute: Institut Pasteur

data_processing:
STAR v2.5.0b was used to map RNA-seq reads to the hg38 reference genome and quantify  gene expression (option--quantMode GeneCounts) by counting the fragments overlapping the Ensembl genes (GRCh38 v. 83).
Genome_build: hg38
Supplementary_files_format_and_content: The raw counts were generated using STAR v2.5.0b for GRCh38 Ensembl genes

source_name: Blood mononuclear cells

growth_protocol: Blood mononuclear cells from 4 healthy volunteers (Etablissement Français du Sang, Paris, France) were isolated by Ficoll-Paque (GE Healthcare Life Sciences) centrifugation. CD14+ monocytes were isolated by positive selection using CD14 microbeads (Miltenyi Biotec). Recovered cells were seeded at 2 × 106 cells/well in six-well plates (Falcon; BD Biosciences) in 3 ml RPMI 1640 (Invitrogen) supplemented with 10% heat-inactivated fetal calf serum (Dutscher), L-glutamine, GM-CSF (20 ng/ml; R&D Systems). Cultures were fed every 2 days with complete medium containing full doses of cytokine. Monocytes were allowed to differentiate into macrophages for 6 days at 37°C in 5% CO2 humidified atmosphere.

extract_protocol:
Total RNA was extracted using QIAzol reagent (Life Technologies) and purified over RNeasy columns (Qiagen). The quality of all samples was assessed with an Agilent 2100 bioanalyzer (Agilent Technologies) to verify RNA integrity. Only samples with a good RNA yield and no RNA degradation (ratio of 28S to 18S, > 1.7; RNA integrity number > 9) were used for further experiments.
cDNA libraries were prepared with the Illumina TruSeq RNA Sample Preparation Kit v2 and were sequenced on an llumina HiSeq 2500

treatment_protocol: Mycobacterium tuberculosis H37Rv (MTB) was grown from a frozen stock to mid-log phase in 7H9 medium (Becton Dickinson), supplemented with albumin-dextrose-catalase (ADC, Becton Dickinson). Before infection, bacteria were washed three times and re-suspended in 1 ml PBS. Clumps were dissociated by 30 passages through a needle and then allowed to sediment for 5 min. Bacteria in the supernatant were then killed by heating at 90°C during 30min (defined heareafter hk-MTB). The density of bacteria in the supernatant was verified by measuring the OD600 and aliquot volumes defined to allow five bacterium-per two cell infection. Cells were infected in 6-well plates with each well containing 1.3 × 106 cells in 3 ml medium containing GM-CSF (R&D Systems), and treated with 20 µg/mL amikacin (AMK), 20 µg/mL ethambutol (EMB), 10 µg/mL isoniazid (INH), 200 µg/mL pyrazinamide (PZA), or 20 µg/mL rifampicin (RIF) for 18 h.

value: human monocyte-derived macrophages

tag: infection status

value: infected

tag: agent

value: Mycobacterium tuberculosis

value: AMK


title: SKM_Control_mouse #6

description: Transcriptomic gastrocnemius - control


title: SKM_ERS_mouse #4


title: Infected_Donor4_EMB_Infected

value: EMB


title: Fet Wk18 AP16

source_name: hindlimb skeletal muscles

value: fetal week 18

value: hindlimb skeletal muscles


title: Fet Wk17 AP17

value: fetal week 17


title: Emb Wk7.75 AP10

source_name: whole hindlimb excluding feet

value: embryonic week 7.76

tag: carnegie stage

value: whole hindlimb excluding feet


title: Infected_Donor4_INH_Infected

value: INH


title: Infected_Donor4_PZA_Infected

value: PZA


title: Infected_Donor4_Untreated_Infected

value: Untreated


title: Uninfected_Donor4_RIF_Uninfected

value: uninfected

value: RIF


title: Infected_Donor4_DMSO_Infected

value: DMSO


title: SKM_ERS_mouse #1

tag: genotype

value: WT

value: tunicamycin


title: MPH Thapsi #3

description: Transcriptomic MPH Thapsi

source_name: MPH Thapsi

growth_protocol: Mice were housed in a temperature-controlled room (22–24°C) with a 12h dark-light cycle. Animal studies were performed in compliance with European Community specifications regarding the use of laboratory animals and approved by the Nord-Pas de Calais Ethical Committee for animal use.

treatment_protocol: Mouse primary hepatocytes were prepared as described in Bantubungi K et al, Diabetes 2014. Hepatocytes were grown in serum free William's medium and treated for 4h with 1µM thapsigargin or vehicle (0.04% DMSO).

tag: strain background

tag: genotype/variation

tag: age

value: adult

tag: Sex

value: male

value: mouse primary hepatocytes (MPH)

value: Thapsi


title: SKM_Control_mouse #2

description: Transcriptomic gastrocnemius - control

value: saline control


title: Uninfected_Donor4_AMK_Uninfected

tag: cell type

value: human monocyte-derived macrophages

value: AMK


title: MPH Thapsi #2

description: Transcriptomic MPH Thapsi


title: Liver NFIL3 KO tunica #5

description: Transcriptomic liver of NFIL3 KO mouse treated with tunicamycin

source_name: Liver NFIL3 KO tunica

treatment_protocol: Mice were treated for 8h with 1 µg/g tunicamycin or vehicle (150 mM dextrose).

value: NFIL3 KO

tag: tissue

value: liver

value: 1 µg/g tunicamycin for 8hrs


title: SKM_Control_mouse #1

description: Transcriptomic gastrocnemius - control


title: Liver NFIL3 KO tunica #4


title: Liver NFIL3 KO tunica #3


title: Uninfected_Donor4_EMB_Uninfected

value: EMB


title: Liver NFIL3 KO vehicle #4

description: Transcriptomic liver of NFIL3 KO mouse treated with vehicle

source_name: Liver NFIL3 KO vehicle

value: vehicle for 8hrs


title: Uninfected_Donor4_PZA_Uninfected

value: uninfected

value: PZA


title: Uninfected_Donor4_INH_Uninfected

value: INH


title: Infected_Donor4_RIF_Infected

value: infected

value: Mycobacterium tuberculosis

value: RIF


title: Uninfected_Donor4_DMSO_Uninfected

value: DMSO


title: Infected_Donor3_PZA_Infected