title: ATT rep2

city: Thuwal, Jeddah

first: Arnab

last: Pain

address: Building 2, Level 4

department: Biological and Environmental Sciences and Engineering

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

description:
miRNA
processed data file: known_miRNA_ODE.count.txt

data_processing:
bcl2fastq2 Conversion Software
Reads were trimmed and made non-redundant using Adaptor_trim.pl script from mirTools2 package
Trimmed reads were aligned on miRBAse v21 for Bos taurus genome and read counts  performed using mirTools2 tool
differential miRNA analysis performed by DESeq2 tool
Genome_build: Bos taurus 4.6.1
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

organism: Bos taurus

source_name: VIR Ode cell line attenuated by passaging

extract_protocol:
Total RNA of Theileria-infected leukocytes was isolated using the miRNA isolation kit (Thermo fisher scientific #AM1560) according to the manufacturer’s instructions. The quality and quantity of RNA was measured by Nanodrop spectrophotometer. Total RNA designated for miRNA experiments was extracted using the mirVana miRNA isolation kit (Thermo Fisher) using the manufacturer’s instructions.  The quantity and quality checked by Qubit and Bioanalyzer 2100, respectively.
The miRNA libraries were prepared using the Truseq Small RNA Sample Preparation kit following the manufacturer’s instructions. Briefly, 1 μg of total RNA was adapter ligated at the 3’ and 5’ ends, reverse transcribed, barcoded then amplified with 11 PCR reactions. Then the cDNA was run on a 6% TBE PAGE gel (Novex, Life Technologies). After staining with SYBR Green the gel is visualized on a UV transluminator (Doc-It imaging system, UVP) and the cDNA constructs of a size between 145-160 bp were cut out and eluted from the gel, concentrated and the libraries validated, quantified and finally pooled.

value: Ode

tag: theileria annulata infection status

value: infected

tag: passage


title: TBL3 rep3

status: Public on Mar 20 2018

type: SRA

description:
miRNA
processed data file: known_miRNA_TBL3.count.txt

library_source: transcriptomic

molecule: total RNA

source_name: BL3 infected by Theileria annulata

tag: cell line

tag: cell type

value: B lymphoblastoid leukemia


title: ATT rep1


title: VIR rep2

source_name: Cell line derived from an infected cow and used at low passage


title: E_minus:AACTATTATTG

city: Monterotondo

first: Christophe

last: Lancrin

state: RM

address: Via Ramarini 32

department: EMBL Rome

country: Italy

institute: EMBL

description: A2lox.Empty without doxycycline

data_processing:
demultiplexing of reads using well barcode in read1 (read1 contains well barcode 11bp directly followed by 10bp molecule barcode (UMI) followed by 9bp of fragment; read2 contains transcript sequence part of fragment). Demultiplexed files (one per barcode) contain read2 and the UMI extracted from read1 has been added to the read name.
trimming of read2 with cutadapt -a AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -a GGGGGGGGGGGGGGGGGGGGG -a AAAAAAAAAAAAAAAAAAAAA -a GCGTCGTGTAGGGAA -g TTCCCTACACGACGC  -n 2 -m 15 --trim-n  -q 25 -f fastq
mapping with STAR  --runMode alignReads --outFilterMismatchNoverLmax 0.1 --outSAMtype BAM SortedByCoordinate
read counting with featureCounts -R -d 15 -s 1 -g gene_id -t exon -a Mus_musculus.GRCm38.79.gtf
UMI counting (UMI barcode correction and filtering)
Genome_build: Mus_musculus.GRCm38
Supplementary_files_format_and_content: The file countMatrix.txt contains a matrix of UMI counts (rows: gene identifiers as in Mus_musculus.GRCm38.79.gtf and columns: well barcodes as sample names).

molecule: polyA RNA

organism: Mus musculus

source_name: BL-CFC day3 of culture (differentiated murine embryonic stem cells)

extract_protocol:
Wafergen iCELL8 standard protocol
Nextera XT DNA (Illumina), sc-RNA Seq (single cell RNA Seq)

tag: wellbarcode

value: AACTATTATTG

tag: sampletype

tag: chiprowid

tag: chipcolumnid


title: ATT rep3


title: TBL3 rep2


title: E_minus:AACCGAGTCAG

description: A2lox.Empty without doxycycline

value: AACCGAGTCAG


title: TBL3 rep1


title: VIR rep1


title: E_minus:AACCGACCATA

description: A2lox.Empty without doxycycline

value: AACCGACCATA


title: BL3 rep2

source_name: Bovine B lymphoblastoid leukemia cell line

value: not infected


title: BL3 rep3


title: E_minus:AACCTCCTGAA

description: A2lox.Empty without doxycycline

value: AACCTCCTGAA


title: E_minus:AACTAACGTCA

description: A2lox.Empty without doxycycline

value: AACTAACGTCA


title: E_minus:AACCGCAACCT

description: A2lox.Empty without doxycycline

value: AACCGCAACCT


title: E_minus:AACGTAGATCT

description: A2lox.Empty without doxycycline

value: AACGTAGATCT


title: TBL20 rep3

description:
miRNA
processed data file: known_miRNA_TBL20.count.txt

source_name: BL20 infected by Theileria annulata

value: B Lymphoblastoid


title: BL3 rep1


title: TBL20 rep2


title: E_minus:AACCAGCAACT

description: A2lox.Empty without doxycycline

value: AACCAGCAACT


title: E_minus:AACCAGATTCC

description: A2lox.Empty without doxycycline

value: AACCAGATTCC


title: VIR rep3


title: E_minus:AACCGGCATTA

description: A2lox.Empty without doxycycline

value: AACCGGCATTA


title: BL20 rep3

source_name: Bovine B Lymphoblastoid cell line


title: BL20 rep2


title: Neg_Ctrl:GGTTCTTATAC

description: control

organism: other sequences

source_name: Buffer without cells

value: GGTTCTTATAC


title: TBL20 rep1


title: E_minus:AACCAGTCAGG

description: A2lox.Empty without doxycycline

value: AACCAGTCAGG


title: E_minus:AACCAATCGTC

description: A2lox.Empty without doxycycline

value: AACCAATCGTC


title: Neg_Ctrl:GTCTGACGGAT

description: control

value: GTCTGACGGAT


title: E_minus:AACCGTAGATT

description: A2lox.Empty without doxycycline

value: AACCGTAGATT


title: Neg_Ctrl:GTTATTGCGTT

description: control

value: GTTATTGCGTT


title: E_minus:AACCATCTATT

description: A2lox.Empty without doxycycline

value: AACCATCTATT


title: E_minus:AACCGTCTCTA

description: A2lox.Empty without doxycycline

value: AACCGTCTCTA


title: Neg_Ctrl:GTATCTACTAC

description: control

value: GTATCTACTAC


title: ERRαγAd-/- PBS rep 3

status: Public on Mar 19 2018

city: Baltimore

first: Anastasia

last: Kralli

state: MD

address: 725 N Wolfe Str

department: Physiology

country: USA

institute: Johns Hopkins University

description:
PBS
BAT-C3_S9

data_processing:
The Illumina Genome Analyzer Data Analysis Pipeline Software (currently bcl2fastq/2.16.0.10) was used to perform the image analysis, base calling, and demultiplexing
Cutadapt was used to trim the adapter and low basepair called scores
STAR 2.3.0 was used to align reads to the mouse genome reference mm9
The RNA-Seq data was analyzed using R Bioconductor package EdgeR program (GLM method) to determine the significantly changed transcripts (DE) between groups, and normalization was performed by the TMM (trimmed mean of M) method where the sample whose 75%-ile (of library-scale-scaled counts) is closest to the mean of 75%-iles as the reference.
The log2 counts-per-million (log2 CPM), greater than 40 counts (gt40) cutoff was used to avoid undefined values and the poorly defined log-fold-changes for low counts shrunk towards zero
Genome_build: mm10
Supplementary_files_format_and_content: txt file: Processed data file 1. RPKM values. File contains RPKM values for all genes.
txt file: Processed data file_logCPM_gt40; Data has been analyzed usnig EdgeR program, and log2 counts per million (CPM) including all values with greater than 40 counts (gt40) are in the file

source_name: Brown adipose tissue

growth_protocol: Mice with floxed ERRα and ERRγ alleles were crossed to ones expressing CRE recombinase driven by the adiponectin promoter to generate mice with adipose-specific deletions of ERRα and ERRγ (ERRαγAd-/-). ERR floxed littermates that did not carry the CRE transgene were used as WT controls. Male mice were housed on a 12-hour light-dark cycle at 30 °C, and fed a standard chow breeder diet (5058, Picolab).

extract_protocol:
Total RNA was isolated from BAT using TRIzol Reagent (Life Technologies). Following separation using chloroform, the upper aqueous phase containing RNA was mixed with equal volume of 70 % EtOH, and transferred to an RNeasy spin column (QIAGEN). RNA isolation was completed using the RNeasy mini kit according to manufacturer’s protocol (QIAGEN), and RNA was treated with DNase I (Zymo Research).
RNA libraries were prepared from 1 µg of total RNA using the TruSeq total RNA Sample Preparation Kit version 2.0 Kit (Illumina) following the manufacturer's instructions

treatment_protocol: At 10-11 weeks of age, mice were given an intraperitoneal injection of the β3-adrenergic agonist CL316,243 (1 mg/kg) or equivalent volume of PBS at Zeitgeber time (ZT) 4 each day for 10 days. Mice were euthanized 24 hours after the last CL316,243 dose for BAT tissue collection.

tag: strain

value: C57BL/6J Bom

tag: tissue

value: Brown adipose

tag: age

value: 12 weeks

tag: genotype

value: ERRalpha-gamma Ad-/-


title: ERRαγAd-/- CL316,243 rep 1

description:
CL316,243
BAT-D1_S10


title: ERRαγAd-/- PBS rep 2

description:
PBS
BAT-C2_S8


title: E_minus:AACCATTGGCT

description: A2lox.Empty without doxycycline

value: AACCATTGGCT


title: ERRαγAd-/- CL316,243 rep 2

description:
CL316,243
BAT-D2_S11


title: ERRαγAd-/- CL316,243 rep 3

description:
CL316,243
BAT-D3_S12


title: WT PBS rep 3

description:
PBS
BAT-A3_S3

value: Wild type (WT)


title: WT CL316,243 rep 2

description:
CL316,243
BAT-B2_S5


title: WT PBS rep 1

description:
PBS
BAT-A1_S1


title: PcGDKO_TAM_NucRNA_rep4

city: London

first: Hamish

middle: W

last: King

address: 4 Newark St

department: Blizard Institute

country: United Kingdom

institute: Queen Mary University of London

data_processing:
RNA-seq reads were initially aligned against the rRNA genomic sequence (GenBank: BK000964.3) using bowtie2 to filter out rRNA fragments, prior to alignment using the STAR RNA-seq aligner (Dobin et al., 2012).
Biological triplicate read counts were determined using custom scripts for a custom-built, non-redundant mm10 gene set. Briefly, mm10 refGene genes were filtered on size (>200bp), gene body and TSS mappability, unique TSS and TTS, so as to remove poorly mappable and highly similar transcripts.
The final set of 20,633 genes were used for differential analysis using DESeq2 (Love et al., 2014), with FDR < 0.05 and fold change > 1.5 considered to be significant.
Genome_build: mm10
Supplementary_files_format_and_content: Stranded bigWig files representing genome coverage for merged biological triplicate, and DESeq2 results table.

source_name: Embryonic stem cells, tamoxifen-treated, NucRNA-seq

growth_protocol: Mouse embryonic stem cell (ESCs) were grown on gelatin-coated plates in DMEM (Gibco) supplemented with 15% FBS, 10ng/mL leukemia-inhibitory factor, penicillin/streptomycin, beta-mercaptoethanol, L-glutamine and non-essential amino acids.

extract_protocol:
1 × 107 cells were resuspended in 1 mL HS Lysis buffer (50 mM KCl, 10 mM MgSO4.7H20, 5 mM HEPES, 0.05 % NP40 (IGEPAL CA630)), 1 mM PMSF, 3 mM DTT)  for 1 min at room temperature to isolate nuclei. Nuclei were centrifuged at 1,000 × g for 5 min at 4°C, followed by a total of three washes with ice-cold RSB buffer. Nuclei were then resuspended in 1mL of TriZOL reagent (ThermoScientific) according to the manufacturer’s protocol. Nuclear RNA was treated with the TURBO DNA-free Kit (ThermoScientific) and depleted for rRNA using the NEBNext rRNA Depletion Kit (NEB).
RNA-seq libraries were prepared using the NEBNext Ultra Directional RNA-seq kit (NEB) and libraries were sequenced on the Illumina NextSeq500 with 80bp paired-end reads.

treatment_protocol: Previously described Ringa-/-;Ring1bfl/fl ESCs (Endoh et al., 2008) were adapted to grow under feeder-free culture conditions and were treated with 800 nM 4-hydroxytamoxifen (TAM) for 72 h to ablate RING1B levels as previously described. To ablate both PRC1 and PRC2 function, Eed was deleted by CRISPR/Cas9 in the Ringa-/-;Ring1bfl/fl ESCs to generate Ringa-/-;Ring1bfl/fl;Eed-/-.

value: Eed-/-;Ring1a-/-;Ring1bfl/fl (PcG DKO)

tag: replicate

tag: clone

tag: treatment

value: tamoxifen


title: WT PBS rep 2

description:
PBS
BAT-A2_S2


title: PcGDKO_TAM_NucRNA_rep2


title: PcGDKO_TAM_NucRNA_rep3


title: PcGDKO_TAM_NucRNA_rep1


title: PcGDKO_UNT_NucRNA_rep4

source_name: Embryonic stem cells, untreated control, NucRNA-seq

value: untreated


title: ERRαγAd-/- PBS rep 1

description:
PBS
BAT-C1_S7


title: PcGDKO_UNT_NucRNA_rep3


title: PcGDKO_UNT_NucRNA_rep2


title: PcGDKO_UNT_NucRNA_rep1


title: RING1Bfl_TAM_NucRNA_rep2


title: WT CL316,243 rep 3

description:
CL316,243
BAT-B3_S6


title: RING1Bfl_TAM_NucRNA_rep3


title: WT CL316,243 rep 1

description:
CL316,243
BAT-B1_S4


title: RING1Bfl_TAM_NucRNA_rep4


title: RING1Bfl_TAM_NucRNA_rep1


title: RING1Bfl_UNT_NucRNA_rep4


title: RING1Bfl_UNT_NucRNA_rep1


title: RING1Bfl_UNT_NucRNA_rep2


title: PcGDKO_TAM_ATAC_rep4

library_source: genomic

data_processing:
Paired-end reads were aligned to the mouse mm10 genome using bowtie2 (Langmead and Salzberg, 2012) with the “—no-mixed” and “—no-discordant” options. Non-uniquely mapping reads and reads mapping to custom “blacklist” of artificially high regions of the genome were discarded. PCR duplicates were removed using SAMtools (Li et al., 2009). Biological replicates were randomly downsampled to contain the same number of reads for each individual replicate and merged.
Merged BAM files were used to make a genome track using DANPOS2, with the Tn5 control provided as background.
Peakcalling was performed using the DANPOS2 dpeak function using untreated and treated samples with biological replicates and a Tn5 gDNA control digestion as background.
Differential chromatin accessibility was identified using DiffBind (Stark and Brown, 2011), with FDR < 0.05 and fold change > 1.5 considered to be significant.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files representing genome coverage (with background subtracted) for merged biological triplicate were generated using DANPOS2.

molecule: genomic DNA

source_name: Embryonic stem cells, tamoxifen-treated

extract_protocol:
Chromatin accessibility was assayed using an adaptation of the assay for transposase accessible-chromatin (ATAC)-seq (Buenrostro et al., 2013). Briefly, 5 × 106 cells were harvested, washed with PBS and nuclei were isolated using 1 mL HS Lysis buffer (50 mM KCl, 10 mM MgSO4.7H20, 5 mM HEPES, 0.05 % NP40 (IGEPAL CA630)), 1 mM PMSF, 3 mM DTT)  for 1 min at room temperature. Nuclei were centrifuged at 1,000 × g for 5 min at 4°C, followed by a total of three washes with ice-cold RSB buffer (10mM NaCl, 10mM Tris (pH 7.4), 3mM MgCl2), to remove as much of contaminating cytoplasmic and mitochondrial material as possible. Nuclei were then counted, and 5×104 nuclei were resuspended in Tn5 reaction buffer (10mM TAPS, 5mM MgCl2, 10% dimethylformamide) and 2 µl of Tn5 transposase (25µM) made in house according to the previously described protocol (Picelli et al., 2014). Nuclei were then incubated for 30 min at 37°C, before isolation and purification of tagmented DNA using QiaQuick MinElute columns (Qiagen). To control for sequence bias of the Tn5 transposase, an ATAC “input” sample was generated, by tagmenting genomic DNA from ESCs with Tn5 for 30 min at 55°C.
ATAC-seq libraries were prepared by PCR amplification using custom made Illumina barcodes previously described (Buenrostro et al., 2013) and the NEBNext® High-Fidelity 2X PCR Master Mix with 8-10 cycles. Libraries were purified with two rounds of AMPure XP bead cleanup (1.5X beads:sample), followed by quantification by qPCR using SensiMix SYBR (Bioline) and KAPA Library Quantification DNA standards (KAPA Biosystems). ATAC-seq libraries were sequenced on Illumina NextSeq500 using 80bp paired-end reads in biological triplicate.

treatment_protocol: Previously described Ringa-/-;Ring1bfl/fl ESCs (Endoh et al., 2008) were adapted to grow under feeder-free culture conditions and were treated with 800 nM 4-hydroxytamoxifen (TAM) for 72 h to ablate RING1B levels as previously described. EED conditional knockout (EED cKO) which express a doxycycline-sensitive Eed4 transgene (Eed4TG) in an Eed-/- background were treated with 1 µg/mL doxycycline (DOX) for 14 days to disrupt PRC2 complex and function, as previously described (Ura et al., 2008, Tavares et al., 2012). To ablate both PRC1 and PRC2 function, Eed was deleted by CRISPR/Cas9 in the Ringa-/-;Ring1bfl/fl ESCs to generate Ringa-/-;Ring1bfl/fl;Eed-/-. E14 ESCs were treated with 500nM triptolide for 50 min to inhibit RNA polymerase II initiation, as previously described (Jonkers et al. 2014)


title: RING1Bfl_UNT_Tn5Control

source_name: Embryonic stem cell genomic DNA, Tn5 tagmented


title: RING1Bfl_TAM_Tn5Control


title: PcGDKO_TAM_ATAC_rep1


title: PcGDKO_TAM_Tn5Control


title: PcGDKO_TAM_ATAC_rep3


title: PcGDKO_UNT_ATAC_rep4

source_name: Embryonic stem cells, untreated control


title: PcGDKO_UNT_ATAC_rep3


title: PcGDKO_UNT_Tn5Control


title: PcGDKO_TAM_ATAC_rep2


title: RING1Bfl_UNT_NucRNA_rep3


title: PcGDKO_UNT_ATAC_rep2


title: PcGDKO_UNT_ATAC_rep1


title: RING1Bfl_TAM_ATAC_rep4


title: RING1Bfl_TAM_ATAC_rep3


title: RING1Bfl_TAM_ATAC_rep2


title: RING1Bfl_TAM_ATAC_rep1


title: RING1Bfl_UNT_ATAC_rep4


title: RING1Bfl_UNT_ATAC_rep3


title: RING1Bfl_UNT_ATAC_rep1


title: RING1Bfl_UNT_ATAC_rep2


title: EEDcKO_DOX_ATAC_rep2

source_name: Embryonic stem cells, doxycycline-treated

value: EED conditional knockout (EED cKO)

value: doxycycline


title: EEDcKO_DOX_ATAC_rep1


title: EEDcKO_UNT_ATAC_rep1


title: TRP_ATAC_rep3

source_name: Embryonic stem cells, triptolide-treated

value: triptolide


title: DMSO_ATAC_rep2

source_name: Embryonic stem cells, DMSO-treated control

value: DMSO control


title: DMSO_ATAC_rep3


title: TRP_ATAC_rep1


title: TRP_ATAC_rep2


title: DMSO_ATAC_rep1


title: E14_ATAC_rep3

source_name: Embryonic stem cells


title: E14_ATAC_rep1


title: E14_ATAC_rep2


title: PTL-007_exosome_depleted

city: Seattle

first: Kai

last: Wang

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

data_processing:
the adaptor sequences, were trimmed and the low quality sequences such as low nucleotide complexity reads – homopolymer sequences or di-, tri-nucleotide repeat sequences were removed. The processed sequences were then mapped against various databases including known human miRNA, human transcripts, followed by human genomic sequence. We also applied three different levels of error tolerance: 0 mismatch, 1 mismatch and 2 mismatches when align to the human sequence databases.  The remaining unmapped sequences were then compared to sequences from other species, and the non-redundant nucleic acid sequence collection from NCBI.  To be considered as expressed RNA, the RNA has to have more than 10 mapped reads and in 70% of the samples.
Supplementary_files_format_and_content: miRNA counts

organism: Homo sapiens

source_name: exosome depleted

extract_protocol:
RNA was isolated from all plasma samples, the 22 EV samples, and 22 corresponding EV-depleted fractions using miRNeasy Micro Kit (Qiagne, Germantown MD).  The quality and quantity of the RNA were evaluated with Agilent 2100 Bioanalyzer (Santa Clara, CA) and NanoDrop 1000 spectrophotometer (Thermo Scientific, Wilmington, DE)
Small RNA sequencing libraries were generated with a modified small RNAseq protocol (manuscript in preparation) that alleviates most of the adapter-miRNA ligation sequence bias problem. Key elements of this small RNA library construction method include the addition of 4 random nucleotides at the appropriate end of the adapters, the use of higher adapter concentrations, and the increased amounts of polyethylene glycol (PEG) in the ligation steps to ensure the completion of ligation reactions. In addition, to reduce the amplification of adapter-dimer, we adapted a two-stage size-selection step in which an initial size selection is performed after 4 cycles of amplification followed by a second size selection after 11 (?) cycles of amplification of ligated fragments from the first size selection step. The quality of libraries was assessed with the Agilent 2100 Bioanalyzer with the DNA 1000 chip.  Individual library concentrations were measured using the NEBNext Library Quant Kit for Illumina (New England Biolabs, Ipswich MA) and adjusted to a final pooled concertation of 2 nM and sequenced using the NEXTseq DNA sequencer (Illumina, San Diego CA).

treatment_protocol: Whole blood samples were collected in EDTA-treated tubes and centrifuged for 15 minutes at 2,000 x g at 4°C. The resulting supernatant is designated plasma. The plasma was transferred to clean polypropylene tubes in 100ul aliquots and frozen at -80°C. Prior to exosome isolation or RNA extraction, plasma was spun at 10,000 x g for 15 minutes at 4°C to remove platelet and large particles. EVs were isolated using size exclusion columns (SEC) (iZON qEV, city state) from a total of 22 selected samples, 11 from each group (Supplemental Table 1). EVs were isolated from 100 ul of plasma using size exclusion columns (iZON qEV, Cambridge MA) with de-gassed 1X PBS from a total of 22 selected samples, 11 from each group (Table 1). Eluate (~500 µl for each fraction) was collected in microfuge tubes individually. The protein contains and concentration for each fraction were assessed by protein gel electrophoresis and Bradford assay (BioRad, Hercules, CA).  The EV fractions (usually from fraction 7 to 10) and EV-depleted fractions (fractions 11 to 35) were pooled and concentrated to ~100 µl using Amicon 10K centrifugation filters (EMD Millipore, Billerica MA) spun in a swing-bucket rotor at 4000 x g at 4oC for 20 minutes.

tag: preterm

value: Preterm Labor (PTL)


title: PTL-015_exosome_depleted


title: PTL-017_exosome_depleted


title: PTL-006_exosome_depleted


title: LSD1

city: Kumamoto

first: Kotaro

last: Anan

state: Kumamoto

address: 2-2-1, Honjo, Chuo-ku

department: Department of Medicall Cell Biology

country: Japan

institute: Kumamoto University

data_processing:
Basecalls and conversion to FASTQ files were performed using BaseSpace Onsite (Illumina)
Sequence data were alignmened onto the mouse reference genome mm9 using the BWA algorithm in Galaxy.
Duplicate reads and low read/mapping quality reads were trimmed out with Galaxy.
Peak detection was done using the MACS algorithm in Galaxy. LSD1 binding sites were detected based on the LSD1 peaks significantly enriched over input peaks at a cutoff value of p=10^-5.
Genome_build: mm9
Supplementary_files_format_and_content: The BED files were generated using MACS algorithm in Galaxy.

growth_protocol: Cells were grown in DMEM containing 25mM glucose and 10% FBS.

extract_protocol:
Cells were crosslinked with formaldehyde and disuccinimidyl glutarate. Cell lysates were subjected to two-step DNA fragmentation by a probe-type sonifier and a water bath sonifier, and chromatin-DNA complexes were pulled down using the specific antibody.
Libraries were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina (New England BioLabs) according to the manufacturer's instructions. Briefly, ChIP DNA was end-repaired using an end prep enzyme. After adapter ligation, DNA was PCR amplified with NEB Index primers for 8-10 cycles. The purified DNA was checked for quality on Agilent TapeStation instrument with an Agilent High Sensitivity D1000 kit. The library DNA was approximately 170–500 bp in length.  Libraries ware quantified using quantitative real-time PCR with the Kapa Library Quantification Kit. Diluted library DNA was subjected NextSeq sequencers (Illumina) according to the manufacturer's protocols.

treatment_protocol: For myogenic induction, medium was changed to DMEM containing 25mM glucose and 2% horse serum, then incubated for 48 hours.

value: differentiating C2C12 myoblasts

tag: antibody

value: Anti-LSD1 polyclonal antibody (Abcam:ab177721)


title: PTL-013_exosome_depleted


title: PTL-016_exosome_depleted


title: Con-038_exosome_depleted

value: Control


title: Con-044_exosome_depleted


title: PTL-002_exosome_depleted


title: input

source_name: input


title: PTL-020_exosome_depleted


title: PTL-010_exosome_depleted


title: Con-036_exosome_depleted


title: EEDcKO_UNT_ATAC_rep2


title: Con-035_exosome_depleted


title: Con-025_exosome_depleted


title: Con-027_exosome_depleted


title: PTL-019_exosome_depleted


title: Con-022_exosome_depleted


title: PTL-018_exosome_depleted


title: Con-020_exosome_depleted


title: Con-018_exosome_depleted


title: Con-011_exosome_depleted


title: PTL-019_exosome

source_name: exosome


title: PTL-018_exosome


title: PTL-016_exosome


title: PTL-017_exosome


title: Con-010_exosome_depleted


title: PTL-015_exosome


title: Con-044_exosome


title: PTL-010_exosome


title: PTL-007_exosome


title: Con-038_exosome


title: PTL-006_exosome


title: Con-036_exosome


title: Con-020_exosome


title: Con-022_exosome


title: Con-018_exosome


title: Con-011_exosome


title: Con-035_exosome


title: Con-010_exosome


title: Con-027_exosome


title: Con-025_exosome


title: PTL-019_plasma

source_name: plasma


title: PTL-018_plasma


title: PTL-002_exosome


title: PTL-020_exosome


title: PTL-017_plasma


title: PTL-016_plasma


title: PTL-015_plasma


title: PTL-012_plasma


title: PTL-014_plasma


title: PTL-013_plasma


title: PTL-010_plasma


title: PTL-013_exosome


title: PTL-020_plasma


title: PTL-003_plasma


title: PTL-004_plasma


title: PTL-006_plasma


title: PTL-005_plasma


title: PTL-002_plasma


title: 4x0506-23

city: Foster City

first: Li

last: Li

address: 333 Lakeside Drive

institute: Gilead Sciences

description: processed data file column header: H36947/4x0506-23_L1.D702

data_processing:
Clipping adapters and low-quality bases.
STAR
RSEM
edgeR
limma
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file with raw gene level counts from RSEM output

organism: Pan troglodytes

source_name: PBMC

extract_protocol:
On-column DNase I treatment was performed during RNA isolation with the RNeasy Mini Kit (Qiagen).
cDNA libraries were constructed using a TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA).

value: PBMC

tag: animal id

tag: infection

value: HBV

tag: day

tag: time


title: PTL-001_plasma


title: Con-049_plasma


title: PTL-007_plasma


title: PTL-008_plasma


title: Con-048_plasma


title: 4x0506-24

description: processed data file column header: H36947/4x0506-24_L1.D703

tag: cell type


title: 4x0506-25

description: processed data file column header: H36948/4x0506-25_L1.D704


title: Con-050_plasma


title: PTL-011_plasma


title: PTL-009_plasma


title: 4x0506-19

description: processed data file column header: H36947/4x0506-19_L1.D710


title: Con-047_plasma


title: Con-046_plasma


title: 4x0506-21

description: processed data file column header: H36947/4x0506-21_L1.D712


title: Con-045_plasma


title: 4x0506-20

description: processed data file column header: H36947/4x0506-20_L1.D711


title: Con-044_plasma


title: 4x0506-17

description: processed data file column header: H36947/4x0506-17_L1.D707


title: 4x0506-16

description: processed data file column header: H36947/4x0506-16_L1.D706


title: 4x0506-15

description: processed data file column header: H36946/4x0506-15_L1.D705


title: Con-043_plasma


title: Con-042_plasma


title: 4x0506-22

description: processed data file column header: H36947/4x0506-22_L1.D701


title: Con-039_plasma


title: 4x0506-12

description: processed data file column header: H36946/4x0506-12_L1.D702


title: 4x0506-14

description: processed data file column header: H37040/4x0506-14_L1.D702


title: 4x0506-11

description: processed data file column header: H36946/4x0506-11_L1.D701


title: 4x0506-13

description: processed data file column header: H36946/4x0506-13_L1.D703


title: Con-040_plasma


title: Con-038_plasma


title: 4x0506-10

description: processed data file column header: H36946/4x0506-10_L1.D712


title: Con-037_plasma


title: 4x0499-3

description: processed data file column header: H36948/4x0499-3_L1.D709

value: HCV


title: 4x0506-18

description: processed data file column header: H36947/4x0506-18_L1.D708


title: Con-036_plasma


title: Con-035_plasma


title: Con-033_plasma


title: Con-034_plasma


title: Con-031_plasma


title: 4x0437-2

description: processed data file column header: H36948/4x0437-2_L1.D712

value: Naive


title: 4x0497-3

description: processed data file column header: H36948/4x0497-3_L1.D707


title: 4x0497-2

description: processed data file column header: H36948/4x0497-2_L1.D705


title: 4x0427-2

description: processed data file column header: H36948/4x0427-2_L1.D710


title: 4x0428-2

description: processed data file column header: H36948/4x0428-2_L1.D711


title: 4x0364-2

description: processed data file column header: H36948/4x0364-2_L1.D701


title: Con-032_plasma


title: Con-029_plasma


title: Con-028_plasma


title: 4x0328-25

description: processed data file column header: H36946/4x0328-25_L1.D711


title: Con-041_plasma


title: Con-027_plasma


title: 4x0328-24

description: processed data file column header: H36946/4x0328-24_L1.D710


title: Con-025_plasma


title: Con-026_plasma


title: 4x0328-22

description: processed data file column header: V12506/4x0328-22_L2


title: 4x0328-23

description: processed data file column header: H36946/4x0328-23_L1.D709


title: Con-023_plasma


title: 4x0328-21

description: processed data file column header: H36945/4x0328-21_L1.D706


title: 4x0328-20

description: processed data file column header: H36945/4x0328-20_L1.D705


title: 4x0499-2

description: processed data file column header: H36948/4x0499-2_L1.D708


title: Con-024_plasma


title: Con-021_plasma


title: 4x0328-19

description: processed data file column header: H36945/4x0328-19_L1.D704


title: Con-022_plasma


title: 4x0328-16

description: processed data file column header: H36945/4x0328-16_L1.D701


title: 4x0328-15

description: processed data file column header: H36945/4x0328-15_L1.D712


title: Con-030_plasma


title: Con-018_plasma


title: Con-017_plasma


title: Con-020_plasma


title: Con-019_plasma


title: 4x0328-17

description: processed data file column header: H36945/4x0328-17_L1.D702


title: 4x0328-13

description: processed data file column header: H36944/4x0328-13_L1.D709


title: Con-016_plasma


title: Con-015_plasma


title: Con-014_plasma


title: 4x0328-12

description: processed data file column header: H36944/4x0328-12_L1.D708


title: 4x0328-11

description: processed data file column header: H36944/4x0328-11_L1.D707


title: Con-013_plasma


title: 4x0328-10

description: processed data file column header: H36944/4x0328-10_L1.D706


title: Con-012_plasma


title: 4x0328-18

description: processed data file column header: H36945/4x0328-18_L1.D703


title: 4x0139-23

description: processed data file column header: H36944/4x0139-23_L1.D704


title: Con-011_plasma


title: 4x0139-22

description: processed data file column header: H36944/4x0139-22_L1.D703


title: 4x0139-20

description: processed data file column header: H36944/4x0139-20_L1.D712


title: 4x0328-14

description: processed data file column header: H36945/4x0328-14_L1.D711


title: 4x0139-19

description: processed data file column header: H36943/4x0139-19_L1.D711


title: 4x0139-21

description: processed data file column header: H36944/4x0139-21_L1.D701


title: Con-007_plasma


title: 4x0139-18

description: processed data file column header: H36943/4x0139-18_L1.D710


title: Con-005_plasma


title: Con-006_plasma


title: 4x0139-16

description: processed data file column header: H36943/4x0139-16_L1.D708


title: Con-004_plasma


title: Con-003_plasma


title: 4x0139-14

description: processed data file column header: H36943/4x0139-14_L1.D706


title: 4x0139-15

description: processed data file column header: H36943/4x0139-15_L1.D707


title: Con-002_plasma


title: 4x0139-17

description: processed data file column header: V12506/4x0139-17_L1


title: Con-001_plasma


title: 4x0139-13

description: processed data file column header: H36943/4x0139-13_L1.D705


title: 4x0139-24

description: processed data file column header: H36944/4x0139-24_L1.D705


title: ChIP-seq_Input_K36M_D0

city: Bethesda

last: Ge

address: 50 South Dr Rm 4154

department: NIDDK

institute: NIH

data_processing:
Basecalls performed using Illumina's CASAVA package v1.8.2 with default parameters
ChIP-seq reads and RNA-seq were aligned to the mm9 genome assembly using Illumina's CASAVA package v1.8.2 with default parameters
Peaks of ChIP-seq were called using SICER with following configuration: For ChIP-seq of H3K4me1 and H3K27ac: Windows (200), Gaps (200), FDR (1e-3); For ChIP-seq of H3K36me2 and H3K27me3: Windows (1000), Gaps (3000), FDR (1e-3).
Aligned reads on exonic regions from RNA-Seq were used to calculate RPKM to measure the gene expression levels.
Genome_build: mm9
Supplementary_files_format_and_content: For ChIP-seq data, wig files were generated using in-house script and the scores represent RPKM; For RNA-seq data, tab-delimited text files were generated to include RPKM values for each gene.

source_name: Brown preadipocyte cell

growth_protocol: Primary preadipocytes were isolated from interscapular BAT of new born GRf/f (Jackson No. 021021) pups and immortalized by SV40T

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq DNA sample prep kit (Cat no. FC-121-2001). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, 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 15-18 cycles and library fragments of 200-400 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 Genome Analyzer following the manufacturer's protocols.

treatment_protocol: After immortalization with SV40T, cells were infected with retroviral Vec or Cre to generate WT or GR KO cells. For adipogenesis assay, cells were plated in growth medium (DMEM plus 10% FBS) at a density of 1.8x106 cells per 15-cm dish 4 days before induction of adipogenesis. The confluent cells (0h) were induced with 0.02 μM insulin, 1 nM T3, 0.5 mM 3-isobutyl-1-methyl-xanthine (IBMX), 2 μg/ml dexamethasone, and 0.125mM indomethacin for 2 day.

value: imortalized GR-flox/flox brown preadipocytes

tag: time point

value: Day 0


title: 4x0139-11

description: processed data file column header: H36943/4x0139-11_L1.D703


title: ChIP-seq_Input_K36M_D2

value: Day 2


title: Con-009_plasma


title: Con-010_plasma


title: ChIP-seq_Input_WT_D2


title: ChIP-seq_Input_WT_D0


title: Con-008_plasma


title: 4x0139-10

description: processed data file column header: H36943/4x0139-10_L1.D702


title: library 10X_P8_15

city: San Francisco

first: Angela

last: Oliveira Pisco

state: CA

address: 499 Illinois St

department: Data Science

institute: Chan Zuckerberg Biohub

description: Single cell

data_processing:
Sequences from the NovaSeq were demultiplexed using CellRanger version 2.0.1, with bcl2fastq 2.19.0.316. Reads were aligned using to a copy of the mm10 genome augmented with ERCC sequences using CellRanger and  STAR version 2.5.2b
cellranger mkfastq --localmem 60
cellranger count --localmem 240 --nosecondary --cells=3000 --transcriptome=MM10-Plus
Genome_build: mm10
Supplementary_files_format_and_content: output of 10X CellRanger: gene lists, barcode lists and UMI count files in mtx format

source_name: Trachea

extract_protocol:
10x Genomics single cell protocol
10x Genomics single cell protocol

value: Trachea

value: 3 months

value: C57BL/6 NIA


title: library 10X_P8_14

description: Single cell


title: ChIP-seq_H3K27ac_K36M_D0

tag: chip antibody

value: H3K27ac Antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #

tag: chip antibody lot/batch #


title: library 10X_P8_13

description: Single cell

source_name: Lung

tag: tissue

value: Lung

tag: age

tag: strain


title: library 10X_P8_12

description: Single cell


title: library 10X_P7_15

description: Single cell

source_name: Muscle

value: Muscle


title: library 10X_P7_14

description: Single cell


title: ChIP-seq_H3K27ac_WT_D2


title: ChIP-seq_H3K27ac_WT_D0


title: library 10X_P7_12

description: Single cell

source_name: Mammary

value: Mammary


title: ChIP-seq_H3K4me1_K36M_D2

value: H3K4me1 Antibody


title: library 10X_P7_11

description: Single cell

source_name: Thymus

value: Thymus


title: ChIP-seq_H3K27me3_K36M_D2

value: H3K27me3 Antibody

value: Millipore


title: library 10X_P7_10

description: Single cell

source_name: Tongue

value: Tongue


title: ChIP-seq_H3K4me1_WT_D0


title: ChIP-seq_H3K27me3_K36M_D0


title: library 10X_P7_9

description: Single cell


title: ChIP-seq_H3K27ac_K36M_D2


title: library 10X_P7_7

description: Single cell

source_name: Bladder

value: Bladder


title: ChIP-seq_H3K27me3_WT_D0

value: imortalized GR-flox/flox brown preadipocytes


title: ChIP-seq_H3K27me3_WT_D2


title: library 10X_P7_8

description: Single cell


title: ChIP-seq_H3K36me2_K36M_D2

value: H3K36me2 Antibody


title: library 10X_P7_5

description: Single cell

source_name: Kidney

value: Kidney


title: ChIP-seq_H3K36me2_K36M_D0

value: Day 0


title: ChIP-seq_H3K36me2_WT_D2

value: Day 2


title: library 10X_P7_4

description: Single cell

source_name: Heart

value: Heart

value: 3 months

value: C57BL/6 NIA


title: ChIP-seq_H3K36me2_WT_D0


title: library 10X_P7_3

description: Single cell

source_name: Marrow

value: Marrow


title: 4x0139-12

description: processed data file column header: H36946/4x0139-12_L1.D704

value: PBMC

value: HBV


title: RNA-seq_shNSD2_D2

extract_protocol:
Total RNA was harvested using Trizol reagent. mRNA wasfurther  purified using Invitrogen Dynabeads® mRNA DIRECT™ Kit  (Cat. 610-11).
RNA libraries were prepared for sequencing using standard Illumina protocols


title: library 10X_P7_13

description: Single cell

value: Mammary


title: ChIP-seq_H3K4me1_WT_D2

value: H3K4me1 Antibody

value: Abcam


title: library 10X_P7_2

description: Single cell


title: ChIP-seq_H3K4me1_K36M_D0


title: RNA-seq_shNSD2_D0


title: RNA-seq_Con_D0


title: library 10X_P7_1

description: Single cell

source_name: Liver

value: Liver


title: library 10X_P4_7

description: Single cell

source_name: Spleen

value: Spleen


title: RNA-seq_Con_D2


title: library 10X_P7_0

description: Single cell


title: library 10X_P4_6

description: Single cell


title: library 10X_P7_6

description: Single cell


title: library 10X_P4_5

description: Single cell


title: library 10X_P4_4

description: Single cell

value: Bladder


title: library 10X_P4_3

description: Single cell


title: RNA-seq_PPARg_ligand_K36M_0h

value: imortalized GR-flox/flox brown preadipocytes

tag: agent

value: DMSO


title: RNA-seq_PPARg_ligand_WT_24h

value: Rosi


title: RNA-seq_PPARg_ligand_WT_0h


title: library 10X_P4_2

description: Single cell


title: RNA-seq_K36M_D7

value: Day 7


title: library 10X_P4_1

description: Single cell

value: Tongue


title: RNA-seq_K36M_D0

value: Day 0


title: RNA-seq_K36M_D2

value: Day 2


title: Trachea

description: single cell

data_processing:
Sequences from the NovaSeq were demultiplexed using bcl2fastq version 2.19.0.316. Reads were aligned using to a copy of the mm10 genome augmented with ERCC sequences, using STAR version 2.5.2b
STAR options are listed below
--outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMstrandField in
Genome_build: mm10
Supplementary_files_format_and_content: comma-separated-value files with raw read counts for each sample

extract_protocol:
single-cell sorting in 96-well plates followed by cDNA preparation using Smart-seq2
Smart-Seq2 for preparation of cDNA followed by library preparation using Nextera XT
Nextera tagmentation according to the standard protocol for single cell RNA-seq following Smart-Seq2

value: Trachea

value: 3 months


title: Tongue

description: single cell


title: Spleen

description: single cell


title: RNA-seq_WT_D2


title: Skin

description: single cell

source_name: Skin

value: Skin


title: Thymus

description: single cell

value: Thymus


title: Pancreas

description: single cell

source_name: Pancreas

value: Pancreas


title: Mammary

description: single cell

value: Mammary


title: Muscle

description: single cell

value: Muscle


title: Marrow

description: single cell

value: Marrow


title: RNA-seq_WT_D0


title: Lung

description: single cell

value: Lung


title: Liver

description: single cell

value: Liver


title: RNA-seq_PPARg_ligand_K36M_24h

value: imortalized GR-flox/flox brown preadipocytes


title: Kidney

description: single cell

value: Kidney


title: Heart

description: single cell

value: Heart


title: Fat

description: single cell

source_name: Fat

value: Fat


title: Colon

description: single cell

source_name: Colon

value: Colon


title: Brain_Neurons

description: single cell


title: library 10X_P4_0

description: Single cell

value: Tongue

value: C57BL/6 NIA


title: RNA-seq_WT_D7

source_name: Brown preadipocyte cell

value: Day 7


title: Bladder

description: single cell

value: Bladder

value: 3 months


title: siUPF1_3

first: Thomas

middle: David

last: Baird

address: 50 South Drive, Room 2339

department: Biochemistry and Biophysics

institute: NIH/NHLBI

data_processing:
Sequencing reads in FASTQ format were aligned to the reference genome hg19 using HISAT2 aligner.
Differential gene expression analysis was performed using the Kallisto and Sleuth packages.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include TPM values and fold expression change.

source_name: HEK-293TO cells

growth_protocol: HEK-293TO cells were maintained in DMEM supplemented with 10% FBS , 100 U/ml of penicillin, 100 μg/ml streptomycin , and 0.3 mg/ml of L-glutamine at 37°C and 5% CO2.

extract_protocol:
Qiagen RNeasy Mini RNA isolation kit
One μg of total RNA was used per sample for library preparation. Ribosomal RNA was depleted from total RNA with the Ribo-Zero rRNA Removal Kit (Epicentre), and purified RNA was then converted to cDNA with the TruSeq RNA Library Preparation Kit (Illumina).

treatment_protocol: Transient depletion for 72 hours by reverse transfection.

tag: sirna

value: Treated with UPF1 siRNA


title: siUPF1_2


title: siNS_3

value: Treated with non-specific (NS) siRNA


title: siUPF1_1


title: siNS_1


title: siICE1_2

value: Treated with ICE1 siRNA


title: siICE1_1


title: Wild type Iron starvation 1h - Biological replicate 2

city: Piracicaba

first: Diego

middle: Mauricio Riano

last: Pachon

state: Sao Paulo

address: Av. CEntenário, 303

department: Center for Nuclear Energy in Agriculture

country: Brazil

institute: University of Sao Paulo

description: Sample name: Sample_WT_1h_starv_II

data_processing:
Basecalls performed using CASAVA version 1.4
Raw reads were quality trimmed with Trimmomatic v0.36 and ribosomal RNA were filterout with SortMeRNA
Reads were mapped to the A. fumigatus A1163 genome sequence available at http://www.aspergillusgenome.org/
Read counts per gene were generated by featureCounts in strand-specific mode
Genome_build: A. fumigatus A1163 genome sequence available at http://www.aspergillusgenome.org/
Supplementary_files_format_and_content: A table with read counts per samples and per gene

organism: Aspergillus fumigatus

source_name: Aspergillus fumigatus wild-type CEA17akuB KU80

growth_protocol: The media used were: complete media composed of 2% w/v glucose, 0.5% w/v yeast extract, trace elements (YAG) and minimal media (MM) consisting of 1% glucose, trace elements and salt solution (Kafer, 1977), pH 6.5, plus or minus 2% w/v agar. Strains were grown at 37°. For the experiments of iron starvation, we grew the strains in MM for 24 hr at 37° and transferred the mycelia to AMM (glucose 1%, trace elements without FeSO₄) plus BPS 200 mM [Bathophenanthrolinedisulfonic acid (4,7-diphenyl-1,10 phenanthrolinedisulfonic acid)] and 3-(2-pyridyl)-5,6-bis(4-phenylsulfonic acid)-1,2,4-triazine (ferrozine) 300 mM for 1 , 2 and 4hr at 37°.

extract_protocol:
Mycelia were harvested, frozen in liquid nitrogen, and ground by mortar and pestle for total RNA isolation. Total RNA was extracted using Trizol (Invitrogen), treated with RNase-free DNase I (Fermentas) and purified using a RNAeasy Kit (Qiagen) according to manufacturer's instructions. The RNA from each treatment was quantified using a NanoDrop and Qubit fluorometer, and analyzed using an Agilent 2100 Bioanalyzer system to assess the integrity of the RNA. RNA Integrity Number (RIN) was calculated; RNA sample had a RIN = 9.0 - 9.5.
Illumina TruSeq Stranded mRNA Sample Preparation kit was used.

value: CEA17akuB KU80

value: mycelia


title: Wild type Iron starvation 1h - Biological replicate 3

description: Sample name: Sample_WT_1h_starv_III


title: Wild type Iron starvation 1h - Biological replicate 1

description: Sample name: Sample_WT_1h_starv_I


title: Wild type Iron starvation 2h - Biological replicate 1

description: Sample name: Sample_WT_2h_starv_I


title: siICE1_3


title: Wild type Iron starvation 0h - Biological replicate 1

description: Sample name: Sample_WT_0_starv_I


title: DeltaPpzA Iron starvation 2h - Biological replicate 3

description: Sample name: Sample_DAfu2g03950_2h_starv_III

source_name: Aspergillus fumigatus ΔppzA


title: Wild type Iron starvation 0h - Biological replicate 2

description: Sample name: Sample_WT_0_starv_II


title: Wild type Iron starvation 2h - Biological replicate 2

description: Sample name: Sample_WT_2h_starv_II


title: DeltaPpzA Iron starvation 1h - Biological replicate 3

description: Sample name: Sample_DAfu2g03950_1h_starv_III


title: DeltaPpzA Iron starvation 1h - Biological replicate 2

description: Sample name: Sample_DAfu2g03950_1h_starv_II


title: Brain_Microglia

description: single cell


title: DeltaPpzA Iron starvation 2h - Biological replicate 1

description: Sample name: Sample_DAfu2g03950_2h_starv_I


title: Wild type Iron starvation 0h - Biological replicate 3

description: Sample name: Sample_WT_0_starv_III


title: siNS_2


title: DeltaPpzA Iron starvation 1h - Biological replicate 1

description: Sample name: Sample_DAfu2g03950_1h_starv_I


title: DeltaPpzA Iron starvation 0h - Biological replicate 3

description: Sample name: Sample_DAfu2g03950_0_starv_III


title: DeltaPpzA Iron starvation 0h - Biological replicate 2

description: Sample name: Sample_DAfu2g03950_0_starv_II


title: DeltaPpzA Iron starvation 0h - Biological replicate 1

description: Sample name: Sample_DAfu2g03950_0_starv_I


title: Aspergillus fumigatus strain Af293 grown on fructose - biological replicate 3

data_processing:
Basecalling bcl2fastq-1.8.4
Data filtering Trimmomatic v0.36; SortMeRNA v2.0
Mapping software Tophat2 v2.1.0
Abundance saturation estimation: RSeQC
Abundance estimation: Rsubread
Genome_build: Aspergillus fumigatus Af293 genome sequence http://www.aspergillusgenome.org/

source_name: conidia

growth_protocol: The A. fumigatus strain Af293 was used for the transcriptome and secretome analyses. To prepare fresh conidia, this strain was cultivated in YAG medium [2% dextrose (w/v), 0.5% yeast extract (w/v), trace elements 0.1% (v/v), and agar 1.8% (w/v)] at 37 °C for two to three days. The conidia were harvested with phosphate buffered saline (PBS) containing 0.1% Tween 20, and the concentration was calculated by counting the conidia with a Newbauer camera. Regarding the growth conditions, the conidia were first inoculated in 50 mL of YNB medium [yeast extract 0.05% (w/v), salt solution 20x 5% (v/v), and trace elements 0.1% (v/v)] containing fructose 1% (w/v) (final concentration of approximately 108 conidia mL-1) at 37 °C for 16 h, in triplicate; the containers were shaken at 200 rpm.

extract_protocol:
For RNA sequencing, total RNA was extracted from SEB- or fructose-induced A. fumigatus mycelia at 24 h by using the “Direct-zolTM RNA MiniPrep” kit according to the manufacturer’s instructions (Zymo Research). The integrity of RNA was verified with Bioanalyzer by using the “Agilent RNA 6000 Nano” kit (Agilent Technologies) and the “Plant Total RNA Nano” protocol. RNA was quantified on a Qubit® 2.0 fluorimeter (Thermo Fisher Scientific) with the Qubit® RNA BR Assay kit (Thermo Fisher Scientific)
TruSeq Stranded mRNA HT Sample prep kit

treatment_protocol: After this first cultivation, the conidia were collected by centrifugation, washed with sterile distilled water, and re-suspended in 50 mL of fresh YNB medium containing fructose 1% (w/v) (control culture) or YNB medium containing SEB 1% (w/v) (steam exploded bagasse) at 37 °C for different periods (3, 6, 12, 18, 24, 48 and 72 h,); the containers were shaken at 200 rpm. SEB was kindly donated by a factory located near Ribeirão Preto, São Paulo, Brazil, and was prepared as follows: in natura bagasse was treated with 14 kg cm-2 water steam for 8 min, which was followed by exhaustive washing with sterile distilled water, to eliminate impurities. Then, SEB was dried at 40 °C for several days, made into SEB powder with a grinder, and stored at room temperature.

tag: treatment

value: growth culture on fructose


title: Wild type Iron starvation 2h - Biological replicate 3

description: Sample name: Sample_WT_2h_starv_III


title: Aspergillus fumigatus strain Af293 grown on fructose - biological replicate 2


title: Aspergillus fumigatus strain Af293 grown on fructose - biological replicate 1


title: Aspergillus fumigatus strain Af293 grown on SEB - biological replicate 2

value: growth culture on SEB


title: Aspergillus fumigatus strain Af293 grown on SEB - biological replicate 3


title: siE2F7 12h

status: Public on Mar 18 2018

city: Bilbao

first: Ana

last: Zubiaga

address: Barrio Sarriena s/n

country: Spain

institute: University of the Basque Country

data_processing:
Image analysis and per-cycle basecalling was performed with Illumina Real Time Analysis software (RTA1.13). Conversion to FASTQ read format and sequence alignment with the ELAND algorithm (v2e) was performed with CASAVA-1.8 (Illumina).
Genome_build: human GRCh37/hg19

growth_protocol: Dulbecco’s modified Eagle’s medium supplemented with 10%  fetalbovine serumbovine serum

extract_protocol:
Total RNA extraction was performed with TRIzol Reagent (Life Technologies) and purified using the RNeasy Mini kit (Qiagen)
Illumina TruSeq RNA Sample Preparation Kit

treatment_protocol: For cell synchronization in G1/S, exponentially growing U2OS cells were incubated with 4 mM hydroxyurea (HU) for 24 h and subsequently washed and cultured in complete medium.

tag: cell line

tag: transfection

tag: cell cycle time point


title: Aspergillus fumigatus strain Af293 grown on SEB - biological replicate 1


title: siNT 12h

value: control siNT


title: siE2F7 3h


title: DeltaPpzA Iron starvation 2h - Biological replicate 2

description: Sample name: Sample_DAfu2g03950_2h_starv_II


title: siNT 3h


title: siNT 0h


title: siE2F7 0h


title: Tet2_Nras_1 (Bisulfite-Seq)

status: Public on Mar 17 2018

city: New York

first: Francine

middle: E.

last: Garrett-Bakelman

state: NY

address: 413 East 69th street, BRB 1426

department: Medicine

institute: Weill Cornell Medicine

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequences and then mapped to mm9 using a whole genome bismark alignment software approach with a maximum of 2 mismatches in a directional manner allowed. Only uniquely aligned reads were retained. Reads which pass filter were considered for mapping. If both matched reads pass filter, the last base of R2 was compared to the first base of R1 (one base overlap); the base with the best quality score was retained and R1 was concatenated to R2 for use in alignment.
methylation score were determined for cytosines with at least 20 phred quality score and 10× coverage
Percentage of bisulfite converted Cytosines (Cs; representing unmethylated Cs) and non-converted Cs (representing methylated Cs) were recorded for each C position in a CpG context
Percent methylation values for CpG dinucleotides are calculated by dividing the number of methylated Cs by total coverage on that base (Cs and Ts).
Genome_build: mm9; NCBIM37
Supplementary_files_format_and_content: tab-delimited text files include the number of methylated Cs and Ts per position (base) covered

source_name: bone marrow

extract_protocol:
Bone marrow was extracted from femurs, tibiae and iliac crests. After red blood cell lysis, cells were FACS-sorted to isolate Lin- Sca1+ cKit+ (LSK) cells. DNA was extracted using AllPrep Kit (Qiagen)
Genomic DNA was digested with MspI restriction enzyme, subjected to end repair and adenylation followed by ligation to cytosine methylated paired-end Illumina Tru-seq adaptors. Fragments of 150-400 bp were isolated by size selection and subjected to bisulfite conversion and PCR amplification using paired-end Illumina primers.  Libraries were sequenced using an Illumina HiSeq2500 per manufacturer’s recommended protocol for 50bp single end read reads

value: LSK

tag: genotype


title: L_Tet2_Nras_3 (Bisulfite-Seq)


title: Tet2_Nras_2 (Bisulfite-Seq)


title: Tet2_Nras_3 (Bisulfite-Seq)


title: HEK293T

city: Guangzhou

first: Jian-Hua

last: Yang

address: No. 135, Xingang Xi Road

department: School of Life Sciences

country: China

institute: Sun Yat-sen University

data_processing:
Mapping  reads to human genome (version: hg38) using bowtie 2.0 with the parameters: -D 200 -R 3 -N 0 -L 20 -i S,1,0.5 -- score-min=C,-16,0. The aligned reads are discarded and the remaining unmapped RNA-seq reads are used to identify circRNAs.
Mapping unmapped reads to human genome (version hg38) with local model. The unmapped reads were aligned again using bowtie2 with the parameters (-- no-unal -- local -- reorder -k 20 -D 200 -R 3 -N 0 -L 20 -i S,1,0.5) and then converted alignment SAM format into the BAM format sorted by name using samtools program.
Predicting circRNAs from the alignments of unmapped reads using circSeeker program (http://starbase.sysu.edu.cn/circTools.php) with default paramerters (-l 18 -d 300000).
Annotating novel circRNAs using the known gene annotation using circAnno software (http://starbase.sysu.edu.cn/circTools.php) with parameters(-m).We kept only the circRNAs that mapped the precise exon boundaries of known genes.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include circRNA locations and their read number

source_name: HEK293T cells

growth_protocol: HEK293T and HeLa cell lines were maintained at 37℃ and 5% CO2 in DMEM media supplemented with 10% fetal bovine serum, 100 I.U./ml Penicillin, 100 μg/ml Streptomycin.

extract_protocol:
RNA isolated using Trizol
The ribosomal RNA was depleted by using a Ribo-Zero rRNA Removal Kit (Epicentre) and then used as input for the Illumina TruSeq® Stranded Total RNA HT/LT Sample Prep Kit.

value: epithelial

tag: cell source

value: embryonic kidney cell line


title: HeLa

source_name: HeLa cells

value: HeLa

tag: cell type

value: cervical cancer cell line


title: Tet2_3 (Bisulfite-Seq)


title: L_Tet2_Nras_2 (Bisulfite-Seq)


title: L_Tet2_Nras_1 (Bisulfite-Seq)

description: TN-BMT


title: Tet2_1 (Bisulfite-Seq)


title: Wild_Type_3 (RNA-Seq)

data_processing:
Illumina bcl2fastq software used for basecalling.
Sequenced reads were aligned using STAR (v 2.4.0f1)
RNAseq counts were annotated  using  STAR (v 2.4.0f1)
normalization factors were computed using calcNormFactor from the edgeR package (v 3.14.0)
RNAseq counts were normalized using VOOM from the limma package (v 3.28.21) following the recommanded protocol
Genome_build: mm10 (NCBIM37) and ensembl v80 transcriptome assembly
Supplementary_files_format_and_content: tab-delimited text file of gene counts where  each row is a gene and every column a sample

extract_protocol:
Bone marrow was extracted from femurs, tibiae and iliac crests. After red blood cell lysis, cells were FACS-sorted to isolate Lin- Sca1+ cKit+ (LSK) cells. RNA was extracted using AllPrep Kit (Qiagen)
Libraries were constructed using using the TruSeq Stranded mRNA Library Prep Kit (Illumina) per manufacturer's recommendations

value: WT


title: Tet2_2 (Bisulfite-Seq)


title: Nras_1 (Bisulfite-Seq)


title: Wild_Type_2 (RNA-Seq)


title: Wild_Type_1 (RNA-Seq)


title: Nras_3 (Bisulfite-Seq)


title: Nras_2 (Bisulfite-Seq)


title: Tet2_Nras_2 (RNA-Seq)


title: Tet2_Nras_3 (RNA-Seq)


title: L_Tet2_Nras_3 (RNA-Seq)


title: L_Tet2_Nras_1 (RNA-Seq)

description: TN-BMT


title: L_Tet2_Nras_2 (RNA-Seq)


title: Tet2_3 (RNA-Seq)


title: Tet2_Nras_1 (RNA-Seq)


title: Tet2_2 (RNA-Seq)


title: Tet2_1 (RNA-Seq)


title: Nras_3 (RNA-Seq)


title: Nras_2 (RNA-Seq)


title: Nras_1 (RNA-Seq)


title: 9797_A

first: Michael

last: Ayars

address: 1550 Orleans St

institute: Johns Hopkins School of Medicine

data_processing:
Basecalls were performed using Illumina CASAVA 1.8.3 software.
Alignments were performed using rsem-1.2.9 with the following options: --calc-ci --output-genome-bam --paired-end --forward-prob 0
FPKM values were calculated using rsem-1.2.9
FPKM values from both datasets were combined and batch-removed using ComBat.
FPKM values were converted to TPM by manual calculation.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file includes TPM values for all samples.

source_name: Laser microdissected patient tissue

extract_protocol:
Gross dissected tissue was mounted on PEN slides and laser microdissected.  RNA was isolated from microdissected samples.
Libraries were prepared using standard ABI and Illumina protocols.

tag: lesion grade


title: 13047_A


title: 12471_B


title: 43581


title: Ni_clone_6

city: Tuxedo

first: Suresh

last: Cuddapah

state: New York

address: 57 Old Forge Road

department: Environmental Sciecne

institute: New York University Langone Medical center

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-Seq data analysis was performed using Biowardrobe experimental management system. Breifly Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh37/hg19 whole genome using STAR version 2.4.oj using default parameters; multi hits removed
Gene expression levels were quantified as reads per kilobase of exon per million fragments mapped (RPKM) using Biowardrobe algorithm
Differential gene expression was calculated using DESeq2
More information on Biowardrobe suite can be found at https://www.biowardrobe.com/
Genome_build: Feb. 2009 (GRCh37/hg19)
Supplementary_files_format_and_content: csv file include RPKM values for each Sample and DESeq Differential expression analysis between control and test samples

source_name: Bronchial epithelial cell

growth_protocol: BEAS-2B cells were cultured in Dulbecco’s Modified Eagle’s Medium (Cellgro).

extract_protocol:
Total RNA was isolated from treated cells  using RNeasy kit (Qiagen)
RNASeq libraries were prepared using Illumina TruSeq RNA Sample Preparation Kit (RS-122-2002), according to the manufacturer’s instructions.

treatment_protocol: For Ni exposure, various concentrations of NiCl2 (Sigma N6136) was added to the media and the cells were cultured for 6 weeks. Following exposure, the cells were washed and cultured in Ni-free medium for 2 weeks to obtain the Ni-washed-out cells. To obtain homogenous populations of Ni-exposed cells, the cells exposed to 100 mM NiCl2 for 6 weeks were plated in 15 cm plates in Ni-free medium at the rate of 1000, 500, 100 and 50 cells per plate. Nicely separated single colonies were picked and the populations were expanded in Ni-free medium.

value: Bronchial epithelial cell


title: 1213

value: Pancreatic normal duct


title: 15043


title: Ni_clone_5


title: Ni_clone_3


title: Ni_clone_2


title: Ni_6W_2


title: Ni_6W_1


title: Ni_3D+14D_2


title: Ni_3D+14D_1


title: Ni_6W+2W_2


title: Ni_clone_1


title: Ni_6W+2W_1


title: Ni_3D_2


title: Control_6W_2


title: Ni_3D_1


title: Control_6W_1


title: Control_3D_4


title: Control_3D_3


title: Control_3D_2


title: Control_3D_1


title: 39851_B


title: 9033_B


title: Parp1 KD Day 4 - 1

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

data_processing:
The RNA-seq reads were aligned to the mm10 mouse reference genome using the Bowtie software package (Langmead et al, 2009) .
Mapped reads were sorted and captured in bam files for further downstream analysis of differential gene expression and  “wiggle” files counting reads in non-overlapping 200-bp windows across the genome for presentation as genome browser tracks by using the BEDTools software package  (Quinlan et al, 2010).
Genome_build: mm10
Supplementary_files_format_and_content: BigWig

source_name: 3T3-L1 cells expressing Parp1 shRNA differentiated with DMI for 96 hours

growth_protocol: 3T3-L1 cells (Green and Kehinde, 1975) were obtained from the American Type Cell Culture (ATCC, CL-173TM) and maintained in DMEM supplemented with 10% fetal bovine serum.

extract_protocol:
Two biological replicates of control, Nmnat1, and Parp1 knockdown 3T3-L1 cells were differentiated as described above.  Total RNA was isolated using the RNeasy kit (Qiagen) according to the manufacturer’s instructions.
The total RNA was then enriched for polyA+ RNA using Dynabeads Oligo(dT)25 (Invitrogen).  The polyA+ RNA was then used to generate strand-specific RNA-seq libraries as described previously (Zhong et al., 2011).  The RNA-seq libraries were subjected to QC analyses (i.e., number of PCR cycles required to amplify each library, the final library yield, and the size distribution of final library DNA fragments) and sequenced using an Illumina HiSeq 2000

treatment_protocol: 3T3-L1 cells were plated in 6 well plates, grown to confluence, and then grown for another two days under contact inhibition. For adipogenic differentiation,cells were treated with 0.25mM IBMX, 1μM Dexamethasone, 10 μg/mL of insulin for 48 hours. After 48 hours, cells were cultured in medium containing 10 μg/mL of insulin for 2 more days.

value: Mouse preadipocytes

value: IBMX+Insulin+Dexamethasone


title: Parp1 KD Day 4 - 2


title: Nmnat1 KD Day 4 - 2

source_name: 3T3-L1 cells expressing Nmnat1 shRNA differentiated with DMI for 96 hours


title: Ni_clone_4


title: Nmnat1 KD Day 4 - 1


title: Parp1 KD Day 2 - 1

source_name: 3T3-L1 cells expressing Parp1 shRNA differentiated with DMI for 48 hours


title: Con KD Day 4 - 1

source_name: 3T3-L1 cells expressing control shRNA differentiated with DMI for 96 hours


title: Parp1 KD Day 2 - 2


title: Nmnat1 KD Day 2 - 2

source_name: 3T3-L1 cells expressing Nmnat1 shRNA differentiated with DMI for 48 hours


title: Con KD Day 4 - 2


title: Con KD Day 2 - 2

source_name: 3T3-L1 cells expressing control shRNA differentiated with DMI for 48 hours


title: Parp1 KD Day 0 - 1

source_name: 3T3-L1 cells expressing Parp1 shRNA without DMI treatment

value: Undifferentiated


title: Con KD Day 2 - 1


title: 69808_3.1

data_processing:
Basecalls were performed using ABI LifeScope software.
Alignments were performed using the Bioscope 1.3 Whole Transcriptome Plugin.
FPKM values were calculated using HTSeq-count.
FPKM values from both datasets were combined and batch-removed using ComBat.
FPKM values were converted to TPM by manual calculation.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file includes TPM values for all samples.


title: Parp1 KD Day 0 - 2


title: Nmnat1 KD Day 0 - 2

source_name: 3T3-L1 cells expressing Nmnat1 shRNA without DMI treatment


title: 77257_3.1


title: Con KD Day 0 - 2

source_name: 3T3-L1 cells expressing control shRNA without DMI treatment


title: Nmnat1 KD Day 0 - 1


title: 77257_3.2


title: Con KD Day 0 - 1


title: 47910_3


title: 12250_2


title: 4699_2


title: 15332_3


title: 66078_3


title: 77668_1A_B


title: 4699_1A


title: 12412N


title: Nmnat1 KD Day 2 - 1


title: 77668_2


title: 6-8hr elav+ Drosophila embryo nuclei DNAse-seq

status: Public on Mar 16 2018

city: Tucson

first: Darren

middle: A.

last: Cusanovich

state: AZ

address: 1230 N Cherry Avenue, BSRL 421

department: Cellular and Molecular Medicine

institute: University of Arizona

description: Accessible genomic DNA

data_processing:
Reads were trimmed for adapter readthrough with Skewer and for read quality with seqtk
Reads were mapped to the genome with bwa
Reads with a mapping quality less than 20 were filtered out
Bam files from sequencing runs were merged and sorted with Samtools
Duplicate reads were filtered out with with a custom version of Picard that considers UMIs
Bam files were converted to bedGraph files with bedtools
BedGraph files were converted to bigWigs with the bedGraphToBigWig program from UCSC
Genome_build: dm3
Supplementary_files_format_and_content: For information on bigWig format see https://genome.ucsc.edu/goldenpath/help/bigWig.html

organism: Drosophila melanogaster

source_name: Nuclei isolated from whole embryos elav+

extract_protocol:
Transgenic Drosophila melanogaster carrying a mesodermally expressed tagged histone marker (Bonn, S., Zinzen, R.P., Perez-Gonzalez, A., Riddell, A., Gavin, A.C., and Furlong,  E.E. (2012). Cell type-specific chromatin immunoprecipitation from multicellula
For DNase digestion, nuclei were resuspended in R-buffer (7.5mM Tris pH8, 45mM NaCl, 30mM KCl, 6mM MgCl2, 1mM CaCl2). Nuclei (4-20x10e6 per digest) were digested in 500uL R-buffer containing 2-20 units of DNaseI depending on nuclei number (where possible

tag: developmental stage

value: 6 to 8 hours after egg laying

value: elav+ nuclei


title: 6-8hr Mef2+ Drosophila embryo nuclei DNAse-seq

description: Accessible genomic DNA

source_name: Nuclei isolated from whole embryos Mef2+

value: Mef2+ nuclei


title: 6-8hr WE Drosophila embryo nuclei DNAse-seq

description: Accessible genomic DNA

source_name: Nuclei isolated from whole embryos ('WE')

value: whole embryo


title: Unt3_Pso_Epi_Iso_FPKM

city: besancon

first: irène

last: gallais sérézal

address: boulevard stalingrad

country: France

institute: CHU Besançon

description: Unt_Pso_Epi_Iso-VS-Unt_Pso_Epi_CD3.GeneDiffExpFilter.txt

data_processing:
SOAPnuke for filtering, Mapping with Bowtie / BWA; Gene/Transcript expression  with RSEM
Primary sequencing data that produced by Illumina HiSeqTM 2000, called as raw reads, is subjected to quality control (QC) that determine if a resequencing step is needed. After QC, raw reads  are filtered into clean reads which will be aligned to the reference sequences. QC of alignment is performed to determine if resequencing is needed. The alignment data is utilized to calculate  distribution of reads on reference genes and mapping ratio. If alignment result passes QC, we will proceed with downstream analysis including gene and isoform expression,deep analysis based  on gene expression(PCA/correlation/screening differentially expressed genes and so on),exon expression, gene structure refinement, alternative splicing, novel transcript prediction and  annotation, SNP detection, Indel detection, gene fusion. Further, we also can perform deep analysis based on DEGs,including Gene Ontology (GO) enrichment analysis,Pathway enrichment  analysis, cluster analysis, protein-protein interaction network analysis and finding transcriptor factor.
Genome_build: hg19
Supplementary_files_format_and_content: textl files with FPKM values for each sample.

extract_protocol:
Skin is sampled, treated with antibodies. The days after epidermis and dermis are separated with dispase, then flash frozen on dry ice. RNA is extracted with Qiazol (qiagen) and send for sequencing
After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA(for eukaryotes) or  by removing rRNAs from the total RNA (for prokaryotes). Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments  as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters.  After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time  PCR System are used in quantification and qualification of the sample library. At last, the library could be sequenced using Illumina HiSeqTM 2000 or other sequencer when necessary.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Epidermis

value: Isotype control

tag: condition

value: patient with untreated Lesional Psoriasis


title: Unt3_Pso_Der_CD3_FPKM

description: Unt_Pso_Der_Iso-VS-Unt_Pso_Der_CD3.GeneDiffExpFilter.txt

value: Dermis

value: CD3 antibody


title: 76746_3.1


title: Unt3_Pso_Epi_CD3_FPKM


title: Unt2_Pso_Der_Iso_FPKM


title: Unt1_Pso_Epi_Iso_FPKM


title: Unt1_Pso_Der_Iso_FPKM


title: Unt1_Pso_Der_CD3_FPKM


title: Unt2_Pso_Der_CD3_FPKM


title: IL12_23_3_Pso_Epi_Iso_FPKM

description: IL12_23_Pso_Epi_Iso-VS-IL12_23_Pso_Epi_CD3.GeneDiffExpFilter.txt

source_name: pp55.15 les h16 iso D 6

value: psoriasis patient treated with Ustekinumab


title: Unt1_Pso_Epi_CD3_FPKM


title: IL12_23_3_Pso_Epi_CD3_FPKM

source_name: pp55.15 les h16 iso E 5


title: IL12_23_3_Pso_Der_Iso_FPKM

description: IL12_23_Pso_Der_Iso-VS-IL12_23_Pso_Der_CD3.GeneDiffExpFilter.txt

source_name: pp55.15 les h16 iso D 4


title: IL12_23_2_Pso_Epi_Iso_FPKM

source_name: pp51.15 les h16 iso D 6


title: IL12_23_2_Pso_Epi_CD3_FPKM

source_name: pp51.15 les h16 iso E 5


title: IL12_23_2_Pso_Der_Iso_FPKM

source_name: pp51.15 les h16 iso D 4


title: IL12_23_3_Pso_Der_CD3_FPKM

source_name: pp55.15 les h16 iso E 3


title: IL12_23_2_Pso_Der_CD3_FPKM

source_name: pp51.15 les h16 iso E 3


title: Unt2_Pso_Epi_Iso_FPKM


title: Unt3_Pso_Der_Iso_FPKM


title: IL12_23_1_Pso_Der_Iso_FPKM


title: IL12_23_1_Pso_Epi_CD3_FPKM


title: IL12_23_1_Pso_Der_CD3_FPKM


title: IL12_23_1_Pso_Epi_Iso_FPKM


title: H3_Epi_Iso_FPKM

description: H_Epi_Iso-VS-H_Epi_CD3.GeneDiffExpFilter.txt

value: Healthy


title: Unt2_Pso_Epi_CD3_FPKM


title: H3_Der_Iso_FPKM

description: H_Der_Iso-VS-H_Der_CD3.GeneDiffExpFilter.txt


title: H3_Epi_CD3_FPKM


title: H2_Epi_Iso_FPKM


title: H2_Epi_CD3_FPKM


title: H2_Der_Iso_FPKM


title: H1_Epi_Iso_FPKM


title: H2_Der_CD3_FPKM


title: H1_Epi_CD3_FPKM


title: H1_Der_CD3_FPKM


title: H1_Der_Iso_FPKM


title: Preterm chorio validation S. epidermidis [CSE]

city: Crawley, Perth

first: Emma

last: de Jong

address: 35 Stirling Hwy

country: Australia

institute: University of Western Australia

description: processed data: ValidationRun_NormalisedData.csv

data_processing:
Image analysis was performed in real time by the HiSeq Control Software (HCS) v1.4.8 and Real Time Analysis (RTA) v1.18.61. RTA performs real-time base calling on the HiSeq instrument computer
The Illumina CASAVA 1.8.2 pipeline was used to generate the sequence data
Read libraries were mapped to the GRCh37 (hg19) Human genome using the R/Subread suite (v1.14.2) with default options
Libraries were summarised against Ensembl (v69) annotations, with a minimum Mapping Quality Score of 30
Genome_build: hg19
Supplementary_files_format_and_content: csv files include a matrix of filtered gene counts (normalised using limma voom)

source_name: Preterm chorio validation S. epidermidis_Monocytes

growth_protocol: Monoytes were purified from cord blood mononuclear cells, then rested for 15 hours in culture media prior to bacterial stimulation

extract_protocol:
Total RNA was extracted from cultured monocytes using the AllPrep DNA/RNA Micro kit (Qiagen), with 1 U/uL of RNase inhibitor (SUPERase In, Ambion) added to each sample. RNA quality was determined using a Bioanalyzer 2100 (Agilent Technologies) and cDNA libraries were constructed using the TruSeq Stranded mRNA Sample Prep Kit (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Monocytes were stimulated for 2 hours with live E. coli or S. epidermidis, or PBS (unstimulated negative control)

tag: culture treatment

value: stimulation with live S. epidermidis

tag: gestational age (weeks)

tag: birth weight

tag: gender

value: M

tag: mode of delivery

value: spontaneous vertex delivery

tag: premature rupture of membranes y/n

value: Y

tag: maternal smoker y/n

value: N

value: neonatal monocyte


title: Preterm chorio validation Unstimulated [CUN]

source_name: Preterm chorio validation Unstimulated_Monocytes

value: Unstimulated


title: Preterm chorio validation E. coli [CEC]

source_name: Preterm chorio validation E. coli_Monocytes

value: stimulation with live E. coli


title: Preterm validation Unstimulated [PUN]

value: cesarean section


title: Preterm validation S. epidermidis [PSE]

source_name: Preterm validation S. epidermidis_Monocytes


title: Set 2, Inducible 3

city: Boulder

first: Glen

last: Bjerke

state: CO

address: 347 UCB

department: MCDB

institute: University of Colorado

data_processing:
Library strategy: CLEAR-CLIP
Reads were quality filtered using the FastX toolkit fastq_filter.pl requiring the first 25 base pairs to have a mean quality of 20.
The 5’ and 3’ adapter sequences were then removed using Cutadapt.  Next the 2 base pairs at the 3’ end of the read that correspond to the NN of the 3’ adapter were trimmed and only reads at least 43 base pairs long were kept (Minimum of 19 base pairs for the miRNA, 20 for mapping the mRNA and 4 base pairs for the barcode at the 5’ end).
Next the barcode was trimmed from the read, but kept as a separate entry in the file using stripbarcode.pl that is part of the CIMS package from the Darnell lab.
Reads were then mapped using BLAST to a Fasta file containing the mouse miRNA database (BLAST settings: -word_size 11, -outfmt 6 –strand plus).  BLAST results were filtered requiring at least 19 matching base pairs matching and E < 0.05.
Only reads containing a miRNA that mapped to the 5’ end of the read were selected and the resulting 3’ end sequence was then mapped to the mouse genome (mm10) using Novoalign.  Reads between 20-24 base pairs were mapped using Novoalign and requiring an exact match to the genome.  Reads 25+ base pairs were mapped using Novoalign and the –t 85 setting which allows two deletions, two substitutions, or one deletion and one substitution.  Novoalign files were parsed using the novoalign2bed.pl program from the Darnell lab CIMS package and then mapped reads corresponding to 20-24 and 25+ base pairs were combined into one file for each sample.
Reads were annotated to regions of the genome using Bedtools intersect against annotated regions of the genome using annotation files downloaded from USCS table browser for the mouse mm10 genome.  Similarly, reads were annotated to genes using Bedtools intersect against gene annotation files for the mouse mm10 genome.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files are in a text format.  Each line corresponds to a miRNA CLEAR-CLIP read that was then mapped to the genome using Novoalign.

source_name: miR-200 Inducible keratinocytes grown in culture, induced with 3 ug/ml doxycycline

growth_protocol: Cells were grown in E-low calcium medium

extract_protocol: One 15cm dish of confluent cells was used per sample.  Cells were washed once with cold PBS.  10mls of cold PBS was added and cells were irradiated with 300mJ/cm2 UVC (254nM wavelength).  Cells were then scraped from the plates in cold PBS and pelleted by centrifugation at 1,000g for 2 minutes.  Pellets were frozen at -80oC until needed.  Cells were then lysed on ice with occasional vortexing in 1ml of lysis buffer (50mM Tris-HCl pH 7.4, 100mM NaCl, 1mM MgCl2, 0.1 mM CaCl2, 1% NP-40, 0.5% Sodium Deoxycholate, 0.1% SDS) containing 1X protease inhibitors (Roche #88665) and RNaseOUT (Invitrogen) at 4ul/ml final concentration.  Next, TurboDNase (10U), RNase A (0.66ug) and RNase T1 (0.66U) were added and samples were incubated at 37oC for 5 minutes with occasional mixing.  Samples were immediately placed on ice and then centrifuged at 16,160g at 4oC for 20 minutes to clear lysate.  25ul of Protein-G Dynabeads were used per IP.  Dynabeads were pre-washed with lysis buffer and pre-incubated with 3ul of Wako Anti-Mouse-Ago2 (2D4) antibody.  The dynabead/antibody mixture was added to the lysate and rocked for 2 hours at 4oC.  All steps after the IP were done on bead until samples were loaded into the polyacrylamide gel.  Beads were captured on a magnetic stand and the supernatant removed, then washed 3 times with cold High Salt Clip Wash Buffer (50mM Tris-HCl pH 7.4, 1M NaCl, 1mM EDTA, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS) for 3 minutes with rocking.  Samples were then washed 2 times with PNK wash buffer (20mM Tris-HCl pH 7.4, 10mM MgCl2, 0.2% Tween-20).  Samples were then phosphorylated at 37oC for 20 minutes in 50ul of PNK mixture: 41.8ul H2O, 5 ul 10X PNK buffer (NEB), 1 ul RNaseOUT, 1.67 ul ATP (30 mM), 0.5 ul T4 PNK - 3’ phosphatase minus (NEB M0236L).  Samples were then washed 3 times on a magnetic rack with PNK wash buffer.  miRNA-mRNA ligation was then carried out overnight at room temperature in 100ul of mixture: 49.25 ul H2O, 30 ul 50% PEG-8000, 10 ul 10X T4 RNA ligation buffer (NEB), 2.5 ul RNaseOUT, 1 ul ATP (100mM), 1 ul BSA (10 mg/ml), 6.25 ul T4 RNA ligase 1 (10U/ul – NEB M0204).  Next morning, an additional 2.5 ul T4 RNA ligase 1 (10U/ul) and 1 ul ATP (100mM) were added and ligation was continued for another 5 hours.  Samples were then washed 2 times with lysis buffer, once with PNK/EDTA/EGTA (50 mM Tris pH 7.4, 10 mM  EDTA, 10 mM EGTA, 0.5% Igepal) and twice more with PNK wash buffer.  Next, samples were treated with phosphatase at 37oC for 20 minutes with 50ul of mix: 41ul H2O, 5ul 10X FastAP buffer, 3ul FastAP enzyme (Thermo Fisher #EF0651) and 1ul RNaseOUT.  Samples were then washed two times with PNK wash buffer.  Next, 3’ adapter ligation was performed on beads overnight in 40 ul of mixture: 17ul H2O, 4ul 10X T4 RNA ligase buffer (NEB), 1ul of 3’linker (5’-Adenylated & 3’ blocked - custom ordered from IDT), 16ul 50% PEG-8000, 1 ul RNaseOUT and 1ul T4 RNA ligase 2 truncated K227Q (NEB M0351).  Samples were then washed twice with PNK buffer.  Next, samples were then radiolabeled on bead with 50ul of the following mix: 5 ul 10X PNK buffer (NEB), 1 ul RNaseOUT, 1.5 ul y-p32-ATP (15mCi), 1 ul PNK enzyme (NEB M0201) and 41.5 ul H2O.  Radiolabeling was carried out for 5 minutes at 37oC, after which another 2 ul of cold ATP (10mM) was added and the samples were then incubated for another 5 minutes at 37oC.  Samples were then washed three times with PNK buffer, and then re-suspended in 25 ul of 1.2X LDS NuPAGE Loading buffer (Thermo Fisher #NP0007) with 60 mM DTT added.  Samples were then heated to 70oC for 10 minutes with occasional agitation and supernatant was separated from beads on a magnetic stand.  Samples were loaded on an 8% Bis-Tris gel and run at 200V for 2 hours on ice.  Protein-RNA complexes were then transferred to nitrocellulose at 90V for 90min.  The membrane was washed with PBS and exposed to a phosphoscreen for 1 hour at -20oC.  Fragments corresponding to the Argonaute complex with the miRNA & mRNA (~110 kDa to 160 kDa) were then excised and RNA was isolated by the following method:  15 ul of Proteinase K at 20 mg/ml was added to 285 ul of Proteinase K/SDS buffer (100 mM Tris-HCl pH 7.5, 50 mM NaCl, 1 mM EDTA, 0.2% SDS).  This solution was heated to 37oC for 20 minutes to inactivate any RNases, added to nitrocellulose membrane fragments and incubated at 50oC for 1 hour.  Samples were briefly centrifuged and then 375 ul of saturated phenol/choloform/isoamyl alcohol (25:24:1) was added and incubated for 10 minutes at 37oC.  Samples were then centrifuged at 16,000g at room temperature for 3 minutes, the aqueous layer was removed to a new tube and precipitated overnight at -20oC with 2 ul Glycoblue (ThermoFisher #AM9516) and 900 ul of 100% ethanol.  RNA was pelleted by centrifugation at 16,160g at 4oC for 20 minutes and the supernatant removed.  Pellet was washed with 70% ethanol and left to air dry at room temperature for 5 minutes.  Next, 5’ adapters were ligated by adding 8ul of the following mix to the pellet and thoroughly resuspending: 2 ul 50% PEG-8000, 1ul 10X NEB RNA ligation buffer, 1 ul 10mM ATP, 4 ul H2O.  Samples were then heated briefly to 95oC, placed on ice and additional components were added: 0.5 ul RNaseOUT, 1 ul T4 RNA ligase 1 (10U/ul – NEB M0204), 0.5 ul 100 uM 5’ RNA linker (Blocked at 5’ end & contains NNNN at 3’ end for barcoding).  Ligation was carried out at 37oC for 4 hours with rocking.  RT-PCR was then carried out in ligation buffer by adding 8.5 ul of the following mix to the sample: 4 ul 5X first-strand buffer (Invitrogen), 1.5 ul 100mM DTT, 2ul 1 uM RT primer, 1 ul 10mM dNTPs.  Samples were heated to 65oC for 5 minutes, transferred to a PCR tube and then enzymes were added: 1 ul Superscript III (Thermo Fisher #18080093) and 0.5 ul RNaseOUT.  RT reaction was then performed in a thermocycler: 50oC for 1 hour, 85oC for 5 minutes, and then hold at 4oC.  Libraries were then amplified from the cDNA by PCR taking aliquots after cycles 12, 17 and 22.  PCR mix: 18.8 ul H2O, 8 ul 5X HF buffer (NEB), 1 ul 25 uM library 1st round forward primer, 1 ul 25 uM RT primer, 0.8 ul 10 mM dNTPs, 0.4 ul Phusion polymerase (NEB M0530) and 10 ul cDNA.  Cycling parameters: Initial denaturation at 98oC for 30 seconds and then amplification cycles at 98oC for 15 seconds, 56oC for 30 seconds and then 72oC for 20 seconds.  PCR products were run on a 9% acrylamide gel and then stained with SYBR gold (ThermoFisher #211494) at 1:10,000 for 10 minutes.  The area corresponding to approximately 73 to 150 base pairs was excised from the lowest cycles condition that showed a product.  Gel pieces were then frozen at -80oC for one hour and centrifuged through a hole in the tube made with a 20G needle to break up the gel.  400 ul HSCB buffer (25 mM Tris-HCl pH 7.5, 400 mM NaCl, 0.1% SDS) was added and samples were then rocked overnight at 4oC.  The next day the gel slurry was transferred to a 0.22 um filter tube and spun at 16,000g for 20 minutes at room temperature.  Samples were then precipitated overnight at -20oC in the presence of 1 ml 100% ethanol and 2ul Glycoblue.  The next day samples were centrifuged at 16,160g at 4oC for 20 minutes.  The pellet was washed with 70% ethanol and then air dried for 5 minutes.  The pellet was then resuspended in 20 ul of H2O.  Next, high throughput sequencing barcodes were added by PCR using the following mix: 10 ul previous PCR product, 3.84 ul H2O, 4 ul 5X HF buffer, 0.66 ul 10mM dNTPs, 0.5 ul 25 uM Illumina Index Primer, 0.5 ul 25 uM Illumina RP1 primer and 0.5 ul Phusion.  Cycling conditions: Initial Denaturation at 98oC for 30 seconds, 2 cycles of: 98oC for 15 seconds, 50oC for 20 seconds, 72oC for 45 seconds and then 4 cycles of: 98oC for 15 seconds and 72oC for 50 seconds and then a final extension at 72oC for 3 minutes.  PCR products were then run on a 9% acrylamide gel and stained with SYBR gold as above.  Products corresponding to sizes approximately 144-200

treatment_protocol: miR-200 inducible cells were treated with 3 ug/ml doxycycline for 24 hours before starting CLEAR-CLIP protocol.

tag: tissue

value: murine keratinocytes


title: Term validation Unstimulated [TUN]

source_name: Term validation Unstimulated_Monocytes

value: F


title: Preterm validation E. coli [PEC]

source_name: Preterm validation E. coli_Monocytes


title: H3_Der_CD3_FPKM

tag: treatment


title: Term validation S. epidermidis [TSE]

source_name: Term validation S. epidermidis_Monocytes


title: Set 2, Inducible 1


title: Term rep4 S. epidermidis [T11540SE]

description: processed data: FullRun_NormalisedData.csv

source_name: Term_S. epidermidis_Monocytes


title: Term rep4 E. coli [T11540EC]

source_name: Term_E. coli_Monocytes


title: Term validation E. coli [TEC]

source_name: Term validation E. coli_Monocytes


title: Term rep4 Unstimulated [T11540UN]


title: Set 2, DKO 3

source_name: miR-200 Double knockout keratinocytes grown in culture


title: Term rep3 Unstimulated [T11512UN]


title: Set 2, DKO 2


title: Set 2, Control 3

source_name: miR-200 Inducible keratinocytes grown in culture, but NOT induced


title: Set 2, DKO 1


title: Term rep2 S. epidermidis [T11510SE]


title: Term rep3 E. coli [T11512EC]


title: Term rep3 S. epidermidis [T11512SE]


title: Term rep2 E. coli [T11510EC]


title: Set 1, DKO 2


title: Set 2, Control 2


title: Set 1, DKO 3


title: Set 2, Inducible 2


title: Set 1, Control 5

source_name: K14-Cre Only keratinocytes grown in culture


title: Term rep1 Unstimulated [T11505UN]


title: Term rep2 Unstimulated [T11510UN]


title: Term rep1 E. coli [T11505EC]


title: Term rep1 S. epidermidis [T11505SE]


title: Set 1, Control 4


title: Preterm rep6 Unstimulated [P31353UN]


title: Set 1, Control 3


title: Set 1, Control 1


title: Set 1, Control 6


title: Set 1, Control 2


title: Preterm rep6 S. epidermidis [P31353SE]

source_name: Preterm_S. epidermidis_Monocytes


title: Set 2, Control 1


title: Preterm rep6 E. coli [P31353EC]

source_name: Preterm_E. coli_Monocytes


title: Set 1, DKO 1


title: Transgenic interfollicular epidermis pup 4

first: Jaimee

last: Hoefert

institute: University of Colorado Boulder

description:
Tg_ife4
Processed data file: normalized_matrix.txt

data_processing:
Adaptor sequences were trimmed, then mapped to mm10 genome using tophat.
Number of reads were counted using HTSeq count.
Normalized read counts were calculated with DESeq2.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_htseqcounts.txt: Tab-delimited text files include HTSeq values for each dataset.
Supplementary_files_format_and_content: Normalized_matrix.txt: Tab-delimited text file includes DESeq2 output for all datasets.

source_name: interfollicular epidermis, transgenic

extract_protocol:
Skin was removed and prepped for FACS; RNA was extracted using Trizol following sorting.
Libraries were prepared using the SMARTer® Stranded Total RNA Sample Prep Kit- Low Input Mammalian (Clontech, catalog #634861).

treatment_protocol: Pregnant females were fed doxycycline chow throughout pregnancy.

tag: strain/background

value: mixed

tag: genotype/variation

tag: age

value: skin

tag: sorting

value: interfollicular epidermis

tag: pup


title: Transgenic interfollicular epidermis pup 6

description:
Tg_ife6
Processed data file: normalized_matrix.txt

tag: cell type


title: Transgenic hair germ pup 6

description:
Tg_hg6
Processed data file: normalized_matrix.txt

source_name: hair germ, transgenic

value: hair germ


title: Transgenic hair germ pup 4

description:
Tg_hg4
Processed data file: normalized_matrix.txt


title: Preterm rep5 E. coli [P21347EC]


title: Preterm  rep5 Unstimulated [P21347UN]

source_name: Preterm _Unstimulated_Monocytes


title: Preterm rep4 E. coli [P11336EC]


title: Control interfollicular epidermis pup 3

description:
ctrl_ife3
Processed data file: normalized_matrix.txt

source_name: interfollicular epidermis, control


title: Preterm rep3 Unstimulated [P11150UN]


title: Preterm rep2 Unstimulated [P11103UN]


title: Control hair germ pup 3

description:
ctrl_hg3
Processed data file: normalized_matrix.txt

source_name: hair germ, control


title: Control interfollicular epidermis pup 5

description:
ctrl_ife5
Processed data file: normalized_matrix.txt


title: Preterm rep4 S. epidermidis [P11336SE]


title: Preterm rep2 E. coli [P11103EC]


title: Preterm rep1 Unstimulated [P11091UN]


title: Preterm rep1 S. epidermidis [P11091SE]


title: Preterm chorio rep5 Unstimulated [C11314UN]

source_name: Preterm chorio_Unstimulated_Monocytes


title: Preterm chorio rep4 S. epidermidis [C11170SE]

source_name: Preterm chorio_S. epidermidis_Monocytes


title: Preterm chorio rep3 Unstimulated [C11164UN]


title: Preterm chorio rep3 S. epidermidis [C11164SE]


title: Preterm chorio rep3 E. coli [C11164EC]

source_name: Preterm chorio_E. coli_Monocytes


title: Preterm chorio rep2 Unstimulated [C11125UN]


title: Preterm chorio rep2 E. coli [C11125EC]


title: Preterm rep4 Unstimulated [P11336UN]


title: Preterm rep5 S. epidermidis [P21347SE]


title: Preterm chorio rep5 S. epidermidis [C11314SE]


title: Preterm chorio rep1 Unstimulated [C11068UN]


title: Preterm chorio rep2 S. epidermidis [C11125SE]


title: Preterm chorio rep1 S. epidermidis [C11068SE]


title: Preterm chorio rep1 E. coli [C11068EC]


title: Preterm chorio rep4 Unstimulated [C11170UN]


title: Preterm rep2 S. epidermidis [P11103SE]


title: Preterm rep3 E. coli [P11150EC]


title: Y27_ExE_EPZ_RNA

city: Shanghai City

first: Naihe

last: Jing

address: Yueyang Road 320

institute: shanghai institute of biochemistry and cell biology

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Sequencing adapters, low quality sequences and amplification primers were trimmed from the raw sequencing reads.
For RNA-seq data, trimmed clean reads were aligned to mouse reference genome (mm10) using TopHat (v2.0.9) with the default parameters
For Bisulfite seq, the trimmed reads were mapped to mm10 mouse genome following our modified bisulfite sequencing pipeline.(H Guo et al, Nature Protocol 10(5):645-59)
For the ChIP-seq data, the trimmed reads were mapped to the mouse genome (mm10 assembly) using BWA sligner (version 0.7.5a-r405) with the options "-I 15 -q 10 -t 4"
Genome_build: mm10
Supplementary_files_format_and_content: The bigwig files for RRBS data include the DNA methylation level of each single CpG site. The tagAlign files show the bed files for aligned reads.

source_name: mouse embryos

growth_protocol: Embryo were collected from pregnant mice at 6.5, 7.0 and 7.5 dpc

extract_protocol:
RNA from embryo samples were extracted by 5M GuSCN (Invitrogen, # 20012-043), then RNA was precipitated by ethanol with the help of RNA carrier; Genomic DNA acquired from ChIP assay (H3K27me3, merck millipore, catlog number: 07-449, lot number: 2275589) of embryo samples were separated and extracted by microChIP. Genomic DNA acquired from embryos were separated and extracted followed by bisulfite sequencing
Libraries of genomic DNA were construted by using NEBNext Ultra DNA Library Prep Kit for Illumina (NEB #7370L); libraries of genomic DNA were construted by using NEBNext Ultra DNA Library Prep Kit for Illumina (NEB #7370L); libraries of single cell based bisulfite seq were constructed according to the protocol described in (H Guo et al, Nature Protocol 10(5):645-59).

treatment_protocol: For samples from Y25,Y26,Y27, the specific inhibitor of EZH2, EPZ005687 (Selleck, S7004), were added in the explant culture of mouse embryo. Embryos are cultured in N2B27 medium for 48 hrs. For samples from Y34, Y35, Y36, equivalent volume of DMSO were added as control group.

tag: strain

value: ICR


title: Y35_P_ctrl_RNA

value: DMSO


title: Y36_ExE_ctrl_RNA


title: Y25_A_EPZ_RNA

value: specific inhibitor of EZH2, EPZ005687 (Selleck, S7004)


title: Y34_A_ctrl_RNA


title: Y26_P_EPZ_RNA


title: Preterm chorio rep5 E. coli [C11314EC]


title: Preterm chorio rep4 E. coli [C11170EC]

value: M


title: E7-5-ExE-RRBS-rep2

tag: developmental stage

value: 7.5 dpc


title: E7-5-ExE-RRBS-rep1


title: E7-5-P-RRBS-rep1


title: E7-5-AM-RRBS-rep2


title: E7-5-A-RRBS-rep2


title: E7-0-ExE-RRBS-rep2

value: 7.0 dpc


title: E7-5-A-RRBS-rep1


title: E7-0-P-RRBS-rep2


title: E7-0-P-RRBS-rep1


title: E7-0-ExE-RRBS-rep1


title: E6-5-ExE-RRBS-rep1

value: 6.5 dpc


title: E6-5-ExE-RRBS-rep2


title: E6-5-Epi-RRBS-rep1


title: E7-0-A-RRBS-rep2


title: E7-0-A-RRBS-rep1


title: E7-5-AM-RRBS-rep1


title: E7-5-P-IP-K27me3

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Sequencing adapters, low quality sequences and amplification primers were trimmed from the raw sequencing reads.
For RNA-seq data, trimmed clean reads were aligned to mouse reference genome (mm10) using TopHat (v2.0.9) with the default parameters
For Bisulfite seq, the trimmed reads were mapped to mm10 mouse genome following our modified bisulfite sequencing pipeline.(H Guo et al, Nature Protocol 10(5):645-59)
For the ChIP-seq data, the trimmed reads were mapped to the mouse genome (mm10 assembly) using BWA sligner (version 0.7.5a-r405) with the options "-I 15 -q 10 -t 4"
Genome_build: mm10
Supplementary_files_format_and_content: the bigwig files for ChIP-seq include the H3K27me3 modification in each sample with merged data from two biological replicates.

source_name: K27me3 microChIP

value: embryo

tag: chip antibody

value: H3K27me3 (merck millipore, cat. 07-449, lot 2275589)


title: E7-5-P-IP-K27me3 rep2


title: E7-5-AM-IP-K27me3


title: E7-5-ExE-IP-K27me3 rep2


title: E7-5-A-IP-K27me3


title: E7-5-AM-IP-K27me3 rep2


title: E7-5-ExE-IP-K27me3


title: E7-5-P-RRBS-rep2


title: E7-0-P-IP-K27me3


title: E7-0-ExE-IP-K27me3 rep2


title: E6-5-ExE-IP-K27me3 rep2


title: E7-0-A-IP-K27me3 rep2


title: E7-0-A-IP-K27me3


title: E6-5-ExE-IP-K27me3


title: E6-5-Epi-RRBS-rep2


title: E6-5-Epi-IP-K27me3


title: E7-5-P-INPUT_rep2

source_name: genomic input sequencing


title: E6-5-Epi-IP-K27me3 rep2


title: E7-5-P-INPUT


title: E7-5-ExE-INPUT


title: E7-5-AM-INPUT_rep2


title: Control hair germ pup 5

description:
ctrl_hg5
Processed data file: normalized_matrix.txt


title: E7-5-ExE-INPUT_rep2


title: E7-5-A-INPUT_rep2


title: E7-0-ExE-INPUT_rep2


title: E7-0-P-INPUT_rep2


title: E7-0-ExE-IP-K27me3


title: E7-0-P-INPUT


title: E7-5-A-INPUT


title: E7-5-AM-INPUT


title: E7-0-P-IP-K27me3 rep2


title: E6-5-ExE-INPUT


title: E7-0-A-INPUT


title: E7-0-A-INPUT_rep2


title: E7-0-ExE-INPUT


title: E6-5-Epi-INPUT_rep2


title: E6-5-ExE-INPUT_rep2


title: W12/16_GF_5_DNA

city: Kiel

first: Wei-Hung

last: Pan

address: Rosalind-Franklin-Straße 12

department: Institute of clinical molecular biology

country: Germany

institute: Christian-Albrechts-Universität zu Kiel

data_processing:
For RNA-Seq, we used Tophat 2  and Bowtie 2  to align reads. Reads were mapped to mouse genome (MGI assembly version 10) using Tophat 2 program
Gene expression values of the transcripts were computed by HTSeq. DEseq2 was used to determine differentially expressed genes.
For RRBS, one sample form CONV-R W1 is excluded during quality control process, the reads from other 29 samples were mapped to mouse genome (MGI version 10) using Bismark.
We used Dispersion shrinkage for sequencing data (R package: DSS) to identify differentially methylated loci based on a beta-binomial regression model with ‘arcsine’ link function
Genome_build: mm10
Supplementary_files_format_and_content: For RNA-Seq, the txt files are generated from Htseq and the numbers in txt file are the reads count. For RRBS, cov files contain the information of chrosome, position, methylated reads, unmethylated reads and methylation rates.

source_name: IECs

extract_protocol:
RNA was isolated the purified small intestinal IECs using the TRIZOL method; DNA was isolated from purified IECs using DNeasy blood & tissue kit (Qiagen) according to manufacturer’s instructions.
RNA libraries were prepared using TruSeq v4 Kit (Illumina) according to manufacturer’s instructions. TrueMethyl®Seq Kit from Cambridge Epigenetix is used for RRBS library preparation.

tag: condition

value: germ-free mice (absence of microbiota)

tag: time point


title: E6-5-Epi-INPUT


title: W12/16_GF_3_DNA


title: W12/16_GF_2_DNA


title: W12/16_GF_1_DNA


title: W4_GF_5_DNA


title: W4_GF_4_DNA


title: W4_GF_3_DNA


title: W1_GF_4_DNA


title: W1_GF_5_DNA


title: W1_GF_3_DNA


title: W1_GF_2_DNA


title: W4_GF_1_DNA


title: W4_GF_2_DNA


title: W1_GF_1_DNA


title: W12/16_CONV-R_4_DNA

value: conventional-raised mice (presence of microbiota)


title: W12/16_CONV-R_3_DNA


title: W12/16_CONV-R_2_DNA


title: W12/16_CONV-R_1_DNA


title: W4_CONV-R_5_DNA


title: W4_CONV-R_4_DNA


title: W12/16_GF_4_DNA


title: W1_CONV-R_4_DNA


title: W1_CONV-R_5_DNA


title: W4_CONV-R_1_DNA


title: W4_CONV-R_2_DNA


title: W1_CONV-R_2_DNA


title: control 3

city: Mishima

first: Hajime

last: Okada

state: Shizuoka

address: Yata 1111

institute: National Institute of Genetics

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Sequenced reads were mapped to mm10 genome with Tophat with Bowtie2 as the aligner.
The abundance of each transcript model and statistical results were computed using DEseq2 based on UCSC genome annotation.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files generated using DEseq2

source_name: intrahepatic bile duct

extract_protocol:
Total RNA was extracted with Trizol reagent (Invitrogen).
Libraries were prepared from 4ng of total RNA with the SMARTer Ultra Low Input RNA Kit for Sequencing - v3 (Takara) and subsequently with the Nextera XT DNA Library Preparation Kit (Illumina) according to the manufacturer’s instructions.  These preparation included 10 cycles of preamiplification PCR and 7 cycles of enrichment PCR after tagmentation.

value: adult

tag: genotype

tag: stress

value: DDC injury for 1wk

value: biliary epithelial cells (BECs)


title: LKO 2


title: control 1


title: control 2


title: W12/16_GF_4_RNA


title: LKO 1


title: W12/16_GF_3_RNA


title: W12/16_GF_1_RNA


title: W12/16_GF_2_RNA


title: W4_GF_5_RNA


title: W4_GF_4_RNA


title: W12/16_CONV-R_5_DNA


title: W4_GF_3_RNA


title: W4_CONV-R_3_DNA


title: W4_GF_2_RNA


title: W1_GF_5_RNA


title: W1_CONV-R_3_DNA


title: W1_GF_4_RNA


title: W1_GF_2_RNA


title: W4_GF_1_RNA


title: W12/16_CONV-R_5_RNA


title: LKO 3


title: W12/16_CONV-R_3_RNA


title: W1_GF_1_RNA


title: W12/16_CONV-R_2_RNA


title: W12/16_CONV-R_1_RNA


title: W1_GF_3_RNA


title: W12/16_GF_5_RNA


title: W12/16_CONV-R_4_RNA


title: W4_CONV-R_4_RNA


title: W4_CONV-R_5_RNA


title: W4_CONV-R_2_RNA


title: W4_CONV-R_3_RNA


title: W1_CONV-R_4_RNA


title: W1_CONV-R_5_RNA


title: W1_CONV-R_3_RNA


title: W1_CONV-R_2_RNA


title: W4_CONV-R_1_RNA


title: W1_CONV-R_1_RNA