title: Ribosome profiling from 72min Replicate 2

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrück Center for Molecular Medicine

description:
Ribosome profiling (Ribo-seq)
RPallreads_counts_combined_CDS_filt.txt.gz
RPallreads_fpkm_CDS.txt.gz
RPlength21_counts_combined_CDS_filt.txt.gz
RPlength21_fpkm_CDS.txt.gz
RPlength29_counts_combined_CDS_filt.txt.gz
RPlength29_fpkm_CDS.txt.gz
RPlength30_counts_combined_CDS_filt.txt.gz
RPlength30_fpkm_CDS.txt.gz

data_processing:
Library strategy: Ribo-seq
Sequencing reads were demultiplexed and adapter-trimmed using flexbar (Dodt et al., 2012) and mapped to the hg19 version of the human genome using tophat2 (Kim et al., 2013) or to the NA construct sequences using bowtie2 (Langmead and Salzberg, 2012).
Only reads with mapping quality 24 or higher were kept, which also filtered out reads mapping to the constant regions at the beginning and end of the NA constructs. Non-coding genes and Histones were filtered out.
For ribosome profiling experiments, read lenghtes with high periodicity (21nt, 29nt, 30nt) were also counted separately. Sequencing reads per gene as annotated in the refSeq database were counted using quasR (Gaidatzis et al., 2015).
Translation efficiencies from readcounts were calculated using RiboDiff (Zhong et al., 2017)
Genome_build: hg19
Supplementary_files_format_and_content: tab separated values

source_name: Transfected HEK 293T cells

growth_protocol: HEK293T cells were grown in DMEM + 10%FCS

extract_protocol:
Cells were lysed in mammalian polysome buffer, digested with RNase I, loaded on a MicroSpin S-400 HR colum (GE Healthcare) and RNA was extracted using Trizol LS as described in Calviello et al. 2016 (doi:10.1038/nmeth.3688)
libraries were constructed as described in Calviello et al. 2016 (doi:10.1038/nmeth.3688)

treatment_protocol: Expression plasmids containing recoded neuraminidase genes have been transfected into HEK 293T cells for 24h

tag: na constructs


title: Ribosome profiling from 72min Replicate 1

status: Public on Jan 01 2020

type: SRA

country: Germany

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens


title: homozygotes of bar-1(ga80) 2

city: Medford

first: David

last: Angeles-Albores

state: MA

address: 61 Locust St

country: USA

institute: Northwestern University

description: bar-1(ga80lf) sample 2

data_processing:
Pseudo-alignment using Kallisto
Differential expression analysis using Sleuth
Genome_build: WBcel235
Supplementary_files_format_and_content: text files with target_id, length, eff_length, est_counts,  tpm  values

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: homozygotes of bar-1(ga80)

growth_protocol: Synchronized growth at 20C on ample OP50

extract_protocol:
Pick 30 worms, use Zymo RNA column to extract
RNA-Seq libraries were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #E7530) following manufacturer’s instructions.

tag: strain

tag: genotype/variation

tag: life stage

value: Young Adult (no eggs visible)


title: Mock-treated SH-SY5Y, rep 1 [NT1]

city: Sacramento

first: Julian

last: Halmai

state: CA

address: 2921 Stockton Blvd

department: Department of Neurology

institute: UC Davis

data_processing:
Sequencing reads were de-multiplexed and aligned to the Hg38 reference genome with STAR Universal Aligner version 2.5.3a using the following settings: Indexed Reference Genome: Ensembl reference genome and annotation files for Hg38 release 77 were downloaded and complied into a single file, Genome was indexed using the following arguments “STAR --runMode genomeGenerate --runThreadN 12 –genomeDir /STAR_INDEX_HG38 --genomeFastaFiles GRCh38_r77.all.fa --sjdbGTFfile Homo_sapiens.GRCh38.77.gtf --sjdbOverhang 149”; Sample Read Alignment: alignment of each sample’s reads was performed with the following arguments: “STAR --runThreadN 24 --genomeDir /STAR_INDEX_HG38 --outFileNamePrefix /STAR/SampleName_ --outSAMtype BAM SortedByCoordinate --outWigType bedGraph --quantMode TranscriptomeSAM GeneCounts --readFilesCommand zcat --readFilesIn Sample-R1.fastq.gz.gz Sample-R2.fastq.gz.gz”.
Differential Expression (DE) analysis was performed with DESeq2  in R Studio
Genome_build: hg38
Supplementary_files_format_and_content: .xlsx file containing normalized read counts per gene

source_name: Mock-treated SH-SY5Y

growth_protocol: SH-SY5Y cells were grown in DME/F12 media containing 20% FBS and 1% L-glut at 37C and 5%CO2

extract_protocol:
Cells were lysed with TriZol reagent and total RNA was extracted using the Direct-zol RNA Miniprep kit (Zymo Research)
Libraries were generated using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina according to protocol using 1ug of input RNA

treatment_protocol: Cells were transduced with lentivirus by protamine sulfate mediated transduction

tag: cell line

tag: treatment

value: non-transduced


title: WBJPE171125603

city: Hangzhou

first: Yixiao

last: Liu

state: 浙江

address: Yuhangtang road

country: China

institute: Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Single-cell RNA sequence reads were evaluated by FastQC
Bad reads were detected automatically and removed. Bases at 3' end of the read were further timmed by NGSQCToolkit if their PHRED quality score were less than 20.
The reads were mapped to the mm9 using bowtie2.
The mapped reads for genes were counted via Htseq.

organism: Mus musculus

source_name: skeleton muscle

extract_protocol:
Cells were isolated by preplating mehods (Nat. Protocols 3, 1501-1509 (2008)).
single cell were captured, lysated, preamplified and library prepared according to "Using the C1 High-Throughput IFC to Generate Single-Cell cDNA Libraries for mRNA Sequencing"

treatment_protocol: 563 mice skeletal muscle derived single cells were form  6~8 weeks old male C57BL/6 mice.

tag: tissue

value: mice skeletal muscle

tag: gender

value: male


title: miR155_40minInducedRNA

city: Berkeley

first: Timothy

middle: J

last: Eisen

state: CALIFORNIA

address: Stanley Hall

institute: UC Berkeley

description:
cytoplasmically-enriched RNA
continuous labeling time course

data_processing:
RPF and RNA-seq reads were mapped to ORFs of representative transcript models as described, which excluded the first 50 nt of each ORF to eliminate signal from ribosomes that initiated after adding cycloheximide (Eichhorn et al., 2014). PAL-seq tags were mapped to 3' UTRs of representative transcript models, and PAL-seq fluorescence intensities were converted to tail lengths according to the pipeline available on github (https://github.com/kslin/PAL-seq/tree/tailSeqPipeline); transcript models available for download (Eichhorn et al., 2014)
Illumina 1.5; Conventional base calls
filtered for only thosed that passed the chastity filter; removed first 8 nt of the read (randomized 5p adapter)
reads aligned with STAR v2.4.2: --alignIntronMax 1 --clip3pAdapterSeq TCGTATGCCGTCTTCTGCTTG --runThreadN 30 --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.04 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSJfilterReads Unique
assigned to features with intersectBed: -wb -s
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPM and RPKM values for each sample. PAL-seq processed files include tab-delimited files of reads.

molecule: cytoplasmic RNA

growth_protocol: Each 3T3 sample was grown or maintained according to standard protocols

extract_protocol:
RNA-seq and RPF libraries were constructed exactly as described in Subtelny et al., 2014 (GSE52809)
PAL-seq libraries were constructed and processed according to the methods.
For RNA-seq or RPF libraries, detailed protocols are available (Subtelny et al., 2014 and Bartel lab website. NEXTflex libraries were prepared according to the manufacturer's instructions. PAL-seq library construction is as follows: Tail-length standard mixes (1 ng of set 1 and 2 ng of set 2 for each 5-EU-selected sample, and twice these amounts for the steady-state sample), and trace 5′-radoiolabeled marker RNAs (Table S2) were added to each sample to assess tail-length measurements and ligation outcomes, respectively. Polyadenylated ends including those with a terminal uridine were ligated to a 3′-biotinylated adapter DNA oligonucleotide (1.8µM) in the presence of two splint DNA oligonucleotides (1.25µM and 0.25µM for the U and A-containing splint oligos, respectively, Table S2) using T4 Rnl2 (NEB) in an overnight reaction at 18 °C. Following 3′-adapter ligation the RNA was extracted with phenol-chloroform (pH 8.0), precipitated, resuspended in 1X RNA T1 sequence buffer (ThemoFisher), heated to 50°C for 5 min and then put on ice. RNA was subsequently captured on streptavidin beads, 5′ phosphorylated, and ligated to a 5′ adapter as described (Subtelny et al., 2014) but using a modified 5′ adapter sequence (Table S2). Following reverse transcription using SuperScript III (Invitrogen) with a barcode-containing DNA primer, cDNA was purified as described (Subtelny et al., 2014), except a 160–810 nt size range was selected. Libraries were amplified by PCR for 8 cycles using Titanium Taq polymerase according to the manufacturer’s protocol with a 1.5 min combined annealing/extension step at 57°C. PCR-amplified libraries were purified using AMPure beads (Agencourt, 40 µL beads per 50 µL PCR, two rounds of purification) according to the manufacturer’s instructions.

treatment_protocol: Cytoplasmically-enriched RNA was extracted, poly(A)-selected, randomly fragmented by partial alkaline hydrolysis and then size-selected RNA fragments were used for library preparation.

tag: cell line background

tag: microrna-inducible cell line

tag: time

tag: micrornainduction

value: TRUE

tag: libraryprepmethod

value: RNAseq matched to RPF


title: homozygotes of bar-1(ga80) 1

description: bar-1(ga80lf) sample 1


title: miR155_40minInduced_PAL_read1

data_processing:
Library strategy: PAL-seq
RPF and RNA-seq reads were mapped to ORFs of representative transcript models as described, which excluded the first 50 nt of each ORF to eliminate signal from ribosomes that initiated after adding cycloheximide (Eichhorn et al., 2014). PAL-seq tags were mapped to 3' UTRs of representative transcript models, and PAL-seq fluorescence intensities were converted to tail lengths according to the pipeline available on github (https://github.com/kslin/PAL-seq/tree/tailSeqPipeline); transcript models available for download (Eichhorn et al., 2014)
Illumina 1.5; Conventional base calls
filtered for only thosed that passed the chastity filter; removed first 8 nt of the read (randomized 5p adapter)
reads aligned with STAR v2.4.2: --alignIntronMax 1 --clip3pAdapterSeq TCGTATGCCGTCTTCTGCTTG --runThreadN 30 --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.04 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSJfilterReads Unique
assigned to features with intersectBed: -wb -s
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPM and RPKM values for each sample. PAL-seq processed files include tab-delimited files of reads.

value: PAL-seq


title: WBJPE171125598


title: homozygotes of bar-1(ga80) 3

description: bar-1(ga80lf) sample 3


title: miR155_2hrUninducedRPF

data_processing:
Library strategy: RPF
RPF and RNA-seq reads were mapped to ORFs of representative transcript models as described, which excluded the first 50 nt of each ORF to eliminate signal from ribosomes that initiated after adding cycloheximide (Eichhorn et al., 2014). PAL-seq tags were mapped to 3' UTRs of representative transcript models, and PAL-seq fluorescence intensities were converted to tail lengths according to the pipeline available on github (https://github.com/kslin/PAL-seq/tree/tailSeqPipeline); transcript models available for download (Eichhorn et al., 2014)
Illumina 1.5; Conventional base calls
filtered for only thosed that passed the chastity filter; removed first 8 nt of the read (randomized 5p adapter)
reads aligned with STAR v2.4.2: --alignIntronMax 1 --clip3pAdapterSeq TCGTATGCCGTCTTCTGCTTG --runThreadN 30 --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.04 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSJfilterReads Unique
assigned to features with intersectBed: -wb -s
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPM and RPKM values for each sample. PAL-seq processed files include tab-delimited files of reads.

value: FALSE

value: RPF


title: Ribosome profiling from 72Hmax/46med Replicate 1

value: 72Hmax and 46med


title: WBJPE171125597


title: WBJPE171125604


title: homozygotes of let-60(n1046gf) 1

description: let-60(n1046gf) sample 1

source_name: homozygotes of let-60(n1046gf)


title: miR155_2hrUninducedRNA


title: RNA from 27wt/72Lmax/27min (pilot experiment)

description:
polyA RNA from input lysate
RNA_Exp1_counts_combined_CDS_filt.txt.gz
RNA_Exp1_fpkm_CDS.txt.gz

data_processing:
Sequencing reads were demultiplexed and adapter-trimmed using flexbar (Dodt et al., 2012) and mapped to the hg19 version of the human genome using tophat2 (Kim et al., 2013) or to the NA construct sequences using bowtie2 (Langmead and Salzberg, 2012).
Only reads with mapping quality 24 or higher were kept, which also filtered out reads mapping to the constant regions at the beginning and end of the NA constructs. Non-coding genes and Histones were filtered out.
For ribosome profiling experiments, read lenghtes with high periodicity (21nt, 29nt, 30nt) were also counted separately. Sequencing reads per gene as annotated in the refSeq database were counted using quasR (Gaidatzis et al., 2015).
Translation efficiencies from readcounts were calculated using RiboDiff (Zhong et al., 2017)
Genome_build: hg19
Supplementary_files_format_and_content: tab separated values

value: 27wt, 72Lmax and 27min


title: Ribosome profiling from 72Hmax/46med Replicate 2


title: WBJPE171125596


title: mdt-12(bx93)/mdt-12(sy622) 3

data_processing:
Pseudo-alignment using Kallisto
Differential expression analysis using Sleuth
Genome_build: WBcel235
Supplementary_files_format_and_content: abundance files, txt
Supplementary_files_format_and_content: target_id       length  eff_length      est_counts      tpm

source_name: trans-heterozygotes


title: Ribosome profiling from 27wt/72Lmax/27min Replicate 1


title: miR155_2hrUninduced_PAL_read1


title: mdt-12(bx93)/mdt-12(sy622) 2


title: miR155_2hrInducedRPF


title: RNA from 72min Replicate 2

description:
polyA RNA from input lysate
RNA_counts_combined_CDS_filt.txt.gz
RNA_fpkm_CDS.txt.gz


title: WBJPE171125595


title: mdt-12(bx93)/mdt-12(sy622) 1


title: RNA from 72min Replicate 1


title: mdt-12(sy622) 3

source_name: homozygotes of the sy622 allele


title: Ribosome profiling from 27wt/72Lmax/27min Replicate 2


title: RNA from 72Hmax/46med Replicate 2


title: WBJPE171125593


title: miR155_2hrInducedRNA


title: WBJPE171125594


title: RNA from 72Hmax/46med Replicate 1


title: miR155_2hrInduced_PAL_read1


title: mdt-12(sy622) 2


title: miR155_1hrUninducedRPF


title: mdt-12(sy622) 1


title: mdt-12(bx93)/mdt-12(sy622) 4


title: RNA from 27wt/72Lmax/27min Replicate 2


title: WBJPE171125590


title: mdt-12(bx93) 3

source_name: homozygotes of the bx93 allele


title: WBJPE171125589


title: miR155_1hrUninducedRNA


title: mdt-12(bx93) 2


title: miR155_1hrUninduced_PAL_read1


title: RNA from 27wt/72Lmax/27min Replicate 1


title: miR155_1hrInducedRPF


title: miR155_1hrInducedRNA


title: mdt-12(bx93) 1


title: wild type control 3

source_name: wild type control sample

value: wild type


title: 83150_ICN-p53-Vav

city: Montreal

first: Möröy

last: Tarik

state: Quebec

address: 110 Pine avenue West

country: Canada

institute: Insititut de Recherches Cliniques

description: ICN induced T-ALL in Miz1 deltaPOZ expressing, p53 KO mouse

data_processing:
RNA-Seq reads were aligned to mm10 using Tophat v2.0.10
Reads were processed with Samtools.
For differential expression, countfiles were generated by mapping reads to Ensembl genes using HTSeq. Further analysis was carried out using the DESeq R package
Genome_build: mm10
Supplementary_files_format_and_content: txt files are tab-delimited text files containing counts on GRCm38 v77 Ensembl genes

source_name: T-ALL

extract_protocol:
RNA was extracted using a MagMax-96 Total RNA Isolation kit (Ambion) and quality-checked with a RNA 6000 Pico kit (Agilent).
RNA-Seq, libraries were prepared from RNA extracts using the TruSeq Stranded mRNA kit from Illumina according to the manufacturer’s instructions and sequenced using using the TruSeq PE Clusterkit v3-cBot-HS.

value: T cell acute lymphoblastic leukemia (T-ALL)

tag: icn induction

value: Yes

tag: miz1/p53 status

value: Miz1 deltaPOZ / p53 ko


title: WBJPE171125587


title: miR155_1hrInduced_PAL_read1


title: KO_10h_RNAseq_1

city: Chicago

first: Qili

last: Fei

state: Illinois

address: 929 E 57th Ave

institute: University of Chicago

data_processing:
After quality control and adapter trimming, readsd were mapped to the human genome hg19 using TopHat v2.1.0 allowing for no more than two mismatches.
For RNA-seq data, cuffnorm from the Cufflinks (v2.2.1) package was used for normalization and FPKM calculation
For RIP-seq data analysis, Cufflinks, combined with Cuffdiff, was employed to quantify gene expression and differential analysis.
For m6A-seq data analysis, the m6A-enriched regions in each m6A-IP sample were identified by MACS2 v2.1.0 with corresponding input library as control.
Genome_build: hg19
Supplementary_files_format_and_content: RNA-seq and RIP-seq data are in tab-delimited text files include RPKM values for each sample.

source_name: HeLa

growth_protocol: HeLa cells were maintained in DMEM (Gibco) with 10% fetal bovine serum and 1% penicillin/streptomycin in a humidified 37°C incubator with 5% CO2.

extract_protocol:
Total RNA was purified from cells with the TRIzol reagent. Polyadenylated RNA was purified from total RNA using the Dynabeads mRNA DIRECT kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HeLa cells were synchronized to G1/S phase using the double thymidine block based on a previous protocol (Ma and Poon, 2011). Cells were collected at indicated hours for each sample following release from the synchronization.

value: HeLa

tag: antibody

tag: genotype

value: YTHDF2 KO


title: WBJPE171125588


title: Jmjd2a-ChIP-seq

city: Taipei

first: Kuo-Hsuan

last: Hung

address: 128 Academia Road, Section 2

department: Genomics Research Center

country: Taiwan

institute: Academia Sinica

library_source: genomic

data_processing:
The sequencing quality of ChIP-Seq libraries was evaluated and assessed by FastQC.
Bowtie ( 0.12.7, Langmead et al., Genome Biol 10, R25 (2009)) was used to align the sequencing reads to the mouse genome. Mouse mm9 (UCSC Genome Browser) were used for gene annotation.
For determining the regulatory landscape and overall number of peaks, we used the Model-based Analysis of ChIP-seq (MACS) program version 1.4.2 (4). Jmjd2a- and Jmjd2c-bound genomic regions were mapped with default parameters, the effective genome size of 2,654,911,517 bp (mm9), and mixed with an anti-rabbit IgG input control sample. Peaks were filtered for p < 10-5. Finally, the Jmjd2a and Jmjd2c arenpmalized to input.
Genome_build: mm9
Supplementary_files_format_and_content: BED file

molecule: genomic DNA

source_name: B220+ B cells

growth_protocol: Mouse splenic B220+ B cells from mouse splenocytes were isolated by magnetic sorting with CD45R (B220) microbeads (Miltenyi Biotec).

extract_protocol:
Lysates were be prepared by the EZ-ChIP kit (EMD Millipore, Cat. #: 17-371), sequentially sonicated to obtain fragmanted DNA,  then complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions by using the DNA Sample Kit (Part# 0801-0303).

treatment_protocol: The purified B220+ B cells were stimulated with anti-mouse CD40 , IL-21 , and HEL.

tag: strain background

value: spleen

tag: cell type

value: splenic B220+ B cells

tag: chip antibody

value: anti-Jmjd2a (abcam, ab70786)


title: wild type control 2

tag: life stage

value: Young Adult (no eggs visible)

tag: genotype/variation


title: WT_10h_RNAseq_2

tag: cell line


title: WBJPE171125585

tag: tissue

value: mice skeletal muscle

tag: strain

value: male


title: WT_10h_RNAseq_1


title: KO_10h_RNAseq_2


title: miR1_4hrUninducedRPF

tag: cell line background


title: wild type control 1


title: KO_8h_RNAseq_2


title: WBJPE171125581

tag: gender


title: miR1_4hrUninducedRNA

tag: microrna-inducible cell line

tag: time

value: RNAseq matched to RPF


title: KO_8h_RNAseq_1


title: WBJPE171125580


title: WT_8h_RNAseq_2


title: miR1_4hrUninduced_PAL_read1

tag: micrornainduction

value: FALSE

tag: libraryprepmethod

value: PAL-seq


title: WBJPE171125586


title: WBJPE171125575


title: WT_8h_RNAseq_1


title: miR1_4hrInducedRPF

value: TRUE

value: RPF


title: miR1_4hrInducedRNA


title: miR1_4hrInduced_PAL_read1


title: WBJPE171125571


title: KO_6h_RNAseq_2


title: miR1_40minUninducedRPF


title: WBJPE171125569


title: WBJPE171125565


title: WT_6h_RNAseq_2

value: wild type


title: KO_6h_RNAseq_1


title: WBJPE171125592


title: WBJPE171125564


title: miR1_40minUninducedRNA


title: WT_6h_RNAseq_1


title: WBJPE171125560


title: KO_4h_RNAseq_2


title: WBJPE171125559


title: miR1_40minUninduced_PAL_read1


title: Tailbud mesoderm rep3

type: RNA

city: London

first: Ravindra

last: Prajapati

address: 123 Coldharbour Lane

country: United Kingdom

institute: King's college London

description:
TBM_R3
Replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The Illumina raw data were processed using the probe intensity transformation (VST) and normalization (RSN) methods from the Bioconductor package lumi (Du et al, 2008), with default settings. No background correction was applied.

label: Biotin

source_name: tail region E10.5 embryos

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: Embryos were collected from 10.5 days pregnanat Mus musculus females

extract_protocol: RNA were extracted using RNeasy Mini Kit (Qiagen Cat. No. 74104). The transcriptional profiling were carried out using Illumina “Ref6v2” beads arrays at the Genome Centre (Barts and the London Medical School, Blizzard Institute)

tag: developmental stage

value: embryo

tag: age

value: Tailbud mesoderm


title: WBJPE171125558


title: miR1_40minInducedRPF


title: KO_4h_RNAseq_1

tag: antibody

tag: genotype


title: miR1_40minInducedRNA


title: Presomitic mdesoderm rep2

description:
PSM_R2
Replicate 2

value: Presomitic mdesoderm


title: Presomitic mdesoderm rep3

description:
PSM_R3
Replicate 3


title: miR155_4hrUninducedRNA


title: WT_4h_RNAseq_2

value: HeLa


title: Presomitic mdesoderm rep1

description:
PSM_R1
Replicate 1


title: miR1_40minInduced_PAL_read1


title: WT_4h_RNAseq_1


title: Tailbud mesoderm rep2

description:
TBM_R2
Replicate 2


title: Chordoneural hinge rep2

description:
CNH_R2
Replicate 2

value: Chordoneural hinge


title: Tailbud mesoderm rep1

description:
TBM_R1
Replicate 1


title: Chordoneural hinge rep3

description:
CNH_R3
Replicate 3


title: miR1_2hrUninducedRPF


title: WBJPE171125555


title: KO_2h_RNAseq_1

value: YTHDF2 KO


title: WBJPE171125557


title: WBJPE171125554


title: miR1_2hrInducedRPF


title: WT_2h_RNAseq_2


title: miR1_2hrUninduced_PAL_read1


title: WBJPE171125553


title: WBJPE171125552


title: miR1_2hrInducedRNA


title: WT_2h_RNAseq_1


title: miR1_2hrInduced_PAL_read1


title: Fat-specific mitochondrial ferritin transgenic mice 2 (FtMT) post HFD feeding

city: Dallas

first: Philipp

middle: E

last: Scherer

state: Texas

address: 5323 Harry Hines Boulevard

department: Touchstone Diabetes Center, Internal Medicine

institute: The University of Texas Southwestern Medical Center

description:
Replicate 2
FtMT-2 HFD

data_processing: The data was normalized using quantile normalization

label: biotin

source_name: Murine adipose tissue

label_protocol: cDNA was prepared by the Genomics & Microarray Core Facility at UTSW. The MouseRef-8 v2 BeadChip was used. Web-link: https://microarray.swmed.edu/products/product/mouseref-8-v2-beadchip/

extract_protocol: Total RNA was extracting using Trizol reagent, followed by DNase I treatment using a Qiagen RNeasy kit, in accordance with the manufacturers' protocol. Quality control was performed using a Bioanalyzer.

value: FtMT-Adip

tag: diet

value: high-fat diet

value: 8-12 weeks old

value: Subcutaneous white adipose tissue


title: Wild-type control 2 post high-fat diet (HFD) feeding

description:
Replicate 2
WT2 HFD

value: Wild-type


title: WBJPE171125551

value: mice skeletal muscle

value: male


title: KO_0h_RNAseq_2


title: KO_0h_RNAseq_1


title: WBJPE171125556


title: WT_0h_RNAseq_2


title: TOX4_ISOL11

city: Philadelphia

first: Rebecca

last: Wells

state: PA

address: 905 BRB, 421 Curie Blvd.

department: Medicine

institute: University of Pennsylvania

description: Gene expression data from primary cholangiocytes from neonatal mice treated with plant toxin or DMSO.

hyb_protocol: Labeled cDNA was added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Mouse Gene 1.0 ST GeneChips

scan_protocol: A GeneChip 3000 7G scanner was used to collect fluorescence signal using default parameters

data_processing: Cel files were RMA normalized and batch corrected in Transcriptome Analysis Console (TAC) Software (v4.0.2, Thermo Fisher) with Isolation Group as batching variable.

source_name: Day 0-3 cholangiocytes

label_protocol: NuGEN Ovation Pico WTA system v2

growth_protocol: Primary neonatal mouse cholangiocytes at 20-22 days after isolation were split and replated; after 48 hours, they were treated as described.

extract_protocol: Qiagen RNeasy

treatment_protocol: 2.0 micrograms/ml of DMSO or a plant toxin in DMSO for 6 hours.

value: BALB/c

tag: treatment

tag: isolationbatch


title: TOX3_ISOL11


title: Fat-specific mitochondrial ferritin transgenic mice 1 (FtMT) post HFD feeding

description:
Replicate 1
FtMT-1 HFD

tag: genotype/variation


title: miR1_1hrUninducedRNA

value: FALSE

value: RNAseq matched to RPF


title: WT_0h_RNAseq_1

tag: cell line

value: wild type


title: Chordoneural hinge rep1

description:
CNH_R1
Replicate 1

value: embryo

tag: tissue


title: WBJPE171125547

tag: strain


title: Wild-type control 1 post high-fat diet (HFD) feeding

description:
Replicate 1
WT1 HFD


title: WBJPE171125545


title: Y2_RIP_IP_2

value: YTHDF2 antibody


title: CtlA4

city: Ann Arbor

first: Adam

last: Helms

state: MI

address: 7220 MSRB3, 1150 W. Medical Center Dr., SPC 5644

department: Internal Medicine

institute: University of Michigan

data_processing:
Illumina HiSeq 4000 reads
Reads aligned to genome using STAR (gene level)
Read counts per gene exported from STAR
Reads normalized to library size for each sample using DESeq2
Read counts controlled for technical and batch variability using RUVseq and housekeeping control gene set
Differential expression quantified using DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed data file containing read counts per gene from STAR

source_name: iPSC-derived cardiomyocytes

growth_protocol: iPSCs were differentiated using standard wnt signaling protocols. Cardiomyocytes were purified using magnetic bead sorting for the SIRPA cell surface marker.

extract_protocol:
Cells were collected in RLT buffer and RNA was extracted using the RNAeasy kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols (stranded, polyA library).

treatment_protocol: All cell lines were treated in the same way.

tag: cell type

value: iPSC-derived cardiomyocytes

value: control


title: miR1_1hrUninduced_PAL_read1

tag: cell line background

value: PAL-seq


title: WBJPE171125549

tag: gender


title: WBJPE171125538


title: DMSO_ISOL11

value: DMSO


title: miR1_1hrUninducedRPF

tag: microrna-inducible cell line

tag: time

value: RPF


title: TOX4_ISOL9


title: WBJPE171125534


title: Y2_RIP_IP_1

value: HeLa


title: miR1_1hrInducedRPF

tag: micrornainduction

value: TRUE

tag: libraryprepmethod


title: TOX3_ISOL9


title: Y2_RIP_input_2


title: TOX2_ISOL11


title: TOX2_ISOL9


title: WBJPE171125532


title: WBJPE171125531


title: Y2_RIP_input_1


title: DMSO_ISOL9


title: 8h_m6A_IP_2

description:
m6A-seq
m6A_8h_merged_peaks.xls

value: m6A antibody


title: directLig_miR1Uninduced_R0_PAL_read1

description:
cytoplasmically-enriched RNA
direct ligation (non-splint) steady state sample

value: Ss


title: WBJPE171125529

value: mice skeletal muscle


title: WBJPE171125527

value: male


title: 8h_m6A_IP_1

description:
m6A-seq
m6A_8h_merged_peaks.xls


title: TOX4_ISOL8

value: BALB/c


title: miR1_1hrInducedRNA


title: WBJPE171125526


title: directLig_miR155Induced_R0_PAL_read1


title: directLig_miR155Uninduced_R0_PAL_read1


title: WBJPE171125521


title: miR1_1hrInduced_PAL_read1


title: 4h_m6A_IP_2

description:
m6A-seq
m6A_4h_merged_peaks.xls


title: 8h_m6A_input_1

description:
m6A-seq
m6A_8h_merged_peaks.xls


title: actD_Total_eluate_read1

description:
cytoplasmically-enriched RNA
actd experimental time course sample

value: FALSE


title: actD_Total_eluate

value: RNA prepared with NEXT-flex kit


title: WBJPE171125520


title: directLig_miR1Induced_R0_PAL_read1


title: TOX2_ISOL8


title: 4h_m6A_IP_1

description:
m6A-seq
m6A_4h_merged_peaks.xls


title: WBJPE171125519


title: DMSO_ISOL8


title: TOX3_ISOL8


title: TOX4_ISOL7


title: 8h_m6A_input_2

description:
m6A-seq
m6A_8h_merged_peaks.xls


title: actD_7hr_input_PAL_read1


title: WBJPE171125518


title: 4h_m6A_input_1

description:
m6A-seq
m6A_4h_merged_peaks.xls


title: WBJPE171125515


title: actD_7hr_eluate_PAL_read1


title: 0h_m6A_IP_2

description:
m6A-seq
m6A_0h_merged_peaks.xls


title: actD_7hr_eluate


title: WBJPE171125513


title: 0h_m6A_IP_1

description:
m6A-seq
m6A_0h_merged_peaks.xls


title: actD_5EU_eluate


title: WBJPE171125514


title: TOX4_ISOL6


title: TOX2_ISOL7


title: 0h_m6A_input_2

description:
m6A-seq
m6A_0h_merged_peaks.xls


title: 4h_m6A_input_2

description:
m6A-seq
m6A_4h_merged_peaks.xls


title: actD_3hr_input_PAL_read1


title: TOX2_ISOL6


title: actD_7hr_input


title: WBJPE171125512


title: 0h_m6A_input_1

description:
m6A-seq
m6A_0h_merged_peaks.xls


title: DMSO_ISOL6


title: TOX3_ISOL7


title: DMSO_ISOL7


title: WBJPE171125511


title: actD_3hr_input


title: WBJPE171125510


title: actD_3hr_eluate_PAL_read1


title: PLC_shDIS3L2

city: Hefei

first: Songge

last: Xing

state: An Hui

address: No.443, Huangshan Road

department: School of Life Sciences

institute: University of Science and Technology of China

data_processing:
As to RNA-seq data, raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
clean reads were aligned to the reference genome hg19 using TopHat v2.0.12.
Cufflinks v2.2.1 was used to count the reads numbers mapped to each gene.
Data filtering parameters：Clean Parameter: SOAPnuke1.5.0 filter -l 5 -q 0.5 -n 0.1 -i -c 25 -Q 2 --seqType 1
Sequenced reads were mapped to the UCSC human genome hg19 using software TopHat v2.0.12.Aligned reads were used for Splicing Express and the detection of alternative splicing evnets.
Genome_build: hg19
Supplementary_files_format_and_content: fpkm

growth_protocol: Human hepatocellular carcinoma PLC cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) with 10% FBS. Cells were maintained in a water-jacketed incubator with 5% CO2 in 37 °C.

extract_protocol:
As to RNA-seq, total RNA was extracted using TRIZOL Reagent (Life technologies) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100.Qualified total RNA was further purified by RNeasy micro kit and RNase-Free DNase Set.Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
RNA-sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: shRNAs were purchased form Sigma. PLC cells were harvested after infecting with viruses containing shRNAs 48 hours.

value: PLC

value: Human hepatocellular carcinoma cells


title: PLC_shhnRNP U

source_name: Human hepatocellular carcinoma PLC cells

value: shhnRNP U


title: WBJPE171125507


title: PLC_NTC

value: NTC


title: TOX3_ISOL6


title: actD_3hr_eluate


title: WBJPE171125505


title: actD_1hr_input_PAL_read1


title: 1905_7d

city: Zurich

first: Nicola

last: Zamboni

state: Zurich

address: Institute of Molecular Systems Biology, Otto-Stern-Weg 3

country: Switzerland

institute: ETH Zurich

hyb_protocol: Agilent Standard Protocol

scan_protocol: Transcriptomics analysis was performed using Whole Human Genome Microarray 4x44K one-color chips (Agilent).

data_processing: Agilent Feature Extraction Software; data processing using LIMMA for R

source_name: Normal Human Epidermal Keratinocytes

label_protocol: Agilent Standard Protocol

growth_protocol: For transcriptomics analysis normal human epidermal keratinocytes (NHEK; Lonza) were cultivated in a humified atmosphere in KBM-2 Basal medium (Lonza) supplemented with KBM-2 SingleQuot Kit Supplements & Growth Factors (Lonza), 0.1 mM CaCl2 (Sigma-Aldrich) and 100 units/ml penicillin/streptomycin (Life Technologies), at 5 % CO2 and 37 °C.

extract_protocol: For microarray analysis RNA of four NHEKs of four individual donors treated for 0, 72 and 168 hours under high calcium conditions was extracted using miRVANA Kit miRNA Isolation Kit (Applied Biosystems).

treatment_protocol: For in vitro differentiation under high calcium conditions, keratinocytes were grown till they reached 80-90% confluency (high confluency) and then media was switched to high calcium media, i.e. media as described before supplement with 1 mM CaCl2 instead of 0.1 mM CaCl2 (Sigma-Aldrich).

tag: donor

value: 7 days


title: 3005_7d


title: WBJPE171125503


title: 2306_7d


title: actD_1hr_input


title: actD_1hr_eluate_PAL_read1

value: PAL-seq


title: SKNAS_shSOX9_0306

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

institute: ETH/University of Zurich

description: SK-N-AS cell was infected with pLKO.1 shSOX9 virus, and stable clone was generated by puromycin selection

data_processing:
bcl2Fastq v2.19 software used for demultiplexing + basecalling.
reads trimmed with trimmomatic, options: ILLUMINACLIP:adapters.fa:1:20:7:5:true AVGQUAL:10 MINLEN:20
reads mapped with STAR  v2.5.4b, options: --sjdbOverhang 150 --twopassMode None --runThreadN 8 --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --outMultimapperOrder Random --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif --outSAMattributes All --outStd BAM_Unsorted --outSAMtype BAM Unsorted
count: FeatureCounts (Bioconductor), options: allowMultiOverlap = true; countPrimaryAlignmentsOnly= true; minFeatureOverlap=10; minMapQuality= 10 ; keepMultiHits=true
differential expression analysis: EdgeR, options: normMethod = TMM; backgroundExpression =10; testMethod = glm; deTest =QL
Genome_build: Homo_sapiens/Ensembl/GRCh38.p10/Annotation/Release_91-2018-02-26
Supplementary_files_format_and_content: tad-delimited, raw counts

source_name: Neuroblasotma cell line

growth_protocol: Cell lines were culture in DMEM/F-12 medium(Thermo Fisher Scientific) supplemented with 10% fetal bovine serum(Dutscher), 1X L-glutamine(Thermo Fisher Scientific), 1X sodium pyruvate(Thermo Fisher Scientific), and 1X MEM non-essential amino acids(Thermo Fisher Scientific), and maintained in a humidified incubator at 37°C, 5% CO2.

extract_protocol:
Total RNA of harvested cells was extracted by RNeasy Kit (QIAGEN) according to manufacturer's instruction
RNA libraries were prepared for sequencing using standard Illumina protocols

value: SK-N-AS

value: Neuroblasotma cell line

value: SOX9 knockdown

tag: plasmid

value: pLKO.1 shSOX9


title: WBJPE171125498


title: SKNAS_shns_0306

description: SK-N-AS cell was infected with pLKO.shns virus, and stable clone was generated by puromycin selection

value: Control


title: WBJPE171125497


title: WBJPE171125500


title: SKNAS_shns_0302


title: SKNAS_shSOX9_0302


title: actD_15hr_input_PAL_read1


title: 0906_7d


title: WBJPE171125490


title: 1905_3d

value: 3 days


title: actD_15hr_input


title: KO_2h_RNAseq_2

value: HeLa

tag: antibody

tag: genotype

value: YTHDF2 KO


title: SKNAS_shns_0227


title: 0906_3d


title: 2306_3d


title: 3005_Control

value: 0 days


title: actD_1hr_eluate

value: FALSE


title: WBJPE171125485

value: mice skeletal muscle

value: male


title: WBJPE171125486


title: TET2 KO+ IFNγ 3-2

city: Chapel Hill

first: Yue

last: Xiong

state: NC

address: 450 West Dr

department: Linebeger Cancer Center

institute: UNC-Chapel Hill

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v2.3.2 with default parameters
Reads/counts  were calculated using R package 'Rsubread' from Liao et al, Nucleic Acids Research, 2019. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted .
Note: In final analysis, we excluded samples CL.1 (CL.1.1 and CL.1.2) after noticing that they look quite different with other CL samples
Genome_build: GRCH37/hg19
Supplementary_files_format_and_content: tab-delimited text file include raw count values (matrix table) for all Samples

source_name: Leukemic monocyte

growth_protocol: THP-1 cells were maintained in RPMI 1640 medium containing 10% FBS, 1% Penicillin/Streptomycin antibiotics, 2mM glutamine, 10mM HEPES and 1x non-essential amino acids.

extract_protocol:
Total RNA was extracted by RNeasy Plus Mini Kit (QIAGEN) according to the manufacturer’s instructions
Library preparation using Illumina TrueSeq mRNA sample preparation kit

treatment_protocol: WT or TET2 KO THP-1 cells were treated with or without 100ng/ml IFNγ for 20hrs

value: Leukemic monocyte

value: TET2 KO

tag: treatment

value: IFNγ


title: actD_15hr_eluate

value: RNA prepared with NEXT-flex kit


title: miR1_2hrUninducedRNA

value: RNAseq matched to RPF


title: actD_15hr_eluate_PAL_read1

value: PAL-seq


title: WBJPE171125483

data_processing:
Illumina Casava1.7 software used for basecalling.
Single-cell RNA sequence reads were evaluated by FastQC
Bad reads were detected automatically and removed. Bases at 3' end of the read were further timmed by NGSQCToolkit if their PHRED quality score were less than 20.
The reads were mapped to the mm9 using bowtie2.
The mapped reads for genes were counted via Htseq.

source_name: skeleton muscle


title: TET2 KO+ IFNγ 3-1


title: TET2 KO+ IFNγ 2-2


title: actD_0hr_input_PAL_read1


title: 1905_Control


title: 3005_3d


title: actD_0hr_input

data_processing:
RPF and RNA-seq reads were mapped to ORFs of representative transcript models as described, which excluded the first 50 nt of each ORF to eliminate signal from ribosomes that initiated after adding cycloheximide (Eichhorn et al., 2014). PAL-seq tags were mapped to 3' UTRs of representative transcript models, and PAL-seq fluorescence intensities were converted to tail lengths according to the pipeline available on github (https://github.com/kslin/PAL-seq/tree/tailSeqPipeline); transcript models available for download (Eichhorn et al., 2014)
Illumina 1.5; Conventional base calls
filtered for only thosed that passed the chastity filter; removed first 8 nt of the read (randomized 5p adapter)
reads aligned with STAR v2.4.2: --alignIntronMax 1 --clip3pAdapterSeq TCGTATGCCGTCTTCTGCTTG --runThreadN 30 --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.04 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSJfilterReads Unique
assigned to features with intersectBed: -wb -s
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPM and RPKM values for each sample. PAL-seq processed files include tab-delimited files of reads.


title: SKNAS_shSOX9_0227

value: SK-N-AS

value: Neuroblasotma cell line


title: WBJPE171125481


title: 2306_Control


title: 0906_Control


title: TET2 KO+ IFNγ 2-1


title: PAL-seq_actD_0hr_eluate_PAL_read1

data_processing:
Library strategy: PAL-seq
RPF and RNA-seq reads were mapped to ORFs of representative transcript models as described, which excluded the first 50 nt of each ORF to eliminate signal from ribosomes that initiated after adding cycloheximide (Eichhorn et al., 2014). PAL-seq tags were mapped to 3' UTRs of representative transcript models, and PAL-seq fluorescence intensities were converted to tail lengths according to the pipeline available on github (https://github.com/kslin/PAL-seq/tree/tailSeqPipeline); transcript models available for download (Eichhorn et al., 2014)
Illumina 1.5; Conventional base calls
filtered for only thosed that passed the chastity filter; removed first 8 nt of the read (randomized 5p adapter)
reads aligned with STAR v2.4.2: --alignIntronMax 1 --clip3pAdapterSeq TCGTATGCCGTCTTCTGCTTG --runThreadN 30 --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.04 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSJfilterReads Unique
assigned to features with intersectBed: -wb -s
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPM and RPKM values for each sample. PAL-seq processed files include tab-delimited files of reads.


title: TET2 KO+ IFNγ 1-2


title: WBJPE171125479


title: TET2 KO+ IFNγ 1-1


title: actD_0hr_eluate


title: WBJPE171125478


title: PM4

city: Beijing

first: Guangfa

last: Wang

address: No.8 Xishiku street

department: Respiratory and Critical care medicine

institute: Peking University First Hospital

description: PM2.5 exposed

data_processing:
bcl2fastq software used for base-calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2 program
Fragments Per Kilo bases per Million fragments (FPKM) were calculated using a protocol from Mortazavi et al., Nat. Methods,, 2008.
Genome_build: mm10
Supplementary_files_format_and_content: trans.xlsx: abundance measurements

source_name: PM2.5 exposed

extract_protocol:
Lungs were removed, snap frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. NEBNext Ultra RNA Library Prep Kit for Illumina (Cat#NEB-E7530S) was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were anesthetized and endotracheal instillation of 50μl saline or 5mg/kg body weight PM2.5 dissolved in the equal volume of saline was performed in the control group or PM2.5 treated group respectively once a week for consecutive eight weeks.

value: BALB/c

value: Lung

tag: age

value: 9 weeks


title: PM3

description: PM2.5 exposed


title: WBJPE171125476


title: CN4

description: saline exposed

source_name: saline exposed


title: WBJPE171125475


title: TET2 KO 2-2

value: control


title: TET2 KO 3-1


title: WBJPE171125480


title: TET2 KO 2-1


title: TET2 KO 3-2


title: WBJPE171125474


title: TET2 KO 1-2


title: CN3

description: saline exposed


title: WBJPE171125473


title: WBJPE171125477


title: WT plants under drought stress condition, biological rep2 [re-analysis]

city: Yangling

first: Kunming

last: Chen

state: Shaanxi

address: Xinong Road 22#

department: College of Life Sciences

institute: Northwest A&F University

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip rice genome arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 (P/N 00-00212, Affymetrix)

data_processing: The data were read with Command Console Software 3.1 (Affymetrix) and normalized using GeneSpring Software 11.0 (Agilent) and the MAS5.0 algorithm.  Data quality was assessed and statistical analysis was performed as described in the Affymetrix GeneChip Expression Analysis and Statistical Algorithms Description Documents. The data were analyzed using Student’s t-test.

organism: Oryza sativa

source_name: The youngest fully expanded leaves from 2.5-month-old WT plants under drought stress condition

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: After germination, rice seeds were transferred into a tray and watered daily with Hoagland’s nutrient solution. After 2 weeks, when the fourth leaf of each seedling had fully expanded, every four seedlings was transferred into a plastic pot, which were each filled with 12.5 kg of soil from a paddy field and cultivated in a greenhouse with a day/night temperature cycle of 36 ℃/28℃, light intensity of 800 μmol m-1 s-1, 16 h day/8 h dark, and 60%–65% relative humidity. The seedlings were watered at 2–3 d intervals to keep the soil submerged in water until the drought treatments were applied.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: For drought treatment, pairs of 10-week-old osnadk1 and WT plants were each grown in the same pot to ensure an identical water-stress condition. The youngest fully expanded leaf from each osnadk1 and WT plant was harvested 0 and 15 days after the commencement of the drought treatment. At these two time points, the soil moisture percentages were 47.3 ± 1.9% and 8.5 ± 2.1%, respectively.

tag: genotype background

value: Oryza sativa ssp. Japonica. cv. Dongjin

tag: genotype/variation

value: wild type

value: drought

value: fresh leaves


title: WT plants under drought stress condition, biological rep1 [re-analysis]

tag: tissue


title: WT plants under drought stress condition, biological rep3 [re-analysis]


title: WT plants under normal growth condition, biological rep1 [re-analysis]

source_name: The youngest fully expanded leaves from 2.5-month-old WT plants under normal condition

value: normal


title: WT plants under normal growth condition, biological rep2 [re-analysis]


title: WT plants under normal growth condition, biological rep3 [re-analysis]


title: PM2

description: PM2.5 exposed

tag: strain


title: osnadk1 mutant under drought stress condition, biological rep3

source_name: The youngest fully expanded leaves from 2.5-month-old osnadk1 plants under drought stress condition


title: osnadk1 mutant under normal growth condition, biological rep3

source_name: The youngest fully expanded leaves from 2.5-month-old osnadk1 plants under normal condition


title: osnadk1 mutant under drought stress condition, biological rep2


title: osnadk1 mutant under normal growth condition, biological rep2


title: TET2 KO 1-1

tag: cell line

tag: cell type

value: Leukemic monocyte


title: osnadk1 mutant under drought stress condition, biological rep1


title: WBJPE171125472

value: mice skeletal muscle

tag: gender

value: male


title: WBJPE171125471


title: W83G

city: Daqing

first: Jiang

last: Zhu

state: Hei Longjiang

address: Xinyang Road 39, Gaoxin District

institute: Daqing Branch of Harbin Medical University

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse genomes using the Illumina Genome Analyzer Pipeline.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Bowtie2.
Genome_build: mm10
Supplementary_files_format_and_content: fold-change, differential expression list

source_name: liver

extract_protocol:
Flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver


title: WT+ IFNγ 3-2

value: WT

value: IFNγ


title: WT+ IFNγ 3-1


title: WBJPE171125470


title: K85G


title: Lymphoma, long, 037A_S37

city: Toronto

first: Miles

last: Mee

address: 661 University Ave Suite 510

institute: Ontario Institute for Cancer Research

data_processing:
Reads aligned to CanFam3.1 reference genome with Hisat2  2.1.0
Gene annotation and expression with StringTie 1.3.3
Raw read counts calculated using prepDE .py from Ballgown R package
FPKM values calculated using the Ballgown R package
Genome_build: CanFam3.1 reference genome
Supplementary_files_format_and_content: Tab-delimited text files include either raw read count or FPKM values

organism: Canis lupus familiaris

source_name: Lymphoma

extract_protocol:
Qiagen Rneasy
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: Lymphoma

tag: immunophenotype

value: B-Cell

tag: survival

value: long


title: W90G


title: W81G


title: Lymphoma, long, 036A_S35

value: T-Cell


title: WT+ IFNγ 2-1


title: K84G


title: Lymphoma, short, 035A_S33

value: Unknown

value: short


title: WBJPE171125468

first: Yixiao

last: Liu

address: Yuhangtang road

institute: Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine

extract_protocol:
Cells were isolated by preplating mehods (Nat. Protocols 3, 1501-1509 (2008)).
single cell were captured, lysated, preamplified and library prepared according to "Using the C1 High-Throughput IFC to Generate Single-Cell cDNA Libraries for mRNA Sequencing"


title: Lymphoma, long, 038A_S39


title: WT+ IFNγ 2-2


title: WBJPE171125469


title: Lymphoma, long, 034A_S31


title: WT+ IFNγ 1-1


title: K82G


title: CN2

description: saline exposed

value: BALB/c

value: Lung

value: 9 weeks


title: WBJPE171125467


title: WBJPE171125466


title: Ago4-/- delNS1-infected rep 1

city: Boston

first: Kate

middle: L

last: Jeffrey

state: Massachusetts

address: 50 Blossom St, Thier 340

institute: Massachusetts General Hospital, Harvard Medical School

description: Supplementary table2.pdf

data_processing:
TrimGalore (v0.4.2) was used to remove Illumina sequencing adaptors, quality score cutoff = 20, stringency = 3, minimum read length = 18
Reads were then aligned to mouse genome build UCSC mm10 using TopHat2 (v2.1.1 with Bowtie2 v2.2.9) maximum mismatches = 2
Unmapped reads were then aligned to influenza genome using Tophat2, with maximum multihit = 1.
Read length distributions were obtained using custom python scripts.
Genome_build: H1N1 influenza (PR/8/1934)
Supplementary_files_format_and_content: Supplementary table2.pdf

source_name: mouse bone marrow derived macrophages

growth_protocol: Bone marrow was flushed from tibia and fibia and allowed to adhere to a non-treated plate for 1 day. Non-adherent cells were differentiated with 5ng/mL of IL-3 and M-CSF for 7 days

extract_protocol:
Cells UV Crosslinked, AGO IP, RNA extraced with Trizol
Libraries of small RNAs were constructed by a method depending on the 5′monophosphate of small RNAs, with a NEBNext Multiplex Small RNA Library Prep Set (Illumina) and sequenced on an Illumina HiSeq System.

treatment_protocol: Infected with  Influenza A (PR/8/1034) or A/PR/8/1934 ΔNS1 , MOI 1 for 24 hours

value: Influenza ΔNS1 (PR/8/1934, MOI 1) 24h

tag: ip antibody

value: pan Ago (2A8, Millipore)

value: Ago4 knockout


title: Lymphoma, long, 033A_S29


title: WBJPE171125465

city: Hangzhou

value: mice skeletal muscle


title: osnadk1 mutant under normal growth condition, biological rep1

value: Oryza sativa ssp. Japonica. cv. Dongjin

value: normal

value: fresh leaves


title: WT delNS1-infected rep 1

description: Supplementary table2.pdf

value: wild-type


title: Ago4-/- Influenza A  infected rep 2

description: Supplementary table2.pdf Ago4 (5) = Ago4 KO rep 2

value: Influenza (PR/8/1934, MOI 1) 24h


title: Lymphoma, short, 030A_S25

value: Lymphoma

value: B-Cell


title: WT 3-1

value: Leukemic monocyte

value: WT

value: control


title: WBJPE171125464

value: male


title: WT 2-2


title: Lymphoma, long, 031A_S27

value: Unknown

value: long


title: Lymphoma, short, 029A_S23

value: short


title: WBJPE171125463


title: WT 2-1


title: WBJPE171125462


title: WT Influenza A  infected rep 2

description: Supplementary table2.pdf WT (5) = WT rep2

value: pan Ago (2A8, Millipore)


title: Ago4-/- Influenza A  infected rep 1

description: Supplementary table2.pdf Ago4 (4) = Ago4 KO rep 1

value: Ago4 knockout


title: WT Influenza A  infected rep 1

description: Supplementary table2.pdf WT (4) = WT rep1


title: WT+ IFNγ 1-2

value: IFNγ


title: WT 1-2


title: Lymphoma, short, 028A_S21

value: T-Cell


title: Lymphoma, short, 027A_S19


title: WT 3-2


title: Ago4-/- mock

description: Supplementary table2.pdf

value: PBS


title: WT 1-1


title: WBJPE171125460

value: mice skeletal muscle


title: LPS+NaHS 3

city: Nanjing

first: xiawei

last: Zhang

address: Weigang NO.1

institute: National Center for International Research on Animal Gut Nutrition

data_processing:
The cleaved RNA fragments werereverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNASeqsample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-endlibraries was 300 bp (±50 bp).
And then we performed the paired-end sequencing on an IlluminaHiseq4000 at the (LC Sceiences,USA) following the vendor’s recommended protocol.
We aligned reads of sample A and sample B to the UCSC (http://genome.ucsc.edu/) homo sapiens reference genome using HISAT package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
Genome_build: UCSC (http://genome.ucsc.edu/) homo sapiens reference genome
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: colonic epithelial cells_LPS+NaHS

extract_protocol:
Total RNA of the Caco-2 cells was extracted using Trizol reagent (Invitrogen, CA, USA). The RNA quantity and purity were determined by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RNA integrity number >7.0.
The RNA was reverse-transcribed to create the cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA). The paired-end sequencing was performed on an Illumina X10 (LC Sceiences, USA) according to the standard protocol.

value: human epithelial colorectal adenocarcinoma cells

tag: passages

value: LPS+NaHS


title: Lymphoma, long, 026A_S17

value: Lymphoma


title: WBJPE171125459


title: LPS+NaHS 2


title: WT mock

description: Supplementary table2.pdf

value: wild-type


title: WBJPE171125458


title: Lymphoma, long, 025A_S15


title: LPS+NaHS 1


title: Lymphoma, short, 024A_S13


title: WBJPE171125455


title: Lymphoma, long, 022_S12

value: B-Cell


title: LPS 3

source_name: colonic epithelial cells_LPS

value: LPS


title: WBJPE171125457


title: Chen2008-25-EnhancerDeletion-150126-H4

city: Stanford

first: Jesse

last: Engreitz

address: 240 Pasteur Drive

institute: Stanford University

description: poly(A)+ RNA-seq with hybrid selection

data_processing:
RNA sequencing analyses were  initially aligned to both the 129S1 and Castanets genomes and reads were merged using pysuspenders, as described in Engreitz et al. Nature (2016). For RNA-seq experiments, reads mapping to specifically to the 129 or Castaneus alleles were counted for each gene (including any read overlapping an intron or exon).
Genome_build: mm9
Supplementary_files_format_and_content: Text file including counts from 129 and Castaneus alleles for each of the genes in the hybrid selection pool

source_name: F1 2-1 129/Castaneus Female mESCs

growth_protocol: Female ES cells were grown on plates coated with 0.2% gelatin and 3.5 ug/mL laminin in serum-free 2i/LIF media composed as follows:  1:1 mix of DMEM/F-12 (Gibco) and Neurobasal (Gibco) supplemented with 1X N2 (Gibco), 0.5X B-27 (Gibco 17504-044), 2 mg/mL bovine insulin (Gemini BioSciences), 1.37 ug/mL progesterone (Sigma), 5 mg/mL BSA Fraction V (Gibco), 0.1 mM 2-mercaptoethanol (Sigma), 5 ng/mL murine LIF (GlobalStem), 0.1 uM PD0325901 (Axon Medchem 1408) and 0.3 uM CHIR99021 (University of Dundee Division of Signal Transduction Therapy).

extract_protocol: p(A)+ RNA-seq with hybrid selection: We generated RNA sequencing + hybrid selection libraries as described in Engreitz et al. Nature (2016) — samples were prepared in parallel with samples in GSE 85798

value: embryonic stem cell

value: female


title: WBJPE171125454

value: male


title: LPS 2


title: WBJPE171125461


title: Lymphoma, long, 017_S11

value: long


title: Chen2008-25-EnhancerDeletion-150126-G2

description: poly(A)+ RNA-seq with hybrid selection


title: Chen2008-25-EnhancerDeletion-150126-H2

description: poly(A)+ RNA-seq with hybrid selection


title: Lymphoma, long, 016_S10


title: WBJPE171125452


title: Chen2008-25-EnhancerDeletion-150126-E6

description: poly(A)+ RNA-seq with hybrid selection


title: Lymphoma, long, 012_S9


title: Chen2008-25-EnhancerDeletion-150126-B4

description: poly(A)+ RNA-seq with hybrid selection


title: Chen2008-25-EnhancerDeletion-150126-C4

description: poly(A)+ RNA-seq with hybrid selection


title: Lymphoma, short, 009_S8

value: short


title: NaHS 3

source_name: colonic epithelial cells_NaHS

value: NaHS


title: LPS 1


title: NaHS 2


title: WBJPE171125451


title: Chen2008-1-EnhancerDeletion-150126-H7

description: poly(A)+ RNA-seq with hybrid selection


title: NaHS 1


title: Lymphoma, long, 006_S6


title: WBJPE171125450


title: Chen2008-1-EnhancerDeletion-150126-G3

description: poly(A)+ RNA-seq with hybrid selection


title: WBJPE171125449


title: Lymphoma, long, 005_S5


title: WBJPE171125446


title: Lymphoma, long, 003A_S3


title: Lymphoma, long, 008_S7


title: WBJPE171125447


title: Lymphoma, long, 002_S2


title: control 1

source_name: colonic epithelial cells_control

value: control


title: WBJPE171125445


title: Chen2008-1-EnhancerDeletion-150126-D2

description: poly(A)+ RNA-seq with hybrid selection


title: Lymphoma, short, 001_S1


title: G164_Adh_r3

first: Eleni

last: Maniati

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

institute: Queen Mary University of London

description:
24h - adherent flask. DMEM/F12 + 10% FBS
RPKM_cqn_monocultures.txt

data_processing:
RNA-Seq reads were mapped to the human genome (hg19, Genome Reference Consortium GRCh37)  using BWA mem (version 0.7.15-r1140) as part of the Oxford Genomics Centre pipeline.
Number of reads aligned to the exonic region of each gene were counted using htseq-count based on the Ensembl annotation.
Genes that achieved at least one read count per million reads (CPM) in at least 25% of the samples were kept. Conditional quantile normalisation (cqn) was performed counting for gene length and GC content and the log2 RPKM expression matrix was generated
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include log2 RPKM values for each Sample

source_name: G164 Adherent

growth_protocol: DMEM/F12 (Gibco, UK)

extract_protocol:
RNA was prepared from cell cultures using the RNeasy Mini Kit and the RNase free DNase set (Qiagen)
Extracted RNA samples were sent to the Oxford Genomics Centre for processing. Library preps were made using RNA-Seq Ribozero kits (Illumina, Inc)

treatment_protocol: SB431542 and GANT61 (Sigma-Aldrich, UK)

tag: cell types

tag: culture type

value: 2D adherent - monoculture

value: Untreated


title: WBJPE171125443


title: Chen2008-1-EnhancerDeletion-150126-B8

description: poly(A)+ RNA-seq with hybrid selection


title: WBJPE171125444


title: Chen2008-1-EnhancerDeletion-150126-D10

description: poly(A)+ RNA-seq with hybrid selection


title: Chen2008-1-EnhancerDeletion-150126-E7

description: poly(A)+ RNA-seq with hybrid selection


title: control 2


title: HSV-1_EPZ6438_RNAseq_rep1

city: Wuhan

first: gao

last: chuan

state: Hubei province

address: bayi road

department: College of life science

institute: Wuhan university

data_processing:
The sequenced reads were first quality-controlled using FASTQC software and then the reads with low-quality were removed with Cutadapt software.
The reads were then mapped to the HSV-1 reference genome (GenBank: JN555585.1) using Bowtie2 with default parameters. Samtools was used to screen out the reads that were uniquely mapped to the HSV-1 genome.
Bedtools was used to quantify the mapped reads across the HSV-1 genome.
The data were normalized by the total number of mapped reads to host genomes and virus copy number of each time point.
Genome_build: HSV-1 reference genome (GenBank: JN555585.1)
Supplementary_files_format_and_content: bigwig files were generated using bdg2bw;Tab-delimited text files include count values for each RNA-Seq sample.

organism:
Homo sapiens
Human alphaherpesvirus 1

extract_protocol:
Total RNA was extracted by using EASYspin RNA Mini Kit (Aidlab RN07). Briefly, tissue was triturated by trituration equipment for 20 s in lysis buffer provided by kit and then centrifuged at 12000 rpm, 4℃ for 5 min. Liquid between precipitates on the bottom and oil on the top was taken out and pipetted 10 times using 1 mL syringe. Entire volume of liquid was added into adsorption column and total RNA eluted with 50 μL RNase-free water. RNA-seq libraries were constructed by NEBNext Poly (A) mRNA Magnetic Isolation Module (NEB E7490) and NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module (NEB E6111). Briefly, poly-A mRNA was prepared with poly-T magnetic beads and transformed into cDNA with first and second strand synthesis. Newly synthesized cDNA were purified by AMPure XP beads (1:1) and eluted in 50 μL nucleotide-free water.
RNA-seq libraries were the same as ChIP-seq library construction described previously except the sequencing depth of 20 million reads per library. RNA-seq libraries were sequenced by Illumina Hiseq X Ten platform with pair-end reads of 150 bp.

tag: host cell line

tag: host cell type

value: monocyte

value: peripheral blood

tag: disease

value: acute monocytic leukemia

value: HSV-1 infect 4h + EPZ6438 4h


title: HSV-1_EPZ6438_RNAseq_rep2

tag: treatment


title: WBJPE171125448

value: mice skeletal muscle


title: G164_Adh_r2


title: SKM_iPSC

city: San Francisco

first: Sheng

last: Ding

address: 1650 Owens Street

institute: Gladstone Institute for Cardiovascular Disease

data_processing:
Total RNA of samples at the indicated times were used for sequencing. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) and then sequenced using Illumina HiSeq 2500 platform and 150 bp paired-end (PE150) reads were generated.
Before alignment, low quality reads and those containing adapter or poly-N were removed using FastQC. The remaining reads were mapped to the assembly mm9 genome using the default parameters in STAR (v2.5.1b) aligner. The read count files which produced by STAR have been merged into the gene expression file.
Genome_build: mm9
Supplementary_files_format_and_content: excel file include raw read count values for each Sample

source_name: SKM iPSC

growth_protocol: MEF cells are cultured in DMEM+10%FBS+1%NEAA, and mESCs and iPSCs are cultured in mESC medium. Reprogramming cells were cultured in mouse ES medium in presence of doxycycline.

extract_protocol:
For cultured cells, total RNA was extracted with RNeasy Plus mini kit (Qiagen, 74136) with QiaShredder (Qiagen, 79656). For sorted cells, samples at the indicated time points were collected and lysed in TRIzolTM Reagent (Invitrogen, 15596026).
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB), according to the manufacturer’s instructions. A total amount of 2µg RNA per sample was used as input material for library preparation. The library fragments were purified with QiaQuick PCR kits (Oiagen, 28106), quality-controlled by Bioanalyzer 2100 and quantified by qPCR.

tag: sample stage

value: SKM iPSC


title: WBJPE171125442

source_name: skeleton muscle

tag: tissue


title: HSV-1_C646_RNAseq_rep2

value: HSV-1 infect 4h + C646 4h


title: Chen2008-1-EnhancerDeletion-150126-E3

description: poly(A)+ RNA-seq with hybrid selection


title: HSV-1_C646_RNAseq_rep1


title: WBJPE171125441

tag: strain


title: G164_Adh_r1

city: London


title: R1_ESC

source_name: R1 mouse ESC

value: R1 mouse ESC


title: WBJPE171125440


title: NPC_D12_GFP_2

source_name: SKM secondary NPC

value: Day 12 of SKM NPC reprogramming


title: NPC_D12_GFP_1


title: HSV-1_DMSO_RNASeq_rep2

description: HSV-RNA-DMSO.bw

value: HSV-1 infect 4h + DMSO 4h


title: RC2

description:
Malignant cell and fibroblast co-cultured in COL1-gels were embedded into adipocyte gels at 7 days, then after a further 24 hours were treated with vehicle for a further 13 days.  Growth medium was DMEM/F12 with 10% FBS and 50 ug/ml Ascorbic-acid-2-phosphate.
RPKM_cqn_tricultures.txt

source_name: 3D-triculture plus vehicle

value: G164, primary omental adipocytes and fibroblasts

value: 3D triculture

value: 0.2 % v/v DMSO


title: WBJPE171125439

value: male


title: control 3

tag: cell line

value: human epithelial colorectal adenocarcinoma cells

value: control


title: HSV-1_DMSO_RNASeq_rep1

description: HSV-RNA-DMSO.bw


title: RC1


title: WBJPE171125438


title: HSV-1_24H_RNASeq_rep2

description:
HSV-RNA-24h.bw
HSV-RNA-24h-count.txt

value: HSV-1 infect 24h


title: NPC_D8_GFP_2

value: Day 8 of SKM NPC reprogramming


title: RI2

description:
Malignant cell and fibroblast co-cultured in COL1-gels were embedded into adipocyte gels at 7 days, then after a further 24 hours were treated with the inhibitor combination for a further 13 days.  Growth medium was DMEM/F12 with 10% FBS and 50 ug/ml Ascorbic-acid-2-phosphate.
RPKM_cqn_tricultures.txt

source_name: 3D-triculture plus inhibitors

value: SB431542 (20 uM) and GANT61 (7.5 uM) both in DMSO


title: RB

description:
Adipocyte gels were cultured for 8 days and then were treated with vehicle for a further 13 days.  Growth medium was DMEM/F12 with 10% FBS and 50 ug/ml Ascorbic-acid-2-phosphate.
RPKM_cqn_tricultures.txt

source_name: adipocytes only plus vehicle

value: Primary omental adipocytes

value: 3D adipocytes


title: HSV-1_24H_RNASeq_rep1

description:
HSV-RNA-24h.bw
HSV-RNA-24h-count.txt

value: monocyte

value: peripheral blood

value: acute monocytic leukemia


title: WBJPE171125436

value: mice skeletal muscle


title: HSV-1_8H_RNASeq_rep2

description:
HSV-RNA-8h.bw
HSV-RNA-8h-count.txt

value: HSV-1 infect 8h


title: WBJPE171125437


title: NPC_D8_GFP_1


title: WBJPE171125435


title: NPC_D4_1

value: Day 2 of SKM NPC reprogramming


title: RI1

description:
Malignant cell and fibroblast co-cultured in COL1-gels were embedded into adipocyte gels at 7 days, then after a further 24 hours were treated with the inhibitor combination for a further 13 days. Growth medium was DMEM/F12 with 10% FBS and 50 ug/ml Ascorbic-acid-2-phosphate.
RPKM_cqn_tricultures.txt

value: G164, primary omental adipocytes and fibroblasts


title: NPC_D2_2

value: Day 0 of SKM NPC reprogramming


title: HSV-1_8H_RNASeq_rep1

description:
HSV-RNA-8h.bw
HSV-RNA-8h-count.txt


title: WBJPE171125433


title: RPE-LINE1-H

city: Baltimore

first: Daniel

last: Ardeljan

address: 733 N Broadway, MRB 432

institute: Johns Hopkins University School of Medicine

description:
poly-A-selected stranded library prep
DESeq2_LINE1_vs_Luciferase.txt
htseq_output_with_stat_summary.txt
93_H_S47

data_processing:
CRISPR KO reads aligned to Brunello Index using Bowtie.
CRISPR KO counts processed with MAGeCK.
RNAseq reads aligned with STAR (hg38), counted with HTSeq, and differential expression was performed with DESeq2.
Genome_build: hg38 or Brunello Index (https://www.addgene.org/pooled-library/broadgpp-human-knockout-brunello/). Brunello citation PMID: 26780180
Supplementary_files_format_and_content: All are .txt files. The DESeq2 file contains differential expression data for cells expressing LINE-1 vs. Luciferase that is standard output from the DESeq2 program. The 'htseq_output_with_stat_summary.txt' file includes the RNA-seq differential expression analysis table to accompany the reads. The MAGeCK files contain screen count data normalized to non-target-controls, as generated by the MAGeCK program.

growth_protocol: RPE cell lines are grown in DMEM/F12 supplemented with sodium bicarbonate and 10% FBS at 37C and 5% CO2. Tet-Free FBS is used in Tet-On expression systems. Tet-On expression systems also require 400 ug/ml G418 and Cas9-expressing cells require 10 ug/ml Blasticidin.

extract_protocol: RNA was isolated using the Quick-RNA microprep kit from Zymo. RNAseq libraries were prepared using the TruSeq stranded mRNA preparation kit from Illumnia (Cat #20020594).

tag: cell type

tag: expression method

value: Tet-On LINE-1

value: cells were treated with doxycycline to induce LINE-1 or Luciferase.


title: HSV-1_4H_RNASeq_rep2

description:
HSV-RNA-4h.bw
HSV-RNA-4h-count.txt

value: HSV-1 infect 4h


title: NPC_D2_1


title: RPE-LINE1-G

description:
poly-A-selected stranded library prep
DESeq2_LINE1_vs_Luciferase.txt
htseq_output_with_stat_summary.txt
93_G_S46


title: HSV-1_4H_RNASeq_rep1

description:
HSV-RNA-4h.bw
HSV-RNA-4h-count.txt


title: WBJPE171125431

tag: gender

value: male


title: RPE-LINE1-F

description:
poly-A-selected stranded library prep
DESeq2_LINE1_vs_Luciferase.txt
htseq_output_with_stat_summary.txt
93_F_S45


title: HSV-1_2H_RNASeq_rep2

description:
HSV-RNA-2h.bw
HSV-RNA-2h-count.txt

value: HSV-1 infect 2h


title: RPE-luciferase_C

description:
poly-A-selected stranded library prep
DESeq2_LINE1_vs_Luciferase.txt
htseq_output_with_stat_summary.txt
91_C_S44

value: Tet-On Luciferase


title: NPC_D4_2


title: NPC_D0_1


title: HSV-1_2H_RNASeq_rep1

description:
HSV-RNA-2h.bw
HSV-RNA-2h-count.txt


title: MEF_D12_GFP_2

source_name: SKM secondary MEF

value: Day 12 of SKM MEF reprogramming


title: RPE-luciferase_B

description:
poly-A-selected stranded library prep
DESeq2_LINE1_vs_Luciferase.txt
htseq_output_with_stat_summary.txt
91_B_S43


title: WBJPE171125429


title: HSV-1_1H_RNASeq_rep2

description:
HSV-RNA-1h.bw
HSV-RNA-1h-count.txt

value: HSV-1 infect 1h


title: RPE-luciferase_A

description:
poly-A-selected stranded library prep
DESeq2_LINE1_vs_Luciferase.txt
htseq_output_with_stat_summary.txt
91_A_S42


title: MEF_D12_GFP_1


title: WBJPE171125432


title: WBJPE171125427


title: WBJPE171125425


title: HSV-1_1H_RNASeq_rep1

description:
HSV-RNA-1h.bw
HSV-RNA-1h-count.txt


title: WBJPE171125424


title: INPUT_HSV-1_24H_ChIPSeq_rep2

data_processing:
The data quality of each sample was controlled using the FASTQC tool and then the reads with low-quality score was removed with Cutadapt tool.
The resulted reads were then mapped to the HSV-1 reference genome (GenBank: JN555585.1) using the Bowtie2 read mapper with default parameters and only uniquely mapped reads were kept by Samtools for further analysis.
Bedtools software was used to calculate histone modifications signals on HSV-1 genome.
The histone modifications were normalized by the total mapped data to the host genome and further divided by the copy number at the corresponding time point.
Genome_build: HSV-1 reference genome (GenBank: JN555585.1)
Supplementary_files_format_and_content: bigwig files were generated using bdg2bw

extract_protocol:
Briefly, approximately 1×10^7 cells were fixed with 1% formaldehyde for 10 min and quenched by glysine. The cells were washed three times with PBS, then harvested in ChIP lysis buffer (50 mM Tris-HCl, pH7.6, 1 mM CaCl2, 0.2% Triton X-100) and incubated for 5 min with gently rotation. After centrifugation at 12000 rpm at 4℃ for 2 min, lysates were washed once by digestion buffer (50 mM Tris-HCl pH 8.0, 1 mM CaCl2, 0.2% Triton X-100). Then lysates were incubated in 630 μL digestion buffer with 1 μL MNase (NEB, M0247S) at 37℃ for 20 min and then quenched with 8 μL 0.5 M EDTA. Whole lysates were sonicated for 5 min (0.5 s on / 0.5 s off, 25% power) and the supernatants were taken out after centrifugation at 12000 rpm, 4℃ for 10 min. Immunopreciptation was performed with 150 μL sheared chromatin, 2 μg antibody, 50 μL Protein G sepharose beads and 800 μL dilution buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS) overnight at 4℃. The immunocomplexes were washed once each with Wash buffer I (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), Wash buffer II (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS) and Wash buffer III (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% Na-deoxycholate, 1% NP-40), and twice with TE (10mM Tris-HCl pH 8.0, 1mM EDTA). The bound materials were eluted twice with 100 μL elution buffer (1% SDS, 0.1M NaHCO3) and 1μL Proteinase K (20 mg/mL) at room temperature for 10 min. Eluted materials were incubated at 65℃ for 6 hr and then purified with DNA purification kit (TIANGEN DP214-03).
ChIP-seq libraries were constructed by VATHS Universal DNA Library Prep Kit for Illumina (Vazyme ND604). Briefly, 50 μL purified ChIP DNA (8-10 ng) was end-reparied for dA tailing, followed by adaptor ligation. Each adaptor marked with a barcode of 6 bp which can be recognized after mixing different sample together. Adaptor-ligated ChIP DNA was purified by AMPure XP beads (1:1) and then amplifying by PCR of 11-13 cycles with the primer matching with adaptor universal part. Amplified ChIP DNA was purified again using AMPure XP beads (1:1) in 35 μL EB elution buffer. For multiplexing, libraries with different barcode were mixed together with equal molar quantities by considering appropriate sequencing depth (30-40 million reads per library). Libraries were sequenced by Illumina Hiseq X Ten platform with pair-end reads of 150 bp.

value: HSV-1 infect 24h

tag: chip antibody


title: INPUT_HSV-1_24H_ChIPSeq_rep3

value: monocyte


title: WBJPE171125430


title: MEF_D4_GFP_3

value: Day 4 of SKM MEF reprogramming


title: WBJPE171125423


title: NPC_D0_2


title: INPUT_HSV-1_8H_ChIPSeq_rep3

value: peripheral blood

value: acute monocytic leukemia


title: INPUT_HSV-1_24H_ChIPSeq_rep1


title: MEF_D8_GFP_1

value: Day 8 of SKM MEF reprogramming


title: MEF_D4_GFP_1


title: WBJPE171125422

value: mice skeletal muscle


title: WBJPE171125421


title: MEF_D2_2

value: Day 2 of SKM MEF reprogramming


title: INPUT_HSV-1_8H_ChIPSeq_rep2

value: HSV-1 infect 8h


title: WBJPE171125428


title: INPUT_HSV-1_8H_ChIPSeq_rep1


title: MEF_D2_1


title: WBJPE171125420


title: MEF_D0_1

value: Day 0 of SKM MEF reprogramming


title: WBJPE171125419


title: MEF_D0_2

value: Day 0 of SKM MEFreprogramming


title: MEF_D8_GFP_2


title: INPUT_HSV-1_4H_ChIPSeq_rep2

value: HSV-1 infect 4h


title: INPUT_HSV-1_4H_ChIPSeq_rep3


title: WBJPE171125418

value: male


title: WBJPE171125417


title: sample_15

city: Zürich

first: Christophe

last: Chabbert

address: Otto-Stern-Weg 7, HPL H 17.2

department: Institute of Molecular Health Sciences

institute: ETH

data_processing:
Base calling and demultiplexing were done with bcl2fastq (v2.17.1.14).
Sequence reads were trimmed for adapter sequences and then aligned to the mm10 reference genome (assembly GRCm38, M14 Gencode annotation) using STAR v 2.4.2a.
Optical and PCR duplicates were flagged and removed using Picard Tools v2.10.3 (MarkDuplicates, with REMOVE_DUPLICATES option).
Overall quality control metrics as well as gene, exon and junction count tables were generated using QoRTs 1.2.42 (default parameters, discarding reads with multiple alignments).
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: _qorts_geneCounts.txt.gz: Raw count tables generated using QoRTs.

source_name: Heart

extract_protocol:
RNA was extracted from tissues using the miRNeasy Mini Kit from Qiagen.
mRNA was isolated from 1μg total RNA by poly-dT enrichment using the NEBNext Poly(A) mRNA Magnetic Isolation Module according to the manufacturer's instructions. Final elution was done in 15ul 2x first strand cDNA synthesis buffer (NEBnext, NEB). After chemical fragmentation by incubating for 15 min at 94°C, the sample was directly subjected to the workflow for strand specific RNA-Seq library preparation (Ultra Directional RNA Library Prep, NEB). For ligation, custom adaptors were used (Adaptor-Oligo 1: 5'-ACA-CTC-TTT-CCC-TAC-ACG-ACG-CTC-TTC-CGA-TCT-3', Adaptor-Oligo 2: 5'-P-GAT-CGG-AAG-AGC-ACA-CGT-CTG-AAC-TCC-AGT-CAC-3'). After ligation, adapters were depleted by an XP bead purification (Beckman Coulter) adding beads in a ratio of 1:1. Indexing was done during the following PCR enrichment (15 cycles) using custom amplification primers carrying the index sequence indicated with ‘NNNNNN’. (Primer1:Oligo_Seq AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, primer2: GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT, primer3: CAAGCAGAAGACGGCATACGAGAT NNNNNN GTGACTGGAGTT.

tag: strain/background

tag: genotype/variation

value: Clk3 KO

tag: conditions

value: TAC

value: Heart

tag: age

value: 10 weeks


title: sample_16


title: WBJPE171125416


title: sample_14


title: sample_13


title: WBJPE171125414


title: INPUT_HSV-1_2H_ChIPSeq_rep3

value: HSV-1 infect 2h


title: INPUT_HSV-1_2H_ChIPSeq_rep1

value: monocyte


title: INPUT_HSV-1_1H_ChIPSeq_rep3

value: HSV-1 infect 1h


title: sample_12

value: WT


title: sample_10


title: sample_8

value: sham


title: INPUT_HSV-1_1H_ChIPSeq_rep1

value: peripheral blood

value: acute monocytic leukemia


title: INPUT_HSV-1_1H_ChIPSeq_rep2


title: WBJPE171125412

value: mice skeletal muscle


title: WBJPE171125411


title: sample_7


title: H3K9ME3_HSV-1_24H_ChIPSeq_rep2

description:
processed data file:
HSV-H3K9me3-24h.bw

value: HSV-1 infect 24h

value: H3K9me3 (Abcam ab176916)


title: INPUT_HSV-1_4H_ChIPSeq_rep1


title: H3K9ME3_HSV-1_24H_ChIPSeq_rep3

description:
processed data file:
HSV-H3K9me3-24h.bw


title: sample_6

value: 11 weeks


title: sample_4


title: sample_5


title: WBJPE171125415


title: Chen2008-1-EnhancerDeletion-150126-D3

description: poly(A)+ RNA-seq with hybrid selection

value: embryonic stem cell

value: female


title: INPUT_HSV-1_2H_ChIPSeq_rep2


title: H3K9ME3_HSV-1_24H_ChIPSeq_rep1

description:
processed data file:
HSV-H3K9me3-24h.bw


title: H3K9ME3_HSV-1_8H_ChIPSeq_rep2

description:
processed data file:
HSV-H3K9me3-8h.bw

value: HSV-1 infect 8h


title: sample_3


title: sample_2


title: WBJPE171125404

value: male


title: WBJPE171125407


title: WBJPE171125405


title: WBJPE171125403


title: H3K9ME3_HSV-1_8H_ChIPSeq_rep1

description:
processed data file:
HSV-H3K9me3-8h.bw


title: sample_1

value: Heart


title: WBJPE171125409


title: H3K9ME3_HSV-1_4H_ChIPSeq_rep3

description:
processed data file:
HSV-H3K9me3-4h.bw

value: HSV-1 infect 4h


title: WBJPE171125401


title: WBJPE171125402


title: WBJPE171125406


title: H3K9ME3_HSV-1_4H_ChIPSeq_rep1

description:
processed data file:
HSV-H3K9me3-4h.bw


title: intra tumoral macs rep5

city: Tel Aviv

first: Hadar

last: Reichman

address: 30 Haim Levanon

department: Microbiology & Immunology

country: Israel

institute: Tel Aviv University

data_processing:
Library quality control: FASTQC version 0.11.5
Quality and adapter trimming: trim_galore (uses catadapt version 1.10)
Mapping: Tophat2 version 2.1.0 (uses Bowtie2 version 2.2.6)
Gene counting: Htseq-count version 0.6.1
Normalization and differential expression analysis: DESeq2 R package version 1.14.1
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: Normalized counts

source_name: intra tumoral macs

growth_protocol: Naive C57/BL6 WT mice or mice bearing tumors following CAC induction

extract_protocol:
RNA extraction: Trizol
samples preparation: CEL-Seq, 3 technical replicates per sample using different primer pools

treatment_protocol: Colons were subjected to enzymatic digestion, then eosinophils and macrophages were isolated using flow cytometry.

tag: disease state

value: CAC

value: colon

value: macs


title: H3K9ME3_HSV-1_8H_ChIPSeq_rep3

description:
processed data file:
HSV-H3K9me3-8h.bw

tag: host cell line

value: monocyte


title: intra tumoral macs rep6


title: WBJPE171125400

data_processing:
Illumina Casava1.7 software used for basecalling.
Single-cell RNA sequence reads were evaluated by FastQC
Bad reads were detected automatically and removed. Bases at 3' end of the read were further timmed by NGSQCToolkit if their PHRED quality score were less than 20.
The reads were mapped to the mm9 using bowtie2.
The mapped reads for genes were counted via Htseq.


title: intra tumoral macs rep3


title: WBJPE171125399


title: intra tumoral macs rep4


title: intra tumoral macs rep2


title: H3K9ME3_HSV-1_2H_ChIPSeq_rep2

description:
processed data file:
HSV-H3K9me3-2h.bw

tag: host cell type

value: HSV-1 infect 2h


title: WBJPE171125398


title: WBJPE171125397


title: intra tumoral macs rep1


title: H3K9ME3_HSV-1_1H_ChIPSeq_rep3

description:
processed data file:
HSV-H3K9me3-1h.bw

value: peripheral blood

tag: disease

value: HSV-1 infect 1h


title: H3K9ME3_HSV-1_2H_ChIPSeq_rep1

description:
processed data file:
HSV-H3K9me3-2h.bw

value: acute monocytic leukemia

tag: treatment


title: naive colonic macs rep5

source_name: naive colonic macs

value: control


title: H3K9ME3_HSV-1_1H_ChIPSeq_rep2

description:
processed data file:
HSV-H3K9me3-1h.bw

value: H3K9me3 (Abcam ab176916)


title: naive colonic macs rep4


title: WBJPE171125396

value: mice skeletal muscle


title: naive colonic macs rep3


title: WBJPE171125394


title: H3K4ME3_HSV-1_24H_ChIPSeq_rep2

description:
processed data file:
HSV-H3K4me3-24h.bw

value: HSV-1 infect 24h

value: H3K4me3 (clone MC315, Millipore 04-745)


title: WBJPE171125393


title: H3K9ME3_HSV-1_4H_ChIPSeq_rep2

description:
processed data file:
HSV-H3K9me3-4h.bw


title: naive colonic macs rep2


title: WBJPE171125413


title: H3K9ME3_HSV-1_2H_ChIPSeq_rep3

description:
processed data file:
HSV-H3K9me3-2h.bw


title: WBJPE171125392


title: H3K4ME3_HSV-1_8H_ChIPSeq_rep2

description:
processed data file:
HSV-H3K4me3-8h.bw

value: HSV-1 infect 8h


title: H3K4ME3_HSV-1_24H_ChIPSeq_rep1

description:
processed data file:
HSV-H3K4me3-24h.bw


title: WBJPE171125391

value: male


title: naive colonic macs rep1


title: intra tumoral eos rep7

source_name: intra tumoral eos

value: eos


title: intra tumoral eos rep6


title: H3K4ME3_HSV-1_8H_ChIPSeq_rep1

description:
processed data file:
HSV-H3K4me3-8h.bw


title: intra tumoral eos rep5


title: H3K4ME3_HSV-1_4H_ChIPSeq_rep2

description:
processed data file:
HSV-H3K4me3-4h.bw

value: HSV-1 infect 4h


title: H3K4ME3_HSV-1_4H_ChIPSeq_rep1

description:
processed data file:
HSV-H3K4me3-4h.bw


title: WBJPE171125390


title: WBJPE171125388


title: H3K9ME3_HSV-1_1H_ChIPSeq_rep1

description:
processed data file:
HSV-H3K9me3-1h.bw


title: H3K4ME3_HSV-1_2H_ChIPSeq_rep2

description:
processed data file:
HSV-H3K4me3-2h.bw


title: WBJPE171125395


title: intra tumoral eos rep4

value: CAC


title: H3K4ME3_HSV-1_2H_ChIPSeq_rep1

description:
processed data file:
HSV-H3K4me3-2h.bw


title: intra tumoral eos rep3

value: colon


title: intra tumoral eos rep2


title: WBJPE171125386


title: WBJPE171125385


title: intra tumoral eos rep1


title: H3K4ME3_HSV-1_1H_ChIPSeq_rep1

description:
processed data file:
HSV-H3K4me3-1h.bw


title: WBJPE171125384


title: naive colonic eos rep2

source_name: naive colonic eos


title: WBJPE171125383


title: H3K27ME3_HSV-1_24H_ChIPSeq_rep2

description:
processed data file:
HSV-H3K27me3-24h.bw


title: naive colonic eos rep1


title: H3K27ME3_HSV-1_8H_ChIPSeq_rep2

description:
processed data file:
HSV-H3K27me3-8h.bw


title: H3K27ME3_HSV-1_24H_ChIPSeq_rep1


title: WBJPE171125389


title: WBJPE171125382


title: E9.5 Oct4 Control_4Cseq_Dsite, rep2

city: Madrid

first: Fatima

last: Sanchez-Cabo

address: Melchor Fernandez Almagro

country: Spain

institute: CNIC

description:
view point primer: GTGTTCCCTCAGTAGGTGGGATC
second primer: TGCCTGTTGACTGGTCTCTCC
first cutter seq: GATC
second cutter seq: CATG
first_library_primer: AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCTGTGTTCCCTCAGTAGGTGGGATC
second_library_primer: CAAGCAGAAGACGGCATACGATGCCTGTTGACTGGTCTCTCC
Oct4_E9.5_dox-_D_2
4C-Seq Illumina DNA-Seq Single End library.

data_processing:
Library strategy: 4C-Seq
Libraries sequenced using Illumina HiSeq 2500 single end at 50 or 60nt.
Base-calling was produced by Illumina RTA Software v 1.18.66.3.
Fastq files were generated from the bcl files using bcl2fastq v1.8.4.
View point specific reads were demultiplexed using cutadapt v1.7.1.
Adaptor sequence contaminants were removed using cutadapt.
Potential chimeric sequences were avoided by removing second cutter sequences to the end of the read.
Resulting reads shorter than 30nt were removed.
Reads were mapped using Bowtie-1.1.2 against mm9 genome.
Mapped reads were then converted to reads per first enzyme fragment ends and smoothed using a 30-fragment mean running window algorithm.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: bedGraph with the smoothened counts.

source_name: E9.5 embryos, control Oct4 levels

growth_protocol: Standard mouse growth conditions. Females between 6-7 weeks are mated with double homozygotes males until plug is observed. ESCs were grown in standard ESC media supplemented with 15% FBS and LIF.

extract_protocol:
4C was done from pools of 60-70 E9.5 embryos or 1-2x10^6 G4 cells per biological replicate. Embryos were minced, treated with collagenase type 2 and passed throw a 70 micrometers cell strainer, and ES cells were harvested and counted. Samples were crosslinked with 2% PFA, frozen with liquid nitrogen and stored at -80º for later processing. After lysis, chromatin was digested with DpnII (New England BioLabs) as primary enzyme and NlaIII (New England BioLabs) as secondary enzyme, and ligated with T4 DNA Ligase (Promega) was used for the two ligation steps.
Circular ligated DNA was amplified using specific primers with the Illumina adaptor library included.

value: ROSA26tg/+; Oct4tg/+

tag: developmental stage

value: whole embryo

tag: doxycycline induction

value: dox-


title: E9.5 Oct4 Control_4Cseq_Dsite, rep1

description:
view point primer: GTGTTCCCTCAGTAGGTGGGATC
second primer: TGCCTGTTGACTGGTCTCTCC
first cutter seq: GATC
second cutter seq: CATG
first_library_primer: AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCTGTGTTCCCTCAGTAGGTGGGATC
second_library_primer: CAAGCAGAAGACGGCATACGATGCCTGTTGACTGGTCTCTCC
Oct4_E9.5_dox-_D_1
4C-Seq Illumina DNA-Seq Single End library.

tag: tissue


title: WBJPE171125381

tag: strain


title: H3K27ME3_HSV-1_8H_ChIPSeq_rep1

description:
processed data file:
HSV-H3K27me3-8h.bw

value: monocyte

value: peripheral blood


title: WBJPE171125380


title: WBJPE171125387


title: G4 ESCs_4Cseq_Dsite, rep2

description:
view point primer: GTGTTCCCTCAGTAGGTGGGATC
second primer: TGCCTGTTGACTGGTCTCTCC
first cutter seq: GATC
second cutter seq: CATG
first_library_primer: AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCTGTGTTCCCTCAGTAGGTGGGATC
second_library_primer: CAAGCAGAAGACGGCATACGATGCCTGTTGACTGGTCTCTCC
G4_ESCs_D_2
4C-Seq Illumina DNA-Seq Single End library.

source_name: G4 cells, WT

value: 129xC57BL/6 F1 Hybrid

value: WT

tag: cell line

tag: cell type

value: ES cells


title: H3K4ME3_HSV-1_1H_ChIPSeq_rep2

description:
processed data file:
HSV-H3K4me3-1h.bw

value: acute monocytic leukemia

value: HSV-1 infect 1h


title: H3K27ME3_HSV-1_4H_ChIPSeq_rep2

description:
processed data file:
HSV-H3K27me3-4h.bw


title: G4 ESCs_4Cseq_Dsite, rep1

description:
view point primer: GTGTTCCCTCAGTAGGTGGGATC
second primer: TGCCTGTTGACTGGTCTCTCC
first cutter seq: GATC
second cutter seq: CATG
first_library_primer: AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCTGTGTTCCCTCAGTAGGTGGGATC
second_library_primer: CAAGCAGAAGACGGCATACGATGCCTGTTGACTGGTCTCTCC
G4_ESCs_D_1
4C-Seq Illumina DNA-Seq Single End library.


title: E9.5 Oct4 Control_4Cseq_Psite, rep2

description:
view point primer: AGTGTTCAAAACTAGTAAAGATC
second primer: CATTTCCCTTCTCCTGTT
first cutter seq: GATC
second cutter seq: CATG
first_library_primer: AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCTAGTGTTCAAAACTAGTAAAGATC
second_library_primer: CAAGCAGAAGACGGCATACGACATTTCCCTTCTCCTGTT
Oct4_E9.5_dox-_P_2
4C-Seq Illumina DNA-Seq Single End library.


title: WBJPE171125375

value: mice skeletal muscle

tag: gender


title: WBJPE171125379


title: WBJPE171125378


title: E9.5 Oct4 Control_4Cseq_Psite, rep1

description:
view point primer: AGTGTTCAAAACTAGTAAAGATC
second primer: CATTTCCCTTCTCCTGTT
first cutter seq: GATC
second cutter seq: CATG
first_library_primer: AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCTAGTGTTCAAAACTAGTAAAGATC
second_library_primer: CAAGCAGAAGACGGCATACGACATTTCCCTTCTCCTGTT
Oct4_E9.5_dox-_P_1
4C-Seq Illumina DNA-Seq Single End library.


title: WBJPE171125374


title: G4 ESCs_4Cseq_Psite, rep1

description:
view point primer: AGTGTTCAAAACTAGTAAAGATC
second primer: CATTTCCCTTCTCCTGTT
first cutter seq: GATC
second cutter seq: CATG
first_library_primer: AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCTAGTGTTCAAAACTAGTAAAGATC
second_library_primer: CAAGCAGAAGACGGCATACGACATTTCCCTTCTCCTGTT
G4_ESCs_P_1
4C-Seq Illumina DNA-Seq Single End library.


title: H3K27ME3_HSV-1_2H_ChIPSeq_rep2

description:
processed data file:
HSV-H3K27me3-2h.bw

value: HSV-1 infect 2h

tag: chip antibody


title: H3K27ME3_HSV-1_2H_ChIPSeq_rep1

description:
processed data file:
HSV-H3K27me3-2h.bw


title: H3K27ME3_HSV-1_4H_ChIPSeq_rep1

description:
processed data file:
HSV-H3K27me3-4h.bw


title: WBJPE171125372

value: male


title: WBJPE171125373


title: H3K27ME3_HSV-1_1H_ChIPSeq_rep2

description:
processed data file:
HSV-H3K27me3-1h.bw


title: H3K27AC_HSV-1_24H_ChIPSeq_rep2

description:
processed data file:
HSV-H3K27ac-24h.bw

value: HSV-1 infect 24h

value: H3K27ac (Abcam Ab4729)


title: H3K27ME3_HSV-1_1H_ChIPSeq_rep1

description:
processed data file:
HSV-H3K27me3-1h.bw


title: E7.5 Oct4 dox+_RNAseq [MTcD2]

description:
Oct4_E7.5_dox+_2
Oct4E75_MTcD2
Processed data file: ALLSamples.NCBIM37.v65.rsem.genes.results.txt

data_processing:
Libraries sequenced using Illumina GAIIx single end 61nt and HiSeq 2500.
Base-calling was produced by Illumina RTA Software v 1.13.48.
Demultiplexed fastq files were generated from the bcl files using picard tools.
Sequencing adaptor contaminations were removed using cutadapt.
Reads were mapped and gene expression quantified using rsem v1.17.
Counts were normalized using voom from Limma R package.
Genome_build: NCBIm37.v65
Supplementary_files_format_and_content: ALLSamples.NCBIM37.v65.rsem.genes.results.txt: Tab-separated text file. Contains estimated counts quantified with rsem.

source_name: E7.5 embryos, high Oct4 levels

growth_protocol: Standard mouse growth conditions. Females between 6-7 weeks are mated with double homozygotes males until plug is observed.

extract_protocol:
Total RNA was purified from E7.5 pull of embryos per triplicate (8-12 embryos/replicate) or E9.5 pull of embryos per triplicate (3 embryos/replicates) following Arcturus PicoPure RNA isolation Kit protocol (Thermo Fisher Scientific).
A cDNA library was prepared according to Illumina recommendations and sequenced in a GAII analyzer or HiSeq 2500.

treatment_protocol: Doxycycline was injected at E4.5 intraperitoneally in the pregnant mother and then continued with the doxycycline treatment in the drinking water until E7.5, when embryos are extracted. For E9.5 embryos, females are treated with doxycycline in the drinking water from E6.5 to E9.5, when embryos are extracted.

tag: strain/background

value: dox+


title: WBJPE171125370


title: H3K27AC_HSV-1_8H_ChIPSeq_rep2

description:
processed data file:
HSV-H3K27ac-8h.bw

value: HSV-1 infect 8h


title: H3K27AC_HSV-1_24H_ChIPSeq_rep1

description:
processed data file:
HSV-H3K27ac-24h.bw


title: E7.5 Oct4 dox+_RNAseq [MTcD1]

description:
Oct4_E7.5_dox+_1
Oct4E75_MTcD1
Processed data file: ALLSamples.NCBIM37.v65.rsem.genes.results.txt

tag: genotype/variation

value: ROSA26tg/+; Oct4tg/+


title: H3K27AC_HSV-1_8H_ChIPSeq_rep1

description:
processed data file:
HSV-H3K27ac-8h.bw


title: WBJPE171125369


title: E7.5 Oct4 Control_RNAseq [MTsD2]

description:
Oct4_E7.5_dox-_2
Oct4E75_MTsD2
Processed data file: ALLSamples.NCBIM37.v65.rsem.genes.results.txt

source_name: E7.5 embryos, control Oct4 levels

value: whole embryo


title: WBJPE171125376


title: WBJPE171125368


title: G4 ESCs_4Cseq_Psite, rep2

description:
view point primer: AGTGTTCAAAACTAGTAAAGATC
second primer: CATTTCCCTTCTCCTGTT
first cutter seq: GATC
second cutter seq: CATG
first_library_primer: AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCTAGTGTTCAAAACTAGTAAAGATC
second_library_primer: CAAGCAGAAGACGGCATACGACATTTCCCTTCTCCTGTT
G4_ESCs_P_2
4C-Seq Illumina DNA-Seq Single End library.


title: E7.5 Oct4 Control_RNAseq [MTsD1]

description:
Oct4_E7.5_dox-_1
Oct4E75_MTsD1
Processed data file: ALLSamples.NCBIM37.v65.rsem.genes.results.txt

value: dox-


title: NZB_Heart_RnaSeq

description: barcode sequence: ATTCCT

data_processing:
libraries sequenced usign Illumina HiSeq 2500
base-calling was produced by Illumina RTA Software v 1.13.48
demultiplexed fastq files were generated from the bcl files using picard tools
sequencing adaptor contaminations were removed using cutadapt
reads were mapped and gene expression quantified using rsem v1.17
counts were normalized using voom from Limma R package
Genome_build: GRXm38 v76
Supplementary_files_format_and_content: tab separated file. Contains expected counts per gene aligned with RSEM. Samples in columns, Genes in rows

extract_protocol:
Mice were killed by cervical decapitation, and heart (left ventricle) tissue were dissected and immediately frozen in liquid nitrogen. Total RNA was extracted with TRIzol reagent and then purified on RNeasy spin columns (Qiagen)
RNA libraries were prepared for sequencing using TrueSeq RNASeq kit from Illumina

tag: genotype

value: 12 weeks-old

value: Heart (left ventricle)

tag: Sex


title: WBJPE171125367


title: WBJPE171125366


title: H3K27AC_HSV-1_2H_ChIPSeq_rep2

description:
processed data file:
HSV-H3K27ac-2h.bw

value: monocyte

value: peripheral blood


title: H3K27AC_HSV-1_4H_ChIPSeq_rep1

description:
processed data file:
HSV-H3K27ac-4h.bw

value: HSV-1 infect 4h


title: H3K27AC_HSV-1_2H_ChIPSeq_rep1

description:
processed data file:
HSV-H3K27ac-2h.bw

value: acute monocytic leukemia


title: C57-NZB(7)_Heart_RnaSeq

description: barcode sequence: GAGTGG

tag: age


title: H3K27AC_HSV-1_1H_ChIPSeq_rep2

description:
processed data file:
HSV-H3K27ac-1h.bw

tag: host cell line

value: HSV-1 infect 1h


title: WBJPE171125364

value: mice skeletal muscle


title: H3K27AC_HSV-1_1H_ChIPSeq_rep1

description:
processed data file:
HSV-H3K27ac-1h.bw

tag: host cell type


title: E7.5 Oct4 Control_RNAseq [MTsD3]

description:
Oct4_E7.5_dox-_3
Oct4E75_MTsD3
Processed data file: ALLSamples.NCBIM37.v65.rsem.genes.results.txt


title: WBJPE171125371


title: C57-NZB(6)_Heart_RnaSeq

description: barcode sequence: GTTTCG


title: C57-NZB(5)_Heart_RnaSeq

description: barcode sequence: GTGGCC


title: H3K27AC_HSV-1_4H_ChIPSeq_rep2

description:
processed data file:
HSV-H3K27ac-4h.bw

tag: disease


title: yl_10_3

city: Tianjin

first: Duo

state: Tianjin

address: No. 92, Weijin Road, Nankai District

institute: Tianjin University

description:
processed data file:
processed data (FPKM).xls
processed data (read count).xls

data_processing:
Quality control
Reads mapping to the reference genome Yarrowia lipolytica CLIB122 (assembly ASM252v1)
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene.
Differential expression analysis was performed using the DESeq R package (1.18.0).
Genome_build: Yarrowia lipolytica CLIB122 (assembly ASM252v1)
Supplementary_files_format_and_content: processed data (read counts) contained RPKM for each gene in different samples

organism: Yarrowia lipolytica

source_name: yl_10_yeast cells

growth_protocol: 72 h cultivation in flask, 250 rpm, 28 ℃

extract_protocol:
RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agelent, USA)
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) and index codes were added to each sample.
The library preparations were sequenced on an Illumina Hiseq 4000 platform. 150 bp paired-end reads were generated as raw data.

treatment_protocol: Yarrowia lipolytica cells were pelleted and quickly frozen by liquid nitrogen.

value: Y. lipolytica strain ATCC 201249

tag: strain name

value: transformation of heterologous genes


title: WBJPE171125361

source_name: skeleton muscle

value: male


title: WBJPE171125360


title: C57-NZB(3)_Heart_RnaSeq

description: barcode sequence: GTCCGC


title: WBJPE171125362


title: yl_10_2

value: 72 h cultivation in flask, 250 rpm, 28 ℃


title: C57-NZB(2)_Heart_RnaSeq

description: barcode sequence: CCGTCC


title: E7.5 Oct4 dox+_RNAseq [MTcD3]

description:
Oct4_E7.5_dox+_3
Oct4E75_MTcD3
Processed data file: ALLSamples.NCBIM37.v65.rsem.genes.results.txt

tag: developmental stage

value: dox+


title: WBJPE171125359


title: C57-NZB(1)_Heart_RnaSeq

description: barcode sequence: AGTTCC


title: C57-NZB(8)_Heart_RnaSeq

description: barcode sequence: ACTGAT


title: yl_10_1


title: WBJPE171125365


title: yl_11_3

source_name: yl_11_yeast cells


title: C57_Heart_RnaSeq

description: barcode sequence: AGTCAA


title: WBJPE171125363


title: WBJPE171125355


title: yl_11_2


title: yl_11_1


title: yl_12_3

source_name: yl_12_yeast cells


title: WBJPE171125354


title: yl_12_2


title: C57-NZB(4)_Heart_RnaSeq

description: barcode sequence: GTGAAA


title: yl_12_1


title: WBJPE171125352


title: WBJPE171125353


title: WBJPE171125351


title: WBJPE171125356


title: WBJPE171125350


title: WBJPE171125349