title: control_ATAC-seq_rep2

data_processing:
Sequence adaptor were first removed using cutadapt (CTGTCTCTTATACACATCTCCGAGCCCACGAGAC for read1 and CTGTCTCTTATACACATCTCCGAGCCCACGAGAC for read2)
Then cutted reads were aligned to human hg19 assembly using Bowtie2 with parameter: -p 4 -X 2000 --no-mixed --no-discordant --no-unal.
ATAC-seq peaks were called by MACS2 with parameter: -s 50 -w.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Tab-delimited table showing the MACS peak calling results

extract_protocol:
samples were lysed in lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2 and NP-40) for 10 min on ice to prepare the nuclei. Immediately after lysis, nuclei were spun to remove the supernatant. Nuclei were then incubated with the Tn5 transposome and tagmentation buffer at 37 °C for 30 min (Vazyme, China). After the tagmentation, the stop buffer was added directly into the reaction to end the tagmentation. PCR was performed to amplify the library for 15 cycles. After the PCR reaction, libraries were purified with the 1.2× AMPure beads (Beckman, Germany).
In house protocol which is similar as NEB library constructions (#7370)


title: OSKM Day 5 HDAC3-YF H3K27ac ChIP-seq

status: Public on Mar 07 2018

type: SRA

city: Shenzhen

first: Andrew

middle: P

last: Hutchins

address: 1088 Xueyuan Rd

department: Bioinformatics

country: China

institute: Southern University of Science and Technology

library_source: genomic

data_processing:
Reads were aligned to the mouse mm10 genome using bowtie2 v2.2.0
Peaks were discovered using MACS 1.4 (NCoR/SMRT)
Peaks were discovered using Dfilter (H3K27ac)
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files are peak bed files and bigWig tracks

molecule: genomic DNA

organism: Mus musculus

source_name: MEFs transfected with OSKM and HDAC3-YF mutant plasmid Day 5

growth_protocol: Maintenance of mouse ESCs and fully reprogramed iPSCs was conducted in chemically defined N2B27-based medium: DMEM/F12 (HyClone) and Neurobasal (Gibco) mixed 1:1, supplemented with N2 (Invitrogene), B27 (Invitrogene), non-essential amino acids, GlutaMAX, sodium-pyruvate (Gibco), penicillin/streptomycin (HyClone), 0.1 mM β-mercaptoethanol (Sigma), 100 units/ml leukemia inhibitory factor (LIF) (Millipore), small-molecule inhibitors CHIR99021 (3 μM, Selleck), and PD0325901 (1 μM, Selleck)

extract_protocol:
Cells were lysed in nuclei extraction buffer (50 mM HEPES KOH (pH 7.5), 140 mM NaCl, 1m M EDTA, 10% glycerol, 0.5% NP-40 alternative, 0.25% Triton X-100) supplemented with protease inhibitor cocktail (Roche) for 10 minutes at 4 °C. Cell pellets were resuspended in protein extraction buffer (10 mM Tris-HCl (pH 8.0), 200 mM NaCl, 1 mM EDTA and 0.5 mM EGTA) supplemented with protease inhibitor cocktail and incubated for 10 minutes at room temperature. For sonication, pellets were resuspended in sonication buffer (10 mM Tris-HCl (pH 8.0), 0.5 mM EGTA, 1% Triton X-100, protease inhibitor cocktail) and then fragmented with a Bioruptor (Diagenode) sonicator at 4°C for 30 cycles using high amplitude and 30 seconds ON and 30 seconds OFF cycles to produce size ranges between 200 and 500 base pairs. 2 mg of each antibody was prebound by incubating with Protein A+G Dynabeads (Invitrogen 100-07D) in blocking buffer (PBS supplemented with 0.5% TWEEN) for 6 hours at 4°C. Washed beads were added to the chromatin lysate and incubated overnight. Samples were washed twice with low salt washing buffer (20 mM Tris-HCl (pH 8.0), 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100), twice with high salt washing buffer (20 mM Tris-HCl (pH 8.0), 500 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100) twice with LiCl buffer (10 mM Tris-HCl, 250mM LiCl, 1mM EDTA, 1% NP-40, 1% Na-deoxycholate), twice with TE (10 mM Tris-HCl pH 8.0, 1mM EDTA), supplemented with 50 mM NaCl and eluted in elution buffer (50 mM Tris-HCl, 10 mM EDTA and 1% SDS). Eluates were incubated at 65°C for 20 minutes, followed by de-crosslinking at 65°C for 6-15 hours. Samples were diluted in TE buffer and then treated with RNaseA (Roche) for 60 minutes at 37°C, followed by incubation with proteinase K (Sigma) for 45 minutes at 56°C. DNA was purified with phenol:chloroform:isoamyl alcohol. The following antibodies were used for ChIP experiments: anti-NCoR (ABE251, Millipore), anti-SMRT (ab24551, Abcam), anti-H3K27ac (ab4729, Abcam).
Standard Illumina protocols

treatment_protocol: 15,000 MEFs were transducted once in 12-well plates using virus-containing supernatants generated by PlatE or HEK293T cells. After infection the medium was changed to mouse ESC serum-based medium (DMEM-High glucose supplemented with 15% FBS, non-essential amino acids, GlutaMAX, sodium-pyruvate, penicillin/streptomycin, 0.1 mM β-mercaptoethanol and 100 units/ml LIF or mouse ESC KSR medium (DMEM-High glucose supplemented with 15% Knockout Serum Replacement (Gibco), non-essential amino acids, GlutaMAX, sodium-pyruvate, penicillin/streptomycin, 0.1 mM β-mercaptoethanol, N2, 5 ng/ml basic fibroblast growth factor (bFGF) (Peprotech) and 100 units/ml LIF, and renewed daily. Cells were cross-linked in freshly prepared formaldehyde solution (1% final concentration for 10 minutes at room temperature), and then quenched with 125 mM glycine (5 minutes at room temperature). Fixed cells were washed with PBS, harvested, flash-frozen in liquid nitrogen and store at -80°C for further use.

tag: day

tag: treatment

value: OSKM+HDAC3-YF transfection

tag: presumed cell type

value: Intermediate pluripotent reprogramed cells

tag: strain

tag: antibody

value: ant-H3K27ac Abcam, GR167929-1 Lot# ab4729


title: OSKM Day 5 FLAG H3K27ac ChIP-seq

source_name: MEFs transfected with OSKM and FLAG control plasmid Day 5

value: OSKM+FLAG control transfection


title: ChIP-Seq_Pc_WT_1

city: Bethesda

first: Mingan

last: Sun

state: Maryland

address: Building 6B, 6 Center Drive

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development

country: USA

institute: National Institute of Health

data_processing:
ChIP-Seq data were first processed using Trim Galore  (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore), then aligned to reference genome (dm3, BDGP Release 5) using Bowtie v1.1.2 (Langmead et al. 2009) with parameters: -n 2 -l 28 -k 1 --best. The PCR duplicates for each dataset were removed using the rmdup function of samtools. The reads from biological replicates were pooled together for further analysis. For H3K27me3 domains which could be of dozens to hundreds of kilobases in length, initial peak calling was performed using SICER v1.1 (Zang et al. 2009) with parameter: window size = 500, fragment size = 200, effective genome fraction = 0.7, gap size = 2000. To focus on canonical H3K27me3 domains, only those with FDR < 0.1, length > 5kb and with at least two-fold enrichment were used for further analysis. For other PcG factors which form punctuated peaks, peak calling was performed using MACS v2.1.1 (Zhang et al. 2008) with parameters: -g dm -q 0.05.
The raw data for RNA-Seq were first processed with Trim Galore, then aligned to the reference genome (dm3, BDGP Release 5) using Tophat v2.1.1 (Ghosh and Chan 2016) with parameter: --no-novel-juncs. Finally, the FPKM for each gene was calculated using cufflinks, and normalized between different datasets using cuffnorm (Ghosh and Chan 2016). To identify differentially expressed genes, we first get the read counts for each gene with htseq-count (Anders et al. 2015), then identified differential genes with FDR<0.05 using DESeq2 (Love et al. 2014).
Genome_build: dm3, BDGP Release 5
Supplementary_files_format_and_content: BED files for broad peaks called by SICER for H3K27me3; BED files for narrow peaks called by macs2 for other factors. Tab-delimited text files include normalized FPKM values for each sample.

organism: Drosophila melanogaster

source_name: third instar larval imaginal discs and brains

growth_protocol: Fly stocks were maintained at 25 0C.

extract_protocol:
Total genomic DNA was extracted from CNS and disc materials using XXX.
Invitrogen Dynabeads (M-280 sheep anti-rabbit IgG) were used for Chromatin immunoprecipitation in place of protein A or G agarose/salmon sperm DNA beads. ChIP reactions were performed with 1:100 dilutions of anti-Pho  (Brown et al., 2003), anti-Spps (Brown and Kassis 2010), anti-Ph (Donna-Arndt-Jovin), 1:200 dilutions of anti-E(z) (rabbit polyclonal raised against bacterially expressed full length E(z)), anti-Psc (Nicole Francis), anti-Pc (Santa Cruz Biotech Inc, sc25762), and anti-H3K27me3 (Millipore, 17-622).

tag: tissue


title: control_ATAC-seq_rep1

city: Beijing

first: Yanjian

last: Li

address: Tsinghua University, Haidian District

institute: Tsinghua University

organism: Homo sapiens

source_name: control HL-60 cells

growth_protocol: HL-60 cells were maintained in RPMI-1640 medium (Gibco) supplemented with 10% fetal bovine serum (FBS, Gibco, USA), 50 units/mL penicillin and streptomycin (Gibco, USA), 1X Non-Essential Amino Acids (Gibco, USA).

treatment_protocol: 2x10^5/ml HL-60 cells in 100mm dish were treated with 1μM ATRA (1 mM stock in ethanol, Sigma, USA) for 4 days , referred as ATRA group. Cells treated with equal amount of ethanol (10μl added in 10ml medium) were referred as control group. Medium was changed and ATRA/ethanol was added again at day2.

tag: cell line

value: HL-60; ATCC CCL-240

tag: tissue origin

value: peripheral blood

tag: disease

value: acute promyelocytic leukemia

tag: treated with

value: ethanol for 4 days


title: OSKM Day 9 SMRT ChIP-seq

source_name: MEFs transfected with OSKM Day 9

value: OSKM

value: anti-SMRT Abcam, ab24551 Lot# GR140820-1


title: ChIP-Seq_Ez_WT_2

value: third instar larval imaginal discs and brains


title: ATRA_ATAC-seq_rep2

source_name: ATRA treated HL-60 cells

value: 1μM ATRA for 4 days


title: ChIP-Seq_Ez_WT_3


title: ChIP-Seq_Ez_WT_1


title: ATRA_ATAC-seq_rep1


title: H3K4me2_siARV_ChIPSeq_R1881

city: San Antonio

first: Zhenqing

last: Ye

state: TX

address: 8403 Floyd Curl Dr

department: 6Department of Population Health Sciences

institute: UT Health San Antonio

data_processing:
Basecalls performed using CASAVA version 1.4
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Cliinc sequence core using the pipeline Cassava 1.7
Raw sequences were mapped to reference genome (hg19) using BWA (v0.5.9) with defautl parameters
Peak calling was performed using MASC2 (v2.0.10)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated from bedGraph files that generated from MACS, Scores represent reads coverage siganl

source_name: Prostate cancer 22Rv1 cells

growth_protocol: Prostate cancer cells were cultures (typically 2–3 × 106 cells into a T75 flask) in RPMI 1640 medium (Gibco, Unite State) with charcoal-stripped (steroid depleted) serum (CSS).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2000 following the manufacturer's protocols.

treatment_protocol: 22Rv1 cells were transfected with non-target siRNA (designated as ARFL+/ARVs+), siRNA targeting ARV1/3/4/7 (designated as ARFL+/ARVs-) or siRNA targeting AR exon7 (designated as ARFL-/ARVs+), cultured with charcoal-stripped serum (CSS) medium for 72 hours, then treated with or without androgen (R1881) .

tag: cell type

value: prostate cancer cells

value: siARV

tag: chip antibody


title: OSKM Day 9 FLAG H3K27ac ChIP-seq

source_name: MEFs transfected with OSKM and FLAG control plasmid Day 9


title: ESC H3K27ac ChIP-seq

source_name: mouse embryonic stem cells

value: Embryonic stem cell


title: H3K4me2_siARV_ChIPSeq

value: EtOH


title: ESC Input

value: No antibody, DNA input control


title: e11a11_R47H_2

city: New York

first: Bin

last: Zhang

state: NY

address: 1470 Madison Avenue

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

library_source: transcriptomic

data_processing:
The raw sequencing reads were aligned to fly genome BDGP6 using star aligner (version 2.5.0b)
Following read alignment, featureCounts was used to quantify the gene expression at the gene level based on Ensembl gene model.
Genes with at least 5 reads in at least one sample were considered expressed and hence retained for further analysis, otherwise removed. Using limma's voom function, the gene level read counts data was normalized as counts per million (CPM) using trimmed mean of M-values normalization (TMM) method and subsequently log2 transformed.
The log2 CPM values were adjusted for RIN score using a linear regression.
Genome_build: BDGP6
Supplementary_files_format_and_content: log2 CPM

molecule: total RNA

source_name: e11a11_R47H_adult heads

growth_protocol: Flies were raised and maitained at 25°C under 12hr light/dak condition.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Flies were quickly frozen in liquid nitrogen and heads were collected on dry ice.

tag: strain information

tag: age

value: 1 week

value: Adult heads

tag: rin


title: ESC SMRT ChIP-seq


title: ESC NCoR ChIP-seq

value: anti-NCoR Millipore, ABE251, Lot#2153059


title: e11a11_Trem2wt_3

source_name: e11a11_Trem2wt_adult heads


title: e11a11_R47H_1


title: e11a11_Trem2wt_2


title: H3K4me1_siARV_ChIPSeq_R1881


title: H3K27ac_siARV_ChIPSeq_R1881


title: H3K27ac_siARV_ChIPSeq


title: OSKM Day 9 NCoR ChIP-seq

value: Intermediate pluripotent reprogramed cells


title: H2AZ_siARV_CHIPSeq_R1881


title: e11a11_3

source_name: e11a11_adult heads


title: e11a11_1


title: e11a11_2


title: MEF H3K27ac ChIP-seq

source_name: mouse embryonic fibroblasts

value: Fibroblast

value: ant-H3K27ac Abcam, GR167929-1 Lot# ab4729


title: eGRL_R47H_3

source_name: eGRL_R47H_adult heads


title: Human cultured adventitial cells ALDH Dim

city: Los Angeles

first: Gay

middle: Miriam

last: Crooks

state: California

address: 610 Charles E. Young Drive, East

department: Pathology & Laboratory Med

institute: University of California Los Angeles

description: GCBPhsCUdim

data_processing:
The STAR aligner (v2.3.0) was used to generate the genome index and perform alignments in paired-end mode. We followed a 2-pass alignment strategy: in the first round, reads were aligned to a genome index that included both the genome sequence (GRCh37 primary assembly) and the exon/intron structure of known gene models (Ensembl GRCh37.71). Novel splice junctions were then included in the junction database to generate a new genome index for re-alignment. Relevant alignment parameters included: multimapping score range=0.66, minimum alignment length=75%, minimum intron length=21, minimum alignment overhang for novel junctions=10, infinite penalty for non-canonical splice sites
Alignment files were used to generate gene-level count summaries with HTSeq (unique hits and “intersection-nonemtpy” mode for version v0.6.1p2). The reference annotation was built using Gencode protein coding genes (GRCh37.71) and an in-house database of long non-coding RNAs (see Supplementary Table 1 in manuscript website).
Expression estimates in units of FPKMs (fragments per kilobase of mappable gene length and million reads) were obtained after normalizing the counts matrix with sequencing depth and gene effective length. These expression levels, which are expected to correlate with mRNA relative abundance within each sample (within-sample normalization), were used for rank-order classifier in comparative analyses for individual samples. Differential expression or global clustering across samples was always carried out after inter-sample normalization.
Genome_build: GRCh37
Supplementary_files_format_and_content: Per sample expression estimates in units of FPKMs. Tab delimited. Format: Gene ids /Description / Average expression estimates for each sample

growth_protocol: Human lipoaspirate was processed for the stroma vascular fraction as descbribed (Corselli et al Blood 2013). Lipoaspirate-derived adventitial cells (CD31-/CD45-/CD34+/CD146-) and pericytes (CD31-/CD45-/CD34-/CD146+) were sorted from two donors. Cells were also stained with aldefluor, an enzyme substrate for ALDH, and the adventitial cells (CD31-/CD45-/CD34+/CD146-) were isolated by FACS according to immunophenotype and ALDH-staining status.

extract_protocol:
All samples were extracted with Trizol and purified using miRNeasy Mini Kit (Qiagen).
500ng-2ug of total RNA was input to generate cDNA using Nugen Ovation RNA-Seq System v2 and the sequencing libraries were generated using prepX DNA library enzyme kit (IntegenX Inc.) per manufacturer’s instructions.
Paired-end 100bp sequencing was performed on Illumina HiSeq 2000

treatment_protocol: The freshly sorted populations were pelleted for RNA extraction and some continue cultured for 3 passages in DMEM containing 20% FBS. Following three passages in culture, the adventitial populations (CD31-/CD45-/CD34+/CD146-/ALDH Bright and (CD31-/CD45-/CD34+/CD146-/ALDH Dim) were pelleted for RNA extraction. Because of phenotype drifting, the pericytes were resorted for a consistent phenotype (CD31-/CD45-/CD34-/CD146+) prior to collection for RNA extraction.

value: human lipoaspirate

value: Human lipoaspirate derived adventitial cells ALDH Dim sorted (sorted and cultured)


title: eGRL_R47H_2


title: Human pericytes

description: GCBPhsFSper

value: Human lipoaspirate derived pericytes (freshly sorted)


title: Human cultured pericytes

description: GCBPhsCUper

value: Human lipoaspirate derived pericytes (freshly sorted and cultured)


title: e11a11_R47H_3


title: eGRL_Trem2wt_2

source_name: eGRL_Trem2wt_adult heads


title: eGRL_R47H_1


title: Human adventitial cells ALDH Dim

description: GCBPhsFSdim

value: Human lipoaspirate derived adventitial cells ALDH Dim sorted (freshly sorted)


title: Human cultured adventitial cells ALDH Bright

description: GCBPhsCUbrite

source_name: CD31-/CD45-/CD34+/CD146-/ALDH Bright

value: Human lipoaspirate derived adventitial cells ALDH Bright sorted (sorted and cultured)


title: eGRL_Trem2wt_3


title: Human adventitial cells

description: GCBPhsFSadv

value: Human lipoaspirate derived adventitial cells (freshly sorted)


title: H3K4me1_siARV_ChIPSeq

value: prostate cancer cells

value: siARV


title: eGRL_Trem2wt_1


title: hPSC-CD146- sample 2

growth_protocol: The hESC line H1 (WiCell, Madison, WI) was maintained on Matrigel coated plates (growth factor reduced, no phenol red; BD Biosciences, San Jose, CA), and cultured in mTESR medium (Stem Cell Technologies, Vancouver, BC). To initiate mesoderm differentiation, mTESR medium was replaced with basal induction medium X-Vivo 15 (Lonza, Walkersville, MD). Basal induction medium was supplemented with human growth factors activin A, BMP4, VEGF and bFGF for 3.5 days (all at 10 ng/mL; R&D Systems, Minneapolis, MN), with the inclusion of activin A only on day 1 (“A-BVF” condition published in Evseenko et al. PNAS. 2010). After mesoderm induction, human embryonic mesodermal progenitor (hEMP) was isolated as CD326−CD56+ cells by fluorescence activated cell sorting (FACS) at day 3.5 of differentiation.

treatment_protocol: To induce mesenchymal differentiation, hEMP were seeded at 50,000 cells/well into 6-well tissue culture plates, pre-coated with matrigel for two hours. For the first 7 days of differentiation, MesenCult Proliferation Kit, Human (STEMCELL Technologies) supplemented with SB-431542 (10uM, R&D Systems) was used. From Day 1-3, 10µM Rock inhibitor (Y27632 hydrochloride; R&D Systems) and 10µg/mL gentamicin (Gibco, Thermo Fisher Scientific, Waltham, MA) were also added. From day 7-14, the media was switched to EGM-2 complete medium (Lonza) supplemented with SB-431542 (10uM, R&D Systems). Half medium change was performed every other day. At day 14-18, cells were dissociated into single cell suspension with Accutase (Innovative Cell Technologies, San Diego, CA), stained with monoclonal antibodies and isolated by FACS according to the aforementioned phenotypes.

value: human embryonic stem cells-derived (H1 line)

value: Mesenchymal subpopulation derived from mesodermal differentiation of human embryonic stem cells


title: eGRL_Control_1

source_name: eGRL_Control_adult heads

value: 1 week


title: eGRL_Control_3

value: Adult heads


title: hPSC-CD146- sample 1


title: eGRL_Control_2


title: hPSC-CD146++ sample 3


title: e11a11_Trem2wt_1


title: H2AZ_siARV_CHIPSeq

value: EtOH


title: Tau_R47H_3

source_name: Tau_R47H_adult heads


title: hPSC-CD146++ sample 2


title: Tau_R47H_2


title: hPSC-CD146++ sample 1


title: Tau_Trem2wt_3

source_name: Tau_Trem2wt_adult heads


title: Tau_R47H_1


title: Tau_Trem2wt_1


title: Tau_Trem2wt_2


title: Input DNA

source_name: 22Rv1_Input DNA


title: FOXA1_ChIPSeq_R1881


title: FOXA1_ChIPSeq


title: Tau_2

source_name: Tau_adult heads


title: H2AZ_CHIPSeq


title: R47H_3

source_name: R47H_adult heads


title: Tau_1


title: H3K27ac_ChIPSeq


title: H3K27ac_ChIPSeq_R1881


title: R47H_2


title: R47H_1


title: H3K4me2_ChIPSeq


title: Trem2wt_3

source_name: Trem2wt_adult heads


title: H3K4me2_ChIPSeq_R1881


title: Trem2wt_1


title: siNT_E_rep2

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
Fragment 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 fragment 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.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include "chrom", "st", "end"," mRNA_size"," strand"," fragment count"," FPM" and "FPKM" values for each Sample.

extract_protocol:
Cells were  flash frozen on dry ice, and RNA was harvested using Trizol reagent.  Ribo-zero rRNA remove Kit was used to remove ribosomal RNAs were removed. 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: 22Rv1 cell were transfected with non-target siRNA (designated as ARFL+/ARVs+) or siRNA targeting ARV1/3/4/7 (designated as ARFL+/ARVs-), then cultured with charcoal-stripped serum (CSS) medium for 72 hours.

tag: transfected with


title: Control_3

source_name: Control_adult heads


title: Human adventitial cells ALDH Bright

description: GCBPhsFSbrite

value: Human lipoaspirate derived adventitial cells ALDH Bright sorted (freshly sorted)


title: H3K4me1_ChIPSeq


title: Control_2


title: H2AZ_CHIPSeq_R1881


title: siARVs_E_rep2

value: siRNA targeting ARV1/3/4/7 (designated as ARFL+/ARVs-)


title: hPSC-CD146- sample 3


title: hEMP sample 2

description: Early mesoderm progenitor derived from human embryonic stem cells

data_processing:
The STAR aligner (v2.3.0) was used to generate the genome index and perform alignments in paired-end mode. Reads were aligned to a genome index that included both the genome sequence (GRCh37 primary assembly) and the exon/intron structure of known gene models (Ensembl GRCh37.71). Relevant alignment parameters included: multimapping score range=0.66, minimum alignment length=75%, minimum intron length=21, minimum alignment overhang for novel junctions=10, infinite penalty for non-canonical splice sites
Alignment files were used to generate gene-level count summaries with HTSeq (unique hits and “intersection-nonemtpy” mode for version v0.6.1p2). The reference annotation was built using Gencode protein coding genes (GRCh37.71) and an in-house database of long non-coding RNAs (see Supplementary Table 1 in manuscript website).
Expression estimates in units of FPKMs (fragments per kilobase of mappable gene length and million reads) were obtained after normalizing the counts matrix with sequencing depth and gene effective length. These expression levels, which are expected to correlate with mRNA relative abundance within each sample (within-sample normalization), were used for rank-order classifier in comparative analyses for individual samples. Differential expression or global clustering across samples was always carried out after inter-sample normalization.
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab delimited. Expression estimates in units of FPKMs. Format: Gene id / Expression estimates for each sample

growth_protocol: The hESC line H1 (WiCell, Madison, WI) was maintained on Matrigel coated plates (growth factor reduced, no phenol red; BD Biosciences, San Jose, CA), and cultured in mTESR medium (Stem Cell Technologies, Vancouver, BC). To initiate mesoderm differentiation, mTESR medium was replaced with basal induction medium X-Vivo 15 (Lonza, Walkersville, MD). Basal induction medium was supplemented with human growth factors activin A, BMP4, VEGF and bFGF for 3.5 days (all at 10 ng/mL; R&D Systems, Minneapolis, MN), with the inclusion of activin A only on day 1 (“A-BVF” condition published in Evseenko et al. PNAS. 2010).

extract_protocol:
All samples wwere extracted with Trizol and purified using miRNeasy Mini Kit (Qiagen).
500ng-2ug of total RNA was input to generate cDNA using Nugen Ovation RNA-Seq System v2 and the sequencing libraries were generated using prepX DNA library enzyme kit (IntegenX Inc.) per manufacturer’s instructions.
Paired-end 100bp sequencing was performed on Illumina HiSeq 2000 with six samples multiplexed per lane.

treatment_protocol: After mesoderm induction, hEMP was isolated as CD326−CD56+ cells by fluorescence activated cell sorting (FACS) at day 3.5 of differentiation.

value: human embryonic stem cells-derived


title: hEMP sample 3


title: hEMP sample 1


title: H1 sample 3

description: human embryonic stem cells cultured on matrigel

value: human embryonic stem cells


title: H1 sample 2


title: Control_1


title: Trem2wt_2


title: H1 sample 1


title: H3K4me1_ChIPSeq_R1881


title: Wild-type in vivo, replicate 3 [HiSeq 2500]

city: Clayton

first: Julian

last: Rood

state: VIC

address: Wellington Rd

department: Microbiology

country: Australia

institute: Monash University

data_processing:
Analysis was performed using the Nesoni pipeline. (https://github.com/Victorian-Bioinformatics-Consortium/nesoni)
Reads were firsted clipped of low quality and adaptor sequence using the Nesoni "clip" tool.
Reads were aligned using SHRiMP 2.2.3.
Fragments (reads or read-pairs) aligning to genes were counted using the Nesoni "count" tool. Where a read aligned equally well to multiple genes, it was counted once toward all best-aligning genes. Reads were produced from multiple sequencing runs for the "in vivo" samples, these have been pooled together to produce a single count for each biological sample.
Genome_build: Clostridium perfringens strain 13, NCBI reference sequences NC_003366.1 and NC_003042.1
Supplementary_files_format_and_content: counts.csv - Fragment counts for each gene and sample in CSV format.

organism: Clostridium perfringens

source_name: Infected murine muscle tissue

growth_protocol:
In vitro cells were grown for 90 min trypticase peptone broth
In vivo cells were injected into murine muscles and the muscle tisses removed and extracted after 90 min

extract_protocol: Total RNA was then isolated using TRIzol reagent. The RNA aliquot was treated with Turbo DNase (Ambion) at 37°C for 30-60 min to eliminate DNA contamination. Contaminating host RNA was depleted from the sample using a MICROBEnrichTM kit (Ambion) in accordance with the manufacturer’s instructions.  A total of 5 μg of pooled RNA was subjected to repeated cycles of bacterial RNA enrichment to ensure the almost complete depletion of the host RNA. Next, bacterial ribosomal RNA (rRNA) was depleted from the preparation using a Ribo-Zero rRNA removal kit (Epicentre) as per the manufacturer’s instructions.  Libraries for bacterial RNA-seq were then prepared using an Illumina TruSeq RNA sample preparation kit v2.  RNA-seq analysis of the enriched RNA samples from the in vivo- and in vitro-derived cells was carried out on Illumina Hi-seq and Mi-seq instruments, respectively.

tag: source

value: Infected murine muscle tissue


title: siNT_E_rep1

value: non-target siRNA (designated as ARFL+/ARVs+)


title: IBD_DSS_NLRX1_RNASEQ_009

city: Blacksburg

first: Monica

last: Viladomiu

state: VA

address: 1015 Life Science Circle

department: Virginia Bioinformatics Institute

institute: Nutritional Immunology and Molecular Medicine Laboratory

data_processing:
Adapter trimming
Bowtie was used to map the reads to RefSeq sequences of mouse (downloaded from UCSC), and RSEM was used to calculate expression values for each gene. FPKM-transformed values were log-transformed followed by normal quantile transformation. Two methods of P-value adjustment (FDR & Bonferroni) were used. Kolmogorov-Smirnov test was used to test normality, followed by parametric 3-way ANOVA to obtain differential expression.
Genome_build: mm9

source_name: Whole colon

growth_protocol: Induction of colitis protocol: C57BL/6 wild-type (WT) and NLRX1-/- mice ranging from 6-8 weeks of age were administered 8% high molecular weight DSS (average 500,000 molecular weight, Fisher Scientific) in drinking water for seven days.  Control mice received normal water. Mice were housed in laboratory animal facilities at the Virginia Tech in a room maintained at 22°C, with a 12-h-light/-dark cycle and fed standard rodent diet free-choice. On day 7, all mice were euthanized via carbon dioxide narcosis with secondary bilateral thoracotomy. All mice were weighed and scored daily. Clinical scores were based physical appearance (0-3), fecal consistency (0-3), presence of rectal bleeding (0-4), and weight loss (0-3) and assigned a compounded score for overall disease activity. All experimental procedures were approved by the Institutional Animal Care and Use Committee of the Virginia Tech.

extract_protocol:
After homogenization of tissue, total RNA was extracted and purified using the RNAeasy system according to manufacturer’s instructions (Qiagen Valencia, CA). The QIAGEN RNase-free DNase supplement kit was used to ensure that the RNA was free from DNA contamination.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After mice were euthanized, colons were excised, scored and washed 3 times in phosphate buffered saline solution. Tissue was homogenized and processed using and RNAeasy MiniKit.

tag: background strain

tag: genotype

value: Wild-type

value: 8% Dextran sodium sulfate

tag: length of treatment

value: 7 days


title: IBD_DSS_NLRX1_RNASEQ_010

tag: treatment


title: IBD_DSS_NLRX1_RNASEQ_012


title: 7m-60-2_WT

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

description: genotype abbreviation: WT

data_processing:
Aligned to mm10 using STAR spliced read aligner
Count read using HT-seq and using mm10 RefSeq as reference
Normalization (TMM), quantitation (FPKM) and differential expression analysis using edgeR and limma voom.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM values

molecule: polyA RNA

growth_protocol: Mice were used in standard mouse cages under conventional SPF laboratory conditions until designated ages (2, 4 and 7 months old).

extract_protocol:
Total RNA was extracted using RNeazy kit (Qiagen)accordance with the prescribed protocol provided with the kit.
Libraries prepared using the Illumina TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq4000 sequencer using strand-specific

tag: strain

value: (C57BL/6J x FvB/NJ) F1

value: WT

value: brain

tag: brain region

value: cortex

tag: gender

value: F


title: 7m-69-3_5xFAD/BAC-TREM2

description: genotype abbreviation: TA

tag: tissue

value: M


title: Wild-type in vivo, replicate 1 [HiSeq 2500]


title: IBD_DSS_NLRX1_RNASEQ_007


title: IBD_DSS_NLRX1_RNASEQ_008


title: IBD_DSS_NLRX1_RNASEQ_004

value: Negative control


title: IBD_DSS_NLRX1_RNASEQ_006


title: IBD_DSS_NLRX1_RNASEQ_005


title: siARVs_E_rep1

tag: cell line

value: prostate cancer cells


title: Wild-type in vivo, replicate 2 [HiSeq 2500]


title: IBD_DSS_NLRX1_RNASEQ_011


title: 7m-51-2_5xFAD

description: genotype abbreviation: AD


title: 7m-60-1_WT

description: genotype abbreviation: WT


title: IBD_DSS_NLRX1_RNASEQ_003


title: 7m-49-3_WT

description: genotype abbreviation: WT


title: 7m-44-4_5xFAD/BAC-TREM2

description: genotype abbreviation: TA


title: 7m-49-4_5xFAD/BAC-TREM2

description: genotype abbreviation: TA


title: 7m-50-3_5xFAD/BAC-TREM2

description: genotype abbreviation: TA


title: 7m-42-2_BAC-TREM2

description: genotype abbreviation: T


title: 7m-50-1_5xFAD/BAC-TREM2

description: genotype abbreviation: TA


title: 7m-49-5_BAC-TREM2

description: genotype abbreviation: T


title: 7m-44-1_5xFAD

description: genotype abbreviation: AD


title: 7m-41-5_WT

description: genotype abbreviation: WT


title: 7m-41-3_5xFAD

description: genotype abbreviation: AD


title: 7m-42-5_5xFAD

description: genotype abbreviation: AD


title: Clostridium perfringens infected rep2

city: Melbourne

first: Jamie

last: Gearing

address: 27-31 Wright St

institute: Hudson Institute of Medical Research

description: Mus musculus tissue infected with Clostridium perfringens

data_processing:
Samples were analysed on the AB SOLiD System and basecalls were  made in colour space using Lifescope.
BAM files were created by mapping reads to the mouse genome using Lifescope with a QV threshold set at 20.  The Clostridium perfringens genome (NC_003366) was included as an artificial chromosome to filter out any bacterial RNA.
The BAM files  for each replicate were merged using samtools merge (v1.3.1).
Counts for each gene were obtained using featureCounts from the Subread package (v1.5.0-p1) with the Mus_musculus.GRCm38.86.gtf Ensembl genome annotation file.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with gene count  values for each Sample

source_name: Muscle

growth_protocol: C. perfringens were incubated under anaerobic conditions (10% (v/v) H2, 10% (v/v) CO2 and 80% (v/v) N2) at 37°C, in tryptone-peptone-glucose (TPG) broth, fluid thioglycolate medium (FTG) (Difco), or nutrient agar supplemented with 10 μg/ml rifampicin and 10 μg/ml nalidixic acid

extract_protocol:
Total RNA from mouse muscle tissue was harvested using Trizol reagent.  The total RNA was further purified through the Qiagen RNeasy mini columns with the additional on column DNase step
RNA libraries were prepared according to the Life Technologies SOLiD Total RNA-Seq Kit.  Briefly 5ug of total RNA was depleted of both eukayotic and bacterial rRNA, using an 8:2 ratio of eukaote:bacteria probe mix.  Following enzymatic shearing, 100ng of ribo-depleted  RNA was used to make whole transcriptome libraires according to the SOLiD Total RNA-Seq protocol; Pub 4452437 RevB

treatment_protocol: Both hind legs of 6-8 week mice were injected with either 50 μl of washed Clostridium perfringens cells in sterile Dulbecco’s phosphate-buffered saline for the Clostridium perfringens infected samples or or 50 μl of PBS only for the mock infected samples.

value: BALB/c

value: Muscle

tag: infectious agent

value: Clostridium perfringens strain JIR325

tag: sample time (hours after infection)


title: Clostridium perfringens infected rep3


title: PBS3 rep3

description: Mus musculus tissue mock infected with PBS

value: Mock infection


title: Clostridium perfringens infected rep1


title: IBD_DSS_NLRX1_RNASEQ_001


title: 7m-41-2_5xFAD/BAC-TREM2

description: genotype abbreviation: TA


title: PBS2 rep1


title: 7m-40-4_5xFAD

description: genotype abbreviation: AD


title: 7m-41-1_5xFAD

description: genotype abbreviation: AD


title: 7m-34-4_BAC-TREM2

description: genotype abbreviation: T


title: 7m-42-4_BAC-TREM2

description: genotype abbreviation: T


title: AOS-14_E-n_H3K4me1

city: Shanghai

first: Weisheng

last: Zheng

address: Siping Road, No.1239

department: Department of Bioinformatics

institute: Tongji University

data_processing:
ChIP-seq reads of each histone modification were aligned to mouse mm10 genome assembly by using Bowtie2 v2.2.9 with parameters: -I 100 -X 500 --no-unal --no-discordant.
The concordant paired reads were used to generate the bigwig signal track files by using Deeptools2.
Genome_build: mm10
Supplementary_files_format_and_content: The processed data file is a bigwig format file for histone modification signal across the mouse genome.

growth_protocol: Mouse haploid embryonic stem cells were derived and constructed from mouse AG-haploid embryos by FACS and then cultured in ES cultrure medium.

extract_protocol:
Lysates were clarified from nuclei and then fragmented with Mnase treatment. Histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit

tag: strain background

tag: cell type

value: mouse haploid embryonic stem cells

tag: chip antibody

value: H3K4me1 (Abcam, ab8895)


title: IBD_DSS_NLRX1_RNASEQ_002

value: Wild-type


title: 7m-31-4_BAC-TREM2

description: genotype abbreviation: T

tag: age


title: A129-2_E-n_H3K4me1


title: 7m-34-1_WT

description: genotype abbreviation: WT


title: 7m-31-2_WT

description: genotype abbreviation: WT


title: 4m-73-1_5xFAD/BAC-TREM2

description: genotype abbreviation: TA


title: 4m-71-1_WT

description: genotype abbreviation: WT


title: 4m-67-2_5xFAD/BAC-TREM2

description: genotype abbreviation: TA


title: PBS1 rep1


title: 4m-63-3_5xFAD/BAC-TREM2

description: genotype abbreviation: TA


title: 4m-64-3_5xFAD/BAC-TREM2

description: genotype abbreviation: TA


title: 4m-59-2_5xFAD

description: genotype abbreviation: AD


title: 4m-58-3_5xFAD/BAC-TREM2

description: genotype abbreviation: TA


title: 4m-58-1_5xFAD/BAC-TREM2

description: genotype abbreviation: TA


title: A129-2_E-n_H3K27ac

value: H3K27ac (Abcam, ab4729)


title: 4m-48-2_5xFAD

description: genotype abbreviation: AD


title: 4m-48-1_WT

description: genotype abbreviation: WT


title: 4m-48-3_5xFAD

description: genotype abbreviation: AD


title: 4m-55-3_BAC-TREM2

description: genotype abbreviation: T


title: 4m-56-1_WT

description: genotype abbreviation: WT


title: 4m-47-2_5xFAD

description: genotype abbreviation: AD


title: 4m-47-3_WT

description: genotype abbreviation: WT


title: AOS-14_E-n_H3K27ac


title: 4m-47-1_5xFAD

description: genotype abbreviation: AD


title: 4m-55-1_BAC-TREM2

description: genotype abbreviation: T


title: 4m-44-2_BAC-TREM2

description: genotype abbreviation: T


title: 4m-43-1_WT

description: genotype abbreviation: WT


title: 2m-93-4_5xFAD

description: genotype abbreviation: AD


title: 4m-44-3_WT

description: genotype abbreviation: WT


title: 7m-31-1_BAC-TREM2

description: genotype abbreviation: T


title: 4m-40-1_BAC-TREM2

description: genotype abbreviation: T


title: 2m-92-1_BAC-TREM2

description: genotype abbreviation: T


title: 2m-88-2_BAC-TREM2

description: genotype abbreviation: T


title: 4m-58-2_5xFAD

description: genotype abbreviation: AD


title: 2m-90-5_5xFAD/BAC-TREM2

description: genotype abbreviation: TA


title: 2m-83-2_5xFAD

description: genotype abbreviation: AD


title: 2m-91-3_WT

description: genotype abbreviation: WT


title: 2m-87-2_5xFAD/BAC-TREM2

description: genotype abbreviation: TA


title: 2m-83-1_BAC-TREM2

description: genotype abbreviation: T


title: 4m-57-1_BAC-TREM2

description: genotype abbreviation: T


title: 2m-82-1_5xFAD/BAC-TREM2

description: genotype abbreviation: TA


title: 2m-81-4_BAC-TREM2

description: genotype abbreviation: T


title: 2m-81-1_5xFAD/BAC-TREM2

description: genotype abbreviation: TA


title: 2m-82-2_WT

description: genotype abbreviation: WT


title: 2m-80-5_5xFAD

description: genotype abbreviation: AD


title: 4m-40-2_BAC-TREM2

description: genotype abbreviation: T


title: 2m-78-2_BAC-TREM2

description: genotype abbreviation: T


title: 2m-79-1_WT

description: genotype abbreviation: WT


title: 2m-79-3_5xFAD/BAC-TREM2

description: genotype abbreviation: TA


title: 2m-79-2_WT

description: genotype abbreviation: WT


title: 2m-78-1_5xFAD/BAC-TREM2

description: genotype abbreviation: TA


title: 2m-77-3_5xFAD

description: genotype abbreviation: AD


title: Wild-type in vivo, replicate 3

value: Infected murine muscle tissue


title: Wild-type in vivo, replicate 2


title: 2m-80-4_WT

description: genotype abbreviation: WT

value: (C57BL/6J x FvB/NJ) F1


title: Wild-type in vivo, replicate 1


title: 2m-77-2_BAC-TREM2

description: genotype abbreviation: T


title: 2m-78-4_5xFAD

description: genotype abbreviation: AD


title: 2m-80-1_5xFAD

description: genotype abbreviation: AD


title: Wild-type in vitro, replicate 3

source_name: Bacterial cells

value: Bacterial cells


title: WT1 GLM

city: OVIEDO

first: Paula

last: Yagüe

state: ASTURIAS

address: JULIAN CLAVERIA SN

department: Biologia funcional

country: Spain

institute: Universidad de Oviedo

data_processing:
lllumina Hiseq 2500 platform, using 100bp paired-end sequencing reads
sequence reads were not trimmed due to its high quality, then they were mapped to Streptomyces coelicolor M145 whole genome.fa (8.6 kb) using Tophat Bowtie2 (V2.1.0)
differential gene expression was analized with Cuffdiff using Streptomyces coelicolor M145 whole genome.gff and the tophat results (accepted_hits.bam) from each sample
The results gene_express.diff were analized using Microsoft Excell
Genome_build: Streptomyes coelicolor: accession number AL645882
Supplementary_files_format_and_content: The format of the processed data files is .txt in which the column "value 1" corresponds to the average readings of each gene in the mutant strain (M25 or D4117) and "value 2" corresponds to the avearge readings of each gene in the wild type strain (S.coelicolor M145)

organism: Streptomyces coelicolor

source_name: WT GLM

growth_protocol: GYM plates covered with cellophane were inoculated with 10^7 spores from a fresh suspension in water and cultured at 30ºC for 44 hours.  100 ml sucrose-free R5A cultures were grown at 30ºC and 200 rpm in 500 ml baffled flasks.

extract_protocol:
Total RNA samples from cultures stabilized with Bacteria RNA protect (Qiagen) were isolated using RNeasy Mini spin columns and treated with DNase I (Qiagen).
cDNA library construction was carried out using TruSeq Stranded mRNA Library Preparation Kit (Illumina) following standard Illumina protocol.

tag: culture medium

value: GYM

tag: time

value: 44 culture hours


title: D4117.1 GLM

source_name: D4117 GLM


title: WT2 GLM


title: D4117.2 GLM


title: Wild-type in vitro, replicate 1

tag: source


title: 3T3 cells with 3'tsRNA-Gly (5 x m5C) transfection rep2

status: Public on Mar 06 2018

city: Riverside

first: Junchao

last: Shi

address: 900 University Ave

department: Division of Biomedical Sciences, School of Medicine

institute: University of California, Riverside

data_processing:
For each RNA library, 4G base pairs (raw data) were generated by Illumina Hi‐Seq 4000.
The filtering process is as follows: (1) Remove reads containing adapters. (2) Remove reads containing N > 10% (N represents the base cannot be determined). (3) Remove reads containing low quality (Qscore<= 5) base which is over 50% of the total base.
RNA sequences were annotated using kallisto with Ensembl mouse cDNA annotation information. Expression level of each gene was normalized to TPM (Transcripts Per Kilobase Million).
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include ensembl transcript ID, transcript length, effective length, estimated counts and TPM.

source_name: 3T3 cells with synthesized tsRNAs

growth_protocol: Seeding 5 x 10^5 3T3 cells (ATCC® CRL-1658) per well into the 12-wells plate the day before transfection and wait the cells reach 70-90% confluent at transfection.

extract_protocol:
Total RNAs are extracted by Trizol (Invitrogen).
Transcriptome libraries were constructed according to TruSeq Stranded mRNA Library Prep Kit (Illumina).

treatment_protocol: For a single well transfection, dilute 9ul Lipofectamine™ 3000 Reagent in 86ul Opti-MEM medium and then add 5ul 10uM synthetic tsRNAs, vortex shortly and incubate 15 minutes at room temperature to form transfection complex. Discard the culture medium, and add 400ul fresh culture medium to the cells. Add 100ul RNA-lipid transfection complex to the cells for transfection. The final RNA concentration for transfection is 100nM. The control group is composed of 9ul Lipofectamine™ 3000 reagent and 91ul Opti-MEM without synthetic tsRNAs. After 4.5h of transfection, change the culture medium, which contain transfection complex, into new fresh culture medium. Harvest the cell total RNA by Trizol® reagent as manufacture instructed at the time point of 12h after transfection.


title: 3T3 cells with 3'tsRNA-Gly (4 x m5C) transfection rep2


title: 2m-80-3_WT

description: genotype abbreviation: WT

tag: genotype

value: WT

value: brain

value: cortex

value: F


title: 3T3 cells with 3'tsRNA-Gly (no m5C) transfection rep2


title: Wild-type in vitro, replicate 2


title: 3T3 cells with 3'tsRNA-Gly (5 x m5C) transfection rep1


title: 3T3 cells with 3'tsRNA-Gly (4 x m5C) transfection rep1


title: 3T3 cells with empty transfection rep2

source_name: 3T3 cells


title: RNASeq_rrr2_2

city: Basel

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

data_processing:
The RNA-seq data (50bp read length) were mapped to the C. elegans genome (ce6) with the R package QuasR (www.bioconductor.org/packages/2.12/bioc/html/QuasR.html) using the included spliced alignment algorithm SpliceMap. The command used to perform the alignments was "proj <- qAlign("samples.txt","BSgenome.Celegans.UCSC.ce6",splicedAlignment=TRUE)". Gene expression was quantified by counting the number of reads that started within any of the exons belonging to a particular gene (WormBase, WS190). The command used to create the count table was qCount(proj,exons,orientation="same"). To compensate for differences in the read depths of the various libraries, each library was normalized to a total of 30.2M reads, which represents the average library size. Log2 expression levels were calculated after adding a pseudocount of 8 (y=log2(x+8). This was done to minimize the large differences in expression that would otherwise be caused by genes with small number of counts. In the processed data files, we also included the two replicates of the matching N2 samples which were published previously (GSM1534604 & GSM1534605).
Genome_build: ce6
Supplementary_files_format_and_content: ce_geneExpression_rrr2_rawCounts.txt: Tab-delimited text file
Supplementary_files_format_and_content: ce_geneExpression_rrr2_normalized.txt: Tab-delimited text file

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: C. elegans eggs were allowed to hatch overnight, hatched L1s were plated on NG 2% plates seeded with OP50, grown to young adult stage and harvested.

extract_protocol:
Total RNA isolation was performed using Trizol Reagent (Life Technologies).
Library preparation was performed using the ScriptSeq v2 RNA-Seq library preparation kit (Epicentre) according to the manufacturer's protocol.

treatment_protocol: Worms were washed off the plates, washed three times with M9 and frozen in liquid nitrogen.

tag: developmental stage

value: young adults

tag: genotype/variation

value: whole body


title: RNASeq_rrr2_1


title: exp3-T0-sporozoites

city: La Jolla

first: Elizabeth

last: Winzeler

address: 9500 Gilman Dr

institute: UCSD

data_processing:
Illumina RTA determined base-calling, bcl2fastq demultiplexes
Total host-pathogen dual RNA-sequencing reads were filtered and aligned to their respective reference genomes (PlasmoDB13.0 P. berghei ANKA; human referecne genome GRCh38 ) . Tophat.2 was used for the alignment (--library-type fr-unstranded) (Kim et al., 2013). PICARD (http://broadinstitute.github.io/picard/) and SAMtools-0.1.19 (http://samtools.sourceforge.net/) were used for processing the aligned reads.
HTSeq (Anders et al., 2015) was used to produce read counts (--stranded=no).
To generate P. berghei filtered reads, the total reads were first aligned to the human reference genome. Any reads that aligned to this genome were removed, and the remaining reads were then aligned to the reference P. berghei-ANKA genome (PlasmoDB-13.0). Similarly, host Huh7.5.1 hepatocyte filtered reads were filtered by the alignment to the P. berghei genome first, removing these reads, and then aligning the remaining reads to the human reference genome (GRCh38).
DESeq2 was used for the differential expression analysis (included in processed data file).

organism: Plasmodium berghei

source_name: P. berghei sporozoites

growth_protocol: Huh7.5.1 hepatocytes were infected in vitro with P. berghei sporozoites freshly dissected from infected A. stephansi mosquitos (100,000 cells to 30,000 sporozoites per well in 24 well plates). Plates were centrifuged at 330xg for 4 minutes to bring sporozoites closer to cells, and plates were then incubated at 37¡C 5% CO2 for 2 hours. During this time the sporozoites traverse and invade hepatocytes (Prudencio et al., 2006b). After 2 hours, the cells were washed, fresh media containing antibiotics/ antimycotics was added, and the cells were returned to the incubator. Cells were collected at time zero (uninfected hepatocytes and sporozoites before infection), time 24 hours post infection (when the sporozoites have transformed into trophozoites), and time 48 hours post infection (when the trophozoites have transformed into liver stage schizonts).  To do this, cells were dissociated from plates using TrypLE (ThermoFisher), washed and resuspended in fresh media, and passed through a 40_M cell strainer (Falcon). Uninfected cells were isolated from infected cells by FACS sorting with BD FACS Aria by gating on GFP mean fluorescence intensity (MFI).

extract_protocol:
Cells were sorted directly into 500_l Qiazol reagent (Qiagen) and total RNA was isolated using a Qiagen miRNEasy kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: host

tag: pathogen

value: Plasmodium berghei

tag: time point

value: 0 hours post infection

tag: p. berghei strain

value: P. berghei-GFP ANKA


title: Pseudomonas aeruginosa Water Rep2

city: Singapore

first: YANG

last: SHEN

address: Genome Institute of Singapore (A*STAR) 60 Biopolis Street, #02-01 Genome

country: Singapore

institute: Genome Institute of Singapore

data_processing:
Short reads from PARCEL libraries (Illumina NextSeq 500, 50 bp, single-end) in P. aeruginosa PAO1 and B. subtilis 168 were aligned to their corresponding reference genomes downloaded from NCBI using the short-read aligner bowtie2 (parameters: -k 1 --local)23. In the case of C. albicans SC5314, we extracted the UTR annotation from Bruno et al and integrated them into their corresponding transcriptomes before alignment by bowtie2. In both cases, only uniquely mapped reads were used for subsequent analysis.
Genome_build: Candida albicans SC5314 (v21)
Genome_build: Bacillus subtilis subsp. subtilis 168. (NC_000964)
Genome_build: Pseudomonas aeruginosa PAO1 (NC_002516)
Supplementary_files_format_and_content: bedgraph file generated using Bedtools

organism: Pseudomonas aeruginosa

source_name: Pseudomonas aeruginosa

growth_protocol: Candida S5314 strain was grown in GMM and YPD media to log phase (OD=0.6-0.8) and to saturated phases (OD>2).  Pseudomonas aeruginosa PAO1 and bacillus subtilis 168 strain are grown in minimal media and LB to log (OD-0.6) and saturated phases (OD>2).

extract_protocol:
Total RNA was extracted from candida albicans using hot acid phenol protocol.  Poly(A)+ selected mRNAs were obtained using Poly(A)purist kit from Ambion.  Total RNA was extracted from pseudomonas aeruginosa using Trizol.  Total RNA was extracted from bacillus subtilis using 1%SDS and lysozyme, followed by Trizol.  Ribosomal depletion on total bacillus and pseudomonas RNA was carried out using RiboZero kit for bacteria (Epicenter)
Poly(A) enriched or ribosomal RNA depleted RNA were structured probed in the presence and absence of ligands using RNase V1.  The structure probed RNA was then fragmented, ligated to adapters, reverse transcribed and PCR amplified.

tag: protocol

value: Water

tag: strain


title: Pseudomonas aeruginosa TPP Rep1

value: TPP


title: Pseudomonas aeruginosa TPP Rep2


title: exp2-T0-sporozoites


title: Pseudomonas aeruginosa FMN Rep2

value: FMN


title: Aged_Input_Rep3

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

country: United Kingdom

institute: Altos Labs

description: log2_RPM_plus_minus_twoandahalf_kb_mRNA_ChIP.txt

data_processing:
Libraries were sequenced on the Illumina NextSeq500 and HiSeq1000/2500 platforms using the default RTA analysis software.
Sequencing reads were trimmed using trim galore v0.4 using default parameters to remove the standard Illumina adapter sequence. Reads were mapped to the mouse GRCm38 genome assembly using bowtie2 v2.2.5 using default parameters. BAM files imported to SeqMonk and reads were extended by 200bp at their 5’ end to approximate the true insert size.
Basecalls were converted to fastq using bcl2fastq v2.15.0.4 and read quality was checked using FastQC v0.10.1. Reads were aligned to the mouse genome (GRCm38) using STAR v2.3.0 with default parameters.
Sequence reads were trimmed to remove poor-quality reads and adapter contamination using Trim Galore (v0.3.7). The remaining sequences were mapped using Bismark (v0.12.5) (Krueger & Andrews 2011) with default parameters to the mouse reference genome GRCm38 in paired-end mode. Reads were deduplicated and CpG methylation calls were extracted from the deduplicated mapping output using the Bismark methylation extractor (v0.13.0).
Genome_build: GRCm38
Supplementary_files_format_and_content: Quantitated ChIP-Seq data file is tab delimited and shows log2 RPM data for -/+2.5kb surrounding each TSS: (1) mRNA transcript associated with TSS (Ensembl); (2) Chromosome; (3) Start; (4) End; (5) Strand; (6) Associated gene name (Ensembl) (7) mRNA ID (Ensembl); (8) Description (Ensembl); (9-29) log2 RPM value
Supplementary_files_format_and_content: Quantitated RNA-Seq data file is tab delimited and contains the following columns: (1) mRNA name (Ensembl); (2) Chromosome; (3) Start; (4) End; (5) Strand; (6) mRNA ID (Ensembl) (7) Description (Ensembl); (8-19) log2 RPM value
Supplementary_files_format_and_content: The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>

growth_protocol: Young adult and aged SVZ NSPCs were derived from 3mo or 18mo male C57Bl/6 mice, respectively. NSPCs were propagated on uncoated T25 flasks (Corning) in chemically-defined media as described (Soldati et al. 2012; De Luca et al. 2013; Soldati et al. 2015), supplemented with 20 ng/ml human recombinant Epidermal Growth Factor (R&D systems), 10 ng/ml human recombinant Fibroblast Growth Factor-basic (Peprotech), 1:50 B27 supplement (Invitrogen) and 2 µg/ml heparin (Sigma-Aldrich). NSPCs grown as neurospheres were passaged approximately once per week by pelleting the cell aggregates, dissociating with Accutase (Sigma-Aldrich) and seeding on new uncoated flasks at a density of 20-50000 cells/ml.

extract_protocol:
Native ChIP for profiling histone marks was performed as described (Gilfillan et al., 2012) with minor modifications. Cell pellets (from 400,000 cells) were thawed and suspended in 95μl MNase Buffer (50mM Tris-HCl pH8, 1mM CaCl2, 0.2% Triton X-100) supplemented with 5mM Sodium Butyrate and 1X Complete EDTA-free Protease Inhibitor (Roche). Chromatin was digested with micrococcal nuclease (3U; NEB) for 8min at 37°C to obtain predominantly mononucleosomes and dinucleosomes. Stop buffer (10μl of 110mM Tris-HCl pH8, 5mM EDTA) was added to inactivate the reaction. Chromatin was solubilised by brief sonication using a Diagenode Bioruptor for 1min on high power. Chromatin was diluted in 100ml RIPA-IP buffer (280mM NaCl, 1.8% Triton X-100, 0.2% SDS, 0.2% Sodium Deoxycholate, 5mM EGTA supplemented with 5mM Sodium Butyrate and 1X Complete EDTA-free Protease Inhibitor) and insoluble material was removed by centrifugation at 14,000 rpm at 4°C for 15 minutes. Supernatant was transferred to a new tube, 10% was removed for the input sample, and the remaining chromatin was pre-cleared with 50μl pre-washed Protein A and Protein G Dynabeads (Thermo Fisher Scientific) at 4°C for 1 hour. Dynabeads were removed, the pre-cleared chromatin was diluted to 500μl in RIPA-IP buffer and split into 5 tubes. Chromatin was incubated overnight with histone antibodies at 4°C with rotation. Antibodies used were H3K27me3 (Millipore, 07-449; 1μg per ChIP) and H4K4me3 (Abcam, ab8580; 0.5μg per ChIP). Pre-washed Dynabeads (10μl) were added to each tube and incubated at 4°C for 2-3 hours with rotation. Beads were washed five times with RIPA buffer, once with LiCl buffer (250mM LiCl, 10mM Tris-HCl pH8, 0.5% NP-40, 0.5% Sodium Deoxycholate, 1mM EDTA) and once with 1xTE. Beads were suspended in 100μl 1X TE supplemented with 50μg Proteinase K and incubated at 55°C for 1 hour. ChIP and Input DNA were purified using Genomic DNA Clean and Concentrator columns (Zymo) and eluted in 50μl 1xTE. ChIP material was examined using a small aliquot of material by qPCR. Indexed ChIP-Seq libraries were generated with the NEBNext Master Kit (NEB) using NEBNext Multiplex Oligos for Illumina indexes (NEB). Library fragment size and concentration was determined using an Aglient Bioanalyzer 2100 and KAPA Library Quantification Kit (KAPA Biosystems). Samples were sequenced on an Illumina NextSeq 500 as 75bp single-end libraries.
Indexed ChIP-Seq libraries were generated with the NEBNext Master Kit (NEB) using NEBNext Multiplex Oligos for Illumina indexes (NEB).

tag: tissue

value: SVZ-derived neural stem / progenitor cells

tag: age of mouse (months)


title: Pseudomonas aeruginosa Water Rep1


title: Aged_Input_Rep2


title: Pseudomonas aeruginosa FMN Rep1


title: Young_Input_Rep2


title: Young_Input_Rep3


title: Young_Input_Rep1


title: Aged_Input_Rep1


title: Aged_H3K4me3_Rep1

value: H3K4me3 (Abcam, ab8580)


title: Aged_H3K4me3_Rep2


title: Young_H3K4me3_Rep2


title: 3T3 cells with empty transfection rep1

tag: cell line


title: Young_H3K4me3_Rep1

tag: chip antibody


title: Aged_H3K27me3_Rep1

value: H3K27me3 (Millipore, 07-449)


title: Aged_H3K27me3_Rep2


title: Young_H3K4me3_Rep3


title: 3T3 cells with 3'tsRNA-Gly (no m5C) transfection rep1


title: Young_H3K27me3_Rep2


title: Young_H3K27me3_Rep3


title: exp1-T0-sporozoites


title: Young_H3K27me3_Rep1


title: Aged_RNA_Validation

extract_protocol:
Total RNA was purified from frozen NSPC pellets using Trizol and indexed mRNA-Seq libraries were constructed and sequenced as described (Collinson et al. 2016).
Indexed mRNA-Seq libraries were constructed from 500ng total RNA using the Tru-Seq RNA Library Prep Kit v2 (Illumina).


title: Aged_RNA_Rep3


title: Aged_H3K4me3_Rep3


title: Aged_RNA_Rep2


title: Aged_RNA_Rep1


title: Young_RNA_Validation


title: Young_RNA_Rep3


title: Hep

first: Kyungtae

last: Lim

address: Tennis Court Road

department: The Wellcome Trust/Cancer Research UK Gurdon Institute

institute: University of Cambridge

description:
Primary hepatocyte freshly isolated from adult mice
Hep

data_processing:
Sequenced reads were mapped to UCSC mm10 Mus musculus genome using STAR 2.4.1c (Dobin et al., 2013) with default parameter setting.
Normalized read count values RPKMs (reads per kilobase of transcript per million mapped reads) were calculated for each gene using featureCounts (Liao et al., 2014) and edgeR 3.16.4 (Robinson et al., 2010).
Pseudo-value 1 was added to all original RPKM scores to compute fold changes.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Expression matrix in tsv format. Genes are represented in NCBI official gene symbols.

extract_protocol:
Total RNA was isolated using an Hybrid-RTM (GeneAll) and 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: passages

value: primarily cultured (P0)

tag: cell type

value: Primary hepatocyte


title: Young_RNA_Rep1


title: LEPCs

description:
Referenced by Li et al. Stem Cells 2006 (doi: 10.1634/stemcells.2005-0108)
LEPCs

source_name: Liver epithelial progenitor cells (LEPCs)

value: Liver epithelial progenitor cells


title: 1b3-iHepSCs

description:
A clonal cell line of iHepSCs were established by sorting using EPCAM.
1b3-p10

source_name: A clonal cell line of induced hepatic stem-like cells (iHepSCs) using Hnf1b and Foxa3

value: clonal cell line of induced hepatic stem-like cells using Hnf1b and Foxa3


title: 1a3_d12

description:
MEFs transduced with Hnf1a and Foxa3 were collected on 12 dpi when the markers of hepatocyte, cholangiocyte, and hepatic stem cells were remarkably activated.
1a3_d12

source_name: MEFs transduced with Hnf1a and Foxa3; collected after 12 days of transdudtion

value: MEFs transduced with Hnf1a and Foxa3


title: 1b3_d12

description:
MEFs transduced with Hnf1b and Foxa3 were collected on 12 dpi.
1b3_d12

source_name: MEFs transduced with Hnf1b and Foxa3; collected after 12 days of transdudtion

value: MEFs transduced with Hnf1b and Foxa3


title: Sample_Plate14_B3

first: Aida

last: Moreno-Moral

address: 8 College Road

institute: Duke-NUS Medical School

description:
Processed data file: gene_counts_SSc_study.txt
Processed data file: TPM_SSc_study.txt

data_processing:
RNA-seq reads were assessed for quality and aligned to hg38 (Ensembl Gene annotation build 79 using STAR 2.5.2b).
RNA-seq reads were quantified with RSEM 1.2.31.
Genome_build: Ensembl version 79 (hg38)
Supplementary_files_format_and_content: TPM_SSc_study.txt: Tab-delimited text file includes TPM values for all genes.
Supplementary_files_format_and_content: gene_counts_SSc_study.txt: Tab-delimited text file includes gene counts for all genes.

source_name: monocyte-derived macrophages, control

growth_protocol: Human MDMs were differentiated from total blood from SSc patients and healthy donors using gradient separation (Histopaque 1077, Sigma) and adhesion purification. Following Histopaque separation, peripheral blood mononuclear cells (PBMCs) were re-suspended in RPMI (Life Technologies) and monocytes were purified by adherence for 1 h at 37 °C, 5% CO2. The monolayer was washed 3 times with HBSS to remove non-adherent cells and monocytes were matured for 5 days in RPMI containing 100 ng ml-1 M-CSF (PeproTech, UK) and 10% Fetal Calf Serum (FCS, Labtech International). Macrophage purity was confirmed by immunohistochemical assessment of CD68 and >99% cells were CD68+.

extract_protocol:
Total RNA was extracted from hMDMs using Trizol (Invitrogen) and RNeasy mini kit (Qiagen) according to manufacturer's instructions, with an additional purification step by on-column DNase treatment using the RNase-free DNase Kit (Qiagen) to ensure elimination of any genomic DNA. The integrity and quantity of total RNA were determined using a NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific) and Agilent 2100 Bioanalyzer (Agilent Technologies).
In total, 500 ng of total RNA was used to generate RNA-seq libraries using TruSeq RNA sample preparation kit (Illumina) according to the manufacturer's instructions. Briefly, RNA was purified and fragmented using poly-T oligo-attached magnetic beads using two rounds of purification followed by the first and second cDNA strand synthesis. Next, cDNA 3' ends were adenylated and adapters ligated followed by 15 cycles of library amplification. Finally, the libraries were size selected using AMPure XP Beads (Beckman Coulter) purified and their quality was checked using Agilent 2100 Bioanalyzer. Samples were randomized to avoid batch effects and multiplexed libraries were run on a single lane (6 samples/lane) of the HiSeq 2500 platform (Illumina) to generate 100bp paired-end reads. An average of 64M reads coverage per samples was achieved.

tag: disease state

value: healthy control

value: monocyte-derived macrophages


title: Sample_Plate14_B6

source_name: monocyte-derived macrophages, SSc

value: scleroderma


title: Sample_Plate14_B4


title: Sample_Plate14_B5


title: Sample_Plate14_B2


title: Sample_Plate14_A12


title: Sample_Plate14_B1


title: Sample_Plate15_B6


title: Sample_Plate14_A11


title: Sample_Plate12_A6


title: Sample_Plate14_A10


title: Sample_Plate12_A5


title: Sample_Plate15_B5


title: Sample_Plate15_B3


title: Young_RNA_Rep2


title: Sample_Plate15_B4


title: 1a3-iHepSCs

description:
A clonal cell line of iHepSCs were established by sorting using EPCAM.
1a3-p12

source_name: A clonal cell line of induced hepatic stem-like cells (iHepSCs) using Hnf1a and Foxa3

value: clonal cell line of induced hepatic stem-like cells using Hnf1a and Foxa3


title: Sample_Plate12_A3


title: Sample_Plate15_B2


title: Sample_Plate14_A9


title: Sample_Plate15_B1


title: Aged_H3K27me3_Rep3


title: Sample_Plate15_A12


title: MEFs

description:
MEFs were isolated from C57BL6 mouse embyos at E13.5 after removing the head and all the internal organs including liver in order to be free from contamination by ectodermal and endodermal cells.
MEFs

source_name: Mouse embryonic fibroblasts (MEFs), isolated at E13.5

value: Mouse embryonic fibroblasts


title: Sample_Plate15_A11


title: Sample_Plate14_A8


title: Sample_Plate5_A5


title: Sample_Plate15_A10


title: Sample_Plate12_A2


title: Sample_Plate12_A1


title: Sample_Plate15_A8


title: Sample_Plate14_A7


title: Sample_Plate15_A9


title: Sample_Plate12_A4


title: Sample_Plate14_A6


title: Sample_Plate14_A5


title: Sample_Plate15_A7


title: Sample_Plate15_A6


title: Sample_Plate15_A5


title: Sample_Plate5_B12


title: Sample_Plate5_A2


title: Sample_Plate5_B8


title: Sample_Plate5_B11


title: Sample_Plate5_B10


title: Sample_Plate5_B9


title: Sample_Plate5_B7


title: Sample_Plate14_A4


title: Sample_Plate15_A4


title: Sample_Plate5_A3


title: Sample_Plate5_B4


title: Sample_Plate5_A4


title: Sample_Plate14_A2


title: Sample_Plate14_A3


title: Sample_Plate14_A1


title: Sample_Plate15_A3


title: Sample_Plate15_A2


title: Sample_Plate5_B2


title: Sample_Plate5_B3


title: Sample_Plate5_A12


title: Sample_Plate15_A1


title: Sample_Plate5_B1


title: Sample_Plate6_A6


title: Sample_Plate6_A5


title: Sample_Plate5_A11


title: Sample_Plate5_A10


title: Sample_Plate6_A4


title: Sample_Plate5_B6


title: Sample_Plate5_B5


title: Sample_Plate5_A9


title: Sample_Plate6_A3


title: Sample_Plate5_A8


title: Sample_Plate5_A7


title: Sample_Plate6_A1


title: Sample_Plate5_A1


title: Control_SMA_02

first: Roland

last: Schmucki

address: Grenzacherstrase

institute: F. Hoffmann - La Roche AG

data_processing:
Basecalling by sequencing provider
Read quality check by using FASTQC version 0.11.5
Read mapping by GSNAP version 2014-10-22 onto human genome hg19
Mapped reads per gene were determined by using human RefSeq mRNA annotations
Reads Per Kilobase of gene per Megabase of library size (RPKM) were calculated.
Reads were mapped onto RefSeq human transcripts using GSNAP version 2014-10-22 with default parameters and the option ‘sam-multiple-primaries’ in order to account for reads that map multiple times to different splice variants.
The numbers of reads mapped to exons, exon junctions, and to exons excluding junction reads was determined by applying the samtools mpileup software with default parameters for each transcript. Reads were excluded from the analysis if their start or end coordinate mapped exactly onto the splice-site.
Insert sizes of mapped read pairs determined by samtools stats software
Genome_build: hg19
Supplementary_files_format_and_content: PK4C9_counts.gct: text files in gct format containing raw read counts per gene, column 1: EntrezGene Index, column 2: Official gene symbol from EntrezGene
Supplementary_files_format_and_content: PK4C9_rpkms.gct: text files in gct format containing normalized read counts (rpkms) per gene, column 1: EntrezGene Index, column 2: Official gene symbol from EntrezGene

source_name: GM03813C fibroblasts

growth_protocol: GM03813C fibroblasts were grown in MEM medium with 15% FBS, 1% penicillin/streptomycin, and 2 mM Glutamine. Cells were kept in a humidified incubator at 37 °C in 5% CO2. 4 x105 cells were seeded per well in 6-well plates (volume 2 mL) and grown to 80% confluence before treatment with PK4C9.

extract_protocol:
GM03813C fibroblasts replicates were obtained using the RNeasy mini kit with on column DNase digestion (Qiagen). RNA concentration was quantified in a Qubit fluorometer and integrity assessed with Agilent’s 2100 bioanalyzer using pico chips. Samples with RIN values >=9.5 were sent to Beckman Coulter Genomics for RNA sequencing.
A poly-A capture protocol was applied to eliminate tRNAs and rRNAs prior to cDNA synthesis.
Eight Illumina TruSEQ RNAseq libraries were constructed and sequencing was perfomed on the Illumina HiSeq 2500 platform using paired-end 125 bp read lengths yielding a total of >400M read pairs.

treatment_protocol: 4 total-RNA replicates of DMSO-treated GM03813C fibroblasts (control) and 4 replicates of PK4C9-treated (40 microM, 24 h)

value: fibroblast

tag: disease

value: SMA Type I

tag: treatment

value: DMSO

tag: group

value: Control

tag: concentration

tag: time


title: Control_SMA_01


title: Treated_SMA_401

value: Treated

value: 40 microM


title: Control_FB13c2


title: Treated_SMA_404


title: Sample_Plate5_A6


title: Treated_SMA_403


title: Treated_SMA_402


title: Control_FB13c1


title: Bulk Day 15 reset H9 rep2

city: Hangzhou

first: Haide

last: Chen

address: 866 Yuhangtang road

institute: Zhejiang University

description: Processed data in Series supplementary file Bulk_FPKM.csv

data_processing:
Basecalls performed using bcl2fastq_2.19.
Sequenced reads were trimmed for adaptor sequence, then mapped to GRCh38 whole genome using STAR v2.5.2a with parameters --runThreadN 2 --genomeDir $Indexpath --readFilesIn $i --outFileNamePrefix $STAROutDIR
The capture efficiency of C1 was measured under microscope. The capture sites without cell or with more than one cell were excluded from further analysis.
scRNA-seq expression  were quantified by counts via featureCounts v1.5.1. Bulk RNA-seq  were quantified by FPKM via RSEM v0.4.6.
scRNA-seq expression data were analyzed with Seurat (filtering, normalization, PCA and t-SNE) and Monocle (pseudotemporal analysis). Bulk RNA-seq data were analyzed with DEseq2 v1.14.1.
Genome_build: GRCh38
Supplementary_files_format_and_content: comma-delimited csv files include DGE values (scRNA-seq data) and FPKM values (Bulk RNA-seq data) for each sample.

source_name: Day 15 reset H9

growth_protocol: Primed H9 was maintained in mTeSR1 media (STEMCELL Technologies) on tissue culture plates coated with Matrigel (BD Bioscience). H9 was reset into a naïve-like state by RSeT media (STEMCELL Technologies). EBs were differentiated in DMEM/F12 (GIBCO) supplemented with 20% FBS (GIBCO), 50 U/mL penicillin/streptomycin (GIBCO), 2 mM L-Glutamine (GIBCO), 1 x non-essential amino acids, and 100 μM ß-mercaptoethanol (Sigma).

extract_protocol:
mRNA Capture Beads (VAHTS mRNA-seq v2 Library Prep Kit for Illumina, Vazyme) were used to extract mRNA from total RNA.
PrimeScript™ Double Strand cDNA Synthesis Kit (TaKaRa) was used to synthesize double-stranded cDNA from purified polyadenylated mRNA templates. We used TruePrep DNA Library Prep Kit V2 for Illumina (TaKaRa) to prepare cDNA libraries for Illumina sequencing.

value: Reset HPSCs

tag: culture media

value: RSeTTM media


title: Bulk Day 15 reset H9 rep1


title: Bulk Day 20 reset H9 rep1

source_name: Day 20 reset H9


title: Bulk Day 10 reset H9 rep1

source_name: Day 10 reset H9


title: Bulk Day 6 reset H9 rep2

source_name: Day 6 reset H9


title: Bulk Day 10 reset H9 rep2


title: Bulk Day 20 reset H9 rep2


title: Bulk Day 3 reset H9 rep1

source_name: Day 3 reset H9


title: Bulk Day 6 reset H9 rep1


title: Bulk Day 3 reset H9 rep2


title: Bulk Primed H9 rep2

source_name: Primed H9

value: Primed HPSCs

value: mTeSR™1 media


title: Bulk Primed H9 rep1


title: Bacillus subtilis FAD Rep2

organism: Bacillus subtilis

source_name: Bacillus subtilis

value: FAD

value: subsp. subtilis 168.


title: single Day 20 reset H9 rep2

extract_protocol:
C1 system and C1 high-throughput integrated fluidics circuits (HT IFCs) were used to capture single cells. Immediately after cell capture, lysis, reverse transcription and preamplification were performed in the HT IFCs.
Samples harvested from HT IFCs were used to create libraries for Illumina sequencing with Illumina Nextera XT DNA Library kit.


title: Bacillus subtilis SAM Rep1

value: SAM


title: Bacillus subtilis FAD Rep1


title: single Day 20 reset H9 rep1


title: single Day 10 reset H9


title: Bacillus subtilis Water Rep2

value: Water


title: single EB rep4

source_name: Day 8 embryoid body

value: Primed HPSCs derived EB

value: EB differentiation media


title: Bacillus subtilis Water Rep1


title: single EB rep3


title: single EB rep2


title: single EB rep1


title: MEF_RNASeq_KO2_20436

city: Vienna

first: Tobias

last: Neumann

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

data_processing:
Adapters were trimmed from the 3' ends of the reads with cutadapt v1.10.
The trimmed reads larger than 18nt were aligned against the Fitz et al 25 rDNA of the respective organism using bowtie2 v 2.1.0  (--sensitive-local --score-min G,30,8 -N 0 --ignore-quals) to remove the rRNA reads.
rRNA cleaned reads were aligned to the genome with the TopHat splice junction mapper for RNA-seq reads v1.4.1.
Reads were quantified with featureCounts v1.5.0-p1.
Differentially expressed genes were obtained using DESeq2 v1.10.1 according to its standard comparison between two experimental conditions vignette. Differentially expressed genes were filtered for a p-adjusted value of < 0.05 and a fold-change greater 1.5 in either direction.
genome build: NCBI mm9
processed data files format and content: Tab-delimited table with raw counts and DESeq2 log2-foldchanges and adjusted p-values

source_name: primary mouse embryonic fibroblasts

growth_protocol: Primary MEFs were prepared from d13.5 Supt5hFl/+Rosa26ERT2-cre/+ and Rosa26ERT2-cre/+ embryos and cultured in complete DMEM medium to passage 3.

extract_protocol:
Cells were harvested as per the instructions in the TruSeq kit from Illumina.
Library preparation for mRNAseq was performed using the TruSeq kit from Illumina following their instructions.

treatment_protocol: Primary MEFs were treated with 2 uM 4-HT for 72h and then harvested for all downstream applications.

value: primary mouse embryonic fibroblasts

tag: genotype

value: Supt5hFl/- Rosa26ERT2-cre/+


title: exp3-T0-huh7_5_1

tag: host

value: human (Huh7.5.1)

tag: pathogen

tag: time point

value: 0 hours post infection

tag: p. berghei strain


title: MEF_RNASeq_KO3_20440

tag: tissue


title: exp1-T0-huh7_5_1


title: MEF_RNASeq_KO1_20435


title: MEF_GROSeq_KO1_18245

description: in vitro transcribed RNA

data_processing:
Library strategy: GRO-Seq
Adapters were trimmed from the 3' ends of the reads with cutadapt (v 1.10), and  a 5nt random linker was removed from the 3' end using fastx_trimmer.
Trimmed reads larger than 10nt were aligned to the genome using bowtie v1.0.0 (-v 2 --best --strata -- tryhard -m 1).
genome build: NCBI mm9
processed data files format and content: bigWig of rpm-normalized read densities

extract_protocol:
Following cell membrane lysis with hypotonic buffer, nuclei were isolated via sucrose gradient density centrifugation. GROseq was performed as described (Core & Lis, 2008). Briefly, 10 million nuclei were used per reaction, and the run-on was performed for 5 minutes with NTPs with a limiting concentration of P32-dCTP and dBrdUTP followed by extraction of RNA with Trizol reagent (Thermo Fisher, 15596026). An updated protocol was kindly provided by Dr. John Lis (Cornell University).
After base hydrolysis and DNA end repair, Illumina compatible 3' RNA adapters were ligated to total RNA. After BrdU- incorporated RNA IP the 5' cap was removed and the 5' DNA end was repaired. Next, the 5' DNA Illumina comaptible adapters were ligated, and the library was reverse transcribed and amplified.


title: MEF_GROSeq_WT2_19965

description: in vitro transcribed RNA


title: exp2-T0-huh7_5_1


title: single Primed H9


title: MEF_GROSeq_KO2_19966

description: in vitro transcribed RNA


title: MEF_S5P_KO_rep1_20447

data_processing:
Adapters were trimmed from the 3' ends of the reads with cutadapt v1.10.
Trimmed reads larger than 18nt were aligned to the genome using bowtie v1.0.0 (-v 2 --best --strata --tryhard -m 1)
genome build: NCBI mm9
processed data files format and content: bigWig of rpm-normalized read densities

extract_protocol:
ChIPseq and ChIP-qPCR were performed as described without modifications (Pavri et al., 2010). In short, 20x10^6 cells were crosslinked with 1% HCHO for 10 min at 37 degree. After quenching with 0,125 M glycine, cells were sonicated with the Diagenode Bioruptor sonication machine.
After chromatin-immunprecipitation, samples were end-repaired with the Epicenter End-Repair Kit. After A-tailing the samples with Klenow (exo-) enzyme, NEXTflex adapters were ligated to the samples and then purified with AMPure XP beads. PCR amplification of the libraries was performed with the Phusion-HF enzyme and the NEXTflex primer mix.

tag: antibody

value: RNA Pol II (Ser5-phospho)


title: Bacillus subtilis SAM Rep2

tag: protocol

tag: strain

tag: chip antibody


title: Sample_Plate6_A2

tag: disease state

value: scleroderma

tag: cell type

value: monocyte-derived macrophages


title: MEF_S2P_KO_rep1_20448

value: RNA Pol II (Ser2-phospho)


title: ZCCHC24 KD, rep1

first: Yu-Ting

last: Tseng

address: 650 Charles E. Young Drive South

department: Department of Microbiology, Immunology, & Molecular Genetics

institute: University of California, Los Angeles

description: ZCCHC24 KD

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to Ensembl transcript (release 72) then hg19 whole genome using tophat v1.4.1 with parameters -a 8 -m 0 -I 300000 -p 8 -g 20 --library-type fr-unstranded --initial-read-mismatches 3 --segment-mismatches 2
Fragments Per Kilobase of exon per Million fragments mapped (FPKM) were calculated using cuffdiff v2.2.0 with uniquely and properly mapped pairs.
Genome_build: hg19
Supplementary_files_format_and_content: an excel file includes FPKM values for each Sample

source_name: Breast cancer cell line

extract_protocol:
1 ug of total RNA was used for  for RNA-seq library preparation using the TruSeq™ Stranded mRNA LT Sample Prep Kit (Illumina). 100x2 bp paired-end RNA-seq reads were generated on a HiSeq 2000 sequencer.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: Breast

tag: age

value: ZCCHC24 KD


title: ZCCHC24 CTRL, rep1

description: ZCCHC24 CTRL

value: ZCCHC24 CTRL


title: ZCCHC24 CTRL, rep3

description: ZCCHC24 CTRL


title: MEF_S5P_WT_rep1_20443


title: ZCCHC24 CTRL, rep2

description: ZCCHC24 CTRL


title: ZCCHC24 KD, rep2

description: ZCCHC24 KD


title: ZCCHC24 KD, rep3

description: ZCCHC24 KD


title: MEF_S2P_WT_rep1_20444


title: MEF_NELF_WT_20470

value: NELF-A


title: Aged_oxBS_Rep2

extract_protocol:
Genomic DNA was extracted using the AllPrep DNA/RNA Mini Kit (QIAGEN).
DNA (250ng per sample) was fragmented by sonication (Covaris) and spiked with pooled sequencing control samples (3% w/w; CEGX). Samples were end-repaired and ligated with Illumina-supplied methylated adaptors using the NEBnext Ultra Kit (NEB). Indexed BS-seq and oxBS-seq libraries were constructed using the TrueMethyl Seq (CEGX) following the manufacturer’s protocol. Final library amplification (11 cycles) was performed with Kapa Uracil Plus (Kapa Biosystems) and purified using 1x XP Ampure beads (Beckman Coulter). Samples were sequenced on an Illumina HiSeq 1000 as 100bp single-end libraries.

value: SVZ-derived neural stem / progenitor cells

tag: age of mouse (months)


title: Aged_oxBS_Rep3


title: Aged_oxBS_Rep1


title: Young_oxBS_Rep1


title: MEF_GROSeq_WT1_18243

description: in vitro transcribed RNA


title: Aged_BS_Rep3


title: MEF_NELF_KO_20475


title: MEF_4H8_KO_rep1_20446

value: RNA Pol II (4H8)


title: Aged_BS_Rep2


title: Aged_BS_Rep1


title: Young_BS_Rep1


title: Dnmt2-/- high fat diet sperm rep1

data_processing:
For each RNA library, more than 10 million reads (raw data) were generated by Illumina Hi-Seq 2000. Sequence reads that fit any of the following parameters were removed with following standard quality control criteria: 1) The reads with N; more than 4 bases whose quality score is lower than 10 or more than 6 bases whose quality score is lower than 13; 2) The reads with 5’ primer contaminants or without 3’ primer; 3) The reads without the insert tag; 4) The reads with ploy A; 5) The reads shorter than 18nt. The clean reads were obtained after data filtration.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *clean_reads.txt: Tab-delimited text files include reads length, reads counts and reads sequence.

source_name: Mature sperm, Dnmt2-/-, high-fat diet

growth_protocol: All animal experiments obey the rules and guidelines of the local animal ethical committee and the Institutional Animal Care and Use Committee of the Institute of Zoology, Chinese Academy of Sciences. For experiments performed, 6-week-old male C57BL/6NCrl mice were purchased from Charles River Laboratories China Inc. Dnmt2 homozygote knock out mice were imported from The Jackson Laboratory (Dnmt2 KO, B6;129-Dnmt2tm1Bes/J) and was backcrossed for more than five generations onto the C57BL/6NCrl genetic background (Charles River Laboratories China Inc) before we start the experiments. These male mice with the genotypes of Dnmt2+/+ and Dnmt2-/- were housed in cages at a temperature of 22-24 °C and randomly divided into two diet groups of each genotype, one group receiving a high-fat diet (HFD, D12492; Research Diets Inc., New Brunswick, NJ) and the other group received a normal diet (Diet 1415, BEIJING HFK BIOSCIENCE CO.,LTD).

extract_protocol:
Sperm total RNAs are extracted by Trizol (Invitrogen).
Small RNA libraries were constructed according to TruSeq Small RNA Sample Pre Kit (Illumina).

treatment_protocol: Briefly, mature sperm were collected in physiological saline at 37 degrees from adult mouse cadua epididymis. Sperm suspension was then centrifuged by 600g to pellet the sperm.

tag: strain/background

tag: genotype/variation

tag: gender

value: male

value: mature sperm

tag: treatment

value: high-fat diet


title: BM iLS  H3K9me3 day7 rep1

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

data_processing:
Basecalls performed using Illumina offline basecaller (OLB) version 1.9.4
Sequences were aligned to mm9 genome using bowtie2 (version 2.1.0) with default parameters.
Peaks were detected using MACS2 (version 2.1.0)
Genome_build: mm9
Supplementary_files_format_and_content: Wiggle files having normalized read count covering whole genome.

source_name: bone marrow induced leukocyte stem

extract_protocol:
Genomic DNA was isolated using QIAGEN All-prep kit.
Library was prepared according to Illumina TruSeq protocol.

value: H3K9me3 antibody (#MABI0308, Medical & Biological Laboratories)


title: Dnmt2-/- normal diet sperm rep1

source_name: Mature sperm, Dnmt2-/-, normal diet

value: normal diet


title: BM iLS  H3K27me3 day7 rep1

value: H3K27me3 antibody (#07-449, Millipore)


title: MEF_S5P_KO_rep2_40949

value: primary mouse embryonic fibroblasts

tag: genotype

value: Supt5hFl/- Rosa26ERT2-cre/+


title: BM iLS  H3K4me3 day4 rep1

value: H3K4me3 antibody (#07-473, Millipore)


title: Dnmt2+/+ high fat diet sperm rep1

source_name: Mature sperm, Dnmt2+/+, high-fat diet


title: BM iLS  H3K27me3 day4 rep1


title: MEF_S5P_WT_rep2_40944

value: RNA Pol II (Ser5-phospho)


title: BM iLS  H3K4me3 day7 rep1


title: MEF_S2P_WT_rep2_40945

value: RNA Pol II (Ser2-phospho)


title: MEF_S2P_KO_rep2_40947


title: Dnmt2+/+ normal diet sperm rep1

source_name: Mature sperm, Dnmt2+/+, normal diet


title: Young_oxBS_Rep2


title: Young_oxBS_Rep3


title: BM iLS  H3K27me3 day2 rep1


title: MEF_4H8_WT_rep2_40942


title: MEF_4H8_KO_rep2_40946


title: Young_BS_Rep3


title: BM iLS  H3K4me3 day2 rep1


title: Young_BS_Rep2


title: Candida albicans  TPP Rep2

organism: Candida albicans

source_name: Candida albicans

value: TPP


title: Candida albicans  TPP Rep1


title: BM iLS  H3K9me3 day1 rep1


title: Candida albicans  Pool of six metabolites Rep2

value: Pool of six metabolites


title: Candida albicans  Pool of six metabolites Rep1


title: BM iLS  H3K4me3 day1 rep1


title: Candida albicans  Water Rep2

value: Water


title: OUTPUT_21

first: Julia

last: Domingo

address: 101 6th Av

institute: New York Genome Center

description:
Sample 6
DNA-seq of PCR amplicon from plasmid library

data_processing:
Read trimming (with cutadapt)
Paired end read merging (PEAR)
Base-calling (custom python scripts)
Supplementary_files_format_and_content: Tabular format. Headers: seq=tRNA genotype; num_vars=Number of mutations compared to S. cerevisiae WT genotype; pos_vars=Position of the mutation/s; ntd_vars=Nucleotide substitutions;  ntd_wt=WT nucleotides.  Columns with "reads" in the headers correspond to raw input reads (after filtering, see Methods); fitness=ln(fitness) values relative to the S. Cerevisiae WT genotype, SE=standard error of the fitness estimate

organism: Saccharomyces cerevisiae

source_name: yeast culture

growth_protocol: Yeast was grown in synthetic complete media -HIS at 30ºC (for input samples) and SC -HIS 1M NaCl at 37ºC (output samples). Cells were harvest, centrifuged and pellets saved at -20ºC for DNA extraction

extract_protocol:
Cell pellets  were resupended in 1.5 mL extraction buffer (2% Triton-X, 1% SDS, 100mM NaCl, 10mM Tris-HCl pH8, 1mM EDTA pH8), frozen by dry ice-ethanol bath and incubated at 62ºC water bath twice. Subsequently, 1.5mL of Phenol/Chloro/Isoamyl 25:24:1 (equilibrated in 10mM Tris-HCl, 1mM EDTA, pH8) was added, together with 1.5 g of glass beads and the samples were vortexed for 10 min. Samples were centrifuged at RT for 30 min at 4,000 rpm to phase separate and the aqueous phase was transferred into new tubes. The same step was repeated twice. 1:10V of NaOAc 3M and 2.2V of cold ethanol 100% were added to the aqueous phase. The mix was incubated at -20ºC for 30 min and after that, centrifuged for 30 min at full speed at 4ºC to precipitate the DNA. The ethanol was removed and the DNA pellet allowed to dry overnight at RT. DNA pellets were resuspended in 900 µL TE 1X and treated with RNAseA (10 mg/mL, Thermo Scientific) for 30 min at 37ºC. To desalt and concentrate the DNA solution, QIAEX II Gel Extraction Kit was used (75 µL of QIagen beads). Finally the sample was washed 3 times with PE and eluted twice in 375 10 mM Tris·Cl, pH 8.5
A 2-step PCR using high fidelity Q5 Hot Start High-Fidelity DNA Polymerase (NEB) was used to amplify the input and output libraries for sequencing. In each sample, ~30 million plasmid molecules were amplified for 10 cycles using oligos with overhang homology to Illumina sequencing adapters (Supplementary Table 3). The first PCR reaction was performed independently for each of the 8 samples. The samples were then treated with ExoSAP (Affymetrix), concentrated by bead purification with a QIAEX II kit. The entire first PCR reaction was used for the second PCR reaction (15 cycles), where the rest of the Illumina adapter was added multiplexed with different indexes. The DNA concentration of each individual second PCR was quantified by fluorometric quantitation (Quant-iT™ PicoGreen® dsDNA Assay Kit) and pooled together in an equimolar ratio. Finally, the pooled sequencing library was run on a gel purified and concentrated (QIAEX II Gel Extraction Kit) and subjected to 125bp paired-end sequencing on an Illumina HiSeq 2500v5 sequencer.

value: BY4742 hsx1::natMX4

tag: growth protocol

value: SC -HIS 1M NaCl at 37ºC


title: H3K27me3 day5 rep1

source_name: bone marrow


title: BM iLS  H3K27me3 day0 rep1


title: BM iLS  H3K9me3 day4 rep1


title: Candida albicans  Water Rep1


title: OUTPUT_13

description:
Sample 5
DNA-seq of PCR amplicon from plasmid library


title: OUTPUT_22

description:
Sample 7
DNA-seq of PCR amplicon from plasmid library


title: BM iLS  H3K9me3 day2 rep1


title: OUTPUT_11

description:
Sample 3
DNA-seq of PCR amplicon from plasmid library


title: H3K9me3 day12 rep1


title: BM iLS  H3K27me3 day1 rep1


title: INPUT_2

description:
Sample 2
DNA-seq of PCR amplicon from plasmid library

value: complete media -HIS at 30ºC


title: H3K27me3 day0 rep1


title: BM iLS  H3K4me3 day0 rep1


title: H3K9me3 day0 rep1


title: INPUT_1

description:
Sample 1
DNA-seq of PCR amplicon from plasmid library


title: H3K9me3 day5 rep1


title: exp3-T48-infected

organism: mixed sample

source_name: Huh7.5.1 infected/ non-infected cells

extract_protocol:
Cells were sorted directly into 500_l Qiazol reagent (Qiagen) and total RNA was isolated using a Qiagen miRNEasy kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: host

value: human (Huh7.5.1)

tag: pathogen

value: Plasmodium berghei

tag: time point

value: 48 hours post infection

tag: p. berghei strain

value: P. berghei-GFP ANKA


title: exp3-T48-non-infected


title: H3K4me3 day0 rep1

tag: strain


title: H3K4me3 day12 rep1

tag: chip antibody


title: H3K4me3 day5 rep1


title: exp3-T24-infected

value: 24 hours post infection


title: OUTPUT_23

description:
Sample 8
DNA-seq of PCR amplicon from plasmid library


title: BM iLS  H3K9me3 day0 rep1

value: H3K9me3 antibody (#MABI0308, Medical & Biological Laboratories)


title: FL iLS_168h after treatment rep1

data_processing:
Basecalls performed using Illumina offline basecaller (OLB) version 1.9.4
Sequences were aligned on mouse genome (mm9) using tophat2 (version 2.1.0) with option "--no-coverage search".
Gene expression (raw counts of mapped reads and FPKM) was obtained using Cufflinks (version 2.1.1)
Genome_build: mm9
Supplementary_files_format_and_content: plain text containig FPKM (fragments per kilobase exon per million reads) values.

source_name: FL iLS_168h after treatment

growth_protocol: Id3-ERT2-induced hematopoietic multipotent progenitors (induced leukocyte stem, or iLS cells) were co-cultured with TSt-4 feeder cells in IMDM medium supplemented with 20 ng/mL IL-7, 10 ng/mL SCF, 10 ng/mL Flt-3L and 40 nM 4-OHT.

extract_protocol:
Total RNA was isolated using Maxwell 16LEV simplyRNA purification kit.
Poly(A)+ mRNA was isolated from total RNA by NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) then library was prepared by NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs). Average size and quantity of each library were measured by Agilent 2100 Bioanalyzer (Agilent Technologies) and KAPA Library Quantification Kit (KAPA Biosystems), respectively. Sequences were read by HiSeq 1500 system (Illumina).

treatment_protocol: To induce B cell differentiation of iLS cells, the cells were co-cultured with TSt-4 cells in IMDM medium supplemented with 5 ng/ml IL-7 in the absence of 4-OHT.

value: fetal liver induced leukocyte stem cell (FL iLS)

value: 168h after treatment


title: exp2-T48-non-infected


title: OUTPUT_12

description:
Sample 4
DNA-seq of PCR amplicon from plasmid library


title: exp2-T48-infected


title: FL iLS_144h after treatment rep3

source_name: FL iLS_144h after treatment

value: 144h after treatment


title: FL iLS_144h after treatment rep2


title: exp2-T24-non-infected


title: exp2-T24-infected


title: FL iLS_144h after treatment rep1


title: FL iLS_120h after treatment rep1

source_name: FL iLS_120h after treatment

value: 120h after treatment


title: exp1-T48-non-infected


title: exp1-T24-non-infected


title: exp3-T24-non-infected


title: exp1-T24-infected


title: FL iLS_96h after treatment rep1

source_name: FL iLS_96h after treatment

value: 96h after treatment


title: FL iLS_96h after treatment rep2


title: FL iLS_96h after treatment rep3


title: FL iLS_72h after treatment rep3

source_name: FL iLS_72h after treatment

value: 72h after treatment


title: FL iLS_72h after treatment rep2


title: exp1-T48-infected


title: VEH3

city: East Lansing

first: Uros

last: Midic

state: MI

address: 474 S. Shaw Lane

department: Animal Sciences

institute: Michigan State University

description: Vehicle control TSCs, repl 3

data_processing:
Illumina Real Time Analysis (RTA) v2.7.6
HISAT 2.0.5 alignment to MacaM v7 genome
Trimming 8 bases from 5' end of unaligned reads (from first alignment); alignment of trimmed reads
Merging accepted_hits.bam from two alignment step (samtools merge)
Removing "ExAmp" duplicates with distance threshold 2500 using proprietary Python code
Cuffdiff 2.2.1 comparisons of 6 Vehicle libraries to each group of toxicant treated libraries (5 groups, 3-6 libraries per group)
Genome_build: MacaM v7 (Macaca Mulatta)
Supplementary_files_format_and_content: gene_exp.diff files (one for each toxicant) produced by Cuffdiff

organism: Macaca mulatta

source_name: Trophoblast stem cells, Methanol (vehicle control)

growth_protocol: Trophoblast stem cells (TSCs) (line 119-T) were isolated previously from rhesus monkey blastocysts and characterized using a panel of antibodies to detect TSC biomarkers. TSCs were maintained in DMEM/F- 12 (Invitrogen) supplemented with 15% fetal bovine serum (FBS; Hyclone), 1% minimum essential medium (MEM) nonessential amino acids (Invitrogen), 1 mM glutamine (Sigma), 0.1 mM  β -mercaptoethanol, and 1X  penicillin/streptomycin sulfate (Invitrogen) on plates coated with human placental collagen (Sigma). Medium was changed daily.

extract_protocol:
Cells were detached with 0.25% trypsin-EDTA (Gibco). They were then centrifuged at 3000 x g for 3 min, supernatant removed, and the cell pellet resuspended in 100 µL Picopure lysis buffer (Applied Biosystems).  Lysates were stored at -80°C until shipment.
100 ng of each RNA sample were processed first using a mixture of random and oligo(dT) primers and reverse transcription to generate double stranded cDNA using the Ovation Universal RNA-Seq System (NuGen, San Carlos, CA). This was followed by cDNA fragmentation to an average of 300 bp using a Covaris-2 sonicator, and then a brief S1 nuclease digestion. After purification, the cDNA was processed further through the Ovation Universal RNA-Seq System (NuGen) for end repair, barcoding, InDA-C mediated ribosomal RNA depletion, and final library production with the addition of unique nucleotide barcodes to each library.

treatment_protocol:
The cells were grown to confluence and passaged weekly by rinsing wells with PBS, incubating with 1.0 mL trypsin-EDTA, and transferring 20% of cell suspension to each new well. Treatments began when cells first reached confluence and continued for 4 weeks, including during passage.
Chemicals for testing were made as 1000x stocks in methanol and were added to aliquots of TSC maintenance medium up to 48 hours before use and stored at 4°C until use. Chemicals were obtained from Sigma (DEHP: Bis(2-ethylhexyl) phthalate – 47994; PFOA: Perfluorooctanoic acid – 171468; ATR: Atrazine – 45330; TBT: Tributyltin chloride – 442869; BPA: Bisphenol A – 133027).  In addition to untreated control, treatment groups included a vehicle control (methanol) and each of five EDCs at environmentally relevant doses [10 nM BPA (36 nM fetal serum), 5 uM DEHP (7.7uM pubertal serum), 30 uM ATR (up to 7 uM drinking water reported), 100 nM PFOA (average 94 nM >12 year old serum), and 25 nM TBT (0.17 – 534 adult nM serum).

value: Methanol (vehicle control)

tag: passages


title: FL iLS_48h after treatment rep3

source_name: FL iLS_48h after treatment

tag: cell type

value: 48h after treatment


title: VEH2

description: Vehicle control TSCs, repl 2

tag: cell line

value: Trophoblast stem cells (TSCs) (line 119-T)


title: FL iLS_48h after treatment rep1


title: FL iLS_48h after treatment rep2


title: VEH1

description: Vehicle control TSCs, repl 1


title: VEH5

description: Vehicle control TSCs, repl 5


title: FL iLS_24h after treatment rep3

source_name: FL iLS_24h after treatment

value: 24h after treatment


title: TBT5

description: Tributyltin chloride treated TSCs, repl 5

source_name: Trophoblast stem cells, Tributyltin chloride

value: Tributyltin chloride


title: TBT4

description: Tributyltin chloride treated TSCs, repl 4


title: FL iLS_24h after treatment rep1


title: FL iLS_12h after treatment rep3

source_name: FL iLS_12h after treatment

value: 12h after treatment


title: TBT3

description: Tributyltin chloride treated TSCs, repl 3


title: TBT2

description: Tributyltin chloride treated TSCs, repl 2


title: H3K27me3 day12 rep1

value: H3K27me3 antibody (#07-449, Millipore)


title: FL iLS_72h after treatment rep1


title: VEH6

description: Vehicle control TSCs, repl 6


title: TBT1

description: Tributyltin chloride treated TSCs, repl 1