title: lrp2 1 mpf eyes 1

description: ZDR(wt) vs lrp2 expression.xlsx


title: shh 11

status: Public on Jun 01 2018

type: SRA

city: Milwaukee

first: Ross

middle: F

last: Collery

state: Wisconsin

address: 8701 Watertown Plank Road

country: USA

institute: Medical College of Wisconsin

description: no shh vs shh expression.xlsx

library_source: transcriptomic

data_processing:
Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads.
Raw reads are subjected to quality control (QC) to determine if a resequencing step is needed. After QC, raw reads are filtered into clean reads which are aligned to the reference sequences.
"Dirty" raw reads are reads which contain the sequence of adaptor, high content of unknown bases and low quality reads, and are removed before analysis.
Bowtie2  was used to map clean reads to reference gene, and HISAT used to reference genome.
The Fragments Per Kilobase of transcript per Million mapped reads (FPKM)  method is used to calculated expression level.
Genome_build: GRCz10 (GCA_000002035.3)
Supplementary_files_format_and_content: Excel files containing FKPM values for expression levels.

molecule: total RNA

organism: Danio rerio

source_name: whole larval eyes

growth_protocol: Zebrafish (Danio rerio) were maintained at 28.5C on an  Aquatic Habitats recirculating filtered water system in reverse-osmosis purified water supplemented  with Instant Ocean salts (60 mg/l) on a 14 h light: 10 h  dark lighting cycle and fed a standard diet

extract_protocol:
Eyes were dissected were removed, stored overnight at 4C in RNAlater, and RNA was harvested using Trizol reagent.
RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low-input Illumina protocol.

tag: genotype

value: Transgenic (hsp70l:shha-eGFP)

tag: age

value: 5 days post-fertilization


title: colo_hrcC_3

city: Thuwal

first: Naganand

last: Rayapuram

address: KAUST

country: Saudi Arabia

institute: KAUST

data_processing:
Sequenced reads were checked for quality.
Low quality reads were trimed using trimmomatic.
Trimmed reads were mapped to TAIR10 genome using TOPHAT.
FPKM was calculated using cufflinks.
Differential analysis was performed using cuffdiff.
Genome_build: TAIR10
Supplementary_files_format_and_content: txt, FPKM values

organism: Arabidopsis thaliana

source_name: 14 day old seedlings

growth_protocol: Plants were grown on sterile one-half-strength Murashige and Skoog (MS) medium with a 16-8h photoperiod for 14 days at 21° C.

extract_protocol:
Total RNA was extracted using NucleoSpin® Plant RNA kit and First-strand complementary DNA was synthesized from 1 μg of total RNA using reverse transcriptase, SuperScript® III First-Strand Synthesis SuperMix kit (Invitrogen).
Libraries were prepared using Illumina TruSeq stranded mRNA kits

treatment_protocol: Plants were treated with Pst DC3000 hrcC- for 24 hours

tag: cell type

value: Whole seedlings

tag: treatment

value: PstDC3000 hrcC-

tag: ecotype

tag: genotype/variation

value: wild type


title: col0_mock_1

value: Mock


title: lrp2 1 mpf sclera 11

description: ZDR(wt) vs lrp2 expression.xlsx

source_name: choroid/sclera

value: 1 month post-fertilization


title: lrp2 1 mpf RPE 13

description: ZDR(wt) vs lrp2 expression.xlsx

source_name: retinal pigment epithelium


title: TH97_HCT8_C6706_Vibrio_cholerae

city: Oslo

first: Siv

last: Gilfillan

address: Gaustadaleen 21

department: Norwegian Center for Molecular Medicine

country: Norway

institute: University of Oslo

library_source: genomic

data_processing:
Reads were mapped to the human reference genome using bowtie version 1.1.2
Filtering of alignment files to identify uniquely mapping, non-duplicate reads, was performed using samtools version 1.3.1
Peak calling was performed by HOMER 4.7.2
Genome_build: hg19
Supplementary_files_format_and_content: peak files from HOMER

molecule: genomic DNA

organism: Homo sapiens

source_name: Cultured HCT8 5h with vesicles from C6706_Vibrio_cholerae

extract_protocol:
Illumina TruSeq™ DNA Sample Preparation
Twenty five microliters of immunoprecipitated, FAIRE or input DNA was used for library preparation. For CHIP samples Illumina (San Diego, CA) TruSeq™ DNA Sample Preparation reagents were used, with ligation of 1/10th the manufacturers recommended adapter amounts and agarose gel selection of DNA fragments in the 200-500 bp size range. For FAIRE samplesThruPLEX DNA-Seq reagents was used (Rubicon Genomics, Ann Arbor, MI, USA), following manufacturer’s instructions”.

tag: cell line

tag: chip antibody


title: DGE_LCC2

city: Aarhus

first: Jian

last: Li

address: The Bartholin Building

department: Institute of Biomedicine

country: Denmark

institute: Aarhus University

description:
derived from LCC1 with increased small-dosage tamoxifen treatment, estrogen-independent, and tamoxifen-resistant
messenger RNA
DGE
processed data file: lcc_dge_cn_ln_20130313.txt

data_processing:
Base calling software: Illumina Casava1.7
FASTX-Toolkit implemented in Perl was used to trim the adaptor sequence. The trimmed tags were subjected to quality filtering, so that only the tags with sequencing quality higher than 30 for more than 80% of the nucleotides of each tag were used for subsequent analysis. The refMrna (hg19, UCSC) was used as reference for mapping cDNA tags. Subsequently, the Burrows–Wheeler Aligner (BWA) procedure was applied for aligning the DGE tags to the refMrna reference library.
Estimation of the expression levels of the identified mRNAs was performed by calculating the value of normalized uniquely mapped tag numbers.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file includes normalized tag numbers for each sample in the LCC cell line model.

source_name: Breast cancer cell line derived from MCF-7

growth_protocol: The LCC cell lines were cultured in DMEM/F12 without phenol red, supplemented with 5% DCC and 1% penicillin/streptomycin. The cells were maintained at 37°C in a humidified atmosphere of 95% ambient air and 5% CO2.

extract_protocol:
Total RNA was extracted from the cell lines with TRI Reagent (Sigma) according to the manufacturer’s protocol. The extracted total RNA was verified by agarose gel electrophoresis, and the concentration was estimated by NanoDrop (Thermo Scientific). Furthermore, BioAnalyzer 2100 RNA Chip (Agilent) were used to ensure the quality, quantity and integrity for the messenger RNA (mRNA). Subsequently, the total RNA was subject to digestion of DNase I (New England BioLabs), and then purified by ethanol precipitation for subsequent analyses.
The DGE analysis used NlaIII and MmeI to produce 20-21 bp tag. The indexed single-end 50 nt sequencing was performed by Illumina HiSeq 2000.

treatment_protocol: The LCC0 is derived from MCF-7 presenting estrogen-dependent and tamoxifen-responsive phenotype. LCC1 was established from the estrogen-dependent parent cell line MCF-7 through prolonged withdrawal from potent estrogenic stimuli both in vivo and in vitro. The above in vivo selected cell line was further passaged in ovary-comprised nude mice and re-established in vitro to generate a new cell line, MCF-7/LCC1, which is estrogen-independent, but tamoxifen-responsive as its parent cell line. Furthermore, a new cell hormone-independent, tamoxifen-resistant subline, LCC2 was developed through growth of LCC1 in incrementally increased dosages of tamoxifen in vitro. And a new cell hormone-independent, cross-resistance to tamoxifen and fluvestrant subline, LCC9 was developed through growth of LCC1 in incrementally increased dosage of fluvestrant.

tag: tissue

value: Breast cancer


title: ZDR 1 mpf sclera 13

description: ZDR(wt) vs lrp2 expression.xlsx

value: wild-type


title: ZDR 1 mpf RPE 13

description: ZDR(wt) vs lrp2 expression.xlsx


title: ZDR 1 mpf sclera 11

description: ZDR(wt) vs lrp2 expression.xlsx


title: ZDR 1 mpf sclera 12

description: ZDR(wt) vs lrp2 expression.xlsx


title: DGE_LCC9

description:
derived from LCC1 with increased small-dosage fluvestrant treatment, estrogen-independent, and cross-resistance to fluvestrant and tamoxifen
messenger RNA
DGE
processed data file: lcc_dge_cn_ln_20130313.txt


title: TH98_HCT8_MC1061_E.coli

source_name: Cultured HCT8 5h with vesicles from MC1061_E.coli


title: TH96_control_HCT8 cells non treated

source_name: Cultured HCT8 control


title: DGE_LCC1

description:
estrogen-independent and tamoxifen sensitive
messenger RNA
DGE
processed data file: lcc_dge_cn_ln_20130313.txt


title: ZDR 1 mpf retina 13

description: ZDR(wt) vs lrp2 expression.xlsx

source_name: retina


title: ZDR 1 mpf retina 12

description: ZDR(wt) vs lrp2 expression.xlsx


title: DGE_LCC0

description:
estrogen-dependent and tamoxifen sensitive
messenger RNA
DGE
processed data file: lcc_dge_cn_ln_20130313.txt


title: TH102_HCT8_C6706_Vibrio_cholerae

extract_protocol:
ThruPLEX, Rubicon Genomics
Twenty five microliters of immunoprecipitated, FAIRE or input DNA was used for library preparation. For CHIP samples Illumina (San Diego, CA) TruSeq™ DNA Sample Preparation reagents were used, with ligation of 1/10th the manufacturers recommended adapter amounts and agarose gel selection of DNA fragments in the 200-500 bp size range. For FAIRE samplesThruPLEX DNA-Seq reagents was used (Rubicon Genomics, Ann Arbor, MI, USA), following manufacturer’s instructions”.


title: RRBS_LCC2

description:
derived from LCC1 with increased small-dosage tamoxifen treatment, estrogen-independent, and tamoxifen-resistant
LB-NB11
processed data file: LCCs_RRBS_processed_data.txt

data_processing:
Base calling software: Illumina Casava1.7
The adaptor sequences were filtered out from the subsequent analysis and the resulting reads were aligned using Bismark software. Only uniquely mapped reads, which had restriction enzyme cutting site at the 5’ end were used to subsequent methylation analysis.
The sequencing depth and the percentage of methylated cytosines/total investigated cytosines for each C location were calculated. The genomic annotation information was based on the hg19 human genome (http://genome.ucsc.edu). Differentially methylated cytosines were identified by QDMR.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file includes the significantly differented cytosines and the correpsonding methylation level (percentage) values for each sample in the LCC cell line model.

extract_protocol:
Genomic DNA was isolated from the LCC cell lines using DNeasy® Blood & Tissue Kit (QIAGEN) following manufacturer's protocol. The extracted genomic DNA was verified by agarose gel electrophoresis, and the concentration was estimated by NanoDrop (Thermo Scientific). Furthermore, BioAnalyzer 2100 DNA Chip was used to ensure the quality, quantity and integrity for the genomic DNA. Subsequently, the genomic DNA was subject to digestion of RNase A (Invitrogen), and then purified by ethanol precipitation for subsequent analyses.
For the RRBS analysis, 5 µg genome DNA from the LCC0, LCC1, LCC2 and LCC9 was digested by restriction enzyme, MspI (New England BioLabs) over night at 37 °C and QIAGEN Mini Purification kit was used to purify the digested products. End repair, adding A and adaptors, where the cytosines in the paired end adaptor sequence were methylated, was performed. The ligated product was subjected to size selection in 2% agarose gel (Bio-RAD) at 100 V for 2 hours. Agarose gel bands with the inserted DNA size 40 ~ 110 bp and the inserted DNA size 110 ~ 220 bp were excised, so that two libraries were generated from each sample (one consisting of 40 ~ 110 bp target sequences and the other of 110 ~ 220 bp target sequences). DNA from the two excised gel pieces was recovered by QIAGEN Gel Extraction Purification Kit, followed by bisulfite treatment using ZYMO EZ DNA Methylation-Gold kit. The resulting converted DNA was amplified by PCR and, following purification, the RRBS libraries were generated by performing paired-end 50 nt sequencing with HiSeq 2000 (Illumina).


title: RRBS_LCC1

description:
estrogen-independent and tamoxifen sensitive
LB-NB10
processed data file: LCCs_RRBS_processed_data.txt


title: ZDR 1 mpf eyes 2

description: ZDR(wt) vs lrp2 expression.xlsx

source_name: whole eyes


title: ZDR 1 mpf RPE 12

description: ZDR(wt) vs lrp2 expression.xlsx


title: ZDR 1 mpf RPE 11

description: ZDR(wt) vs lrp2 expression.xlsx


title: RNA-Seq_LCC9

description:
derived from LCC1 with increased small-dosage fluvestrant treatment, estrogen-independent, and cross-resistance to both fluvestrant and tamoxifen
messenger RNA
LB_new1
processed data file: LCCs_RNAseq_processed_data.txt

data_processing:
Base calling software: Illumina Casava1.7
Sequenced reads were trimmed for adaptor sequence, then mapped to hg19 using TopHat
Estimation of the expression levels of the identified mRNAs was performed by calculating the value of FPKM (Fragments Per Kilobase of exon per Million fragments mapped) using TopHat and Cufflinks. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Significantly differented expressed genes were revealed between the tamoxifen-resistant cell lines and their parental cell lines in the two cell line models.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample.

growth_protocol: The TAMR cell lines were maintained in DME/F12 (1:1) medium supplemented with 1% FCS and 1 μM tamoxifen. The LCC cell lines were cultured in DMEM/F12 without phenol red, supplemented with 5% DCC and 1% penicillin/streptomycin. The cells were maintained at 37°C in a humidified atmosphere of 95% ambient air and 5% CO2.

extract_protocol:
Total RNA was extracted from the cell lines with TRI Reagent (Sigma) according to the manufacturer’s protocol. The extracted total RNA was verified by agarose gel electrophoresis, and the concentration was estimated by NanoDrop (Thermo Scientific). Furthermore, BioAnalyzer 2100 RNA Chip (Agilent) were used to ensure the quality, quantity and integrity for the messenger RNA (mRNA). Subsequently, the total RNA was subject to digestion of DNase I (New England BioLabs), and then purified by ethanol precipitation for subsequent analyses.
RNA libraries were prepared for sequencing using standard Illumina  RNA-seq protocol.

treatment_protocol: For the TAMR cell line model, the MCF-7 cells were gradually adapted to grow in low serum concentration (initially 0.5% fetal calf serum (FCS) and 1% FCS  after phenol-red was omitted from the culture medium) and the tamoxifen-sensitive sub-line MCF-7/S0.5 was used to establish tamoxifen-resistant (TAMR) cell lines by extended treatment with 1 µM tamoxifen. The 4 TAMR cell lines:  MCF-7/TAMR-1 (TAMR-1), MCF-7/TAMR-4 (TAMR-4), MCF-7/TAMR-7 (TAMR-7) and MCF-7/TAMR-8 (TAMR-8) were derived from distinct colonies that emerged in cultures of MCF-7/S0.5 cells treated with 1 µM tamoxifen. For the LCC cell line model, LCC0 is derived from MCF-7 presenting estrogen-dependent and tamoxifen-responsive phenotype. LCC1 was established from the estrogen-dependent parent cell line MCF-7 through prolonged withdrawal from potent estrogenic stimuli both in vivo and in vitro. The above in vivo selected cell line was further passaged in ovary-comprised nude mice and re-established in vitro to generate a new cell line, MCF-7/LCC1, which is estrogen-independent, but tamoxifen-responsive as its parent cell line. Furthermore, a new cell hormone-independent, tamoxifen-resistant subline, LCC2 was developed through growth of LCC1 in incrementally increased dosages of tamoxifen in vitro. And a new cell hormone-independent, cross-resistance to tamoxifen and fluvestrant subline, LCC9 was developed through growth of LCC1 in incrementally increased dosage of fluvestrant.


title: RRBS_LCC0

description:
estrogen-dependent and tamoxifen sensitive
LB-NB9
processed data file: LCCs_RRBS_processed_data.txt


title: RNA-Seq_LCC2

description:
derived from LCC1 with increased small-dosage tamoxifen treatment, estrogen-independent, and tamoxifen-resistant
messenger RNA
LB_new2
processed data file: LCCs_RNAseq_processed_data.txt


title: RNA-Seq_LCC1

description:
estrogen-independent and tamoxifen sensitive
messenger RNA
LB_new3
processed data file: LCCs_RNAseq_processed_data.txt


title: RNA-Seq_LCC0

description:
estrogen-dependent and tamoxifen sensitive
messenger RNA
LB_new4
processed data file: LCCs_RNAseq_processed_data.txt


title: RNA-Seq_TAMR8

description:
tamoxifen-resistant
messenger RNA
LB_new12
processed data file: TAMRs_RNAseq_processed_data.txt


title: RNA-Seq_TAMR7

description:
tamoxifen-resistant
messenger RNA
LB_new11
processed data file: TAMRs_RNAseq_processed_data.txt


title: ZDR 1 mpf retina 11

description: ZDR(wt) vs lrp2 expression.xlsx


title: RRBS_LCC9

description:
derived from LCC1 with increased small-dosage fluvestrant treatment, estrogen-independent, and cross-resistance to fluvestrant and tamoxifen
LB-NB12
processed data file: LCCs_RRBS_processed_data.txt


title: wt_xyl1

city: Utrecht

first: Wieke

middle: R

last: Teertstra

address: Padualaan 8

department: Science, Biology

country: Netherlands

institute: Utrecht University

data_processing:
Illumina Casava pipeline version 1.8.3 was used for base calling
The RNA-Seq pipeline used the TRIMMOMATIC read trimmer version 0.32 (Bolger et al., 2014) to remove low quality regions and the Illumina adapters from the reads
Tophat version 2.1.13 (Trapnell et al., 2009) was used to align sequence reads to the A. niger ATCC 1015 genome assembly
The program Cuffdiff (version 2.2.1), which is part of Cufflinks (Trapnell et al., 2010), was used to identify reads mapping to predicted genes and to identify differentially expressed genes.
Genome_build: http://genome.jgi.doe.gov/Aspni7/Aspni7.home.html
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Aspergillus niger

source_name: Mycelium

growth_protocol: Conidia of Aspergillus niger strains MA234.1 and ΔrpnR were grown as liquid shaken cultures at 200 rpm and 30 °C in 300 ml Transformation Medium + 1% glucose for 16 hours. Subsequently, the mycelium was transferred to 150 ml Minimal Medium + 25 mM xylose and grown for another 4 hours at 250 rpm and 30 °C.

extract_protocol:
Mycelium was flash-frozen in liquid nitrogen and ground using the TissueLyzer II (Qiagen, Venlo, The Netherlands). RNA was isolated using a standard TRIzol isolation procedure, followed by purification using the Nucleospin® RNA kit (Macherey-Nagel, Düren, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain


title: RNA-Seq_MCF-7/S0.5

description:
estrogen-dependent and tamoxifen sensitive
messenger RNA
LB_new8
processed data file: TAMRs_RNAseq_processed_data.txt


title: RNA-Seq_TAMR4

description:
tamoxifen-resistant
messenger RNA
LB_new10
processed data file: TAMRs_RNAseq_processed_data.txt


title: RNA-Seq_TAMR1

description:
tamoxifen-resistant
messenger RNA
LB_new9
processed data file: TAMRs_RNAseq_processed_data.txt


title: d06850_xyl3

value: delta-rpnR


title: ZDR 1 mpf eyes 3

description: ZDR(wt) vs lrp2 expression.xlsx


title: TGFb+BMP+TNF_L46

city: Nashville

first: Jing

last: Zhu

state: TN

institute: Vanderbilt University

description:
L48-4 (L46 colonoid) 3ng/mL TGFB1, 10ng/mL BMP2, 100ng/mL TNFa
Total RNA was isolated from mouse colonoid treated with or without TNF, TGFb1, and BMP2 using RNeasy kit (Qiagen)
group_TGFb+BMP+TNF_vs_TNF_DEG.txt

data_processing:
Casava and bcl2fastq v2.16 were used for demultiplexing data from HiSeq2500 and HiSeq3000, seperately.
We mapped the reads to the mouse genome mm10 using TopHat-2.1.0 (Kim et al. 2013). Then, following the method of Anders (Anders et al. 2013), we counted the number of reads that fall into annotated genes by samtools-1.3.1 (Li et al. 2009) and HTSeq-0.5.4p5 (Anders et al. 2014).
Finally, we performed count-based differential expression analysis using edgeR_3.4.2 (McCarthy et al. 2012) which implements general differential analyses based on the negative binomial model.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized count values and differential expression analysis results for each Sample

organism: Mus musculus

source_name: Colonoid

extract_protocol:
Total RNA was isolated using RNeasy kit (Qiagen). Processing of RNA using a TruSeq Stranded mRNA sample prep kit was conducted according to the manufacturer’s instructions (Illumina, San Diego, CA)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Colonoid


title: d06850_xyl2


title: ZDR 1 mpf eyes 1

description: ZDR(wt) vs lrp2 expression.xlsx


title: TGFb+BMP_L46

description:
L48-2 (L46 colonoid) 3ng/mL TGFB1, 10ng/mL BMP2
Total RNA was isolated from mouse colonoid treated with or without TNF, TGFb1, and BMP2 using RNeasy kit (Qiagen)
group_TGFb+BMP_vs_Ctl_DEG.txt


title: TNF_L43

description:
L45-7 (L43 colonoid) 100ng/mL TNFa
Total RNA was isolated from mouse colonoid treated with or without TNF, TGFb1, and BMP2 using RNeasy kit (Qiagen)
group_TNF_vs_Ctl_DEG.txt


title: wt_xyl2


title: F_oxysporum_SX2_Dark_rep2

first: Javier

last: Avalos

address: Av. Reina Mercedes sn

department: Genetics

country: Spain

institute: University of Seville

data_processing:
Quality control  was performed using the software packges FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Read mapping to the reference genome was performed using Tophat (https://ccb.jhu.edu/software/tophat/index.shtml)
Transcript assembly was performed using Cufflinks and Cuffmerge (http://cole-trapnell-lab.github.io/cufflinks/)
Gene expression level measured in FPKM (fragments per kilobase of exon and million of mapped reads) was perfomed using Cufflinks and Cuffdiff
Subsequent data analysis and visualization was performed using the R bioconductor package cummeRbund (http://bioconductor.org/packages/release/bioc/html/cummeRbund.html)
Genome_build: EF1.27 (fusarium fujikuroi) and FO2.27 (fusarium oxysporum)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

organism: Fusarium oxysporum f. sp. lycopersici

source_name: carS mutant SX2 in the dark

growth_protocol: 106 conidia were inoculated into 100 ml of DG medium in 500-ml Erlenmeyer flasks and incubated in the dark for three days in an orbital shaker. For illumination 25 ml samples of the cultures were transferred to Petri dishes under red safelight and incubated for one hour either in the dark or under white light The process with F. oxysporum was the same, except that the 3-day cultures were incubated in 145-mm Petri dishes with 80 ml of DGasn medium.

extract_protocol:
RNA samples were extracted with Trizol (Invitrogen, Paisley, UK) using the protocol described by the manufacturer
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Illumination was achieved with a set of four fluorescent tubes (Philips TL-D 18W/840) at a distance of ca. 60 cm, providing a light intensity of 0.25 m

value: SX2 (derived from 4287)

value: carS mutant

value: mycelium


title: wt_xyl3


title: Ctl_L46

description:
L48-1 (L46 colonoid) vehicle treated
Total RNA was isolated from mouse colonoid treated with or without TNF, TGFb1, and BMP2 using RNeasy kit (Qiagen)
group_TNF_vs_Ctl_DEG.txt


title: TNF_L46

description:
L48-3 (L46 colonoid) 100ng/mL TNFa
Total RNA was isolated from mouse colonoid treated with or without TNF, TGFb1, and BMP2 using RNeasy kit (Qiagen)
group_TNF_vs_Ctl_DEG.txt


title: TGFb+BMP+TNF_L43

description:
L45-8 (L43 colonoid) 3ng/mL TGFB1, 10ng/mL BMP2, 100ng/mL TNFa
Total RNA was isolated from mouse colonoid treated with or without TNF, TGFb1, and BMP2 using RNeasy kit (Qiagen)
group_TGFb+BMP+TNF_vs_TNF_DEG.txt


title: TGFb+BMP_L43

description:
L45-6 (L43 colonoid) 3ng/mL TGFB1, 10ng/mL BMP2
Total RNA was isolated from mouse colonoid treated with or without TNF, TGFb1, and BMP2 using RNeasy kit (Qiagen)
group_TGFb+BMP_vs_Ctl_DEG.txt


title: F_oxysporum_SX2_Dark_rep1


title: d06850_xyl1


title: F_oxysporum_SX1_Dark_rep2

source_name: carS mutant SX1 in the dark

value: SX1 (derived from 4287)


title: F_oxysporum_SX1_Dark_rep1


title: TGFb+BMP+TNF_L42

description:
L45-4 (L42 colonoid) 3ng/mL TGFB1, 10ng/mL BMP2, 100ng/mL TNFa
Total RNA was isolated from mouse colonoid treated with or without TNF, TGFb1, and BMP2 using RNeasy kit (Qiagen)
group_TGFb+BMP+TNF_vs_TNF_DEG.txt


title: F_oxysporum_WT_Light_rep2

source_name: Wild type after 1h light


title: F_oxysporum_WT_Light_rep1


title: TNF_L42

description:
L45-3 (L42 colonoid) 100ng/mL TNFa
Total RNA was isolated from mouse colonoid treated with or without TNF, TGFb1, and BMP2 using RNeasy kit (Qiagen)
group_TNF_vs_Ctl_DEG.txt


title: F_oxysporum_WT_Dark_rep2

source_name: Wild type in the dark


title: TGFb+BMP_L42

description:
L45-2 (L42 colonoid) 3ng/mL TGFB1, 10ng/mL BMP2
Total RNA was isolated from mouse colonoid treated with or without TNF, TGFb1, and BMP2 using RNeasy kit (Qiagen)
group_TGFb+BMP_vs_Ctl_DEG.txt


title: Ctl_L42

description:
L45-1 (L42 colonoid) vehicle treated
Total RNA was isolated from mouse colonoid treated with or without TNF, TGFb1, and BMP2 using RNeasy kit (Qiagen)
group_TNF_vs_Ctl_DEG.txt


title: F_oxysporum_WT_Dark_rep1


title: Flx_TGFb+BMP2_3

description:
Flx_TGFb+BMP2
Total RNA was isolated from colonocytes treated with or without TNF, TGFb1, and BMP2 using RNeasy kit (Qiagen)
group_Flx_TGFb+BMP2_vs_Flx_Ctl_DEG.txt

source_name: Colonocytes

value: IMCfl/fl Smad4+ colonocytes

value: Colonocytes


title: Flx_TNFa+TGFb+BMP2_3

description:
Flx_TNFa+TGFb+BMP2
Total RNA was isolated from colonocytes treated with or without TNF, TGFb1, and BMP2 using RNeasy kit (Qiagen)
group_Flx_TNFa+TGFb+BMP2_vs_Flx_TNFa_DEG.txt


title: Flx_Ctl_3

description:
Flx_Ctl
Total RNA was isolated from colonocytes treated with or without TNF, TGFb1, and BMP2 using RNeasy kit (Qiagen)
group_Flx_TNFa_vs_Flx_Ctl_DEG.txt


title: Flx_TNFa+TGFb+BMP2_2


title: Flx_TGFb+BMP2_1


title: Flx_TNFa+TGFb+BMP2_1


title: Flx_TGFb+BMP2_2


title: Flx_TNFa_1

description:
Flx_TNFa
Total RNA was isolated from colonocytes treated with or without TNF, TGFb1, and BMP2 using RNeasy kit (Qiagen)
group_Flx_TNFa_vs_Flx_Ctl_DEG.txt


title: Ctl_L43

description:
L45-5 (L43 colonoid) vehicle treated
Total RNA was isolated from mouse colonoid treated with or without TNF, TGFb1, and BMP2 using RNeasy kit (Qiagen)
group_TNF_vs_Ctl_DEG.txt


title: GRA18+++_LPS

city: La Tronche

first: Alexandre

last: Bougdour

state: Isère

address: Domaine de la Merci, Campus santé

department: Prevention and Therapy of Chronic diseases

country: France

institute: Centre de Recherche Inserm U1209 / CNRS UMR5309 / UGA

data_processing:
The RNA-Seq reads (FASTQ) were processed and analyzed using the Lasergene Genomics Suite version 14 (DNASTAR, Madison, WI, USA) using default parameters.
The paired-end reads were uploaded onto the SeqMan NGen (version 14, DNASTAR. Madison, WI, USA) platform for reference-based assembly using either the Mus musculus genome package (GRCm38.p3) or the Toxoplasma Type II ME49 strain (ToxoDB-24, ME49 genome) as reference template.
The ArrayStar module (version 14, DNASTAR. Madison, WI, USA) was used for normalization, differential gene expression and statistical analysis of uniquely mapped paired-end reads using the default parameters.
The expression data quantification and normalization were calculated using the RPKM (Reads Per Kilobase of transcript per Million mapped reads) normalization method.
Genome_build: Mus musculus genome package (GRCm38.p3)
Genome_build: Toxoplasma Type II ME49 strain (ToxoDB-24, ME49 genome)
Supplementary_files_format_and_content: xlsx format. The matrix table includes RPKM values and log2 transformed values for each Sample for both BMDM and T. gondii transcripts.

organism:
Toxoplasma gondii
Mus musculus

source_name: BMDMs and parasites

growth_protocol: Cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen) supplemented with 10% heat-inactivated FBS (Invitrogen), 20% conditioned medium from macrophage-colony stimulating factor-secreting L929 fibroblasts (Aziz et al., 2009), 50 μM 2-mercaptoethanol, 1X non-essential amino acids (Thermo Fisher Scientific), 10 mM Hepes buffer, pH 7.2, 2 mM L-glutamine, and 50 μg/ml penicillin and streptomycin (Thermo Fisher Scientific). Cells were incubated at 37°C in 5% CO2.

extract_protocol:
Total RNAs were extracted and purified using TRIzol (Invitrogen, Carlsbad, CA, USA) and RNeasy Plus Mini Kit (Qiagen). RNA quantity and quality were measured by NanoDrop 2000 (Thermo Scientific). RNA integrity was assessed by standard non-denaturing 1.2% TBE agarose gel electrophoresis. The ribosomal large subunits from Toxoplasma and the host cells was used to verify that the ratio between Toxoplasma RNA versus host RNA was equivalent between the different biological samples, thus indicating that the samples had equivalent infection rates.
RNA libraries were prepared for sequencing using standard Illumina protocols (Illumina TruSEQ RNA library prep).

treatment_protocol: 18 hours after infection, cells were subjected or not to LPS stimulation for 4 hours before being harvested for RNA extraction.

tag: mice strain

value: BALB/c

tag: parasite strain

value: Prugniaud

value: Macrophages

value: LPS

tag: parasite genotype

value: GRA18 complemented


title: Flx_Ctl_2


title: F_fujikuroi_SG256_Light_rep1

organism: Fusarium fujikuroi

source_name: Complementing strain after 1h light

value: SG256 (derived from SG39)

value: complementation of carS mutant


title: gra18

value: gra18 mutant


title: Pru_LPS

value: wt


title: F_fujikuroi_SG256_Light_rep2


title: Pru


title: F_fujikuroi_SG256_Dark_rep2

source_name: Complementing strain in the dark


title: F_fujikuroi_SG39_Light_rep2

source_name: carS mutant SG39 after 1h light

value: SG39 (derived from IMI58289)


title: F_fujikuroi_SG39_Light_rep1


title: F_fujikuroi_SG39_Dark_rep2

source_name: carS mutant SG39 in the dark


title: F_fujikuroi_WT_Light_rep2

value: wild type


title: F_fujikuroi_SG39_Dark_rep1


title: F_fujikuroi_WT_Light_rep1


title: Flx_TNFa_3


title: Flx_TNFa_2


title: F_fujikuroi_WT_Dark_rep2


title: Flx_Ctl_1


title: gra18_LPS


title: F_fujikuroi_WT_Dark_rep1


title: pRnhA_DRIPcseq_RIII

city: Davis

first: Frederic

last: Chedin

state: CA

address: 1 Shields Avenue

department: MCB

institute: UC Davis

description:
RNA/DNA hybrids
DRIPc-seq
2x75 bp FC Mid Output Illumina NextSeq500

data_processing:
DRIPc-seq and RNA-seq: All fastq files were trimmed with fastq-mcf before mapping.
DRIPc-seq: Trimmed fastq reads were mapped to hg19 using Bowtie2.1.0. DRIPc-seq peak calling was performed using HMM as described in methods.
RNA-seq: Trimmed fastq reads were mapped to S.pombe genome version ASM294v2 using TopHat 2.0.5. Normalized count table and log2 fold change were generated using DESeq2
Genome_build: ASM294v2
Supplementary_files_format_and_content: tsv: DESeq2 table count and log2Fold change. bigWig: binary of wiggle file

organism: Schizosaccharomyces pombe

source_name: Schizosaccaromyces pombe

growth_protocol: For RNA-seq analysis, cells were grown in PMG medium and shifted at 34°C for 3 hours before being collected. For DRIPc-seq, cells were grown at 30°C, in PMG or in YES as indicated

extract_protocol:
Genomic DNA was extracted from Schizosaccaromyces pombe and fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI. Monoclonal S9.6 antibody was used to enrich for RNA/DNA hybrids.
NEXTflex™ Rapid Directional mRNA-Seq Kit
For RNA-seq, total RNA were extracted with hot phenol according to the classic procedure. For DRIPc-seq, genomic DNA was extracted after spheroplasting S.pombe cells.
RNA-seq: according ot the manufacturer's instructions. DRIPc-seq: according to the manusfacturer's instructions omitting the step of poly-A enrichment and the step of RNA fragmentation.

treatment_protocol: DRIPc-seq samples were either treated with RNase A alone, RNase A + RNase H or RNase A + RNase III as indicated.

tag: mutation

value: E.coli rnhA o/e

value: RNaseA + RNaseIII


title: rrp6∆_DRIPcseq_RH_rep2

description:
dsRNA + RNA/DNA hybrids
DRIPc-seq
2x75 bp FC Mid Output Illumina NextSeq500

value: RNaseA + RNaseH


title: rnh1∆rnh201∆_DRIPcseq_RH_rep2

value: rnh1delta rnh201delta


title: rrp6∆_DRIPcseq_RH_rep1


title: WT_DRIPcseq_RH_rep1


title: rnh1∆rnh201∆_DRIPcseq_RH_rep1


title: GRA18+++


title: F_fujikuroi_SG256_Dark_rep1

value: mycelium


title: rrp6∆_DRIPcseq_rep1

value: RNase A


title: pRnhA_DRIPcseq_RH


title: rnh1∆rnh201∆_DRIPcseq_rep2


title: edIs6 thoc-5(wy822), 2

city: STANFORD

first: Jin

middle: Billy

address: 300 Pasteur Dr.

institute: Stanford University

data_processing:
Raw reads were filtered using Trim Galore! to remove low quality and adaptor bases. Reads shorter than 16nt were discarded.
Filtered reads were mapped to ce10 genome sequences using STAR v2.4.2a with parameters: --outFilterMultimapNmax 20   --outFilterMismatchNmax 999  --outFilterMismatchNoverReadLmax 0.1   --alignIntronMin 20   --alignIntronMax 1000000   --alignMatesGapMax 1000000
The number of reads mapped to genes were counted using gene models  downloaded from UCSC on: July 17, 2015.
DESeq2 was used to perform differential gene expression analysis between thoc-5 mutant and the control.
Genome_build: ce10
Supplementary_files_format_and_content: Comma-separated values (csv) file with normalized gene expression levels (read count) and results from DESeq2

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: neurons

growth_protocol: Worms were synchronized and grown on 8PP plates + NA22 bacteria to young adulthood at 16 degree

extract_protocol:
single cell suspension and FACS sorting  was done as described according to Kaletsky et al. Nature, 2016. RNA was extracted with RNAeasy Micro kit
cDNA was generated with SMARTR v4 kit from Clontech, libraries were made with the Nextera XT kit according to manufacturer's protocol.

tag: Stage

value: Day 1 Adult

value: neurons

value: thoc-5(wy822) mutant


title: WT_DRIPcseq_RH_rep2


title: rrp6∆_DRIPcseq_rep2


title: edIs6 thoc-5(wy822), 3


title: edIs6, 1

value: wildtype


title: edIs6, 2


title: edIs6 thoc-5(wy822), 1


title: WT_DRIPcseq_rep2


title: rnh1∆rnh201∆_DRIPcseq_rep1


title: pRnhA_DRIPcseq


title: dis354_DRIPcseq


title: GcC1_h_rep3

city: Rockville

first: Shunyuan

last: Xiao

state: MD

address: 9600 Gudelsky Drive

department: Institute of Bioscience and Biotechnology Research

institute: University of Maryland

description:
Golovinomyces cichoracearum UCSC1
GcC1_cuffdiff.result.txt

data_processing:
We performed pair-end 100 bp sequencing on the HiSeq1500 Sequencing System. Sequenced reads were quality trimmed using Trimmomatic and adapters were removed with Cutadapt. Then, we used TopHat2 (v2.0.10) with parameters  "-g 1". The bam files from TopHat2, mapped reads at the gene-level were processed with cufflinks to get the expression value.
Genome_build: Gene structural prediction was performed using MAKER2 (Holt and Yandell 2011)
Supplementary_files_format_and_content: Tab limited text files that are generated from Cufflinks by using TopHat2 mapped reads. Each file contains fpkm value at gene level.
Supplementary_files_format_and_content: Tab limited text files that are generated from Cuffdiff by using TopHat2 mapped reads. Each file contains fpkm value at gene level.
Supplementary_files_format_and_content: The gff files contain the annotation for OnM2, GcM3 and GcC1

organism: Golovinomyces cichoracearum

source_name: Haustoria

growth_protocol: All powdery mildew fungi were respectively maintained on sow thistle (for GcM1), tomato (for OnM2), or tobacco (for GcM3) plants in separate plant growth chambers (8 h light at ~125 µmol.m-2.S-1, 16 h dark) at The University of Maryland, Shady grove campus.

extract_protocol:
The samplels are collected at 6 days post inoculation. The infected leaves were used for mycelium collection by gently brushing the mycelia off from leaves using TRIzol reagent. Then the haustorium-containing leaves with surface mycelia and spores removed at 6 dpi were further washed with ddH2O, frozen in liquid N2 and stored at -80°C for extraction of total plant and fungal RNA. Total RNA extraction and purification from mycelia or haustorium-containing host cells was conducted using TRIzol reagent (Cat. No. 15596026, Thermo Fisher Scientific) after grinding harvested mycelia or plant tissue with a pestle.
The cDNA libraries were prepared using Illumina TruSeq™ RNA Sample Preparation Kit v2 and transcriptome sequencing was performed on Illumina Hiseq 1500 at the UM-IBBR Sequencing Core at the University of Maryland.

value: Haustoria

tag: time point

value: 6 dpi

tag: biotype


title: GcC1_m_rep1

source_name: Mycelia

value: Mycelia


title: GcC1_h_rep2


title: CG1

city: Nanjing

first: Changfa

last: Zhou

state: Jiangsu

address: Wenyuan Road 1st

country: China

institute: Nanjing Normal University

data_processing:
The library for sequencing was generated using an Illumina TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA). analysis.
Transcriptome sequencing was carried out on an Illumina HiSeq 2500 platform that generated approximately 125-bp paired-end (PE) raw reads by SBC (Shanghai Biotechnology Corporation, Shanghai, China).
After removing adaptor sequences, ambiguous ‘N’ nucleotides (with the ratio of ‘N’ greater than 5%) and low quality sequences (with quality score less than 20), the remaining clean reads were assembled using trinity software as described for de novo transcriptome assembly without a reference genome. The quality of the assembly was critically assessed by SBC before subsequent edition.
For homology annotation, non-redundant sequences were annotated based on the following databases:  UniProt (SWISS-PROT and TrEMBL; manually annotated and reviewed protein sequence databases); Nr (NCBI non-redundant protein sequences); GO (Gene Ontology); KEGG (KEGG Ortholog database); and KOG (euKaryotic Ortholog Groups).
Supplementary_files_format_and_content: The expression level of each transcript was measured as the number of clean reads mapped to its sequence. The mapped clean read number was normalized to FPKM (FPKM- Fragments Per Kilobase of transcript per Million fragments mapped). We used DESeq to determine the FDR threshold. FDR < 0.05 and fold change > 2 were considered to indicate significant expression abundance.

organism: Cloeon viridulum

source_name: the whole body of five YL, two ML, two SI, and two IM, each represented by a male and a female individual

growth_protocol: The young C. viridulum larvae used in this study were collected in the Caiyue pool or lake, Nanjing Normal University, Nanjing, Jiangsu province, eastern China. This species can be found in most of China and is very common. The locality of collection is open to public.  Young larvae were reared in an insectary, at 22 ± 1 °C, 60% relative humidity, and under 16:8-h (light:dark) photoperiod, using water and plants from the pool they were collected from. Mature larva, subimagoes, and imagoes were reared from young larvae in the laboratory. Young larvae samples comprised 10 individuals, ML, SI, and IM samples comprised three males and three females each, and CG samples comprised five YL, and two ML, two SI, and two IM, each represented by a male and a female individual. Each sample had three biological replicates (YL1, YL2, YL3; ML1, ML2, ML3; SI1, SI2, SI3; IM1, IM2, IM3; CG1, CG2, CG3). Samples were cryopreserved in liquid nitrogen and stored at -80 °C until use.

extract_protocol:
Total RNA was extracted from each sample using TRIZOL Reagent (Cat#15596-018, Life Technologies, Carlsbad, CA, US), following the manufacturer’s instructions, and their RNA integrity was checked in the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, US). Qualified total RNA was further purified using the RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN).
Approximately 1 μg of total RNA per sample was used to construct the corresponding cDNA libraries. The library used in RNA-Seq was generated using the Illumina TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA). Transcriptome sequencing was carried out by SBC (Shanghai Biotechnology Corporation, Shanghai, China) on the Illumina HiSeq 2500 platform, and approximately 125-bp paired-end raw reads were generated. Reads with low overall quality (proportion of identified bases below 50%), adaptor sequences, ambiguous nucleotides (“Ns”), low quality (quality score below 20), and shorter than 20 nucleotides, and ribosome RNA reads were removed. The remaining clean reads were firstly assembled using CLC Genomics Workbench to obtain the primary unigenes, which were then assembled using CAP3 EST [21] to obtain the final unigenes of real animals, as described for de novo transcriptome assemblies without a reference genome.

tag: developmental stage

value: mixture

value: whole body


title: WT_DRIPcseq_RIII


title: rnh1∆rnh201∆_DRIPcseq_RIII


title: WT_DRIPcseq_rep1


title: CG2


title: IM3

source_name: the whole body of imago

value: imago


title: IM2


title: GcM3_h_rep2

description:
Golovinomyces cichoracearum UMSG3
GcM3_cuffdiff.result.txt


title: GcM3_m_rep1


title: GcM3_h_rep3


title: CG3


title: SI2

source_name: the whole body of subimago

value: subimago


title: IM1


title: GcM3_h_rep1


title: SI3


title: SI1


title: ML3

source_name: the whole body of mature larva

value: mature larva


title: ML2


title: YL3

source_name: the whole body of young larva

value: young larva


title: ML1


title: YL1


title: YL2


title: human_ESC_w5_fj194

status: Public on May 31 2018

city: Boston

first: Andrew

middle: Ryan

last: Field

state: MA

address: 45 Shattuck St

department: BCMP

institute: Harvard Medical School

description:
fj194
Processed data file: hg19.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt

data_processing:
Paired-end Illumina reads were trimmed from the 3’ end of read1 and read2 to 100x100bp for human and rhesus libraries and 80x80bp for chimpanzee and orangutan based on sequence quality. Bowtie2 v2.2.1 was used with the “--very-sensitive” parameter to filter reads against the repeatMasker library for each respective species which were removed from further analysis.
STAR v2.5.1b was used to map RNA-seq reads to hg19 (human, Genome Reference Consortium GRCh37, 2009), panTro4 (chimpanzee, CGSC Build 2.1.4, 2011), ponAbe2 (orangutan, WUSTL Pongo_albelii-2.0.2, 2007), and rheMac8 (rhesus macaque, Baylor College of Medicine HGSC Mmul_8.0.1, 2015) respective to the origin species. STAR was run with the default parameters with the following exceptions: --outFilterMismatchNmax 999, --outFilterMismatchNoverLmax 0.04, --alignIntronMin 20, --alignIntronMax 1000000, and --alignMatesGapMax 1000000. STAR alignments were converted to genomic position coverage with the bedtools command genomeCoverageBed -split.
DESeq2 v1.14.1 was used to provide basemean expression values and differential expression analysis across the time course in each species using FANTOM5 lv3 (Hon et al., 2017) transcript annotations (lifted to other species by transMap). Total gene coverage for a gene was converted to read counts by dividing the coverage by N+N (100+100 for human and rhesus and 80+80 for chimpanzee and orangutan) since each paired-end NxN mapped read induces a total coverage of N+N across its genomic positions.
Cufflinks v2.0.2 suite was used to assemble transcript predictions of potentially unannotated lncRNAs in each species and the Cuffmerge tool was used to combine these annotations with FANTOM5 transcripts.
Cufflinks-assembled and merged transcript sets were then projected through the cactus alignment to each of the other three genomes (hg19, panTro4, ponAbe2, and rheMac8, respectively).
RSEM v1.3.0 was used to provide TPM expression values for Cufflinks generated transcripts.
Genome_build: hg19, panTro4, ponAbe2, and rheMac8
Supplementary_files_format_and_content: *tsv, *txt: Tab-delimited text files include either basemean values (DESeq) or TPM values (RSEM) for each time point in each of the respective species.

source_name: embryonic stem cells

growth_protocol: The Eiraku et al., 2008 protocol was optimized for use with human ESCs, rhesus ESCs, chimpanzee iPSCs, and orangutan iPSCs. Human H9 and rhesus LyonESC1 embryonic stem cells were cultured on mouse embryonic fibroblasts with KSR-8 media (KO DMEM/F-12 + 20% KOSR, 1% NEAA, 1% GlutaMAX, 1% Pen-strep, and 0.1mM 2-mercaptoethanol supplemented with 8ng/mL bFGF). Embryonic stem cells were manually lifted from MEF feeders and allowed to self-form into embryoid bodies on low attachment plates (Corning) in KSR media. Chimpanzee and orangutan induced pluripotent stem cells were grown in feeder-free conditions on matrigel (Corning) with mTeSR-1 (Stem Cell Tech) or vitronectin (ThermoFisher) with Essential-8 Flex media (ThermoFisher), respectively, and 10,000 cells per EB were aggregated using AggreWell-800 plates (Stem Cell Technologies) in Aggrewell media (Stem Cell Technologies) supplemented with 10 uM Y-27632 rock inhibitor (ATCC) and transferred to low attachment plates (Corning) on day 2. Both methods supplemented the respective media with 500ng/mL DKK1 (Peprotech), 500 ng/mL NOGGIN (R & D Systemes), 10 uM SB431542 (Sigma), and 1 uM Cyclopamine V. californicum (VWR) for the first 18 days of differentiation. The media was changed to Neuralbasal (Invitrogen) supplemented with N2 (Gibco) and 1 uM Cyclopamine on day 18. At this time, chimpanzee and orangutan neurospheres were also supplemented with 10ng/mL bFGF and 10ng/mL EGF to improve survivability in Neuralbasal media. After day 26, all cultures were grown in Neuralbasal/N2 media without any added factors. Total RNA was extracted at weekly time points for each species. This timeline was adjusted accordingly in rhesus, harvesting on days 6, 11, 17, 22, and 28, to account for differences in gestational timing.

extract_protocol:
Trizol + RNeasy or Direct-zol cleanup, followed by ribozero rRNA depletion.
Strand-specific dUTP followed by TruSeq DNA library prep kit.

value: week 5


title: human_ESC_w5_fj193

description:
fj193
Processed data file: hg19.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt


title: GcC1_h_rep1


title: human_ESC_w4_fj108

description:
fj108
Processed data file: hg19.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt

value: week 4


title: human_ESC_w4_fj107

description:
fj107
Processed data file: hg19.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt


title: human_ESC_w3_fj105

description:
fj105
Processed data file: hg19.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt

value: week 3


title: human_ESC_w2_fj104

description:
fj104
Processed data file: hg19.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt

value: week 2


title: human_ESC_w2_fj103

description:
fj103
Processed data file: hg19.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt


title: human_ESC_w1_fj102

description:
fj102
Processed data file: hg19.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt

value: week 1


title: human_ESC_w1_fj101

description:
fj101
Processed data file: hg19.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt


title: human_ESC_w0_fj096

description:
fj096
Processed data file: hg19.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt

value: week 0


title: RNA-Seq NEU APOE3_rep1

city: Cambridge

first: Li-Huei

last: Tsai

state: Massachusetts

department: Picower Institute for Learning and Memory

institute: MIT

description:
COUNTS_NEU.txt
Parental iPSC ine derived neuron

data_processing:
RNA-seq data analysis: The generated fastq files were aligned to the UCSC human reference genome assembly hg19 using STAR 2.4. The aligned reads were processed by featureCounts tool ro calculate gene count matrix. Differential expression test between different groups was performed with Cuffdiff module, and genes with adjusted p-value < 0.05 were selected as differentially expressed genes. The GTF annotation files for UCSC hg19 was used for gene annotation.
Genome_build: hg19
Supplementary_files_format_and_content: Text table format for gene expression raw counts.

source_name: iPSC-derived neurons

growth_protocol:
astrocyte: Modified by Nat Commun 2014 July; 4430
Coated one well of 6-well cell culture plate with hESC-qualified matrigel (Corning) for 2h at 37 plated iPSCs colonies from irradiated mouse embryonic fibroblasts (MEFs, Globalstem) onto matrigel pre-coated well. Keep feeding the cells with mTeSRTM1 medium (STEMCELL Technologies) until the cells had reached ~100% confluence. Washed the cells with DPBS and add 2 ml of neural induction media (This is the neural maintenance media with a 1:1 mixture of N-2 and B-27 media. N-2 media includes DMEM/F-12 GlutaMAX (Thermo Fisher Scientific), 1× N-2 (Thermo Fisher Scientific,), 5 μg/ml insulin (Sigma-Aldrich), 100 μM nonessential amino acids (Sigma-Aldrich), 100 μM 2-mercaptoethanol (Sigma-Aldrich), 200 U/ml penicillin and 0.2 mg/ml streptomycin (Gemini Bio-products). B-27 media includes Neurobasal medium (Thermo Fisher Scientific), 1× B-27 (Thermo Fisher Scientific), 1× GlutaMAX (Thermo Fisher Scientific), 200 U/ml penicillin and 0.2 mg/ml streptomycin. And then the maintenance media was supplemented with 1 μM Dorsomorphin and 10 μM SB431542 every day for 12 days. After neural induction for 12 days, using accutase (Thermo Fisher Scientific) to passage the cells. Changed the media with neural maintenance media until the neural rosette structures were viewed obviously with the microscope around days 16-24 after neural induction. Passaged the cells again with accutase and plated 4×106 cells into one well of matrigel pre-coated well in 6-well plate. The day after passage the cells, started to add 20 ng/ml FGF2 (Peprotech) and 10 ng/ml BMP4 (Peprotech) into neural maintenance medium. Changed the medium every other day for further 28 days. Once astroglia induction finished, using GLAST antibody (Miltenyi Biotec) to perform Fluorescence-activated cell sorting (FACS) in order to purify the astrocytes from the wells. By FACS, we plated 2.5×105 cells into one well of 6-well plate and changed with astrocyte medium (Sciencell) every other day for 7 days. 7 days after, we performed FACS with GLAST antibody again to purify the astrocytes second time. After purification twice, we further used the cells for the biochemical analysis.
microglia: Nat Med. 2016 November ; 22(11): 1358–1367
We followed the protocol published by Muffat (Nature Medicine, 2016). Briefly, iPSCs were prepared on MEFs and used Collagenase IV (Thermo Fisher Scientific) to dissociate iPSCs colonies from MEFs. iPSCs colonies resuspended by  MGdM {NGD medium [Neurobasal medium with Gem21 (Gemini Bio-products), Neuroplex N2 (Gemini Bio-products), Albumax I (Thermo Fisher Scientific), Sodium chloride (Sigma-Aldrich), sodium pyruvate (Thermo Fisher Scientific), penicillin-streptomycin (Gemini Bio-products), GlutaMAX, biotin (Sigma-Aldrich), ascorbic acid (Sigma-Aldrich), and lactic syrup (Sigma-Aldrich)] plus 10 ng/ml IL-34 (Peprotech) and 10 ng/ml M-CSF1(Peprotech)} in ultra-low attachment 6-well plates (Corning) and further formed the EBs. Once the phase-bright neutralized spheroids and cystic bodies appeared, EBs were gently triturated to shear off cells of interest and transfered the supernatant in a single well of Primaria 6-well plate (Corning). Unattached cells and EBs were washed out by MGdM and attached cells were morphological characteristics of microglia and microglia precursors. Wells from 6 consecutive productions were pooled and purified by FACS using CD11b antibody (Miltenyi Biotec). Collected cells were further maintained in MGM (NGD plus 100 ng/ml IL-34 and 5 ng/ml M-CSF) for different analysis.
neuron: Modified by Neuron. 2013 June 5; 78(5): 785–798
We followed and modified the protocol published by Zhang (Neuron, 2013). Briefly, iPSCs were prepared from matrigel coated plates and used accutase to dissociate iPSCs and further plated 4×106 cells into one well of matrigel coated 6-well plate on day -1. Two hours later, lentivirus with rtTA and Ngn2-GFP expression vectors were suspended with mTeSRTM1 medium plus 2 μM thiazovivin (Tocris) and added onto the iPSCs. After 24 hrs (day 0), the culture medium were full changed with N2/DMEM/F12/NEAA (Thermo Fisher Scientific) medium containing 10 ng/ml BDNF (Peprotech), 10 ng/ml NT-3 (Peprotech), 0.2 μg/ml laminin (Corning), and 2 μg/ml doxycycline (Sigma-Aldrich) to induce TetO gene expression, and full changed the same medium on day 1. On day 2, a 48 hrs puromycin selection was started and the culture medium were full changed with Neurobasal/B27/GlutaMAX (Thermo Fisher Scientific) medium containing 10 ng/ml BDNF, 10 ng/ml NT-3, 0.2 μg/ml laminin, 2 μg/ml doxycycline, and 1 μg/ml puromycin (Millipore). On day 4, Ngn2-GFP expression cells were purified by FACS and replated GFP expressing cells onto matrigel coated plates with astrocyte conditioned medium containing 10 ng/ml BDNF, 10 ng/ml NT-3, 0.2 μg/ml laminin, 2 μg/ml doxycycline, and 1 μg/ml puromycin. On day 5, a 72 hrs Ara-C selection was started and used the same medium as day 4 plus 1 μM Ara-C (Sigma-Aldrich). On day 8, full changed the medium with astrocyte conditioned medium containing 10 ng/ml BDNF, 10 ng/ml NT-3, 0.2 μg/ml laminin, and 0.5 μg/ml doxycycline, and half changed the medium every 4 days until performing functional analysis.

extract_protocol:
We used the Rneasy plus mini kit from Qiagene to extract RNA samples and followed the manufacturer's instructions.
Total RNA samples were subject to Illumina strand-specific total RNA library preparation (Neoprep). A QC step was performed to check RIN number of the RNA samples before library preparation.

value: neuron

tag: passages


title: RNA-Seq NEU APOE4_rep3

description:
COUNTS_NEU.txt
isogenic iPSC line derived neuron

tag: cell type


title: RNA-Seq NEU APOE3_rep2


title: RNA-Seq NEU APOE4_rep2


title: RNA-Seq NEU APOE4_rep1


title: RNA-Seq NEU APOE3_rep3


title: RNA-Seq AST APOE3_rep3

description:
COUNTS_AST.txt
Parental iPSC ine derived astrocyte

source_name: iPSC-derived astrocytes

value: astrocytes


title: RNA-Seq AST APOE4 rep1

description:
COUNTS_AST.txt
isogenic iPSC line derived astrocyte


title: RNA-Seq AST APOE4 rep2


title: human_ESC_w3_fj106

description:
fj106
Processed data file: hg19.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt


title: RNA-Seq AST APOE3_rep1


title: RNA-Seq AST APOE3_rep2


title: RNA-Seq iPSC APOE4 rep1

description:
COUNTS_IPS.txt
isogenic iPSC line

source_name: iPSC

value: iPSCs


title: RNA-Seq iPSC APOE4 rep3

description:
COUNTS_IPS.txt
isogenic iPSC line


title: RNA-Seq iPSC APOE3_rep2

description:
COUNTS_IPS.txt
Parental iPSC ine


title: RNA-Seq iPSC APOE3_rep3

description:
COUNTS_IPS.txt
Parental iPSC ine


title: RNA-Seq iPSC APOE4 rep2

description:
COUNTS_IPS.txt
isogenic iPSC line


title: human_ESC_w0_fj095

description:
fj095
Processed data file: hg19.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt


title: RNA-Seq iPSC APOE3_rep1

description:
COUNTS_IPS.txt
Parental iPSC ine


title: RNA-Seq AST APOE4 rep3


title: CTCF_siRNA_MCF10A_RNA-seq_1

city: Madrid

first: Ana

last: Losada

state: Madrid

address: C/ Melchor Fernández Almagro, 3.

department: Molecular Oncology Programme

institute: Centro Nacional de Investigaciones Oncológicas (CNIO)

data_processing:
ChIP-SEQ processing. Image analysis, per-cycle basecalling and quality score assignment was performed with Illumina Real Time Analysis software. Conversion of Illumina BCL files to bam format was performed with the Illumina2bam tool (Wellcome Trust Sanger Institute - NPG).
ChIP-seq reads were aligned to the hg19 genome assembly using bwa (version 0.6.1-r104) under default parameters. Unmapped reads were removed using samtools (version 1.3.1) running 'samtools view -F 4'. Reads were sorted and replicates removed using picardtools (version 1.60). Peak calling was performed using macs2 (version 2.1.1.20160309) setting following parameters: '-q 0.05' and  '-extsize (value obtained from macs2 predictd step)' and using input as the control.
RNA-SEQ processing. Read files were quality-checked with FastQC. Reads were aligned to the human genome (GRCh37/hg19) with TopHat-2.0.10 (using Bowtie 1.0.0 and Samtools 0.1.19), allowing 2 mismatches and 5 multihits. Transcripts quantification and differential expression calculated with Cufflinks 2.2.1. Homo sapiens GRCh37/hg19 transcript annotations from the UCSC Genome Browser were used.
4C-SEQ processing. Read files were feeded to HTSstation following indicated steps: demultiplexing, mapping, 4c. David, FPA et al. HTSstation: A Web Application and Open-Access Libraries for High-Throughput Sequencing Data Analysis. PLoS ONE 9, e85879 (2014). Noordermeer et al., The dynamic architecture of Hox gene clusters, Science, 334:222-225, 2011
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bigwig files were generated using ucsc's bedGraphToBigWig tool converting begraph (output of peakcalling step) to bigwig

source_name: Human Mammary Epithelial Cells

growth_protocol: MCF10A cells were grown in DMEM/F12 supplemented with 20ng/ml of EGF, 0.5mg/ml hydrocortisone, 100ng/ml of cholera toxin, 10mg/ml of insulin and 5% of horse serum.

extract_protocol: 1 µg of total RNA sample was used as provided by the user. Sample RNA Integrity Numbers were in the range 9.6-10 when assayed on an Agilent 2100 Bioanalyzer. PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq Stranded mRNA Sample Preparation Part # 15031047 Rev. D" kit (this kit incorporates dUTP during 2nd strand cDNA synthesis, which implies that only the cDNA strand generated during 1st strand synthesis is eventually sequenced). Adapter-ligated library was completed by PCR with Illumina PE primers (8 cycles). The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument (see below) by following manufacturer's protocols.

value: Transformed nontumorigenic

tag: experiment

value: RNA-SEQ

tag: treatment

value: Cells were transfected with 50 nM onTARGETplus SMARTpool CTCF siRNAs (Dharmacon L-020165) at seeding in high confluency using DharmaFECT reagent 1.


title: SA2_siRNA_MCF10A_RNA-seq_3

value: Cells were transfected with 50 nM onTARGETplus SMARTpool STAG2 siRNAs (Dharmacon L-021351) at seeding in high confluency  using DharmaFECT reagent 1.


title: CTCF_siRNA_MCF10A_RNA-seq_2


title: SA2_siRNA_MCF10A_RNA-seq_1


title: SA2_siRNA_MCF10A_RNA-seq_2


title: CONTROL_MCF10A_RNA-seq_3


title: SA1_siRNA_MCF10A_RNA-seq_1

value: Cells were transfected with 50 nM onTARGETplus SMARTpool STAG1 siRNAs at seeding in high confluency (Dharmacon L-010638)  using DharmaFECT reagent 1.


title: SA1_siRNA_MCF10A_RNA-seq_3


title: Input_HCAEC_ChIP-seq

source_name: Human Coronary Artery Endothelial Cells (HCAEC)

growth_protocol: HCAEC were grown in EBM2 basal medium (CC-3156) supplemented EGM2-MV Bulletkit (CC-4147)

extract_protocol: Samples went through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters with "NEBNext Ultra II DNA Library Prep Kit for Illumina" from New England BioLabs (catalog # E7645). Adapter-ligated library was completed by limited-cycle PCR and extracted with a [single] double-sided SPRI size selection. Median fragment size is 360 bp from which 120 bp correspond to adaptor sequences. Library was applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument (see below) by following manufacturer's protocols.

value: Primary cells

value: ChIP-SEQ

tag: catalogue number

value: Lonza CC-2585

value: less than 10


title: CONTROL_MCF10A_RNA-seq_1


title: SMC1_MCF10A_ChIP-seq

value: custom made antibody for SMC1


title: SMC1_HCAEC_ChIP-seq


title: SA1_HCAEC_ChIP-seq

value: custom made antibody for SA1 (STAG1)


title: SA2_HCAEC_ChIP-seq

value: custom made antibody for SA2 (STAG2)


title: Input_MCF10A_ChIP-seq


title: SA2_MCF10A_ChIP-seq


title: ZMYM2_MCF10A_ChIP-seq

value: Zmym2 antibody was a generous gift from H. Yu (UT Southwestern, US)


title: CONTROL_MCF10A_RNA-seq_2


title: SA1_MCF10A_ChIP-seq


title: Input_HMEC_ChIP-seq

source_name: Human Mammary Epithelial Cells (HMEC)

growth_protocol: HMEC were cultured in MEBM basal medium (CC-3171) supplemented with MEGM Bulletkit (CC-3150)

value: Lonza CC-2551


title: SA2_HMEC_ChIP-seq


title: SMC1_HMEC_ChIP-seq


title: NO2-CLA2

city: Shanghai

first: Shengdi

address: 320 Yueyang Road

institute: SIBS

description: cDNA sample from hCASMC cells treated with NO2-CLA, replicate 2

data_processing:
Read quality check using FastQC
Read mapping to reference genome using Cufflinks, FPKM values were generated
Genome_build: GRCh37 (Ensembl)
Supplementary_files_format_and_content: fpkm_gene.txt

source_name: hCASMC

growth_protocol: Human coronary artery smooth muscle cells (hCASMCs) were purchased from PromoCell (Germany) and cultured in Smooth Muscle Cell Growth Medium 2 from same company at 37 °C, 5% CO2 in a standard cell culture incubator

extract_protocol:
The total RNA from hCASMCs were isolated and purified using RNeasy mini kit (Qiagen) and subjected to on-column RNase-free DNase treatment following the manufacturer’s recommendation (Qiagen)
RNA-seq library was prepared using the EnCore Complete RNA Seq Library System (NuGen, San Carlos, CA)

treatment_protocol: The cells at 80% confluence were maintained in 0.5% FBS medium for overnight and subsequently treated with NO2-CLA, CLA or vehicle control for 6 hours

value: human coronary artery smooth muscle cell

tag: agent


title: NO2-CLA3

description: cDNA sample from hCASMC cells treated with NO2-CLA, replicate 3


title: NO2-CLA4

description: cDNA sample from hCASMC cells treated with NO2-CLA, replicate 4


title: SA1_HMEC_ChIP-seq

tag: chip antibody


title: CLA4

description: cDNA sample from hCASMC cells treated with CLA,replicate 4

value: CLA


title: NO2-CLA1

description: cDNA sample from hCASMC cells treated with NO2-CLA, replicate 1


title: SA1_siRNA_MCF10A_RNA-seq_2


title: Control4

description: cDNA sample from hCASMC cells treated with vehicle control, replicate 4

value: vehicle control


title: Control1

description: cDNA sample from hCASMC cells treated with vehicle control, replicate 1


title: Control2

description: cDNA sample from hCASMC cells treated with vehicle control, replicate 2


title: CLA1

description: cDNA sample from hCASMC cells treated with CLA,replicate 1


title: CLA3

description: cDNA sample from hCASMC cells treated with CLA,replicate 3


title: Control3

description: cDNA sample from hCASMC cells treated with vehicle control, replicate 3


title: CLA2

description: cDNA sample from hCASMC cells treated with CLA,replicate 2


title: A3_RNAseq, Biological replicate 2

city: Durham

first: Zhong

last: Chen

state: NC

address: 905 S. LaSalle Street

department: Pathology

institute: Duke University

description:
Biological replicate 2
RNAseq_A3_gene.read.counts

data_processing:
ChIP-exo Alignment: Sequence reads were obtained and mapped to the human (hg19) genomes using the Bowtie2. All reads mapping with two or fewer mismatches were retained. Peaks were called using Partek Suits and BELT with default setting.
RNA-seq process: The RNA-seq data was aligned by TopHat 2.0. Reads were mapped to the reference genome build (hg19). Read counts were calculated with Partek. The reads count in exon regions was used to estimate the expression level of the genes.
Genome_build: hg19
Supplementary_files_format_and_content: For ChIP-seq, bigwig files were generated using bedtools, scores represent normalized peaks genomic coverage. For RNA-seq, tab-delimited text files include read counts of all genes for each Sample.

source_name: prostate cancer tissues

growth_protocol: The androgen-independent prostate cancer cell line 22RV1 was cultured in the RPMI complete medium (10% FBS).The androgen-independent prostate cancer cell line LN95 was cultured in the RPMI complete medium (10% CSFBS).

extract_protocol:
For ChIP-exo, cells were crosslinked with 1% formaldehyde for 10 min. With sufficient lysis, the samples were enriched by immunoprecipatation with antibodes and then processed according to ChIP-exo procedures. For RNA-seq, total RNA was isolated using an RNeasy kit (QIAGEN). Next, mRNA was enriched using NEBNext Poly(A) mRNA Magnetic Isolation Module. After two rounds of processes, the  mRNA was recovered for library generation.
For ChIP-exo, T4 DNA polymerase, T4 PNK, and Klenow DNA Polymerase were used together for end polishing. The ligation step was performed with less reducing agent. Protein A Dynal magnetic beads were washed using modified RIPA buffer (50mM Tris-HCL pH 7.8, 1mM EDTA, 0.25% Na Deoxycholate, 1% NP-40, 0.5M LiCl). The library was amplified with only 10 or 12 PCR cycles, and prepared without gel-based size selection. For RNA-seq, the library preparation was performed with NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina following the manufacturer’s instructions. The cDNA molecules were amplified by 8 cycles of PCR. Non-size selection libraries were then sequenced for using Illumina HiSeq 2000 at the OSUCCC sequencing core.

treatment_protocol: For all experiments, cells were maintained in phenol red-free RPMI medium with 5-10% charcoal-stripped FBS for 3 days before collection.

tag: cell line

tag: cancer

value: Prostate adenocarcinoma

tag: chip andtibody


title: A3_RNAseq, Biological replicate 1

description:
Biological replicate 1
RNAseq_A3_gene.read.counts


title: A31_RNAseq, Biological replicate 2

description:
Biological replicate 2
RNAseq_A31_gene.read.counts


title: A31_V7_ChIPexo

value: AR-V7 (AG10008) from Precision Antibody (Columbia, MD )


title: A17_RNAseq, Biological replicate 1

description:
Biological replicate 1
RNAseq_A17_gene.read.counts


title: A3_V7_ChIPexo


title: A17_V7_ChIPexo


title: A31_RNAseq, Biological replicate 1

description:
Biological replicate 1
RNAseq_A31_gene.read.counts


title: A3_HoxB13_ChIPexo

value: HoxB13 (H80) from Santa Cruz Biotechnology (Santa Cruz, CA)


title: A17_RNAseq, Biological replicate 2

description:
Biological replicate 2
RNAseq_A17_gene.read.counts


title: A31_HoxB13_ChIPexo


title: A17_HoxB13_ChIPexo


title: LN95_siHoxB13_RNAseq, Biological replicate 2

description:
Biological replicate 2
RNAseq_LN95_gene.read.counts

source_name: prostate cancer cells


title: LN95_siHoxB13_RNAseq, Biological replicate 1

description:
Biological replicate 1
RNAseq_LN95_gene.read.counts


title: LN95_siControl_RNAseq, Biological replicate 1


title: LN95_siAR-V7_RNAseq, Biological replicate 1


title: 22RV1_siHoxB13_RNAseq, Biological replicate 2

description:
Biological replicate 2
RNAseq_22RV1_gene.read.counts


title: LN95_siControl_RNAseq, Biological replicate 2


title: 22RV1_siAR-V7_RNAseq, Biological replicate 1

description:
Biological replicate 1
RNAseq_22RV1_gene.read.counts


title: 22RV1_siAR-V7_RNAseq, Biological replicate 2


title: 22RV1_siHoxB13_RNAseq, Biological replicate 1


title: 22RV1_siControl_RNAseq, Biological replicate 2


title: LN95_HoxB13_ChIPexo, Biological replicate 2

description:
Biological replicate 2
LN95_hox.bw


title: LN95_HoxB13_ChIPexo, Biological replicate 1

description:
Biological replicate 1
LN95_hox.bw


title: 22RV1_siControl_RNAseq, Biological replicate 1


title: LN95_V7_ChIPexo, Biological replicate 2

description:
Biological replicate 2
LN95_v7.1.bw


title: LN95_C19_ChIPexo, Biological replicate 1

description:
Biological replicate 1
LN95_c19.bw

value: AR (C19) from Santa Cruz Biotechnology (Santa Cruz, CA)


title: LN95_C19_ChIPexo, Biological replicate 2

description:
Biological replicate 2
LN95_c19.bw


title: LN95_V7_ChIPexo, Biological replicate 1

description:
Biological replicate 1
LN95_v7.1.bw


title: 22RV1_HoxB13_ChIPexo, Biological replicate 1

description:
Biological replicate 1
CW22RV1_vehicle_Hox.bw


title: 22RV1_HoxB13_ChIPexo, Biological replicate 2

description:
Biological replicate 2
CW22RV1_vehicle_Hox.bw


title: 22RV1_C19_ChIPexo, Biological replicate 1

description:
Biological replicate 1
CW22RV1_vehicle_C19.bw


title: 22RV1_V7_ChIPexo, Biological replicate 2

description:
Biological replicate 2
CW22RV1_vehicle_V7.bw


title: LN95_siAR-V7_RNAseq, Biological replicate 2


title: mNPC clone#035 technical rep 3

city: Stanford

first: Howard

middle: Y.

last: Chang

state: CALIFORNIA

address: 269 Campus Drive, CCSR 2130

institute: Stanford

data_processing:
Basecalls
paired-end reads were merged using PEAR
Reads were counted using Fastx-collapser
Genome_build: Hg19
Supplementary_files_format_and_content: Allele frequency counted using Fastx-collapser,  X is the order of each allele abundance, y is the read counts.

source_name: neuronal progenitor cells

growth_protocol: Cultured in N2B27 media supplemted with 1X Glutamx, 0.1mM of b-mercaptoethanol, 10 ng/ul of EGF and 10 ng/ul of FGF

extract_protocol:
Min-elute column (Qiagen)
Amplicon PCR (Truseq adaptor)
mmPVT1_F1_adapter: GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGAAAGGTGCCTAGAAATCCTGA
mmPVT1_R1_adapter: ACACTCTTTCCCTACACGACGCTCTTCCGATCTGGAAGTGAGGTGGGAACTTG
mmPVT1_F2_adapter: GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCATCCTCTAAAGTGTGCCCC
mmPVT1_R2_adapter: ACACTCTTTCCCTACACGACGCTCTTCCGATCTCATCCTGGAAAGAAATGCTAACA
mmMYC_F1_adapter: GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCTGTGGAGAAGAGGCAAACC
mmMYC_R1_adapter: ACACTCTTTCCCTACACGACGCTCTTCCGATCTGAGGACCAGTGGGCTGTG
mmMYC_F2_adapter: GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGGGGAGGGAATTTTTGTCTA
mmMYC_R2_adapter: ACACTCTTTCCCTACACGACGCTCTTCCGATCTAAATCCAGCCTTCAAACAGC
mmTBP_F_adapter: GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCCACAGCCTATTCAGAACACC
mmTBP_R_adapter: ACACTCTTTCCCTACACGACGCTCTTCCGATCTCTACTGCCTGCTGTTGTTGC

treatment_protocol: Reverse transcription using qRT-PCR master mix

value: neuronal progenitor cells


title: mNPC clone#034 technical rep 3


title: 22RV1_C19_ChIPexo, Biological replicate 2

description:
Biological replicate 2
CW22RV1_vehicle_C19.bw


title: mNPC clone#031 technical rep 3


title: mNPC clone#033 technical rep 3


title: 22RV1_V7_ChIPexo, Biological replicate 1

description:
Biological replicate 1
CW22RV1_vehicle_V7.bw


title: mNPC clone#032 technical rep 3


title: mNPC clone#036 technical rep 3


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title: agb1-BL rep1

first: weiwei

last: Qi

address: No 99 Shangda Road

institute: Shanghai  University

description: rep1=biological replicate 1

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to  primaryTranscript dataset obtained from primaryTranscript of  Arabidopsis thaliana TAIR10 gene set  using Bowtie 2 version 2.2.2  with default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample.

source_name: agb1-BL, seedling

growth_protocol: seeds were germinated in 1/2 MS plus 1% sucrose and placed at 4 degree centigrade for 3 days and then tranferred to white light for 12 h before placed in blue light for another 4.5 days

extract_protocol:
Total RNA was extracted from samples including WT, agb1, cry1 cry2 and hy5 with RNAprep plant kit (TIANGEN), and followed by DNase I (Takara) treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: ecotype

tag: genotype

value: agb1-2 mutant

tag: light condition

value: blue light

tag: growth time

value: 4.5 days

tag: tissue

value: seedling


title: agb1-BL rep2

description: rep2=biological replicate 2


title: cry1 cry2-BL rep1

description: rep1=biological replicate 1

source_name: cry1 cry2-BL, seedling

value: cry1 cry2 double mutant


title: B cells 2

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
Reads pairs from each sample were aligned to the mouse genome and counted into 50 kB bin pairs using the R package diffHic v1.6.0.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files give the number of reads supporting each interaction, where an interaction corresponds to a pair of 50 kB bins. The .mtx files are space-delimited text files in Matrix Market Exchange format with integer entries. The first two columns give the indices of the two interacting genomic bins and the third column gives the read count. Bin pairs with no reads are omitted. The indices correspond to rows of the BED format file GenomicRegions.bed.gz. The processed data files can be read into R using the readMTX2IntSet function of the diffHic package or the readMM function of the Matrix package.

source_name: B cells

extract_protocol: In situ HiC was performed as described by Rao et al (Cell 2014; PMID: 25497547).

tag: strain

value: C57B/6 male

value: Spleen

value: B lymphocytes


title: CD4+ T cells 2

source_name: Naïve CD4+ T cells

value: T lymphocytes


title: CD8+ T cells 1

source_name: Naïve CD8+ T cells


title: CD4+ T cells 1


title: cry1 cry2-BL rep2

description: rep2=biological replicate 2


title: hy5-BL rep2

description: rep2=biological replicate 2

source_name: hy5-BL, seedling

value: hy5 mutant


title: B cells 1


title: hy5-BL rep1

description: rep1=biological replicate 1


title: CD8+ T cells 2


title: MTSF1-B [Ribo-seq]

city: ORSAY

first: Pierre

last: Bertin

address: Batiment 400, Université Paris Sud

institute: Institut de Biologie Intégrative de la Cellule

description: Processed data file: genes_normacounts_processeddata.txt

data_processing:
Library strategy: Ribo-seq
Quality assessment with FastQC.
Low quality reads (< 30) and read’s adapters were trimmed using Cutadapt version 1.9.1 (selected kmer sizes were between 24 and 35 nucleotides).
RNA filtering was conducted mapping all reads on Arabidopsis RNA genes (www.arabidopsis.org). Unmapped reads with bowtie1.1.2 were conserved.
Filtered reads were mapped using bowtie 1.1.2 on the Col-0 genome (JF729201.1) allowing 2 mismatches.
Uniquely mapped reads were counted using featureCounts v1.5.0-p2 and normalised by the size of the genes to generate the processed file used in the study.
Genome_build: Col0 mitochondrial genome JF729201.1
Supplementary_files_format_and_content: genes_normacounts_processeddata.txt: Tabular file containing the count on each mitochondrial gene normalised by the size of the gene itself.

source_name: Arabidopsis mitochondria

growth_protocol: Plants were grown in a greenhouse in long day conditions for 10 to 12 weeks. Flowers were harvested simultaneously for all genotypes, snap-frozen in liquid nitrogen and stored at -80°C until use.

extract_protocol:
About 2.5 g of flowers were ground in liquid nitrogen and resuspended in 15 mL of ribosome extraction buffer.
Illumina TruSeq Small RNA RS-200-0012.

tag: ecotype/background

tag: genotype/variation

value: ppr mutant (nad4 mRNA stability)

value: flower

tag: organelle

value: mitochondria


title: WT-BL rep1

description: rep1=biological replicate 1

source_name: WT-BL, seedling

value: wild type


title: MTSF1-A [Ribo-seq]


title: MTL1-A [Ribo-seq]

value: ppr mutant (nad7 mRNA translation)


title: input rep2

first: Venkatesan

last: Sundaresan

address: One Shields Ave

department: Plant Biology

institute: University of California Davis

description: Chromatin IP against H3K27me3

data_processing:
Illumina Casava1.8 software used for basecalling.
The ChIP and input (non-IP) DNA sequencing data was subjected to trimming of adaptor biased 30 bp from 5’ end of reads using NGS QC Toolkit (Patel and Jain, 2012). These trimmed datasets were mapped to the rice genome (RGAP v7.0) using bowtie v2.0.0.7 (Langmead et al., 2009). SICER (Zang et al., 2009) with suitable parameters for H3K27me3 modification (200 bp window size and 600 bp gap size) was used to identify significantly ChIP-enriched domains (1% FDR) from ChIP DNA data against input DNA data in background. The normalized read count per 200 bp bins for 2 kb upstream region and the gene body were extracted using custom Perl script.
Genome_build: RGAP vs 7.0
Supplementary_files_format_and_content: wig file format with ChIP enriched peaks 1% FDR

organism: Oryza sativa

source_name: WT

growth_protocol: All rice plants were grown in greenhouse conditions of 30oC daytime and 25oC nighttime temperatures. Light regimes were dictated by natural light conditions.

extract_protocol:
Chromatin from approximately 1.6g of mature leaf tissue or 100 mg of immature panicle stage In7 was used for each immunoprecipitation with H3K27me3 antibody (Millipore 07-449). Chromatin Immunoprecipitation was performed essentially according to (Bowler et al., 2004) with the following exceptions. All three extraction buffers contained 1mM PMSF and lacked protease inhibitors. The nuclei lysis buffer was modified from (Saleh et al., 2008) with only 0.1% SDA and no protease inhibitors. Chromatin was sonicated on the high setting of a Bioruptor UCD-200 (Diagenode) for 8 thirty-second cycles to produce approximately 500 bp fragments. Immunoprecipitation was performed using Pierce Protein A/G Magnetic Beads (Thermo Scientific). Elution and reverse crosslinking of chromatin was performed simultaneously for 2 hours at 65oC. ChIP purified DNA was amplified using the Sigma Genomeplex Whole Genome Amplification (WGA2) kit following the manufacturer’s protocol (Sigma-Aldrich Co.).  Quantification of ChIP enrichment was performed by Quantitative PCR with ChIP and input (no IP) DNA samples. Primers were designed using the Beacon Designer software (BioRad). The rice ACTIN gene (Os03g50885) was utilized as a negative control for H3K27me3 with the following primers: Actin ChIP qPCR Forward: 5’-GCTGTTTGGATCTCAGGGTGGTTTC-3’ Actin ChIP qPCR Reverse: 5’-GCCGACAATGCTGGGGAAGAC-3’. Primers used to assayed OsMADS1, OsMADS22 and OsMADS34 are as follows: OsMADS1 qPCR For: 5’-GTAGCCAAACCACACCACCATAAAG-3’ OsMADS1 qPCR Rev: 5’-ATCTTCTTCCTCCTCCTCTCCTCTC-3’. OsMADS22 qPCR For4: 5’-GCCTTTGCCAGTTGCGGTGTTG-3’ OsMADS22 qPCR Rev4: 5’-GAGGGTGAGGTGAGGTGAGGTGAG-3’. OsMADS34 qPCR For: 5’-GTTTGTGTTGATTTGCTGGTCTGCTAGAG-3’ OsMADS34 qPCR Rev: 5’-CGATCCGCTGAAGCACCACCTTG-3’. OsMADS6 primers (MADS1506f and MADS1645r) can be found in (Zhang et al., 2010). Fold enrichment was calculated relative to ACTIN.
ChIP DNA samples described above were prepared for high throughput Illumina sequencing using the NuGEN Ovation Ultra Low DR Multiplex System 1-8 (NuGEN). 1ug of amplified ChIP DNA for each sample was sheared using the Covaris S220 Focused Ultrasonicator (Covaris Inc.) and approximately 166ng of this sheared DNA was put into each library. One hundred cycles of single read sequencing was performed on the Illumina HiSeq2000 machine (Illumina).

tag: cultivar

value: Dongjin

value: panicle

tag: age

value: WT


title: input rep3

description: Chromatin IP against H3K27me3


title: WT-BL rep2

description: rep2=biological replicate 2

value: blue light


title: ChIP rep2

description: Chromatin IP against H3K27me3

value: H3K27me3 (Millipore 07-449)


title: MTL1-B [Ribo-seq]


title: COL0-A [Ribo-seq]


title: COL0-B [Ribo-seq]


title: input rep1

description: Chromatin IP against H3K27me3


title: ChIP rep3

description: Chromatin IP against H3K27me3


title: ChIP rep1

description: Chromatin IP against H3K27me3


title: COL0-B [RNA-seq]

description:
Processed data file: col0_B_editing_summary.txt
Processed data file: sites_details.txt

data_processing:
Quality assessment with FastQC.
Low quality reads (< 30) were trimmed using Cutadapt version 1.9.1.
RNA filtering was conducted mapping all reads on Arabidopsis RNA genes (www.arabidopsis.org). Unmapped reads with bowtie1.1.2 were conserved.
Reads were mapped using bowtie 1.1.2 on the Col-0 genome (JF729201.1) allowing 0 mismatch. Mapping was done on the edited and non-edited version of the genome.
Uniquely mapped reads were used to generate the editing report for Col0 replicates.
Genome_build: Col0 mitochondrial genome JF729201.1 (edited and non-edited)
Supplementary_files_format_and_content: site_details.txt: Tabular file which contains the Gene (gene name), TrCoord (relative position in transcript) and TrSeq (sequence around the editing site) from the article of Bentolila S et al. (2013) Comprehensive High-Resolution Analysis of the Role of an Arabidopsis Gene Family in RNA Editing.
Supplementary_files_format_and_content: col0_[A,B]_editing_summary.txt: Tabular files containing the report from nucleotide counting at each editing site. GeneName, TrPos (relative position in transcript), Std (Standard deviation in Bentolila), Expected (editing ratio measured in Bentolila), Observed (editing ratio observed in our RNAseq data), Coverage (Number of read in the editing site), Status (Verified if close to the expected value, the margin used is expected_value +/- 2*std for value > 0.1. Otherwise, 0.1 is used as std), A T G and C (counts of each nucleotide at the editing site).

source_name: Arabidopsis whole cells

extract_protocol:
Total RNA extraction in Trizol from flowers. Total RNA were treated with DNase and rRNA were removed using Ribozero Plant Leaf.
Standard RNA-seq sequencing at Genewiz company (TruSeq RNA sample preparation v2).


title: COL0-A [RNA-seq]

description:
Processed data file: col0_A_editing_summary.txt
Processed data file: sites_details.txt


title: B cells 2

data_processing:
Reads pairs from each sample were aligned to the human genome and counted into 50 kB bin pairs using the R package diffHic v1.6.0.
Genome_build: hg38
Supplementary_files_format_and_content: Processed data files give the number of reads supporting each interaction, where an interaction corresponds to a pair of 50 kB bins. The .mtx files are space-delimited text files in Matrix Market Exchange format with integer entries. The first two columns give the indices of the two interacting genomic bins and the third column gives the read count. Bin pairs with no reads are omitted. The indices correspond to rows of the BED format file GenomicRegions.bed.gz. The processed data files can be read into R using the readMTX2IntSet function of the diffHic package or the readMM function of the Matrix package.

tag: subject

value: Peripheral blood

tag: cell type


title: B cells 1


title: RNA-Seq MIC APOE4_rep4

description:
COUNTS_MIC.txt
isogenic iPSC line derived microglia-like cells

source_name: iPSC-derived microglia

value: microglia-like cells

tag: passages


title: RNA-Seq MIC APOE4_rep1


title: RNA-Seq MIC APOE3_rep3

description:
COUNTS_MIC.txt
Parental iPSC ine derived microglia-like cells


title: CD8+ T cells 1


title: MHH-JK-11-Acu-1

city: MELBOURNE

first: SANGKYU

last: KIM

state: VICTORIA

address: 305 GRATTAN ST

department: RESEARCH

institute: PETER MACCALLUM CANCER CENTRE

data_processing:
Illumina CASAVA 1.8.2 software was used for base calling and low-quality reads (Q<30) were removed
Adapters were trimmed using Cutadapt v1.9
Reads were mapped to the human reference genome (hg10) using HISAT2
Read counting was performed using featureCounts part of the subread v1.5.0 software package
Limma-Voom method was applied for data normalisation and differential gene expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: csv file includes normalised counts for each sample

growth_protocol: MHH-CALL4 cells were cultured in RPMI 1640 media supplemented with penicillin (100 u/mL), streptomycin (100 mg/mL) and 20% FCS at 37°C under 5% CO2.

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA isolation kit (Macherey-Nagel) as per manufacturer's instructions
RNA libraries were prepared for sequencing according to standard protocols (QuantSeq 3’ mRNA-Seq FWD, Lexogen)

treatment_protocol: MHH-CALL4 cells were treated with vehicle (DMSO), CHZ868 (300 nM) or ruxolitinib (1000 nM) for 24 hours in duplicate and total RNA was freshly extracted for 3'-RNA-Seq. MHH-CALL4 cells were transduced with constitutive (pLMS-GFP) retroviral vectors harbouring shRNAs targeting JAK2 (shJAK2.209 or shJAK2.2826) or scrambled (shSCR) in duplicate and GFP+ cells were harvested at day 5 post-transduction for 3'-RNA-Seq.

tag: cell line

value: expressing CRLF2-rearranged/JAK2I682F

tag: replicate

value: replicate 1

tag: transduced with

tag: timepoint

value: Day 5 post-transduction


title: CD8+ T cells 2

value: T lymphocytes


title: MHH-JK-3-Acu-1


title: MHH-Scr-Acu-2

source_name: MHH-Scr-Acu

value: replicate 2

value: pLMS-shSCR


title: MHH-JK-3-Acu-2


title: MHH-JK-11-Acu-2


title: RNA-Seq MIC APOE3_rep1


title: RNA-Seq MIC APOE3_rep2


title: MHH-CHZ-1

source_name: MHH-CHZ

tag: treated with

value: 24 hr


title: MHH-Rux-2

source_name: MHH-Rux

value: 1000 nM Ruxolitinib


title: RNA-Seq MIC APOE3_rep4


title: CD4+ T cells 2


title: MHH-Rux-1


title: MHH-Veh-1

source_name: MHH-Veh

value: Vehicle


title: MHH-CHZ-2


title: MHH-Scr-Acu-1


title: CD4+ T cells 1


title: RNA-Seq MIC APOE4_rep3


title: RNA-Seq MIC APOE4_rep2


title: NPC_XY9 rep2

data_processing:
The raw data was first examed by fastqc to valid the sequencing quality
The raw data was mapped to mofidifed mouse reference genome(mm9) with SNP information between 129 and Cast strains(Xu et. al. Nature Genetics 49, 377–386 , 2017).
The mapped reads were assigned to each parental genome according to the SNP information.
Bam files were first converted into bedGraph using bedtools, then coverted into bigwig for visualization from UCSC brower.   Besides the genome-wide  bigwig file for each bam file,  we added two  bigwig files with allelic specific reads.  Genome1 files represent signal from the reads mapped to 129S1 genome only, genome2 files represnt the signal from the reads mapped to Cast genome only.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

source_name: neural progenitor cells

growth_protocol: NPCs were grown in N2/B27 media supplemented with 10 ng/mL FGF and EGF on 0.2% gelatin coated plates

extract_protocol:
RNA-seq data for NPC  cell lines was generated using the TruSeq protocol (Illumina) following ribosomal RNA depletion.
Briefly, 400 ng of RNA was fragmented and then reverse transcribed using SuperScript III.  After second strand synthesis, RNA cDNA was A-tailed and adapters were ligated.  DNA was cleaned up using Ampure XP beads and then PCR amplified using the TruSeq PCR cocktail.  Libraries were sequenced on a HiSeq instrument with 2x75 bp reads.

value: neural progenitor cells

tag: cell clone

tag: background strain (cross)

value: 129S1 x Cast:EiJ F1

tag: gender

value: male


title: NPC_XY9 rep1


title: NPC_XY10 rep2


title: NPC_XY10 rep1


title: NPC_XY8 rep1


title: Input (NPC_XX1)

data_processing:
The raw data was first examined by fastqc to valid the sequencing quality
The raw data was mapped to modified mouse reference genome(mm9) with SNP information between 129 and Cast strains.
Mapped reads with mapping quality more than 10 were kept
PCR duplications(redundancy reads ) were removed by Picard
The remained reads were assigned to each parental genome according to the SNP information
Final bam files from each replicates or re-sequencing runs were merged together. Bam files were first converted into bedGraph using bedtools, then coverted into bigwig for visualization from UCSC brower.   Besides the genome-wide  bigwig file for each bam file,  we added two  bigwig files with allelic specific reads.  Genome1 files represent signal from the reads mapped to 129S1 genome only, genome2 files represent the signal from the reads mapped to Cast genome only.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

extract_protocol:
Nuclei were lysed and chromatin was resuspended in sonication buffer
The chromatin was sonicated to average 220 bp and incubated with antibody overnight at 4'C.  Antibody-bound chromatin was incubated with Protein G Dynabeads (Invitrogen, 10004D) for 4 hours at 4’C and eluted in Tris buffer (10mM Tris pH 8.0, 10mM EDTA, 1% SDS).  Crosslinks were reversed by incubation overnight at 65’C followed by treatment with 0.2 mg/mL proteinase K (Life Technologies, AM2548) and 0.2 mg/mL RNAse A (Qiagen).
DNA was purified using Qiagen Minelute Columns (Qiagen, 28006).  Libraries were prepared by DNA tagmentation (Nextera) followed by PCR amplification.

treatment_protocol: Cells were fixed 1% formaldehyde for 10 minutes at room temperature and subsequently quenched with 0.125 M glycine.

tag: cell number

value: 5M per replicate

value: female

tag: chip antibody

value: IgG


title: NPC_XY7 rep1


title: H3K4me3 ChIP-seq (NPC_XX1)

value: H3K4me3 (Active Motif, Cat#39159)


title: H3K9me3 ChIP-seq (NPC_XX1)

value: H3K9me3 (Abcam, Cat#ab8898)


title: H3K9me3 ChIP-seq (ESC_XX1)

source_name: mouse embryonic stem cells

growth_protocol: mESCs were grown in medium supplemented with fetal bovine serum (FBS) and mLIF on 0.2% gelatin-coated plates.

value: mouse embryonic stem cells


title: MHH-Veh-2

tag: genotype/variation

value: expressing CRLF2-rearranged/JAK2I682F


title: DPL2KO_C7

city: wuhan

first: Wei

last: Miao

state: hubei

address: donghu south road #7

institute: Institute of hydrobiology, CAS

data_processing:
Adaptors of raw reads were trimmed by Trim-Galore (version 0.4.0)
mRNA-Seq data processing: Trimmed-reads were mapped to the Tetrahymena themophila MAC genome (version 2014: http://ciliate.org/index.php/home/downloads) using TopHat (version 2.0.9).Genes expression values were quantify to the number of fragments per kilobase of exon per million fragments mapped (FPKM) using Cuffdiff (version 2.1.1).
Genome_build: Tetrahymena themophila MAC genome (version 2014: http://ciliate.org/index.php/home/downloads)
Supplementary_files_format_and_content: FPKM table matrix

organism: Tetrahymena thermophila

source_name: Conjugation cells

growth_protocol: Tetrahymena thermophila cells were grown in SPP medium at 30 oC.  For conjugation, log-phase growing cells (~200k cells/ml) of two different mating types were washed, starved (~16 hrs) and mixed in Dryl’s buffer (2 mM sodium citrate, 1 mM NaH2PO4, 1 mM Na2HPO4, 1.5 mM CaCl2, pH 6.8) at 30°C.

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols. First strand specific libraries were constructed using the Illumina TruSeq Stranded mRNA Sample Prep Kit (RS-122-2101). The Poly-A tailed mRNA as purified using the Sera‐Mag Magnetic Oligo(dT) Beads. The mRNA fragmentation, first strand cDNA synthesis, second strand cDNA synthesis, A tailing, adaptor ligation and PCR amplification were performed according to the stranded mRNA sample preparation guide of the kit.  Sequencing (Single-end (52X1) for C3 and C6, Paired-end (101x2) FOR C10) was performed using an Illumina HiSeq 2000 sequencer (DNA Sequencing Core of University of Michigan).

tag: strain

tag: genotype

value: DPL2 Knock out

tag: time point

value: Conjugation 7 hours


title: H3K4me3 ChIP-seq (ESC_XX1)


title: DPL2KO_C6

value: Conjugation 6 hours


title: wildtype_C7

value: WT


title: DPL2KO_C3

value: Conjugation 3 hours


title: NPC_XY8 rep2


title: DPL2KO_C4

value: Conjugation 4 hours


title: wildtype_C5

value: Conjugation 5 hours


title: wildtype_C4


title: wildtype_C3


title: wildtype_C6


title: set9set26_rep1_H3ChIPseq

city: Ithaca

first: Siu

middle: Sylvia

last: Lee

state: NY

address: 520 Campus road

institute: Cornell University

description: set9set26H3K4me3ChIP_pooled_bedgraph_forIGFview.bedgraph

data_processing:
Two replicate ChIP-Seq raw data were pooled. Raw data were first filtered by fastx_trimmer and fastq_quality_filter
bowtie2 was used to align reads to WS250 genome
PCR duplicate was removed by samtools and the data were converted to bam files
bamCoverage was used to generate bedgraph files
Genome build: WS250
Supplementary_files_format_and_content: bedgraph containing z-score in 50bp window

growth_protocol: L4 worms were cultured and harvested on NGM plates

extract_protocol:
Crosslinked protein-DNA complex were isolated with antibody.
ChIP-seqw libraries were prepared for sequencing using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB)

value: set-9 set-26

tag: developmental stage


title: wt_rep1_H3K4me3ChIPseq

description: wtH3K4me3ChIP_pooled_bedgraph_forIGFview.bedgraph


title: wt_rep2_H3K4me3ChIPseq


title: set9set26_rep2_ribominusRNAseq

description:
total RNA after removing ribo-RNA
n2set9set26set9set26rnaseq.txt

data_processing:
Rawdata was filtered by fastq_quality_filter, adaptor was cut by cutadapt  and rRNA was  removed by bowtie2;
tophat2 was used to align reads to WS250 genome
cufflink was used to generate raw count for each gene
EdgeR was used to calculate the significant changed gene
Genome build: WS250
Supplementary_files_format_and_content: excel containing raw counts

extract_protocol:
RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using Ovation Human FFPE RNA-Seq Library Systems (NuGEN) kit


title: set9set26_rep1_H3K4me3ChIPseq


title: set9set26_rep2_H3K4me3ChIPseq


title: wt_rep1_H3ChIPseq


title: NPC_XY7 rep2

tag: cell type

value: neural progenitor cells

value: 129S1 x Cast:EiJ F1


title: set9set26_rep1_ribominusRNAseq


title: set26_rep2_ribominusRNAseq


title: DPL2KO_C5


title: set9_rep2_ribominusRNAseq


title: Input (ESC_XX1)

value: 5M per replicate


title: set26_rep1_ribominusRNAseq


title: set9_rep1_ribominusRNAseq


title: wt_rep2_ribominusRNAseq


title: set9set26_rep2_H3ChIPseq