title: HIV-1 CEM-SS PA-m6A-seq

city: Durham

first: Edward

middle: Matthew

last: Kennedy

state: NC

address: Department of Molecular Genetics and Microbiology, Box 3025

department: Molecular Genetics and Microbiology

institute: Duke University

data_processing:
Library strategy: PA-m6A-seq
Initial reads were quality filtered with Cassava 1.8.2.
Reads >14 nt were collapsed into FASTA format with the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html) using the following pipeline: fastq_quality_filter –Q 33| fastq_to_fasta –Q 33 | fastx_clipper -a TruSeq-Index# -l 15 –c | fastx_collapser.
All reads were then subject to alignment using Bowtie v.0.12.7 (Langmead et al., 2009) with the following options: –a --best --strata –m 25.  The reads were sequentially aligned and filtered to adapter sequences, then the human genome 19 with one mismatch, and then the HIV-1 strain of interest with one mismatch.
Bowtie alignments were then used for direct visualization with IGV or PARLyzer V 1.1 with default parameterization, these data were further processesed with an in house Perl scripts.
Genome_build: HIV-1 genomes were constructed from the publically available molecular clone sequences for NL4-3 and JR-CSF, the BaL sequence was used previously in Whisnant,A 2014 (PMID: 23592263)
Supplementary_files_format_and_content: Processed data are in a tab-delineated BED format presented as chromosome/gene, starting location for aligned read relative to the start of the gene beginning at 1, ending position of the aligned read, aligned reads per million of total library reads, and these are aligned to the HIV-1 strain of interest.

source_name: CEM-SS

growth_protocol: DMEM or RPMI 1640  where appropriate for cell type, and 4-thiouridine for all experiments

extract_protocol: All samples were processed with the Illumina Tru-seq small RNA-seq kit

treatment_protocol: 16-24hr 4-thiouridine pulse

tag: cell line

value: CEM-SS

tag: virus

value: HIV-1 NL4-3


title: HIV-1 YTHDF2-FL PAR-CLIP U3TM

status: Public on May 01 2016

type: SRA

country: USA

library_source: transcriptomic

data_processing:
Library strategy: PAR-CLIP
Initial reads were quality filtered with Cassava 1.8.2.
Reads >14 nt were collapsed into FASTA format with the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html) using the following pipeline: fastq_quality_filter –Q 33| fastq_to_fasta –Q 33 | fastx_clipper -a TruSeq-Index# -l 15 –c | fastx_collapser.
All reads were then subject to alignment using Bowtie v.0.12.7 (Langmead et al., 2009) with the following options: –a --best --strata –m 25.  The reads were sequentially aligned and filtered to adapter sequences, then the human genome 19 with one mismatch, and then the HIV-1 strain of interest with one mismatch.
Bowtie alignments were then used for direct visualization with IGV or PARLyzer V 1.1 with default parameterization, these data were further processesed with an in house Perl scripts.
Genome_build: HIV-1 genomes were constructed from the publically available molecular clone sequences for NL4-3 and JR-CSF, the BaL sequence was used previously in Whisnant,A 2014 (PMID: 23592263)
Supplementary_files_format_and_content: Processed data are in a tab-delineated BED format presented as chromosome/gene, starting location for aligned read relative to the start of the gene beginning at 1, ending position of the aligned read, aligned reads per million of total library reads, and these are aligned to the HIV-1 strain of interest.

molecule: total RNA

organism: Homo sapiens

value: 293T clonally expressing YTHDF2-FL

tag: transfection

value: U3/NF-kB/TAR mutant indicator


title: NOMO-1_BRD9_ab66443_ChIPSeq

city: Cold Spring Harbor

first: Anja

middle: Fides

last: Hohmann

state: NY

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

description: ChIP-Seq

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the mm9 or hg19 genome assembly using bowtie with default parameters.
To call the peaks, MACS 1.4.2 software was used.
To generate density maps, all Brg1 peaks with an FDR <0.05% and a minimal fold enrichment of 5 over input were used. Heatmaps matrices were created by counting tags using 20 kb windows with 50 bp bins. Heatmap matrices were visualized by Java TreeView 1.1.6r4.
To generate hockeystick plots of Brd9 peaks in RN2 cells, peaks were called using MACS 1.4.2 software with a 50bp shift size and all peaks with a FDR <25% and a minimal fold enrichment of 3.5 over input were used.
To quantify FLAG-BRD9 and Brg1 chromatin occupancy after BI-7273 treatment, high confidence peaks (FDR <10%, minimal fold enrichment of 10 over input) were identified among DMSO treated RN2 FLAG-BRD9 and untransduced RN2 cells. Tag counts for these locations were then re-calculated from uniquely mapped reads in both, DMSO and BI-7273 treated samples, and normalized to the total number of uniquely mapped reads in each data set. Changes in occupancy after BI-7273 treatment were then quantified as the fold change of normalized tag counts between BI-7273 and DMSO treated samples for each of the identified high confidence peaks. To exclude regions of minimal occupancy, peaks with tag counts between 40 and 200 were excluded from the analysis of FLAG-BRD9 and Brg1 binding alterations, respectively.
Genome_build: murine: mm9, human: hg19
Supplementary_files_format_and_content: peak information was generated by MACS software

molecule: genomic DNA

growth_protocol: Cultures were maintained in RPMI medium 1640 supplemented with 10% FBS, 1% Pen/Strep.

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with appopriate sizes were prepared for sequencing.
These libraries were made following the instructions of illumina Truseq DNA sample prep kit v2.

treatment_protocol: To assess changes in chromatin binding upon BI-7273 treatment, cells were cultured in DMSO or BRD9 inhibitor for 24 hours before harvest.

tag: cell type

value: Acute myeloid leukemia

tag: genotype

tag: treatment

tag: antibody

value: BRD9 (ab66443; Abcam)


title: HIV-1 YTHDF2-FL PAR-CLIP U3T

value: U3/NF-kB/TAR indicator


title: HIV-1 BaL YTHDF1-FL PAR-CLIP

value: 293T clonally expressing YTHDF1-FL

value: HIV-1 BaL


title: HIV-1 NL4-3 GFP-FL PAR-CLIP

value: 293T clonally expressing GFP-FL


title: HIV-1 BaL YTHDF2-FL PAR-CLIP


title: HIV-1 NL4-3 YTHDF2-FL PAR-CLIP


title: HIV-1 JR-CSF YTHDF2-FL PAR-CLIP

value: HIV-1 JR-CSF


title: HIV-1 NL4-3 YTHDF1-FL PAR-CLIP


title: HIV-1 JR-CSF YTHDF1-FL PAR-CLIP


title: KYSE510_6hr_50 nM

city: Singapore

first: Phillip

middle: H

last: Koeffler

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute

data_processing:
Fastq files were aligned to reference genome using STAR aligner by providing ensemble75 gtf file as known junctions.
Gene expression was quantified (in terms of FPKM) against ensemble v75 genes using Cufflinks programme with arguments -G ens75.gtf -b -u –max-bundle-frags 1000000
Genome_build: hg19
Supplementary_files_format_and_content: Expression abundances in terms of FPKM as measured by cufflinks against ensemble version 75 genes.

molecule: polyA RNA

growth_protocol: KYSE510 cell lines is cultured in RPMI-1640 medium; TE7 is maintained in Dulbecco’s modiﬁed Eagle medium (DMEM). All media are supplemented with 10% fetal bovine serum (Invitrogen, San Diego, CA), penicillin (100 U/mL) and streptomycin (100 mg/mL).

extract_protocol:
Total RNA from each sample was extracted according to the manufacturer’s instruction of RNeasy Mini kit (QIAGEN).
RNA library was prepared using TruSeq Library Prep Kit (Illumina) according to the manufacturer’s instructions and subjected to massive parallel sequencing using Hiseq (Illumina) at Beijing Genomics Institute.

treatment_protocol: TE7 and KYSE510 cells were treated with either THZ1 or DMSO, and harvested at indicated time points, with indicated concentrations.

value: Esophageal squamous cell carcinoma (ESCC)

tag: drug

tag: concentration

tag: time point (hrs)


title: HIV-1 NL4-3 YTHDF3-FL PAR-CLIP

value: 293T clonally expressing YTHDF3-FL


title: TE7_2hr_50 nM


title: KYSE510_12hr_50 nM


title: KYSE510_6hr_200nM


title: TE7_0hr

value: DMSO


title: TE7_6hr_50 nM


title: TE7_6hr_200nM


title: TE7_12hr_50 nM


title: TE7_4hr_50 nM


title: TE7_Input

data_processing:
Raw fastq files were aligned to reference genome using bowtie aligner with parameters -e 70 -m 2 -k 2 -n 2 –best –strata
Peak calling was done using MACS14 with default paraemeters.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files representing pileup for every 50 base pair bins normalized to reads per million (RPM)

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
DNA fragments were end-pair repaired foloowed by adapter ligation. Later these fragments were PCR-amplified and size selected (100-300 bp).

tag: chip antibody


title: KYSE510_2hr_50 nM


title: KYSE510_H3K27Ac

tag: chip antibody vendor

value: AbCam

tag: chip antibody cat. #

tag: chip antibody lot #


title: TE7_H3K27Ac


title: RNA-seq_Control_rep2

city: Chong Qing

first: Xianfeng

last: Li

address: Da ping

department: Department of Gastroenterology, Daping Hospital

country: China

institute: Army Medical University (Third Military Medical University)

data_processing:
Basecalls performed using CASAVA version 1.8
The low quality reads and adapter sequences were firstly removed from the raw reads. The quality of resulted clean reads was checked by FastQC
To estimate gene expression level and identify differentially expressed genes between H2O2-treated and untreated HCT116 cells, sequencing library derived from poly(A)-enriched cellular RNA were sequenced on Illumina high throughput sequencing platform in paired-end mode. After using script Trim Galore to trim off sequencing adaptors, low quality sequencing reads and then estimate sequencing data qualities, reads with Phered-scaled quality<20 were discarded. Software STAR was used to map reads to genome with default parameters.
We used bioconductor package DESeq to identify differentially expressed genes between H2O2-treated HCT116 and untreated HCT116 based on number of mapped paired-end reads counted by python package HTSeq (http://www.htseq.org/) for each gene. Each sample has two biological replicates, respectively. The method for estimateDispersions in DESeq was set to "pooled" and the fit type was set "local".
Genome_build: UCSC hg19
Supplementary_files_format_and_content: Tab-delimited text files include DESeq output information.

source_name: human colon cancer cells

extract_protocol:
Total RNA was harvested using RNeasy Mini Kit (QIAGEN, Germany). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
Total RNAs were extracted from H2O2-treated HCT116 and untreated HCT116 cells with RNeasy Mini Kit (QIAGEN, Germany). Quality control was performed using Bioanalyser 2100 (RNA nano kits, Agilent). mRNA-Seq libraries were generated from total RNA with polyA+ selection of mRNA using the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA), and then subjected to transcriptome sequencing on the Illumina Hiseq 2000

tag: agent

value: Control

value: colon cancer cells


title: RRBS_Control_HCT116

data_processing:
Basecalls performed using CASAVA version 1.8
The low quality reads and adapter sequences were firstly removed from the raw reads. The quality of resulted clean reads was checked by FastQC
RRBS reads were aligned to the hg19 genome assembly using SOAP2 with two mismatches allowed in the seed (40 bp)
Unique mapped reads were used for DNA methylation information extraction with software RRBS-Analyser
Genome_build: UCSC hg19
Supplementary_files_format_and_content: Tab-delimited text files include methylation information of each chromosone for each Sample.Scores represent chromosone,position,strand,Cpattern,Csequence,copy number,methylC reads number,unmethylC reads number,binomial expection

extract_protocol:
Total DNA of HCT116 cell line with or without H2O2 treatment was extracted by proteinase K/phenol.
For each library, 500 ng of genomic DNA was digested overnight with MspI (20 units). After purification, the digested products were blunt-ended. Then dA was added, followed by methylated-adapter (Illumina, CA, USA) ligation. To obtain DNA fractions in 40-120 bp and 120-220 bp range of MspI-digested products, two ranges (160-240 bp and 240-340 bp) of adapter-ligated fractions were excised from 2% agarose gel. The size-selected DNA was bisulfite-treated for two rounds using EpiTect Bisulfite Kit (Qiagen, Venlo, Netherlands) following the manufacturer’s standard protocol. Finally, libraries were generated by amplification with HiFi HotStart Uracil+ ReadyMix (KAPA, MA，USA) and Illumina Multiplexing PCR Primers. Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA) and RT-PCR were used to guarantee the quality and quantity of RRBS library. After RRBS library construction, Illumina HiSeq 2000 was used to sequence those libraries according to the manufacturer’s protocol.


title: RRBS_H2O2_HCT116


title: RNA-seq_H2O2_rep1


title: KYSE510_4hr_50 nM


title: KYSE510_0hr


title: KYSE510_Input


title: RNA-seq_Control_rep1


title: SH-SY5Y

city: St Lucia

first: Kathleen

last: Yin

state: Queensland

address: 306 Carmody Rd

department: Institute of Molecular Biosciences

country: Australia

institute: University of Queensland

data_processing:
FASTQ data generation: CASAVA 1.8.2. Reads were screened for the presence of any adaptor or overrepresented sequences, ambiguous characters were clipped where required, and sequence bias was corrected.
Alignment: performed with Tophat with default analysis parameters in single-end mode. The number of mismatches were restricted to no more than 2 bases.
Assembly: Performed by Cufflinks with the reference annotation-based assembly option (RABT) using the UCSC annotation, and multi-reads correction was used.
Count: Gene counts were compiled using the HTSeq software
Genome_build: mm9 (DRGs, F-11, ND7/23), hg19 (SH-SY5Y), rn5 (F-11, ND7/23)
Supplementary_files_format_and_content: .txt files, tab-delimited.

source_name: SH-SY5Y human neuroblastoma immortal cells

extract_protocol:
Whole DRGs were removed and immediately put into RNALater and cut into pieces in RNA later. RNA was extracted using the Rneasy Mini kit (Qiagen). Cultured cells were trypsinised and centrifuged and RNA was processed.
RNA libraries were prepared using for RNA-Seq

tag: strain

tag: tissue


title: SSEA1 posB biological replicate 2

city: London

first: Paola

last: Scaffidi

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

description: FAIRE-Seq

data_processing:
Alignments were performed using the CASAVA pipeline (version 1.8.2) with default parameters.
Nucleosome-depleted regions were  identified by the peak calling program F-seq (Boyle, Bioinformatics., 2008).
Genome_build: hg19
Supplementary_files_format_and_content: Bed files containing coordinates of FAIRE peaks for each FAIRE-Seq samples generated in the study. Called sites were filtered to only include the top 50000 regions for each sample.

source_name: in vitro transformed human skin fibroblasts

growth_protocol: Cells were grown in minimum essential medium (MEM) containing  15% fetal bovine serum (FBS), 2 mM L-glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin, at 37 °C in 5% CO2.

extract_protocol:
FAIRE DNA was purified by phenol-chloroform extraction follwing the protocol decribed in Simon et al. Nat Protocols, 2012.
Library construction (Illumina TruSeq 2.0 protocol) and sequencing was performed at NCI sequencing facility (SAIC-Frederick, MD) on the Illumina HiSeq 2000.

treatment_protocol: SSEA1+ cells were isolated by cell sorting from a population of in vitro-transformed fibrobalsts derived from hTERT-immortalized skin fribroblasts.

tag: cell line

value: SSEA1+ CSCs


title: RNA-seq_H2O2_rep2


title: RKO_uv0.5h

city: Seoul

first: Jiyeon

last: Park

address: 222, Banpo-daero

department: Catholic Center for Precision Medicine Research

country: South Korea

institute: The Catholic University of Korea

description: nuclear RNA

data_processing:
Basecalls performed using CASAVA (Illumina).
Reads were mapped to reference genome using bowtie2 (local mode)
The poly(A) site supporting (PASS) reads are those with unique alignment with the genome and having at least two extra 5’Ts (corresponding to the poly(A) sequence) after alignment.
Poly(A) sites identified by PASS reads were clustered if located within 24 nt from each other, and were further assigned to genes using the RefSeq information.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each pA

source_name: RKO colon cancer cell

growth_protocol: RKO cell lines were cultured in Eagle's minimal essential medium (EMEM) and Dulbecco’s modified Eagles medium (DMEM) respectively. Media were supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin antibiotic.

extract_protocol:
Nuclear RNA was purified using the RNeasy kit (Qiagen) following manufacturer’s protocol.
Total RNA was processed by the 3’ READS method as previously described (Nat Methods. 2013 Feb;10(2):133-9.)
3'READS (a recently developed deep sequencing method for analysis of APA isoform expression genome-wide)

treatment_protocol: Colon carcinoma RKO cells were treated with UV irradiation and allowed to recover for 0.5 hr or 2 hr.

value: a poorly differentiated colon carcinoma cell line

value: RKO

value: UV 0.5h


title: hTERT 66A biological replicate 1

description: FAIRE-Seq

source_name: hTERT-immortalized human skin fibroblasts

value: hTERT skin fibroblasts


title: genomic_activated_memory

city: Bruce

first: Kristine

last: Hardy

state: ACT

address: University of Canberra

institute: University of Canberra

data_processing:
Adapters stripped using cutadapt -m 10
Reads mapped with Bowtie2 using local alignment. Only uniquely mapped reads used.
Duplicates removed using Picard
Wig files from HTSEQ, reads extended 200bp.
Peaks called for PKC against relevant TI, called with MACS2 (parameters --keep-dup all  -g hs -s 50 --bw 200 -q 0.05 then qvalue filtered to be < 0.01)
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files show tag densities for the different cell types/treatments for antibody (PKC) and Total Input (TI). Bed files are peaks for PKC against TI.

source_name: primary T cells

growth_protocol: Isolation of primary human CD4+ T cells from Buffy Coats was performed at the AMR, Sydney. Buffy Coats were obtained from the Australian Red Cross Institute, Sydney. Peripheral mononuclear cells (PBMCs) from these individuals were isolated using Ficoll-Hypaque extraction (GE Healthcare, 17-1440-03) and the Dynabeads® UntouchedTM Human CD4+ T Cells Kit (Invitrogen, Cat. Num. 113.46D) was used to negatively isolate total CD4+ T cells. Flow cytometry was used to isolate distinct primary human memory CD4+ T cell subsets. The isolation is based on the combination of cell-type specific surface markers namely, anti-CD4, CD25, CD62L, CD45RO, CD127.

extract_protocol:
ChIP samples were prepared with anti-PKC-theta (sc-212, SantaCruz), according to the protocol supplied by Upstate Biotechnology.
10ng of PKC-theta immunoprecipitated ChIP-DNA, and the corresponding total input (TI), were used to prepare the ChIP-seq DNA library using the NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina® (New England BioLabs Inc, NEB#E6240L) according to the manufacturer’s instructions. ChIP-DNA size was selected with AMPure XP beads (Beckman Coulter, Inc., Part #: A63881). The selected DNA was repaired with NEBNext End Repair Enzyme Mix and Buffer, followed by treatment with Klenow fragment (3’-5’ exo-) to generate “A” base overhangs. Subsequent adaptor ligation of the dA-tailed DNA was performed with 1.5μM NEBNext adaptor primers, Quick Ligation Reaction Buffer, and Quick T4 DNA ligase. AMPure beads were used to isolate library fragments ranging between 175 and 225bp in size and the purified DNA was combined with the NEBNext High-Fidelity 2X PCR Master mix, 25μM Universal PCR primer, and 25μM index primer for multiplexing purposes (New England BioLabs Inc, NEBNext® Multiplex Oligos for Illumina®, NEB#E7335L). A total of 15 cycles were used for PCR amplification of the adaptor-ligated DNA. The resultant ChIP-DNA library was subjected to DNA purification with AMPure beads. The quality of the ChIP-DNA library was assessed on a Bioanalyzer. A total of 2nM was captured on the Illumina flow cell for cluster generation

value: CD4+ primary T cells

tag: cell surface markers

value: none (total input)


title: genomic_jurkat

description:
Jurkat_TI
This sample is an equal mixture of total input from Jurkat cells unstimulated and stimulated with PMA and Ionomycin

source_name: Jurkat cell line

growth_protocol: The Jurkat T cell line (Clone E6-1, ATCC® TIB-152) was cultured at 37C  in complete  RPMI medium with FCS

treatment_protocol: The Jurkat T cell line (Clone E6-1, ATCC® TIB-152) was cultured at 37C  in complete  RPMI medium.

value: Jurkat T-cell leukemia cell line


title: genomic_naive

value: CD4+ CD45RO- CD62L+ CD127hi CD25-


title: genomic_resting_memory


title: genomic_effector_memory


title: PKC_jurkat_re-stim

description:
Re-ST_PKC
Jurkat cells stimulated for 4h with PMA and Ionomycin and then washed and cultured for 9 days and restimulated with PMA and Ionomycin for 2 h.

treatment_protocol: The Jurkat T cell line was activated at 5x105 cells/mL by using 24ng/mL of phorbol 12-myristate 13-acetate (PMA; Sigma-Aldrich, P8139) and 1μM calcium ionophore (I; Sigma-Aldrich, A23187).  The process of stimulus withdrawal involved centrifuging Jurkat T cells for 10 minutes, at 1200rpm, room temperature. Supernatant was discarded followed by re-suspension in stimulus-free complete RPMI-1640 medium. This was repeated 3 times before re-suspending these previously activated Jurkat T cells at a density of 5x105 cells/mL in complete stimulus-free RPMI medium for cell resting. After 9 days of resting cells were re-stimulated with PMA and calcium ionophore.

value: prestimulation and PMA and Ionomycin

value: PKCtheta (SantaCruz, catalog# sc-212, lot# K0713)


title: PKC_jurkat_resting

description:
SW_PKC
Jurkat cells stimulated for 4h with PMA and Ionomycin and then washed and cultured for 9 days

treatment_protocol: The Jurkat T cell line was activated at 5x105 cells/mL by using 24ng/mL of phorbol 12-myristate 13-acetate (PMA; Sigma-Aldrich, P8139) and 1μM calcium ionophore (I; Sigma-Aldrich, A23187).  The process of stimulus withdrawal involved centrifuging Jurkat T cells for 10 minutes, at 1200rpm, room temperature. Supernatant was discarded followed by re-suspension in stimulus-free complete RPMI-1640 medium. This was repeated 3 times before re-suspending these previously activated Jurkat T cells at a density of 5x105 cells/mL in complete stimulus-free RPMI medium for cell resting.

value: prestimulation


title: PKC_jurkat_stim

description:
ST_PKC
Jurkat cells stimulated for 4h with PMA and Ionomycin

treatment_protocol: The Jurkat T cell line was activated at 5x105 cells/mL by using 24ng/mL of phorbol 12-myristate 13-acetate (PMA; Sigma-Aldrich, P8139) and 1μM calcium ionophore (I; Sigma-Aldrich, A23187).

value: PMA and Ionomycin


title: PKC_effector_memory

value: PKCtheta (SantaCruz, catalog# sc-212, lot# I2110)


title: PKC_jurkat_nonstim


title: RKO_uv0.0h

description: nuclear RNA

value: baseline


title: PKC_activated_memory


title: RKO_uv2.0h

description: nuclear RNA

value: UV 2 h


title: 1-L

city: Wuhan

first: xiaoyi

last: wang

address: Xudong 2nd Road,Hubei,P.R.ChinaWuha

institute: Oil crops research institute, Chinese academy of agriculture sciences

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the SoyBase soybean genomics database (http://www.soybase.org/)
Clean tags mapped to reference sequences from multiple genes were filtered, and the remaining clean tags were designated as unambiguous clean tags. The number of unambiguous clean tags for each gene was calculated and then normalized to TPM (number of transcripts per million clean tags)
A rigorous algorithm was used to identify DEGs between two samples. Using this algorithm, statistical information (e.g., p value, FDR, expression level, and log2 ratio) corresponding to the DEGs was obtained. In this study, we used “FDR ≤ 0.001 and the absolute value of log2 ratio ≥ 1” as the threshold to determine the significance of gene expression differences.
Genome_build: the SoyBase soybean genomics database (http://www.soybase.org/)
Supplementary_files_format_and_content: Excell files include TPM values for each gen in each Sample

organism: Glycine max

source_name: plant

growth_protocol: The cultivated soybean (Tianlong 2) and wild soybean (ED059) varieties used in this study were acquired from the Institute of Oil Crops Research, Chinese Academy of Agricultural Sciences, Wuhan, China. Seeds were pre-germinated on moistened filter paper in a plant growth chamber at 27 °C, 85% ambient humidity, and 16:8 (light: dark) photoperiod for 3–4 d. The seedlings were then transferred into 18 cm × 18 cm individual plastic pots with nutrient-rich soil (Pinnstrup Substrate, Denmark) and vermiculite at a ratio of 2:3 at 27 C under 16 h of light. All plants used in the experiments had three fully expanded trifoliates.

extract_protocol:
Total RNA was extracted using Trizol reagent (Sigma). Using Oligo(dT) magnetic beads adsorption to purify mRNA, and then use Oligo(dT) as primer to synthesize cDNA.
At least 10 µg of total RNA (≥300 ng/µL) was extracted from samples for Solexa sequencing. Sample preparation, library construction, sequencing, and bioinformatics analysis were prepared for sequencing using standard Illumina protocols. The samples were sequenced by an Illumina HiSeq2000 platform, and 35 bp paired-end reads were produced.

treatment_protocol: The second fully expanded leaves were used. For H. armigera treatment, the second fully expanded leaves were infected with three third-instar larvae of H. armigera. After 24 h, the wounded local leaves were harvested (1-L and 2-L), flash frozen in liquid nitrogen, and stored at −80 °C until RNA isolation. Samples from untreated plants were used as controls (1L and 2L).

value: leaf

tag: age

value: three fully expanded trifoliates

value: soybean (Tianlong 2)


title: hERT 66B biological replicate 2

description: FAIRE-Seq


title: P3_G12 - BT20_5000_day2

city: Boston

first: Marc

last: Hafner

state: MASSACHUSETTS

address: WAB 438, 200 Longwood Av.

department: Systems Biology

institute: Harvard Medical School

description: BT20 cells seeded at 5000 cells per well (384-well plate), harvasted 3 days after seeding

data_processing:
Paired reads were used for analysis if all sixteen bases of the first read had quality scores of at least 10 and the first six bases corresponded exactly to a designed well-barcode.
All second sequence reads were aligned to a reference database consisting of all human RefSeq mRNA sequences (hg19) and the ERCC RNA spike-in reference sequences using bwa version 0.7.4 4 with non-default parameter “-l 24”.
Reads mapped to multiple genes were excluded from further analysis.
Digital gene expression (DGE) profiles were then generated by counting, for each microplate well and RefSeq gene, the number of unique molecular identifiers (UMIs) associated with alignments to that gene in that well.
Genome_build: hg19
Supplementary_files_format_and_content: tab-separated file with columns as samples (labelled as P3_*) and genes as rows with UMI count for each gene/sample pair.

growth_protocol: All cells lines were obtained from the ATCC and grown according to their recommendations.

extract_protocol:
RNA was extracted using the RNeasy mini kit (Qiagen).
The 3’-DGE libraries were prepared from total RNA according to the Single Cell RNA Barcoding and Sequencing method originally developed for single cell RNA-seq (SCRB-seq, Soumillon et al., 2014) and adapted to extracted total RNA. Briefly, Poly(A)+ mRNA from extracted total RNA are converted to cDNA decorated with universal adapters, sample-specific barcodes and unique molecular identifiers (UMIs) using a template-switching reverse transcriptase. Decorated cDNA from multiple samples are then pooled, amplified and prepared for multiplexed sequencing using a modified transposon-based fragmentation approach that enriches for 3’ ends and preserves strand information.

treatment_protocol: No treatment

tag: growth time (days)

tag: seeding density (cell/well)


title: SSEA1 posA biological replicate 1

description: FAIRE-Seq

value: SSEA1+ CSCs


title: 1L

tag: genotype

value: Soybean (Tianlong 2)


title: P3_D12 - BT20_1250_day2

description: BT20 cells seeded at 1250 cells per well (384-well plate), harvasted 3 days after seeding


title: P3_C12 - BT20_1250_day2


title: P3_F12 - BT20_2500_day2

description: BT20 cells seeded at 2500 cells per well (384-well plate), harvasted 3 days after seeding


title: P3_E12 - BT20_2500_day2


title: PKC_resting_memory

tag: treatment

tag: cell type


title: P3_B12 - BT20_625_day2

description: BT20 cells seeded at 625 cells per well (384-well plate), harvasted 3 days after seeding


title: PKC_naive


title: P3_F11 - BT20_2500_day1

description: BT20 cells seeded at 2500 cells per well (384-well plate), harvasted 2 days after seeding


title: P3_H11 - BT20_5000_day1

description: BT20 cells seeded at 5000 cells per well (384-well plate), harvasted 2 days after seeding


title: P3_E11 - BT20_2500_day1


title: P3_D11 - BT20_1250_day1

description: BT20 cells seeded at 1250 cells per well (384-well plate), harvasted 2 days after seeding


title: P3_C11 - BT20_1250_day1


title: P3_G11 - BT20_5000_day1


title: P3_B11 - BT20_625_day1

description: BT20 cells seeded at 625 cells per well (384-well plate), harvasted 2 days after seeding


title: P3_A11 - BT20_625_day1


title: P3_A10 - BT20_625_day0

description: BT20 cells seeded at 625 cells per well (384-well plate), harvasted 1 days after seeding


title: P3_E10 - BT20_2500_day0

description: BT20 cells seeded at 2500 cells per well (384-well plate), harvasted 1 days after seeding


title: P3_D10 - BT20_1250_day0

description: BT20 cells seeded at 1250 cells per well (384-well plate), harvasted 1 days after seeding


title: P3_B10 - BT20_625_day0


title: P3_C10 - BT20_1250_day0


title: P3_F10 - BT20_2500_day0


title: P3_F9 - SKBR3_2500_day2

description: SKBR3 cells seeded at 2500 cells per well (384-well plate), harvasted 3 days after seeding


title: P3_H10 - BT20_5000_day0

description: BT20 cells seeded at 5000 cells per well (384-well plate), harvasted 1 days after seeding


title: P3_E9 - SKBR3_2500_day2


title: P3_H12 - BT20_5000_day2


title: P3_D9 - SKBR3_1250_day2

description: SKBR3 cells seeded at 1250 cells per well (384-well plate), harvasted 3 days after seeding


title: P3_C9 - SKBR3_1250_day2


title: P3_A9 - SKBR3_625_day2

description: SKBR3 cells seeded at 625 cells per well (384-well plate), harvasted 3 days after seeding


title: P3_A12 - BT20_625_day2


title: P3_G9 - SKBR3_5000_day2

description: SKBR3 cells seeded at 5000 cells per well (384-well plate), harvasted 3 days after seeding


title: P3_F8 - SKBR3_625_day1

description: SKBR3 cells seeded at 625 cells per well (384-well plate), harvasted 2 days after seeding


title: P3_B9 - SKBR3_625_day2


title: P3_G10 - BT20_5000_day0


title: P3_G8 - SKBR3_2500_day1

description: SKBR3 cells seeded at 2500 cells per well (384-well plate), harvasted 2 days after seeding


title: P3_E8 - SKBR3_313_day1

description: SKBR3 cells seeded at 313 cells per well (384-well plate), harvasted 2 days after seeding


title: P3_H9 - SKBR3_5000_day2


title: P3_D8 - SKBR3_156_day1

description: SKBR3 cells seeded at 156 cells per well (384-well plate), harvasted 2 days after seeding


title: P3_H7 - MCF10A_2500_day2

description: MCF10A cells seeded at 2500 cells per well (384-well plate), harvasted 3 days after seeding


title: P3_B8 - MCF10A_5000_day2

description: MCF10A cells seeded at 5000 cells per well (384-well plate), harvasted 3 days after seeding


title: P3_F7 - MCF10A_1250_day2

description: MCF10A cells seeded at 1250 cells per well (384-well plate), harvasted 3 days after seeding


title: C5 mRNA

city: Edmonton

first: Guanxiang

last: Liang

state: Alberta

address: 410 Agriculture/Forestry Centre

country: Canada

institute: University of Alberta

data_processing:
All the RNA-seq reads were demultiplexed according to their index sequences using CASAVA version 1.8 (Illumina)
Paired end fastq files were mapped to refenrence genome by using Tophat 2.0.10 with default parameters.
The output mapping files from the TopHat2 alignment, along with the GTF file from ENSEMBL (http://uswest.ensembl.org/) bovine gene annotation v75.30, were used in the htseq-count (http://www-huber.embl.de/users/anders/HTSeq/) to count the total number of reads mapped to each gene.
The expression level of mRNAs in each library was obtained by normalizing reads number to counts per million reads (CPM): CPM = (gene reads number / total mapped reads number per library) × 1,000,000.
All the small RNA reads were demultiplexed according to their index sequences using CASAVA version 1.8 (Illumina)
The small RNAs sequencing reads with good quality were subjected to 3’ adaptor sequence trimming by miRDeep2
The miRNA expression (CPM) were identified by miRDeep2, while piRNA expression (CPM) were identified by costumised Perl program based on method descibed by other studies (Liu et al., 2012.PLoS ONE 7(4): e34770).
Genome_build: UMD3.1
Supplementary_files_format_and_content: Tab-delimited text files include CPM values for each Sample

organism: Bos taurus

source_name: Non-infected ileal tissues

extract_protocol:
The tissue samples were frozen on liquid nitrogen, and RNA was extracted using Trizol reagent. Illumina TruSeq small RNA Sample Prep Kit (Cat#RS-200-0012) was used with 1 ug of total RNA for the construction of small RNA sequencing libraries.  Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2001) was used with 1 ug of total RNA for the construction of RNA sequencing libraries.
RNA-seq libraries and small RNA libraries were prepared for sequencing using standard Illumina protocols

value: Non-infected ileal tissues

tag: infection

value: Non-Infected


title: P3_A7 - MCF10A_313_day2

description: MCF10A cells seeded at 313 cells per well (384-well plate), harvasted 3 days after seeding


title: P3_C7 - MCF10A_625_day2

description: MCF10A cells seeded at 625 cells per well (384-well plate), harvasted 3 days after seeding


title: P3_D5 - SKBR3_2500_day1


title: P3_C8 - SKBR3_156_day1


title: P3_G5 - SKBR3_313_day1


title: P3_B5 - SKBR3_1250_day1

description: SKBR3 cells seeded at 1250 cells per well (384-well plate), harvasted 2 days after seeding


title: P3_G7 - MCF10A_2500_day2


title: P3_D7 - MCF10A_625_day2


title: P3_F5 - SKBR3_5000_day1

description: SKBR3 cells seeded at 5000 cells per well (384-well plate), harvasted 2 days after seeding


title: C2 mRNA


title: P3_C5 - SKBR3_2500_day1


title: P3_E7 - MCF10A_1250_day2


title: C1 mRNA


title: C4 mRNA


title: P3_A8 - MCF10A_5000_day2


title: M5 mRNA

source_name: MAP-infected ileal tissue

value: MAP-infected ileal tissue

value: MAP-Infected


title: P3_B7 - MCF10A_313_day2


title: P3_A5 - SKBR3_1250_day1


title: M4 mRNA


title: P3_H4 - SKBR3_625_day1


title: M2 mRNA


title: P3_G4 - SKBR3_625_day1


title: M3 mRNA


title: M1 mRNA


title: P3_F4 - SKBR3_5000_day0

description: SKBR3 cells seeded at 5000 cells per well (384-well plate), harvasted 1 days after seeding


title: C5 microRNA


title: P3_E4 - SKBR3_5000_day0


title: C4 microRNA


title: C1 microRNA


title: M3 microRNA


title: M4 microRNA


title: P3_G3 - SKBR3_625_day0

description: SKBR3 cells seeded at 625 cells per well (384-well plate), harvasted 1 days after seeding


title: M5 microRNA


title: P3_B4 - SKBR3_1250_day0

description: SKBR3 cells seeded at 1250 cells per well (384-well plate), harvasted 1 days after seeding


title: M1 microRNA


title: P3_F3 - MCF10A_5000_day1

description: MCF10A cells seeded at 5000 cells per well (384-well plate), harvasted 2 days after seeding


title: M2 microRNA


title: P3_E3 - MCF10A_5000_day1


title: IL_42_5

data_processing:
All the reads were demultiplexed according to their index sequences using CASAVA version 1.8 (Illumina)
Paired end fastq files were mapped to refenrence genome by using Tophat 2.0.10 with default parameters.
The output mapping files from the TopHat2 alignment, along with the GTF file from ENSEMBL (http://uswest.ensembl.org/) bovine gene annotation v75.30, were used in the htseq-count (http://www-huber.embl.de/users/anders/HTSeq/) to count the total number of reads mapped to each gene.
The expression level of mRNAs in each library was obtained by normalizing reads number to counts per million reads (CPM): CPM = (gene reads number / total mapped reads number per library) × 1,000,000.
Genome_build: UMD3.1
Supplementary_files_format_and_content: Tab-delimited text files include CPM values for each Sample

source_name: ileum, D42

extract_protocol:
The tissue samples were frozen on liquid nitrogen, and RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#RS-200-0012) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tag

value: ileum, D42

value: ileum


title: IL_42_4


title: P3_B3 - MCF10A_2500_day1

description: MCF10A cells seeded at 2500 cells per well (384-well plate), harvasted 2 days after seeding


title: IL_42_3


title: IL_42_2


title: P3_A3 - MCF10A_1250_day1

description: MCF10A cells seeded at 1250 cells per well (384-well plate), harvasted 2 days after seeding


title: P3_H2 - MCF10A_1250_day1


title: IL_42_1


title: IL_21_5

source_name: ileum, D21

value: ileum, D21


title: P3_D3 - MCF10A_2500_day1


title: P3_D4 - SKBR3_2500_day0

description: SKBR3 cells seeded at 2500 cells per well (384-well plate), harvasted 1 days after seeding


title: IL_21_4


title: IL_21_3


title: P3_C2 - MCF10A_313_day1

description: MCF10A cells seeded at 313 cells per well (384-well plate), harvasted 2 days after seeding


title: IL_21_2


title: C3 microRNA


title: IL_7_5

source_name: ileum, D7

value: ileum, D7


title: P3_F2 - MCF10A_625_day1

description: MCF10A cells seeded at 625 cells per well (384-well plate), harvasted 2 days after seeding


title: C2 microRNA


title: IL_21_1


title: P3_B2 - MCF10A_156_day1

description: MCF10A cells seeded at 156 cells per well (384-well plate), harvasted 2 days after seeding


title: P3_A4 - SKBR3_1250_day0


title: P3_C4 - SKBR3_2500_day0


title: C3 mRNA


title: P3_E5 - SKBR3_5000_day1


title: P3_A2 - MCF10A_156_day1


title: P3_G2 - MCF10A_625_day1


title: P3_H1 - MCF10A_5000_day0

description: MCF10A cells seeded at 5000 cells per well (384-well plate), harvasted 1 days after seeding


title: P3_E2 - MCF10A_625_day1


title: P3_D2 - MCF10A_313_day1


title: P3_F1 - MCF10A_2500_day0

description: MCF10A cells seeded at 2500 cells per well (384-well plate), harvasted 1 days after seeding


title: IL_7_3


title: IL_7_2


title: IL_7_1


title: P3_E1 - MCF10A_2500_day0


title: P3_D1 - MCF10A_1250_day0

description: MCF10A cells seeded at 1250 cells per well (384-well plate), harvasted 1 days after seeding


title: IL_0_2

source_name: ileum, D0

value: ileum, D0


title: IL_0_1


title: P3_B1 - MCF10A_625_day0

description: MCF10A cells seeded at 625 cells per well (384-well plate), harvasted 1 days after seeding


title: P3_C1 - MCF10A_1250_day0


title: DJ_42_5

source_name: distal-jejunum, D42

value: distal-jejunum, D42

value: distal-jejunum


title: DJ_42_4


title: P3_H3 - SKBR3_625_day0


title: DJ_42_1


title: 4121_DAPT_shRBPJ-2

city: Cleveland

first: Tyler

middle: E

last: Miller

state: Ohio

department: Stem Cell Biology and Regenerative Medicine

institute: Cleveland Clinic Lerner Research Institute

data_processing:
For gene expression analysis, reads were aligned to the hg19 genome build (retrieved from http://cufflinks.cbcb.umd.edu/igenomes.html), using Tophat v2.0.6 (Trapnell et  al., 2009).
The distribution of alignments was analyzed using the CollectRnaSeqMetrics module of Picard v1.89 (http://picard.sourceforge.net/).
FPKM values for known genes were calculated using Cufflinks v2.0.2 (Trapnell et al., 2010) provided with the GTF file via the -G (known genes only) option. FPKM values were Quantile Normalized.
Genome_build: Hg19
Supplementary_files_format_and_content: FPKM values from Cufflinks

source_name: Primary Patient Derived Tumor Model

growth_protocol: See Individual Samples

extract_protocol:
RNA was extracted from ~1x10^6 cells with TRIzol (Invitrogen), separated using Phase Lock Gel tubes (5 Prime), and purified using the miRNAeasy kit (Qiagen) according to the manufacturer’s protocol.
Total RNA was prepared for sequencing by the CWRU Genomics Core using the Illumina stranded TruSeq RNA Sample Preparation Kit according to the manufacturer's protocol.
RNA-seq libraries were sequenced on the Illumina HiSeq 2500 platform at the Case Western Reserve University Genomics Core Facility.

tag: tumor model

tag: treatment 1

value: shRNA #2 against RBPJ

tag: treatment 2

value: 5uM DAPT


title: DJ_42_3


title: DJ_21_5

source_name: distal-jejunum, D21

value: distal-jejunum, D21


title: P3_A1 - MCF10A_625_day0


title: 4121_DAPT_NT

value: Nontargeting shRNA


title: 4121_DAPT_shRBPJ-1

value: shRNA #1 against RBPJ


title: IL_7_4


title: 4121_DMSO_shRBPJ-2

value: DMSO


title: 4121_DMSO_shRBPJ-1


title: P3_G1 - MCF10A_5000_day0


title: DJ_21_4


title: P3_H8 - SKBR3_313_day2

description: SKBR3 cells seeded at 313 cells per well (384-well plate), harvasted 3 days after seeding


title: IL_0_3


title: 4121_DMSO_NT


title: DJ_21_3


title: DJ_21_2


title: 3691_DAPT_10um

value: 10uM DAPT


title: 3691_DAPT_5um


title: DJ_21_1


title: DJ_7_5

source_name: distal-jejunum, D7

value: distal-jejunum, D7


title: DJ_7_3


title: 3691_DMSO


title: DJ_7_2


title: 3691_NT


title: 3691_shRBPJ-1


title: DJ_7_1


title: FBL_T1RNase_HEK_rep2

city: Basel

first: Rafal

last: Gumienny

state: CH

address: Im Ettingerhof 8

department: Biozentrum

country: Switzerland

institute: University of Basel

description: snoRNA and target chimera

data_processing:
The raw reads were processed on the CLIPZ server (www.clipz.unibas.ch; Khorshid et al., Nucleic Acids Research 2011, 39:D245 (PMID 21087992)).
For subsequent analysis multimapping reads were also considered
Calculations were done directly on the bed (with genomic coordinates of reads mapped) and fasta files (with sequences of reads unmapped).
Genome_build: hg19 Feb 2009
Supplementary_files_format_and_content: bed file with genomic coordinates of reads mapped; columns: chromosome, start, end, name, count, strand.  Fasta file with sequences of reads unmapped.

growth_protocol: HEK-293 cells grown in DMEM Sigma) with 10% FCS

extract_protocol:
Immunoprecipitation with anti-Fibrillarin Antibody
CLIP protocol executed as described in Martin et al., Cell Reports, 2012,  Vol 1, p. 753, PMID:22813749

treatment_protocol: 2x 10^8 Cells UV crosslinked with 254 nm. Cell lysis in lysis buffer and treatment with RNAse I to fragment the RNA.

value: Flp-In 293 cell line (from Invitrogen)

tag: ip antibody

value: anti-Fibrillarin; mouse monoclonal (Cytoskeleton, catalog# AFB01, lot# 011)


title: Lea1 rep1 ChIP-nexus in T4V1-26 mutant

first: Stirling

last: Churchman

state: MA

address: NRB Rm 356, 77 Ave Loius Pasteur

department: Genetics

description: DNA isolated by ChIP against Lea1-TAP

data_processing:
Library strategy: ChIP-nexus
For NET-seq libraries were sequened in 76 base pair reads for all NextSeq libraires. For reads shorter than 75 basepairs respectively the adapter sequenice  (ATCTCGTATGCCGTCTTCTGCTTG) was trimmed from the fastq files and files were filtered using PrinSeq version prinseq-lite-0.20.2 (http://prinseq.sourceforge.net). For ChIP-nexus reads were filtered for the presence of the fixed barcode CTGA, and for reads shorter than 60 basepairs the adapter sequence (AGATCGGAAGAGCACACGTCT) was trimmed.
For NET-seq the linker contained a molecular barcode with a random hexamer sequence. These random hexamers were removed using custom python scripts.For ChIP-nexus the remaining molecular barcode sequence was removed before alignment to the genome.
For NET-seq data were then aligned to the SacCer3 genome using the TopHat2 aligner v2.0.5 and reverse transcription mispriming events are identified and removed where molecular barcode sequences correspond exactly to the genomic sequence adjacent to the aligned read. For ChIP-nexus data were aligned to the sacCer3 genome using Bowtie version 1.1.1 .
For both NET-seq and ChIP-nexus only the 5' position of the read is recorded with a custom python script using HTSeq package in python . NET-seq data are stranded while ChIP-nexus contain strand data merged into a single file that is unstranded.
Genome_build: sacCer3
Supplementary_files_format_and_content: bedgraph: Chromosome, Start, End, Score

organism: Saccharomyces cerevisiae BY4741

source_name: yeast BY4741, mid-exponential phase

growth_protocol: Yeast strains were grown in YPD at 30°C with shaking from an initial OD of 0.05 to mid-log phase with an OD of 0.6-0.8. For NET-seq in pSMF2 WT1-8 CTD and yKH303 T4V 1-8 CTD cells were grown at  30°C in sc-Lue media in the presense of 50 microgram per mL doxycylcine with shaking from an initial OD of 0.05 to mid-log phase with an OD of 0.6-0.8.

extract_protocol:
For NET-seq frozen cells were cryogenically pulverized for lysis and nascent RNA was isolated via an immunoprecipitation at 4°C of Rpb3-3xFLAG and purified using the miRNeasy kit (Qiagen, 217004). For ChIP-nexus cells were crosslinked in 1% formaldehyde, lysed by bead beating, and sonicated. Chomatin was isolated via immunoprecipitation using phospoh-CTD antibodies or TAP tagged subunits.
For NET-seq nascent immunoprecipitated RNA was fragmented by alkaline hydrolysis followed by size selection after electrophoresis on a polyacrylamide gel.RNA was treated with polynucleotide kinase (NEB) followed by ligation to a preadenylated RNA linker. The remainder of the library construction was done as described inte NET-seq library construction. All samples were sequenced using an Illumina NextSeq 500 in 75 base pair reads. For ChIP-nexus the library constrution was preformed as desribed in He, Q., Johnston, J., Zeitlinger, J. (2015) "ChIP-nexus enables improved detection of in vivo transcription factor binding footprints." Nature Biotechnology. Samples were sequenced on an Illumina MiSeq in 60 bp single end reads.

tag: genotype/variation

value: BY4741, rpb3::rpb3-3xFLAG NAT, , lea1::lea1-TAP HIS3, rpo21::rpo21-CTDT4V KAN


title: Lea1 rep2 ChIP-nexus in T4V1-26 mutant

description: DNA isolated by ChIP against Lea1-TAP

tag: strain


title: Mud1 rep2 ChIP-nexus in T4V1-26 mutant

description: DNA isolated by ChIP against Mud1-TAP

value: BY4741, rpb3::rpb3-3xFLAG NAT, mud1::mud1-TAP HIS3, rpo21::rpo21-CTDT4V KAN


title: RiboMethSeq_HEK_nuclear2

data_processing:
The 3' adapter was trimmed with cutadapt (cutadapt v1.8, --adapter TGGAATTCTCGGGTGCCAAGG) , --minimum-length 15)
Reads were mapped to custom genome with STAR (STAR_2.4.0j, --outFilterMultimapNmax 20,  --outFilterMismatchNoverLmax 0.05, --scoreGenomicLengthLog2scale 0, --outSAMattributes All).
Output from STAR was converted from SAM to BED with samtools v1.2 and bamToBed (bedtools v2.25.0) (samtools view -S input.sam -b -u | bamToBed -tag NH > output.bed)
Positions of 5' (beginnings) and 3' (ends) were extracted and converted to bedGraph using custom python script with HTSeq
Genome_build: Custom STAR index base.d on ENSEMBL GRCh37/hg19 unspliced protein coding genes extracted with BioMart, rRNAs, snRNAs, snoRNAs, lincRNAs and miscRNAs. The custom genome is a human hg19 assembly version-based transcriptome composed of rRNAs, snRNAs, snoRNAs, lincRNAs, miscRNAs, and all unspliced protein coding genes (obtained from hg19 version of ENSEMBL, http://grch37.ensembl.org/index.html), supplemented with a set of tRNAs.
Supplementary_files_format_and_content: bedGraph files were generated using custom script with HTSeq python package.  Columns: chromosome (transcript) name, start, end, coverage.

extract_protocol:
total RNA was extracted using TRI Reagent (#T9424), poly(A)+ RNA was enriched using Dynabeads mRNA direct kit (# 61012), according to manufacturer's instructions. Nuclear and cytoplasmic RNA fraction were collected with the REAP method (PMID: 21067583)
Libraries were prepared following the protocol of Birkedal et al. (PMID: 25417815) using Illumina-compatible adapters and primers. After adapter ligation DNA was PCR amplified with Illumina primers for 16 cycles and library fragments of ~140-160 bp (insert plus adaptor and PCR primer sequences) were band isolated from an non-denaturing polyacrylamide gel. The purified DNA was captured on an Illumina HiSeq2500 flow cell for cluster generation. Libraries were sequenced following the manufacturer's protocols.

tag: passages

tag: origin

value: ATCC CRL-1573

tag: rna fraction

value: nuclear


title: RN2_BI-7273_Input_ChIPSeq

data_processing:
ChIP-seq reads were aligned to the mm9 or hg19 genome assembly using bowtie with default parameters.
To call the peaks, MACS 1.4.2 software was used.
To generate density maps, all Brg1 peaks with an FDR <0.05% and a minimal fold enrichment of 5 over input were used. Heatmaps matrices were created by counting tags using 20 kb windows with 50 bp bins. Heatmap matrices were visualized by Java TreeView 1.1.6r4.
To generate hockeystick plots of Brd9 peaks in RN2 cells, peaks were called using MACS 1.4.2 software with a 50bp shift size and all peaks with a FDR <25% and a minimal fold enrichment of 3.5 over input were used.
To quantify FLAG-BRD9 and Brg1 chromatin occupancy after BI-7273 treatment, high confidence peaks (FDR <10%, minimal fold enrichment of 10 over input) were identified among DMSO treated RN2 FLAG-BRD9 and untransduced RN2 cells. Tag counts for these locations were then re-calculated from uniquely mapped reads in both, DMSO and BI-7273 treated samples, and normalized to the total number of uniquely mapped reads in each data set. Changes in occupancy after BI-7273 treatment were then quantified as the fold change of normalized tag counts between BI-7273 and DMSO treated samples for each of the identified high confidence peaks. To exclude regions of minimal occupancy, peaks with tag counts between 40 and 200 were excluded from the analysis of FLAG-BRD9 and Brg1 binding alterations, respectively.
Genome_build: murine: mm9, human: hg19
Supplementary_files_format_and_content: peak information was generated by MACS software

organism: Mus musculus

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with appopriate sizes were prepared for sequencing.
These libraries were made following the instructions of illumina Truseq DNA sample prep kit v2.

value: Acute myeloid leukemia

tag: antibody


title: Mud1 rep1 ChIP-nexus in T4V1-26 mutant

description: DNA isolated by ChIP against Mud1-TAP


title: P3_C3 - MCF10A_2500_day1

tag: growth time (days)


title: DJ_0_3

source_name: distal-jejunum, D0

value: distal-jejunum, D0

tag: tissue


title: RiboMethSeq_HEK_nuclear1

tag: cell line


title: DJ_0_2

value: distal-jejunum


title: RN2_DMSO_Input_ChIPSeq

tag: genotype

tag: treatment


title: Lea1 rep2 ChIP-nexus

description: DNA isolated by ChIP against Lea1-TAP

value: BY4741, rpb3::rpb3-3xFLAG NAT, , lea1::lea1-TAP HIS3


title: DJ_7_4


title: DJ_0_1


title: RiboMethSeq_HEK_cytoplasmic2

value: cytoplasmic


title: Lea1 rep1 ChIP-nexus

description: DNA isolated by ChIP against Lea1-TAP


title: Mud1 rep2 ChIP-nexus

description: DNA isolated by ChIP against Mud1-TAP

value: BY4741, rpb3::rpb3-3xFLAG NAT, mud1::mud1-TAP HIS3


title: 3691_shRBPJ-2

value: shRNA #2 against RBPJ


title: RN2_FLAG-BRD9_BI-7273_Input_ChIPSeq

tag: cell type


title: MJ_42_4

source_name: mid-jejunum, D42

tag: tag

value: mid-jejunum, D42

value: mid-jejunum


title: MJ_42_3


title: RN2_FLAG-BRD9_BI-7273_FLAG_ChIPSeq

value: FLAG (F1804; Sigma)


title: RN2_BI-7273_Brg1_ChIPSeq

value: Brg1 (ab110641; Abcam)


title: Mud1 rep1 ChIP-nexus

description: DNA isolated by ChIP against Mud1-TAP


title: Ser5P rep2 ChIP nexus

description: DNA isolated by ChIP against Ser5P

value: BY4741, rpb3::rpb3-3xFLAG NAT


title: RiboMethSeq_HEK_totalRNA_20min

value: total RNA

tag: protocol

value: alkaline hydrolysis

tag: time

value: 20 min


title: Ser5P rep1 ChIP nexus

description: DNA isolated by ChIP against Ser5P


title: MJ_42_2


title: RN2_FLAG-BRD9_DMSO_FLAG_ChIPSeq

value: DMSO


title: RiboMethSeq_HEK_polyARNA_8min

value: ATCC CRL-1573

value: polyA RNA

value: 8 min


title: RiboMethSeq_HEK_totalRNA_8min


title: RN2_FLAG-BRD9_DMSO_Input_ChIPSeq

value: Acute myeloid leukemia


title: RN2_DMSO_Brg1_ChIPSeq


title: MJ_21_5

source_name: mid-jejunum, D21

value: mid-jejunum, D21


title: MJ_42_5


title: Thr4P rep2 ChIP-nexus

description: DNA isolated by ChIP against THr5


title: 231/DKG_rep2

city: Duarte

first: Ching-Ying

last: Kuo

state: California

address: 1500 Duarte Rd.

institute: City of Hope/Beckman Research Institute

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using software Partek
Genome_build: hg19

source_name: breast cancer cells

growth_protocol: MDA-MB-231 cells were grown in DMEM supplemented with 10% FBS and pen/strep.

extract_protocol:
RNA was extracted using Trizol protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MDA-MB-231 cells were treated with daily DKG (10 mM, 4-days).

value: breast cancer

tag: gender

value: female


title: Thr4P rep1 ChIP-nexus

description: DNA isolated by ChIP against THr4


title: RiboMethSeq_HEK_totalRNA_14min

value: 14 min


title: RN2_Brg1_ChIPSeq

description: ChIP-Seq


title: RN2_Input_ChIPSeq

description: ChIP-Seq


title: pKH303_T4VCTD1-8 NET-seq

description: nascent RNA isolated by IP against Rpb3-3x FLAG affinity label

data_processing:
Library strategy: NET-Seq
For NET-seq libraries were sequened in 76 base pair reads for all NextSeq libraires. For reads shorter than 75 basepairs respectively the adapter sequenice  (ATCTCGTATGCCGTCTTCTGCTTG) was trimmed from the fastq files and files were filtered using PrinSeq version prinseq-lite-0.20.2 (http://prinseq.sourceforge.net). For ChIP-nexus reads were filtered for the presence of the fixed barcode CTGA, and for reads shorter than 60 basepairs the adapter sequence (AGATCGGAAGAGCACACGTCT) was trimmed.
For NET-seq the linker contained a molecular barcode with a random hexamer sequence. These random hexamers were removed using custom python scripts.For ChIP-nexus the remaining molecular barcode sequence was removed before alignment to the genome.
For NET-seq data were then aligned to the SacCer3 genome using the TopHat2 aligner v2.0.5 and reverse transcription mispriming events are identified and removed where molecular barcode sequences correspond exactly to the genomic sequence adjacent to the aligned read. For ChIP-nexus data were aligned to the sacCer3 genome using Bowtie version 1.1.1 .
For both NET-seq and ChIP-nexus only the 5' position of the read is recorded with a custom python script using HTSeq package in python . NET-seq data are stranded while ChIP-nexus contain strand data merged into a single file that is unstranded.
Genome_build: sacCer3
Supplementary_files_format_and_content: bedgraph: Chromosome, Start, End, Score

value: Mat-alpha, his3delta, leu2delta, lys2delta, met15delta, trp1delta, hisG URA CMV-tTA, kanRPtetO7-TATA-RPB1 rpb3::rpb3-3xFLAG NAT pKH301


title: RN2_Brd9_ChIPSeq

description: ChIP-Seq

value: Brd9 (ab66443; Abcam)


title: MJ_21_4

value: mid-jejunum


title: 231/DKG_rep1


title: RiboMethSeq_HEK_cytoplasmic1

value: cytoplasmic


title: MJ_21_3


title: RI48; smallRNA-Seq

city: New Haven

first: Haifan

last: Lin

state: Connecticut

address: 10 Amistad St.

department: Cell Biology

institute: Yale Univeristy

description:
small RNA-Seq
Sample 10

data_processing:
The raw sequence reads were first processed to remove reads with no 3' sequencing adaptor or of low quality. The trimmed reads were mapped against Oryza sativa and Magnaporthe oryzae genomes.
Genome_build: O. sativa ssp. indica; Magnaporthe oryzae
Supplementary_files_format_and_content: Supplementary_files_format_and_content: txt format. Content: 1st column is SEQUENCE; 2nd column is COUNT

organism: Oryza sativa Indica Group

source_name: fully expanded third leaf

growth_protocol: The rice seeds were sown in 30 cm ×20 cm×5 cm trays in a greenhouse, in seven rows and each row with 15-20 plants. Inoculation with blast spore was performed at the 3.5 leaf stage. A 20-ml spore suspension (105 spores/ml) was applied to each tray using an airbrush connected to a source of compressed air. The plants were then held in dark for 24 h at 95–100% relative humidity and 28℃, after which they were transferred to a greenhouse where the ambient temperature was maintained at 28℃. The fully expanded third leaf, which would show most severe symptom, was collected from 25 individual seedlings as one sample at each time point. Samples were collected at 8, 24 and 48 hours post inoculation, control samples were collected at 0 and 8 hours after being sprayed with water.

extract_protocol: Small RNA libraries were constructed using previously described methods. Briefly, 10–30 nt small RNAs were purified using a 15 % denaturing polyacrylamide gel , then ligated with 5′ and 3′ adapters, then converted to cDNA by RT-PCR using Superscript II reverse transcriptase (Invitrogen), small RNAs were amplified by PCR, gel-purified then submitted for deep sequencing using the Illumina Genome analyzer (Illumina) at the Beijing Genomics Institute (BGI, Shenzhen, China).

value: leaf

tag: cultivar

tag: condition

value: 48 hpi


title: MJ_21_2


title: SI48; smallRNA-Seq

description:
small RNA-Seq
Sample 9


title: 231_rep1


title: RN2 LP99 2

description: Samples28_29_31_32_RN2_DMSO_LP99_Rep1_2.txt

data_processing:
Sequenced reads were trimmed for adaptor sequence and mapped to mouse (mm9) or human (hg19) genome using Tophat with default parameters.
Cuffdiff software was used to compare gene expression profiles by calculting Fragments Per Kilobase of exon per Megabase of library size (FPKM) for each sample.
For biological replicates of shRNA experiments, two - three individual shRNAs were used. For BRD9 inhibitor assessement, all experiments were performed with two independent biological replicates
To define the expressed genes in further analysis of PolyA+ RNA-Seq, only the genes with FPKM≥5 in the control samples and FPKM>0 in the test samples were considered.
Processed data files contain a list of filtered genes with log-transformed fold change  of averaged FPKM values from two-three independent hairpins (shRNA experiments) or two biological replicates (inhibitor experiments) to their respective negative controls.
Genome_build: mouse: mm9; human: hg19
Supplementary_files_format_and_content: tab-delimited text file with FPKM values for samples

growth_protocol: Leukemia cell cultures were maintained in RPMI medium 1640 supplemented with 10% FBS, 1% Pen/Strep. Fibroblasts and HeLa cells were cultured in DMEM supplemented with 10% FBS, 1% Pen/Strep.

extract_protocol:
Total RNAs were extracted using Trizol reagent.
These libraries were prepared following the instructions of illumina Truseq RNA sample prep kit v2.

treatment_protocol: To define genes affected by BRD9 knockdown, cells which express dox-inducible shRNAs were cultured with Doxycyclin for 48 hour before harvest. To define genes affected by BRD9 inhibitor treatment, cells were cultured in DMSO or BRD9 inhibitor for 24 hours before harvest.

tag: strain


title: MJ_42_1

value: mid-jejunum, D42


title: MJ_21_1


title: sh55 hairpin AFTER biological replicate 3

description: RNA-Seq

data_processing:
Alignments were performed to human RefSeq genes archived in the Illumina iGenomes resource using RSEM (version 1.2.4; Li and Dewey 2011).
An existing pipeline developed within the Trinity software package (Grabherr et al., 2011) was used to perform differential expression analysis with DESeq (Anders and Huber, 2010) which is available as part of the Bioconductor project (Gentleman et al., 2004).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file containing TPM values generated by RSEM where gene names are rows and columns represent all RNA-Seq samples generated in the study

source_name: in vitro transformed human skin fibroblasts

growth_protocol: Cells were grown in minimum essential medium (MEM) containing Tet-free 15% fetal bovine serum (FBS), 2 mM L-glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin, at 37 °C in 5% CO2. Inducible cell lines were generated by introducing inducible pTRIPZ constructs V2THS_38052 (shH1.0-1) and V2THS_38055 (shH1.0-2) (Open Biosystems) in the cells.

extract_protocol:
Total cell RNA was prepared from the cells using RNAeasy reagents (Qiagen).
The Total RNA samples were quality controlled (QC) by using the 6000 Nano RNA Chip on the BioAnalyser 2100 (Agilent, Santa Clara, CA, USA) to insure RNA integrity and concentration before starting the procedure.  The Total RNA samples were subjected to Ribozero Gold (Epicentre Madison, U.S.A.) treatment to remove the rRNA fraction from the samples.  After this treatment we QC the samples again using the 6000 mRNA RNA Chip on the BioAnalyser 2100 (Agilent, Santa Clara, CA, USA) to check that there was sufficient reduction in the rRNA.  If the reduction in the rRNA was sufficient we continue to library preparation (TruSeq Stranded Total RNA-Seq Library Prep 15031048-E. Illumina San Diego, CA, USA).  This protocol by Illumina was adjusted to fit the samples sets.  We optimised this protocol to make better use of samples of lower RNA integrity and concentration.  The standard PCR cycling was also changed to match the concentration of the total RNA from the mRNA QC We also found that the final elution of 32.5µl with resuspension buffer was over diluting the libraries so we eluted using 16µl.  After this clean up stage the final QC on the DNA 1000 BioAnalyser 2100 chip (Agilent, Santa Clara, CA, USA) was performed. After passing the final QC the stranded total RNA-seq libraries were ready for Flowcell cluster formation on a cBot and then 101bp Paired End Sequencing by synthesis on the HiSeq 2500 was performed.

treatment_protocol: Cells were treated with 1µg/ml Doxycicline (dox) for 16h or 14d to induce knock-down, or let re-express the knocked-down protein by removing dox for 4d after the 14d dox treatment.

value: washDOX  (4d after Dox removal)


title: 231_rep2


title: RN2 DMSO 2_2

description: Samples28_29_31_32_RN2_DMSO_LP99_Rep1_2.txt and Samples28_30_31_33RN2_DMSO_I-BRD9_Rep1_2.txt

value: DMSO


title: RI24; smallRNA-Seq

description:
small RNA-Seq
Sample 8

value: 24 hpi


title: RN2 I-BRD9 1

description: Samples28_30_31_33RN2_DMSO_I-BRD9_Rep1_2.txt

value: BRD9 inhibitor


title: SI24; smallRNA-Seq

description:
small RNA-Seq
Sample 7


title: RN2 LP99 1


title: MJ_7_3

source_name: mid-jejunum, D7

value: mid-jejunum, D7


title: RC08; smallRNA-Seq

description:
small RNA-Seq
Sample 6

value: control 8 hour


title: SC08; smallRNA-Seq

description:
small RNA-Seq
Sample 5


title: MJ_7_4


title: sh55 hairpin AFTER biological replicate 1

description: RNA-Seq


title: sh55 hairpin DOX biological replicate 3

description: RNA-Seq

value: DOX  (14d Dox)


title: RI08; smallRNA-Seq

description:
small RNA-Seq
Sample 4

value: 8 hpi


title: RN2 DMSO 1_2

value: Acute myeloid leukemia


title: MJ_7_2


title: sh55 hairpin DOX biological replicate 2

description: RNA-Seq


title: RN2 I-BRD9 2


title: iMEF BI-7273 2

description: Samples12-15_iMEF_DMSO_vs_BI2_Rep1_2.txt

source_name: iMEF

value: Immortalized fibroblasts


title: MJ_7_1


title: iMEF DMSO 2


title: RC00; smallRNA-Seq

description:
small RNA-Seq
Sample 2

value: control 0 hour


title: iMEF BI-7273 1


title: sh55 hairpin DOX biological replicate 1

description: RNA-Seq


title: sh55 hairpin SHOT biological replicate 3

description: RNA-Seq

value: SHOT (16h Dox)


title: MJ_7_5

value: mid-jejunum


title: iMEF DMSO 1


title: SI08; smallRNA-Seq

description:
small RNA-Seq
Sample 3


title: sh55 hairpin SHOT biological replicate 2

description: RNA-Seq


title: MJ_0_2

source_name: mid-jejunum, D0

value: mid-jejunum, D0


title: sh55 hairpin AFTER biological replicate 2

description: RNA-Seq


title: MJ_0_3


title: MJ_0_1


title: sh55 hairpin NT biological replicate 3

description: RNA-Seq

value: NT  (uninduced)


title: RI48; RNA-Seq

description: Sample 10

data_processing:
We aligned short reads against genome sequences and annotations from both organisms as the reference. The O. sativa indica genome and annotations were retrieved from the Ensemble Plants Repository Release 8. For M. oryzae, sequences and annotations of super contigs of version 8 were downloaded from the Magnaporthe comparative Database. All reads mapping was carried out using TopHat 2.0.11. HTSeq 0.6.1p2  with intersection-nonempty option was adopted to count the number of reads in each gene given the alignment results of Tophat. Differentially expressed (DE) transcripts were then identified using edgeR, a count-based differential expression test tool based on Negative Binomial Distribution, with a False Discovery Rate (FDR) no more than 1%. The DE test is performed on rice and fungal genes altogether.
Genome_build: O. sativa ssp. indica; Magnaporthe oryzae
Supplementary_files_format_and_content: Supplementary_files_format_and_content: txt format. Content: output file genes.fpkm_tracking from cufflinks

extract_protocol:
Total RNA was extracted with TRIzol (Invitrogen, USA) from each sample according to the manufacturer's protocol. NanoDrop ND-1000 spectrophotometer (NanoDrop, USA) was used to quantify the concentration of total RNA.
RNA-seq was performed via HiSeq 2000(Illumina, USA) at Beijing Genome Institute (BGI) (Shenzhen, CHN).Briefly, oligo(dT) magnetic beads was employed to enrich mRNA and then interrupted mRNA to short fragments (about 200 bp), the mRNA fragments was treated as templates to synthesizethe first and second strand cDNA. Following by ligating sequencing adaptors to the fragments, the fragments were purified by agarose gel electrophoresis and enriched by PCR amplification. HiSeq 2000 was used to sequence the library products.

value: leaf

value: 48 hpi


title: SI48; RNA-Seq

description: Sample 9


title: RN2 DMSO 2


title: RN2 BI-7273 2


title: sh55 hairpin SHOT biological replicate 1

description: RNA-Seq


title: RU_42_5

source_name: rumen, D42

value: rumen, D42

value: rumen


title: RU_42_4


title: RN2 BI-7273 1


title: RI24; RNA-Seq

description: Sample 8

value: 24 hpi


title: RN2 DMSO 1

value: DMSO


title: sh55 hairpin NT biological replicate 2

description: RNA-Seq


title: RU_42_2


title: SI24; RNA-Seq

description: Sample 7


title: RC08; RNA-Seq

description: Sample 6


title: sh55 hairpin NT biological replicate 1

description: RNA-Seq


title: RU_42_3


title: sh52 hairpin AFTER biological replicate 3

description: RNA-Seq

value: washDOX  (4d after Dox removal)


title: sh52 hairpin AFTER biological replicate 2

description: RNA-Seq


title: iMEF shBrd9.1116

tag: shRNA


title: SC00; smallRNA-Seq

description:
small RNA-Seq
Sample 1


title: RU_42_1


title: SC08; RNA-Seq

description: Sample 5

value: control 8 hour


title: RI08; RNA-Seq

description: Sample 4


title: RU_21_5

source_name: rumen, D21

value: rumen, D21


title: sh52 hairpin AFTER biological replicate 1

description: RNA-Seq


title: iMEF shRen

value: shRen


title: SI08; RNA-Seq

description: Sample 3

value: 8 hpi


title: RU_21_4


title: sh52 hairpin DOX biological replicate 3

description: RNA-Seq

value: DOX  (14d Dox)


title: RU_21_3


title: sh52 hairpin DOX biological replicate 2

description: RNA-Seq


title: RC00; RNA-Seq

description: Sample 2

value: control 0 hour


title: RN2 shBrd9.1061

value: Acute myeloid leukemia


title: RN2 shBrd9.1116


title: SC00; RNA-Seq

description: Sample 1


title: RU_21_2


title: sh52 hairpin SHOT biological replicate 3

description: RNA-Seq

value: SHOT (16h Dox)


title: RN2 shBrd9.783


title: sh52 hairpin DOX biological replicate 1

description: RNA-Seq


title: RU_7_5

source_name: rumen, D7

value: rumen, D7


title: RU_21_1


title: DRG

data_processing:
FASTQ data generation: CASAVA 1.8.2. Reads were screened for the presence of any adaptor or overrepresented sequences, ambiguous characters were clipped where required, and sequence bias was corrected.
Alignment: performed with Tophat with default analysis parameters in single-end mode. The number of mismatches were restricted to no more than 2 bases.
Assembly: Performed by Cufflinks with the reference annotation-based assembly option (RABT) using the UCSC annotation, and multi-reads correction was used.
Count: Gene counts were compiled using the HTSeq software
Genome_build: mm9 (DRGs, F-11, ND7/23), hg19 (SH-SY5Y), rn5 (F-11, ND7/23)
Supplementary_files_format_and_content: .txt files, tab-delimited.

source_name: Mouse DRG neurons

extract_protocol:
Whole DRGs were removed and immediately put into RNALater and cut into pieces in RNA later. RNA was extracted using the Rneasy Mini kit (Qiagen). Cultured cells were trypsinised and centrifuged and RNA was processed.
RNA libraries were prepared using for RNA-Seq

value: L3, L4, L5 whole DRG neurons

value: Wild-type


title: RU_7_3


title: sh52 hairpin NT biological replicate 3

description: RNA-Seq

value: NT  (uninduced)


title: iMEF shBrd9.783

value: Immortalized fibroblasts


title: sh52 hairpin SHOT biological replicate 2

description: RNA-Seq


title: RN2 shRen


title: RU_7_2

value: rumen


title: RU_7_4


title: sh52 hairpin SHOT biological replicate 1

description: RNA-Seq


title: Parental Ba/F3

city: Worcester

first: Michael

middle: R.

last: Green

address: 364 Plantation Street

department: Molecular, Cell and Cancer Biology

institute: University of Massachusetts Medical School

data_processing:
Images were analyzed using OLB 1.9 and CASAVA_v1.8.2
TopHat v2.0.6 was used to map the sequences to mouse genome mm10
cuffdiff v2.0.1 was used to generate the differentially spliced isoforms.
Genome_build: mm10

source_name: cell line

growth_protocol: RPMI (10% FBS)

extract_protocol:
Trizol reagent
Illumina TruSeq RNA Sample Preparation Kit

tag: phenotype

value: parental (wild type)


title: Ba/F3-U2AF35(S34F)


title: sh52 hairpin NT biological replicate 1

description: RNA-Seq


title: RU_7_1


title: RU_0_3

source_name: rumen, D0

value: rumen, D0


title: APL 3

city: Shanghai

first: Jiang

last: Zhu

address: 197, rui-jin 2nd Road

institute: Shanghai institute of hematology

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
mRNA-seq reads were aligned to the mm10 genome assembly using Tophat version 2.0.6 with parameters: -r 100 -I 50000  --max-segment-intron 50000 -a 10 -g 10
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed  using DEGseq function package in R program version 2.10.0
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: leukemia progenitor

growth_protocol: GFP-labled APL cells were expanded in vivo via transplantation into syngeneic mice.

extract_protocol:
Total RNA was extracted with AMBION AM1560 kit.
Following "TruSeq RNA Sample Preparation Guide".

tag: sample type

value: GFP-labeled c-Kit+ mouse APL cells

value: FVB N/J


title: APL 1


title: RU_0_2


title: MP 3

source_name: bone marrow progenitor

value: Lin-Sca-1-c-Kit+ mouse bone marrow cells


title: MP 2


title: MP 1


title: mRNA_WT2

city: Bethesda

first: Hossein

last: Zare

address: 5o South Dr #1347

institute: NIH

description:
RNA-seq for E13.5 Wild type cerebellum No.2
processed data file: RPKMGeneList_cerebellum.xlsx

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were mapped to mm9 whole genome using Bowtie(Langmead et al, 2009), and TopHat(Trapnell C, et.al 2009) for RNA-Seq
H3k27me3 peaks were called using SICER Algorithm ( Zang et al, 2009) with the following setting: window size (200bp), window pvalue (0.2), gap size(600bp) and the FDR of 0.05
FPKM(RPKM) and differential expression analysis was done using Cufflink/Cuffdiff (Trapnell C, et.al 2009) with multi-reads correction and geometric normalization
Genome_build: mm9

source_name: WT_embryonic cerebellum

growth_protocol: The cerebella were directly dissected out from E13.5 embryos.

extract_protocol:
We abstracted mRNA by using the Rneasy mini kit (Qiagen). For genomic DNA, we use Qiaquick Mini kit (Qiagen)
For ChIPSeq, tissues were cross-linked in 1% formaldehyde. The chromatin was sonicated to 250 bp fragments. Histone-DNA complexes were isolated with H3K27me3 antibody (Millipore). Purified DNA was processed according to manufacturer's protocol. For polyA RNA-Seq, Illumina protocol was followed.

treatment_protocol: For RNA-seq samples, we dropped the freshly dissected tissues into RNAlater (Ambion). For ChIP-seq samples, we fixed the freshly dissected cerebellar with 1%PFA for 15 minutes at room temperature.

tag: strain background

tag: developmental stage

tag: genotype/variation

value: wild type

value: embryonic cerebellum


title: H3K27me3_Ezh2KO

description: ChIP-seq for E13.5 Ezh2KO cerebellum No.1

source_name: H3K27me3_Ezh2KO_embryonic cerebellum

value: Ezh2 deletion

tag: tissue

tag: chip antibody

value: anti-trimethyl-histone H3 (Lys27) (Millipore, Cat# 07-449, Lot# 2607758)


title: mRNA_WT4

description:
RNA-seq for E13.5 Wild type cerebellum No.4
processed data file: RPKMGeneList_cerebellum.xlsx


title: mRNA_WT3

description:
RNA-seq for E13.5 Wild type cerebellum No.3
processed data file: RPKMGeneList_cerebellum.xlsx


title: mRNA_WT1

description:
RNA-seq for E13.5 Wild type cerebellum No.1
processed data file: RPKMGeneList_cerebellum.xlsx


title: sh52 hairpin NT biological replicate 2

description: RNA-Seq

tag: cell line

tag: treatment


title: mRNA_Ezh2KO4

description:
RNA-seq for E13.5 Ezh2KO cerebellum No.4
processed data file: RPKMGeneList_cerebellum.xlsx

source_name: Ezh2KO_embryonic cerebellum


title: mRNA_Ezh2KO3

description:
RNA-seq for E13.5 Ezh2KO cerebellum No.3
processed data file: RPKMGeneList_cerebellum.xlsx


title: mRNA_Ezh2KO1

description:
RNA-seq for E13.5 Ezh2KO cerebellum No.1
processed data file: RPKMGeneList_cerebellum.xlsx


title: mRNA_Ezh2KO2

description:
RNA-seq for E13.5 Ezh2KO cerebellum No.2
processed data file: RPKMGeneList_cerebellum.xlsx


title: uMT_197_Div3.RNAseq

city: Atlanta

first: Benjamin

middle: G

last: Barwick

state: GA

address: 1365 Clifton Rd. NE WCI-C 4th Floor Benches 36-37

department: Hematology and Medical Oncology

institute: Emory University

description: Cell division 3 of adoptively transferred B cells in uMT host #197

data_processing:
RNA-seq data was mapped back to the UCSC mouse genome mm9 using Tophat254 (v.2.0.13) with the following parameters "-p 8 -N2 -max-multihits 1 -read-gap-length 1" and the UCSC Known Genes mm9 transcript file as a guide.  The 92 ERCC sequences were added to the mm9 genome as artificial chromosomes.
PCR duplicates were determined using Picard (http://broadinstitute.github.io/picard/) and removed from subsequent analyses.
Reads that uniquely overlapped mm9 exons were determined in R (v.3.2.2) using the 'summarizeOverlaps' function in mode 'IntersectionNotEmpty' of the 'GenomicAlignments' package55 (v.1.6.3).
Reads per million (RPM) were calculated for each gene based on the number reads in all potential exons for a given gene and the total number of uniquely mappable reads per sample.
Fragments per kilobase per million (FPKM) were calculated based on RPM and the total size of non-overlapping exons for a gene.
The number of mRNAs per cell were calculated with the following equation:
mRNAs_geneA/cell = (FPKM_geneA/#cells) x ({Sigma}Molecules_ERCC/{Sigma}FPKM_ERCC)
Genome_build: mm9
Supplementary_files_format_and_content: [erccCts.csv]: Read counts for ERCC spike-ins
Supplementary_files_format_and_content: [erccCts.rpm.fpkm.csv]: Normalized read counts for ERCC spike-ins expressed in reads per million (RPM) and fragments per kilobase per million (FPKM)
Supplementary_files_format_and_content: [geneCts.exon.csv]: Read counts for exons of UCSC mm9 KnownGenes
Supplementary_files_format_and_content: [geneCts.exon.fpkm.csv]: Normalized read counts expressed in fragments per kilobase per million (FPKM) for UCSC mm9 KnownGenes
Supplementary_files_format_and_content: [geneCts.exon.mRNAsPerCell.csv]: Normalized read counts expressed in mRNAs per cell for UCSC mm9 KnownGenes
Supplementary_files_format_and_content: [geneCts.exon.rpm.csv]: Normalized read counts expressed in reads per million (RPM) for UCSC mm9 KnownGenes

source_name: Adoptively transferred B cells in uMT Spleen Day 3 post LPS Mouse

extract_protocol:
For RNA-seq analysis, 40,000 cells were sorted into RLT buffer (Qiagen) with 1% 2-mercaptoethanol (Sigma), vortexed and snap frozen.  Prior to extraction 5 µl of 1:2000 dilution of ERCC synthetic RNAs (ThermoFisher) were added to each sample.  RNA was extract using RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol.  DNA was removed with RQ1 DNase (Promega) at 37˚C for 30 minutes and RNA was purified using 3x AMPPure XP clean up (Beckman Coulter).
Stranded mRNA-seq libraries were constructed using KAPA Biosystems Stranded mRNA-Seq Kit following the manufacturer’s protocol (KAPA Biosystems). Equal molar amounts of mRNA-seq libraries were amplified for 11 PCR cycles and purified using a 1.5x ratio of AMPPure XP beads (Beckman Coulter).  Libraries were pooled in equal molar ratios based on the KAPA Library Quantification Kit (Kapa Biosystems) and sequenced on an Illumina HiSeq2500 with 50 bp paired-end reads.
stranded mRNA-seq

value: female

value: B6.SJL-Ptprca Pepcb/BoyJ

value: Spleen

tag: age

value: 8 weeks

tag: cell type

tag: host id

tag: agent

value: LPS

tag: cell division


title: uMT_196_Div8neg.RNAseq

description: Cell division 8- of adoptively transferred B cells in uMT host #196

tag: gender


title: uMT_196_Div8pos.RNAseq

description: Cell division 8+ of adoptively transferred B cells in uMT host #196

tag: strain


title: APL 2


title: uMT_197_Div1.RNAseq

description: Cell division 1 of adoptively transferred B cells in uMT host #197


title: uMT_197_Div5.RNAseq

description: Cell division 5 of adoptively transferred B cells in uMT host #197


title: H3K27me3_WT

description: ChIP-seq for E13.5 Wild type cerebellum No.1

source_name: H3K27me3_WT_embryonic cerebellum


title: uMT_196_Div3.RNAseq

description: Cell division 3 of adoptively transferred B cells in uMT host #196


title: uMT_197_Div8pos.RNAseq

description: Cell division 8+ of adoptively transferred B cells in uMT host #197


title: uMT_197_Div8pos.RRBS

data_processing:
RRBS FASTQ files were aligned to the in silico bisulfite converted genome (mm9) using Bismark with the Bowtie2 option.
Binary Alignment Map (BAM) files were parsed to derive DNA methylation calls that were collapsed to the CpG level using custom R scripts that made use of the ‘Rsamtools’ and ‘data.table’ packages (available upon request)
Data were summarized for CpGs that were covered at 10x in all samples and CpGs that were covered at 10x by all groups
Genome_build: mm9
Supplementary_files_format_and_content: annotated CpG coverage file

extract_protocol:
Overnight digestion in Proteinase K and RNase followed by isolation with Phenol Chloroform and isoamyl alcohol and ethanol precipitation
Reduced Representation Bisulfite Sequencing (RRBS) libraries were made from 20 ng of DNA that was digested overnight with 20 U MspI (New England Biolabs) and 20 U TaqI following the manufacturer’s protocol.  Digested DNA was purified using a 1.8X Solid Phase Reversible Immobilization (SPRI) clean-up with Agencourt AMPure XP beads (Beckman Coulter).  Illumina compatible sequencing adaptors were used and contained fully methylated cytosine residues and were designed similar to those previously described () and synthesized by Integrated DNA Technologies.  DNA was end-repaired and A-tailed and sequencing adaptors were ligated using the Hyper Prep Kit (KAPA Biosystems) following the manufacturer’s protocol.  Adaptor-ligated DNA was bisulfite treated using the EpiTect Bisulfite Kit (Qiagen), modifying the manufacturer’s protocol by extending the denaturation thermocycler step from 5 to 10 minutes at 99ᵒC.  Adaptor-ligated bisulfite treated libraries were amplified 10-15 times using HiFi Uracil+ Polymerase (KAPA Biosystems) and library concentration was estimated using the KAPA quantification kit (KAPA Biosystems).  Size was estimated using a high sensitivity DNA chip (Agilent Technologies) at the Emory Integrated Genomics Core.  Libraries were sequenced using 50 bp single-end reads on a HiSeq2500 by the Genome Technology Center at New York University (NYU).

value: adoptively transferred B cells in uMT host


title: uMT_196_Div0.RNAseq

description: Cell division 0 of adoptively transferred B cells in uMT host #196


title: RU_0_1

data_processing:
All the reads were demultiplexed according to their index sequences using CASAVA version 1.8 (Illumina)
Paired end fastq files were mapped to refenrence genome by using Tophat 2.0.10 with default parameters.
The output mapping files from the TopHat2 alignment, along with the GTF file from ENSEMBL (http://uswest.ensembl.org/) bovine gene annotation v75.30, were used in the htseq-count (http://www-huber.embl.de/users/anders/HTSeq/) to count the total number of reads mapped to each gene.
The expression level of mRNAs in each library was obtained by normalizing reads number to counts per million reads (CPM): CPM = (gene reads number / total mapped reads number per library) × 1,000,000.
Genome_build: UMD3.1
Supplementary_files_format_and_content: Tab-delimited text files include CPM values for each Sample

extract_protocol:
The tissue samples were frozen on liquid nitrogen, and RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#RS-200-0012) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tag


title: uMT_196_Div5.RNAseq

description: Cell division 5 of adoptively transferred B cells in uMT host #196


title: uMT_196_Div1.RNAseq

description: Cell division 1 of adoptively transferred B cells in uMT host #196


title: uMT_197_Div3.RRBS


title: uMT_197_Div8neg.RRBS

description: Cell division 8- of adoptively transferred B cells in uMT host #197


title: uMT_197_Div5.RRBS


title: uMT_197_Div1.RRBS


title: uMT_197_Div8neg.RNAseq


title: uMT_196_Div8pos.RRBS


title: uMT_196_Div5.RRBS


title: uMT_197_Div0.RRBS

description: Cell division 0 of adoptively transferred B cells in uMT host #197


title: uMT_196_Div3.RRBS


title: 2L

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the SoyBase soybean genomics database (http://www.soybase.org/)
Clean tags mapped to reference sequences from multiple genes were filtered, and the remaining clean tags were designated as unambiguous clean tags. The number of unambiguous clean tags for each gene was calculated and then normalized to TPM (number of transcripts per million clean tags)
A rigorous algorithm was used to identify DEGs between two samples. Using this algorithm, statistical information (e.g., p value, FDR, expression level, and log2 ratio) corresponding to the DEGs was obtained. In this study, we used “FDR ≤ 0.001 and the absolute value of log2 ratio ≥ 1” as the threshold to determine the significance of gene expression differences.
Genome_build: the SoyBase soybean genomics database (http://www.soybase.org/)
Supplementary_files_format_and_content: Excell files include TPM values for each gen in each Sample

organism: Glycine soja

source_name: plant

extract_protocol:
Total RNA was extracted using Trizol reagent (Sigma). Using Oligo(dT) magnetic beads adsorption to purify mRNA, and then use Oligo(dT) as primer to synthesize cDNA.
At least 10 µg of total RNA (≥300 ng/µL) was extracted from samples for Solexa sequencing. Sample preparation, library construction, sequencing, and bioinformatics analysis were prepared for sequencing using standard Illumina protocols. The samples were sequenced by an Illumina HiSeq2000 platform, and 35 bp paired-end reads were produced.

value: leaf

value: three fully expanded trifoliates

tag: genotype

value: Wild soybean (ED059)


title: uMT_197_Div0.RNAseq


title: uMT_196_Div1.RRBS


title: uMT_196_Div0.RRBS


title: 2-L

value: wild soybean (ED059)


title: Pearl sac development 60th_DGE

city: zhanjiang

first: xiaoxia

last: zhao

state: guangdong

address: huguangyaneast

department: Fisheries University

institute: Guangdong Ocean University

description: Sample 5

data_processing:
The sequenced raw data were filtered to remove low quality tags (tags with unknown nucleotide ‘‘N’’), empty tags (no tag sequence between the adaptors) and tags with only one copy number using SOAPfilter software (v1.0)
Supplementary_files_format_and_content: The text files include Mapped-Tag,anntation and TPM (tag) for each Sample

organism: Pinctada imbricata

source_name: pearl sac

extract_protocol:
Pearl sac were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: surgical implantation day 60

value: pearl sac

value: post natal year 1.5


title: Pearl sac development 10th_DGE

description: Sample 1

value: surgical implantation day 10


title: Pearl sac development 15th_DGE

description: Sample 2

value: surgical implantation day 15


title: Spleen.NaiveMouse.Bcell.3.RRBS

description:
Naïve B cell replicate 3
Bcell.3.RRBS

data_processing:
RRBS FASTQ files were aligned to the in silico bisulfite converted genome (mm9) using Bismark with the Bowtie2 option.
Binary Alignment Map (BAM) files were parsed to derive DNA methylation calls that were collapsed to the CpG level using custom R scripts that made use of the ‘Rsamtools’ and ‘data.table’ packages (available upon request)
Genome_build: mm9
Supplementary_files_format_and_content: annotated CpG coverage file

source_name: Spleen Naive Mouse

extract_protocol:
Overnight digestion in Proteinase K and RNase followed by isolation with Phenol Chloroform and isoamyl alcohol and ethannol precepitation
Reduced Representation Bisulfite Sequencing (RRBS) libraries were made from 10 to 500 ng of DNA and were digested overnight with 20 U MspI (New England Biolabs) following the manufacturer’s protocol.  Digested DNA was purified using a 1.8X Solid Phase Reversible Immobilization (SPRI) clean-up with Agencourt AMPure XP beads (Beckman Coulter).  Illumina compatible sequencing adaptors were used and contained fully methylated cytosine residues and were either NEXTflex Bisulfite-Seq Barcodes  (BIOO Scientific) or were designed similar to those previously described 76 and synthesized by Integrated DNA Technologies.  DNA was end-repaired and A-tailed and sequencing adaptors were ligated using the Hyper Prep Kit (KAPA Biosystems) following the manufacturer’s protocol.  Adaptor-ligated DNA was bisulfite treated using the EpiTect Bisulfite Kit (Qiagen), modifying the manufacturer’s protocol by extending the denaturation thermocycler step from 5 to 10 minutes at 99ᵒC.  Adaptor-ligated bisulfite treated libraries were amplified 10-15 times using HiFi Uracil+ Polymerase (KAPA Biosystems) and library concentration was estimated using the KAPA quantification kit (KAPA Biosystems).  Size was estimated using a high sensitivity DNA chip (Agilent Technologies) at the Emory Integrated Genomics Core.  Libraries were sequenced using 50 bp single-end reads on a HiSeq2500 by the Genome Technology Center at New York University (NYU).

value: 10 weeks

value: B cell

value: control


title: Spleen.NaiveMouse.Bcell.1.RRBS

description:
Naïve B cell replicate 1
Bcell.1.RRBS

value: female


title: Spleen.NaiveMouse.Bcell.2.RRBS

description:
Naïve B cell replicate 2
Bcell.2.RRBS

value: Spleen


title: Spleen.Day3LPS.Plasmablast.2.RRBS

description:
LPS Plasmablast replicate 2
Plasmablast.2.RRBS

source_name: Spleen Day 3 LPS Mouse

value: Plasmablast


title: Spleen.Day3LPS.PlasmaCell.1.RRBS

description:
LPS Plasma Cell replicate 1
PlasmaCell.1.RRBS

value: Plasma cell

value: LPS


title: Spleen.Day3LPS.Plasmablast.1.RRBS

description:
LPS Plasmablast replicate 1
Plasmablast.1.RRBS


title: Spleen.Day3LPS.Plasmablast.3.RRBS

description:
LPS Plasmablast replicate 3
Plasmablast.3.RRBS


title: uMT_196_Div8neg.RRBS

value: B6.SJL-Ptprca Pepcb/BoyJ

value: 8 weeks

value: adoptively transferred B cells in uMT host


title: Lsd1 mko/wt two-cell embyo 7 RNA seq

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

data_processing:
Quality control: Reads characterized by at least one of the following criteria were discarded from the analysis i) >50% of low quality bases (Phred score <5) ii) >5% of N bases iii) >80% of AT rate iv) ≥30% of continuous A and/or T
Gene analysis: Reads were aligned to the mouse mm10 genome using the TopHat software v2.0.6. Count tables of gene expression were then generated using HTSeq v0.6.1 software. The DESeq R package v1.16.0 was used to normalize and identify the differentially expressed genes between control and mutant embryos.
Repeats analysis: Reads were aligned to the mouse mm10 genome using the Bowtie v1.0.0 software. Aligned reads were then annotated and intersected with repeats annotation from the repeatMasker database. The number of reads falling in repeats were counted and normalized by the total number of reads aligned on repeats. Differential analysis was performed using the limma R package v3.20.4 .
Genome_build: mm10
Supplementary_files_format_and_content: excel files with 2 sheets: Count read tables i) for each gene ii) for each repeat family

source_name: Lsd1 mat ko/wt_two-cell stage embryo

extract_protocol:
two-cell stage embryos were recovered and flash frozen;reverse transcription was carried out directly on the whole  embryos lysate, and total cDNA were then prepared according to Tang et al Nature Protocol  2010 to be used to  construct sequencing libraries
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: stain

value: mouse preimplantation two-cell stage embryos

value: Lsd1 mat ko/wt


title: Lsd1 mko/wt two-cell embyo 6 RNA seq


title: Lsd1 mko/wt two-cell embyo 8 RNA seq


title: Lsd1 mko/wt two-cell embyo 2 RNA seq


title: Lsd1 mko/wt two-cell embyo 3 RNA seq


title: Lsd1 mko/wt two-cell embyo 1 RNA seq


title: f/wt two cell embryo 8 RNA seq

source_name: Lsd1/Kdm1a flox/wt_two-cell stage embryo

value: Lsd1/Kdm1a flox/wt


title: f/wt two cell embryo 6 RNA seq


title: Spleen.Day3LPS.PlasmaCell.2.RRBS

description:
LPS Plasma Cell replicate 2
PlasmaCell.2.RRBS


title: Pearl sac development 30th_DGE

description: Sample 4

value: surgical implantation day 30

value: pearl sac

value: post natal year 1.5


title: Pearl sac development 20th_DGE

description: Sample 3

value: surgical implantation day 20


title: f/wt two cell embryo 7 RNA seq


title: f/wt two cell embryo 4 RNA seq


title: Spleen.Day3LPS.PlasmaCell.3.RRBS

description:
LPS Plasma Cell replicate 3
PlasmaCell.3.RRBS

value: 10 weeks


title: Lsd1 mko/wt two-cell embyo 4 RNA seq


title: f/wt two cell embryo 1 RNA seq


title: f/wt two cell embryo 2 RNA seq


title: YAP_Knockdown_rep3

status: Public on Apr 30 2016

city: Jupiter

first: Joseph

last: Kissil

state: Florida

address: 130 Scripps Way

department: Cancer Biology

institute: The Scripps Research Institute

description: Mouse cells isolated from Nf2-null schwannoma

data_processing:
Adaptor trimming was performed by 'flexbar 2.41 beta' for csfasta files and using an internal perl script for qual files
Quality trimming was performed using an internal perl script
Reads were aligned to mm9 reference genome using 'Tophat 2.0.9'
Raw read counts generated using HTSeq 0.6.1
Normalized counts and a list of differentially expressed genes generated using DESeq 1.14.0
Genome_build: mm9
Supplementary_files_format_and_content: Processed data file is a text file and contains normalized counts obtained from DESeq 1.14.0

source_name: Nf2-null Schwann cells treated with YAP pooled siRNA

growth_protocol: SC4 cells were maintained in DMEM media with 10% FBS at 37 degrees C, and 5% CO2.  Standard cell culture techniques were employed.

extract_protocol:
Media was aspirated and cells were washed twice with sterile PBS.  0.5 ml of Trizol reagent (Life Technologies) was added to each well.  Cell lysates were collected and frozen immediately and stored at -80 degrees C overnight.
For RNA-Seq analysis, 5-10 μg of total RNA was used to isolate poly(A) RNA using the micropoly(A)purist kit (Ambion). The whole transcriptome library kit (Life Technologies) was used to prepare paired-end sequencing libraries. Briefly, 100 ng of poly(A)+ RNA was enzymatically fragmented to an average size of 150 nt, ligated to directional adapters and reverse-transcribed, and the cDNA was size-selected on denaturing 6% TBE-Urea polyacrylamide gels, amplified for 15 cycles with barcoded primers and purified using AmpPure XP beads. The resulting libraries were quantified using Bioanalyzer (Agilent) and Taqman (Life Technologies) assays. Barcoded libraries from each sample were combined at equimolar amounts and the mixture was used at a final concentration of 0.4 pM in emulsion PCR to link the libraries to the sequencing beads.

treatment_protocol: SC4 cells were passaged into 6-well plates at a concentration of 5.0 x 10^4 cells/well and were grown for 24 hours before treatment.  siRNAs were transfected in OptiMem(Life Technologies) using Lipofectamine 2000 reagent(Life Technologies) at a final concentration of 40 nL of siRNA .  Transfected cells were grown for 48 hours before RNA extraction.

value: Nf2-null schwannoma

value: SC4 Schwann cells

value: YAP Smartpool siRNA (GE Life Sciences)


title: 1_odIs77

city: Piscataway

first: Christopher

last: Rongo

state: NJ

address: 190 Frelinghuysen Road

department: Department of Genetics

institute: Waksman Institute, Rutgers The State University of New Jersey

data_processing:
Libraries were sequenced on an Illumina HiSeq 2500 in Rapid Run Mode, resulting in high quality sequence reads (FAST QC Phred score average of 40 out to the full 50 bp length).
Reads (45-49 million per genome and replicate) were analyzed using Geospiza Genesifter, with alignment to the C. elegans genome (WS220) via Illumina WTS BWA (GATKv3).
From 89-90% of reads mapped to the genome (72-74% mapped to annotated ORFs).
Normalization and statistical analysis was performed with EdgeR with a Benjamini and Hochberg correction.

organism: Caenorhabditis elegans

source_name: whole animals

growth_protocol: Developmentally synchronized animals were obtained by hypochlorite treatment of gravid adults to release embryos. Synchronized embryos were hatched on NGM plates and grown at 20°C until 48 h after the L4 stage of development. Fluorodeoxyuridine was used to prevent the development of second-generation embryos once animals reached fertile adulthood

extract_protocol:
For each RNA-seq experiment, populations for odIs77[Pcol-19::UbG76V-GFP] and dop-1(vs100); [Pcol- 19::UbG76V-GFP] were grown simultaneously under the same conditions. Total RNA was isolated from animals using trizol (Invitrogen) combined with Bead Beater lysis in 3 biological replicates
mRNA library (single-end, 50-bp reads) was prepared for each sample/replicate using Illumina Truseq with PolyA selection. Libraries were sequenced on an Illumina HiSeq 2500 in Rapid Run Mode, resulting in high quality sequence reads (FAST QC Phred score average of 40 out to the full 50 bp length).

value: whole animals


title: Drosophila S2 cell iCLIP

city: Berkeley

first: Qingqing

last: Wang

state: CA

address: 161 Koshland Hall, UC Berkeley

department: Molecular and Cell Biology

institute: University of California, Berkeley

description:
iCLIP
Two replicates were pooled before sequencing: rep1 barcode = AACC; rep2 barcode = CGGA
processed data files: Dataset S5

data_processing:
Read alignment: iCLIP samples using Novoalign, map to Drosophila dm3 genome
iCLIP tag enrichment analyses: author-developed method, see associated manuscript
genome build: dm3
processed data files format and content: Dataset S5: bed format; Genomic coordinates of significantly enriched PSI iCLIP tag clusters at single nucleotide resolution

molecule: nuclear RNA

organism: Drosophila melanogaster

source_name: S2 cell_iCLIP

extract_protocol:
For RNA-seq, Drosophila heads were isolated from 50mL of manually sorted and frozen males from the v16/v16 PSI mutant fly strain (PSI-null) carrying either the PSI genomic-cDNA wild-type or PSIΔAB transgenes.  Total RNA was isolated using Qiagen RNA Easy kits and polyA (+) RNA was purified using oligo (dT) Dynabeads (Life Technologies).  For iCLIP, Nuclei were isolated from suspension cultures of S2 cells by hypotonic lysis and Dounce homogenization.  Nuclei were resuspended in isotonic buffer and irradiated on ice with 150 mJ/cm2 at 254 nm in a Stratalinker 2400.
NEBNext® mRNA Sample Prep kit (cat # E6110S; New England Biolabs)

value: S2 cell wildtype