title: HDAC2 KD cells, shRNA 2

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: HDAC2 KD cells, shRNA 2

data_processing:
RNA-Seq data analyzing was done with rsem (ver. 1.2.3) and hg19 genome with ensemble transcriptome information
edgeR was used for differentail expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: Prosessed files contains the raw counts for each gene

source_name: TOV21G cell line, HDAC2 knockdown

growth_protocol: ARID1A-mutated clear cell ovarian cancer TOV21G cells were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin at 37°C supplied with 5% CO2

extract_protocol:
RNA was extracted with Trizol (Invitrogen) and subsequently cleaned and DNase-treated using RNeasy columns (Qiagen).
Libraries for RNA-seq were prepared with ScriptSeq complete Gold kit (Epicentre) and subjected to a 75 bp sequencing run on NextSeq 500, using Illumina’s NextSeq 500 high output sequencing kit following the manufacturer’s instructions.

treatment_protocol: ARID1A-mutated clear cell ovarian cancer TOV21G cells were transduced with lentivirus encoding shHDAC2. Lentivirus was packaged using the Virapower Kit from Life Technologies (Carsbad, CA). pLenti shHDAC2 was constructed by inserting pLKO.1-shHDAC2 obtained from the Molecular Screening Facility at the Wistar Institute. (Cat. No: TRCN0000004819 5′-CCGGCAGTCTCACCAATTTCAGAAACTCGAGTTTCTGAAATTGGTGAGACTGTTTTT-3′ and TRCN0000004823 5′-CCGGGCAAATACTATGCTGTCAATTCTCGAGAATTGACAGCATAGTATTTGCTTTTT-3′ )

value: HDAC2 knockdown


title: Highaltitude 10

status: Public on Mar 09 2018

type: SRA

city: Chongqing

first: Chang

last: Liu

address: 30 Gaotanyan street

country: China

institute: 3rd Military Medical University

library_source: transcriptomic

data_processing:
Illumina HCS2.0 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 Bowtie2 version 2.2.5 software, with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p l -k 200
FPKM were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: Highaltitude, blood

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used  for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: stress

value: High altitude exposure

tag: tissue

value: blood


title: Highaltitude 9


title: HDAC2 WT cells

state: PA

country: USA

description: HDAC2 WT cells

source_name: TOV21G cell line

tag: cell line

tag: genotype/variation

value: WT


title: normal PDLSCs

city: Hangzhou

first: Jianning

address: 866 Yuhangtang Road

institute: Zhejiang University

data_processing:
The clean reads from two cDNA libraries were mapped to the human genome sequence in GENCODE Release 19 using TopHat version 2.0.9. The transcripts were then assembled and annotated using Cufflinks.
According to the annotation of the human genome sequence, the known lncRNAs and mRNAs were identified. The coding potential for of the remaining unknown transcripts was calculated by thewith a coding potential calculator based on quality, completeness, and sequence similarity of the open reading frame to the proteins in the protein databases. The remaining unknown transcripts of more than 200 base pairs (bp) were considered as novel lncRNAs with the a score of coding potential score of less than −1, which suggested that a transcript has had no protein- coding capacity of coding for proteins. Expression The expression levels of lncRNAs and mRNAs were quantified as FPKM (fragments per kilobase of exon per million fragments mapped) using the Cuffdiff program. Differential expression of lncRNAs and mRNAs was determined using DESeq, with P < 0.05 and fold change (FC) ≥ 2.
Compared with linear RNAs, circRNAs exhibited distinct patterns of alternative back-splicing and alternative splicing. An upgraded computational pipeline (CIRCexplorer2) was used to systematically identify and annotate circRNAs. Expression The expression levels of circRNAs were quantified as RPM (mapped backsplicing junction reads per million mapped reads) using the EBSeq package. Differential expression of circRNAs was determined with P < 0.05, FC ≥ 2, and circRNA junction reads ≥5.
Genome_build: human genome sequence in GENCODE Release 19

source_name: periodontal ligament stem cells

growth_protocol: PDLSCs were derived from the middle third of the root surface of healthy human impacted third molars, which were collected from 18- to 20-year-old patients

extract_protocol:
Total RNA was extracted from three samples using Trizol (Invitrogen) according to the manufacturer’s protocols.
Libraries were prepared for sequencing using standard Illumina protocols by performing a paired-end run with a 100 bp read length.

treatment_protocol: Normal PDLSCs were cultured with normal media, consisting of α-modification of Eagle's media (HyClone, South Logan, UT, USA), 10% fetal calf serum (Gibco BRL, Grand Island, NY, USA), 100 U/ml penicillin and 100 μg/ml streptomycin (Invitrogen, Carlsbad, CA, USA) at 37°C in 5% carbon dioxide. Osteogenic inductive PDLSCs were cultured  with osteogenic inductive media supplemented with 10 nM dexamethasone, 10 mM β-glycerophosphate and 50 μg/ml vitamin C (Sigma-Aldrich, St. Louis, MO, USA). Stretch-induced PDLSCs were stretched in a Flexcell® FX-5000™ Tension system with 10% equibiaxial strain at 1.0 Hz for 12 h.

tag: treatment

value: PDLSCs cultured with  normal media

tag: passage

value: cell line

tag: origin

value: the middle third of the root surface of healthy human impacted third molars of 18- to 20-year-old patients


title: HDAC2 KD cells, shRNA 1

description: HDAC2 KD cells, shRNA 1


title: Highaltitude 4


title: stretch-induced PDLSCs

value: PDLSCs stretched for 12h in a Flexcell® FX-5000™ Tension system


title: Highaltitude 6


title: Highaltitude 3


title: Highaltitude 7


title: OMA_2

city: Madrid

first: Carlos

last: Torroja

state: Madrid

address: Melchor Fernandez Almagro, 3

department: Bioinformatics Unit

country: Spain

institute: Centro Nacional de Investigaciones Cardiovasculares (CNIC)

description: Processed data file: RSEMNormExpectedCounts.txt

data_processing:
Libraries sequenced using Illumina HiSeq 2500.
Base-calling was produced by Illumina RTA Software v 1.13.48.
Demultiplexed fastq files were generated from the bcl files using bclToFastq v1.18 from Illumina.
Sequencing adaptor contaminations were removed using cutadapt.
Reads were mapped and gene expression quantified using rsem v1.17.
Counts were normalized using voom from Limma R package.
Genome_build: GRCm38 v70
Supplementary_files_format_and_content: RSEMNormExpectedCounts.txt: Tab-separated text file. Contains expected counts per gene aligned with RSEM. Samples in columns, Genes in rows.

organism: Mus musculus

source_name: Heart, OMA1 KO, non-treated

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

treatment_protocol: Isoproterenol (ISO; 10 mg/kg/day, Sigma) was chronically administered with minipumps (Mini-Osmotiz Pump Model 2004, Alzet) for 7 days before sample collection for RNA.

tag: strain/background

value: OMA1 KO

tag: age

value: 12 weeks

tag: Sex

value: male

value: Heart

value: control


title: Plain 11

source_name: Plain, blood


title: Highaltitude 2


title: Highaltitude 8


title: Highaltitude 1


title: Plain 9


title: C57_2_mp

source_name: Heart, WT, isoproterenol

value: wild type

value: Isoproterenol


title: Plain 10


title: OMA_1


title: Plain 7


title: Plain 5


title: Plain 6


title: osteogenic inductive PDLSCs

value: PDLSCs cultured with osteogenic induction for seven days


title: Plain 2


title: Plain 3


title: Plain 4


title: Highaltitude 5


title: Plain 1


title: U2OS Input

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

description:
library strategy: DRIP-seq
Sample was prepared by pooling input DNA from both NT and Etop samples

library_source: genomic

data_processing:
Short reads were aligned to hg19 using BWA with default alignment parameters, and then post processed to limit to unique alignment and no more than 2 mis-match base-pairs
Peak calling by using MACS2 with parameters as follows: -g 2.7e9 -q 0.05 -B -m 3 30, and using corresponding Input as control sample
peaks (in bed file format) were further annotated to gene by using CEAS (v1.0.2)
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files are in bed format, which are the peak calling results by using MACS2.

molecule: genomic DNA

source_name: Osteosarcoma U2OS

growth_protocol: Cells were passaged in 10cm corningware dishes using media described in Samples section in a 37°C humidified incubator

extract_protocol:
Genomic DNA was extracted from sub-confluent dishes and fragment with HindIII, EcoRI, BsrGI, XbaI and SspI (NEB). Half the samples were further treated to RNASEH (NEB). 10% of the samples from each cell line were pooled to form the Input. Monoclonal antibody S9.6 that recognizes DNA:RNA hybrids was used to enrich for R-loops.
Sequencing library was prepared using standard Illumina protocols

treatment_protocol: Samples were treated with either vehicle (DMSO) or indicated doses of etoposide for indicated amout of time before extraction of RNA

tag: cell type

value: Osteosarcoma

tag: growth protocol

value: Cells were grown in DMEM supplemented with 10%FBS

tag: transfection protocol

tag: treatment protocol

value: DMSO

tag: sample preparation

value: pooled

tag: drip antibody


title: U2OS RNH

description:
library strategy: DRIP-seq
Sample was prepared by pooling RNH treated from both NT and Etop samples


title: U2OS-siEWSR1-1 Etop DRIP

description: library strategy: DRIP-seq

value: Transfected with 40nmol of siRNA against EWSR1  (Santa Cruz, Cat#sc-35347) using Lipofectamine RNAiMax (Invitrogen)

value: 6μM Etoposide for 6 hours

value: S9.6 (Kerafast, Cat#ENH001)


title: U2OS-siEWSR1-2 NT DRIP

description: library strategy: DRIP-seq

value: Transfected with 40nmol of pooled siRNA against EWSR1 (ON-TARGETplus, Dharmacon, Cat#L-005119-02) using Lipofectamine RNAiMax (Invitrogen)

value: DMSO (NT:No Treatment)


title: U2OS-siCtrl Etop DRIP

description: library strategy: DRIP-seq

value: Transfected with 40nmol of control siRNA (Santa Cruz, Cat#sc-37007) using Lipofectamine RNAiMax (Invitrogen)


title: TC32 NT RNAPII

source_name: Ewing's sarcoma TC32

growth_protocol:
Cells were grown in RPMI-40 supplemented with 10%FBS
Cells were passaged in 10cm corningware dishes using media described in Samples section in a 37°C humidified incubator.

extract_protocol:
Genomic DNA was extracted from sub-confluent dishes, fixed and sheared to an average length of 200-1500bp. 10% of the samples from each cell line were pooled to form the Input. RNAPII/BRCA1 antibody was used for immunoprecipitation. ChIP DNA was purified, sheared further to an average length of 350 bp and sequenced after library construction.
Sequencing library was prepared using standard Illumina protocols

treatment_protocol: Samples were treated with either vehicle or indicated doses of etoposide for indicated amout of time before extraction of DNA.

value: Ewing's sarcoma

tag: treatment agent

tag: chip antibody

value: RNA Polymerase II (Qiagen, Cat# GAH-111)


title: TC32 Etop Input

value: IgG (Qiagen, Cat# GAH-111)


title: U2OS NT RNAPII

growth_protocol:
Cells were grown in DMEM supplemented with 10%FBS
Cells were passaged in 10cm corningware dishes using media described in Samples section in a 37°C humidified incubator.


title: U2OS-siEWSR1-1 NT DRIP

description: library strategy: DRIP-seq


title: U2OS-siEWSR1-2 Etop DRIP

description: library strategy: DRIP-seq


title: Plain 8

tag: stress

value: control

tag: tissue

value: blood


title: U2OS-siCtrl NT DRIP

description: library strategy: DRIP-seq

tag: cell line

value: Transfected with 40nmol of control siRNA (Santa Cruz,Cat#sc-37007) using Lipofectamine RNAiMax (Invitrogen)


title: U2OS-pMSCV Etop DRIP

description: library strategy: DRIP-seq

value: Transfected with 20μg of empty vector (pMSCV, Clontech Cat#634401 ) using Lipofectamine 3000 (Invitrogen)


title: IMR90 Input

source_name: Fetal lung fibroblasts IMR90

value: Human fetal lung fibroblasts


title: IMR90 Etop DRIP

description: library strategy: DRIP-seq

value: Cells were grown in DMEM supplemented with 10%FBS


title: CHLA10 Input

source_name: Ewing's sarcoma CHLA10

value: Cells were grown in IMDM supplemented with 10%FBS

value: DMSO


title: CHLA10 RNH

value: pooled


title: IMR90 NT DRIP

description: library strategy: DRIP-seq


title: CHLA10 NT DRIP

description: library strategy: DRIP-seq


title: CHLA10 Etop DRIP

description: library strategy: DRIP-seq

value: 0.15μM Etoposide for 6 hours


title: EWS502 Input

source_name: Ewing's sarcoma EWS502

value: Cells were grown in RPMI-40 supplemented with 10%FBS


title: EWS502 NT DRIP

description: library strategy: DRIP-seq

value: S9.6 (Kerafast, Cat#ENH001)


title: EWS502 RNH


title: TC32 Input


title: EWS502 Etop DRIP

description: library strategy: DRIP-seq

value: 0.25μM Etoposide for 6 hours


title: TC32 RNH


title: TC32 Etop DRIP

description: library strategy: DRIP-seq

value: 0.05μM Etoposide for 6 hours


title: U2OS-pMSCV NT DRIP

description: library strategy: DRIP-seq

value: Osteosarcoma

value: DMSO (NT:No Treatment)


title: TC32 NT DRIP

description: library strategy: DRIP-seq

source_name: Retina

value: Ewing's sarcoma


title: IMR90 RNH


title: CHLA10 Etop_12

data_processing:
Illumina Casava v1.8.2 software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat v2.0.8b
gene count measurements were obtained using HTSeq-count
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

extract_protocol:
Total RNA was extracted from sub-confluent 10cm dishes using Qiagen RNeasy kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: treatment prototcol

value: 0.15μM Etoposide for 12 hours


title: CHLA10 Etop_24

value: 0.15μM Etoposide for 24 hours


title: IMR90 Etop_12

value: 6μM Etoposide for 12 hours


title: CHLA10 Etop_6


title: U2OS Etop_6

value: 6μM Etoposide for 6 hours


title: IMR90 Etop_18

value: Human fetal lung fibroblasts

value: 6μM Etoposide for 18 hours


title: CHLA10 Etop_18

value: Cells were grown in IMDM supplemented with 10%FBS

value: 0.15μM Etoposide for 18 hours


title: U2OS NT

value: Cells were grown in DMEM supplemented with 10%FBS


title: IMR90 Etop_6


title: CHLA258 Etop_12

source_name: Ewing's sarcoma CHLA258

value: 0.1μM Etoposide for 12 hours


title: CHLA10 NT


title: Highaltitude 11

value: High altitude exposure

value: blood


title: DLL4- HE cells with 2ug/ml Dox treatment at Day5 of Differentiation

city: Madison

first: Oleg

last: Moskvin

state: WI

address: 1220 Capitol Court

institute: University of Wisconsin-Madison

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads filtered and trimmed to eliminate low-quality reads and adapter sequences
Gene expression estimates obtained using RSEM v 1.2.3, with Bowtie 0.12.9 for alignment. Parameters to rsem-calc-expression include: "--bowtie-m 200 --bowtie-n 2 --forward-prob 1 --seed-length 25 "
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited files containing non-normalized "Expected Counts" and normalized "Transcripts Per Million" expression estimates calculated by RSEM.

source_name: inducible ETS1 H1 human embryonic stem cells (iETS1-hESCs)

growth_protocol: Single cells were plated at 10,000 cells/cm2 onto six-well plates coated with 0.5μg/cm2 of ColIV (Sigma-Aldrich) in E8 medium supplemented with 10 μM Rho kinase inhibitor (Tocris Y-27632). After 24 hr (day 0), the medium was changed to IF9S medium supplemented with 50ng/ml FGF2 (Miltenyi Biotech), 50ng/ml BMP4 (Peprotech), 15ng/ml Activin A (Peprotech) and 2 mM LiCl (Sigma). On day 2, the medium was changed to IF9S medium supplemented with 50ng/ml FGF2 and VEGF with or without Doxycycline (1, 1.5 and 2ug/ml). On day 4, the medium was changed to IF9S medium supplemented with 50ng/ml FGF2, VEGF, TPO, SCF and IL-6 and 10ng/ml IL3 with or without Doxycycline (1, 1.5 and 2ug/ml). On day5, DLL-/+ HE cells were sorted from differentiation cultures

extract_protocol:
Total RNA was isolated using RNeasy Plus Micro Kit (Qiagen)
DNA libraries were prepped using the LM-Seq protocol described in  Hou et al 2015 (PMID 25831155)

treatment_protocol: iETS1-hESCs were differentiated in defined conditions for 5 days with Day 2-5 of Dox treatment (No, 1, 1.5 and 2ug/ml) and DLL-/+ HE cells were sorted using a FACSAria cell sorter.


title: DLL4- HE cells at Day5 of Differentiation

source_name: H1 human embryonic stem cells (H1-hESCs)


title: CHLA258 Etop_6

value: 0.1μM Etoposide for 6 hours


title: EWS502 Etop_24

value: Cells were grown in RPMI-40 supplemented with 10%FBS

value: 0.25μM Etoposide for 24 hours


title: CHLA258 Etop_18

value: 0.1μM Etoposide for 18 hours


title: DLL4+ HE cells with No Dox treatment at Day5 of Differentiation

value: inducible ETS1 H1 human embryonic stem cells (iETS1-hESCs)


title: DLL4+ HE cells at Day5 of Differentiation

value: H1 human embryonic stem cells (H1-hESCs)


title: CHLA258 NT

value: Ewing's sarcoma

value: DMSO (NT:No Treatment)


title: DLL4+ HE cells with 1ug/ml Dox treatment at Day5 of Differentiation


title: EWS502 Etop_18

value: 0.25μM Etoposide for 18 hours


title: DLL4- HE cells with 1ug/ml Dox treatment at Day5 of Differentiation


title: IMR90 NT

value: Human fetal lung fibroblasts


title: IMR90 Etop_24

value: 6μM Etoposide for 24 hours


title: CHLA258 Etop_24

value: Cells were grown in IMDM supplemented with 10%FBS

value: 0.1μM Etoposide for 24 hours


title: DLL4- HE cells with No Dox treatment at Day5 of Differentiation


title: EWS502 Etop_12

value: 0.25μM Etoposide for 12 hours


title: EWS502 Etop_6

value: 0.25μM Etoposide for 6 hours


title: DLL4+ HE cells with 1.5ug/ml Dox treatment at Day5 of Differentiation


title: TC32 Etop_24

value: 0.05μM Etoposide for 24 hours


title: SIPS1201_3

city: Vienna

first: Markus

last: Schosserer

address: Waehringer Strasse 10

department: Center for Pathobiochemistry and Genetics

country: Austria

institute: Medical University of Vienna

description: Senescent cells treated with 1201 replicate 3

data_processing:
Illumina Casava 1.8.2 software was used for basecalling.
RNA-seq reads were aligned to hg19 genome assembly using TOPHAT Version 2.0.13 with default parameters
Cufflinks Version 2.2.1 was used to calculate Fragments Per Kilobase of transcript per Million mapped reads (FPKM) based on .bam files from TOPHAT results
Genome_build: hg19
Supplementary_files_format_and_content: Output files from cufflinks (.gtf) for each sample include FPKM values as feature abundance measurement

source_name: dermis from human abdominoplasty

growth_protocol: Fibroblasts were cultivated in DMEM/Ham's F12 supplemented with 4 mM L-glutamine and 10 % fetal calf serum at 37 °C, 7% CO2 and ambient oxygen. Cells were usually passaged twice a week at a 1:2 ratio.

extract_protocol:
Total RNA was isolated with TRIreagent (Sigma) following the recommended protocol. RNA concentration and quality was analysed with a Bioanalyzer 2100 using the RNA 6000 Nano Kit (Agilent Technologies) before the samples were sent for next generation sequencing.
RNA libraries were prepared for sequencing on HiSeq 2500 (Illumina) using standard Illumina protocols by GATC BIOTECH (Konstanz, Germany)

treatment_protocol: Prior to treatment fibroblasts were seeded at 3,500 cells /cm2 and quiescent cells were allowed to reach confluence for the next 11 days with a media change on day 4, 7 and 11, whereas premature senescence was induced by exposing the cells 1 hour per day to growth medium supplemented with 100 µM H2O2 on day 1, 2, 3, 4, 7, 8, 9, 10 and 11. On day 11 after the last H2O2 treatment was conducted, half of the SIPS and quiescent cells were cultivated with growth medium supplemented with 0.01 % of 1201. On day 14 the medium was refreshed. On day 15 cells were harvested.

tag: cells type

value: human dermal fibroblasts

tag: population doubling


title: DLL4+ HE cells with 2ug/ml Dox treatment at Day5 of Differentiation


title: EWS502 NT


title: TC32 Etop_18

value: 0.05μM Etoposide for 18 hours


title: SIPS1201_1

description: Senescent cells treated with 1201 replicate 1


title: TC32 Etop_6

value: Cells were grown in RPMI-40 supplemented with 10%FBS

value: 0.05μM Etoposide for 6 hours


title: TC32 Etop_12

value: 0.05μM Etoposide for 12 hours


title: TC32 NT


title: SIPS_3

description: Senescent cells replicate 3


title: D4 HEP

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads filtered and trimmed to eliminate low-quality reads and adapter sequences
Gene expression estimates obtained using RSEM v 1.3.0, with Bowtie 1.1.2 for alignment
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited files containing  "Expected Counts" (posterior mean estimate) and  "Transcripts Per Million" expression estimates calculated by RSEM.

source_name: differentiated WA01 human embryonic stem cells

growth_protocol: WA01 human embryonic stem cells were differentiated into hematoendothelial lineages in serum- and feeder-free conditions, using a modified version of a protocl previously described (Uenishi et al, 2015). After 4 days of differentiation (D4), EMHlin-CD31+CD144+ hemogenic endothelial progenitors were magnetically purified and plated onto collagen-coated plates with either DAPT or DMSO (vehicle control), or plated onto collagen- and DLL1-coated plates with DMSO. Additional growth factors of EGF, IGF-I, and IGFII (all 50ng/ml) were added on top of the original cytokines to improve endothelial growth. Where indicated, the cells were collected 24 hours later and plated onto either OP9 or OP9-DLL4 in a-MEM with 10% FBS containing IL-6, TPO (50ng/ml), IL3 (10ng/ml), and SCF (20ng/ml).

extract_protocol:
MicroRNeasy Plus RNA Extraction kit (Qiagen)
One hundred nanograms of total RNA was used to prepare sequencing libraries using the TruSeq RNA Sample Preparation kit (Illumina, San Diego, CA).  Final cDNA libraries were quantitated with the Qubit Fluorometer (Life Technologies, Carlsbad, CA) and multiplexed with eighteen total indexed libraries per lane.  Sequencing was performed using the HiSeq 3000 (Illumina, San Diego, CA) with a single read of 64 bp and index read of 7 bp.

treatment_protocol: Where indicated, the D4 hemogenic endothelial progenitors were plated onto collagen IV- and IgG-Fc fragment-coated plates (IgG Control) and treated with either DAPT (NOTCH inhibition condition), DMSO (control condition), or were plated ontol collagen IV- and DLL1-Fc-coated plates and treated with DMSO (NOTCH activation condition). Where indicated, 24 hours later the CD144+ endothelial subsets were FACSorted for HE:DLL4-, HE:DLL4+, AHP, and nonAHPs and plated the HE:DLL4- and HE:DLL4+ were plated either onto OP9 (no NOTCH activation), or OP9-DLL4 (NOTCH activation).


title: SIPS1201_2

description: Senescent cells treated with 1201 replicate 2


title: SIPS_1

description: Senescent cells replicate 1


title: Q1201_3

description: Quiescent cells treated with 1201 replicate 3


title: Q1201_2

description: Quiescent cells treated with 1201 replicate 2


title: SIPS_2

description: Senescent cells replicate 2


title: VE-cadherin+ endothelial cells with iETS1 expression (Day 2-4 of Dox) at Day4 of Differentiation

value: inducible ETS1 H1 human embryonic stem cells (iETS1-hESCs)


title: VE-cadherin+ endothelial cells with No Dox treatment at Day4 of Differentiation


title: Q1201_1

description: Quiescent cells treated with 1201 replicate 1


title: D4+1(DLL1 HE:DLL4-)+5(OP9) lin-CD34+CD43+CD45+

tag: cell line source

value: human embryonic stem cells

tag: cell subtype


title: D4+1(DLL1 HE:DLL4-)+5(OP9DLL4) lin-CD34+CD43+CD45+


title: U2OS RNAp2

value: Osteosarcoma

value: RNA Polymerase II (Qiagen, Cat# GAH-111)


title: D4+1(DLL1 HE:DLL4+)+5(OP9DLL4) lin-CD34+CD43+CD45+


title: TC32 RNAp2

value: Ewing's sarcoma

value: DMSO (NT:No Treatment)


title: U2OS NT Input

value: DMSO

value: IgG (Qiagen, Cat# GAH-111)


title: U2OS Etop Input


title: DLL4- HE cells with 1.5ug/ml Dox treatment at Day5 of Differentiation


title: Q_3

description: Quiescent cells replicate 3


title: Q_2

description: Quiescent cells replicate 2


title: U2OS Etop BRCA1

value: 6μM Etoposide for 6 hours

value: BRCA1 (Santa Cruz, Cat# sc-646)


title: U2OS Etop RNPII


title: U2OS NT BRCA1


title: IMR90 Etop Input

value: Human fetal lung fibroblasts


title: IMR90 NT Input


title: IMR90 NT BRCA1


title: IMR90 Etop BRCA1


title: IMR90 Etop RNPII


title: EWS502 Etop Input


title: IMR90 NT RNAPII


title: EWS502 NT Input


title: Adelman_Dmel_S2_Start-seq_TSScall_rep1

city: Boston

first: Karen

last: Adelman

state: MA

address: 45 Shattuck St. LHRRB-201a

department: Biological Chemistry and Molecular Pharmacology

institute: Harvard Medical School

description:
short capped RNA isolated from drosophila S2 nuclei
processed data file:
Adelman_Dmel_S2_Start-seq_TSScall_rep1to4_GSM463298_5prRNA_forward.bedGraph.gz
Adelman_Dmel_S2_Start-seq_TSScall_rep1to4_GSM463298_5prRNA_reverse.bedGraph.gz

data_processing:
Base calling and generation of FASTQ files performed using standard CASAVA pipeline for HiSeq runs, bcl2fastq2 for NextSeq
4sU read pairs containing one or more members with mean quality score <20 filtered; start-seq trimmed for adapter using cutadapt 1.9.1, pairs containing reads trimmed shorter than 20 nt filtered
4sU mapped to reference using tophat 2.0.4, in a strand-specific manner, with bowtie1 as the underlying aligner, also to index of ERCC spikes using bowtie 0.12.8; start-seq mapped to index composed of annotated rRNA/tRNA and spike-in sequences, successfully aligned pairs filtered, remaining mapped to reference using bowtie 0.12.8 retaining uniquely mappable pairs only, allowing 2 mismatches; ChIP-seq mapped using bowtie 0.12.8 retaining uniquely mapped pairs only, allowing 2 mismatches
4sU strand-specific coverage tracks were generated using genomeCoverageBed, normalized with custom scripts using factors determined by DESeq 1.12.2 based on ERCC spike counts and combined with unionBedGraphs and custom scripts (mean count); start-seq strand-specific bedGraphs generated using custom scripts based on 5' mapping location of end 1 reads only, with all replicates combined; ChIP-seq bedGraphs were generated by removing duplicate fragments, filtering fragments of length <50 and >400, and determining counts of fragment centers in 25 nt bins tiling the genome, using custom scripts
Genome_build: dm3 (ChIP-seq, start-seq), mm9 (4sU)
Supplementary_files_format_and_content: 4sU: bigWig containing mean normalized coverage of all replicates; start-seq: bedGraph containing combined count of end 1 5' mapping locations for all replicates; ChIP-seq: bedGraph containing combined count of fragment centers for all replicates

organism: Drosophila melanogaster

growth_protocol: Drosophila S2 cells from the DGRC were grown in M3 media supplemented with bactopeptone, yeast extract and 10% FBS. For all experiments, cells were harvested at a consistent cell density of 4-6x10^6 cells/ml. mESC culture was conducted at 37°C in 5% CO2. NELF-BFl/Fl, CreER+/- ESCs were maintained without feeders in 2i media (knockout DMEM (KO-DMEM), 15% knockout serum replacement (KOSR, Invitrogen), 1 mM NaPyruvate (Millipore), 1% NEAA, 1% BME, 1% Pen/Strep, 1% Glutamax, 1000 U/ml ESGRO, 1 µM MEK inhibitor (PD0325901, Stemgent), and 3 µM GSK3 inhibitor (CHIR99021, Stemgent)) and passaged every 2 days.

extract_protocol:
4sU experiments: metabolically labeled RNA was extracted with Trizol. Equal amounts of total RNA were biotinylated and pulled down with streptavidin beads. 4-thiouridine labeled RNA was eluted with DTT, ethanol precipitated and resuspended in RNAse-free H2O. Start-seq experiments: nascent RNA was isolated from nuclei. ChIP-seq experiments: Sonicated genomic DNA was extracted after IP with respective antibody, Phenol-Chloform extracted and ethanol precipitated.
4sU experiments: TruSeq Stranded Total RNA, with Ribozero Gold and ERCC spikes. Start-seq experiments: TruSeq Small RNA, with homemade spike-in RNAs. ChIP-seq experiments: NextFlex Rapid DNA-seq on IPed or digested genomic DNA

treatment_protocol: 4sU experiments: Two independent biological replicates were generated for Control and 4OHT treated C2 embryonic stem cells to ablate NELF-KO where RNA was metabolically labeled for 10minutes using 500 μM 4-thiouridine. To activate Cre recombinase and recombine out the floxed NELF-B allele, NELF-BFl/Fl, CreER+/- ESCs were treated with 100 nM 4OHT (Sigma) for 5 days. ESCs were then grown in 2i media without 4OHT for the completion of the experiment. Start-seq experiments: Start-RNA libraries were prepared as described in (Nechaev et al., Science 2010 and Henriques et al. 2013). ChIP-seq experiments: ChIP-seq libraries were prepared as described in (Muse et al., Nat Genetics 2007 and Henriques et al. 2013).

tag: treatment

value: control

tag: molecule subtype

value: nascent RNA


title: EWS502 Etop BRCA1

tag: cell type

value: 0.25μM Etoposide for 6 hours


title: EWS502 NT BRCA1


title: EWS502 NT RNAPII


title: EWS502 Etop RNAPII


title: TC32 Etop BRCA1


title: TC32 Etop RNPII


title: TC32 NT Input


title: Adelman_Dmel_S2_Start-seq_TSScall_rep4


title: TC32 NT BRCA1


title: Adelman_Dmel_S2_Start-seq_TSScall_rep3


title: Adelman_Dmel_S2_Start-seq_TSScall_rep2


title: Adelman_Dmel_S2_Cohesin_ChIP-seq_rep2

description:
processed data file:
Adelman_Dmel_S2_Cohesin_ChIP-seq_rep1and2.bedgraph.gz

value: untreated

value: SA-Cohesin (gift from D. Dorsett)


title: Q_1

description: Quiescent cells replicate 1

value: human dermal fibroblasts


title: Adelman_Dmel_S2_H3K27ac_ChIP-seq_rep1

description:
immunoprecipitated chromatin fragments
processed data file: Adelman_Dmel_S2_H3K27ac_ChIP-seq_rep1and2.bedgraph.gz

data_processing:
Base calling and generation of FASTQ files performed using standard CASAVA pipeline for HiSeq runs, bcl2fastq2 for NextSeq
RNA-seq and 4sU read pairs containing one or more members with mean quality score <20 filtered; start-seq trimmed for adapter using cutadapt 1.9.1, pairs containing reads trimmed shorter than 20 nt filtered; iCLIP sequencing reads were collapsed for PCR duplicates, trimmed of 5' and 3' adaptors
RNA-seq and 4sU mapped to reference using tophat 2.0.4, in a strand-specific manner, with bowtie1 as the underlying aligner, also to index of ERCC spikes using bowtie 0.12.8; start-seq mapped to index composed of FlyBase annotated rRNA/tRNA and spike-in sequences, successfully aligned pairs filtered, remaining mapped to reference using bowtie 0.12.8 retaining uniquely mappable pairs only, allowing 2 mismatches; PolII ChIP-seq mapped against both mm9 and dm3 reference genomes, retaining uniquely aligned reads only, allowing two mismatches using bowtie 0.12.8; MNase-seq and other ChIP-seq mapped using bowtie 0.12.8 retaining uniquely mapped pairs only, allowing 2 mismatches; iCLIP-seq mapped to the mouse (mm9) genome using STAR
RNA-seq and 4sU strand-specific coverage tracks were generated using genomeCoverageBed, normalized with custom scripts using factors determined by DESeq 1.12.2 based on ERCC spike counts and combined with unionBedGraphs and custom scripts (total count per nt for RNA-seq, mean count for 4sU); start-seq strand-specific bedGraphs generated using custom scripts based on 5' mapping location of end 1 reads only, normalized by linear regression slope of spike-in counts per sample versus mean of control samples, total normalized counts per condition determined using custom scripts; MNase-seq alignments were concatenated and fragments of length <120 and >180 filtered and converted to BED format using custom script, coverage track generated using genomeCoverageBed; ChIP-seq bedGraphs were generated by removing duplicate fragments, filtering very short or long fragments (NELF-B: <60, >410; PolII and Spt5: <60, >380; H3K4me1: <70, >500; H3K4me3: <70, >525; H3K27ac: <50, >450), and determining counts of fragment centers in 25 nt bins tiling the genome, using custom scripts, PolII samples were normalized such that the counts aligning to mm9 were equal, and replicates combined using custom scripts; iCLIP-seq RT stop identificaiton, gene assignment, and peak calling was performed as in FAST-iCLIP (PMID: 25411354)
Genome_build: dm3 (ChIP-seq, RNA-seq, 4sU, start-seq), mm9 (MNase,iClip)
Supplementary_files_format_and_content: RNA-seq and 4sU: bigWig containing combined normalized coverage of all replicates; start-seq: bedGraph containing combined normalized count of end 1 5' mapping locations for all replicates; MNase-seq: bedGraph containing combined coverage of 120-180 nt fragments for all replicates; ChIP-seq: bedGraph containing combined count of fragment centers for all replicates, in 25 nt bins

source_name: Drosophila S2 cells

growth_protocol: Drosophila S2 cells from the DGRC were grown in M3 media supplemented with bactopeptone, yeast extract and 10% FBS.

extract_protocol:
Pol II ChIP material was prepared as described previously (Muse et al., 2007).
Immunoprecipitated material was purified using the Qiaquick PCR purification kit

value: H3K27ac (Abcam, ab4729)


title: Adelman_Dmel_S2_H3K27ac_ChIP-seq_rep2


title: Adelman_Dmel_S2_Cohesin_ChIP-seq_rep1


title: Adelman_Dmel_S2_4sU-RNA-seq_Spt5-depleted_rep3

description:
4sU labeled RNA-seq
processed data file: Adelman_Dmel_S2_4sU-RNA-seq_Spt5-depleted_rep1to5_mean_normalized_coverage_plus.bw
processed data file: Adelman_Dmel_S2_4sU-RNA-seq_Spt5-depleted_rep1to5_mean_normalized_coverage_minus.bw

extract_protocol:
Total RNA was extracted from nuclei using Trizol reagent (Invitrogen).
RNA quality was assessed using a Bioanalyzer NanoChIP (Agilent). Ribosomal RNA was removed prior to library construction by hybridizing to ribo-depletion beads that contain biotinylated capture probes (Ribo-Zero, Epicentre). RNA was then fragmented and libraries were prepared according to the TruSeq Stranded Total RNA Gold Kit (Illumina) using random hexamer priming. Illumina Spike-ins were used for normalization.

treatment_protocol: Spt5 RNAi was performed for 48h and cells harvested at a consistent cell density of 4–6 x 106 cells/ml, using the same method as previously described (PMID: 24184211)


title: Adelman_Dmel_S2_4sU-RNA-seq_Spt5-depleted_rep4


title: JNK_KO_3D_3

city: Worcester

first: Dr Yvonne

last: Edwards

address: 373 Plantation Street

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

data_processing:
Bowtie2 (v 2-2.1.0) and Tophat2 (v 2.0.14) were used for alignment
Cufflinks(v2.2.1) was used to determine fpkms and cuffmerge and cuffdiff were used to identify differentially expressed genes
Genome_build: Ensembl GRCm38
Supplementary_files_format_and_content: tab-delimited txt file includes FPKM values for all samples

source_name: JNK-/-_3 days_mammary gland

extract_protocol:
Pieces of mammary glands were flash frozen in liquid nitrogen and RNA was extracted using the RNEasy kit from Qiagen (#74106).
Illumina Neoprep kit

tag: strain

tag: time of involution

value: 3 days

tag: genotype/variation

value: JNK-/-

value: mammary gland


title: Adelman_Dmel_S2_H3K4me3_ChIP-seq_rep2

description:
immunoprecipitated chromatin fragments
processed data file: Adelman_Dmel_S2_H3K4me3_ChIP-seq_rep1and2.bedgraph.gz

value: H3K4me3 (Millipore #07-473)


title: Adelman_Dmel_S2_4sU-RNA-seq_Spt5-depleted_rep2


title: Adelman_Dmel_S2_4sU-RNA-seq_Spt5-depleted_rep1


title: JNK_KO_3D_2


title: Adelman_Bl6_mESC_C2cells_2i_MNase-seq_rep2

description:
MNase-digested chromatin mononucleosomal fragments
processed data file: Adelman_Bl6_mESC_C2cells_2i_MNase-seq_rep1to3_fragment_coverage_120_180.bedgraph.gz

source_name: C2 embryonic stem cell

growth_protocol: mES cells were grown on gelatin plates with 2i and LIF.

extract_protocol:
Nuclei were pelleted at 1000 X G for 5 minutes and 5 × 106 nuclei were resuspended in 400 μl digest buffer (15 mM Tris pH 8, 60 mM KCl, 15 mM NaCl, 1 mM CaCl2, 0.25 M sucrose, 0.5 mM DTT), and incubated with varying concentrations of MNase (Worthington) for 5 minutes. 400 μl stop solution (1% SDS, 0.1 M sodium bicarbonate, 20 mM EDTA) was added and digested nuclei were incubated at 65°C for 90 minutes. 24 μl Tris pH 7.6, 3 μl Proteinase K (Life Technologies), and 3 μl GlycoBlue (Life Technologies) were added and digestions were incubated for 12 hours at 65°C. DNA was extracted and mono-nucleosome fragments were gel-purified from fractions digested to ~60% mono-nucleosome, ~30% di-nucleosome, and ~10% tri-nucleosome- sized fragments.
MNase-seq libraries were prepared as described in (Gilchrist et al., 2010)

tag: gender

value: male


title: JNK_KO_3D_1


title: Adelman_Dmel_S2_4sU-RNA-seq_control_rep5

description:
4sU labeled RNA-seq
processed data file: Adelman_Dmel_S2_4sU-RNA-seq_control_rep1to5_mean_normalized_coverage_plus.bw
processed data file: Adelman_Dmel_S2_4sU-RNA-seq_control_rep1to5_mean_normalized_coverage_minus.bw

treatment_protocol: LacZ RNAi was performed for 48h and cells harvested at a consistent cell density of 4–6 x 106 cells/ml, using the same method as previously described (PMID: 24184211)


title: Adelman_Bl6_mESC_C2cells_2i_MNase-seq_rep1


title: Adelman_Dmel_S2_H3K4me1_ChIP-seq_rep1

description:
immunoprecipitated chromatin fragments
processed data file: Adelman_Dmel_S2_H3K4me1_ChIP-seq_rep1and2.bedgraph.gz

value: H3K4me1 (Millipore #07-436)


title: Adelman_Dmel_S2_4sU-RNA-seq_Spt5-depleted_rep5


title: WT_3D_2

source_name: wild type_3 days_mammary gland

value: wild type


title: Adelman_Dmel_S2_RNAPolII_ChIP-seq_Spt5-depleted_rep2

description:
immunoprecipitated chromatin fragments
processed data file: Adelman_Dmel_S2_RNAPolII_ChIP-seq_Spt5-depleted_rep1and2_normalized.bedgraph.gz

value: Pol II (anti-Rpb3, Drosophila; H-224, Santa Cruz Biotechnology #SC-9001, mouse)


title: WT_3D_3


title: Adelman_Dmel_S2_RNAPolII_ChIP-seq_Spt5-depleted_rep1


title: WT_3D_1


title: JNK_KO_0D_3

source_name: JNK-/-_0 day_mammary gland

value: 0 days


title: Adelman_Dmel_S2_4sU-RNA-seq_control_rep2


title: Adelman_Dmel_S2_RNAPolII_ChIP-seq_control_rep2

description:
immunoprecipitated chromatin fragments
processed data file: Adelman_Dmel_S2_RNAPolII_ChIP-seq_control_rep1and2_normalized.bedgraph.gz


title: JNK_KO_0D_2


title: Adelman_Bl6_mESC_C2cells_2i_MNase-seq_rep3


title: Adelman_Dmel_S2_RNAPolII_ChIP-seq_control_rep1


title: Ethylene Rep 3

city: Knoxville

first: Brad

middle: M

last: Binder

state: Tennessee

address: 309 Ken and Blaire Mossman Bldg.

department: Biochemistry & Cellular and Molecular Biology

institute: University of Tennessee

data_processing:
Read trimming with a 4:15 sliding window and a minimum read length of 75
Trimmed reads mapped to reference genome using Bowtie2 and Tophat
BAM files were sorted then converted to SAM format files
Mapped reads were sorted and counted using SamTools and HTSeq
Differential epxression analysis performed using DESeq2
Genome_build: ASM972v1
Supplementary_files_format_and_content: The counts.txt files contain abundance data for each sample. WTair_WTeth_results.txt contains comparison of transcript levels in air versus ethylene.

organism: Synechocystis sp. PCC 6803

source_name: Ethylene, Synechocystis Cells

growth_protocol: Cells were grown on soft agar containing BG-11 medium in directional white  light (30 µmol/m^2/s) at 24˚C for 4d

extract_protocol:
RNA extracted using Trizol extraction
Libraries were constructed according to Illumina protocols.

treatment_protocol: Treated with ethylene-free air or 1 ppm ethylene

tag: agent

value: Ethylene


title: JNK_KO_0D_1


title: Ethylene Rep 2


title: Adelman_Dmel_S2_4sU-RNA-seq_control_rep1

value: control

tag: chip antibody


title: Adelman_Dmel_S2_H3K4me3_ChIP-seq_rep1


title: WT_0D_3

source_name: wild type_0 day_mammary gland


title: Adelman_Dmel_S2_H3K4me1_ChIP-seq_rep2


title: Ethylene Rep 1


title: Adelman_Dmel_S2_4sU-RNA-seq_control_rep4


title: Adelman_Dmel_S2_Start-seq_5pr_and_3pr_Spt5-depleted_rep1

description:
short capped RNA isolated from drosophila S2 nuclei
processed data file: Adelman_Dmel_S2_Start-seq_5prRNA_Spt5-depleted_rep1and2_forward_normalized.bedGraph.gz
processed data file: Adelman_Dmel_S2_Start-seq_5prRNA_Spt5-depleted_rep1and2_reverse_normalized.bedGraph.gz
processed data file: Adelman_Dmel_S2_Start-seq_3prRNA_Spt5-depleted_rep1and2_forward_normalized.bedGraph.gz
processed data file: Adelman_Dmel_S2_Start-seq_3prRNA_Spt5-depleted_rep1and2_reverse_normalized.bedGraph.gz
Start-seq (Nechaev, Science 2010) isolates the transcription start site (TSS) associated RNAs. Paired-end sequencing is performed on the short RNAs isolated, such that the first end sequenced gives the precise 5'-end of the transcript, corresponding to the TSS. The second read gives the transcript 3'-end, which corresponds to the place the polymerase pauses. So the two reads in the fastq are parsed separately because they give different information.

extract_protocol:
Total RNA was extracted from nuclei using Trizol reagent (Invitrogen).
Start-RNA libraries were prepared as described in (Nechaev et al., Science 2010) except reads were size selected in the range 20-80 nt to exclude full length snRNA species.


title: Air Rep 3

source_name: Air, Synechocystis Cells

value: Air


title: WT_0D_2


title: Adelman_Dmel_S2_Start-seq_5pr_and_3pr_control_rep2

description:
short capped RNA isolated from drosophila S2 nuclei
processed data file: Adelman_Dmel_S2_Start-seq_5prRNA_control_rep1and2_forward_normalized.bedGraph.gz
processed data file: Adelman_Dmel_S2_Start-seq_5prRNA_control_rep1and2_reverse_normalized.bedGraph.gz
processed data file: Adelman_Dmel_S2_Start-seq_3prRNA_control_rep1and2_forward_normalized.bedGraph.gz
processed data file: Adelman_Dmel_S2_Start-seq_3prRNA_control_rep1and2_reverse_normalized.bedGraph.gz
Start-seq (Nechaev, Science 2010) isolates the transcription start site (TSS) associated RNAs. Paired-end sequencing is performed on the short RNAs isolated, such that the first end sequenced gives the precise 5'-end of the transcript, corresponding to the TSS. The second read gives the transcript 3'-end, which corresponds to the place the polymerase pauses. So the two reads in the fastq are parsed separately because they give different information.


title: Air Rep 2


title: Adelman_Dmel_S2_4sU-RNA-seq_control_rep3


title: WT_0D_1


title: Air Rep 1


title: Adelman_Dmel_S2_Start-seq_5pr_and_3pr_control_rep1


title: WT_10

status: Public on Mar 08 2018

city: Beijing

first: yanling

last: sun

state: Beijing

address: No.1, Beichen West Road  Chaoyang District

institute: Beijing Institute of Genomics

description: RNA-seq

data_processing:
RNA-seq reads were aligned to the mouse genome reference sequence (GRCm38/mm10) and RefSeq annotation (Release May 23, 2014) obtained from UCSC using TopHat (v2.0.9) with a parameter of --max-multihits=1. FastQC (v0.10.1) (http://www.bioinformatics.babraham.ac.uk/projects/fastq) and RseQC (v2.3.8) software were used to check the quality of the raw reads. The quality score of each read reached an average of 25. The rates of overall mapped reads reached approximately 95%.
Cufflink software (v2.0.2) was used to quantify the gene expression values by calculating the FPKM value (the fragment per kilobase of transcript per million fragments mapped). Cuffdiff was used to detect the differentially expressed genes (DEGs), and DEGs with a cutoff of P < 0.05 were selected for further pathway analyses.
GSEA analysis was performed with gene signatures in GESA/MSigDB v5.1, including Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway signatures and Gene Ontology (GO) signatures. Enriched gene sets or pathways were selected using a cut-off of false discovery rate (FDR) < 0.25.
Genome_build: GRCm38/mm10

source_name: BM LK cells

extract_protocol: Total RNA was isolated from mouse Asxl2-/- and WT LK cells following standard protocol with TRIZol reagent (Life Technologies) followed by RNA library preparation with the Illumina TruSeq strand-specific mRNA sample preparation system. All RNA-seq libraries were sequenced with a read length of single-end 75bp using the Illumina NextSeq 500, and final of over 45 million reads per sample.

tag: age

tag: genotype

value: WT

value: LK cells


title: KO_09

description: RNA-seq


title: KO_08

description: RNA-seq


title: WT_09

description: RNA-seq


title: KO_10

description: RNA-seq


title: WT_08

description: RNA-seq


title: KO_H3K4me1

data_processing:
ChIP-seq libraries for H3K27ac, H3K4me1, and H3K4me2 were prepared and sequenced with a read length of single-end 75bp on NextSeq 500, and final of over 45 million reads per sample. The sequence reads were aligned to the mouse genome (GRCm38/mm10) using the bowtie2 (v2.1.0) algorithm with default settings. The rates of overall mapped reads were at least 95%. Reads that aligned to the same position and strand were only counted once to avoid potential PCR bias. Finally, 40-70% of total reads were kept for further analysis.
Enrichment peaks of histone modifications were called using the MACS (v14) with parameters of --fe-min=1 --fe-max=40, and filtered in according to FDR ≤ 0.01, mean signal≥0.02 and enrichment fold≥2.5. The resulting genomic signals in wiggle files were visualized using UCSC genome browser (http://genome.ucsc.edu/). MAnorm was used to identify differential enrichment regions (DERs) for each histone modification between Asxl2-/- and WT LK cells, with P ≤ 0.01 and read count after normalization to reads per million (RPM) ≥ 32.
Peaks, binding sites, and DERs were assigned to its nearest genes within 100 Kb using RefSeq annotation (Release May 23, 2014) from UCSC. Peaks overlapping with the regions from upstream 2Kb to downstream 2Kb of TSS (TSS ± 2Kb) were allocated to the promoter. Peaks overlapping with gene body rather than promoter were allocated to gene body. The remaining intergenic peaks were assigned to both the nearest 5’ and 3’ genes within its 100 Kb. If no gene was found within 100 Kb of an intergenic peak, it was not assigned to any gene.
Peak overlapping and merging were done with multovl (v1.2). ChIP-seq read counts were normalized to reads per kilobase per million reads (RPKM) and combined into one matrix with deeptools (http://deeptools.ie-freiburg.mpg.de/) for heatmap visualization.
Given 80% of histone modification peaks were located in regions ranging from upstream 10 Kb to downstream 10Kb of gene body (Gene ± 10 Kb), the ChIP-seq reads within Gene ± 10 Kb were counted using cisgenome (v2) with a parameter of –e200, and normalized to RPM for integrational analysis of ChIP-seq and gene expression data.39 For each gene, enrichment fold was defined as log2 transformed RPM in ChIP divided by RPM in input, log2-(ChIP/input), and revised to zero when it was smaller than zero. This enrichment fold matrix was used to do GESA analysis of DEGs (http://software.broadinstitute.org/gsea)32, to examine whether DEGs have differential enrichment signals of H3K27ac and H3K4me1/2.
Genome_build: GRCm38/mm10

extract_protocol:
LK cells of each mouse genotype were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine.
Chromatin was isolated by the addition of lysis buffer, followed by shearing with Bioruptor Pico with water cooler (Diagenode, Seraing, Belgium). The DNA was sheared to an average length of 300-500 bp. Genomic DNA regions of interest were isolated using antibodies against H3K27ac (Diagenode, C15410196), H3K4me1 (C15410194), and H3K4me2 (Abcam, ab32356). Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. After the measurement of DNA concentration with Qubit3.0, the libraries were prepared and sequenced on an Illumina NextSeq 500.


title: Adelman_Dmel_S2_Start-seq_5pr_and_3pr_Spt5-depleted_rep2

tag: cell line


title: KO_H3K27ac


title: KO_H3K4me2


title: KO_Input


title: WT_H3K4me1


title: WT_H3K4me2


title: WT_Input


title: two-weeks seedling plants_307T3_Bisulfite-seq

city: Shanghai

first: yiwen

last: Deng

state: Shanghai

address: 300 Fenglin Road

department: Institute of Plant Physiology and Ecology

institute: Shanghai Institute for Biological Sciences, Chinese Academy of Sciences

data_processing:
Illumina Casava1.8 software used for basecalling.
Low-quality reads and reads containg adaptor/primer were filtered.  The filtered reads were mapped to rice reference genome (pseudomolecules/MSUv7.0 ) by software BSMAP, allowing up to 2 mismatches and retaining only uniquely-mapping, only the unique mapping were retained for further analysis.
Genome_build: Os-Nipponbare-MSUv7.0
Supplementary_files_format_and_content: tar archives of text files with methylation status data

organism: Oryza sativa

source_name: leaf_Resui retrotransposition insertion line 307T3 (three copies)

growth_protocol: The genomic DNA  samples were isolated from the shoots of the variety 308D, 307T1 and 307T3 grown in soil under 12-h-light/12-h-dark at 28°C in a greenhouse for 15 days.

extract_protocol:
For each sample, about 20 individual plants were pooled and total genomic DNA was extracted using CTAB method. DNA samples were treated with RNase A and DNA was purified from the supernatant using chloroform.  About 5 microgram of genomic DNA was sheared by sonication to fragments of 100-500 bp, and the adapters were ligated following the Illumina protocol. The library was then treated twice with sodium bisulfite (which converts unmethylated Cs to Us) using the Qiagen EpiTect kit, and amplified by 18 cycles of PCR using PfuTurboCx DNA polymerase (Stratagene), The PCR product was purified with AMpure XP beads to obtain the final library DNA. BS-seq libraries were sequenced using an Illumina HiSeq 2000.
libraries were prepared for sequencing using standard Illumina protocols

tag: development stage

value: seedling

tag: tissue

value: leaf

value: WT-3 copies


title: two-weeks seedling plants_308D_MeDIPseq

data_processing:
Illumina Casava1.8 software used for basecalling.
Low-quality reads and reads containg adaptor/primer were filtered.  The filtered reads were mapped to rice reference genome using BOWTIE2 with default settings. The duplicated reads were removed, and only alignments with MAPQ score > 20 were kept for further analysis.  Enriched regions of DNA methylation were identified using MACS14.
Genome_build: Os-Nipponbare-MSUv7.0
Supplementary_files_format_and_content: peak files. Columns contain the following: 1) Chromosome, 2) start peak position, 3) end peak position, and 4) number of reads.

growth_protocol: The genomic DNA  samples were isolated from the shoots of the variety 308D and 307T3 grown in soil under 12-h-light/12-h-dark at 28°C in a greenhouse for 15 days.

extract_protocol:
For each sample, about 20 individual plants were pooled and total genomic DNA was extracted using CTAB method. DNA samples were treated with RNase A and DNA was purified from the supernatant using chloroform.For each sample, about 20 individual plants were pooled and total genomic DNA was extracted using CTAB method. DNA samples were treated with RNase A and DNA was purified from the supernatant using chloroform.  About 5 microgram of genomic DNA was sheared by sonication to fragments of 100-500 bp. Sonicated DNA was end-repaired, A-tailed, and ligated to single-end adapters following the standard Illumina protocol. After agarose size-selection to remove unligated adapters, 2–5 μg of adaptor-ligated DNA was used for each immunoprecipitation using a mouse monoclonal anti-methylcytidine antibody, following performed by Magnetic Methylated DNA Immunoprecipitation kit (Diageno,Catalog No:  mc-magme-048). MeDIP DNA was purified using Qiagen MinElute columns and eluted in 16 μl EB (Qiagen). Fifteen cycles of PCR were performed on 5 μl of the immunoprecipitated DNA using the single-end Illumina PCR primers. Libraries were quality controlled by spectrophotometry and Agilent DNA Bioanalyzer analysis. Libraries were sequenced on the Hiseq2000 following the manufacturer's protocols.
libraries were prepared for sequencing using standard Illumina protocols.


title: two-weeks seedling plants_307T1_smallRNAseq

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the rice reference genome Nipponbare genome using software SOAP  with parameters -v 0 -r 2 -M 0 -a clean.fa -D ref_genome.fa.index -o match_genome.soap
Genome_build: Os-Nipponbare-Reference-IRGSP-1.0 pseudomolecules
Supplementary_files_format_and_content: .fa file reports raw counts of small RNA reads

source_name: leaf_Resui retrotransposon insertion line 307T1 (one copy)

growth_protocol: The RNA samples were isolated from the shoots of the variety 308D, 307T1 and 307T3 grown in soil under 12-h-light/12-h-dark at 28°C in a greenhouse for 15 days

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: WT-1 copy


title: two-weeks seedling plants_307T3_smallRNAseq

source_name: leaf_Resui retrotransposon insertion line 307T3 (three copies)


title: two-weeks seedling plants_308D_smallRNAseq


title: two-weeks seedling plants_308D_Bisulfite-seq


title: two-weeks seedling plants_307T1_Bisulfite-seq

source_name: leaf_Resui retrotransposition insertion line 307T1 (one copy)


title: WT_H3K27ac


title: RNA_BRDs OE Sample 2

city: Rochester

first: LIGUO

last: WANG

state: MN

address: 200 1st St SW

department: Division of Computational Biology

institute: Mayo Clinic

data_processing:
Basecalls performed using CASAVA version 1.4
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Cliinc sequence core using the pipeline Cassava 1.7
Raw sequences were mapped to reference genome (hg19) using Tophat2 (v2.1.0) with default parameters.
RPKM and BIGWIG were calcualted using RSeQC (v2.3.6).
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated from bedGraph files that generated from MACS, Scores represent reads coverage signal

source_name: Prostate cells

growth_protocol: C4-2 were routinely generated by regular cultures (typically 5 × 106 cells into a T75 flask) on uncoated plastic in RPMI1640 medium (Gibco, USA) supplemented with Charcoal stripped serum (Gibco, USA). Cells were transfected with empty vectors or BRD2/3/4 overexpressed vectors.

extract_protocol:
RNAs were extracted as as described previously (Zhao Y, Wang L, Huang H, et al., Cell Rep. 2016).
Libraries were prepared according to Illumina's instructions accompanying the Total RNA-seq Sample Kit.

treatment_protocol: no treatment

value: Prostate

tag: transfection

value: BRD2/3/4 overexpressed vector


title: two-weeks seedling plants_308D_RNAseq

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the rice reference genome Nipponbare genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Os-Nipponbare-Reference-IRGSP-1.0 pseudomolecules
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample


title: two-weeks seedling plants_307T1_RNAseq


title: RNA_BRDs OE Sample 1


title: RNA_control Sample 1

value: empty vector


title: RNA_control Sample 2


title: two-weeks seedling plants_307T3_MeDIPseq

source_name: leaf_Resui retrotransposon line 307T3 (three copies)


title: 220510

first: Avrum

last: Spira

address: 72 E Concord Street

department: Computational Biomedicine

institute: Boston University

description: removed by QC filter

data_processing:
To estimate microRNA expression we used the small RNA sequencing pipeline previously described (Campbell et al., RNA 2015). Briefly, the 3′ adapter sequence was trimmed using the FASTX toolkit. Reads longer than 15 nt were aligned to hg19 using Bowtie v0.12.7 allowing up to one mismatch and alignment to up to 10 genomic locations. MicroRNA expression was quantified by counting the number of reads aligning to mature microRNA loci (miRBase v20) using Bedtools v2.9.0.
The distribution of read lengths present in each sample was examined to ensure that the sequences were of the proper length for microRNA. The read length distribution ought to follow a normal distribution with a mean of 22 bases. We filtered out 6 samples whose distribution had an abundance of reads well below or above the mean of 22 bases (with less than one million reads aligned to 22 read length), indicating that the sample was not properly sequenced, the adapters were improperly trimmed, or the sample was of poor quality.
microRNA loci with a low number of aligned reads (less than 20 on average) were removed. A total of 463 microRNA loci passed our filter and were included in the analysis.
microRNA counts within each sample were normalized to log2 RPM values by adding a pseudocount of one to each microRNA, dividing by the total number of reads that aligned to all microRNA loci within that sample, multiplying by 1 × 106, and then applying a log2 transformation.
ComBat (Johnson et al., Biostatistics 2007) was applied toremove the batch effects across the three different batches.
Genome_build: hg19
Supplementary_files_format_and_content: expression_matrix.csv contains the matrix of the normalized log2 RPM values where the rows correspond to the 463 filtered microRNAs (miRBase ID) and the columns correspond to the samples.

source_name: Mainstem Bronchus

extract_protocol:
200 ng of total RNA from each sample was used for library preparation.
The TruSeq Small RNA Sample Prep Kit (Illumina) was used for the first batch, while the NEBNext Multiplex Small RNA Library Prep Set (Illumina) was used for the second and third batches. RNA adapters were ligated to 3’ and 5’ ends of the RNA and the adapter-ligated RNA was reverse transcribed into single-stranded cDNA. The RNA 3’ adapter was designed to target microRNAs and other small RNAs that have a 3’ hydroxyl group resulting from enzymatic cleavage by Dicer or other RNA processing enzymes. The adapter used for the first batch has the following sequence: TGGAATTCTCGGGTGCCAAGG, while the one used for the second and the third batches has the following sequence: AGATCGGAAGAGCACACGTCT. The cDNA was then amplified by PCR, using a common primer and a primer containing one of 12 index sequences. The introduction of the six-base index tag at the PCR step allowed multiplexed sequencing of different samples in a single lane of a flowcell. A 0.5% PhiX spike-in was also added in all lanes for quality control. Each multiplexed library was hybridized to one lane of the two 8-lane High-Output single-read flow cells on a cBot Cluster Generation System (Illumina) using TruSeq Single-Read Cluster Kit (Illumina). The clustered flowcell was loaded onto a HiSeq 2000 sequencer for a multiplexed sequencing run which consists of a standard 36-cycle sequencing read with the addition of a 7-cycle index read.

value: Bronchial Epithelium

tag: patient clinical diagnosis

value: Primary Lung

tag: patient smoking status

value: Former

tag: patient history of smoking (pack years)

tag: patient gender

value: Male

tag: patient age

tag: sequencing batch

tag: used as training or test


title: 120006

description: removed by QC filter

value: Declared Negative

value: Current


title: 240508

description: removed by QC filter

value: Female


title: 150507

description: removed by QC filter


title: 250526

value: training


title: 1-25-0516-2


title: 250529


title: 250523


title: 140453


title: 130115

description: removed by QC filter


title: two-weeks seedling plants_307T3_RNAseq


title: 141242


title: 1-25-0511-2


title: 1-25-0509-2


title: 220521


title: 250501


title: 1-22-0507-2


title: 210524


title: 220513


title: 138568


title: 210520


title: 200506


title: 30028

description: removed by QC filter


title: 124402


title: 190509


title: 1-18-0505-2


title: 1-19-0508-3


title: 170516


title: 160600


title: 160612


title: 160590


title: 118280


title: 1-16-0574-2


title: 1-16-0528-2


title: 160542


title: 160553


title: 170506


title: 160580


title: 160520


title: 160519


title: 1-22-0509-2


title: 150519


title: 1-14-0131-2


title: 160543


title: 1-15-0506-2


title: 119680


title: 150527


title: 140435


title: 140125


title: 115897


title: 140069


title: 140094


title: 123218


title: 140088


title: 140008


title: 93486


title: 1-14-0054-2


title: 93674


title: 97448


title: 1-15-0502-2


title: 89926


title: 89121


title: 89119


title: 93672


title: 1-14-0103-2


title: 87340


title: 120535


title: 120524


title: 1-12-0049-2


title: 120522


title: 109569


title: 99930


title: 130121


title: 83893


title: 120505


title: 140106


title: 1-12-0032-2


title: HLe115_Hoxc10_santacruz_mm10

city: Montreal

first: Amandine

last: Bemmo

state: QC

address: 110 Avenue des Pins

country: Canada

institute: IRCM

description: ChIP-seq

data_processing:
Paired-end reads were mapped using Bowtie2 version 2.2.6 in paired-end mode, e.g. "bowtie2 -t -p 12 --fr -I 0 -X 1000 -x /gs/project/feb-684-aa/BIF/genomes/BOWTIE2_INDEXES/mm10 -1 R1.fastq -2 R2.fastq -S HLe115_Tbx4_mm10PE.sam"
Peak calling was performed on Tbx4 and HoxC10 datasets with MACS version 2.1.1.20160309 in paired-end mode, using otherwise default parameters for mm10.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files were generated with HOMER with read counts normalized per 10000000 reads (default). Summit files are in BED format, with the score in the 5th column indicating the -LOG10(qvalue) as output by MACS.

growth_protocol: Timed breedings of wild type CD1 were collected at the indicated embryonic stages.

extract_protocol:
Tissue was fixed with 1% formaldehyde, nuclei were isolated, genomic DNA was sheared by sonication, and protein:DNA complexes were pulled down with the indicated antibodies.
Illumina

tag: Stage

value: hindlimb

value: wild type

tag: strain

value: HoxC10(L-17) sc-33003 Santa Cruz Lot L1015


title: HLe115_Hoxc10_abcam_mm10

description: ChIP-seq

tag: chip antibody

value: ab153904  AbCam


title: 92640


title: 89366


title: HLe115_Tbx4_mm10

description: ChIP-seq

value: homemade anti-Tbx4 (1695a)


title: 120002


title: 110526


title: 1-11-0512-2


title: 89929


title: RA8: Ezh2-KO CD44- NK1.1-

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
FASTQ files were output using standard Illumina protocols and Illumina CASAVA sofware version 1.8.2.
Reads were aligned to the mouse genome with Subread 1.4.3-p1.
Read counts were summarized by Entrez Gene ID using featureCounts and Rsubread's built-in RefSeq annotation.
Read counts from the four technical replicates of the same sample were summed.
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: tab-delimited text files; columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene.

source_name: Thymic natural killer T cells

extract_protocol:
Total RNA was prepared using a RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s instructions.
mRNA reverse transcription and cDNA libraries were prepared using the TruSeq RNA Sample preparation kit (Illumina) following the manufacturer’s instructions.

tag: background strain

value: Ezh2 knock-out

tag: cell surface markers

tag: cell type

value: Thymic natural killer T cells


title: 130114


title: 1-11-0508-2


title: 100090


title: RA6: Ezh2-KO CD44+ NK1.1-

tag: genotype


title: RA7: Ezh2-KO CD44+ NK1.1+


title: RA5: Ezh2-KO CD44+ NK1.1-


title: 94800

tag: tissue


title: 98401


title: RA4: WT CD44- NK1.1-

value: Wild-type


title: 93538


title: 88733


title: 80527


title: 91159


title: 92641


title: 1-14-0066-3


title: 104936


title: 70527


title: RA3: WT CD44+ NK1.1+


title: 130122


title: 1-8-0015-2


title: 1-7-0513-2


title: RA1: WT CD44+ NK1.1-


title: 70002


title: 88689


title: 60022


title: 60030


title: 60014


title: 91758


title: 1-5-0545-2


title: 50570


title: 1-5-0552-2


title: 1-5-0538-2


title: 50510


title: 1-5-0509-2


title: 50540


title: RA2: WT CD44+ NK1.1-


title: 115650


title: 1-5-0058-2


title: 90008-2


title: 87000


title: 1-5-0505-2


title: 50023


title: 50028


title: 87498


title: 1-5-0019-2


title: 92018


title: 1-5-0002-2


title: 60026


title: 86179


title: 100958


title: 84488


title: 30026


title: 50525


title: 100099


title: 90787


title: 90533


title: 99924


title: 99451


title: 97350


title: 10085


title: 87312


title: 86923


title: 86925


title: 86288


title: 139428

value: test


title: 250502

value: Bronchial Epithelium


title: 230530


title: 230520


title: 230521

value: Primary Lung


title: 230506

value: Former


title: 60019

value: Male


title: 220555


title: 220561


title: 220546

value: Declared Negative


title: 93533


title: 220538

value: Current


title: 98253

value: Female


title: 1-22-0516-2


title: 220534


title: 220570


title: 220544


title: 220501


title: 230527


title: 10051

value: training


title: 210562


title: 124410


title: 210573


title: 210564


title: 240507


title: 210557


title: 1-21-0509-2


title: 1-21-0512-2


title: 1-21-0516-2


title: 230505


title: 1-21-0517-2


title: 122840


title: 210508


title: 210507


title: 220518


title: 200507


title: 180508


title: 190515


title: 1-18-0501-2


title: 210535


title: 200505


title: 170550


title: 170549


title: 170548


title: 170541


title: 99927


title: 170531


title: 1-17-0501-2


title: 170517


title: 160745


title: 160703


title: 170513


title: 160700


title: 160711


title: 160689


title: 160688


title: 160691


title: 200512


title: 160675


title: 160679


title: 160665


title: 160669


title: 160654


title: 160664


title: 160653


title: 160630


title: 160632


title: 160638


title: 160629


title: 160652


title: 160562


title: 160619


title: 1-16-0603-2


title: 160613


title: 160614


title: 1-16-0566-2


title: 160685


title: 123093


title: 160558


title: 160597


title: 160549


title: 121705


title: 160659


title: 150599


title: 160531


title: 118294


title: 1-16-0561-2


title: 150575


title: 150558


title: 150549


title: 150542


title: 140141


title: 150532


title: 140076


title: 138941


title: 140113


title: 122620


title: 140064


title: 140058


title: 1-16-0539-2


title: 115901


title: 109394


title: 109323


title: 230515


title: 100362


title: 150585


title: 96789


title: 95856


title: 150554


title: 96788


title: 140004


title: 130165


title: 130170


title: 1-13-0164-2


title: 130148


title: 140132


title: 130147


title: 150530


title: 93478


title: 120566


title: 85403


title: 89927


title: 120561


title: 89925


title: 120562


title: 1-12-0541-2


title: 120534


title: 1-12-0545-2


title: 110339


title: 95339


title: 1-12-0523-2


title: 1-12-0531-2


title: 120526


title: 120512


title: 120540


title: 120539


title: 89599


title: 120028


title: 1-12-0011-2


title: 1-12-0511-2


title: 120021


title: 97446


title: 141093


title: 110540


title: 110506


title: 110502


title: 88083


title: 100018


title: 95344


title: 70551


title: 120516


title: 1-10-0014-3


title: 97806


title: 93940


title: 220539


title: 70543


title: 118173


title: 70546


title: 70536


title: 70535


title: 70519


title: 88081


title: 88840


title: 112407


title: 50610


title: 70531


title: 70014


title: 60023


title: 50604


title: 112579


title: 50595


title: 104883


title: 50622


title: 50594


title: 50582


title: 50588


title: 50578


title: 50574


title: 50572


title: 1-5-0530-2


title: 50571


title: 50569


title: 108949


title: 99364


title: 108950


title: 1-5-0504-2


title: 50034


title: 89996


title: 88453


title: 85393


title: 50018


title: 86184


title: 89398


title: 85976


title: 84883


title: 40003


title: 84887


title: 96603


title: 10078


title: 96594


title: 90987


title: 10070


title: 50580


title: 50544


title: 1-1-0005-2


title: 87494


title: input DNA

city: Kocaeli

first: Tamer

last: Yagci

address: Istanbul Street

department: Molecular Biology and Genetics

country: Turkey

institute: Gebze Technical University

data_processing:
Sequences: Standard Illumina software base-calling and quality-control filtering was applied
Sequences (75 nt reads, single end) were aligned to the human genome (hg19) using the BWA algorithm (v0.6.1, default parameters).
Aligns were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWIG files.
Peak locations were determined using the MACS algorithm (v1.4.2) with a cutoff of pvalue = 1E-6.
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations
Genome_build: hg19
Supplementary_files_format_and_content: BW = signal map in bigWIG format (UCSC)

source_name: liver

growth_protocol: SNU398 cells were grown in RPMI1640 supplemented with 10% FBS and grown to 80% confluency

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine.  Lysates were sonicated with a microtip sonicator to shear the DNA. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. For each ChIP reaction, 30 ug of chromatin was precleared with protein G Dynabeads (Invitrogen). ChIP reaction was set up using precleared chromatin and antibody and incubated overnight at 4 C. Dynabeads were added and incubation at 4 C was continued for another 3 hr. Immune complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by DNA purification kit (Qiagen).
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on NextSeq 500.

value: pooled cells from hepatocellular carcinoma cell lines SNU398 and PLC/PRF/5

tag: tumor type

value: Hepatocellular Carcinoma Cell Line


title: ZEB2 ChIP-Seq

tag: tiisue

value: SNU398 cell line

value: clone 6E5 (homemade antibody; also available at Active Motif Inc. catalog#61095)


title: 2h salt stress Rep 1

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

country: Germany

institute: Ludwig-Maximilians-Universität München

description:
ATAC-seq (Transposon accessible chromatin)
Prepared following protocol by Buenrostro et al. Nature Methods 2013

data_processing:
Reads were mapped against the human genome (GRCh37/hg19) and rRNA sequences using ContextMap v2.7.9
Open chromatin regions were identified using F-Seq v1.85
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bed files with identified open chromatin regions

source_name: HFF_2h_80 mM KCl_ATAC-seq

growth_protocol: Human foreskin fibroblasts were cultured in DMEM supplements with 10% FBS and P/S. Cells at passage 15 were exposed to the salt or heat stress 24h after the last split.

extract_protocol:
Samples were processed according to the original ATAC-seq protocol (Buenrostro et al. Nature Methods 2013)
See Buenrostro et al, Nature Methods 2013
NextSeq 500 sequencing 75bp paired-end reads

treatment_protocol: Cells were exposed to either 80mM KCl (increase in final concentration) or heat stress (44ºC) by exchange of cell culture media. Samples were harvested at the indicated time points and all samples were processed according to the standard ATAC-seq protocol.

value: Primary human foreskin fibroblasts (HFF)

tag: stress with

value: 80 mM KCl

tag: replicate

value: Repicate 1


title: 2h salt stress Rep 2

value: Replicate 2


title: 2h heat stress Rep 2


title: 50017

tag: patient clinical diagnosis

tag: patient smoking status

tag: patient history of smoking (pack years)

value: test


title: 2h heat stress Rep 1


title: 1h salt stress Rep 1

source_name: HFF_1h_80 mM KCl_ATAC-seq


title: 1h heat stress Rep 2


title: 1h salt stress Rep 2


title: Mock Rep 4

value: mock

value: Repicate 4


title: Mock Rep 1


title: Mock Rep 3

value: Repicate 3


title: 86190

value: Bronchial Epithelium

value: Primary Lung

tag: patient gender

tag: patient age

tag: sequencing batch


title: Mock Rep 2

value: Repicate 2


title: ATAC-seq 8hpi Rep 1

description:
Prepared following protocol by Buenrostro et al. Nature Methods 2013
ATAC-seq (Transposon accessible chromatin)

data_processing:
Reads were mapped against the human genome (GRCh37/hg19), HSV-1 genome (Human herpesvirus 1 strain 17, JN555585, terminal repeats masked) and rRNA sequences using ContextMap v2.7.9
Open chromatin regions were identified using F-Seq v1.85
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bed files with identified open chromatin regions

source_name: HFF, 8hpi

growth_protocol: Human foreskin fibroblasts were cultured in DMEM supplements with 10% FBS and P/S. Cells at passage 15 were infected with HSV-1 strain 17 at an MOI of 10

treatment_protocol: Cells were infected with wildtype HSV-1 for 15min using an MOI of 10. 15min after infection (time point 0h), cell culture media was replaced with fresh media. Samples were harvested at the indicated time points and all samples were processed according to the standard ATAC-seq protocol.

value: human foreskin fibroblasts

tag: infection

value: HSV-1 strain 17

tag: time


title: ATAC-seq 4hpi Rep 1

source_name: HFF, 4hpi


title: ATAC-seq 2hpi Rep 1

source_name: HFF, 2hpi


title: ATAC-seq 2hpi Rep 2


title: ATAC-seq 1hpi Rep 2

source_name: HFF, 1hpi


title: ATAC-seq mock Rep 2

source_name: HFF, mock


title: ATAC-seq mock Rep 1


title: ATAC-seq 6hpi Rep 2

source_name: HFF, 6hpi


title: ATAC-seq 8hpi Rep 2


title: ATAC-seq 6hpi Rep 1


title: ATAC-seq 1hpi Rep 1


title: ATAC-seq 4hpi Rep 2


title: 1h heat stress Rep 1


title: Nucleoplasmic RNA, HSV-1 8h p.i., Rep 2

description:
Nucleoplasmic RNA isolated from HSV-1 infected HFF at 8h p.i.
Subcellular RNA fraction

data_processing:
Reads were mapped against the human genome (GRCh37/hg19), HSV-1 genome (Human herpesvirus 1 strain 17, JN555585, terminal repeats masked) and rRNA sequences using ContextMap v2.7.9
Number of read fragments per gene were determined using featureCounts and gene annotations from Ensembl (version 87 for GRCh37). HSV-1 gene annotations were obtained from GenBank (GenBank accession code: JN555585).
Expression of cellular protein-coding and lincRNAs was quantified in terms of fragments per kilobase of exons per million mapped reads (FPKM)
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: FPKM

source_name: Nucleoplasmic RNA

extract_protocol:
Subcellular RNA fractions were prepared combinig the following two protocols (PMID: 19656867, RNA 2009; and PMID: 23449254, Nature Protocols 2013)
Sequencing libraries were prepared using the TruSeq Stranded Total RNA kit (Illumina)  with Ribo-Zero Human/Mouse/Rat (only for total RNA).
NextSeq 500 sequencing 75bp paired-end reads

treatment_protocol: Cells were infected with wildtype HSV-1 for 15min using an MOI of 10. 15min after infection (time point 0h), cell culture media was replaced with fresh media. Cells were harvested prior to or at 8h p.i. Subcellular RNA fractions were prepared and subjected to standard RNA-seq including rRNA deplation

tag: time post infection

value: HSV-1 8h p.i.


title: Chromatin-associated RNA, Mock, Rep 2

description:
Chromatin-associated RNA isolated from mock infected HFF
Subcellular RNA fraction

source_name: Chromatin-associated RNA

value: Mock


title: Chromatin-associated RNA, HSV-1 8h p.i., Rep 2

description:
Chromatin-associated RNA isolated from HSV-1 infected HFF at 8h p.i.
Subcellular RNA fraction


title: Cytoplasmic RNA, HSV-1 8h p.i., Rep 2

description:
Cytoplasmic RNA isolated from HSV-1 infected HFF at 8h p.i.
Subcellular RNA fraction

source_name: Cytoplasmic RNA


title: Cytoplasmic RNA, HSV-1 8h p.i., Rep 1


title: Total RNA, Mock, Rep 2

description:
Total RNA isolated from mock infected HFF
Subcellular RNA fraction

source_name: Total RNA


title: Nucleoplasmic RNA, HSV-1 8h p.i., Rep 1


title: Cytoplasmic RNA, Mock, Rep 2

description:
Cytoplasmic RNA isolated from mock infected HFF
Subcellular RNA fraction


title: Total RNA, HSV-1 8h p.i., Rep 1

description:
Total RNA isolated from HSV-1 infected HFF at 8h p.i.
Subcellular RNA fraction


title: Total RNA, HSV-1 8h p.i., Rep 2


title: Nucleoplasmic RNA, Mock, Rep 1

description:
Nucleoplasmic RNA isolated from mock infected HFF
Subcellular RNA fraction


title: Chromatin-associated RNA, HSV-1 8h p.i., Rep 1


title: Cytoplasmic RNA, Mock, Rep 1


title: Total RNA, Mock, Rep 1


title: Mock 1 4sU-RNA - Rep 2

description:
mock1_2
Purified from total RNA using 4sU-tagging

source_name: Mock 1 4sU-RNA

extract_protocol:
Total RNA was prepared using Trizol. Newly transcribed RNA was purified as described in Rädle et al., JoVE 2013.
Sequencing libraries were prepared using the TruSeq Stranded Total RNA kit (Illumina)
NextSeq 500 sequencing 75bp paired-end reads

treatment_protocol: Cells were exposed to either 80mM KCl (increase in final concentration) or heat stress (44ºC) by exchange of cell culture media. 500uM 4-thiouridine was added to the cell culture at the indicated time points.

value: 60 min 500 uM 4sU prior to stress

tag: molecule subtype

value: newly transcribed RNA (4sU-RNA)


title: Nucleoplasmic RNA, Mock, Rep 2

tag: cell type


title: Mock 1 4sU-RNA - Rep 1

description:
mock1_1
Purified from total RNA using 4sU-tagging


title: 0-1 h Heat stress 4sU-RNA -  Rep 2

description:
heat_1h_2
Purified from total RNA using 4sU-tagging

source_name: 0-1 h Heat stress 4sU-RNA

value: 60 min 500 uM 4sU at 0-1 h


title: 0-1 h Heat stress 4sU-RNA - Rep 1

description:
heat_1h_1
Purified from total RNA using 4sU-tagging


title: Mock 2 4sU-RNA - Rep 1

description:
mock2_1
Purified from total RNA using 4sU-tagging

source_name: Mock 2 4sU-RNA


title: 0-1 h Salt stress 4sU-RNA - Rep 2

description:
salt_1h_2
Purified from total RNA using 4sU-tagging

source_name: 0-1 h Salt stress 4sU-RNA

value: 80 mM KCl


title: 1-2 h Salt stress 4sU-RNA -  Rep 2

description:
salt_2h_2
Purified from total RNA using 4sU-tagging

source_name: 1-2 h Salt stress 4sU-RNA

value: 60 min 500 uM 4sU at 1-2 h


title: 1-2 h Heat stress 4sU-RNA - Rep 1

description:
heat_2h_1
Purified from total RNA using 4sU-tagging

source_name: 1-2 h Heat stress 4sU-RNA


title: 0-1 h Salt stress 4sU-RNA -  Rep 1

description:
salt_1h_1
Purified from total RNA using 4sU-tagging


title: 1-2 h Heat stress 4sU-RNA -  Rep 2

description:
heat_2h_2
Purified from total RNA using 4sU-tagging


title: Mock 2 4sU-RNA - Rep 2

description:
mock2_2
Purified from total RNA using 4sU-tagging


title: da-Gal4/+ (Ctrl-D)2

city: linkoping

first: shahrzad

last: Bahrampour

address: Campus HU: Lab 1, floor 13

department: IKE

country: Sweden

institute: Linkoping University

description: Experiment 2

data_processing: Expression profiling was conducted using DNAStar 14.1, SeqMan NextGen software, adjusted for reads per kilobase per million mapped sequence reads (RPKM), and we have showne the linear and log2 PRKM and raw reads for each sample also the fold change (Control VS Test).

source_name: Drosophila embryo

extract_protocol:
Drosophila embryos at stages 8-16 have been collected in two biological replicates per genoptype (50 mg of frozen collection); sampel collections were used for RNA extraction, using RNeasy Mini Kit (Qiagen, Hilden, Germany).
RNA sequencing was performed by (GeneWiz, New Jersey, NJ), in 1x50 bp single-read sequencing configuration, which yielded 15-35 M reads/sample ( each set of experiment had been sequencing on 1 lane of Illumina HiSeq2500 platform in a 1X50bp single-read (SR) configuration. receive on average ~25M reads/sample with a total data output of ~150M reads/lane).

tag: embryonic stage

value: whole embryo - St8-St16

tag: strain

value: da-Gal4 (BDSC# 55849)/OregonR (BDSC# 2376)


title: da-Gal4/+ (Ctrl-D)1

description: Experiment 2


title: da-Gal4>UAS- (ase-Vp16,  Kr,  wor-EnR, SoxN-EnR); denoted UAS-QuadD#1

description: Experiment 2

value: da-Gal4 (BDSC# 55849)/ UAS-(ase-Vp16, Kr, wor-EnR, SoxN-EnR)


title: 5month-frontal-cortex[Q331K/Q331K]8

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

country: United Kingdom

institute: Altos Labs

data_processing:
Libraries were sequenced with 2x100bp paired-end reads on a HiSeq2500 platform.
Reads were trimmed using Trim Galore v0.4.3 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the standard Illumina adapter sequence. They were mapped to the mouse GRCm38 genome assembly using HISAT2 v2.0.5. BAM files were imported to Seqmonk v1.37.0 (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/). Raw read counts per transcript were calculated using the RNA-Seq quantitation pipeline using opposit-stranded counts.
Genome_build: GRCm38
Supplementary_files_format_and_content: The Quantitated RNA-Seq report file is tab delimited and contains the following columns: (1) mRNA name (Ensembl); (2) Chromosome; (3) Start; (4) End; (5) Strand; (7) mRNA ID (Ensembl) (8) Description (Ensembl); (13-end) raw counts

molecule: polyA RNA

extract_protocol:
Total RNA was extracted from 5 month old frontal cortex tissue using TRIsure reagent (Bioline) and the RNeasy extraction kit (Qiagen).
Libraries were prepared using the TrueSeq Stranded mRNA kit (Illumina) following the low sample protocol. RNA fragmentation time was reduced to 3 minutes at 94°C.

treatment_protocol:
Frontal cortex tissues were collected from either wild type, heterozygous or homozygous TDP-43 Q331K knock-in mice, at 5 months of age.
Tissues were snap frozen on liquid nitrogen and stored at -80°C until processing

tag: strain background

tag: genotype/variation

tag: age

value: 5 months

tag: tissue

value: Frontal cortex


title: Chromatin-associated RNA, Mock, Rep 1

description:
Chromatin-associated RNA isolated from mock infected HFF
Subcellular RNA fraction

tag: replicate

value: Repicate 1


title: da-Gal4/+ (Ctrl)2

description: Experiment 1


title: da-Gal4>UAS- (ase, Kr, wor, SoxN); denoted UAS-Quad#2

description: Experiment 1

value: da-Gal4 (BDSC# 55849)/ UAS-(ase, Kr, wor, SoxN)


title: da-Gal4/+ (Ctrl)1

description: Experiment 1


title: 5month-frontal-cortex[Q331K/Q331K]4


title: 5month-frontal-cortex[Q331K/Q331K]7


title: 5month-frontal-cortex[Q331K/Q331K]5


title: Sample 24 [CTRL 2 d14]

city: Martigny

first: Raphaelle

last: Luisier

state: Valais

address: Rue Marconi 19, PO Box 592

country: Switzerland

institute: Idiap Research Institute

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and then mapped to h19 ribosomal RNA using bowtie v1.1.2 with parameters -q -p 8 -v 0. Unmapped reads were finally mapped to hg19 whole genome using tophat2 with parameters  -g 1 -p 8  --library-type fr-firststrand.
For differential gene and transcript expression analysis we ran Kallisto and Sleuth. Kallisto was used to 1) build a transcript index from the Ensembl GRC38 release 85 Homo sapiens transcriptome (-k 31), 2) pseudo-align the RNA-seq reads to the transcriptome and 3) quantify transcript abundances (-b 100 --single -l 275 -s 50 --rf-stranded). We next identified differentially expressed transcripts and genes with Sleuth, a companion program that uses Kallisto results to differentiate between true biological expression differences and variation resulting from sources of experimental noise.
Genome_build: hg19
Supplementary_files_format_and_content: Relative transcript abundance and transcript per million as obtained from Kallisto software.

source_name: pMN progenitor cells

growth_protocol: Dermal fibroblasts were cultured in OptiMEM +10% FCS medium. The following episomal plasmids were transfected for iPSC generation: pCXLE hOct4 shp53, pCXLE hSK and pCXLE hUL (Addgene), as previously reported [15].Details of the lines used in thus study are reported in Supplementary table 1. Two of the control lines used (control 2 and control 3) are commercially available and were purchased from Coriell (cat. number ND41866*C ) and ThermoFisher Scientific (cat. number A18945) respectively. Induced PSCs were maintained on Geltrex (Life Technologies) with Essential 8 Medium media (Life Technologies) and passaged using EDTA (Life Technologies, 0.5mM). All cell cultures were maintained at 37°Cand 5% carbon dioxide.

extract_protocol:
Total RNA was extracted from cells using the Maxwell RSC simplyRNA cells kit (Promega), that includes DNase treatment, according to manufacturer’s instructions.
1 ug of total RNA was subjected to Ribo-Zero treatment TruSeq Stranded mRNA preparation Kit (Illumina).

treatment_protocol: Motor neuron (MN)differentiation was carried out using an adapted version of a previously published protocol [Gupta et al. 2012]. Briefly, iPSCs were first differentiated to neuroepithelium by plating to 100% confluency in chemically defined medium consisting of DMEM/F12 Glutamax, Neurobasal, L-Glutamine, N2 supplement, non essential amino acids, B27 supplement, β-mercaptoethanol (all from Life Technologies) and insulin (Sigma). Treatment with small molecules from day 0-7 was as follows: 1μM Dorsomorphin (Millipore), 2μM SB431542 (TocrisBioscience), and 3μM CHIR99021 (MiltenyiBiotec) for 7 days. At day 8, the neuroepithelial layer was enzymatically dissociated using dispase(GIBCO, 1 mg/ml), plated onto laminin coated plates and next patterned for 7days with 0.5μM retinoic acid and 1μMPurmorphamine. At day 14 spinal cord MN precursors were treated with 0.1μM Purmorphamine for a further 4 days before being terminally differentiated in 0.1 mM Compound E (Enzo Life Sciences) to promote cell cycle exit.

value: pMN progenitor cells

tag: diagnosis

value: none (control)

tag: patient id

value: Patient 3

tag: cell line id

value: CTRL 2

tag: genotype

value: Control

tag: days of differentiation


title: 5month-frontal-cortex[Q331K/Q331K]6


title: 1-2 h Salt stress 4sU-RNA - Rep 1

description:
salt_2h_1
Purified from total RNA using 4sU-tagging

value: human foreskin fibroblasts

tag: stress with


title: 5month-frontal-cortex[Q331K/Q331K]3


title: 5month-frontal-cortex[Q331K/Q331K]2


title: Sample 22 [CTRL 2 d14]


title: 5month-frontal-cortex[Q331K/Q331K]1


title: Sample 21 [CTRL 2 d7]

source_name: Neural precursor cells

value: Neural precursor cells


title: Sample 20 [CTRL 1 d7]

value: Patient 4

value: CTRL 1


title: 5month-frontal-cortex[Q331K/+]6


title: da-Gal4>UAS- (ase-Vp16,  Kr,  wor-EnR, SoxN-EnR); denoted UAS-QuadD#2

description: Experiment 2


title: 5month-frontal-cortex[Q331K/+]4


title: 5month-frontal-cortex[Q331K/+]5


title: 5month-frontal-cortex[Q331K/+]3


title: 5month-frontal-cortex[Q331K/+]2


title: Sample 8 [MUT 2 d14]

value: amyotrophic lateral dystrophy (ALS)

value: Patient 1

value: MUT 2


title: 5month-frontal-cortex[Q331K/+]1


title: 5month-frontal-cortex[+/+]6


title: Sample 4 [MUT 1 d7]

value: MUT 1


title: Sample 6 [MUT 3 d7]

value: Patient 2

value: MUT 3


title: Sample 5 [MUT 2 d7]


title: 5month-frontal-cortex[+/+]5

value: 5 months

value: Frontal cortex


title: da-Gal4>UAS- (ase, Kr, wor, SoxN); denoted UAS-Quad#1

description: Experiment 1

value: whole embryo - St8-St16

value: da-Gal4 (BDSC# 55849)/ UAS-(ase, Kr, woR, SoxN)


title: Sample 23 [CTRL 1 d14]

value: pMN progenitor cells

value: none (control)


title: pubertal rat

city: Hefei

first: Fugui

last: Fang

state: Anhui

address: No. 130 of Changjiang West Road

department: College of Animal Sciences and Technology

institute: Anhui Agricultural University

data_processing:
Total RNA was used as input material for the RNA sample preparations. Ribosomal RNA was removed by Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA). Sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). Products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the libraries were  sequenced on an Illumina Hiseq 4000 platform and 150 bp paired-end reads were generated.
Inorder to identify the lncRNAs,the prelimilary scanning was conducted by Scripture (beta2)and Cufflinks (v2.1.1) in a reference-based approach, follwed by coding poteintial analysis using CNCI (v2), CPC (0.9-r2),Pfam Scan (v1.3) and phyloCSF.
Cuffdiff (v2.1.1) was used to calculate FPKMs of both lncRNAs and coding genes in each sample (Trapnell,C.et al.2010).
Genome_build: Rnor_5.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values, gene type,chromosome, and strand information for each Sample.

organism: Rattus norvegicus

source_name: Hypothalamus

extract_protocol:
Hypothalamic tissues were surgically removed immediately frozen, and RNA derived from rat hypothalamus was obtained using TRIzol Reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Sprague Dawley

value: Hypothalamus

tag: developmental stage

value: Puberty


title: 5month-frontal-cortex[+/+]2


title: 5month-frontal-cortex[+/+]1


title: 5month-frontal-cortex[+/+]3


title: prepubertal rat

value: Prepuberty


title: 5month-lower-motor-neuron[Q331K/Q331K]4

data_processing:
Libraries were sequenced with 2x100bp paired-end reads on a HiSeq2500 platform.
Reads were trimmed using Trim Galore v0.4.3 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the standard Illumina adapter sequence.  They were mapped to the mouse GRCm38 genome assembly using HISAT2 v2.0.5. BAM files were imported to Seqmonk v1.37.0 (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/). Raw read counts per transcript were calculated using the RNA-Seq quantitation pipeline using non-stranded counts.
Genome_build: GRCm38
Supplementary_files_format_and_content: The Quantitated RNA-Seq report file is tab delimited and contains the following columns: (1) mRNA name (Ensembl); (2) Chromosome; (3) Start; (4) End; (5) Strand; (7) mRNA ID (Ensembl) (8) Description (Ensembl); (13-end) raw counts

extract_protocol:
RNA was immediately extracted using the Arcturus PicoPure kit (ThermoFisher) and stored at -80°C
Libraries were prepared using the SMART-seq v4 Ultra Low Input RNA kit (Clontech) with a 10 cycle PCR amplification protocol. 150pg cDNA per library was used as input to the Nextera XT DNA Library Prep Kit (Illumina) to generate sequence ready libraries.

treatment_protocol: tissue collection: Laser captured lumbar motor neurons were collected from either wild type, heterozygous or homozygous TDP-43 Q331K knockin mice, at 5 months of age.

value: Lower motor neurons


title: 5month-lower-motor-neuron[Q331K/Q331K]3


title: Sample 7 [MUT 1 d14]

value: amyotrophic lateral dystrophy (ALS)


title: 5month-lower-motor-neuron[Q331K/Q331K]2


title: 5month-lower-motor-neuron[Q331K/+]4


title: Sample 19 [CTRL 2 d7]

value: Neural precursor cells

value: Patient 3

value: CTRL 2

value: Control


title: 5month-lower-motor-neuron[Q331K/Q331K]1


title: 5month-lower-motor-neuron[Q331K/+]3


title: 5month-lower-motor-neuron[Q331K/+]2


title: 5month-lower-motor-neuron[Q331K/+]1


title: 5month-lower-motor-neuron[+/+]3


title: 5month-lower-motor-neuron[+/+]2


title: 5month-lower-motor-neuron[+/+]4


title: 5month-lower-motor-neuron[+/+]1


title: Veh RNAseq rep2

city: Univeristy Park

first: Gary

middle: H

last: Perdew

address: 309A Life Sciences Building

institute: The Pennsylvania State University

data_processing:
RNAseq reads were aligned to the mouse genome (mm10) using TopHat version 2.0.13 with default parameters
Reads mapping to genes were counted using HTseq-count version 0.5.4p3 with parameters ‘-s no -a 10’
Genome_build: mm10 mouse genome
Supplementary_files_format_and_content: tag counts (output of the HTseq-count tool) are given for each gene

source_name: peritoenal macrophages

growth_protocol: Wild-type male mice of the C57BL6/J strain were used for all experiments, with adults ranging in age from 6 to 8 weeks.

extract_protocol:
Total RNA from cultured primary macrophages were extracted with trizol. RNAseq libraries were made from polyA enriched toRNA.
Libraries were preapred as described in the Illumina RNAseq cloning kit

treatment_protocol: Cells were pre-treated with 10 uM SGA360 for 1 h, then with 10 ng/ml LPS for 4 h. Cells were harvested at the end of treatment.

tag: expression

value: endogenous

value: C57BL6/J wild-type

tag: treatment

value: Vehicle 5 h


title: Veh RNAseq rep1


title: LPS-SGA RNAseq rep1

value: 10 µM SGA360 1 h, 10 ng/ml LPS 4 h


title: 5month-frontal-cortex[+/+]4

value: 5 months

value: Frontal cortex


title: LPS RNAseq rep2

value: 10 ng/ml LPS 4 h


title: LPS RNAseq rep1


title: MAM3842

city: Wuhan

first: Yang

last: Zhou

state: Hubei

address: Shizishanjie #1

department: College of animal science

institute: Huazhong Agricultural University

description: different lane for MAM3842 whole genome bisufite sequencing

data_processing:
Programs FastQC (0.11.2) and Trim Galore (0.4.0) were used to generate sequence quality reports and to trim/filter the sequences, respectively.
The cleaned data for each sample were merged and aligned to the reference genome (Bos taurus UMD3.1) using bowtie2 under the Bismark software (0.14.5)
The methylcytosine information was extracted using the bismark_methylation_extractor after deduplicating the duplication reads.
Genome_build: UMD3.1
Supplementary_files_format_and_content: The data files contain the methylatin information for the CG detected. The column names are: chrmosome, position, position (same as the second column), methylation level, coverage for methylated cytosine, coverage for unmethylated cytosine, total coverage

organism: Bos taurus

source_name: mammary gland

extract_protocol:
Genomic DNA was isolated according to the QIAamp DNA Mini Kit protocol (QIAGEN, Valencia, CA, USA).
The qualified genomic DNA from somatic tissues and sperm were used to construct libraries. Briefly, 3 μg of genomic DNA spiked with unmethylated lambda DNA were fragmented into 200-300 bp using a Covaris S220 (Covaris, Inc., Woburn, MA, USA), followed by teriminal repairing and A-ligation. Different cytosine methylated barcodes were ligated to sonicated DNA for different samples. The DNA bisufite conversion was performed using the EZ DNA Methylation Gold Kit (Zymo Research, Irvine, CA, USA). Then single-stranded DNA fragments were amplified using the KAPA HiFi HotStart Uracil + ReadyMix (2 X) (Kapa Biosystems, Wilmington, MA, USA). The library concentration was quantified using a Qubit 2.0 fluorometer (Life Technologies, Carlsbad, CA, USA) and qPCR (iCycler, BioRad Laboratories, Hercules, CA, USA), and the insert size was checked using the Agilent 2100.

value: mammary gland

tag: breed

value: Holstein

value: adult


title: CORTEX3886

description: different lane for CORTEX3886 whole genome bisufite sequencing

source_name: brain

value: brain


title: CORTEX3842

description: different lane for CORTEX3842 whole genome bisufite sequencing


title: sperm2B

description: different lane for sperm2B whole genome bisufite sequencing

source_name: sperm

value: sperm