title: K562 NaBut 72hr DNase-seq Rep 3

source_name: K562 NaBut 72hr DNase-seq

extract_protocol:
30-50 million nuclei were digested with a range of recombinant DNase I enzyme (Roche) concentrations (between 1.2 and 12U) for 15 minutes at 37°C in 120uL 1X DNase buffer. Libraries constructed according to PMID: 20150158
Cell pellets were washed twice with 1xPBS and nuclei isolated by 0.1% NP-40 lysis

value: 0.5 mM NaBut


title: K562 High NaBut 72hr DNase-seq Rep 1

status: Public on Apr 10 2016

type: SRA

city: Durham

first: Christopher

middle: L

last: Frank

state: NC

address: 101 Science Dr.

country: USA

institute: Duke University

library_source: genomic

data_processing:
Basecalls performed using CASAVA v1.8
DNase-seq (first 20 bp) and ChIP-seq reads mapped to UCSC hg19 with Bowtie v1.1.0 allowing only unique alignments with up to 1 mismatch, RNA-seq reads mapped to UCSC knownGenes reference with Tophat v2.0 allowing up to 2 mismatches
Putative PCR artifacts (pileup of identical reads) filtered from mapped DNase-seq and ChIP-seq prior to peak calls
DNase-seq and ChIP-seq peak calls made with MACS2 v2.1.0, FPKM expression values estimated by Cufflinks v2.2.1
Genome_build: hg19
Supplementary_files_format_and_content: DNase-seq and ChIP-seq .bed files of peak calls contain chromosome, start, stop, name, score, fold-change, -log10 p-value, -log10 q-value, summit position; RNA-seq Cufflinks text files contain gene-level FPKM abundances with gene name and locus

molecule: genomic DNA

organism: Homo sapiens

source_name: K562 High NaBut 72hr DNase-seq

growth_protocol: K562 cells were obtained from ATCC (CCL-243) and maintained in 1x RPMI1640 media (with L-glutamine) supplemented with 10% FBS and 1x penicillin/streptomycin (Life Technologies). GM12878 lymphoblasts obtained from Coriell and maintained in 1x RPMI 1640 media (with L-glutamine) supplemented with 15% FBS and 1x penicillin/streptomycin (Life Technologies). CRC119 cells maintained in 1x RPMI 1640 media (with L-glutamine) supplemented with 10% FBS, 1x NaPyruvate, 0.02 M HEPES, and 1x penicillin/streptomycin (Life Technologies).

extract_protocol:
30-50 million nuclei were digested with a range of recombinant DNase I enzyme (Roche) concentrations (between 1.2 and 12U) for 15 minutes at 37°C in 120uL 1X DNase buffer. Libraries constructed according to PMID: 20150159
Cell pellets were washed twice with 1xPBS and nuclei isolated by 0.1% NP-40 lysis

tag: cell line

tag: cell type

value: myelogenous leukemia cell line

tag: treated with

value: 2 mM NaBut

tag: duration of treatment

value: 72 hours


title: K562 NaBut 72hr DNase-seq Rep 2

extract_protocol:
30-50 million nuclei were digested with a range of recombinant DNase I enzyme (Roche) concentrations (between 1.2 and 12U) for 15 minutes at 37°C in 120uL 1X DNase buffer. Libraries constructed according to PMID: 20150157
Cell pellets were washed twice with 1xPBS and nuclei isolated by 0.1% NP-40 lysis


title: drug_st2_DNase-seq

city: chapel hill

first: Yunjung

last: Kim

state: North Carolina

address: 120 Mason farm road

institute: UNC at Chapel Hill

data_processing:
read sequences were aligned to mm9 using bowtie with parameters (-m 1 --best --strata)
we filtered to remove quality score < 10, PCR duplicates.
We used F-seq for estimation of enriched peaks to identify potential open chromatin regions
Genome_build: mm9
Supplementary_files_format_and_content: bed files for DNase I cut peak regions

organism: Mus musculus

source_name: C57BL/6J, striatum, DNase-seq

extract_protocol:
Genomic DNA was extracted from mouse brain samples
The extracted nuclei were digested with different amounts of DNase I for 16 min at 37° C. The reactions were terminated by the addition of 50 mM EDTA. Libraries were constructed from pooled digests and sequenced.

treatment_protocol: All animals were bred at UNC from mice that were less than six generations removed from founders acquired from the Jackson Laboratory (Bar Harbor, ME).

tag: strain

tag: treatment

value: drug

tag: tissue

value: striatum

tag: lane


title: placebo_G872_ATACseq

data_processing:
library strategy: ATAC-seq
read sequences were aligned to mm9 using bowtie with parameters (-m 1 --bset --strata)
we filtered to remove quality score < 10, PCR duplicates.
We used F-seq for estimation of enriched peaks to identify potential open chromatin regions
Genome_build: mm9
Supplementary_files_format_and_content: Wig files were generated using F-seq and converted to bigwig format

source_name: C57BL/6J, striatum, ATACseq

extract_protocol:
Genomic DNA was extracted from mouse brain samples
Libraries were amplified for a total of 10–12 cycles, purified using 1.2X Ampure beads and eluted in 20ul H2O. Following purification, library fragments were amplified using 1x NEBnext PCR master mix and 1.25 μM of custom Nextera PCR primers. To reduce GC and size bias in our PCR we monitored the PCR reaction using qPCR in order to stop amplification prior to saturation. The libraries were amplified for 5 cycles, a 5ul aliquot was run in a qPCR side reaction for 20 cycles, to determine the additional number of cycles needed for the remaining 45 μL reaction. The libraries were purified using 1.2X Ampure beads and eluted in 20ul H2O. Libraries were amplified for a total of 10–12 cycles.

value: placebo


title: drug_G868_ATACseq


title: placebo_G871_ATACseq


title: K562 PBS Vehicle Control DNase-seq Rep 3

source_name: K562 PBS Vehicle Control DNase-seq

extract_protocol:
30-50 million nuclei were digested with a range of recombinant DNase I enzyme (Roche) concentrations (between 1.2 and 12U) for 15 minutes at 37°C in 120uL 1X DNase buffer. Libraries constructed according to PMID: 20150155
Cell pellets were washed twice with 1xPBS and nuclei isolated by 0.1% NP-40 lysis

value: 0.5% 1xPBS vehicle


title: K562 PU.1 shRNA1 DMSO DNase-seq Rep 2

source_name: K562 PU.1 shRNA1 DMSO DNase-seq

extract_protocol:
30-50 million nuclei were digested with a range of recombinant DNase I enzyme (Roche) concentrations (between 1.2 and 12U) for 15 minutes at 37°C in 120uL 1X DNase buffer. Libraries constructed according to PMID: 20150166
Cell pellets were washed twice with 1xPBS and nuclei isolated by 0.1% NP-40 lysis

tag: genotype/variation

value: PU.1 shRNA; PU.1 depletion

value: 0.01% DMSO vehicle


title: drug_G866_ATACseq


title: K562 SAHA 72hr DNase-seq Rep 2

source_name: K562 SAHA 72hr DNase-seq

extract_protocol:
30-50 million nuclei were digested with a range of recombinant DNase I enzyme (Roche) concentrations (between 1.2 and 12U) for 15 minutes at 37°C in 120uL 1X DNase buffer. Libraries constructed according to PMID: 20150151
Cell pellets were washed twice with 1xPBS and nuclei isolated by 0.1% NP-40 lysis

value: 1 μM SAHA


title: K562 PBS Vehicle Control DNase-seq Rep 2

extract_protocol:
30-50 million nuclei were digested with a range of recombinant DNase I enzyme (Roche) concentrations (between 1.2 and 12U) for 15 minutes at 37°C in 120uL 1X DNase buffer. Libraries constructed according to PMID: 20150154
Cell pellets were washed twice with 1xPBS and nuclei isolated by 0.1% NP-40 lysis


title: K562 SAHA 72hr DNase-seq Rep 1

extract_protocol:
30-50 million nuclei were digested with a range of recombinant DNase I enzyme (Roche) concentrations (between 1.2 and 12U) for 15 minutes at 37°C in 120uL 1X DNase buffer. Libraries constructed according to PMID: 20150150
Cell pellets were washed twice with 1xPBS and nuclei isolated by 0.1% NP-40 lysis


title: placebo_G865_ATACseq


title: placebo_G864_ATACseq


title: drug_G874_ATACseq


title: drug_G873_ATACseq


title: K562 SAHA 72hr DNase-seq Rep 3

extract_protocol:
30-50 million nuclei were digested with a range of recombinant DNase I enzyme (Roche) concentrations (between 1.2 and 12U) for 15 minutes at 37°C in 120uL 1X DNase buffer. Libraries constructed according to PMID: 20150152
Cell pellets were washed twice with 1xPBS and nuclei isolated by 0.1% NP-40 lysis


title: K562 DMSO Vehicle Control DNase-seq Rep 3

source_name: K562 DMSO Vehicle Control DNase-seq

extract_protocol:
30-50 million nuclei were digested with a range of recombinant DNase I enzyme (Roche) concentrations (between 1.2 and 12U) for 15 minutes at 37°C in 120uL 1X DNase buffer. Libraries constructed according to PMID: 20150149
Cell pellets were washed twice with 1xPBS and nuclei isolated by 0.1% NP-40 lysis


title: K562 PBS Vehicle Control DNase-seq Rep 1

extract_protocol:
30-50 million nuclei were digested with a range of recombinant DNase I enzyme (Roche) concentrations (between 1.2 and 12U) for 15 minutes at 37°C in 120uL 1X DNase buffer. Libraries constructed according to PMID: 20150153
Cell pellets were washed twice with 1xPBS and nuclei isolated by 0.1% NP-40 lysis


title: drug_G869_ATACseq


title: K562 DMSO Vehicle Control DNase-seq Rep 2

extract_protocol:
30-50 million nuclei were digested with a range of recombinant DNase I enzyme (Roche) concentrations (between 1.2 and 12U) for 15 minutes at 37°C in 120uL 1X DNase buffer. Libraries constructed according to PMID: 20150148
Cell pellets were washed twice with 1xPBS and nuclei isolated by 0.1% NP-40 lysis


title: dms3_RNAseq

status: Public on Apr 09 2016

city: Beijing

first: Yongqiang

last: Li

address: 7 Science Park Rd., ZGC life science park

country: China

institute: NIBS

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced clean reads were mapped to Arabidopsis thaliana (tair10) whole genome using tophat v2.0.6 with parameters --bowtie1 --no-coverage-search --segment-length 20 -g 10 -p 10
Gene annotation and calculation of FPKM values was carried out using Cufflinks (v2.0.1) with the provision of a GTF annotation file (tair10)
Gene expression differences were assessed by Cuffdiff use upper-quartile normalization, with false discovery rate correction for multiple testing
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

molecule: total RNA

organism: Arabidopsis thaliana

growth_protocol: The seedlings were grown on MS medium plates under long-day conditions (16 h day time and 8 h night time) at 22°C.

extract_protocol:
Seeding materials was ground into powder in liquid nitrogen; total RNA was harvested using TRIzol® Reagent (Invitrogen); then total RNA samples were treated with DNase I and the mRNA is enriched by using the oligo(dT) magnetic beads.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age

tag: ecotype

value: Columbia


title: K562 DMSO Vehicle Control DNase-seq Rep 1

extract_protocol:
30-50 million nuclei were digested with a range of recombinant DNase I enzyme (Roche) concentrations (between 1.2 and 12U) for 15 minutes at 37°C in 120uL 1X DNase buffer. Libraries constructed according to PMID: 20150147
Cell pellets were washed twice with 1xPBS and nuclei isolated by 0.1% NP-40 lysis


title: K562 NaBut 72hr DNase-seq Rep 1

extract_protocol:
30-50 million nuclei were digested with a range of recombinant DNase I enzyme (Roche) concentrations (between 1.2 and 12U) for 15 minutes at 37°C in 120uL 1X DNase buffer. Libraries constructed according to PMID: 20150156
Cell pellets were washed twice with 1xPBS and nuclei isolated by 0.1% NP-40 lysis


title: WT_RNAseq

value: WT


title: drug_G870_ATACseq


title: nrpe1_RNAseq


title: suvh2suvh9_RNAseq


title: YAP_5SA_HaCAT_rep1

city: London

first: Barry

middle: J

last: Thompson

state: London

address: 44 Lincoln's Inn Fields

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
RNA-seq: The 100 bp paired-end read data was trimmed to 75 bp. The RSEM package (version 1.2.11) (Li and Dewey, 2011) was used for the alignment and subsequent gene-level counting of the sequenced reads with respect to hg19 RefSeq genes downloaded from the UCSC Table Browser (Karolchik et al., 2004) on 27th May 2015. Differential gene expression analysis was performed with the Bioconductor package EdgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text file containing raw counts per gene for all samples

source_name: HaCat cell line

growth_protocol: DMEM + 10 % FCS

extract_protocol:
RNA-seq: All RNA-seq experiments, except for control samples,  were performed in triplicate. Total RNA was prepared and the quality of the RNA was assessed using a Bioanalyzer (Agilent).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: siRNAs were transfected twice with 24 hours inbetween transfections. RNA-Seq analysis performed 48 hours after the second transfection.

value: HaCat

tag: sirna treatment

tag: expression vector

value: YAP1 S5A (constitutively active YAP1 mutant)


title: YAP_5SA_HaCAT_rep3


title: YAP_5SA_HaCAT_rep2


title: empty_vector_HaCAT

value: empty vector


title: siYAP_HaCAT_rep3

value: YAP1 siRNA


title: siYAP_HaCAT_rep2


title: placebo_G867_ATACseq


title: YAP_5SA_A431_rep3

source_name: A431 cell line


title: YAP_5SA_A431_rep2


title: empty_vector_A431


title: siCTRL_HaCAT

value: control siRNA


title: YAP 5SA_A431_rep1


title: siYAP_A431_rep3


title: Healthy3

city: Shenzhen

first: Wangmin

last: Qiao

address: Building NO.7, BGI Park, No.21 Hongan 3rd Street, Yantian District

institute: BGI

description: granulocytes from Healthy

data_processing:
We define "dirty" raw reads as reads which contain the sequence of adapter, high content of unknown bases and low quality reads.
Clean reads are mapped to rRNA  reference using short reads alignment software SOAPaligner/SOAP2 (4)  to remove the remain rRNA reads.
we use Cuffdiff 2 version 2.1.1 to calculate gene and transcript expression levels in more than one condition and test them for significant differences on the basis of FPKM value.
Genome_build: hg19
Supplementary_files_format_and_content:
'All_samples_FPKM.txt' contains all genes' FPKM result
'All_samples_FPKM_filter.txt' was generated with  filetering parameters of FPKM >1.(If the FPKM of a gene is less than 1, it will be regarded as unconvincing expression and then the gene will be filtered).

source_name: healthy_GPI-AP+ granulocyte

extract_protocol: RNA extraction using the RNeasy Mini kit (Qiagen); Samples were prepared with the Illumina TruSeq Stranded Total RNA Library Prep Kit.

tag: subject status

value: healthy control

value: blood

value: GPI-AP+ granulocyte cell


title: Healthy2

description: granulocytes from Healthy


title: PNH1_PNH

description: GPI-AP- granulocytes from PNH patients

source_name: PNH_GPI-AP- granulocyte

value: paroxysmal nocturnal hemoglobinuria (PNH)  patient

value: GPI-AP- granulocyte cell


title: Healthy1

description: granulocytes from Healthy


title: PNH2_PNH

description: GPI-AP- granulocytes from PNH patients


title: siYAP_A431_rep2


title: siYAP_HaCAT_rep1


title: PNH1_WT

description: GPI-AP+ granulocytes from PNH patients

data_processing:
We define "dirty" raw reads as reads which contain the sequence of adapter, high content of unknown bases and low quality reads.
Clean reads are mapped to rRNA  reference using short reads alignment software SOAPaligner/SOAP2 (4)  to remove the remain rRNA reads.
we use Cuffdiff 2 version 2.1.1 to calculate gene and transcript expression levels in more than one condition and test them for significant differences on the basis of FPKM value.
Genome_build: hg19
Supplementary_files_format_and_content:
'All_samples_FPKM.txt' contains all genes' FPKM result.
'All_samples_FPKM_filter.txt' was generated with  filetering parameters of FPKM >1.(If the FPKM of a gene is less than 1, it will be regarded as unconvincing expression and then the gene will be filtered).

source_name: PNH_GPI-AP+ granulocyte


title: Dex rep#1 DNase-seq GH1564

status: Public on Apr 08 2016

city: Bethesda

first: Songjoon

last: Baek

state: MD

address: 41 Library Drive

department: CCR

institute: NCI / NIH

description: hs_RC_ZR-75-1_Dex_RC_GH1564xGH1568_FDR0.csv

data_processing:
RTA 1.12.42 was used for Basecalling and Casava 1.8.2 ws used for demultiplexing.
Alignment was performed by Bowtie2 software with the hg19 reference genome.
Areas of enrichment were identified using DNase2Hotspots software(http://sorceforge.net/proujects/dnase2hotspots/) software with FDR 0%.
Raw signal density graphs were generated by counting tags at each genomic coordinate after extending the length of sequences to 150bp by strands.
Values for tag densities were normalized to 10 million reads to adjust for differences in the sequencing depth between samples.
Genome_build: hg19
Supplementary_files_format_and_content: comma-delimited (CSV)  text files include genomic locations (Chromosome, start,  end ), z-score, p-value and the maximum density of hotspots. Bedgraph files contain genomic locations and normalized tag density profiles.

source_name: MCF-7 breast cancer cell line

growth_protocol: see additional columns of the SAMPLES section

extract_protocol: Lysates were digested with DNase-I and DNA fragments of 100-500bp were purified using a sucrose gradient.

treatment_protocol: Cells were plated for experiments in phenol red free growth medium supplemented with 10% charcoal-dextran serum twenty-four hours before hormone treatment.  Cells were left untreated or induced with 100nM dexamethasone or 100nM estradiol for 30 minutes.

value: Ascites from a ductal carcinoma of the breast

value: Dexamethasone

tag: concentration

tag: time

value: 30 minutes

tag: replicate

value: replicate 1

tag: growth proptocol

value: For maintenance cells were cultured in RPMI containing 2mM L-glutamine supplemented 10% calf serum, 1mM sodium pyruvate, 1X non-essential amino acids, and 1% penicillin-streptomycin


title: untreated rep#2 DNase-seq GH1567

description: hs_RC_ZR-75-1_untreated_RC_GH1563xGH1567_FDR0.csv

tag: cell line

tag: cell type

value: untreated

value: replicate 2


title: implantation with ion fluence of 1×1017N+/cm2 and 2×1017N+/cm2

city: Luoyang

first: Huiyuan

last: Ya

state: Henan

address: 71# Longmen Road

department: Life science Department

institute: Luoyang Nornal University

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 MSUv7 whole genome using Tophat v2.0.5 with default parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CLC Genomics Workbench 5.1.5
Genome_build: MSU v7
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Oryza sativa Japonica Group

growth_protocol: An aseptic filter paper is placed on the bottom of an aseptic culture dish after moistened with aseptic water. Put all the experimental materials on this filter paper, and then put the culture dish into a climate box (with12 h in light /12 h in dark) with constant temperature (28 ℃). For every 12 h, uniformly drip 10 ml aseptic water on the filter paper in culture dish to keep the filter paper be moist.

extract_protocol:
Total RNA was subsequently extracted with RNAisoPlus reagent from 70 mg of tissue powder according to the manufacturer’s instructions (Takara, Otsu, Shiga, Japan). All RNA samples were checked for DNA contamination.
Purified RNA was analyzed on a ND-8000 spectrophotometer (Nanodrop, Technologies, Wilmington, DE), agarose electrophoresis or a 2100-Bioanalyzer (Agilent Technologies, Santa Clara, CA), to determine the quantity. RNA samples were used if there was no smear on the agarose. RNA samples were also used if the 260/280 ratio was above 2.0 and the RIN (RNA integrity number) was greater than 7.0.

treatment_protocol: Since the biological effect of the seventh day should be early gene expression result, the rice buds cultured for 96 h are selected as the material for RNA extraction and RNA-seq. We choose 50 complete buds cultured for 96 h and in similar height from each treated material group for the total RNA pool (TRIZOL) extraction of mixed strain. In this experiment, we get one RNA pool of blank control (control is taken as a sequencing sample: Sample1) and five RNA pools treated with five ion fluences Then according to the biological effect measured, separately collect 10 ug of each RNA pool treated by ion fluence of 1×1017 N+/cm2 and 2×1017 N+/cm2, and mix the two RNA pools collected into one sequencing sample (Sample 2: The sample that has no significant growth inhibition effect differences with the control). And then separately take 10 ug of each RNA pool treated by ion fluence of 6×1017 N+/cm2 and 8×1017 N+/cm2, and mix the two RNA pools collected into one sequencing sample (Sample3: the sample that has significant growth inhibition effect differences with the control).

tag: response

value: No-significant damage

value: whole rice seedling

tag: cultivar


title: implantation with ion fluence of 6×1017N+/cm2 and 8×1017N+/cm2

value: Significant damage

tag: treatment


title: control

value: control

tag: tissue


title: E2 rep#1 DNase-seq GH1565

description: hs_RC_ZR-75-1_E2_RC_GH1565xGH1569_FDR0.csv


title: E2 rep#2 DNase-seq GH1569


title: E2 rep#1 DNase-seq GH1503

description: hs_RC_MCF7_DHS_E2_RC_GH1503_3xGH1573_3_FDR0.csv

value: Pleural effusion from an adenocarcinoma of the breast

value: For maintenance cells were cultured in DMEM supplemented 10% calf serum, 2mM L-glutamine, 1mM sodium pyruvate, 1X non-essential amino acids, and 1% penicillin-streptomycin


title: Dex rep#2 DNase-seq GH1572

description: hs_RC_MCF7_DHS_Dex_RC_GH1502_3xGH1572_3_FDR0.csv


title: Dex rep#1 DNase-seq GH1502


title: untreated rep#1 DNase-seq GH1501

description: hs_RC_MCF7_DHS_unt_RC_GH1501_3xGH1571_3_FDR0.csv


title: Input in FoxAflox;Alfp-Cre Mice

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

data_processing:
Demultiplexing: data were demultiplexed using Illumina's BaseSpace online utilities.
Alignment: data were aligned to genomic build mm8 using bowtie 0.12.7 (-m 1 --best).
Track generation: track files (bigWigs) were created by (i) pooling aligned tags from replicate data, (ii) making coverage maps of pooled tags using BEDTools' genomeCoverageBed utility (option -bg to produce bedGraphs), then (iii) multiplying these by the RPM coefficient (inverse of the number of millions of tags aligned), and finally (iv) generating bigWigs with UCSC Genome Browser's bedGraphToBigWig utility.
Genome_build: mm8
Supplementary_files_format_and_content: BigWig files describing RPM-adjusted genomic tracks with RPM-adjusted input subtracted are provided for visualization. These files represent two pooled replicates each.

source_name: Liver

growth_protocol: Mice were anesthetized in a chamber with isoflurane (Butler Animal Health Supply).  When the mouse was completely under anesthetic, it was transferred to a surgical surface and its head was inserted into a nose cone containing isoflurane.

extract_protocol:
The nuclear suspension was layered onto a 1.5 ml cushion of 1:1 of buffer A: buffer B (15 mM Hepes [pH 7.6], 60 mM KCl, 15 mM NaCl, 0.1 mM EDTA, 0.1 mM EGTA, 2.1 M sucrose, 0.15 mM 2-mercaptoethanol) in 15 ml Corex tubes, centrifuged at 7.5-10K rpm for 10 min at 4°C, and the supernatant was removed.  The pellets were suspended in 5-10 ml Buffer A and layered again onto 1:1 of buffer A:B, and centrifuged at 5K rpm for 10 min at 4°C, and the supernatant was removed.  The pellet was suspended into 4 ml sonication buffer (50 mM Tris [pH8], 2 mM EDTA, 0.5 % N-Lauroylsarcosine, complete EDTA-free protease inhibitor cocktail (Roche), 0.5 mM PMSF) for Bioruptor sonication, or about 8 ml sonication buffer as adjusted the concentration at 2-2.4 x 107 nuclei/ml for Covaris sonication, and incubated for 5 min at room temperature, then 5 min on ice. The nuclear lysate was transferred to milliTUBE ATA Fiber tubes (#520130) and sonicated for 8 min (Temperature: 5-9 C, PP: 200, DF 10, CB 200) using Covaris S220. A portion of chromatin was reverse-crosslinked and confirmed, by agarose gel electrophoresis, that their average DNA fragment size was around 200 bp.  RNase A was added to 12.5-25 ng/ul and incubated at room temperature for 10 min.  Debris was removed by centrifugation at 14K rpm for 10 min at 4°C.  The supernatant was dialyzed in TE (10 mM Tris [pH8], 1 mM EDTA) using 3500 MWCO Slide-A Lyzer Dialysis cassette (Thermo Scientific) at 4°C for several hours, and move into new TE and dialyzed overnight. 20 ul (for H1 ChIP) or 50 ul (for FoxA3, C/EBPβ, and HNF4α ChIP) Dynabeads Protein G (Life technologies) were washed three times with 500 ul blocking solution (0.5 % w/v BSA in PBS).  The beads were resuspended in 20 ul or 50 ul blocking solution and saturated with 2.5 ug H1 antibody (Millipore, 05-457), 5 ug FoxA3 antibody (Santa Cruz, sc-5361), 5 ug C/EBPβ antibody (Santa Cruz, sc-150), 5 ug HNF4α antibody (Abcam, ab42898) by rotating the mixture for 2-6 hr at 4°C.  The antibody-beads were washed two times with 500 ul blocking solution and two times with 500 ul ChIP buffer (50 mM Hepes-KOH [pH 7.5], 140 mM NaCl, 1 mM EDTA, 0.1 % Triton X-100, 1 mM PMSF, Complete EDTA free protease inhibitor cocktail (Roche)).  ChIP was performed in 100 ul (for H1) or 250 ul (for FoxA3, C/EBPβ, and HNF4α) ChIP buffer containing antibody-beads mixture and 4-12.5 ug (for H1) or 50 ug (for FoxA3, C/EBPβ, and HNF4α) of sonicated chromatin, which was based on O.D. A260 of reverse-crosslinking DNA, and rotated for 16 hr at 4°C.  The ChIP-beads mixture was washed for 5 min with rotation successively two times with 500 ul ChIP buffer, one time with 500 ul ChIP buffer plus 500 mM NaCl, two times with 500 ul LiCl solution (10 mM Tris-HCl [pH 8], 250 mM LiCl, 1 mM EDTA, 0.5% NP-40), and two times with 500 ul TE plus 0.1% NP-40.  The chromatin was eluted from the beads in 67 ul TES (50 mM Tris-HCl [pH 8], 10 mM EDTA, 1% SDS) and incubated at 65°C for 15 min.  The supernatant was placed in a fresh tube and the elution was repeated two more times, combining all supernatants.  The eluted chromatin and input chromatin were reverse-crosslinked by adding NaCl (final 200 mM) and incubating at 65°C for 4 to 16 hr. The chromatin was treated with 0.2 mg/ml Proteinase K and incubated at 37°C for 2 hr.  DNA was purified by phenol-chloroform extraction followed by ethanol precipitation.
We prepared multiplexed libraries from two biological replicates of H1, FoxA3, C/EBPβ and HNF4α ChIP and Input from FoxA1/FoxA2 flox;Alfp-Cre and WT.  We used NEBNext Ultra DNA Library Prep Kit for Illumina (#E7370). Libraries from FoxA1/FoxA2 flox;Alfp-Cre and WT were sequenced as 75-bp single-end, using Illumina NextSeq500.

treatment_protocol: Mouse liver was perfused with 10 ml of 50 ng/ml heparin in PBS, followed by 5 ml 1% formaldehyde in PBS.  Perfused livers sat for 10 min including formaldehyde perfusion time at room temperature.  The mouse was then sacrificed by cervical dislocation.  The livers were removed and placed in 6 ml Buffer A (15 mM Hepes [pH 7.6], 60 mM KCl, 15 mM NaCl, 0.2 mM EDTA, 0.5 mM EGTA, 0.34 M sucrose, 0.15 mM 2-mercaptoethanol) supplied with 125 mM glycine, and were minced with scalpels on ice.  The liver was homogenized with a Teflon pestle in a glass homogenizer.  The nuclear suspension was filtered through a 100 mm cell strainer.

tag: strain

tag: background

value: FoxAflox;Alfp-Cre

value: 1 and 2

tag: ChIP


title: Dex rep#2 DNase-seq GH1568


title: Input in WT Mice

value: WT


title: FoxA3 ChIP-seq in FoxAflox;Alfp-Cre Mice

tag: antibody vendor/catalog

value: Santa Cruz, sc-5361


title: E2 rep#2 DNase-seq GH1573


title: untreated rep#2 DNase-seq GH1571


title: siCTRL_A431_rep1

tag: sirna treatment

value: control siRNA


title: untreated rep#1 DNase-seq GH1563

value: Ascites from a ductal carcinoma of the breast


title: H1 ChIP-seq in FoxAflox;Alfp-Cre Mice

value: Millipore, 05-457


title: PNH2_WT

description: GPI-AP+ granulocytes from PNH patients

value: paroxysmal nocturnal hemoglobinuria (PNH)  patient

value: blood

value: GPI-AP+ granulocyte cell


title: FoxA3 ChIP-seq in WT Mice


title: HNF4a ChIP-seq in WT Mice

value: Abcam, ab42898


title: siYAP_A431_rep1

value: YAP1 siRNA

tag: expression vector


title: HNF4a ChIP-seq in FoxAflox;Alfp-Cre Mice


title: CEBPb ChIP-seq in FoxAflox;Alfp-Cre Mice

value: CEBPb

value: Santa Cruz, sc-150


title: CEL-Seq2 vs Smart-Seq [dend_cells_6_sample_0006]

city: Haifa

first: Naftalie

last: Senderovich

state: International

address: Technion city, Faculty of biology

department: Biology

country: Israel

institute: Technion - Israel Institute of Technology

description:
CS2 on DC.txt
dend_cells_6_sample_0006

data_processing:
Libraries were sequenced on the Illumina HiSeq2500 according to standard, paired-end sequencing, protocols. Primary analysis done in RTA 1.17.20,1.13.48
Conversion from BCL to FASTQ and deumltiplexing using CASAVA-1.8 (configureBclToFastq.pl--fastq-cluster-count 1234567890 --mismatches 0 --use-bases-mask Y15n,I6n,Y35n)
Filter and read trimming (barcode minimum quality of 20. trimming of read2 to 35 bases - not required).
CEL-Seq (Hashimshony, et al. 2012) demultiplexing of second mate, using first mate barcode, allowing no mismatches in barcode.
bowtie2, version 2.1.0, against various genomes
Read counting with htseq-count version 0.5.4p3. Reads with the same unique molecular identifiers (UMIs) were colapsed for transcript counting.
Genome_build: GRCm38
Genome_build: mm9 for comparison to Smart-Seq data
Genome_build: WS230
Supplementary_files_format_and_content: Tabular expression matrix includes number of transcript molecules.

source_name: BMDCs

growth_protocol:
Mouse ear fibroblasts were derived from 1 month-old CyclinB1-GFP mice. Briefly, a small piece of mouse ear was collected, digested overnight in DMEM containing Collagenase /Dispase. The tissue was then dissociated by gentle pipetting and cells were washed in DMEM/10% FBS/1% Pen-Strep/1% L-Glutamine, pelleted, seeded and cultured for 2-4 days before sorting on a FACS ARIA (Becton Dickinson).
Bone marrow dendritic cells (BMDCs) were collected from 6-8 weeks old female C57BL/6J mice from femora and tibiae and plated. At day 9 post-bone marrow extraction non-adherent cells were collected and stained for CD11c to collect BMDCs.  day 5, floating CD11c+ cells were sorted on the

extract_protocol:
C. elegans total RNA was isolated using TRIzol with addition of ERCC spike-ins and GenElute LPA (Sigma).  BMDCs were lysed by sorting directly into a hypotonic solution before freezing on dry ice. Mouse fibroblasts were lysed in lysis buffer 0.2% NP-40 on C1 IFC. Manually collected fibroblasts were lysed by freezing in liquid nitrogen.
For RNA amplification and library construction see the detailed protocol in "CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq"

value: femora and tibiae

value: unstimulated

tag: age

value: 6-8 weeks

tag: experimental design

value: Previously described BMDCs were FACS sorted into microtiter plate. CEL-Seq2 protocol was applied on 48 single cells.


title: H1 ChIP-seq in WT Mice

value: 1 and 2


title: CEL-Seq2 vs Smart-Seq [dend_cells_43_sample_0043]

description:
CS2 on DC.txt
dend_cells_43_sample_0043


title: CEL-Seq2 vs Smart-Seq [dend_cells_45_sample_0045]

description:
CS2 on DC.txt
dend_cells_45_sample_0045


title: CEBPb ChIP-seq in WT Mice

value: WT


title: CEL-Seq2 vs Smart-Seq [dend_cells_4_sample_0004]

description:
CS2 on DC.txt
dend_cells_4_sample_0004


title: CEL-Seq2 vs Smart-Seq [dend_cells_47_sample_0047]

description:
CS2 on DC.txt
dend_cells_47_sample_0047


title: CEL-Seq2 vs Smart-Seq [dend_cells_7_sample_0007]

description:
CS2 on DC.txt
dend_cells_7_sample_0007


title: CEL-Seq2 vs Smart-Seq [dend_cells_8_sample_0008]

description:
CS2 on DC.txt
dend_cells_8_sample_0008


title: CEL-Seq2 vs Smart-Seq [dend_cells_5_sample_0005]

description:
CS2 on DC.txt
dend_cells_5_sample_0005


title: CEL-Seq2 vs Smart-Seq [dend_cells_41_sample_0041]

description:
CS2 on DC.txt
dend_cells_41_sample_0041


title: CEL-Seq2 vs Smart-Seq [dend_cells_44_sample_0044]

description:
CS2 on DC.txt
dend_cells_44_sample_0044


title: CEL-Seq2 vs Smart-Seq [dend_cells_42_sample_0042]

description:
CS2 on DC.txt
dend_cells_42_sample_0042


title: CEL-Seq2 vs Smart-Seq [dend_cells_38_sample_0038]

description:
CS2 on DC.txt
dend_cells_38_sample_0038


title: CEL-Seq2 vs Smart-Seq [dend_cells_39_sample_0039]

description:
CS2 on DC.txt
dend_cells_39_sample_0039


title: CEL-Seq2 vs Smart-Seq [dend_cells_37_sample_0037]

description:
CS2 on DC.txt
dend_cells_37_sample_0037


title: CEL-Seq2 vs Smart-Seq [dend_cells_48_sample_0048]

description:
CS2 on DC.txt
dend_cells_48_sample_0048


title: CEL-Seq2 vs Smart-Seq [dend_cells_35_sample_0035]

description:
CS2 on DC.txt
dend_cells_35_sample_0035


title: CEL-Seq2 vs Smart-Seq [dend_cells_34_sample_0034]

description:
CS2 on DC.txt
dend_cells_34_sample_0034


title: CEL-Seq2 vs Smart-Seq [dend_cells_32_sample_0032]

description:
CS2 on DC.txt
dend_cells_32_sample_0032


title: CEL-Seq2 vs Smart-Seq [dend_cells_3_sample_0003]

description:
CS2 on DC.txt
dend_cells_3_sample_0003


title: CEL-Seq2 vs Smart-Seq [dend_cells_31_sample_0031]

description:
CS2 on DC.txt
dend_cells_31_sample_0031


title: CEL-Seq2 vs Smart-Seq [dend_cells_30_sample_0030]

description:
CS2 on DC.txt
dend_cells_30_sample_0030


title: placebo_G876_ATACseq

extract_protocol:
Genomic DNA was extracted from mouse brain samples
Libraries were amplified for a total of 10–12 cycles, purified using 1.2X Ampure beads and eluted in 20ul H2O. Following purification, library fragments were amplified using 1x NEBnext PCR master mix and 1.25 μM of custom Nextera PCR primers. To reduce GC and size bias in our PCR we monitored the PCR reaction using qPCR in order to stop amplification prior to saturation. The libraries were amplified for 5 cycles, a 5ul aliquot was run in a qPCR side reaction for 20 cycles, to determine the additional number of cycles needed for the remaining 45 μL reaction. The libraries were purified using 1.2X Ampure beads and eluted in 20ul H2O. Libraries were amplified for a total of 10–12 cycles.

value: placebo

value: striatum

tag: lane


title: CEL-Seq2 vs Smart-Seq [dend_cells_28_sample_0028]

description:
CS2 on DC.txt
dend_cells_28_sample_0028


title: CEL-Seq2 vs Smart-Seq [dend_cells_29_sample_0029]

description:
CS2 on DC.txt
dend_cells_29_sample_0029


title: CEL-Seq2 vs Smart-Seq [dend_cells_33_sample_0033]

description:
CS2 on DC.txt
dend_cells_33_sample_0033


title: CEL-Seq2 vs Smart-Seq [dend_cells_46_sample_0046]

description:
CS2 on DC.txt
dend_cells_46_sample_0046


title: CEL-Seq2 vs Smart-Seq [dend_cells_36_sample_0036]

description:
CS2 on DC.txt
dend_cells_36_sample_0036


title: CEL-Seq2 vs Smart-Seq [dend_cells_26_sample_0026]

description:
CS2 on DC.txt
dend_cells_26_sample_0026


title: CEL-Seq2 vs Smart-Seq [dend_cells_24_sample_0024]

description:
CS2 on DC.txt
dend_cells_24_sample_0024


title: CEL-Seq2 vs Smart-Seq [dend_cells_27_sample_0027]

description:
CS2 on DC.txt
dend_cells_27_sample_0027


title: CEL-Seq2 vs Smart-Seq [dend_cells_21_sample_0021]

description:
CS2 on DC.txt
dend_cells_21_sample_0021


title: CEL-Seq2 vs Smart-Seq [dend_cells_22_sample_0022]

description:
CS2 on DC.txt
dend_cells_22_sample_0022


title: CEL-Seq2 vs Smart-Seq [dend_cells_25_sample_0025]

description:
CS2 on DC.txt
dend_cells_25_sample_0025


title: CEL-Seq2 vs Smart-Seq [dend_cells_23_sample_0023]

description:
CS2 on DC.txt
dend_cells_23_sample_0023


title: CEL-Seq2 vs Smart-Seq [dend_cells_20_sample_0020]

description:
CS2 on DC.txt
dend_cells_20_sample_0020


title: CEL-Seq2 vs Smart-Seq [dend_cells_1_sample_0001]

description:
CS2 on DC.txt
dend_cells_1_sample_0001


title: CEL-Seq2 vs Smart-Seq [dend_cells_2_sample_0002]

description:
CS2 on DC.txt
dend_cells_2_sample_0002


title: CEL-Seq2 vs Smart-Seq [dend_cells_13_sample_0013]

description:
CS2 on DC.txt
dend_cells_13_sample_0013


title: Automated CEL-Seq2 on C1 [C1_n.a._sample_0056]

description:
Expression_C1_96_cells.txt
C1_n.a._sample_0056

source_name: Fibloblasts

value: CyclinB1-GFP strain

value: Ear

value: cultered for 2-4 days before sorting

value: 1 month old

value: Mixed population of negative and positive CyclinB1-GFP cells were analysed by an automated CEL-Seq2 protocol on Fluidigm C1. GFP signal of each captured single cell was examined visually. A number, representing the signal strength, was assigned to each cell; 0-no fluorescence, 0.3 low fluorescence, 0.5-2 cells or more cells with mixed signal, n.a - no cell, ? - fluorescence wasn't assigned, 1- postive GFP fluorescence.


title: CEL-Seq2 vs Smart-Seq [dend_cells_12_sample_0012]

description:
CS2 on DC.txt
dend_cells_12_sample_0012


title: CEL-Seq2 vs Smart-Seq [dend_cells_9_sample_0009]

description:
CS2 on DC.txt
dend_cells_9_sample_0009


title: Automated CEL-Seq2 on C1 [C1_1_sample_0090]

description:
Expression_C1_96_cells.txt
C1_1_sample_0090


title: Automated CEL-Seq2 on C1 [C1_1_sample_0094]

description:
Expression_C1_96_cells.txt
C1_1_sample_0094


title: CEL-Seq2 vs Smart-Seq [dend_cells_18_sample_0018]

description:
CS2 on DC.txt
dend_cells_18_sample_0018


title: CEL-Seq2 vs Smart-Seq [dend_cells_17_sample_0017]

description:
CS2 on DC.txt
dend_cells_17_sample_0017


title: CEL-Seq2 vs Smart-Seq [dend_cells_15_sample_0015]

description:
CS2 on DC.txt
dend_cells_15_sample_0015


title: CEL-Seq2 vs Smart-Seq [dend_cells_14_sample_0014]

description:
CS2 on DC.txt
dend_cells_14_sample_0014


title: Automated CEL-Seq2 on C1 [C1_1_sample_0071]

description:
Expression_C1_96_cells.txt
C1_1_sample_0071


title: CEL-Seq2 vs Smart-Seq [dend_cells_10_sample_0010]

description:
CS2 on DC.txt
dend_cells_10_sample_0010


title: CEL-Seq2 vs Smart-Seq [dend_cells_11_sample_0011]

description:
CS2 on DC.txt
dend_cells_11_sample_0011


title: Automated CEL-Seq2 on C1 [C1_1_sample_0066]

description:
Expression_C1_96_cells.txt
C1_1_sample_0066


title: Automated CEL-Seq2 on C1 [C1_n.a._sample_0028]

description:
Expression_C1_96_cells.txt
C1_n.a._sample_0028


title: Automated CEL-Seq2 on C1 [C1_1_sample_0065]

description:
Expression_C1_96_cells.txt
C1_1_sample_0065


title: Automated CEL-Seq2 on C1 [C1_n.a._sample_0023]

description:
Expression_C1_96_cells.txt
C1_n.a._sample_0023


title: Automated CEL-Seq2 on C1 [C1_1_sample_0096]

description:
Expression_C1_96_cells.txt
C1_1_sample_0096


title: Automated CEL-Seq2 on C1 [C1_1_sample_0055]

description:
Expression_C1_96_cells.txt
C1_1_sample_0055


title: Automated CEL-Seq2 on C1 [C1_1_sample_0054]

description:
Expression_C1_96_cells.txt
C1_1_sample_0054


title: Automated CEL-Seq2 on C1 [C1_1_sample_0076]

description:
Expression_C1_96_cells.txt
C1_1_sample_0076


title: Automated CEL-Seq2 on C1 [C1_1_sample_0072]

description:
Expression_C1_96_cells.txt
C1_1_sample_0072


title: Automated CEL-Seq2 on C1 [C1_1_sample_0095]

description:
Expression_C1_96_cells.txt
C1_1_sample_0095


title: Automated CEL-Seq2 on C1 [C1_1_sample_0051]

description:
Expression_C1_96_cells.txt
C1_1_sample_0051


title: Automated CEL-Seq2 on C1 [C1_1_sample_0068]

description:
Expression_C1_96_cells.txt
C1_1_sample_0068


title: Automated CEL-Seq2 on C1 [C1_1_sample_0050]

description:
Expression_C1_96_cells.txt
C1_1_sample_0050


title: Automated CEL-Seq2 on C1 [C1_1_sample_0043]

description:
Expression_C1_96_cells.txt
C1_1_sample_0043


title: Automated CEL-Seq2 on C1 [C1_1_sample_0049]

description:
Expression_C1_96_cells.txt
C1_1_sample_0049


title: CEL-Seq2 vs Smart-Seq [dend_cells_16_sample_0016]

description:
CS2 on DC.txt
dend_cells_16_sample_0016


title: CEL-Seq2 vs Smart-Seq [dend_cells_19_sample_0019]

description:
CS2 on DC.txt
dend_cells_19_sample_0019


title: Automated CEL-Seq2 on C1 [C1_1_sample_0031]

description:
Expression_C1_96_cells.txt
C1_1_sample_0031


title: Automated CEL-Seq2 on C1 [C1_1_sample_0029]

description:
Expression_C1_96_cells.txt
C1_1_sample_0029


title: Automated CEL-Seq2 on C1 [C1_1_sample_0064]

description:
Expression_C1_96_cells.txt
C1_1_sample_0064


title: Automated CEL-Seq2 on C1 [C1_1_sample_0024]

description:
Expression_C1_96_cells.txt
C1_1_sample_0024


title: Automated CEL-Seq2 on C1 [C1_1_sample_0061]

description:
Expression_C1_96_cells.txt
C1_1_sample_0061


title: Automated CEL-Seq2 on C1 [C1_1_sample_0060]

description:
Expression_C1_96_cells.txt
C1_1_sample_0060


title: Automated CEL-Seq2 on C1 [C1_1_sample_0059]

description:
Expression_C1_96_cells.txt
C1_1_sample_0059


title: Automated CEL-Seq2 on C1 [C1_1_sample_0083]

description:
Expression_C1_96_cells.txt
C1_1_sample_0083


title: Automated CEL-Seq2 on C1 [C1_1_sample_0053]

description:
Expression_C1_96_cells.txt
C1_1_sample_0053


title: Automated CEL-Seq2 on C1 [C1_1_sample_0033]

description:
Expression_C1_96_cells.txt
C1_1_sample_0033


title: Automated CEL-Seq2 on C1 [C1_1_sample_0016]

description:
Expression_C1_96_cells.txt
C1_1_sample_0016


title: Automated CEL-Seq2 on C1 [C1_1_sample_0012]

description:
Expression_C1_96_cells.txt
C1_1_sample_0012


title: Automated CEL-Seq2 on C1 [C1_1_sample_0014]

description:
Expression_C1_96_cells.txt
C1_1_sample_0014


title: Automated CEL-Seq2 on C1 [C1_1_sample_0038]

description:
Expression_C1_96_cells.txt
C1_1_sample_0038


title: Automated CEL-Seq2 on C1 [C1_1_sample_0032]

description:
Expression_C1_96_cells.txt
C1_1_sample_0032


title: Automated CEL-Seq2 on C1 [C1_1_sample_0026]

description:
Expression_C1_96_cells.txt
C1_1_sample_0026


title: Automated CEL-Seq2 on C1 [C1_0_sample_0092]

description:
Expression_C1_96_cells.txt
C1_0_sample_0092


title: Automated CEL-Seq2 on C1 [C1_0_sample_0088]

description:
Expression_C1_96_cells.txt
C1_0_sample_0088


title: Automated CEL-Seq2 on C1 [C1_1_sample_0018]

description:
Expression_C1_96_cells.txt
C1_1_sample_0018


title: Automated CEL-Seq2 on C1 [C1_0_sample_0084]

description:
Expression_C1_96_cells.txt
C1_0_sample_0084


title: Automated CEL-Seq2 on C1 [C1_1_sample_0001]

description:
Expression_C1_96_cells.txt
C1_1_sample_0001


title: Automated CEL-Seq2 on C1 [C1_0_sample_0067]

description:
Expression_C1_96_cells.txt
C1_0_sample_0067


title: Automated CEL-Seq2 on C1 [C1_1_sample_0005]

description:
Expression_C1_96_cells.txt
C1_1_sample_0005


title: Automated CEL-Seq2 on C1 [C1_0_sample_0091]

description:
Expression_C1_96_cells.txt
C1_0_sample_0091


title: Automated CEL-Seq2 on C1 [C1_1_sample_0002]

description:
Expression_C1_96_cells.txt
C1_1_sample_0002


title: Automated CEL-Seq2 on C1 [C1_1_sample_0008]

description:
Expression_C1_96_cells.txt
C1_1_sample_0008


title: Automated CEL-Seq2 on C1 [C1_0_sample_0087]

description:
Expression_C1_96_cells.txt
C1_0_sample_0087


title: Automated CEL-Seq2 on C1 [C1_0_sample_0093]

description:
Expression_C1_96_cells.txt
C1_0_sample_0093


title: Automated CEL-Seq2 on C1 [C1_0_sample_0057]

description:
Expression_C1_96_cells.txt
C1_0_sample_0057


title: Automated CEL-Seq2 on C1 [C1_0_sample_0089]

description:
Expression_C1_96_cells.txt
C1_0_sample_0089


title: Automated CEL-Seq2 on C1 [C1_0_sample_0080]

description:
Expression_C1_96_cells.txt
C1_0_sample_0080


title: Automated CEL-Seq2 on C1 [C1_0_sample_0086]

description:
Expression_C1_96_cells.txt
C1_0_sample_0086


title: Automated CEL-Seq2 on C1 [C1_0_sample_0078]

description:
Expression_C1_96_cells.txt
C1_0_sample_0078


title: CEL-Seq2 vs Smart-Seq [dend_cells_40_sample_0040]

description:
CS2 on DC.txt
dend_cells_40_sample_0040


title: Automated CEL-Seq2 on C1 [C1_0_sample_0058]

description:
Expression_C1_96_cells.txt
C1_0_sample_0058


title: Automated CEL-Seq2 on C1 [C1_1_sample_0010]

description:
Expression_C1_96_cells.txt
C1_1_sample_0010


title: Automated CEL-Seq2 on C1 [C1_0_sample_0052]

description:
Expression_C1_96_cells.txt
C1_0_sample_0052


title: Automated CEL-Seq2 on C1 [C1_0_sample_0048]

description:
Expression_C1_96_cells.txt
C1_0_sample_0048


title: Wildtype head X2 single cell 70

city: Portland

first: Bret

last: Pearson

state: OR

address: 3181 SW Sam Jackson Park Rd., BRB Room 305

department: Pediatrics

institute: Oregon Health and Science University

data_processing:
Base calls and demultiplexing was performed with Illumina bcl2fastq version 1.8.3
Trimmed reads (3' 15 bp) were aligned to the transcriptome associated with BioProject 215411 using the program Bowtie2 version 2.2.4.  Raw counts were extracted from resulting SAM files and normalized using DESeq2.
The 1000 most highly variable transcripts across the single cell data were extracted based on mean and coefficient of variation values. The expression values for these transcripts in each cell were log transformed with a small pseudo-counts (+ 0.001) and used for heirarchical clustering and t-distributed stocastic neighbor embedding. Cell groups were defined by producing a dendrogram of the heirarchical clustering results and cutting the tree into 10 groups.
Genome_build: NCBI BioProject PRJNA215411  SmedASXL_transcripts_20130210.nt
Supplementary_files_format_and_content: [Molinaro_NCBI_rawcounts.txt] Raw counts values for each sample for each transcript are listed.  Only transcripts that were detected in at least one sample are listed. [Molinaro_NCBI_normalizedcounts.txt] single cell DESeq2-normalized counts.

molecule: polyA RNA

organism: Schmidtea mediterranea

source_name: Wildtype animal heads

growth_protocol: The clonal strain of Schmidtea mediterranea, CIW4, was grown in a milli-Q-based salt solution on beef liver.  Organisms were starved for 1 week prior to tissue collection.

extract_protocol:
All samples were prepared using the Smartseq2 protocol and the Nextera XT DNA library preparation kit from Illumina.
Illumina V4 chemistry and reagents

treatment_protocol: Cells from the heads of 30 animals were FACS sorted to obtain 96 single X1s and 72 single X2s and cDNA was prepared from poly-A+ mRNA for each cell using Smartseq2 and deep sequenced to a depth of 5M reads, as illustrated in Figure 1A of the manuscript. cDNA from two X1 and 1 X2 bulk tube controls of 200 cells each was prepared using the same protocol and sequenced to a depth of 10-20M reads each.

value: Asexual CIW4

tag: facs gate

value: Amputation fragment

value: heads

tag: sample type

value: single cell


title: Automated CEL-Seq2 on C1 [C1_0_sample_0034]

description:
Expression_C1_96_cells.txt
C1_0_sample_0034


title: Automated CEL-Seq2 on C1 [C1_0_sample_0045]

description:
Expression_C1_96_cells.txt
C1_0_sample_0045


title: Automated CEL-Seq2 on C1 [C1_0_sample_0044]

description:
Expression_C1_96_cells.txt
C1_0_sample_0044


title: Automated CEL-Seq2 on C1 [C1_0_sample_0042]

description:
Expression_C1_96_cells.txt
C1_0_sample_0042


title: Automated CEL-Seq2 on C1 [C1_0_sample_0017]

description:
Expression_C1_96_cells.txt
C1_0_sample_0017


title: Wildtype head X2 single cell 68


title: Automated CEL-Seq2 on C1 [C1_0_sample_0041]

description:
Expression_C1_96_cells.txt
C1_0_sample_0041


title: Wildtype head X2 single cell 72


title: Automated CEL-Seq2 on C1 [C1_0_sample_0007]

description:
Expression_C1_96_cells.txt
C1_0_sample_0007


title: Wildtype head X2 single cell 69


title: Wildtype head X2 single cell 71


title: Automated CEL-Seq2 on C1 [C1_0_sample_0040]

description:
Expression_C1_96_cells.txt
C1_0_sample_0040


title: Automated CEL-Seq2 on C1 [C1_0_sample_0035]

description:
Expression_C1_96_cells.txt
C1_0_sample_0035


title: Wildtype head X2 single cell 65


title: Automated CEL-Seq2 on C1 [C1_0_sample_0075]

description:
Expression_C1_96_cells.txt
C1_0_sample_0075


title: Automated CEL-Seq2 on C1 [C1_0_sample_0006]

description:
Expression_C1_96_cells.txt
C1_0_sample_0006


title: Automated CEL-Seq2 on C1 [C1_0_sample_0004]

description:
Expression_C1_96_cells.txt
C1_0_sample_0004


title: Wildtype head X2 single cell 59


title: Wildtype head X2 single cell 58


title: Automated CEL-Seq2 on C1 [C1_0.5_sample_0063]

description:
Expression_C1_96_cells.txt
C1_0.5_sample_0063


title: Automated CEL-Seq2 on C1 [C1_0.5_sample_0039]

description:
Expression_C1_96_cells.txt
C1_0.5_sample_0039


title: Automated CEL-Seq2 on C1 [C1_0_sample_0019]

description:
Expression_C1_96_cells.txt
C1_0_sample_0019


title: Wildtype head X2 single cell 67


title: Wildtype head X2 single cell 64


title: Automated CEL-Seq2 on C1 [C1_0_sample_0015]

description:
Expression_C1_96_cells.txt
C1_0_sample_0015


title: Wildtype head X2 single cell 66


title: Wildtype head X2 single cell 51


title: Wildtype head X2 single cell 54


title: Automated CEL-Seq2 on C1 [C1_0.5_sample_0027]

description:
Expression_C1_96_cells.txt
C1_0.5_sample_0027


title: Automated CEL-Seq2 on C1 [C1_0.5_sample_0025]

description:
Expression_C1_96_cells.txt
C1_0.5_sample_0025


title: Wildtype head X2 single cell 49


title: Automated CEL-Seq2 on C1 [C1_0.5_sample_0022]

description:
Expression_C1_96_cells.txt
C1_0.5_sample_0022


title: Wildtype head X2 single cell 63


title: Wildtype head X2 single cell 50


title: Wildtype head X2 single cell 61


title: Automated CEL-Seq2 on C1 [C1_0_sample_0003]

description:
Expression_C1_96_cells.txt
C1_0_sample_0003


title: Automated CEL-Seq2 on C1 [C1_0.3_sample_0085]

description:
Expression_C1_96_cells.txt
C1_0.3_sample_0085


title: Wildtype head X2 single cell 60


title: Automated CEL-Seq2 on C1 [C1_0_sample_0011]

description:
Expression_C1_96_cells.txt
C1_0_sample_0011


title: Automated CEL-Seq2 on C1 [C1_0.3_sample_0081]

description:
Expression_C1_96_cells.txt
C1_0.3_sample_0081


title: Automated CEL-Seq2 on C1 [C1_0.5_sample_0082]

description:
Expression_C1_96_cells.txt
C1_0.5_sample_0082


title: Automated CEL-Seq2 on C1 [C1_0.5_sample_0074]

description:
Expression_C1_96_cells.txt
C1_0.5_sample_0074


title: Wildtype head X2 single cell 45


title: Wildtype head X2 single cell 57


title: Automated CEL-Seq2 on C1 [C1_0.5_sample_0077]

description:
Expression_C1_96_cells.txt
C1_0.5_sample_0077


title: Wildtype head X2 single cell 56


title: Automated CEL-Seq2 on C1 [C1_0.3_sample_0079]

description:
Expression_C1_96_cells.txt
C1_0.3_sample_0079


title: Wildtype head X2 single cell 55


title: Automated CEL-Seq2 on C1 [C1_0.5_sample_0070]

description:
Expression_C1_96_cells.txt
C1_0.5_sample_0070


title: Automated CEL-Seq2 on C1 [C1_0.5_sample_0047]

description:
Expression_C1_96_cells.txt
C1_0.5_sample_0047


title: Wildtype head X2 single cell 62


title: Automated CEL-Seq2 on C1 [C1_0.3_sample_0073]

description:
Expression_C1_96_cells.txt
C1_0.3_sample_0073


title: Automated CEL-Seq2 on C1 [C1_0.3_sample_0069]

description:
Expression_C1_96_cells.txt
C1_0.3_sample_0069


title: Wildtype head X2 single cell 41


title: Automated CEL-Seq2 on C1 [C1_0.5_sample_0037]

description:
Expression_C1_96_cells.txt
C1_0.5_sample_0037


title: Automated CEL-Seq2 on C1 [C1_0.3_sample_0046]

description:
Expression_C1_96_cells.txt
C1_0.3_sample_0046


title: Wildtype head X2 single cell 40


title: Wildtype head X2 single cell 52


title: Wildtype head X2 single cell 39


title: Automated CEL-Seq2 on C1 [C1_0.5_sample_0036]

description:
Expression_C1_96_cells.txt
C1_0.5_sample_0036


title: Wildtype head X2 single cell 36


title: Wildtype head X2 single cell 34


title: manual_CEL-Seq1 [Manual_pos_sample_0108]

description:
CS1_manual.txt
Manual_pos_sample_0108

value: Analysis of manually collected CyclinB1-GFP negative (neg) or positive (pos) single cells by CEL-Seq1 protocol.


title: Automated CEL-Seq2 on C1 [C1_0.3_sample_0009]

description:
Expression_C1_96_cells.txt
C1_0.3_sample_0009


title: Automated CEL-Seq2 on C1 [C1_?_sample_0021]

description:
Expression_C1_96_cells.txt
C1_?_sample_0021


title: Wildtype head X2 single cell 37


title: manual_CEL-Seq1 [Manual_pos_sample_0106]

description:
CS1_manual.txt
Manual_pos_sample_0106


title: manual_CEL-Seq1 [Manual_pos_sample_0107]

description:
CS1_manual.txt
Manual_pos_sample_0107


title: manual_CEL-Seq1 [Manual_pos_sample_0105]

description:
CS1_manual.txt
Manual_pos_sample_0105


title: Wildtype head X2 single cell 48


title: Automated CEL-Seq2 on C1 [C1_0.5_sample_0020]

description:
Expression_C1_96_cells.txt
C1_0.5_sample_0020


title: Wildtype head X2 single cell 32


title: Wildtype head X2 single cell 47


title: manual_CEL-Seq1 [Manual_pos_sample_0103]

description:
CS1_manual.txt
Manual_pos_sample_0103


title: Wildtype head X2 single cell 46


title: Automated CEL-Seq2 on C1 [C1_0.5_sample_0013]

description:
Expression_C1_96_cells.txt
C1_0.5_sample_0013


title: Wildtype head X2 single cell 31


title: Wildtype head X2 single cell 30


title: Wildtype head X2 single cell 44


title: Wildtype head X2 single cell 53


title: Wildtype head X2 single cell 43


title: Wildtype head X2 single cell 26


title: Wildtype head X2 single cell 25


title: manual_CEL-Seq1 [Manual_pos_sample_0100]

description:
CS1_manual.txt
Manual_pos_sample_0100


title: manual_CEL-Seq1 [Manual_pos_sample_0098]

description:
CS1_manual.txt
Manual_pos_sample_0098


title: Wildtype head X2 single cell 42


title: Automated CEL-Seq2 on C1 [C1_0.3_sample_0030]

description:
Expression_C1_96_cells.txt
C1_0.3_sample_0030


title: Wildtype head X2 single cell 38


title: Automated CEL-Seq2 on C1 [C1_0.3_sample_0062]

description:
Expression_C1_96_cells.txt
C1_0.3_sample_0062


title: manual_CEL-Seq1 [Manual_neg_sample_0119]

description:
CS1_manual.txt
Manual_neg_sample_0119


title: manual_CEL-Seq1 [Manual_neg_sample_0117]

description:
CS1_manual.txt
Manual_neg_sample_0117


title: Wildtype head X2 single cell 21


title: Wildtype head X2 single cell 35


title: Wildtype head X2 single cell 19


title: Wildtype head X2 single cell 27


title: Wildtype head X2 single cell 18


title: manual_CEL-Seq1 [Manual_pos_sample_0097]

description:
CS1_manual.txt
Manual_pos_sample_0097


title: manual_CEL-Seq1 [Manual_pos_sample_0104]

description:
CS1_manual.txt
Manual_pos_sample_0104


title: Wildtype head X2 single cell 14


title: Wildtype head X2 single cell 29


title: Wildtype head X2 single cell 13


title: Wildtype head X2 single cell 33


title: Wildtype head X2 single cell 28


title: Wildtype head X2 single cell 24


title: manual_CEL-Seq1 [Manual_neg_sample_0120]

description:
CS1_manual.txt
Manual_neg_sample_0120


title: manual_CEL-Seq1 [Manual_pos_sample_0102]

description:
CS1_manual.txt
Manual_pos_sample_0102


title: Wildtype head X2 single cell 23


title: Wildtype head X2 single cell 22


title: manual_CEL-Seq1 [Manual_neg_sample_0118]

description:
CS1_manual.txt
Manual_neg_sample_0118


title: manual_CEL-Seq1 [Manual_neg_sample_0116]

description:
CS1_manual.txt
Manual_neg_sample_0116


title: Wildtype head X2 single cell 20


title: manual_CEL-Seq1 [Manual_neg_sample_0114]

description:
CS1_manual.txt
Manual_neg_sample_0114


title: manual_CEL-Seq1 [Manual_neg_sample_0115]

description:
CS1_manual.txt
Manual_neg_sample_0115


title: manual_CEL-Seq1 [Manual_pos_sample_0099]

description:
CS1_manual.txt
Manual_pos_sample_0099


title: Wildtype head X2 single cell 17


title: manual_CEL-Seq1 [Manual_neg_sample_0113]

description:
CS1_manual.txt
Manual_neg_sample_0113


title: Wildtype head X2 single cell 16


title: Wildtype head X2 single cell 15


title: manual_CEL-Seq1 [Manual_neg_sample_0112]

description:
CS1_manual.txt
Manual_neg_sample_0112


title: Wildtype head X2 single cell 8


title: Wildtype head X2 single cell 9


title: Wildtype head X2 single cell 11


title: Wildtype head X2 single cell 10


title: Wildtype head X2 single cell 5


title: Wildtype head X2 single cell 12


title: manual_CEL-Seq1 [Manual_neg_sample_0110]

description:
CS1_manual.txt
Manual_neg_sample_0110


title: manual_CEL-Seq2 [Cel_Seq2-IVT2_pos_sample_0017]

description:
CS2_manual.txt
Cel_Seq2-IVT2_pos_sample_0017

value: Analysis of manually collected CyclinB1-GFP negative (neg) or positive (pos) single cells by CEL-Seq2 protocol. Two seperarte IVT reactions (IVT1,IVT2) were used in the RNA amplification step.


title: manual_CEL-Seq2 [Cel_Seq2-IVT2_pos_sample_0015]

description:
CS2_manual.txt
Cel_Seq2-IVT2_pos_sample_0015


title: manual_CEL-Seq1 [Manual_neg_sample_0111]

description:
CS1_manual.txt
Manual_neg_sample_0111


title: manual_CEL-Seq2 [Cel_Seq2-IVT2_neg_sample_0020]

description:
CS2_manual.txt
Cel_Seq2-IVT2_neg_sample_0020


title: manual_CEL-Seq1 [Manual_neg_sample_0109]

description:
CS1_manual.txt
Manual_neg_sample_0109


title: manual_CEL-Seq2 [Cel_Seq2-IVT2_pos_sample_0019]

description:
CS2_manual.txt
Cel_Seq2-IVT2_pos_sample_0019


title: Wildtype head X2 single cell 4


title: manual_CEL-Seq2 [Cel_Seq2-IVT2_pos_sample_0013]

description:
CS2_manual.txt
Cel_Seq2-IVT2_pos_sample_0013


title: manual_CEL-Seq2 [Cel_Seq2-IVT2_neg_sample_0016]

description:
CS2_manual.txt
Cel_Seq2-IVT2_neg_sample_0016


title: Wildtype head X2 single cell 7


title: Wildtype head X2 single cell 2


title: Wildtype head X2 single cell 3


title: Wildtype head X1 single cell 96


title: manual_CEL-Seq2 [Cel_Seq2-IVT2_pos_sample_0011]

description:
CS2_manual.txt
Cel_Seq2-IVT2_pos_sample_0011


title: manual_CEL-Seq2 [Cel_Seq2-IVT2_neg_sample_0018]

description:
CS2_manual.txt
Cel_Seq2-IVT2_neg_sample_0018


title: manual_CEL-Seq2 [Cel_Seq2-IVT2_neg_sample_0014]

description:
CS2_manual.txt
Cel_Seq2-IVT2_neg_sample_0014


title: manual_CEL-Seq2 [Cel_Seq2-IVT1_pos_sample_0010]

description:
CS2_manual.txt
Cel_Seq2-IVT1_pos_sample_0010


title: Wildtype head X2 single cell 1


title: manual_CEL-Seq2 [Cel_Seq2-IVT2_neg_sample_0012]

description:
CS2_manual.txt
Cel_Seq2-IVT2_neg_sample_0012


title: Wildtype head X1 single cell 94


title: manual_CEL-Seq2 [Cel_Seq2-IVT1_pos_sample_0006]

description:
CS2_manual.txt
Cel_Seq2-IVT1_pos_sample_0006


title: manual_CEL-Seq2 [Cel_Seq2-IVT1_pos_sample_0002]

description:
CS2_manual.txt
Cel_Seq2-IVT1_pos_sample_0002


title: manual_CEL-Seq2 [Cel_Seq2-IVT1_pos_sample_0004]

description:
CS2_manual.txt
Cel_Seq2-IVT1_pos_sample_0004


title: manual_CEL-Seq2 [Cel_Seq2-IVT1_pos_sample_0008]

description:
CS2_manual.txt
Cel_Seq2-IVT1_pos_sample_0008


title: Wildtype head X1 single cell 93


title: Wildtype head X1 single cell 95


title: manual_CEL-Seq2 [Cel_Seq2-IVT1_neg_sample_0007]

description:
CS2_manual.txt
Cel_Seq2-IVT1_neg_sample_0007


title: manual_CEL-Seq2 [Cel_Seq2-IVT1_neg_sample_0003]

description:
CS2_manual.txt
Cel_Seq2-IVT1_neg_sample_0003


title: manual_CEL-Seq2 [Cel_Seq2-IVT1_neg_sample_0005]

description:
CS2_manual.txt
Cel_Seq2-IVT1_neg_sample_0005


title: Wildtype head X1 single cell 92


title: Wildtype head X1 single cell 90


title: manual_CEL-Seq2 [Cel_Seq2-IVT1_neg_sample_0001]

description:
CS2_manual.txt
Cel_Seq2-IVT1_neg_sample_0001


title: Wildtype head X1 single cell 88


title: Wildtype head X1 single cell 91


title: Wildtype head X1 single cell 85


title: Wildtype head X1 single cell 89


title: CL -10

first: Integrative

last: Bioinformatics

address: 111 TW Alexander Drive

department: BCBB

institute: NIEHS

description:
LeftColonProcessed.xlsx
89NS

data_processing:
Fastq data files were aligned to the human Hg19 Ensembl genome with Novoalign read aligner version 2.08.02
Novoaligned SAM files were parsed into binary BAM files using SamTransriptomeParser application from USeq software version 8.8.5
Differentially expressed genes were identified using the DefinedRegionDifferentialSeq application from USeq software version 8.8.5
SAMtoUSeq application was used to make normalized read data tracks (FPKM) for visualization in the Integrated Genome Browser from USeq software version 8.8.5
Genome_build: Ensembl Homo sapiens Hg19
Supplementary_files_format_and_content: Excel file with Ensembl IDs, chromosome coordinates, individual sample raw read counts and normalized read counts (FPKM)

source_name: Colon

extract_protocol:
TriZOL
Illumina TruSeq mRNA Sequencing with oligo dT selection

tag: patient cohort

value: Control

value: Control left colon


title: Wildtype head X1 single cell 84


title: E14_d0_H3K27me3_ChIP-seq

city: La Jolla

first: Pengfei

last: Yu

state: CA

address: 9500 Gilman Drive MC 0419

department: Bioengineering

institute: University of California San Diego

description: This sample replaces the previously submitted GSM881350.

data_processing:
Sequence reads were obtained and mapped to mouse genomes (mm9) using Bowtie 0.12.7.
Only reads with one or fewer mismatches and uniquely mapped onto the genome were retained.
Genome_build: mm9
Supplementary_files_format_and_content: BED

source_name: mouse embryonic stem cells (E14)

growth_protocol: E14(mESC) were plated onto gelatin-coated dishes in Dulbecco's modified Eagle medium (DMEM; GIBCO), supplemented with 15% heat-inactivated fetal bovine serum (FBS; GIBCO), 0.055 mM -mercaptoethanol (GIBCO), 2 mM L-glutamine, 0.1 mM MEM nonessential amino acid, 5,000 units/ml penicillin/streptomycin and 1,000 units/ml of LIF (Millipore ESG1107) in incubator set at 37 ºC in 5% CO2.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
DNA products for ChIP-seq are immuno-precipitated by antibodies of H3K27me3(Millipore, 07-449),H2AZ(Abcam, ab4174). MRE-seq was performed as described (NATURE| Vol 466|8 July 2010). DNA product for 5-hmC_ChIP-seq is generated by a selctive chemical labeling method (Nat. Methods 2011, 9, 75-77). Four parallel digests were performed (HpaII, Hin6I and SsiI are from Fermentas; HpyCH4IV is from NEB), each with 1 ug of DNA. Five units of enzyme per microgram DNA were added and incubated at 37˚C for 3 hrs. A second dose of five units-enzyme was added and the DNA was incubated for an additional 3 hrs. Digested DNA was precipitated with sodium acetate and ethanol, and 500 ng of each digest were combined into one tube.  Combined DNA was size-selected by electrophoresis on a 1% agarose gel. A 100-500 bp gel slice was excised and gel-purified using Qiagen Qiaquick columns, eluting in 30 ul of Qiagen EB buffer. Library construction was performed using the Illumina Genomic DNA Sample kit with paired-end adapters, following the manufacturer’s instructions with the following changes. For the end repair reaction, T4 DNA polymerase and T4 polynucleotide kinase were excluded and the klenow DNA polymerase was diluted 1:5 in water and 1 ul used per reaction. For paired-end oligo adapter ligation, adapters were diluted 1:10 in water and 1 ul used per reaction. After the second size selection, DNA was eluted in 36 ul EB buffer using Qiagen Qiaquick columns, and 12 ul used as template for PCR, using Illumina reagents and cycling conditions with 15 cycles. After cleanup with Qiagen MinElute columns, each library is examined by Quant-iT™ dsDNA HS Assay Kit (Qubit, Invitrogen, USA) and Agilent DNA Biaanalyzer (Agilent, USA). The libraries were sequenced with an Illunima Hi-seq Sequencing Systems. MeDIP-seq was performed as described (NATURE| Vol 466|8 July 2010). 3 ug DNA isolated as described above was sonicated to ,100–500 bp with a Bioruptor sonicator (Diagenode). Sonicated DNA was end-repaired, A-tailed, and ligated to paired-end adapters following the standard Illumina protocol. After agarose size-selection to remove unligated adapters, 1 ug of adaptor-ligated DNA was used for each immunoprecipitation using a mouse monoclonal anti-methylcytidine antibody (1 mg/ml, Eurogentec). For this, DNA was heat-denatured at 95 ˚C for 10 min, rapidly cooled on ice, and immunoprecipitated with 1 ul primary antibody per microgram of DNA overnight at 4 ˚C with rocking agitation in 500 ml immunoprecipitation buffer (10mMsodium phosphate buffer, pH 7.0, 140mMNaCl, 0.05% Triton X-100). To recover the immunoabsorbed DNA fragments, 2ul of rabbit anti-mouse IgG secondary antibody (2.5 mg/ml, Jackson Immunoresearch) and 100 ml Protein A/G beads (Pierce Biotechnology) were added and incubated for an additional 2 h at 4 ˚C with agitation. After immunoprecipitation a total of six to ten immunoprecipitation washes were performed with ice-cold immunoprecipitation buffer. A nonspecific mouse IgG immunoprecipitation (Jackson Immunoresearch) was performed in parallel to methyl DNA immunoprecipitation as a negative control. Washed beads were resuspended in TE buffer with 0.25% SDS and 0.25 mg/ml proteinase K for 2 h at 55 ˚C and then allowed to cool to room temperature. MeDIP and supernatant DNA were purified using Qiagen Qiaquic columns and eluted in 30 ul EB (Qiagen). Twelve cycles of PCR were performed on 10 ul of the immunoprecipitated DNA using the paired-end Illumina PCR primers. The resulting reactions were purified with Qiagen MinElute columns, after which a final size selection (192–592 bp) was performed by electrophoresis in 2% agarose. Libraries were quality controlled by Qubit and Agilent DNA Bioanalyzer analysis. An aliquot of each library was diluted in EB to 5 ng/ul and 1 ul used as template in four independent PCR reactions to confirm enrichment for methylated and de-enrichment for unmethylated sequences, compared to 5 ng of input (sonicated DNA). Two positive controls (SNRPN and MAGEA1 promoters) and two negative controls (a CpG-less sequence on chromosome 15 and GAPDH promoter) were amplified (Supplementary). Cycling was 95 ˚C for 30 s, 58 ˚C for 30 s, 72 ˚C for 30 s with 30 cycles. PCR products were visualized by 1.5% agarose gel electrophoresis.

tag: cell type

value: mouse embryonic stem cells (E14)


title: CL -9

description:
LeftColonProcessed.xlsx
88NS


title: Wildtype head X1 single cell 87


title: Wildtype head X1 single cell 86


title: Wildtype head X1 single cell 83


title: Input_DNA

city: Hong Kong

first: Kwok Ming

last: YAO

address: L3-69, Laboratory Block, 21 Sassoon Road

department: School of Biomedical Sciences

country: Hong Kong

institute: The University of Hong Kong

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2.
Peaks were called using MACS2 version 2.1.0.20140616.
Genome_build: hg19
Supplementary_files_format_and_content: bigWigs were created using UCSC utilities, to summarize read counts overlapping genomic regions. narrowPeak file was generated using MACS2; Columns include chrom, chromStart, chromEnd, name, score, strand, fold-change, -log10pvalue, -log10qvalue, and relative summit position to peak start.

source_name: human embryonic stem cell

growth_protocol: The human embryonic stem cell line VAL-3 was cultured on plates coated with BD MatrigelTM hESC-qualified Matrix in mTeSRTM1 Maintenance Medium at 37°C in 5% CO2. Cell passage was performed by enzymatic dissociation using Accutase, and culture media were supplemented with 10 μM ROCK inhibitor (Y-27632) for the first day after cell seeding.

extract_protocol:
VAL-3 cells were treated with 1% paraformaldehyde for chromatin cross-linking before cell lysis and sonication to generate DNA fragments. Fragmented chromatin mixed with Dynabeads protein G was incubated with either FOXM1 antibody or rabbit IgG at 4°C overnight. Successive rounds of magnetic clearance were performed, followed by crosslink reversal with NaCl incubation and protein digestion with proteinase K. DNA was purified using the Wizard® PCR clean-up system (Promega)
Libraries were prepared according to Illumina's instructions. Briefly, DNA-end was repaired to overhang a 3'-dA, then adapters were ligated to the end DNA fragments. DNA fragments with proper size (usually 100-300bp, including adaptor sequence) were selected after PCR amplification, followed by library construction.

value: ES cells

tag: passage

tag: cell line

tag: chip-antibody


title: CL -7

description:
LeftColonProcessed.xlsx
86NS

tag: tissue


title: CL -8

description:
LeftColonProcessed.xlsx
87NS


title: manual_CEL-Seq2 [Cel_Seq2-IVT1_neg_sample_0009]

description:
CS2_manual.txt
Cel_Seq2-IVT1_neg_sample_0009

tag: strain

tag: treatment


title: Wildtype head X2 single cell 6


title: Wildtype head X1 single cell 79


title: Wildtype head X1 single cell 80


title: CL -3

description:
LeftColonProcessed.xlsx
74NS


title: CL -6

description:
LeftColonProcessed.xlsx
85NS


title: CL -5

description:
LeftColonProcessed.xlsx
84NS


title: Wildtype head X1 single cell 78


title: CL -4

description:
LeftColonProcessed.xlsx
81NS


title: Wildtype head X1 single cell 77


title: Wildtype head X1 single cell 74


title: CR -9

description:
RightColonProcessed.xlsx
88NA

value: Control right colon


title: Wildtype head X1 single cell 82


title: FOXM1_ChIPSeq

value: Santa Cruz FOXM1-C20 (sc-502)


title: Wildtype head X1 single cell 75


title: CR -10

description:
RightColonProcessed.xlsx
89NA


title: Wildtype head X1 single cell 73


title: Wildtype head X1 single cell 72


title: CR -6

description:
RightColonProcessed.xlsx
85NA


title: Wildtype head X1 single cell 81


title: CR -5

description:
RightColonProcessed.xlsx
84NA


title: Wildtype head X1 single cell 69


title: Wildtype head X1 single cell 70


title: CR -4

description:
RightColonProcessed.xlsx
81NA


title: Wildtype head X1 single cell 67


title: CR -3

description:
RightColonProcessed.xlsx
74NA


title: CR -2

description:
RightColonProcessed.xlsx
72NA


title: CL -2

description:
LeftColonProcessed.xlsx
72NS


title: Wildtype head X1 single cell 66


title: Wildtype head X1 single cell 68


title: CR -1

description:
RightColonProcessed.xlsx
71NA


title: Wildtype head X1 single cell 76


title: CL -1

description:
LeftColonProcessed.xlsx
71NS


title: Wildtype head X1 single cell 64


title: CR -8

description:
RightColonProcessed.xlsx
87NA


title: CR -7

description:
RightColonProcessed.xlsx
86NA


title: UL -6

description:
LeftColonProcessed.xlsx
144NS

value: Sporadic

value: Uninvolved left colon


title: UL -5

description:
LeftColonProcessed.xlsx
133NS


title: Wildtype head X1 single cell 63


title: UL -4

description:
LeftColonProcessed.xlsx
105NS


title: Wildtype head X1 single cell 62


title: Wildtype head X1 single cell 71


title: Wildtype head X1 single cell 61


title: Wildtype head X1 single cell 60


title: UL -3

description:
LeftColonProcessed.xlsx
111NS


title: UL -1

description:
RightColonProcessed.xlsx
18ND

value: Serrated Polyposis


title: UL -2

description:
LeftColonProcessed.xlsx
100NS


title: Wildtype head X1 single cell 59


title: UR -14

description:
RightColonProcessed.xlsx
15NT

value: Uninvolved right colon


title: Wildtype head X1 single cell 57


title: Wildtype head X1 single cell 56


title: UR -13

description:
RightColonProcessed.xlsx
13NC


title: UR -12

description:
RightColonProcessed.xlsx
11NA


title: Wildtype head X1 single cell 65


title: Wildtype head X1 single cell 55


title: UR -10

description:
RightColonProcessed.xlsx
144NA


title: Wildtype head X1 single cell 54


title: UR -11

description:
RightColonProcessed.xlsx
14NA


title: UR -8

description:
RightColonProcessed.xlsx
200NA


title: Wildtype head X1 single cell 53


title: UR -9

description:
RightColonProcessed.xlsx
203NA


title: UR -7

description:
RightColonProcessed.xlsx
111NA


title: Wildtype head X1 single cell 49


title: UR -4

description:
RightColonProcessed.xlsx
103NA


title: UR -6

description:
RightColonProcessed.xlsx
109NA


title: Wildtype head X1 single cell 52


title: Wildtype head X1 single cell 46


title: UR -5

description:
RightColonProcessed.xlsx
104NA


title: Wildtype head X1 single cell 51


title: Wildtype head X1 single cell 45


title: UR -2

description:
RightColonProcessed.xlsx
101NA


title: Wildtype head X1 single cell 48


title: Wildtype head X1 single cell 44


title: UR -15

description:
RightColonProcessed.xlsx
17NA


title: Wildtype head X1 single cell 43


title: Wildtype head X1 single cell 42


title: CA -4

description:
ColonCancerProcessed.xlsx
CA764

value: Colon adenocarcinoma


title: Wildtype head X1 single cell 40

value: Asexual CIW4


title: CA -2

description:
ColonCancerProcessed.xlsx
CA087


title: CA -1

description:
ColonCancerProcessed.xlsx
CA040


title: Wildtype head X1 single cell 50

value: Amputation fragment


title: AP -9

description:
RightColonProcessed.xlsx
111AP_A

value: Adenomatous polyp


title: Wildtype head X1 single cell 39

value: heads

value: single cell


title: Wildtype head X1 single cell 38


title: AP -8

description:
RightColonProcessed.xlsx
109AP_A


title: AP -10

description:
RightColonProcessed.xlsx
200AP_A


title: Wildtype head X1 single cell 37


title: AP -6

description:
RightColonProcessed.xlsx
104AP_C


title: AP -7

description:
RightColonProcessed.xlsx
104AP_T


title: Wildtype head X1 single cell 34


title: UR -3

description:
RightColonProcessed.xlsx
102NT


title: Wildtype head X1 single cell 35


title: CA -3

description:
ColonCancerProcessed.xlsx
CA365


title: Wildtype head X1 single cell 33


title: AP -2

description:
RightColonProcessed.xlsx
101AP_D


title: Wildtype head X1 single cell 41


title: Wildtype head X1 single cell 32


title: AP -3

description:
RightColonProcessed.xlsx
102AP_T


title: AP -5

description:
RightColonProcessed.xlsx
103AP_T


title: Wildtype head X1 single cell 47


title: Wildtype head X1 single cell 36


title: AP -1

description:
RightColonProcessed.xlsx
76AP_A


title: HP -10

description:
LeftColonProcessed.xlsx
144HP_SF

value: Hyperplastic polyp


title: Wildtype head X1 single cell 29


title: Wildtype head X1 single cell 31


title: Wildtype head X1 single cell 30


title: HP -9

description:
LeftColonProcessed.xlsx
133HP_S


title: Wildtype head X1 single cell 28


title: HP -8

description:
LeftColonProcessed.xlsx
132HP_R


title: HP -7

description:
LeftColonProcessed.xlsx
132HP_S


title: HP -6

description:
LeftColonProcessed.xlsx
131HP_R


title: AP -4

description:
RightColonProcessed.xlsx
103AP_A


title: Wildtype head X1 single cell 27


title: Wildtype head X1 single cell 26


title: Wildtype head X1 single cell 25


title: HP -4

description:
LeftColonProcessed.xlsx
105HP_S


title: Wildtype head 200 X2s

value: bulk (200 cells)


title: SSA/P -21

description:
RightColonProcessed.xlsx
133SSP_R

value: Sessile serrated adenoma/polyp


title: Wildtype head 200 X1s 2


title: HP -2

description:
LeftColonProcessed.xlsx
103HP_S


title: HP -1

description:
LeftColonProcessed.xlsx
76HP_S


title: HP -3

description:
LeftColonProcessed.xlsx
111HP_R


title: SSA/P -17

description:
RightColonProcessed.xlsx
203SSP_C


title: SSA/P -20

description:
RightColonProcessed.xlsx
127SSP_A


title: SSA/P -15

description:
RightColonProcessed.xlsx
101SSP_A


title: SSA/P -19

description:
RightColonProcessed.xlsx
118SSP_C2


title: SSA/P -12

description:
RightColonProcessed.xlsx
19SSP_A2


title: SSA/P -14

description:
RightColonProcessed.xlsx
100SSP_S


title: SSA/P -18

description:
RightColonProcessed.xlsx
12SSP_T


title: SSA/P -11

description:
RightColonProcessed.xlsx
19SSP_A1


title: SSA/P -13

description:
RightColonProcessed.xlsx
110SSP_A


title: SSA/P -9

description:
RightColonProcessed.xlsx
18SSP_D1


title: SSA/P -10

description:
RightColonProcessed.xlsx
18SSP_D2


title: SSA/P -6

description:
RightColonProcessed.xlsx
15SSP_T


title: HP -5

description:
LeftColonProcessed.xlsx
111HP_HF


title: SSA/P -8

description:
RightColonProcessed.xlsx
17SSP_A


title: SSA/P -16

description:
RightColonProcessed.xlsx
118SSP_C1


title: SSA/P -7

description:
RightColonProcessed.xlsx
8SSP_A


title: SSA/P -3

description:
RightColonProcessed.xlsx
11SSP_T


title: SSA/P -5

description:
RightColonProcessed.xlsx
13SSP_A


title: SSA/P -1

description:
RightColonProcessed.xlsx
14SSP_A


title: SSA/P -4

description:
RightColonProcessed.xlsx
13SSP_C


title: FB nascent 120min ribo-RNA replicate 2

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

description: Nascent RNA labeled with 4sU 120min ribo-RNA

data_processing:
Basecalling using Illumina Casava1.8.2 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
Reads were aligned against the GRCh37/hg19 human reference genome with the UCSC Genes annotation (hg19 knownGene.txt updated at 2013/6/30) using TopHat2 (Kim et al., 2013) 2.0.9 (parameters: -g 1 -a 6 --microexon-search -m 2).
Bam to Bedgraph using genomeCoverageBed
Bedgraph to bigwig using UCSC bedGraphToBigWig
Genome_build: hg19 for human samples
Supplementary_files_format_and_content: bigwig file (UCSC bigwig in an indexed binary format. http://genome.ucsc.edu/goldenPath/help/bigWig.html)

source_name: FB nascent 4sU-labeled 120min ribo-RNA technical replicate 2

growth_protocol: Human embryonal carcinoma (EC) line PA1 were cultured with MEMα medium supplemented with L-Glutamine and 10% FBS. H9 hESCs were cultured on plates coated with growth-factor-depleted Matrigel in fibroblast-conditional medium (CM) supplemented with 4ng/mL human Basic Fibroblast Growth Factor (bFGF). hESCs-derived forebrain neuron progenitor cells (FB D26) were cultured on laminin-coated substrate with NDM medium.

extract_protocol:
100-140 μg total RNA was used for biotinylation and purification of 4sU labeled nascent RNA. 4sU labeled RNA was biotinylated in biotinylation buffer (10 mM Tris pH 7.4, 1 mM EDTA) with 0.2 mg/ml EZ-link biotin-HPDP (Pierce, 21341), which was dissolved in dimethylformamide (DMF, Sigma, D4551) at a concentration of 1 mg/ml, and incubated at room temperature for 1.5 h with rotation. Unbound biotin-HPDP was removed by equal volume chloroform extraction twice, and RNA was precipitated at 1,3000 rpm for 15min at 4℃ with 1:10 volume of 5 M NaCl and an equal volume of isopropanol. The RNA pellet was washed twice with 75% ethanol and resuspended in 150 μl DEPC•H2O. RNA quality was checked by electrophoretical analysis to exclude RNA degradation. 4sU labeled and unlabeled RNA was separated by using Streptavidin-coated magnetic beads (Invitrogen). Biotinylated RNA was incubated with 150 μl Streptavidin beads at room temperature for 20 min. Beads were washed four times with 0.9 ml of 65 ℃ washing buffer (100 mM Tris pH 7.4, 10 mM EDTA, 1 M NaCl, 0.1% Tween 20), followed by four times with 0.9 ml of room temperature washing buffer. Nascent RNA was eluted with 100 μl 0.1 M dithiotheitol (DTT) twice, and RNA was precipitated with 40 μl of 4 M LiCl, 2 μl glycogen and 600 μl ice-cold ethanol. Before preparation of nascent RNA-seq library, ribosomal RNA was depleted from 4sU labeled RNAs with RiboMinusTM Human/Mouse Transcriptome Isolation Kit (Invitrogen, K1550-01) according to the manufacturer’s protocol.
4sUDRB and ribo-RNA-seq libraries were prepared with Illumina TruSeq Total RNA LT Sample Prep Kit (P/N 15026495) without oligo(dT) enrichment. Deep sequencing was performed on Illumina Hiseq 2000 at CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai, China.

treatment_protocol: PA1, H9 and FB cells were incubated with 100 μM DRB (Sigma, D1916) for 3 h to block Pol II transcription. Transcription was recovered after DRB release and newly transcribed RNA was labeled with 300 μM 4sU (Sigma, T4509). TRizol (Invitrogen) was added to stop transcription and total RNA was extracted at each indicated transcription elongation time point.

value: forebrain neuron progenitor cells (Day 26)

tag: assayed molecule

value: ribo-RNA

value: 3 h DRB 120 min 4sU-labeled


title: FB nascent 120min ribo-RNA replicate 1

source_name: FB nascent 4sU-labeled 120min ribo-RNA technical replicate 1


title: FB nascent 60min ribo-RNA replicate 2

description: Nascent RNA labeled with 4sU 60min ribo-RNA

source_name: FB nascent 4sU-labeled 60min ribo-RNA technical replicate 2

value: 3 h DRB 60 min 4sU-labeled


title: FB nascent 30min ribo-RNA replicate 2

description: Nascent RNA labeled with 4sU 30min ribo-RNA

source_name: FB nascent 4sU-labeled 30min ribo-RNA technical replicate 2

value: 3 h DRB 30 min 4sU-labeled


title: p35S:LFYTERE, rep1

city: Grenoble

first: Francois

last: Parcy

address: 17, av. des Martyrs

country: France

institute: CNRS

description:
Plant expressing a mutant version of Arabidopsis thaliana LFY cDNA (mutation T75E R112E) under the control of the 35S promoter.
Processed data file: peaks_p35SLFYTERE.bed

data_processing:
Read mapping and duplicates removal were performed using the SHORE pipeline (preprocess, import, mapflowcell subprocesses) using -H 1,1 -M 0,4 -X 130 -B 1 as parameters. Peakfinding was performed with the shore subprogram using -B 1 as parameters. We kept as bound regions all peaks with a BH-FDR q < 10-7 in all 4 comparisons of the two replicates against the 2 controls. We obtained 1954 peaks for p35S:LFY and 176 for p35S:LFYTERE. Corresponding bed files with peak rank and CFR values are linked to the GEO Series record.
For each genomic position, the read number corresponds to the number of reads extended by 130 bp covering this position. For each bound region (ChIP-Seq peak), the coverage is defined as the area above the read count curve.
The normalization procedure was performed in two steps: 1) Intra genotype normalization between ChIP-seq replicates for the same genotype (Col-0, p35S:LFY or p35S:LFYTERE). For each genotype, we used the most significant peaks and plotted the coverage values of one replicate against the other. Replicates were then fused by calculating a normalized read count at each position. 2) Inter genotype normalization was performed based on the highest background peaks detected in the Col-0 control sample. For each background peak, coverages were compared between normalized p35S:LFY or p35S:LFYTERE and the Col-0 control sample and the regression coefficient was computed and used for final normalization for p35S:LFY and p35S:LFYTERE ChIP-seq.
The coverage fold reduction (CFR) due to the TERE mutation was computed : CFR = coverage(p35S :LFY)/coverage(p35S :LFYTERE)
Genome_build: TAIR10
Supplementary_files_format_and_content: Bed files with the peaks found by comparing p35S:LFY, or p35S :LFYTERE, and Col-0. Files contain position of the genome (TAIR10) and the rank of the bound regions (according to the FDR-BH q) and the CFR calculated by comparing the region in p35S:LFY and p35S:LFYTERE.

source_name: A. thaliana 15-day-old seedlings, p35S:LFYTERE

growth_protocol: 15-day-old p35S:LFY, p35S:LFYTERE and Col-0 (control) seedlings (complete seedlings, including aerial part+roots) grown under long day photoperiods at 23 °C on MS plates.

extract_protocol:
The entire experiment from seed sowing through deep sequencing was performed twice to produce independent biological replicates. ChIP-seq was performed with an antibody raised in rabbit (#4028) against the LFY C-terminal amino acids 223-424 (BioGenes, Berlin, Germany). Briefly, 15-day-old 35S:LFY (pCA26) and 35S:LFYTERE (pCA29) and Col-0 (control) seedlings grown under long day photoperiods at 23 °C on MS plates were harvested and fixed as described previously. Frozen tissue was ground, filtered three times through Miracloth (Calibrochem), and washed as described previously thorough buffers M1, M2, and M3. Nuclear pellets were resuspended in sonic buffer as described (1 mM PEFA BLOC SC (Roche Diagnostics) was substituted for PMSF), split into technical duplicate samples, and sonicated with a Branson sonifier at continuous pulse (output level 3) for 8 rounds of 2 x 6 seconds and allowed to cool on ice between rounds. IP reactions were performed by incubating chromatin with 2.5 μl anti-LFY serum overnight at 4 °C as described. The immunoprotein-chromatin complexes were captured by incubating with protein A-agarose beads (Santa Cruz Biotechnology), followed by consecutive washes in IP buffer and then elution as described. Immunoprotein-DNA was then incubated consecutively in RNase A/T1 mix (Fermentas) and Proteinase K (Roche Diagnostics) as described, after which DNA was purified using Minelute columns (Qiagen). ChIP samples were tested for enrichment by QPCR.
Deep sequencing libraries were produced by standard Illumina protocols.

treatment_protocol: No treatment.

tag: strain/background

tag: genotype/variation

value: seedlings

tag: Stage

value: 15 days

tag: chip antibody


title: p35S:LFYTERE, rep2

value: rabbit (#4028) against the LFY C-terminal amino acids 223-424


title: WT Col-0, rep2

description:
Wild-type Arabidopsis thaliana Col-0.
Processed data file: peaks_p35SLFY.bed, peaks_p35SLFYTERE.bed

source_name: A. thaliana 15-day-old seedlings, WT

value: WT


title: FB nascent 60min ribo-RNA replicate 1

source_name: FB nascent 4sU-labeled 60min ribo-RNA technical replicate 1


title: WT Col-0, rep1


title: FB nascent 30min ribo-RNA replicate 1

source_name: FB nascent 4sU-labeled 30min ribo-RNA technical replicate 1


title: FB nascent 15min ribo-RNA replicate 2

description: Nascent RNA labeled with 4sU 15min ribo-RNA

source_name: FB nascent 4sU-labeled 15min ribo-RNA technical replicate 2

value: 3 h DRB 15 min 4sU-labeled


title: p35S:LFY, rep1

description:
Plant expressing the Arabidopsis thaliana LFY cDNA under the control of the 35S promoter.
Processed data file: peaks_p35SLFY.bed

source_name: A. thaliana 15-day-old seedlings, p35S:LFY


title: FB nascent 0min ribo-RNA

description: Nascent RNA labeled with 4sU 0min ribo-RNA

source_name: FB nascent 4sU-labeled 0min ribo-RNA

value: 3 h DRB 0 min 4sU-labeled


title: FB nascent 15min ribo-RNA replicate 1

source_name: FB nascent 4sU-labeled 15min ribo-RNA technical replicate 1


title: p35S:LFY, rep2


title: FB steady-state ribo-RNA

description: steady-state ribo-RNA

source_name: FB steady-state ribo-RNA

value: untreated


title: SSA/P -2

description:
RightColonProcessed.xlsx
11SSP_A

value: Serrated Polyposis


title: Jak1_44176_KO_Involution

city: Daejeon

first: Taemook

address: 291 Daehak-ro, Yuseong-gu

department: Biological sciences

country: South Korea

institute: Korea Advanced Institute of Science and Technology

data_processing:
Basecalls performed using the CASAVA software
Sequenced reads were trimmed for adaptor sequence using cutadapt, and masked for low-complexity or low-quality sequence using Sickle, Sequenced reads were aligned to the mm9 genome assembly using the TopHat program
Fragment Per Kilobase of exon per million fragments mapped (FPKM) were calculated using a protocol. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files (Lactation and Involution) include FPKM values for each Sample

source_name: Mammary gland tissue

extract_protocol:
Total RNA was extracted from flash-frozen mammary gland tissues of seven conditional knockout femalesand six wildtype control mice using the RNeasy Mini Kit (Qiagen).
RNA samples were processed using the TruSeq RNA Sample kit and sequenced using a HiSeq2000 sequencer (Illumina).

value: Mammary gland

tag: developmental stage

value: Day 2 of Involution


title: Jak1_44440_KO_Involution


title: H9 nascent 120min ribo-RNA replicate 1

source_name: H9 nascent 4sU-labeled 120min ribo-RNA technical replicate 1

value: H9 human embryonic stem cells (hESCs)  (Day 0)

value: 3 h DRB 120 min 4sU-labeling


title: H9 nascent 120min ribo-RNA replicate 2

source_name: H9 nascent 4sU-labeled 120min ribo-RNA technical replicate 2


title: Jak1_43767_KO_Involution


title: H9 nascent 30min ribo-RNA replicate 2

source_name: H9 nascent 4sU-labeled 30min ribo-RNA technical replicate 2

value: 3 h DRB 30 min 4sU-labeling


title: H9 nascent 60min ribo-RNA replicate 1

source_name: H9 nascent 4sU-labeled 60min ribo-RNA technical replicate 1

value: ribo-RNA

value: 3 h DRB 60 min 4sU-labeling


title: H9 nascent 30min ribo-RNA replicate 1

source_name: H9 nascent 4sU-labeled 30min ribo-RNA technical replicate 1


title: H9 nascent 15min ribo-RNA replicate 2

source_name: H9 nascent 4sU-labeled 15min ribo-RNA technical replicate 2

value: 3 h DRB 15 min 4sU-labeling


title: FB nascent 10min ribo-RNA

description: Nascent RNA labeled with 4sU 10min ribo-RNA

source_name: FB nascent 4sU-labeled 10min ribo-RNA

value: forebrain neuron progenitor cells (Day 26)

value: 3 h DRB 10 min 4sU-labeled


title: H9 nascent 10min ribo-RNA replicate 2

source_name: H9 nascent 4sU-labeled 10min ribo-RNA technical replicate 2

value: 3 h DRB 10 min 4sU-labeling


title: H9 nascent 0min ribo-RNA

source_name: H9 nascent 4sU-labeled 0min ribo-RNA

value: 3 h DRB 0 min 4sU-labeling


title: H9 nascent 10min ribo-RNA replicate 1

source_name: H9 nascent 4sU-labeled 10min ribo-RNA technical replicate 1


title: Jak1_43196_KO_Involution


title: H9 steady-state ribo-RNA

description: steady-state ribo-RNA

source_name: H9 steady-state ribo-RNA


title: 100pgTechRepUMI_primer_no_lig [no_lig_sample_0050]

description:
100pgTechRepUMI_primer_no_lig.txt
no_lig_sample_0050

organism: Caenorhabditis elegans

source_name: total RNA

value: embryos

tag: age

value: mixed stages

tag: experimental design

value: 100pg of C. elegans isloted total RNA was used to calibrate the new CEL-Seq2 protocol. Each sample set represent different parameters; old_bc - the original CEL-Seq primer, UMI - unique molecular identifier, short - a shorter version of the original primer with UMI, no_lig - ligation free 3 prime illumina adapter introduction.


title: 100pgTechRepUMI_primer_no_lig [no_lig_sample_0049]

description:
100pgTechRepUMI_primer_no_lig.txt
no_lig_sample_0049


title: 100pgTechRepUMI_primer_no_lig [no_lig_sample_0048]

description:
100pgTechRepUMI_primer_no_lig.txt
no_lig_sample_0048


title: Wildtype head X1 single cell 58

source_name: Wildtype animal heads

value: Asexual CIW4

tag: facs gate

value: Amputation fragment

value: heads

tag: sample type

value: single cell


title: H9 nascent 60min ribo-RNA replicate 2

source_name: H9 nascent 4sU-labeled 60min ribo-RNA technical replicate 2

value: H9 human embryonic stem cells (hESCs)  (Day 0)


title: 100pgTechRepUMI_primer_no_lig [no_lig_sample_0047]

description:
100pgTechRepUMI_primer_no_lig.txt
no_lig_sample_0047


title: PA1 nascent 120min ribo-/RNase R RNA replicate 1

description: Nascent RNA labeled with 4sU 120min ribo-/RNase R RNA

source_name: PA1 nascent 4sU-labeled 120min ribo-/RNase R RNA technical replicate 1

value: ribo-/RNase R RNA

value: 3 h DRB 120 min 4sU-labeling


title: PA1 nascent 120min ribo-/RNase R RNA replicate 2

source_name: PA1 nascent 4sU-labeled 120min ribo-/RNase R RNA technical replicate 2


title: PA1 nascent 120min ribo-/RNase R RNA replicate 3

source_name: PA1 nascent 4sU-labeled 120min ribo-/RNase R RNA technical replicate 3


title: PA1 nascent 60min ribo-/RNase R RNA replicate 2

description: Nascent RNA labeled with 4sU 60min ribo-/RNase R RNA

source_name: PA1 nascent 4sU-labeled 60min ribo-/RNase R RNA technical replicate 2


title: Jak1_42734_KO_Lactation

source_name: Mammary gland tissue

value: Mammary gland

value: Day 7 of Lactation


title: Jak1_43768_Con_Involution

value: Day 2 of Involution


title: 100pgTechRepUMI_primer_no_lig [no_lig_sample_0046]

description:
100pgTechRepUMI_primer_no_lig.txt
no_lig_sample_0046


title: Jak1_44448_Con_Involution


title: Jak1_44174_KO_Lactation


title: Jak1_44175_Con_Lactation


title: 100pgTechRepUMI_primer_no_lig [no_lig_sample_0045]

description:
100pgTechRepUMI_primer_no_lig.txt
no_lig_sample_0045


title: PA1 nascent 60min ribo-/RNase R RNA replicate 1

source_name: PA1 nascent 4sU-labeled 60min ribo-/RNase R RNA technical replicate 1

value: 3 h DRB 60 min 4sU-labeling


title: Jak1_43767_KO_Lactation


title: H9 nascent 15min ribo-RNA replicate 1

source_name: H9 nascent 4sU-labeled 15min ribo-RNA technical replicate 1

value: ribo-RNA

value: 3 h DRB 15 min 4sU-labeling


title: Jak1_43914_Con_Involution


title: Jak1_43768_Con_Lactation


title: 100pgTechRepUMI_primer_no_lig [no_lig_sample_0044]

description:
100pgTechRepUMI_primer_no_lig.txt
no_lig_sample_0044


title: Jak1_42186_Con_Lactation


title: 100pgTechRepUMI_primer_no_lig [no_lig_sample_0043]

description:
100pgTechRepUMI_primer_no_lig.txt
no_lig_sample_0043


title: PA1 nascent 30min ribo-/RNase R RNA replicate 4

description: Nascent RNA labeled with 4sU 30min ribo-/RNase R RNA

source_name: PA1 nascent 4sU-labeled 30min ribo-/RNase R RNA technical replicate 4

value: 3 h DRB 30 min 4sU-labeling


title: PA1 nascent 30min ribo-/RNase R RNA replicate 3

source_name: PA1 nascent 4sU-labeled 30min ribo-/RNase R RNA technical replicate 3


title: 100pgTechRepUMI_primer_no_lig [no_lig_sample_0042]

description:
100pgTechRepUMI_primer_no_lig.txt
no_lig_sample_0042

value: embryos


title: PA1 nascent 30min ribo-/RNase R RNA replicate 1

source_name: PA1 nascent 4sU-labeled 30min ribo-/RNase R RNA technical replicate 1


title: 100pgTechRepUMI_primer_no_lig [no_lig_sample_0041]

description:
100pgTechRepUMI_primer_no_lig.txt
no_lig_sample_0041

value: mixed stages


title: LsATF4-KO 6 hr 0.3% DMSO [TY011_GGCTAC_L005_R1_001]

city: Indianapolis

first: Ronald

middle: C

last: Wek

state: IN

address: 635 Barnhill Dr

department: Biochemistry and Molecular Biology

institute: IU School of Medicine

data_processing:
RTA for base calling
bcl2fastq for converting BCL to fastq format, coupled with adaptor trimming
Mapped to mm9 with Tophat (2.0.4) with 4 mismatches and 10 maxiumum multiple hits
Assembled transcripts using default options for cufflinks
Merged transcripts with cuffmerge
Examined diferential expression with cuffdiff
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text abundance measurements

source_name: Mouse Liver

extract_protocol:
Livers were removed, flash frozen on dry ice, and RNA was harvested using Trizol.  Illumina TruSeq RNA Sample prep kit was used, and ERCC ExFold Spike Ins were added to Total RNA to normalize upon polyA selection
Prepared using standard Illumina protocol

treatment_protocol: 0.3% DMSO or 1 mg/kg Tunicamycin for 6 hours delivered via IP Injection

value: 6 hr 0.3% DMSO

value: Liver

tag: genotype


title: LsATF4-KO 6 hr 0.3% DMSO [TY010_TAGCTT_L005_R1_001]


title: PA1 nascent 30min ribo-/RNase R RNA replicate 2

source_name: PA1 nascent 4sU-labeled 30min ribo-/RNase R RNA technical replicate 2


title: 100pgTechRepShort_primer [short_sample_0030]

description:
100pgTechRepShort_primer.txt
short_sample_0030

value: 100pg of C. elegans isloted total RNA was used to calibrate the new CEL-Seq2 protocol. Each sample set represent different parameters; old_bc - the original CEL-Seq primer, UMI - unique molecular identifier, short - a shorter version of the original primer with UMI, no_lig - ligation free 3 prime illumina adapter introduction.


title: Wild Type 6 hr 0.3% DMSO [TY009_GATCAG_L004_R1_001]

value: wild type


title: PA1 nascent 120min ribo-RNA replicate 3

description: Nascent RNA labeled with 4sU 120min ribo-RNA

source_name: PA1 nascent 4sU-labeled 120min ribo-RNA technical replicate 3


title: PA1 nascent 120min ribo-RNA replicate 2

source_name: PA1 nascent 4sU-labeled 120min ribo-RNA technical replicate 2


title: 100pgTechRepShort_primer [short_sample_0029]

description:
100pgTechRepShort_primer.txt
short_sample_0029

source_name: total RNA


title: 100pgTechRepShort_primer [short_sample_0027]

description:
100pgTechRepShort_primer.txt
short_sample_0027


title: LsATF4-KO 6 hr 1 mg/kg Tunicamycin [TY007_CAGATC_L004_R1_001]

value: 6 hr 1 mg/kg Tunicamycin


title: PA1 nascent 120min ribo-RNA replicate 1

source_name: PA1 nascent 4sU-labeled 120min ribo-RNA technical replicate 1


title: 100pgTechRepShort_primer [short_sample_0026]

description:
100pgTechRepShort_primer.txt
short_sample_0026


title: LsATF4-KO 6 hr 1 mg/kg Tunicamycin [TY005_ACAGTG_L004_R1_001]


title: Wild Type 6 hr 1 mg/kg Tunicamycin [TY008_ACTTGA_L004_R1_001]


title: PA1 nascent 60min ribo-RNA replicate 2

description: Nascent RNA labeled with 4sU 60min ribo-RNA

source_name: PA1 nascent 4sU-labeled 60min ribo-RNA technical replicate 2


title: PA1 nascent 60min ribo-RNA replicate 3

source_name: PA1 nascent 4sU-labeled 60min ribo-RNA technical replicate 3


title: 100pgTechRepShort_primer [short_sample_0025]

description:
100pgTechRepShort_primer.txt
short_sample_0025


title: 100pgTechRepShort_primer [short_sample_0028]

description:
100pgTechRepShort_primer.txt
short_sample_0028


title: LsATF4-KO 6 hr 0.3% DMSO [TY012_CTTGTA_L005_R1_001]


title: Wild Type 6 hr 1 mg/kg Tunicamycin [TY004_TGACCA_L004_R1_001]


title: PA1 nascent 30min ribo-RNA replicate 2

description: Nascent RNA labeled with 4sU 30min ribo-RNA

source_name: PA1 nascent 4sU-labeled 30min ribo-RNA technical replicate 2


title: PA1 nascent 60min ribo-RNA replicate 1

source_name: PA1 nascent 4sU-labeled 60min ribo-RNA technical replicate 1


title: LsATF4-KO 6 hr 1 mg/kg Tunicamycin [TY003_TTAGGC_L004_R1_001]


title: 100pgTechRepShort_primer [short_sample_0024]

description:
100pgTechRepShort_primer.txt
short_sample_0024


title: 100pgTechRepShort_primer [short_sample_0023]

description:
100pgTechRepShort_primer.txt
short_sample_0023


title: PA1 nascent 15min ribo-RNA replicate 2

description: Nascent RNA labeled with 4sU 15min ribo-RNA

source_name: PA1 nascent 4sU-labeled 15min ribo-RNA technical replicate 2


title: 100pgTechRepShort_primer [short_sample_0021]

description:
100pgTechRepShort_primer.txt
short_sample_0021


title: Wild Type 6 hr 0.3% DMSO [TY002_CGATGT_L004_R1_001]


title: PA1 nascent 15min ribo-RNA replicate 1

source_name: PA1 nascent 4sU-labeled 15min ribo-RNA technical replicate 1


title: Wild Type 6 hr 1 mg/kg Tunicamycin [TY001_ATCACG_L004_R1_001]


title: 100pgTechRepUMI_primer [UMI_primer_sample_0020]

description:
100pgTechRepUMI_primer.txt
UMI_primer_sample_0020


title: Wild Type 6 hr 0.3% DMSO [TY006_GCCAAT_L004_R1_001]


title: PA1 nascent 10min ribo-RNA

description: Nascent RNA labeled with 4sU 10min ribo-RNA

source_name: PA1 nascent 4sU-labeled 10min ribo-RNA

value: 3 h DRB 10 min 4sU-labeling


title: 100pgTechRepUMI_primer [UMI_primer_sample_0019]

description:
100pgTechRepUMI_primer.txt
UMI_primer_sample_0019


title: PA1 steady-state ribo-RNA replicate 2

description: steady-state ribo-RNA

source_name: PA1 steady-state ribo-RNA technical replicate 2

value: untreated


title: PA1 nascent 0min ribo-RNA

description: Nascent RNA labeled with 4sU 0min ribo-RNA

source_name: PA1 nascent 4sU-labeled 0min ribo-RNA

value: 3 h DRB 0 min 4sU-labeling


title: 100pgTechRepUMI_primer [UMI_primer_sample_0017]

description:
100pgTechRepUMI_primer.txt
UMI_primer_sample_0017


title: PA1 nascent 30min ribo-RNA replicate 1

source_name: PA1 nascent 4sU-labeled 30min ribo-RNA technical replicate 1


title: 100pgTechRepUMI_primer [UMI_primer_sample_0018]

description:
100pgTechRepUMI_primer.txt
UMI_primer_sample_0018


title: PA1 steady-state ribo-RNA replicate 1

description: steady-state ribo-RNA

source_name: PA1 steady-state ribo-RNA technical replicate 1


title: 100pgTechRepUMI_primer [UMI_primer_sample_0016]

description:
100pgTechRepUMI_primer.txt
UMI_primer_sample_0016