title: DMF 6hour biological rep2

city: Memphis

first: JUN

last: YANG

state: TN

address: 262 Danny Thomas Place

department: Surgery

institute: St Jude Children's Research Hospital

hyb_protocol: The WT Plus assay from Affymetrix fragments and labels 5.5 ug of ss-cDNA of which 2.3 ug is hybridized on the Clariom S mouse array with a constant temperature of 45° C for 16 hours while rotating at 60 rpm.

scan_protocol: The samples were the stained and washed using the Affymetrix Fluidics 450 stations and  recommended protocol. Then the Clariom S mouse arrays were then scanned by the Affymetrix GeneChip Scanner 3000 7G

data_processing: Data were background adjusted, normalized and summarized by the RMA method.

source_name: Cells treated with DMF for 6h

label_protocol: The protocol used for the samples run on the Clariom S mouse arrays was the Whole Transcript Plus assay from Affymetrix.  The initial input of RNA was 100 ng

growth_protocol: Cells were cultured in IMDM medium (10%FBS).

extract_protocol: Qiagen RNeasy mini kit

treatment_protocol: Cells were  treated with 50 uM of DMF for 6 and 12 hours.


title: DLBCL_LS155

status: Public on May 01 2018

type: RNA

city: Boston

first: Björn

last: Chapuy

state: MA

address: 450 Brookline Ave.

department: Medical Onology

country: USA

institute: Dana-Farber Cancer Institute

hyb_protocol: Following fragmentation, cRNA was hybridized overnight according to the Affymetrix protocol.

scan_protocol: GCS3000 (Affymetrix)

data_processing: The raw cel files were converted into probeset-specific expression values using Affymetrix RMA summarization method as implemented in the BioConductor package simpleaffy (Gentleman et al., 2004) using Brainarray custom chip definition files (Version 16) based on Ensemble IDs.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: DLBCL

label_protocol: cRNA was biotinylated according to the standard Affymetrix protocol.

growth_protocol: 10-20 x 20 um sections from snap-frozen tumor specimens from newly diagnosed previously untreated samples were directly transferred to Trizol.

extract_protocol: For total RNA, cells were homogenized in Trizol and RNA was extracted according to standard protocols.

tag: tissue type

value: primary Diffuse Large B-cell Lymphoma


title: indrops_nextseq06: visual cortices

status: Public on Apr 30 2018

type: SRA

city: Dallas

first: Hume

last: Stroud

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern

library_source: transcriptomic

data_processing:
We used the published inDrops sequencing read mapping Python pipeline from Klein et al. (Klein et al., 2015)(https://github.com/indrops/indrops) with default parameters (umi quantification - m:10, u:1, d:600, split-ambigs:False, min_non_polyA:15, bowtie [v 1.1.1] - m:200, n:1, l:15, e:80, trimmomatic [v 0.33] - LEADING: "28", SLIDINGWINDOW: "4:20", MINLEN: "16", max_low_complexity_fraction : 0.50) on a custom built transcriptome (made with default parameters of same Python pipeline using the GRCm38.p5 mouse genome assembly with the Ensembl transcript annotation build 85) The data were clustered using Seurat (Satija et al., 2015). Nuclei with at least 500 unique molecular identifiers (UMIs) with at least 200 genes covered were retained for analyses and genes expressed in at least 3 nuclei were kept for analyses. Furthermore, nuclei with greater than 15,000 UMIs or nuclei in which >10% of UMI came from mitochrondial genes were excluded from the analyses. T-distributed stochastic neighbor embedding (t-SNE) plots were generated using the “TSNEplot” function. Gene expression overlays were visualized using the  “FeaturePlot” function. We used known neuronal and non-neuronal markers “Slc17a7”, “Gad1”, “Aldoc”, “Olig1”, ”Cx3cr1”, “Cldn5”, “Mrc1” and “Vtn” genes, to identify potential doublets. All nuclei expressing more than one of the above markers were excluded from the analyses. Furthermore, nuclei that expressed more that one of either “Sst”, ”Pvalb” and “Vip” genes were marked as potential doublets of inhibitory neurons and excluded from the analyses.  Average normalized gene expression in Pv and Vip expressing nuclei was quantified using Monocle (Trapnell et al., 2014),
Genome_build: mm10
Supplementary_files_format_and_content: Normalized gene expression levels in all Pv and Vip expressing nuclei. All data from the same genotype were merged. Column 1: Gene name; Column 2: Gene expression in wild type Pv neurons; Column 3: Gene expression in mutant Pv neurons; Column 4: Gene expression in wild type Vip neurons; Column 5: gene expression in mutant Vip neurons.

organism: Mus musculus

source_name: Visual cortex

growth_protocol: Adult mice were dark-reared for one week prior to dissecting the visual cortices to reduce variation in transcription caused by light exposure (Mardinly et al., 2016). Nuclei from Dnmt3a cKO and Mecp2 KO visual cortices along with those from the respective littermate wild type controls were isolated as previously described (Mo et al., 2015).

extract_protocol:
SUN1-GFP expressing nuclei were isolated as previously described (Mo et al., 2015) using GFP antibodies (Fisher G10362) coupled with Protein G Dynabeads (Invitrogen 10003D). RNasein Plus RNase Inhibitors (Promega N2611) were added to the buffers to prevent degradation of RNA.
Co-encapsulation into microfluidic droplets of nuclei, polyacrylamide gels containing barcoded reverse transcription primers, reverse-transcriptase enzyme, and lysis buffer were performed as previously described to generate barcoded cDNA from single nuclei (Klein et al., 2015; Zilionis et al., 2017). We added 57µL of FD pre-mix (5µL 10X FD buffer; 45µL ddH20; 3µL ExoI (NEB M0293S, 20U/µL); 4µL HinFI (Thermo FD0804) to every 40 µl of sample. Samples were filtered through a 0.45 µm cellulose acetate filter, and incubated at 30 min at 37 °C. Samples were purified with 1.2X volume Agencourt AMPure XP beads (Beckman Coulter A63881). Second strand complementary DNA synthesis was performed by adding 10X NEB Second Strand Synthesis Buffer and NEB Second Strand Synthesis Enzyme Mix (New England Biolabs E6111S) and incubated at 16°C for 2.5 hours, then heat inactivated at 65 °C for 20min. In vitro transcription was performed with NEB T7 High Yield 10X Buffer, dNTPs, NEB T7 High Yield Enzyme Mix (NEB E2040S) and incubating at 37 °C for 13 hours. Samples were purified with 1.3X volume AMPure beads. RNA was fragmented with Fragmentation reagent (Ambion AM8740) by incubating at at 70°C for 3 min, stopped with the STOP mix, and purified with the 1.2X volume AMPure beads. Reverse transcription was performed using random hexamers: Fragmented RNA were incubated with 10 µM primers (TCGGCATTCCTGCTGAACCGCTCTTCCGATCTNNNNNN) and 10mM dNTPs for 3 min at 70°C. Then added RNase Inhibitor, 5X PrimeScript Buffer, 0.5 µL PrimeScript Reverse Transcriptase (Takara Clontech 2680A), and incubated at 30 °C for 10 min, 42 °C for 1 hour, then 70 °C for 15 min. The product was purified with 1.2X volume AMPure beads. The product was amplified using 2X KAPA HiFi HotStart ReadyMix (KAPA Biosystems KK2601), 5 µM primer mix (PE1: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGA; PE2: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAAC) using the following conditions 98°C 2 min, 2 cycles of (98°C 20sec, 55°C 30sec, 72°C 40sec), 9 to 14 cycles of (98°C 20sec, 65°C 30sec, 72°C 40sec), 72°C 5 min, 4°C hold.

tag: background

tag: age

value: 10 week

tag: tissue

value: Visual cortex

tag: genotype

value: mixed sample (non-demultiplexed)


title: indrops_nextseq03: visual cortices


title: DLBCL_LS146


title: DLBCL_LS1395


title: indrops_nextseq08: visual cortices


title: indrops_nextseq04: visual cortices


title: indrops_nextseq05: visual cortices


title: indrops_nextseq07: visual cortices


title: DLBCL_LS1304


title: DMF 12hour biological rep1

source_name: Cells treated with DMF for 12h

tag: cell type


title: indrops_nextseq02: visual cortices


title: DMF 12hour biological rep2


title: DMF biological rep2

source_name: Cells treated with DMF for 0h


title: Hoxb3os GapMir Treated cells Replicate 1

city: Minneapolis

first: Micah

last: Gearhart

state: MN

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

institute: University of Minnesota

description:
hoxb3osKD_log2fc_padj_counts.csv
Hoxb3os_KD_1_S51

data_processing:
Reads were adapter trimmed (Trimmomatic v0.32), mapped to the GRCm38 reference genome with STAR (2.4.2a_modified), indexed and sorted with Samtools (v1.0).   The number of reads mapping to each transcript in ENSEMBL annotation set (v84) was estimated with summarizeOverlaps (v1.8.3). Moderated log2 fold change values and Benjamini-Hochberg corrected p-values were calculated using DESeq2 (1.12.3). BigWig files were created using rtracklayer (1.32.2) and scaled based on the normalization in DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: Cultured mIMCD-3 Cells (ATCC CRL-2123)

growth_protocol: mICMD-3 cells were cultured in DMEM with 10% FBS.

extract_protocol:
Trizol (Invitrogen)
TruSeq (Illumina)

treatment_protocol: Cultured cells were transfected with 10 nM GapmeR against Hoxb3os (ATTACTGCTTCTTCCA) using Lipofectamine 3000 and harvested after 48 h.

tag: strain


title: Pkd2 f/f Kidney (WT) Replicate 2

description:
Pkd1_Pkd2_summary.csv
Pkd2WT_2

data_processing:
Paired-end reads were checked for quality using fastqc (v0.11.2) and fastq_screen (v0.4.4) and were quality trimmed using fastq-mcf (ea-utils/v1.1.2-806). Trimmed reads were aligned to the mouse reference genome (UCSC mm10 version from igenomes) using STAR (v2.4.2a) and known transcripts from gencode (vM9). Cufflinks (v2.2.1) was then used for reference annotation based transcript assembly (RABT) of the transcriptome for each of the individual samples. These individual assemblies were then merged and annotated using gencode (vM9) into a single collection of transcripts using Cuffmerge. Expression quantification and differential expression analysis were performed on the transcript using RSEM (v1.2.22) and edgeR respectively.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: kidney

value: Postnatal day 20


title: Control Treated cells Replicate 1

description:
hoxb3osKD_log2fc_padj_counts.csv
Control_1_S52

treatment_protocol: Cultured cells were transfected with 10 nM GapmeR negative control (Exiqon) using Lipofectamine 3000 and harvested after 48 h.


title: Control Treated cells Replicate 2

description:
hoxb3osKD_log2fc_padj_counts.csv
Control_2_S53


title: Hoxb3os GapMir Treated cells Replicate 2

description:
hoxb3osKD_log2fc_padj_counts.csv
Hoxb3os_KD_2_S49


title: Pkhd1/Cre; Pkd2 f/f Kidney (WT) Replicate 2

description:
Pkd1_Pkd2_summary.csv
Pkd2KO_2


title: Hoxb3os GapMir Treated cells Replicate 3

description:
hoxb3osKD_log2fc_padj_counts.csv
Hoxb3os_KD_3_S50


title: DMF biological rep1


title: Pkhd1/Cre; Pkd2 f/f Kidney (WT) Replicate 1

description:
Pkd1_Pkd2_summary.csv
Pkd2KO_1


title: DMF 6hour biological rep1


title: Pkd2 f/f Kidney (WT) Replicate 1

description:
Pkd1_Pkd2_summary.csv
Pkd2WT_1


title: Ksp/Cre; Pkd1 f/f Kidney (KO) Replicate 2

description:
Pkd1_Pkd2_summary.csv
Pkd1KO_2

value: Postnatal day 10


title: Pkd1 f/f Kidney (WT) Replicate 2

description:
Pkd1_Pkd2_summary.csv
Pkd1WT_2


title: Ksp/Cre; Pkd1 f/f Kidney (KO) Replicate 1

description:
Pkd1_Pkd2_summary.csv
Pkd1KO_1


title: Pkd1 f/f Kidney (WT) Replicate 1

description:
Pkd1_Pkd2_summary.csv
Pkd1WT_1


title: Antisense oligonucleotide SPC3847, biological rep1

city: Horsholm

first: Peter

middle: H

last: Hagedorn

state: Danmark

address: Fremtidsvej 3

department: Research

country: Denmark

institute: Roche Innovation Center Copenhagen A/S

hyb_protocol: Labeled ssDNA was hybridized to arrays in a GeneChip Hybridization Oven 640 (Affymetrix).

scan_protocol: The arrays were washed and stained in a GeneChip Fluidics Station 450 (Affymetrix), and subsequently scanned with a GeneChip Scanner 3000 (Affymetrix).

data_processing: The raw cel files were converted into probeset-specific expression values using Robust Multiarray Averaging (Bioconductor package Affy) with summarization method using Brainarray cdf annotations.

source_name: Liver, 4d after first dose

label_protocol: Total RNA was amplified and labeled using the Whole Transcript (WT) Sense Target Labeling Assay (Affymetrix).

growth_protocol: Inbred C57BL/6J female mice were obtained from Taconic (Denmark) and fed standard diet ad libitum. At study start, the mice weighed 20±2g (arithmetic mean ± standard deviation). The animal facility was maintained on a 12-hour light-dark cycle throughout each study.

extract_protocol: Total RNA from liver was isolated using Trizol (Invitrogen), purified using mini RNeasy columns (Qiagen), and the integrity and purity assessed using an Agilent Bioanalyzer and a Nanodrop RNA 6000 spectrophotometer.

treatment_protocol: Mice were dosed intravenously on days 0, 1, and 2, and anesthetized (70% CO2/30% O2) before sacrifice by cervical dislocation on day 3.

tag: Sex

value: female

value: liver

tag: treatment

tag: dose

value: 10 mg/kg


title: Antisense oligonucleotide SPC3833, biological rep1

value: 5 mg/kg


title: Antisense oligonucleotide SPC4955, biological rep1


title: Antisense oligonucleotide SPC4061, biological rep3


title: Antisense oligonucleotide SPC3847, biological rep2


title: Antisense oligonucleotide SPC4061, biological rep2


title: Antisense oligonucleotide SPC3847, biological rep4


title: Antisense oligonucleotide SPC4061, biological rep1


title: Antisense oligonucleotide SPC3833, biological rep_1

value: Antisense oligonucleotide


title: Antisense oligonucleotide SPC3847, biological rep3


title: Antisense oligonucleotide SPC3833, biological rep2


title: Antisense oligonucleotide SPC3833, biological rep3


title: Antisense oligonucleotide SPC4061, biological rep4


title: Saline, biological rep_2

value: Saline


title: Antisense oligonucleotide SPC3833, biological rep_3


title: Saline, biological rep3


title: Antisense oligonucleotide SPC4955, biological rep2


title: Saline, biological rep4


title: Saline, biological rep_3


title: Saline, biological rep2


title: Antisense oligonucleotide SPC4955, biological rep4


title: Antisense oligonucleotide SPC3833, biological rep4


title: Antisense oligonucleotide SPC3833, biological rep_4


title: Saline, biological rep_4


title: Antisense oligonucleotide SPC4955, biological rep3


title: Antisense oligonucleotide SPC3833, biological rep_2


title: Saline, biological rep1


title: Saline, biological rep_1


title: alpha-Amanitin_8cell_embryo3_6

city: Guangzhou

first: Lin

last: Li

address: Shatai South Road

department: Pathophysiology

country: China

institute: Southern Medical University

description: bisulfite treated  genomic DNA

library_source: genomic

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
We used Trim Galore (v0.3.3) to remove the first 6 bases of random primer, adaptor sequences and low quality bases were also trimmed with the command ‘trim_galore --quality 20 --stringency 3 --length 50 --clip_R1 6 --clip_R2 6 --paired --trim1 --phred33’.
In order to recover more sequencing reads, we used Bismark (v0.7.6) to map the clean reads to human reference genome hg19 with paired-end and non-directional module, and then the unmapped reads were realigned to the same reference genome in single-end and non-directional module (paired-end parameters: bismark --fastq --non_directional –unmapped --phred33-quals -1 $trim_fq1 -2 $trim_fq2; unmapped read1 single-end parameters: bismark –fastq --non_directional --phred33-quals $unmap_fq1; unmapped read2 single-end parameters: bismark –fastq --non_directional --phred33-quals $unmap_fq2). After alignment, PCR duplicates were removed with the command ‘samtools rmdup’ (v0.1.18) for paired-end reads and ‘samtools rmdup -s’ for single-end reads.
WCG and GCH methylation level of cytosines was estimated using comstomized scripts.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files which include the methylation level of cytosines in WCG and GCH context respectively

molecule: genomic DNA

source_name: 8-cell blastomere

extract_protocol:
The single cell of early embryos were picked into PCR tube containing lysis buffer (10 mM Tris-HCl pH 7.4, 0.25 mM EDTA, 0.25 mM PMSF, 0.5% NP-40, 10 mM DDT, 50 mM NaCl and 1 pg unmethylated lambda DNA) by mouth pipette, in order to release genomic DNA.
After pick a single cell into lysis buffer, the tube was vortexed violently for 30 s to lyse efficiently. After spinning down, the lysate was incubated in 5 U GpC MTase (NEB, M0227L) and 160 μM S-adenosylmethionine at 37 ℃ for 45 min and 65 ℃ for 25 min. To release the genomic DNA, 0.5 μl 20 mg/ul protease (QIAGEN) was added and the sample was incubated at 50 ℃ for 3 hrs, 20 ℃ for 20 min. The scCOOL-seq libraries were constructed with slight modification. Briefly, the bisulfite conversion was performed using EZ-96 DNA Methylation-DirectTMMagPrep (Zymo, D5044) according to the user guide. After purification, 10 rounds of amplification were completed in the presence of Klenow exo- (Enzymics) and scBS-seq-P5-N6-oligo1  (CTACACGACGCTCTTCCGATCTNNNNNN). The amplification product was purified by 0.8x Agencourt AMPure XP beads (Beckman). The second strand was synthesied using scBS-seq-P7-N6-oligo2 (AGACGTGTGCTCTTCCGATCTNNNNN), followed by 0.8x Agencourt AMPure XP beads (Beckman). 13 cycles of PCR were performed to amplify the library using index primer and universal primer (NEB). The libraries were sequenced on Illumina Hiseq 4000 platform on pair-end 150 bp mode.

value: 8-cell embryo

tag: developmental stage / passages


title: alpha-Amanitin_8cell_embryo3_3

description: bisulfite treated  genomic DNA


title: alpha-Amanitin_8cell_embryo3_4

description: bisulfite treated  genomic DNA


title: alpha-Amanitin_8cell_embryo3_2

description: bisulfite treated  genomic DNA


title: alpha-Amanitin_8cell_embryo2_8

description: bisulfite treated  genomic DNA


title: alpha-Amanitin_8cell_embryo2_7

description: bisulfite treated  genomic DNA


title: alpha-Amanitin_8cell_embryo3_1

description: bisulfite treated  genomic DNA


title: alpha-Amanitin_8cell_embryo2_4

description: bisulfite treated  genomic DNA


title: alpha-Amanitin_8cell_embryo2_1

description: bisulfite treated  genomic DNA


title: alpha-Amanitin_8cell_embryo2_5

description: bisulfite treated  genomic DNA


title: alpha-Amanitin_8cell_embryo2_6

description: bisulfite treated  genomic DNA


title: alpha-Amanitin_8cell_embryo3_5

description: bisulfite treated  genomic DNA


title: alpha-Amanitin_8cell_embryo1_5

description: bisulfite treated  genomic DNA


title: alpha-Amanitin_8cell_embryo1_3

description: bisulfite treated  genomic DNA


title: alpha-Amanitin_8cell_embryo1_2

description: bisulfite treated  genomic DNA


title: alpha-Amanitin_8cell_embryo2_3

description: bisulfite treated  genomic DNA


title: alpha-Amanitin_8cell_embryo1_6

description: bisulfite treated  genomic DNA


title: alpha-Amanitin_7cell_embryo1_1

description: bisulfite treated  genomic DNA

source_name: 7-cell blastomere

value: 7-cell embryo


title: alpha-Amanitin_8cell_embryo1_1

description: bisulfite treated  genomic DNA


title: alpha-Amanitin_8cell_embryo1_4

description: bisulfite treated  genomic DNA


title: alpha-Amanitin_8cell_embryo2_2

description: bisulfite treated  genomic DNA


title: alpha-Amanitin_7cell_embryo1_2

description: bisulfite treated  genomic DNA


title: alpha-Amanitin_6cell_embryo1_1

description: bisulfite treated  genomic DNA

source_name: 6-cell blastomere

value: 6-cell embryo


title: TE_embryo5_6

description: bisulfite treated  genomic DNA

source_name: Blastocyst

value: Trophoectoderm cells

value: Blastocyst


title: TE_embryo5_12

description: bisulfite treated  genomic DNA


title: TE_embryo5_5

description: bisulfite treated  genomic DNA


title: TE_embryo5_10

description: bisulfite treated  genomic DNA


title: TE_embryo5_8

description: bisulfite treated  genomic DNA


title: TE_embryo5_7

description: bisulfite treated  genomic DNA


title: TE_embryo5_13

description: bisulfite treated  genomic DNA


title: TE_embryo5_9

description: bisulfite treated  genomic DNA


title: TE_embryo5_11

description: bisulfite treated  genomic DNA


title: TE_embryo4_10

description: bisulfite treated  genomic DNA


title: TE_embryo5_1

description: bisulfite treated  genomic DNA


title: TE_embryo4_11

description: bisulfite treated  genomic DNA


title: TE_embryo4_12

description: bisulfite treated  genomic DNA


title: TE_embryo5_4

description: bisulfite treated  genomic DNA


title: TE_embryo5_2

description: bisulfite treated  genomic DNA


title: TE_embryo4_13

description: bisulfite treated  genomic DNA


title: TE_embryo4_7

description: bisulfite treated  genomic DNA


title: TE_embryo4_8

description: bisulfite treated  genomic DNA


title: TE_embryo4_5

description: bisulfite treated  genomic DNA


title: TE_embryo5_3

description: bisulfite treated  genomic DNA


title: TE_embryo4_2

description: bisulfite treated  genomic DNA


title: TE_embryo4_9

description: bisulfite treated  genomic DNA


title: TE_embryo4_4

description: bisulfite treated  genomic DNA


title: TE_embryo4_3

description: bisulfite treated  genomic DNA


title: TE_embryo3_4

description: bisulfite treated  genomic DNA


title: TE_embryo2_16

description: bisulfite treated  genomic DNA


title: TE_embryo4_6

description: bisulfite treated  genomic DNA


title: TE_embryo2_14

description: bisulfite treated  genomic DNA


title: TE_embryo3_3

description: bisulfite treated  genomic DNA


title: TE_embryo3_1

description: bisulfite treated  genomic DNA


title: TE_embryo2_10

description: bisulfite treated  genomic DNA


title: TE_embryo2_4

description: bisulfite treated  genomic DNA


title: TE_embryo2_3

description: bisulfite treated  genomic DNA


title: TE_embryo4_1

description: bisulfite treated  genomic DNA


title: TE_embryo2_15

description: bisulfite treated  genomic DNA


title: TE_embryo2_7

description: bisulfite treated  genomic DNA


title: TE_embryo2_11

description: bisulfite treated  genomic DNA


title: TE_embryo2_12

description: bisulfite treated  genomic DNA


title: TE_embryo2_8

description: bisulfite treated  genomic DNA


title: TE_embryo3_2

description: bisulfite treated  genomic DNA


title: TE_embryo2_5

description: bisulfite treated  genomic DNA


title: ICM_embryo7_6

description: bisulfite treated  genomic DNA

value: Inner cell mass


title: TE_embryo1_1

description: bisulfite treated  genomic DNA


title: TE_embryo1_2

description: bisulfite treated  genomic DNA


title: ICM_embryo8_1

description: bisulfite treated  genomic DNA


title: ICM_embryo8_2

description: bisulfite treated  genomic DNA


title: ICM_embryo7_7

description: bisulfite treated  genomic DNA


title: TE_embryo2_13

description: bisulfite treated  genomic DNA


title: ICM_embryo7_5

description: bisulfite treated  genomic DNA


title: ICM_embryo7_9

description: bisulfite treated  genomic DNA


title: ICM_embryo7_4

description: bisulfite treated  genomic DNA


title: ICM_embryo7_8

description: bisulfite treated  genomic DNA


title: ICM_embryo7_2

description: bisulfite treated  genomic DNA


title: ICM_embryo6_5

description: bisulfite treated  genomic DNA


title: ICM_embryo7_3

description: bisulfite treated  genomic DNA


title: ICM_embryo7_1

description: bisulfite treated  genomic DNA


title: ICM_embryo6_4

description: bisulfite treated  genomic DNA


title: TE_embryo2_6

description: bisulfite treated  genomic DNA


title: TE_embryo2_1

description: bisulfite treated  genomic DNA


title: TE_embryo2_2

description: bisulfite treated  genomic DNA


title: ICM_embryo6_2

description: bisulfite treated  genomic DNA


title: ICM_embryo6_3

description: bisulfite treated  genomic DNA


title: ICM_embryo4_13

description: bisulfite treated  genomic DNA


title: ICM_embryo6_1

description: bisulfite treated  genomic DNA


title: ICM_embryo5_5

description: bisulfite treated  genomic DNA


title: ICM_embryo5_2

description: bisulfite treated  genomic DNA


title: ICM_embryo5_4

description: bisulfite treated  genomic DNA


title: ICM_embryo5_1

description: bisulfite treated  genomic DNA


title: ICM_embryo4_11

description: bisulfite treated  genomic DNA


title: TE_embryo2_9

description: bisulfite treated  genomic DNA


title: ICM_embryo4_12

description: bisulfite treated  genomic DNA


title: ICM_embryo5_3

description: bisulfite treated  genomic DNA


title: ICM_embryo4_6

description: bisulfite treated  genomic DNA


title: ICM_embryo4_3

description: bisulfite treated  genomic DNA


title: ICM_embryo4_5

description: bisulfite treated  genomic DNA


title: ICM_embryo4_4

description: bisulfite treated  genomic DNA


title: ICM_embryo4_10

description: bisulfite treated  genomic DNA


title: ICM_embryo4_2

description: bisulfite treated  genomic DNA


title: ICM_embryo4_7

description: bisulfite treated  genomic DNA


title: ICM_embryo4_1

description: bisulfite treated  genomic DNA


title: ICM_embryo3_5

description: bisulfite treated  genomic DNA


title: ICM_embryo3_7

description: bisulfite treated  genomic DNA


title: ICM_embryo4_8

description: bisulfite treated  genomic DNA


title: ICM_embryo4_9

description: bisulfite treated  genomic DNA


title: ICM_embryo3_6

description: bisulfite treated  genomic DNA


title: ICM_embryo3_3

description: bisulfite treated  genomic DNA


title: ICM_embryo3_4

description: bisulfite treated  genomic DNA


title: ICM_embryo3_1

description: bisulfite treated  genomic DNA


title: ICM_embryo2_4

description: bisulfite treated  genomic DNA


title: ICM_embryo2_2

description: bisulfite treated  genomic DNA


title: ICM_embryo2_1

description: bisulfite treated  genomic DNA


title: ICM_embryo1_2

description: bisulfite treated  genomic DNA


title: ICM_embryo2_3

description: bisulfite treated  genomic DNA


title: ICM_embryo3_2

description: bisulfite treated  genomic DNA


title: ICM_embryo2_5

description: bisulfite treated  genomic DNA


title: ICM_embryo1_1

description: bisulfite treated  genomic DNA


title: Morula_embryo3_3

description: bisulfite treated  genomic DNA

source_name: Morula blastomere

value: Morula


title: ICM_embryo1_3

description: bisulfite treated  genomic DNA


title: ICM_embryo1_4

description: bisulfite treated  genomic DNA


title: Morula_embryo3_4

description: bisulfite treated  genomic DNA


title: Morula_embryo3_2

description: bisulfite treated  genomic DNA


title: Morula_embryo2_10

description: bisulfite treated  genomic DNA


title: Morula_embryo2_8

description: bisulfite treated  genomic DNA


title: Morula_embryo2_9

description: bisulfite treated  genomic DNA


title: Morula_embryo3_1

description: bisulfite treated  genomic DNA


title: Morula_embryo2_7

description: bisulfite treated  genomic DNA


title: Morula_embryo2_1

description: bisulfite treated  genomic DNA


title: Morula_embryo1_11

description: bisulfite treated  genomic DNA


title: Morula_embryo1_10

description: bisulfite treated  genomic DNA


title: Morula_embryo2_5

description: bisulfite treated  genomic DNA


title: Morula_embryo2_6

description: bisulfite treated  genomic DNA


title: Morula_embryo1_9

description: bisulfite treated  genomic DNA


title: Morula_embryo2_2

description: bisulfite treated  genomic DNA


title: Morula_embryo2_4

description: bisulfite treated  genomic DNA


title: Morula_embryo1_7

description: bisulfite treated  genomic DNA


title: Morula_embryo2_3

description: bisulfite treated  genomic DNA


title: Morula_embryo1_6

description: bisulfite treated  genomic DNA


title: Morula_embryo1_4

description: bisulfite treated  genomic DNA


title: 8cell_embryo11_3

description: bisulfite treated  genomic DNA


title: Morula_embryo1_1

description: bisulfite treated  genomic DNA


title: 8cell_embryo11_2

description: bisulfite treated  genomic DNA


title: Morula_embryo1_2

description: bisulfite treated  genomic DNA


title: Morula_embryo1_3

description: bisulfite treated  genomic DNA


title: 8cell_embryo12_1

description: bisulfite treated  genomic DNA


title: Morula_embryo1_5

description: bisulfite treated  genomic DNA


title: 8cell_embryo10_6

description: bisulfite treated  genomic DNA


title: 8cell_embryo11_1

description: bisulfite treated  genomic DNA


title: Morula_embryo1_8

description: bisulfite treated  genomic DNA


title: 8cell_embryo10_3

description: bisulfite treated  genomic DNA


title: 8cell_embryo10_4

description: bisulfite treated  genomic DNA


title: 8cell_embryo10_5

description: bisulfite treated  genomic DNA


title: 8cell_embryo10_2

description: bisulfite treated  genomic DNA


title: 8cell_embryo9_4

description: bisulfite treated  genomic DNA


title: 8cell_embryo9_1

description: bisulfite treated  genomic DNA


title: 8cell_embryo9_2

description: bisulfite treated  genomic DNA


title: 8cell_embryo9_3

description: bisulfite treated  genomic DNA


title: 8cell_embryo10_1

description: bisulfite treated  genomic DNA


title: 8cell_embryo7_1

description: bisulfite treated  genomic DNA


title: 8cell_embryo8_1

description: bisulfite treated  genomic DNA


title: 8cell_embryo7_2

description: bisulfite treated  genomic DNA


title: 8cell_embryo8_2

description: bisulfite treated  genomic DNA


title: 8cell_embryo8_3

description: bisulfite treated  genomic DNA


title: 8cell_embryo6_6

description: bisulfite treated  genomic DNA


title: 8cell_embryo6_1

description: bisulfite treated  genomic DNA


title: 8cell_embryo6_5

description: bisulfite treated  genomic DNA


title: 8cell_embryo4_3

description: bisulfite treated  genomic DNA


title: 8cell_embryo5_2

description: bisulfite treated  genomic DNA


title: 8cell_embryo5_3

description: bisulfite treated  genomic DNA


title: 8cell_embryo5_5

description: bisulfite treated  genomic DNA


title: 8cell_embryo6_4

description: bisulfite treated  genomic DNA


title: 8cell_embryo5_4

description: bisulfite treated  genomic DNA


title: 8cell_embryo4_5

description: bisulfite treated  genomic DNA


title: 8cell_embryo4_4

description: bisulfite treated  genomic DNA


title: 8cell_embryo4_2

description: bisulfite treated  genomic DNA


title: 8cell_embryo6_2

description: bisulfite treated  genomic DNA


title: 8cell_embryo6_3

description: bisulfite treated  genomic DNA


title: 8cell_embryo5_1

description: bisulfite treated  genomic DNA


title: 8cell_embryo3_2

description: bisulfite treated  genomic DNA


title: 8cell_embryo2_2

description: bisulfite treated  genomic DNA


title: 8cell_embryo3_3

description: bisulfite treated  genomic DNA


title: 8cell_embryo3_5

description: bisulfite treated  genomic DNA


title: 4cell_embryo11_3

description: bisulfite treated  genomic DNA

source_name: 4-cell blastomere

value: 4-cell embryo


title: 8cell_embryo3_1

description: bisulfite treated  genomic DNA


title: 8cell_embryo4_1

description: bisulfite treated  genomic DNA


title: 8cell_embryo2_3

description: bisulfite treated  genomic DNA


title: 8cell_embryo2_5

description: bisulfite treated  genomic DNA


title: 8cell_embryo2_4

description: bisulfite treated  genomic DNA


title: 8cell_embryo3_4

description: bisulfite treated  genomic DNA


title: 8cell_embryo1_3

description: bisulfite treated  genomic DNA


title: 8cell_embryo1_2

description: bisulfite treated  genomic DNA


title: 8cell_embryo1_1

description: bisulfite treated  genomic DNA


title: 4cell_embryo10_1

description: bisulfite treated  genomic DNA


title: 4cell_embryo11_2

description: bisulfite treated  genomic DNA


title: 4cell_embryo8_2

description: bisulfite treated  genomic DNA


title: 4cell_embryo9_1

description: bisulfite treated  genomic DNA


title: 4cell_embryo9_2

description: bisulfite treated  genomic DNA


title: 4cell_embryo7_1

description: bisulfite treated  genomic DNA


title: 4cell_embryo10_2

description: bisulfite treated  genomic DNA


title: 4cell_embryo8_1

description: bisulfite treated  genomic DNA


title: 4cell_embryo7_2

description: bisulfite treated  genomic DNA


title: 4cell_embryo11_1

description: bisulfite treated  genomic DNA


title: 4cell_embryo7_3

description: bisulfite treated  genomic DNA


title: 4cell_embryo6_1

description: bisulfite treated  genomic DNA


title: 4cell_embryo5_1

description: bisulfite treated  genomic DNA


title: 4cell_embryo4_3

description: bisulfite treated  genomic DNA


title: 4cell_embryo5_2

description: bisulfite treated  genomic DNA


title: 4cell_embryo4_2

description: bisulfite treated  genomic DNA


title: 8cell_embryo2_1

description: bisulfite treated  genomic DNA


title: 4cell_embryo2_2

description: bisulfite treated  genomic DNA


title: 4cell_embryo4_1

description: bisulfite treated  genomic DNA


title: 4cell_embryo3_3

description: bisulfite treated  genomic DNA


title: 4cell_embryo1_1

description: bisulfite treated  genomic DNA


title: 4cell_embryo2_1

description: bisulfite treated  genomic DNA


title: 4cell_embryo1_2

description: bisulfite treated  genomic DNA


title: 4cell_embryo2_3

description: bisulfite treated  genomic DNA


title: 4cell_embryo3_2

description: bisulfite treated  genomic DNA


title: 4cell_embryo3_1

description: bisulfite treated  genomic DNA


title: 2cell_embryo7_2

description: bisulfite treated  genomic DNA

source_name: 2-cell blastomere

value: 2-cell embryo


title: 2cell_embryo9_1

description: bisulfite treated  genomic DNA


title: 2cell_embryo8_1

description: bisulfite treated  genomic DNA


title: 2cell_embryo7_1

description: bisulfite treated  genomic DNA


title: 2cell_embryo10_1

description: bisulfite treated  genomic DNA


title: 2cell_embryo6_2

description: bisulfite treated  genomic DNA


title: 2cell_embryo4_1

description: bisulfite treated  genomic DNA


title: 2cell_embryo6_1

description: bisulfite treated  genomic DNA


title: 2cell_embryo5_2

description: bisulfite treated  genomic DNA


title: 2cell_embryo1_1

description: bisulfite treated  genomic DNA


title: 2cell_embryo2_1

description: bisulfite treated  genomic DNA


title: 2cell_embryo3_1

description: bisulfite treated  genomic DNA


title: 2cell_embryo4_2

description: bisulfite treated  genomic DNA


title: 2cell_embryo5_1

description: bisulfite treated  genomic DNA


title: Zygote_5

description: bisulfite treated  genomic DNA

source_name: Zygote

value: Zygote


title: Zygote_9

description: bisulfite treated  genomic DNA


title: Zygote_7

description: bisulfite treated  genomic DNA


title: Zygote_6

description: bisulfite treated  genomic DNA


title: Zygote_10

description: bisulfite treated  genomic DNA


title: Zygote_8

description: bisulfite treated  genomic DNA


title: Zygote_2

description: bisulfite treated  genomic DNA


title: Zygote_4

description: bisulfite treated  genomic DNA


title: Oocyte_2

description: bisulfite treated  genomic DNA

source_name: Oocyte

value: Oocyte

value: MII oocyte


title: Oocyte_1

description: bisulfite treated  genomic DNA


title: Zygote_3

description: bisulfite treated  genomic DNA


title: Oocyte_4

description: bisulfite treated  genomic DNA


title: Oocyte_7

description: bisulfite treated  genomic DNA


title: Oocyte_9

description: bisulfite treated  genomic DNA


title: Oocyte_8

description: bisulfite treated  genomic DNA


title: Oocyte_5

description: bisulfite treated  genomic DNA


title: Oocyte_3

description: bisulfite treated  genomic DNA


title: Oocyte_6

description: bisulfite treated  genomic DNA


title: Zygote_1

description: bisulfite treated  genomic DNA


title: hESC_6

description: bisulfite treated  genomic DNA

source_name: Embryonic stem cell

value: Embryonic stem cell


title: hESC_15

description: bisulfite treated  genomic DNA


title: hESC_18

description: bisulfite treated  genomic DNA


title: hESC_16

description: bisulfite treated  genomic DNA


title: hESC_19

description: bisulfite treated  genomic DNA


title: hESC_4

description: bisulfite treated  genomic DNA


title: hESC_7

description: bisulfite treated  genomic DNA


title: hESC_2

description: bisulfite treated  genomic DNA


title: hESC_21

description: bisulfite treated  genomic DNA


title: hESC_12

description: bisulfite treated  genomic DNA


title: hESC_13

description: bisulfite treated  genomic DNA


title: hESC_20

description: bisulfite treated  genomic DNA


title: hESC_8

description: bisulfite treated  genomic DNA


title: hESC_11

description: bisulfite treated  genomic DNA


title: hESC_17

description: bisulfite treated  genomic DNA


title: hESC_1

description: bisulfite treated  genomic DNA


title: hESC_22

description: bisulfite treated  genomic DNA


title: hESC_9

description: bisulfite treated  genomic DNA


title: hESC_14

description: bisulfite treated  genomic DNA


title: Sperm_10

description: bisulfite treated  genomic DNA

source_name: Sperm

value: Sperm


title: Sperm_9

description: bisulfite treated  genomic DNA


title: hESC_10

description: bisulfite treated  genomic DNA


title: hESC_5

description: bisulfite treated  genomic DNA


title: Sperm_11

description: bisulfite treated  genomic DNA


title: Sperm_12

description: bisulfite treated  genomic DNA


title: Sperm_13

description: bisulfite treated  genomic DNA


title: Sperm_7

description: bisulfite treated  genomic DNA


title: Sperm_6

description: bisulfite treated  genomic DNA


title: Sperm_8

description: bisulfite treated  genomic DNA


title: PBMC rep 1

status: Public on Apr 28 2018

city: Stanford

first: Cheen Euong

last: Ang

state: CA

address: 265 Campus Drive, G3145

institute: Stanford University

description:
P939
processed data file: FPKM_table.txt

data_processing:
Fastq files were mapped using Tophat.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cuffdiff.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: FPKM table.txt: Tab-delimited text file includes FPKM values for each Sample.

source_name: Peripheral blood

growth_protocol: PBMCs were isolated using density gradient centrifugation with Ficoll-paque Plus.

extract_protocol:
RNA were extracted using Trizol according to manufacturer's protocol.
Libraries were generated using Clontech Smarter kit according to manufacturer's protocol.

treatment_protocol: Three micrograms of vectors of reprogramming factors were electroporated into isolated PBMCs. Transduced cells were cultured for 3 days in six-well plates in X-vivo10 supplemented with 30 U/ml IL-2 and 3.4µl/ml of Dynabeads Human T-activator CD3/CD28. Three days after electroporation, the transduced cells were seeded on primary glia culture in a well of 12 well-plates. Two days after seeding, medium were replaced to DMEM/F12 including N2, B27 and insulin. The medium was changed every 7 days.

value: peripheral blood mononuclear cells (PBMCs)


title: PSA-NCAM+ GFP- rep 1

description:
iN860-PSA
processed data file: FPKM_table.txt

source_name: In vitro derived neuronal cells

value: induced neuronal cells


title: PSA-NCAM+ GFP+ rep 1

description:
iN013-PSAG
processed data file: FPKM_table.txt


title: hESC_3

description: bisulfite treated  genomic DNA


title: PSA-NCAM+ GFP- rep 2

description:
iN948-PSA
processed data file: FPKM_table.txt


title: Sperm_4

description: bisulfite treated  genomic DNA


title: AM-wt, rep 3

status: Public on Apr 27 2018

city: Vienna

first: Nadine

middle: Elpida

last: Tatto

address: Muthgasse 18

department: Department of Biotechnology

country: Austria

institute: University of Natural Resources and Life Sciences

description: PolyA enriched RNA

data_processing:
Conversion BAM → FASTQ with bam2fastx 2.1.0 (TopHat2).
Quality Control with FastQC 0.11.2 with UGENE workflow designer (Unipro UGENE IDE v1.9.8).
Read trimming with TrimGalore 0.4.2.
Read quantification with kallisto and samtools (kallisto index based on K. phaffii CBS7435 genomic sequence as reference).
Differential expression analysis with R (DESeq2).
Genome_build: K. phaffii CBS7435 (PicPas_Mar2011 / GCA_000223565.1).
Supplementary_files_format_and_content: *.tsv: Tab-delimited text files include raw read counts and TPMs.
Supplementary_files_format_and_content: *_normalizedCounts.csv: Semi-colon-delimited text files include abundance measurements (DESeq2).

organism: Komagataella phaffii

source_name: Wild type grown in acetate medium

growth_protocol: Cells were grown in YPD and harvested during exponential growth. The same cultures were then shifted to acetate medium for 24h to induce mating gene expression.

extract_protocol:
Cells were disrupted mechanically and RNA was extracted using TRI reagent (Sigma-Aldrich) according to the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols (PolyA RNA (NEB)).

tag: strain/background

tag: genotype/variation

value: Wild type

tag: medium

value: acetate


title: AM-alpha, rep 2

description:
PolyA enriched RNA
dic1-2Δ(α)

source_name: α-type grown in acetate medium


title: AM-alpha, rep 1

description:
PolyA enriched RNA
dic1-2Δ(α)


title: AM-a, rep 1

description:
PolyA enriched RNA
dic1-2Δ(a)

source_name: a-type grown in acetate medium


title: PSA-NCAM+ GFP+ rep 2

description:
iN948-PSAG
processed data file: FPKM_table.txt


title: AM-a, rep 2

description:
PolyA enriched RNA
dic1-2Δ(a)


title: Sperm_5

description: bisulfite treated  genomic DNA


title: PBMC rep 2

description:
P940
processed data file: FPKM_table.txt


title: AM-a, rep 3

description:
PolyA enriched RNA
dic1-2Δ(a)


title: AM-wt, rep 2

description: PolyA enriched RNA


title: YPD-wt, rep 1

description: PolyA enriched RNA

source_name: Wild type grown in YPD medium

value: YPD


title: Sperm_1

description:
bisulfite treated  genomic DNA
single cell


title: Sperm_2


title: AM-wt, rep 1

description: PolyA enriched RNA


title: Sperm_3


title: YPD-alpha, rep 1

description:
PolyA enriched RNA
dic1-2Δ(α)

source_name: α-type grown in YPD medium


title: YPD-wt, rep 3

description: PolyA enriched RNA


title: YPD-a, rep 3

description:
PolyA enriched RNA
dic1-2Δ(a)

source_name: a-type grown in YPD medium


title: YPD-alpha, rep 2

description:
PolyA enriched RNA
dic1-2Δ(α)


title: YPD-alpha, rep 3

description:
PolyA enriched RNA
dic1-2Δ(α)


title: YPD-a, rep 2

description:
PolyA enriched RNA
dic1-2Δ(a)


title: YPD-a, rep 1

description:
PolyA enriched RNA
dic1-2Δ(a)


title: AM-alpha, rep 3

description:
PolyA enriched RNA
dic1-2Δ(α)


title: YPD-wt, rep 2

description: PolyA enriched RNA


title: XEN_R1 – Late S Fraction

status: Public on Apr 26 2018

city: Tallahassee

first: David

middle: M

last: Gilbert

state: FL

address: 319 Stadium Drive

department: Biology

institute: Florida State University

description:
Allele-specificRT.txt
Processed File Header 1: XEN_C57B6_R1
Processed File Header 2: XEN_Cas_R1

data_processing:
Reads are mapped to corresponding genome (C57BL/6, 129/sv and CAST/Ei) using bowtie2.
Coverage data are calculated from mapped reads using samtools and bedtools
Base 2 log of early to late coverage ratio was calculated in 5kb windows
Log 2 ratio data were quantile normalized using R package preprocessCore
Data were loess smoothed and binned into 50kb windows
Genome_build: mm10
Supplementary_files_format_and_content: processed data are 50kb windows in mm10 genome.

source_name: hybrid mouse XEN cells

growth_protocol: Hybrid mouse ES cell lines V6.5, F121, F121-6, F121-9, F123 and Cas129, were grown in two different conditions: a) on mitomycin-C-inactivated MEFs in ES media and b)  feeder-free in 2i medium. For feeder free/serum free conditions cells were grown on 0.1% gelatin-coated dish in N2B27 media supplemented with 1 μM MEK inhibitor , 4.25 μM GSK3 inhibitor (1-Azakenpaullone), 2 mM glutamine and 1,000U/ml LIF (Cell Guidance Systems GFM200), 0.15 mM monothioglycerol. Hybrid XEN cells were derived and maintained as previously described  (Kunath, et al 2005) in RPMI supplemented with 15% FBS (Life Tech), 100mM sodium pyruvate, 10mM B-mercaptoehanol and 200mM L-glutamine. Hybrid MEFs were grown in DMEM supplemented with 10% FBS, 1X NAAs, 2mM L-glutamine and 10mM B-mercaptoethanol. Neural precursor cells were derived from hybrid mouse ES cell lines with opposite parental configurations (F121-9 and Cas129). Hybrid mouse ESCs were grown in a monolayer culture at high density (1.5^105 cells/cm2) onto 0.1% (v/v) gelatin-coated 6-wells in serum-free medium ESGRO Complete Clonal Grade medium (CCGM). After 24 hours, cells were dissociated with 0.1% trypsin and then were plated onto 0.1% (v/v) gelatin-coated 10cm dishes at 1^104 cells/cm2 in RHB-A media (Takara), the media was changed every other day and NPCs were analyzed at day 11.

extract_protocol:
Genome-wide replication timing profiles were constructed as previously described (Hiratani et al. 2008; Ryba et al. 2011; Marchal et al., 2017). Briefly, cells were pulse labeled with BrdU and separated into early and late S-phase fractions by flow cytometry and processed  by NGS.
Sequencing libraries of BrdU-substituted DNA from early and late fractions were prepared by NEBNext Ultra DNA Library Prep Kit for Illumina (E7370).

tag: cross

value: hybrid C57B6 / cas

tag: s phase fraction

value: Late S fraction

tag: gender

value: Female

value: XEN cells

tag: replicate


title: XEN_R1 – Early S Fraction

value: Early S fraction


title: XEN_R2 – Early S Fraction

description:
Allele-specificRT.txt
Processed File Header 1: XEN_C57B6_R2
Processed File Header 2: XEN_Cas_R2


title: Cas129_ESC_2i_R2 – Late S Fraction

description:
Allele-specificRT.txt
Processed File Header 1: Cas129_ESC_2i_129_R2
Processed File Header 2: Cas129_ESC_2i_Cas_R2

source_name: hybrid mouse ESCs

value: hybrid cas / 129

value: ESCs


title: Cas129_NPC_R1 – Early S Fraction

description:
Allele-specificRT.txt
Processed File Header 1: Cas129_NPC_129_R1
Processed File Header 2: Cas129_NPC_Cas_R1

source_name: hybrid mouse NPCs

value: NPCs


title: Cas129_NPC_R1 – Late S Fraction


title: Cas129_ESC_2i_R1 – Early S Fraction

description:
Allele-specificRT.txt
Processed File Header 1: Cas129_ESC_2i_129_R1
Processed File Header 2: Cas129_ESC_2i_Cas_R1


title: V65_ESC_2i_R1 – Early S Fraction

description:
Allele-specificRT.txt
Processed File Header 1: V65_ESC_2i_129_R1
Processed File Header 2: V65_ESC_2i_C57B_R1

value: hybrid C57B6 / 129

value: Male


title: MEF_EMB1_R2 – Early S Fraction

description:
Allele-specificRT.txt
Processed File Header 1: MEF_EMB1_129_R2
Processed File Header 2: MEF_EMB1_Cas_R2

source_name: hybrid MEFs

value: MEFs


title: MEF_EMB1_R1 – Late S Fraction

description:
Allele-specificRT.txt
Processed File Header 1: MEF_EMB1_129_R1
Processed File Header 2: MEF_EMB1_Cas_R1


title: Cas129_NPC_R2 – Late S Fraction

description:
Allele-specificRT.txt
Processed File Header 1: Cas129_NPC_129_R2
Processed File Header 2: Cas129_NPC_Cas_R2


title: Cas129_NPC_R2 – Early S Fraction


title: XEN_R2 – Late S Fraction


title: MEF_EMB1_R1 – Early S Fraction


title: Cas129_ESC_2i_R1 – Late S Fraction


title: MEF_EMB1_R2 – Late S Fraction


title: Cas129_ESC_2i_R2 – Early S Fraction


title: V65_ESC_2i_R1 – Late S Fraction


title: MEF_EMB4_R2 – Late S Fraction

description:
Allele-specificRT.txt
Processed File Header 1: MEF_EMB4_129_R2
Processed File Header 2: MEF_EMB4_Cas_R2


title: MEF_EMB4_R2 – Early S Fraction


title: MEF_EMB3_R2 – Late S Fraction

description:
Allele-specificRT.txt
Processed File Header 1: MEF_EMB3_129_R2
Processed File Header 2: MEF_EMB3_Cas_R2


title: MEF_EMB2_R1 – Late S Fraction

description:
Allele-specificRT.txt
Processed File Header 1: MEF_EMB2_129_R1
Processed File Header 2: MEF_EMB2_Cas_R1


title: MEF_EMB4_R1 – Early S Fraction

description:
Allele-specificRT.txt
Processed File Header 1: MEF_EMB4_129_R1
Processed File Header 2: MEF_EMB4_Cas_R1


title: MEF_EMB2_R1 – Early S Fraction


title: MEF_EMB3_R1 – Early S Fraction

description:
Allele-specificRT.txt
Processed File Header 1: MEF_EMB3_129_R1
Processed File Header 2: MEF_EMB3_Cas_R1


title: MEF_EMB3_R2 – Early S Fraction


title: MEF_EMB3_R1 – Late S Fraction


title: F123_ESC_2i_R2 – Early S Fraction

description:
Allele-specificRT.txt
Processed File Header 1: F123_ESC_2i_129_R2
Processed File Header 2: F123_ESC_2i_Cas_R2

value: hybrid 129 / cas


title: MEF_EMB2_R2 – Early S Fraction

description:
Allele-specificRT.txt
Processed File Header 1: MEF_EMB2_129_R2
Processed File Header 2: MEF_EMB2_Cas_R2


title: MEF_EMB4_R1 – Late S Fraction


title: MEF_EMB2_R2 – Late S Fraction


title: F123_ESC_2i_R2 – Late S Fraction


title: F1219_ESC_2i_R2 – Early S Fraction

description:
Allele-specificRT.txt
Processed File Header 1: F1219_ESC_2i_129_R2
Processed File Header 2: F1219_ESC_2i_Cas_R2


title: F1219_NPC_R1 – Early S Fraction

description:
Allele-specificRT.txt
Processed File Header 1: F1219_NPC_129_R1
Processed File Header 2: F1219_NPC_Cas_R1


title: F123_ESC_2i_R1 – Late S Fraction

description:
Allele-specificRT.txt
Processed File Header 1: F123_ESC_2i_129_R1
Processed File Header 2: F123_ESC_2i_Cas_R1


title: F1219_ESC_2i_R1 – Early S Fraction

description:
Allele-specificRT.txt
Processed File Header 1: F1219_ESC_2i_129_R1
Processed File Header 2: F1219_ESC_2i_Cas_R1


title: F1219_ESC_MEF_R1 – Late S Fraction

description:
Allele-specificRT.txt
Processed File Header 1: F1219_ESC_MEF_129_R1
Processed File Header 2: F1219_ESC_MEF_Cas_R1


title: siRNA-NEDD9+V rep1

first: Bradley

last: Maron

address: 77 Avenue Louis Pasteur

department: Medicine

institute: Brigham & Women's Hospital

description: replicate 1

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Tophat2
Counting reads was done by HTSeq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include counts for each sample ...

growth_protocol: Cells were grown to confluence using EBM-2TM medium supplemented with 5% fetal bovine serum.

extract_protocol:
RNA was extracted using RNeasy mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Six samples were transfected with NEDD9 siRNA (40nM) using Lipofectamine TM2000 and 24 hours later treated with aldosterone (10-7mol/L) or vehicle control for 24 hours. Other 12 samples were directly treated with aldosterone (10-7mol/L) or vehicle control for 24 hours.

tag: transfection

value: NEDD9 siRNA

value: vehicle

value: pulmonary artery endothelial cells

value: male


title: siRNA-NEDD9+V rep3

description: replicate 3


title: F123_ESC_2i_R1 – Early S Fraction


title: F1219_NPC_R1 – Late S Fraction


title: siRNA-NEDD9+V rep2

description: replicate 2


title: Chomala_Panicle_Repl2  [ncRNA-seq]

status: Public on Apr 25 2018

city: Bangalore

first: Shivaprasad

last: Padubidri V.

address: GKVK Campus, Bellary road

department: Plant epigenetics

country: India

institute: National Center for Biological Sciences

description: Oryza sativa subspecies: Chomala

data_processing:
3’ adapter (5’-TGGAATTCTCGGGTGCCAAGG-3’) was removed from sequenced reads using UEA small RNA workbench.
The small RNA reads of length 16nt-35nt were filtered and analyzed.
Supplementary_files_format_and_content: Text file containing 16nt-35nt long unique reads and their raw abundance after removal of adapter.

organism: Oryza sativa aus subgroup

source_name: Panicle

extract_protocol:
Total RNA from three different tissues, 4-week old seedling, flagleaf and panicle of selected rice species were extracted using Trizol (Invitrogen) reagent.
Size fractionation

tag: cultivar

value: Chomala

value: Panicle


title: F1216_ESC_MEF_R2 – Late S Fraction

description:
Allele-specificRT.txt
Processed File Header 1: F1216_ESC_MEF_129_R2
Processed File Header 2: F1216_ESC_MEF_Cas_R2

value: Late S fraction


title: F1216_ESC_MEF_R1 – Early S Fraction

description:
Allele-specificRT.txt
Processed File Header 1: F1216_ESC_MEF_129_R1
Processed File Header 2: F1216_ESC_MEF_Cas_R1

value: Female


title: F1216_ESC_MEF_R2 – Early S Fraction


title: F1219_ESC_MEF_R1 – Early S Fraction


title: F1219_ESC_2i_R1 – Late S Fraction


title: F1219_ESC_MEF_R2 – Early S Fraction

description:
Allele-specificRT.txt
Processed File Header 1: F1219_ESC_MEF_129_R2
Processed File Header 2: F1219_ESC_MEF_Cas_R2


title: F1219_ESC_MEF_R2 – Late S Fraction


title: F1216_ESC_MEF_R1 – Late S Fraction


title: F1219_ESC_2i_R2 – Late S Fraction


title: F121_ESC_2i_R1 – Late S Fraction

description:
Allele-specificRT.txt
Processed File Header 1: F121_ESC_2i_129_R1
Processed File Header 2: F121_ESC_2i_Cas_R1


title: F1216_ESC_2i_R2 – Late S Fraction

description:
Allele-specificRT.txt
Processed File Header 1: F1216_ESC_2i_129_R2
Processed File Header 2: F1216_ESC_2i_Cas_R2


title: siRNA-NEDD9+ALDO rep1

description: replicate 1

value: aldosterone


title: Chomala_Flagleaf_Repl1  [ncRNA-seq]

description: Oryza sativa subspecies: Chomala

source_name: Flagleaf

tag: tissue

value: Flagleaf


title: F1216_ESC_2i_R1 – Late S Fraction

description:
Allele-specificRT.txt
Processed File Header 1: F1216_ESC_2i_129_R1
Processed File Header 2: F1216_ESC_2i_Cas_R1


title: siRNA-NEDD9+ALDO rep3

description: replicate 3


title: F1216_ESC_2i_R2 – Early S Fraction

value: Early S fraction


title: siRNA-NEDD9+ALDO rep2

description: replicate 2


title: F1216_ESC_2i_R1 – Early S Fraction

value: ESCs


title: Chomala_Flagleaf_Repl2  [ncRNA-seq]

description: Oryza sativa subspecies: Chomala


title: F121_ESC_2i_R1 – Early S Fraction


title: Chomala_Flagleaf_Repl2 [RNA-seq]

description: Oryza sativa subspecies: Chomala

data_processing:
Adapter was removed and low quality bases were trimmed from sequenced reads.
The processed reads were aligned to the rice genome using TopHat (v2.1.1).
Gene expressions were calculated using CuffLinks (v2.2.1) as mentioned in Cole Trapnell et al, 2012.
Genome_build: Oryza sativa japonica nipponbare genome – IRGSP1
Supplementary_files_format_and_content: Tab delimited text files including FPKM for each sample.

extract_protocol:
Total RNA from two different tissues, flagleaf and panicle of selected rice species were extracted using Trizol (Invitrogen) reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: flagleaf


title: Chomala_Panicle_Repl1  [ncRNA-seq]

description: Oryza sativa subspecies: Chomala


title: Chomala_Flagleaf_Repl1 [RNA-seq]

description: Oryza sativa subspecies: Chomala


title: Whiteponni_Flagleaf_Repl1  [ncRNA-seq]

description: Oryza sativa subspecies: Whiteponni

organism: Oryza sativa Indica Group

value: Whiteponni


title: Whiteponni_Panicle_Repl1  [ncRNA-seq]

description: Oryza sativa subspecies: Whiteponni


title: Whiteponni_Flagleaf_Repl2  [ncRNA-seq]

description: Oryza sativa subspecies: Whiteponni


title: Chomala_Seedling_Repl2  [ncRNA-seq]

description: Oryza sativa subspecies: Chomala

source_name: Four weeks old seedlings

value: Four weeks old seedlings


title: Chomala_Seedling_Repl1  [ncRNA-seq]

description: Oryza sativa subspecies: Chomala


title: Doddabyranel_Flagleaf_Repl2 [RNA-seq]

description: Oryza sativa subspecies: Doddabyranel

value: Doddabyranel


title: Whiteponni_Seedling_Repl1  [ncRNA-seq]

description: Oryza sativa subspecies: Whiteponni


title: Whiteponni_Seedling_Repl2  [ncRNA-seq]

description: Oryza sativa subspecies: Whiteponni


title: Kavuni_Flagleaf_Repl1 [RNA-seq]

description: Oryza sativa subspecies: Kavuni

value: Kavuni


title: Whiteponni_Panicle_Repl2  [ncRNA-seq]

description: Oryza sativa subspecies: Whiteponni


title: IN-wholefishtranscriptome_RNAseq rep3

status: Public on Apr 24 2018

city: Baltimore

first: yang

last: song

state: MD

address: HSF-3, 3rd Floor; 670 W Baltimore St.

department: Department: Institute for Genome Sciences

institute: University of Maryland in Baltimore

data_processing:
Base calls were performed using the built-in Illumina basecaller
Sequenced reads were trimmed for adaptor sequence, and then mapped to Mouse GRCm38 reference using the TopHat splice-aware aligner
Reads Per Kilobase of gene per Million mapped reads (RPKM) were calculated for each sample.
Differential expression of genes were computed between infected and uninfected samples
Genome_build: Danio_rerio(GRCz10)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

organism: Danio rerio

growth_protocol: embryos were grown at 28 degrees C in E3 media until 5dpf

extract_protocol:
RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit (Cat#74104).HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody (see manuscript for full protocol)
Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit (Illumina) per manufacturer’s instructions, with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Untreated

tag: developmental stage

value: whole fish

tag: antibody


title: Whiteponni_Flagleaf_Repl1 [RNA-seq]

description: Oryza sativa subspecies: Whiteponni


title: Whiteponni_Flagleaf_Repl2 [RNA-seq]

description: Oryza sativa subspecies: Whiteponni


title: IP-HCtranslatome_RNAseq rep2

value: hair cells (enriched)

value: HA


title: ChIP-seq from A549 (ENCLB227RQN)

status: Public on Apr 20 2018

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR984DZW/
***************
biological replicate number: 3
technical replicate number: 1
description: RAD21 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 8 hours.
experiment encode accession: ENCSR984DZW
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR233BJW
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB227RQN
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Homo sapiens A549 cell line treated with 100 nM dexamethasone for 8 hours

tag: line

value: cell line

tag: biosample encode accession

value: male

tag: dev stage

value: adult

tag: age

value: 58 year

tag: lab

value: Tim Reddy, Duke

tag: treatments

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:8; duration_units:hour;

tag: link

value: ENCBS058QGC at ENCODE; https://www.encodeproject.org/ENCBS058QGC/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: IN-wholefishtranscriptome_RNAseq rep2


title: IP-HCtranslatome_RNAseq rep1


title: ChIP-seq from A549 (ENCLB527YNF)

description:
https://www.encodeproject.org/experiments/ENCSR984DZW/
***************
biological replicate number: 2
technical replicate number: 1
description: RAD21 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 8 hours.
experiment encode accession: ENCSR984DZW
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR233BJW
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB527YNF
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

tag: Sex

value: ENCBS997NQT at ENCODE; https://www.encodeproject.org/ENCBS997NQT/


title: IN-wholefishtranscriptome_RNAseq rep1


title: Kavuni_Flagleaf_Repl2 [RNA-seq]

description: Oryza sativa subspecies: Kavuni

value: flagleaf


title: Doddabyranel_Flagleaf_Repl1 [RNA-seq]

description: Oryza sativa subspecies: Doddabyranel


title: ChIP-seq from A549 (ENCLB135NMZ)

description:
https://www.encodeproject.org/experiments/ENCSR981FDC/
***************
biological replicate number: 3
technical replicate number: 1
description: SMC3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 2 hours.
experiment encode accession: ENCSR981FDC
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR088SOR
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB135NMZ
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 cell line treated with 100 nM dexamethasone for 2 hours

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:2; duration_units:hour;

value: ENCBS061UZO at ENCODE; https://www.encodeproject.org/ENCBS061UZO/


title: ChIP-seq from A549 (ENCLB865MRK)

description:
https://www.encodeproject.org/experiments/ENCSR981FDC/
***************
biological replicate number: 2
technical replicate number: 1
description: SMC3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 2 hours.
experiment encode accession: ENCSR981FDC
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR088SOR
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB865MRK
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS826RWQ at ENCODE; https://www.encodeproject.org/ENCBS826RWQ/


title: IP-HCtranslatome_RNAseq rep3


title: ChIP-seq from A549 (ENCLB407IFI)

description:
https://www.encodeproject.org/experiments/ENCSR806UKK/
***************
biological replicate number: 2
technical replicate number: 1
description: SMC3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 5 hours.
experiment encode accession: ENCSR806UKK
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR565ZHQ
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB407IFI
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 cell line treated with 100 nM dexamethasone for 5 hours

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:5; duration_units:hour;

value: ENCBS934GIO at ENCODE; https://www.encodeproject.org/ENCBS934GIO/


title: ChIP-seq from A549 (ENCLB851RQU)

description:
https://www.encodeproject.org/experiments/ENCSR853VWZ/
***************
biological replicate number: 3
technical replicate number: 1
description: RAD21 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 6 hours.
experiment encode accession: ENCSR853VWZ
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR366VPA
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB851RQU
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 cell line treated with 100 nM dexamethasone for 6 hours

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS012TTG at ENCODE; https://www.encodeproject.org/ENCBS012TTG/


title: ChIP-seq from A549 (ENCLB779KYC)

description:
https://www.encodeproject.org/experiments/ENCSR895JMI/
***************
biological replicate number: 2
technical replicate number: 1
description: RAD21 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0.5 hours.
experiment encode accession: ENCSR895JMI
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR216DMN
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB779KYC
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 cell line treated with 100 nM dexamethasone for 30 minutes

value: cell line

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:30; duration_units:minute;

value: ENCBS274ZVG at ENCODE; https://www.encodeproject.org/ENCBS274ZVG/


title: ChIP-seq from A549 (ENCLB758CPG)

description:
https://www.encodeproject.org/experiments/ENCSR768DOX/
***************
biological replicate number: 2
technical replicate number: 1
description: SMC3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 1 hours.
experiment encode accession: ENCSR768DOX
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR560DEL
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB758CPG
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 cell line treated with 100 nM dexamethasone for 1 hour

value: male

value: adult

value: 58 year

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:1; duration_units:hour; UCSC-ENCODE-cv:DEX_100nM;

value: ENCBS380CAL at ENCODE; https://www.encodeproject.org/ENCBS380CAL/


title: ChIP-seq from A549 (ENCLB165EVI)

description:
https://www.encodeproject.org/experiments/ENCSR944ZCT/
***************
biological replicate number: 3
technical replicate number: 1
description: SMC3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 3 hours.
experiment encode accession: ENCSR944ZCT
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR266YIS
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB165EVI
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 cell line treated with 100 nM dexamethasone for 3 hours

value: Tim Reddy, Duke

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:3; duration_units:hour;

value: ENCBS806ZLH at ENCODE; https://www.encodeproject.org/ENCBS806ZLH/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: ChIP-seq from A549 (ENCLB203LGT)

description:
https://www.encodeproject.org/experiments/ENCSR956LGB/
***************
biological replicate number: 3
technical replicate number: 1
description: RAD21 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 1 hours.
experiment encode accession: ENCSR956LGB
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR560DEL
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB203LGT
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS915ELT at ENCODE; https://www.encodeproject.org/ENCBS915ELT/


title: ChIP-seq from A549 (ENCLB606GUT)

description:
https://www.encodeproject.org/experiments/ENCSR807WAC/
***************
biological replicate number: 3
technical replicate number: 1
description: RAD21 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 3 hours.
experiment encode accession: ENCSR807WAC
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR266YIS
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB606GUT
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS665VWV at ENCODE; https://www.encodeproject.org/ENCBS665VWV/


title: ChIP-seq from A549 (ENCLB765TMP)

description:
https://www.encodeproject.org/experiments/ENCSR806UKK/
***************
biological replicate number: 3
technical replicate number: 1
description: SMC3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 5 hours.
experiment encode accession: ENCSR806UKK
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR565ZHQ
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB765TMP
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:5; duration_units:hour;

value: ENCBS856DBT at ENCODE; https://www.encodeproject.org/ENCBS856DBT/


title: ChIP-seq from A549 (ENCLB434LJG)

description:
https://www.encodeproject.org/experiments/ENCSR944ZCT/
***************
biological replicate number: 2
technical replicate number: 1
description: SMC3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 3 hours.
experiment encode accession: ENCSR944ZCT
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR266YIS
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB434LJG
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS847XVV at ENCODE; https://www.encodeproject.org/ENCBS847XVV/


title: ChIP-seq from A549 (ENCLB598CUI)

description:
https://www.encodeproject.org/experiments/ENCSR853VWZ/
***************
biological replicate number: 2
technical replicate number: 1
description: RAD21 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 6 hours.
experiment encode accession: ENCSR853VWZ
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR366VPA
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB598CUI
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: cell line

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS237PGF at ENCODE; https://www.encodeproject.org/ENCBS237PGF/


title: ChIP-seq from A549 (ENCLB637TQB)

description:
https://www.encodeproject.org/experiments/ENCSR895JMI/
***************
biological replicate number: 3
technical replicate number: 1
description: RAD21 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0.5 hours.
experiment encode accession: ENCSR895JMI
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR216DMN
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB637TQB
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: male

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:30; duration_units:minute;

value: ENCBS539ECE at ENCODE; https://www.encodeproject.org/ENCBS539ECE/


title: ChIP-seq from A549 (ENCLB915YZN)

description:
https://www.encodeproject.org/experiments/ENCSR807WAC/
***************
biological replicate number: 2
technical replicate number: 1
description: RAD21 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 3 hours.
experiment encode accession: ENCSR807WAC
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR266YIS
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB915YZN
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: adult

value: 58 year

value: ENCBS910NQY at ENCODE; https://www.encodeproject.org/ENCBS910NQY/


title: ChIP-seq from A549 (ENCLB462JPY)

description:
https://www.encodeproject.org/experiments/ENCSR956LGB/
***************
biological replicate number: 2
technical replicate number: 1
description: RAD21 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 1 hours.
experiment encode accession: ENCSR956LGB
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR560DEL
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB462JPY
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: Tim Reddy, Duke

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:1; duration_units:hour; UCSC-ENCODE-cv:DEX_100nM;

value: ENCBS555SMT at ENCODE; https://www.encodeproject.org/ENCBS555SMT/


title: ChIP-seq from A549 (ENCLB181MRI)

description:
https://www.encodeproject.org/experiments/ENCSR768DOX/
***************
biological replicate number: 3
technical replicate number: 1
description: SMC3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 1 hours.
experiment encode accession: ENCSR768DOX
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR560DEL
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB181MRI
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS303AZP at ENCODE; https://www.encodeproject.org/ENCBS303AZP/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: ChIP-seq from A549 (ENCLB500WPM)

description:
https://www.encodeproject.org/experiments/ENCSR767DFK/
***************
biological replicate number: 3
technical replicate number: 1
description: SMC3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 12 hours.
experiment encode accession: ENCSR767DFK
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR382EJS
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB500WPM
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 cell line treated with 100 nM dexamethasone for 12 hours

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:12; duration_units:hour;

value: ENCBS793IHC at ENCODE; https://www.encodeproject.org/ENCBS793IHC/


title: ChIP-seq from A549 (ENCLB984ZSW)

description:
https://www.encodeproject.org/experiments/ENCSR767DFK/
***************
biological replicate number: 2
technical replicate number: 1
description: SMC3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 12 hours.
experiment encode accession: ENCSR767DFK
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR382EJS
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB984ZSW
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS311ILN at ENCODE; https://www.encodeproject.org/ENCBS311ILN/


title: ChIP-seq from A549 (ENCLB512LQF)

description:
https://www.encodeproject.org/experiments/ENCSR760NPX/
***************
biological replicate number: 3
technical replicate number: 1
description: RAD21 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 5 hours.
experiment encode accession: ENCSR760NPX
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR565ZHQ
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB512LQF
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: cell line

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:5; duration_units:hour;

value: ENCBS591HRC at ENCODE; https://www.encodeproject.org/ENCBS591HRC/


title: ChIP-seq from A549 (ENCLB613RPF)

description:
https://www.encodeproject.org/experiments/ENCSR760NPX/
***************
biological replicate number: 2
technical replicate number: 1
description: RAD21 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 5 hours.
experiment encode accession: ENCSR760NPX
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR565ZHQ
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB613RPF
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: male

value: ENCBS194BUG at ENCODE; https://www.encodeproject.org/ENCBS194BUG/


title: ChIP-seq from A549 (ENCLB108SOB)

description:
https://www.encodeproject.org/experiments/ENCSR537EFT/
***************
biological replicate number: 3
technical replicate number: 1
description: SMC3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 7 hours.
experiment encode accession: ENCSR537EFT
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR701MJQ
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB108SOB
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 cell line treated with 100 nM dexamethasone for 7 hours

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:7; duration_units:hour;

value: ENCBS745PHH at ENCODE; https://www.encodeproject.org/ENCBS745PHH/


title: ChIP-seq from A549 (ENCLB366KEL)

description:
https://www.encodeproject.org/experiments/ENCSR620NWG/
***************
biological replicate number: 3
technical replicate number: 1
description: SMC3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0.5 hours.
experiment encode accession: ENCSR620NWG
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR216DMN
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB366KEL
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: adult

value: 58 year

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:30; duration_units:minute;

value: ENCBS848GZD at ENCODE; https://www.encodeproject.org/ENCBS848GZD/


title: ChIP-seq from A549 (ENCLB246XQG)

description:
https://www.encodeproject.org/experiments/ENCSR676MJK/
***************
biological replicate number: 3
technical replicate number: 1
description: RAD21 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 7 hours.
experiment encode accession: ENCSR676MJK
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR701MJQ
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB246XQG
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: Tim Reddy, Duke

value: ENCBS488JXY at ENCODE; https://www.encodeproject.org/ENCBS488JXY/


title: ChIP-seq from A549 (ENCLB303WLH)

description:
https://www.encodeproject.org/experiments/ENCSR676MJK/
***************
biological replicate number: 2
technical replicate number: 1
description: RAD21 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 7 hours.
experiment encode accession: ENCSR676MJK
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR701MJQ
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB303WLH
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS258YUU at ENCODE; https://www.encodeproject.org/ENCBS258YUU/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: ChIP-seq from A549 (ENCLB919URI)

description:
https://www.encodeproject.org/experiments/ENCSR495WGO/
***************
biological replicate number: 2
technical replicate number: 1
description: RAD21 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 10 hours.
experiment encode accession: ENCSR495WGO
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR328BXP
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB919URI
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 cell line treated with 100 nM dexamethasone for 10 hours

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:10; duration_units:hour;

value: ENCBS821YWV at ENCODE; https://www.encodeproject.org/ENCBS821YWV/


title: ChIP-seq from A549 (ENCLB530PJE)

description:
https://www.encodeproject.org/experiments/ENCSR537EFT/
***************
biological replicate number: 2
technical replicate number: 1
description: SMC3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 7 hours.
experiment encode accession: ENCSR537EFT
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR701MJQ
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB530PJE
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: cell line

value: ENCBS253PKE at ENCODE; https://www.encodeproject.org/ENCBS253PKE/


title: ChIP-seq from A549 (ENCLB826ODD)

description:
https://www.encodeproject.org/experiments/ENCSR620NWG/
***************
biological replicate number: 2
technical replicate number: 1
description: SMC3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0.5 hours.
experiment encode accession: ENCSR620NWG
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR216DMN
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB826ODD
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS911XCD at ENCODE; https://www.encodeproject.org/ENCBS911XCD/


title: ChIP-seq from A549 (ENCLB791AHO)

description:
https://www.encodeproject.org/experiments/ENCSR501LQA/
***************
biological replicate number: 2
technical replicate number: 1
description: SMC3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 6 hours.
experiment encode accession: ENCSR501LQA
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR366VPA
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB791AHO
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: male

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:6; duration_units:hour;

value: ENCBS998IQV at ENCODE; https://www.encodeproject.org/ENCBS998IQV/


title: ChIP-seq from A549 (ENCLB766MNY)

description:
https://www.encodeproject.org/experiments/ENCSR748MVX/
***************
biological replicate number: 2
technical replicate number: 1
description: RAD21 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 4 hours.
experiment encode accession: ENCSR748MVX
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR748SVE
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB766MNY
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 cell line treated with 100 nM dexamethasone for 4 hours

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS194DFG at ENCODE; https://www.encodeproject.org/ENCBS194DFG/


title: ChIP-seq from A549 (ENCLB314CBF)

description:
https://www.encodeproject.org/experiments/ENCSR495WGO/
***************
biological replicate number: 3
technical replicate number: 1
description: RAD21 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 10 hours.
experiment encode accession: ENCSR495WGO
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR328BXP
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB314CBF
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: adult

value: 58 year

value: ENCBS685FEM at ENCODE; https://www.encodeproject.org/ENCBS685FEM/


title: ChIP-seq from A549 (ENCLB009DBW)

description:
https://www.encodeproject.org/experiments/ENCSR501LQA/
***************
biological replicate number: 3
technical replicate number: 1
description: SMC3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 6 hours.
experiment encode accession: ENCSR501LQA
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR366VPA
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB009DBW
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: Tim Reddy, Duke

value: ENCBS909XAR at ENCODE; https://www.encodeproject.org/ENCBS909XAR/


title: ChIP-seq from A549 (ENCLB224LLL)

description:
https://www.encodeproject.org/experiments/ENCSR748MVX/
***************
biological replicate number: 3
technical replicate number: 1
description: RAD21 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 4 hours.
experiment encode accession: ENCSR748MVX
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR748SVE
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB224LLL
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS743GRW at ENCODE; https://www.encodeproject.org/ENCBS743GRW/


title: ChIP-seq from A549 (ENCLB880PVQ)

description:
https://www.encodeproject.org/experiments/ENCSR335RKQ/
***************
biological replicate number: 3
technical replicate number: 1
description: SMC3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 4 hours.
experiment encode accession: ENCSR335RKQ
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR748SVE
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB880PVQ
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS278VLL at ENCODE; https://www.encodeproject.org/ENCBS278VLL/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: ChIP-seq from A549 (ENCLB523OHG)

description:
https://www.encodeproject.org/experiments/ENCSR217ELF/
***************
biological replicate number: 2
technical replicate number: 1
description: RAD21 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 12 hours.
experiment encode accession: ENCSR217ELF
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR382EJS
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB523OHG
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:12; duration_units:hour;

value: ENCBS600GFD at ENCODE; https://www.encodeproject.org/ENCBS600GFD/


title: ChIP-seq from A549 (ENCLB429FZC)

description:
https://www.encodeproject.org/experiments/ENCSR247LSH/
***************
biological replicate number: 3
technical replicate number: 1
description: RAD21 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 2 hours.
experiment encode accession: ENCSR247LSH
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR088SOR
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB429FZC
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: cell line

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:2; duration_units:hour;

value: ENCBS509STK at ENCODE; https://www.encodeproject.org/ENCBS509STK/


title: ChIP-seq from A549 (ENCLB343GDD)

description:
https://www.encodeproject.org/experiments/ENCSR199XBQ/
***************
biological replicate number: 2
technical replicate number: 1
description: SMC3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 8 hours.
experiment encode accession: ENCSR199XBQ
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR233BJW
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB343GDD
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: male

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:8; duration_units:hour;

value: ENCBS844UJU at ENCODE; https://www.encodeproject.org/ENCBS844UJU/


title: ChIP-seq from A549 (ENCLB177RPA)

description:
https://www.encodeproject.org/experiments/ENCSR330ELC/
***************
biological replicate number: 2
technical replicate number: 1
description: SMC3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 10 hours.
experiment encode accession: ENCSR330ELC
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR328BXP
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB177RPA
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:10; duration_units:hour;

value: ENCBS685PHX at ENCODE; https://www.encodeproject.org/ENCBS685PHX/


title: ChIP-seq from A549 (ENCLB267FQH)

description:
https://www.encodeproject.org/experiments/ENCSR330ELC/
***************
biological replicate number: 3
technical replicate number: 1
description: SMC3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 10 hours.
experiment encode accession: ENCSR330ELC
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR328BXP
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB267FQH
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: adult

value: 58 year

value: ENCBS214HMB at ENCODE; https://www.encodeproject.org/ENCBS214HMB/


title: ChIP-seq from A549 (ENCLB768BID)

description:
https://www.encodeproject.org/experiments/ENCSR217ELF/
***************
biological replicate number: 3
technical replicate number: 1
description: RAD21 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 12 hours.
experiment encode accession: ENCSR217ELF
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR382EJS
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB768BID
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: Tim Reddy, Duke

value: ENCBS737LUY at ENCODE; https://www.encodeproject.org/ENCBS737LUY/


title: ChIP-seq from A549 (ENCLB464VAG)

description:
https://www.encodeproject.org/experiments/ENCSR335RKQ/
***************
biological replicate number: 2
technical replicate number: 1
description: SMC3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 4 hours.
experiment encode accession: ENCSR335RKQ
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR748SVE
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB464VAG
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:4; duration_units:hour;

value: ENCBS991JCM at ENCODE; https://www.encodeproject.org/ENCBS991JCM/


title: ChIP-seq from A549 (ENCLB091AHH)

description:
https://www.encodeproject.org/experiments/ENCSR247LSH/
***************
biological replicate number: 2
technical replicate number: 1
description: RAD21 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 2 hours.
experiment encode accession: ENCSR247LSH
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR088SOR
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB091AHH
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS361ETR at ENCODE; https://www.encodeproject.org/ENCBS361ETR/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: ChIP-seq from A549 (ENCLB060EJS)

description:
https://www.encodeproject.org/experiments/ENCSR981FDC/
***************
biological replicate number: 1
technical replicate number: 1
description: SMC3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 2 hours.
experiment encode accession: ENCSR981FDC
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR088SOR
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB060EJS
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: cell line

value: ENCBS255OGK at ENCODE; https://www.encodeproject.org/ENCBS255OGK/


title: ChIP-seq from A549 (ENCLB439ZIA)

description:
https://www.encodeproject.org/experiments/ENCSR193NSH/
***************
biological replicate number: 3
technical replicate number: 1
description: RAD21 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0 hours.
experiment encode accession: ENCSR193NSH
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR139PCE
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB439ZIA
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

source_name: Homo sapiens A549 cell line

value: ENCBS608SQG at ENCODE; https://www.encodeproject.org/ENCBS608SQG/


title: ChIP-seq from A549 (ENCLB603ASI)

description:
https://www.encodeproject.org/experiments/ENCSR199XBQ/
***************
biological replicate number: 3
technical replicate number: 1
description: SMC3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 8 hours.
experiment encode accession: ENCSR199XBQ
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR233BJW
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB603ASI
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: male

value: ENCBS267EOV at ENCODE; https://www.encodeproject.org/ENCBS267EOV/


title: ChIP-seq from A549 (ENCLB715LEN)

description:
https://www.encodeproject.org/experiments/ENCSR150EFU/
***************
biological replicate number: 3
technical replicate number: 1
description: SMC3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0 hours.
experiment encode accession: ENCSR150EFU
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR139PCE
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB715LEN
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS975BCL at ENCODE; https://www.encodeproject.org/ENCBS975BCL/


title: ChIP-seq from A549 (ENCLB957RZS)

description:
https://www.encodeproject.org/experiments/ENCSR193NSH/
***************
biological replicate number: 2
technical replicate number: 1
description: RAD21 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0 hours.
experiment encode accession: ENCSR193NSH
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR139PCE
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB957RZS
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: ENCBS461IGF at ENCODE; https://www.encodeproject.org/ENCBS461IGF/


title: ChIP-seq from A549 (ENCLB262ING)

description:
https://www.encodeproject.org/experiments/ENCSR984DZW/
***************
biological replicate number: 1
technical replicate number: 1
description: RAD21 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 8 hours.
experiment encode accession: ENCSR984DZW
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR233BJW
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB262ING
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:8; duration_units:hour;

value: ENCBS484NJJ at ENCODE; https://www.encodeproject.org/ENCBS484NJJ/


title: ChIP-seq from A549 (ENCLB946HBE)

description:
https://www.encodeproject.org/experiments/ENCSR807WAC/
***************
biological replicate number: 1
technical replicate number: 1
description: RAD21 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 3 hours.
experiment encode accession: ENCSR807WAC
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR266YIS
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB946HBE
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: adult

value: 58 year

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:3; duration_units:hour;

value: ENCBS465PUD at ENCODE; https://www.encodeproject.org/ENCBS465PUD/


title: ChIP-seq from A549 (ENCLB400ZAP)

description:
https://www.encodeproject.org/experiments/ENCSR806UKK/
***************
biological replicate number: 1
technical replicate number: 1
description: SMC3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 5 hours.
experiment encode accession: ENCSR806UKK
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR565ZHQ
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB400ZAP
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: Tim Reddy, Duke

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:5; duration_units:hour;

value: ENCBS016VTZ at ENCODE; https://www.encodeproject.org/ENCBS016VTZ/


title: ChIP-seq from A549 (ENCLB715DRH)

description:
https://www.encodeproject.org/experiments/ENCSR767DFK/
***************
biological replicate number: 1
technical replicate number: 1
description: SMC3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 12 hours.
experiment encode accession: ENCSR767DFK
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR382EJS
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB715DRH
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:12; duration_units:hour;

value: ENCBS358PMO at ENCODE; https://www.encodeproject.org/ENCBS358PMO/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/


title: ChIP-seq from A549 (ENCLB272EBJ)

description:
https://www.encodeproject.org/experiments/ENCSR537EFT/
***************
biological replicate number: 1
technical replicate number: 1
description: SMC3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 7 hours.
experiment encode accession: ENCSR537EFT
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR701MJQ
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB272EBJ
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: cell line

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:7; duration_units:hour;

value: ENCBS426JGZ at ENCODE; https://www.encodeproject.org/ENCBS426JGZ/


title: ChIP-seq from A549 (ENCLB719QKT)

description:
https://www.encodeproject.org/experiments/ENCSR620NWG/
***************
biological replicate number: 1
technical replicate number: 1
description: SMC3 ChIP-seq on A549 cell line treated with 100 nM dexamethasone for 0.5 hours.
experiment encode accession: ENCSR620NWG
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR216DMN
encode release date: 2018-03-15
lab: Tim Reddy, Duke
library encode accession: ENCLB719QKT
size range: >200
nucleic acid starting quantity: 7
nucleic acid starting quantity units: ng

value: male

value: treatment_term_id:CHEBI:41879; treatment_term_name:dexamethasone; treatment_type:chemical; duration:30; duration_units:minute;

value: ENCBS475OAC at ENCODE; https://www.encodeproject.org/ENCBS475OAC/