title: D-6 ESC +Dox

description: D-2 ES infected with pLV-tetO-Dusp9-IRES-Tomato. Induced for 3 passages.

data_processing:
Alignment: bisulfite-converted reads were aligned to a MspI-digested mm9 mouse  genome using MAQ in bisulfite alignment mode using the following parameters: -D -s 0 -M c -e 100
Methylation calling: CpGs in the reference sequence were compared to the sequence in the aligned read. If bisulfite conversion (signifying an unmethylated cytosine) was detected, the read added to the unmethylated count for that CpG, otherwise, it added to the methylated count.
Genome_build: mm9
Supplementary_files_format_and_content: Bed files contain the number of methylated and total reads for CpGs covered by RRBS with the columns: chromosome, start, end, number of reads methylated divided by number of reads seen, methylation percent/1000

extract_protocol:
generation protocol: D-2 ESCs were infected with a dox-inducible virus expressing additional DUSP protein. Induced for 3 passages.
Genomic DNA was collected using phenol/chloroform extraction
RRBS libraries were prepared using a commercial kit (Ovation RRBS Methyl-Seq System, NuGen, San Carlos, CA) following the manufacturer's protocol except that we pooled 12 individually barcoded reactions after the final repair step and performed the bisulfite conversion and library amplification as a pool. Libraries were sequenced on an Illumina HiSeq2500 high-output flowcell without a PhiX spike-in using Nugen's custom sequencing primer for read 1 (36 bases) and standard Illumina sequencing primers to read the 8-base sample barcodes.

tag: sex chromosomes

value: XX

value: ESC


title: Control2_3

status: Public on Apr 12 2017

type: SRA

city: Cambridge

first: David

middle: A

last: Bulger

address: Box 289, Addenbrooke's Hospital

department: Institute of Metabolic Science

country: United Kingdom

institute: University of Cambridge

library_source: transcriptomic

data_processing:
RNA-seq reads were aligned to GRCh37 genome assembly using Tophat V2.0.8
Fragment counts were determined using Cufflinks V2.2.1
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited files include ENSEMBL_ID, gene_short_name, tss_id, locus, and raw count values

molecule: total RNA

organism: Homo sapiens

source_name: Interscapular subcutaneous adipose tissue

extract_protocol:
Adipose tissue was removed surgically, dissected from surrounding connective and vascular tissue on dry ice and frozen in liquid nitrogen, 2-3 frozen aliquots per subject were transferred into 1 mL QIAzol (Qiagen) and homogenized on thawing with a hand-held TissueRuptor (Qiagen) before centrifugation at 13,000g for 3 minutes, and infranatant beneath the fatty layer was mixed with 1 ML 100% ethanol before binding to RNeasy columns and purifying using the RNAeasy kit according to manufacturer's instructions.
RNA was concentrated with the Rneasy MinElute Cleanup Kit (Qiagen) and the RNA samples were whole transcriptome-amplified with NuGEN RNA-Seq System V2 and converted to indexed libraries with NuGEN Ovation Rapid DR Multiplex Library System following manufacturer's instructions.

tag: tissue

tag: gender

value: female

tag: genotype

value: WT


title: Control3_2

value: Interscapular subcutaneous adipose tissue


title: Control5_2


title: D-2 ESC +Dox

first: Kendell

last: Clement

state: MA

address: 7 Divinity Ave.

country: USA

institute: Harvard University

description: KH2 targeted with Dusp9. Induced for 3 passages.

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: ESC

extract_protocol:
generation protocol: D-2 ESCs were induced with doxycyclin for 3 passages.
Genomic DNA was collected using phenol/chloroform extraction
RRBS libraries were prepared using a commercial kit (Ovation RRBS Methyl-Seq System, NuGen, San Carlos, CA) following the manufacturer's protocol except that we pooled 12 individually barcoded reactions after the final repair step and performed the bisulfite conversion and library amplification as a pool. Libraries were sequenced on an Illumina HiSeq2500 high-output flowcell without a PhiX spike-in using Nugen's custom sequencing primer for read 1 (36 bases) and standard Illumina sequencing primers to read the 8-base sample barcodes.

tag: cell type


title: D-2 ESC

description: KH2 targeted with Dusp9. No induction.

extract_protocol:
generation protocol: Dusp9 cDNA was cloned into the shuttle plasmid pBS31 using NotI and MfeI digestion. The resulting plasmid was electroporated into KH2 ESCs together with a plasmid driving expression of Flp recombinase (Beard et al., 2006).
Genomic DNA was collected using phenol/chloroform extraction
RRBS libraries were prepared using a commercial kit (Ovation RRBS Methyl-Seq System, NuGen, San Carlos, CA) following the manufacturer's protocol except that we pooled 12 individually barcoded reactions after the final repair step and performed the bisulfite conversion and library amplification as a pool. Libraries were sequenced on an Illumina HiSeq2500 high-output flowcell without a PhiX spike-in using Nugen's custom sequencing primer for read 1 (36 bases) and standard Illumina sequencing primers to read the 8-base sample barcodes.


title: Nr1d1_ko_CT12_rep2

city: San Francisco

first: Zenghua

last: Fan

state: CA

address: 1550 4th Street

institute: University of California, San Francisco

description: Nr1d1_ko_CT12_rep2, paired-end read1&2

data_processing:
Fastq files containing raw sequence reads were aligned to mouse genome (mm9) by Tophat2. Then bedtools (v2.19.1) were applied to calculate the number of reads of each transcript based on the gene annotations from Ensembl annotation(v69). The reads numbers were normalized to reads per kilobase per million mapped reads (RPKM).
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values of genes for RNA-seq.

source_name: liver

growth_protocol: The mice were housed under a 12-h light/12-h dark regimen with food and water available ad libitum for one week before being switched to complete darkness. The mice were switched to complete darkness two days before execution. CT0 is defined as the time when the lights are turned on.

extract_protocol:
Livers of all mice were quickly dissected and snap-frozen in liquid nitrogen and stored at −80 °C. Total RNA was extracted from each liver sample using Trizol reagent. For genomic DNA extraction, cells were first lysed in cold lysis buffer (10mMTris HCl, 10mMNaCl, 0.2% NP-40, 1×protease inhibitor) for 15 min on ice. After being washed twice, cell nuclei were re-suspended in Buffer 2.1 (New England Biolabs) including 0.1% SDS and were incubated for 10 min at 65°C. 1% (final concentration) of Triton X-100 was added to quench SDS and centri- fuged to remove SDS and Triton.
The RNA samples  were converted into Illumina sequencing libraries by using Illumina TruSeq RNA Sample Prep Kit v2 as per manufacturer’s protocol.

treatment_protocol: Two pairs of Nr1d1 KO and WT mice were sacrificed at CT0 and CT12 respectively after at least one week entrainment.

tag: strain

value: Nr1d1 knockout

value: liver

tag: age

value: 8 weeks


title: 520B_BK

city: Stanford

first: Thomas

last: Quertermous

address: 300 Pasteur Drive

department: Medicine Cardiology

institute: Stanford University

data_processing:
Reads contained in raw fastq files were mapped to hg19 using the RNA-seq aligner STAR (v2.4.0i), that processes data with short run times and yields high numbers of uniquely mapped reads (https://github.com/alexdobin/STAR). Second pass mapping with STAR was then performed using a new index that is created with splice junction information contained in the file SJ.out.tab from the first pass STAR mapping. Read that have been mapped with STAR second pass mapping algorithm were subsequently counted using the htseq-count script distributed with the HTSeq Python package (https://pypi.python.org/pypi/HTSeq). Differential expression of exons, genes, and transcripts were assayed using the DESeq2 R package from Bioconductor (http://bioconductor.org/packages/release/bioc/html/DESeq2.html), which uses negative binomial distribution to estimate dispersion and model differential expression such as to permit biological variability to be different among tested genes (transcripts).
Genome_build: hg19
Supplementary_files_format_and_content: [.txt] FeatureCounts - with Gencode annotation - gencode.v19.annotation.gtf
Supplementary_files_format_and_content: [.csv] DESeq output table

source_name: Control - biological replicate 2

growth_protocol: Primary human coronary artery smooth muscle cells (HCASMC) were purchased from three different manufacturers, Lonza, PromoCell and Cell Applications and were cultured in complete smooth muscle basal media (Lonza, #CC-3182) according to the manufacturer's instructions. All experiments were performed with HCASMC between passages 4–7.

extract_protocol:
HCASMC were cultured as described in Nurnberg at al, Plos Genetics 2015 ,and total RNA was purified from 5.0x10e5 cells using the Qiagen miRNeasy kit. RNA was isolated using RNeasy mini kit (Qiagen) and total cDNA was prepared using iScript cDNA synthesis kit (Biorad).
RNA libraries were prepared using the Illumina TruSeq library kit as described by the manufacturer. RNA molecules were sequenced using Illumina HiSeq 2500.

treatment_protocol: For the TCF21 overexpression study, HCASMC were transduced with 2nd generation lentivirus with TCF21 cDNA cloned into pWPI (Addgene #12254). The cells were collected 48 hours after transduction and processed using RNeasy kit (Qiazol) for RNA isolation.

tag: genotype/variation

value: control


title: Nr1d1_ko_CT0_rep2

description: Nr1d1_ko_CT0_rep2, paired-end read1&2


title: Control2_2


title: Nr1d1_control_CT12_rep2

description: Nr1d1_control_CT12_rep2, paired-end read1&2


title: Control2_1


title: Nr1d1_control_CT0_rep2

description: Nr1d1_control_CT0_rep2, paired-end read1&2


title: Control1_2


title: Control1_1


title: P3_2

value: male


title: 4C_CT6 rep1

data_processing:
Library strategy: 4C-Seq
Fastq files containing raw sequence reads were aligned to mouse genome (mm9) by Tophat2. Then bedtools (v2.19.1) were applied to calculate the number of reads of each transcript based on the gene annotations from Ensembl annotation(v69).  The reads numbers were normalized to reads per kilobase per million mapped reads (RPKM).
4C-seq fastq files were aligned to mouse genome (mm9) by Bowtie and others were aligned by Tophat2 and . Then bedtools (v2.19.1) were applied to calculate the number of reads of each transcript based on the gene annotations from Ensembl annotation(v69).  The reads numbers were normalized to reads per kilobase per million mapped reads (RPKM).
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values of genes for RNA-seq and reads count of HindIII fragments for 4C-seq.

extract_protocol: For 4C libraray construction, nuclei were digested overnight by 800U HindIII (New England Biolabs) at 37°C with shaking. After inactivation by 1.6% (final concentration) of SDS at 65°C for 20 min, samples were washed and re-suspended in ligation buffer and ligated by 100U T4 DNA ligase (Thermo Fisher Scientific) at 16°C for 4 hr and then room temperature for 30 min. Ligated chromatin was digested by proteinase K before DNA purification. The purified DNA was further digested by DpnII (New England Biolabs) and then circularized using T4 DNA ligase (Thermo Fisher Scientific). After purification, 200 ng of DNA fromthe 4C library was used as the template for the PCR amplification using DyNAzyme EXT (Finn- zymes). Primers specific to bait region were applied for amplification by PCR. PCR products were used as the templates for a second PCR reaction utilizing the primers with the addition of Illumina adaptors.

treatment_protocol: Three WT mice were sacrificed at CT6 and CT18 respectively after at least one week entrainment.


title: 4C_CT18 rep2


title: 4C_CT6 rep3


title: P3_3


title: 4C_CT18 rep3


title: 4C_CT6 rep2


title: 4C_CT18 rep1


title: Control3_1


title: Nr1d1_ko_CT12_rep1

data_processing:
Fastq files containing raw sequence reads were aligned to mouse genome (mm9) by Tophat2. Then bedtools (v2.19.1) were applied to calculate the number of reads of each transcript based on the gene annotations from Ensembl annotation(v69).  The reads numbers were normalized to reads per kilobase per million mapped reads (RPKM).
4C-seq fastq files were aligned to mouse genome (mm9) by Bowtie and others were aligned by Tophat2 and . Then bedtools (v2.19.1) were applied to calculate the number of reads of each transcript based on the gene annotations from Ensembl annotation(v69).  The reads numbers were normalized to reads per kilobase per million mapped reads (RPKM).
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values of genes for RNA-seq and reads count of HindIII fragments for 4C-seq.


title: P3_1


title: P2_3


title: Nr1d1_ko_CT0_rep1


title: Nr1d1_control_CT12_rep1


title: Bmal1_ko_CT12_rep3

extract_protocol:
Livers of all mice were quickly dissected and snap-frozen in liquid nitrogen and stored at −80 °C. Total RNA was extracted from each liver sample using Trizol.
The RNA samples were converted into Illumina sequencing libraries by using Illumina TruSeq RNA Sample Prep Kit v2 as per manufacturer’s protocol.

treatment_protocol: Three pairs of Bmal1 liver-specific knockout mice and wild-type mice were sacrificed at CT0 and CT12 respectively after at least one week entrainment.

value: Bmal1 knockout


title: P2_2


title: Bmal1_ko_CT12_rep1


title: P2_1


title: Bmal1_control_CT12_rep3


title: Bmal1_ko_CT0_rep1


title: Bmal1_ko_CT12_rep2


title: Bmal1_control_CT12_rep1


title: Bmal1_control_CT0_rep3


title: Bmal1_control_CT12_rep2


title: Bmal1_ko_CT0_rep2


title: Bmal1_ko_CT0_rep3


title: Bmal1_control_CT0_rep1


title: J-56

description: Fusion hybrid between J-30 ESC and XX MEF

data_processing:
Alignment: bisulfite-converted reads were aligned to a MspI-digested mm9 mouse  genome using MAQ in bisulfite alignment mode using the following parameters: -D -s 0 -M c -e 100
Methylation calling: CpGs in the reference sequence were compared to the sequence in the aligned read. If bisulfite conversion (signifying an unmethylated cytosine) was detected, the read added to the unmethylated count for that CpG, otherwise, it added to the methylated count.
Genome_build: mm9
Supplementary_files_format_and_content: Bed files contain the number of methylated and total reads for CpGs covered by RRBS

source_name: ESC XX x MEF XX

extract_protocol:
generation protocol: One million EGCs or ESCs were combined with one million MEFs and fused with PEG-1500 (Roche) according to the manufacturer’s directions. Selection was initiated 24 hr post-fusion with puromycin (2 mg/mL) and neomycin (300 mg/mL). Cell-cycle analysis was performed on a FACSCalibur (BD) with propidium iodide; signal area was used as a measure of DNA content.
Genomic DNA was collected using phenol/chloroform extraction
mRRBS libraries were prepared as previously described (Boyle et al. 2012). Briefly, genomic sequences were digested using the MspI restriction enzyme, which cuts at the sequence CCGG. Digested fragments were subjected to bisulfite treatment which converts unmethylated cytosine residues to uracil

value: XXXX


title: J-57


title: Nr1d1_control_CT0_rep1


title: snrk2.2/3/6_rep2_sRNA_Seq_1727

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

description: small RNA

data_processing:
The adapter was trimmed using fastx_clipper command line tool of the FASTX-Toolkit. Only clean reads with length 18-32 nt were retained for the following analysis. The known Arabidopsis miRNA sequences were counted in each library. miRBase release 21 was used.
Supplementary_files_format_and_content: Identical_miRNA_count_upload.txt is the processed file. The file has 14 colunms: (1) miRNA_ID, if different miRNA has the same sequence, the IDs were seperated by ";". (2) miRNA_Seq: the sequence of the miRNA (3)-(8) the raw counts of miRNA sequences in each library. (9)-(14) The normalized counts in each library. The RPTM means "Reads Per Ten Million clean reads".

organism: Arabidopsis thaliana

source_name: rosette leaves

extract_protocol: Total RNA was isolated from rosette leaves of 3-week-old plants grown in soil using TriPure Isolation Reagent (Roche). Total RNA Samples were sent to Genomics Core Facility of Shanghai Center for Plant Stress Biology for library preparation and Illumina sequencing.

value: snrk2.2/3/6 mutant

value: rosette leaves


title: Col_rep2_sRNA-Seq_1723

description: small RNA


title: J-59

description: Fusion hybrid between J-17 EGC and XY MEF

source_name: EGC XY x MEF XY

value: XXYY


title: J-52

description: Fusion hybrid between J-20 EGC and XX MEF

source_name: EGC XX x MEF XX


title: hyl1-2_rep1_sRNA_Seq_1728

description: small RNA

value: hyl1-2 mutant


title: J-53


title: hyl1-2_rep2_sRNA_Seq_1729

description: small RNA


title: J-62

description: Fusion hybrid between J-34 ESC and XY MEF

source_name: ESC XY x MEF XY


title: snrk2.2/3/6_rep1_sRNA_Seq_1725

description: small RNA


title: J-55


title: J-58


title: J-51


title: J-61


title: J-32 ESC

description: E3.5 ESC (XX)

extract_protocol:
generation protocol: E3.5 blastocysts were retrieved from the uterine horn by flushing and collected under a dissection microscope. A whole blastocyst was plated onto MEF feeder (Globalstem) containing 2i-LIF medium (Ying et al., 2008).  The cells were cultured for 4 days without changing medium. After that, the cells were cultured for additional 3-4 days and fed every two days with fresh 2i-LIF medium until picking. Outgrowth from the culture was picked, trypsinized, and re-plated onto MEF feeders containing KO DMEM (Invitrogen) supplemented with 15% FBS (Hyclone), 1mM L- glutamine, 100 uM MEM non-essential amino acids, and 0.1 mM beta-mercaptoethanol, and LIF.
Genomic DNA was collected using phenol/chloroform extraction
mRRBS libraries were prepared as previously described (Boyle et al. 2012). Briefly, genomic sequences were digested using the MspI restriction enzyme, which cuts at the sequence CCGG. Digested fragments were subjected to bisulfite treatment which converts unmethylated cytosine residues to uracil


title: J-31 ESC

description: E3.5 ESC (XX)


title: J-30 ESC

description: E3.5 ESC (XX)


title: J-37 ESC

description: E3.5 ESC (XY)

value: XY


title: Mouse_M2255-F8-M15-LZ

city: Los Angeles

first: Benjamin

middle: E

last: Decato

address: 1050 Childs Way

department: Molecular and Computational Biology

institute: University of Southern California

description: C57Bl/6 females were housed under dark:light 12:12 conditions with free access to water and the standard diet used in the University of Cambridge Animal Facility. At 8-10 weeks, females were mated with C57Bl/6 males and the day a copulatory plug was found was denoted as embryonic day 1 of pregnancy (term=20.5 days). On embryonic days 15 or 18 of pregnancy (days correspond to the periods of rapid placental and fetal growth respectively), mouse dams were schedule 1 killed by cervical dislocation. Uteri were collected and the number of viable conceptuses counted. Embryos and placentas were dissected and weighed. Each placenta from the litter was rapidly separated into the functionally distinct zones, the labyrinthine transport and junctional endocrine zones (Sferruzzi-Perri et al., 2009), in ice cold sterile PBS before rapid snap freezing in liquid nitrogen. Fetal tails were kept for sexing using standard genotyping methods including using primers to detect the SRY gene (5’-CCCAGCATGCAAAATACAGA -3’ and 5’-TCAACAGGCTGCCAATAAAA-3’), an internal control gene (5’-AGTGGCTAACGCTGAGTGGT-3’ and 5’-GTGCCTGTCGGAGGAGAAC-3’) and with agarose gel electrophoresis. From each litter, the male and female placenta with its weight closest to the litter mean was used for further analysis.

data_processing:
Reads aligned to mm10 reference genome using WALT (https://github.com/smithlabcode/walt)
Methylation levels computed from reads using methpipe v3.4.2
Genome_build: mm10
Supplementary_files_format_and_content: All processed data files are bigWig format with the value equal to the methylation level for .meth.bw files and coverage depth for .read.bw files.

organism: Mus musculus domesticus

source_name: Placental labyrinthine zone

growth_protocol: See individual samples: the two datasets (interspecific and intraspecific) were grown using separate growth protocols.

extract_protocol:
Using a Qiagen DNA extraction kit, DNA was extracted and purified for all whole placental, labyrinthine, and junctional zone samples. Samples were sent to the Beijing Genomics Institute for bisulfite conversion and sequencing.
BGI library construction protocols for WGBS samples

value: placental labyrinthine zone

tag: Sex


title: Mouse_M2255-F8-M15-JZ

source_name: Placental junctional zone

value: placental junctional zone


title: J-35 ESC

description: E3.5 ESC (XY)


title: J-34 ESC

description: E3.5 ESC (XY)


title: J-29 EGC

description: E11.5 EGC (XX)

source_name: EGC

extract_protocol:
generation protocol: Genital ridges containing primordial germ cells (PGCs) were retrieved from E11.5/12.5 mouse embryos. PGCs were collected from the genital ridges by trypsinization and centrifugation. Subsequently, isolated PGCs were cultured on stem cell factor (SCF)-secreting MEF feeder containing 2i-LIF medium (Ying et al., 2008) supplemeted with 60 ng/ml exogenous SCF and 10 ng/ml bFGF.  The cells were cultured for 3 days without changing medium. After that, the cells were cultured for additional 7-11 days and fed every other day with fresh 2i-LIF medium until picking. Outgrowth from the culture was picked, trypsinized, and re-plated onto MEF feeders containing KO DMEM (Invitrogen) supplemented with 15% FBS (Hyclone), 1mM L- glutamine, 100 uM MEM non-essential amino acids, and 0.1 mM beta-mercaptoethanol, and LIF.
Genomic DNA was collected using phenol/chloroform extraction
mRRBS libraries were prepared as previously described (Boyle et al. 2012). Briefly, genomic sequences were digested using the MspI restriction enzyme, which cuts at the sequence CCGG. Digested fragments were subjected to bisulfite treatment which converts unmethylated cytosine residues to uracil

value: XX


title: Mouse_M2255-F6-F15-LZ

value: female


title: J-27 EGC

description: E11.5 EGC (XO)

value: XO


title: J-26 EGC

description: E11.5 EGC (XX)


title: J-24 EGC

description: E11.5 EGC (XY)


title: J-25 EGC

description: E11.5 EGC (XY)


title: Col_rep1_sRNA-Seq_1722

description: small RNA

value: WT


title: Mouse_M2253-F3-F15-LZ


title: Mouse_M2253-F3-F15-JZ


title: EL16.7

description: M. Musculus x M. Castaneous hybrid F1 ESC line (XX)

data_processing:
Sequencing reads were trimmed using timgalore, as well as NuGEN-provided script for diversity trimming and filtering.
Alignment: bisulfite-converted reads were aligned to a the mm9 genome using Bsmap version 2.89 with the following flags: -v 0.05 -s 16 -w 100 -S 1 -p 8 -u
Methylation calling: CpGs in the reference sequence were compared to the sequence in the aligned read. If bisulfite conversion (signifying an unmethylated cytosine) was detected, the read added to the unmethylated count for that CpG, otherwise, it added to the methylated count.
Genome_build: mm9
Supplementary_files_format_and_content: Bed files contain the number of methylated and total reads for CpGs covered by RRBS with the columns: chromosome, start, end, number of reads methylated divided by number of reads seen, methylation percent/1000

organism: Mus musculus musculus x Mus musculus castaneus

growth_protocol: generation protocol: Lee and Lu, 1999

extract_protocol:
Genomic DNA was collected using phenol/chloroform extraction
RRBS libraries were prepared using a commercial kit (Ovation RRBS Methyl-Seq System, NuGen, San Carlos, CA) following the manufacturer's protocol except that we pooled 12 individually barcoded reactions after the final repair step and performed the bisulfite conversion and library amplification as a pool. Libraries were sequenced on an Illumina HiSeq2500 high-output flowcell without a PhiX spike-in using Nugen's custom sequencing primer for read 1 (36 bases) and standard Illumina sequencing primers to read the 8-base sample barcodes.


title: Mouse_M2255-F6-F15-JZ


title: J-20 EGC

description: E12.5 EGC (XX)


title: J-17 EGC

description: E12.5 EGC (XY)


title: Mouse_M1054-F7-M18-LZ


title: siRNA_ccr4Δdcr1Δ

city: Munich

first: Mario

last: Halic

department: Biochemistry - Gene Center

country: Germany

institute: Ludwig-Maximilians-Universität

data_processing:
base calling with RTA1.18.64
Sequenced reads were trimmed for the adaptor sequence, then mapped to the S.pombe genome with Novoalign (http://www.novocraft.com) randomly assigned.
Reads mapping with two or fewer mismatches were retained.
Enrichments were calculated with our house Perl scripts
Normalisation to reads per million for siRNA and ChIP experiments, normalisation to reads mapping to protein coding genes for RNAseq /RIPseq
Genome_build: Schizosaccharomyces_pombe.ASM294v1.18
Supplementary_files_format_and_content: can be viewed with IGV browser: http://www.broad.mit.edu/igv

organism: Schizosaccharomyces pombe

growth_protocol: cells were grown in liquid, rich YES medium

extract_protocol:
RNA libraries were prepared with NEBnext Ultra Directional RNA Library Prep Kit for Illumina (NEB); DNA library construction with NEBNext Ultra II DNA Library Prep Kit for Illumina kit (NEB). siRNA library: ligation of 3’ adapter (5'-App CTG TAG GCA CCA TCA AT/ddC/-3') and 5’ adapter (5'-GUU CAG AGU UCU ACA GUC CGA CGA UC-3'), reverse transcription, PCR of cDNA with Illumina P5 5' primer and barcoded llumina P7 3' primer.
Endogenous 3xFLAG-tagged Ago1-bound siRNA were purified by protein affinity purification and subsequent size selection on an 18% acrylamide gel. 2 pmol of a preadenylated 3' adaptor oligonucleotide (miRNA Cloning Linker-1 from IDT, 5'-App CTG TAG GCA CCA TCA AT/ddC/-3') were ligated in a 10 µl reaction with 5 U T4 RNA ligase (TaKaRa), ligation buffer without ATP and 5 U RNasin (Promega) at 20°C for 2 hours. The 3' ligated products were purified on an 18% acrylamide urea gel with subsequent phenol-chloroform purification and ethanol purification. The 5' adaptor ligation was performed in a 10 µl reaction with 2 pmol 5' adaptor oligonucleotide (5'-GUU CAG AGU UCU ACA GUC CGA CGA UC-3'), 5 U RNasin (Promega), 0.06 µg BSA, 5 U T4 RNA ligase (Thermo Scientific) and 1x ligation buffer with ATP (Thermo Scientific) for 2 h at 20°C. The ligated products were gel purified and reverse transcribed with 10 pmol primer (RT primer: 5'- GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC GAT TGA TGG TGC CTA CAG-3') and the SuperScript III First Strand Synthesis System (Thermo Scientific). The cDNA was PCR-amplified with Q5 High-Fidelity 2x Master Mix (NEB) for 14-20 cycles using the Illumina P5 5' primer (5' -AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC G -3') and the Illumina P7 3' primer with inserted barcode (5'-CAA GCA GAA GAC GGC ATA CGA GAT XXXXXX GTG ACT GGA GTT CAG ACG TG -3').

tag: antibody for ip

value: anti-FLAG

tag: strain number

tag: target molecule

value: siRNA


title: H3RIP_caf1Δdcr1Δ 2

extract_protocol:
RNA libraries were prepared with NEBnext Ultra Directional RNA Library Prep Kit for Illumina (NEB); DNA library construction with NEBNext Ultra II DNA Library Prep Kit for Illumina kit (NEB). siRNA library: ligation of 3’ adapter (5'-App CTG TAG GCA CCA TCA AT/ddC/-3') and 5’ adapter (5'-GUU CAG AGU UCU ACA GUC CGA CGA UC-3'), reverse transcription, PCR of cDNA with Illumina P5 5' primer and barcoded llumina P7 3' primer.
Immunoprecipitation of crosslinked (1% formaldehyde, 15 min) cells, decrosslinking, protein degradation and DNA depletion.

value: Anti-H3:ab1791, abcam

value: H3 bound RNA


title: siRNA_taz1Δdcr1Δ


title: Mouse_M2253-F2-M15-LZ

value: male


title: siRNA_ccr4Δ


title: H3RIP_wild_type 3

source_name: wild type


title: DRIP_caf1Ddcr1D_+RNaseH 2

data_processing:
Library strategy: DRIP-seq
base calling with RTA1.18.64
Sequenced reads were trimmed for the adaptor sequence, then mapped to the S.pombe genome with Novoalign (http://www.novocraft.com) randomly assigned.
Reads mapping with two or fewer mismatches were retained.
Enrichments were calculated with our house Perl scripts
Normalisation to reads per million for siRNA and ChIP experiments, normalisation to reads mapping to protein coding genes for RNAseq /RIPseq
Genome_build: Schizosaccharomyces_pombe.ASM294v1.18
Supplementary_files_format_and_content: can be viewed with IGV browser: http://www.broad.mit.edu/igv

extract_protocol:
RNA libraries were prepared with NEBnext Ultra Directional RNA Library Prep Kit for Illumina (NEB); DNA library construction with NEBNext Ultra II DNA Library Prep Kit for Illumina kit (NEB). siRNA library: ligation of 3’ adapter (5'-App CTG TAG GCA CCA TCA AT/ddC/-3') and 5’ adapter (5'-GUU CAG AGU UCU ACA GUC CGA CGA UC-3'), reverse transcription, PCR of cDNA with Illumina P5 5' primer and barcoded llumina P7 3' primer.
DNA purification, S1 nuclease digest, RNaseH treatment ON, immunoprecipitation.

value: S9.6, Kerafast

value: background


title: DRIP_caf1Ddcr1D_-RNaseH 2

extract_protocol:
RNA libraries were prepared with NEBnext Ultra Directional RNA Library Prep Kit for Illumina (NEB); DNA library construction with NEBNext Ultra II DNA Library Prep Kit for Illumina kit (NEB). siRNA library: ligation of 3’ adapter (5'-App CTG TAG GCA CCA TCA AT/ddC/-3') and 5’ adapter (5'-GUU CAG AGU UCU ACA GUC CGA CGA UC-3'), reverse transcription, PCR of cDNA with Illumina P5 5' primer and barcoded llumina P7 3' primer.
DNA purification, S1 nuclease digest, no RNaseH treatment ON, immunoprecipitation.

value: DNA:RNA hybrids DNA


title: Mouse_M1054-F3-F18-LZ


title: DRIP_wild_type_-RNaseH 2

extract_protocol:
RNA libraries were prepared with NEBnext Ultra Directional RNA Library Prep Kit for Illumina (NEB); DNA library construction with NEBNext Ultra II DNA Library Prep Kit for Illumina kit (NEB). siRNA library: ligation of 3’ adapter (5'-App CTG TAG GCA CCA TCA AT/ddC/-3') and 5’ adapter (5'-GUU CAG AGU UCU ACA GUC CGA CGA UC-3'), reverse transcription, PCR of cDNA with Illumina P5 5' primer and barcoded llumina P7 3' primer.
DNA purification, S1 nuclease digest, no RNaseH treatment, immunoprecipitation.


title: DRIP_wild_type_+RNaseH 2


title: 520A_BK

source_name: Control - biological replicate 1

value: human coronary artery smooth muscle cells (HCASMC)

value: control


title: Mouse_M1054-F3-F18-JZ


title: DRIP_caf1Ddcr1D_-RNaseH 1


title: J-23 EGC

description: E11.5 EGC (XY)

value: XY


title: Mouse_M2253-F2-M15-JZ


title: siRNA_taz1Δ


title: Mouse_M1053-F7-F18-LZ

value: placental labyrinthine zone


title: DRIP_wild_type_+RNaseH 1


title: Mouse_M1053-F7-F18-JZ

value: placental junctional zone


title: DRIP_caf1Ddcr1D_+RNaseH 1


title: H3K9me2_ChIP_caf1Δtaz1Δ

extract_protocol:
RNA libraries were prepared with NEBnext Ultra Directional RNA Library Prep Kit for Illumina (NEB); DNA library construction with NEBNext Ultra II DNA Library Prep Kit for Illumina kit (NEB). siRNA library: ligation of 3’ adapter (5'-App CTG TAG GCA CCA TCA AT/ddC/-3') and 5’ adapter (5'-GUU CAG AGU UCU ACA GUC CGA CGA UC-3'), reverse transcription, PCR of cDNA with Illumina P5 5' primer and barcoded llumina P7 3' primer.
Immunoprecipitation of crosslinked (1% formaldehyde, 15 min) cells, decrosslinking, protein degradation and RNA degradation.

value: H3K9me2:ab1220 abcam

value: H3K9me2 bound DNA


title: DRIP_wild_type_-RNaseH 1


title: H3K9me2_ChIP_taz1Δ


title: H3K9me2_ChIP_caf1Δdcr1Δ


title: H3K9me2_ChIP_caf1Δ


title: Mouse_M1054-F7-M18-JZ


title: H3K9me2_ChIP_wild_type


title: Mouse_M1053-F3-M18-LZ


title: Mouse_M1053-F3-M18-JZ


title: H3RIP_dcr1Δ 1


title: Mouse_M1049-F6-F18-JZ

value: female


title: H3RIP_caf1Δ 2


title: Mouse_M1049-F5-M18-LZ


title: H3RIP_mock

extract_protocol:
RNA libraries were prepared with NEBnext Ultra Directional RNA Library Prep Kit for Illumina (NEB); DNA library construction with NEBNext Ultra II DNA Library Prep Kit for Illumina kit (NEB). siRNA library: ligation of 3’ adapter (5'-App CTG TAG GCA CCA TCA AT/ddC/-3') and 5’ adapter (5'-GUU CAG AGU UCU ACA GUC CGA CGA UC-3'), reverse transcription, PCR of cDNA with Illumina P5 5' primer and barcoded llumina P7 3' primer.
Immunoprecipitation of crosslinked (1% formaldehyde, 15 min) cells, decrosslinking, protein degradation and DNA depletion. For mock: beads without antibody were used instead of IP.

value: background RNA


title: Mouse_M1049-F6-F18-LZ


title: H3RIP_wild_type 2


title: H3RIP_caf1Δ 1


title: Mouse_M1049-F5-M18-JZ


title: H3RIP_wild_type 1


title: Mouse_M1043-F5-F15-JZ


title: H3RIP_caf1Δdcr1Δ 1


title: H3ChIP_caf1Δdcr1Δ

value: H3 bound DNA


title: Mouse_M1043-F3-M15-LZ


title: H3ChIP_wild_type


title: Mouse_M1043-F3-M15-JZ


title: H3RIP_dcr1Δ 2


title: Caf1RIP_chr_untagged 2

extract_protocol:
RNA libraries were prepared with NEBnext Ultra Directional RNA Library Prep Kit for Illumina (NEB); DNA library construction with NEBNext Ultra II DNA Library Prep Kit for Illumina kit (NEB). siRNA library: ligation of 3’ adapter (5'-App CTG TAG GCA CCA TCA AT/ddC/-3') and 5’ adapter (5'-GUU CAG AGU UCU ACA GUC CGA CGA UC-3'), reverse transcription, PCR of cDNA with Illumina P5 5' primer and barcoded llumina P7 3' primer.
Crosslinked cells with 1% Formaldehyde for 15 minutes used. Caf1-associated RNA IP with chromatin fractionation: before sonication, the sample was centrifuged for 20 min at 21 000 x g at 4°C. The supernatant was taken as “soluble fraction”, the pellet was washed twice with lysis buffer, then resuspended in lysis buffer, which formed the “chromatin fraction”. Subsequent immunoprecipitation, decrosslinking, protein degradation and DNA depletion.

value: anti-FLAG M2-Magnetic Beads (Sigma-Aldrich)


title: Caf1RIP_chr_clr4Δ 2

source_name: Clr4Δ, 3x FLAG-Caf1

value: Caf1 bound RNA


title: DOT2381P5

description: Mice were housed under a 14:10 hour light cycle with food and water ad libidum. For all crosses, a single stud and dam were housed together for four and a half days, and then split. 10 days later, females were euthanized, uteri were collected and the number of viable conceptuses counted. The embryos and placenta were dissected and weighed. Two placentae were sampled from a single litter in each cross direction and snap frozen in liquid nitrogen. For M. domesticus, reciprocal crosses between strains BIK (originally isolated from Kefar Galim, Israel) and DOT (Tahiti) were generated; for M. musculus, MPB (Bialowieza, Poland) and MBS (Sokolovo, Bulgaria) were crossed; and for M. spretus, STF (Fondouk Djedid, Tunisia) and SFM (Montpellier, France) were mated. Placenta are named according to their maternal strain.

source_name: Whole placenta

value: whole placenta

value: DOTxBIK


title: DOT2381P2


title: Caf1RIP_chr_wild_type 2

source_name: wild type, 3x FLAG-Caf1


title: Caf1RIP_sol_clr4Δ 2


title: Caf1RIP_sol_wild_type 2


title: Caf1RIP_sol_untagged 2


title: 2131271_TimePoint3_BoneMarrow

city: Atlanta

first: Mary

last: Galinski

state: GA

address: 954 Gatewood Road

department: Vaccine Center at Yerkes

institute: Emory University

data_processing:
Bases were called with Illumina RTA (Real-Time Analysis, v1.13.48) with default parameters.  FASTQC (v0.10.1) was used to assess data quality, but the data were not filtered at this stage.
To quantify gene expression,  RNA-Seq reads were mapped to the listed assembly and annotation using Tophat2 (Trapnell et al, 2013).  Default options were used with the exception that the command --library-type fr-secondstrand was used since reads were generated using a stranded library preparation method from Illumina.  This allowed differentiation between sense and antisense transcripts.  Only reads that map to a single location in the genome were included, to ensure high-confidence mapping.
Several quality control steps were used to verify the reliability of the data: linear correlation of estimated abundance of ERCC spike-in controls with known concentration; confirmation of 99.9% strand-specificity of the controls; less than 0.1% control fusion transcripts; and absence of 3’ bias in the controls was confirmed with RSeqC software (https://code.google.com/p/rseqc).  Transcript abundance levels were inferred using HTSeq v0.5.4 (http://www-huber.embl.de/users/anders/HTSeq/doc/).  HTSeq takes the short-read mapping file (bam) from tophat2 and the gene annotation file which contains the locations of all annotated genes.  Since some libraries were sequenced more deeply than others, the libraries were normalized before determining differential gene expression using the gene level expression files with the default parameters of DESeq v1.10.1 (http://www.bioconductor.org/packages/release/bioc/html/DESeq.html).
Genome_build: RNA-Seq reads were mapped to both a host and parasite genome.  Host: An early version of a new  assembly (as of 5/2014) of the rhesus macaque (MacaM assembly, v4.0, created by Aleksey Zimin at the University of Maryland, Rob Norgren at the University of Nebraska Medical Center and their colleagues.  The MacaM assembly has been deposited in GenBank under accession  PRJNA214746 ID: 214746. Parasite: PlasmoDB version 9.3 of the Plasmodium cynomolgi B strain genome assembly was used. The assembly has been deposited in GenBank under the accession PRJDA49901 ID: 49901.
Supplementary_files_format_and_content: Excel files contain normalized transcript abundances at the gene level, for each individual.  Abundances are further classified by experimental Time Point (1-7), and Specimen Type (Bone Marrow).
Supplementary_files_format_and_content: Gene Data Column headers are defined as follows:
Supplementary_files_format_and_content: 'gene_name':  Identifiers of all Genes in the reference annotation.
Supplementary_files_format_and_content: 'gene_symbol': Symbols of all Genes in the reference annotation.
Supplementary_files_format_and_content: 'Sample ID / Raw File 1 / Raw File 2 /Normalized Read Counts':  Sample ID, Raw sequence file names for the sample, and Library size normalized and Log2 transformed read counts of all genes, from the Specimen Type, Individual ID, and Time Point listed directly below.
Supplementary_files_format_and_content: Notes:
Supplementary_files_format_and_content: There will be one read count column per specimen per NHP  (Non-Human-Primate) per Time Point. So, 1 * 5 * 7 = 35 columns with read counts.  Note that one NHP was euthanized during the experiment, so the total number of samples is 31.
Supplementary_files_format_and_content: 0 as value for read counts of some genes Overlapping genes (sharing exons) were "collapsed" into a single gene for the purposes of RNA-Seq read assignments. So, the read count at such a locus is representative of the cumulative expression of all the genes at that locus. BUT, the entire read count is assigned to only one of the genes and the others in the locus are assigned 0.

organism:
Macaca mulatta
Plasmodium cynomolgi strain B

source_name: Bone Marrow

growth_protocol: Animals approved for use were moved into experimental housing 10 days prior to the start of the experiment.

extract_protocol:
Bone marrow (1ml) was collected into 1.5 ml tubes with EDTA, and the mononuclear cells were purified by density gradient centrifugation on Lymphoprep (Stem Cell Technologies) solution and preserved in RLT buffer (Qiagen) to stabilize mRNA.  Whole blood (3 ml) was collected in Tempus tubes (Applied Biosystems) that also preserve mRNA; these samples include erythrocytes, platelets and granulocytes in addition to mononuclear lymphocytes.  RNA was extracted from the BM samples using Qiagen RNEasy Mini-Plus kits following the manufacturer-recommended procedures, and from PB samples using Tempus-Spin RNA isolation kits. The quality of all RNA samples was confirmed using a Bioanalyzer, with an RNA Integrity Number (RIN) greater than 8 recorded for all samples.
Approximately 1 μg of total RNA per sample was converted to double-stranded cDNA using poly-A beads to enrich for mRNA, and Illumina TruSeq Stranded mRNA Sample Prep kits to generate strand-specific libraries.   As a quality control, 96 spike-in RNAs of known concentration and GC proportions (ERCC Spike-In Control, Life Technologies) were added to constitute approximately 1% of the total RNA for each library.  Adapters were ligated to facilitate 3-plex sequencing on an Illumina HiSeq2000 at the Yerkes Genomics Core, aiming for 80 million paired-end 100 base pair (bp) reads per library.

treatment_protocol: During the 100-day experiment, artemether was delivered on days 27 and 53 (corresponding to time points 3 and 4), for blood-stage treatment.  Chloroquine and primaquine were administered at the end of the study to treat liver- and blood-stages.

tag: time point

value: Male

tag: mahpic non human primate individual id

tag: infected with

value: Plasmodium cynomolgi strain B


title: BIK2380P2

value: BIKxDOT


title: 2130100_TimePoint7_BoneMarrow


title: BIK2380P1


title: 2130108_TimePoint7_BoneMarrow


title: 2130103_TimePoint7_BoneMarrow


title: Caf1RIP_chr_wild_type 1


title: Caf1RIP_sol_clr4Δ 1


title: Caf1RIP_chr_untagged 1


title: 2130111_TimePoint7_BoneMarrow


title: 2131274_TimePoint6_BoneMarrow


title: 2131276_TimePoint6_BoneMarrow


title: Caf1ChIP_clr4Δ 2

value: Caf1 bound DNA


title: 2131267_TimePoint6_BoneMarrow


title: Caf1ChIP_wild_type 2


title: 2131279_TimePoint5_BoneMarrow


title: Caf1RIP_chr_clr4Δ 1


title: Caf1ChIP_ChIP_clr4Δ 1


title: Caf1_exoChIP_wild_type 2


title: Caf1ChIP_wild_type 1


title: PolII_ChIP_wild_type

value: anti-RNA polymerase II CTD repeat YSPTSPS antibody [8WG16]:ab817, abcam

value: RNA-PolII bound DNA


title: 2130099_TimePoint6_BoneMarrow


title: 2130113_TimePoint5_BoneMarrow


title: PolII_RIP_mock 2


title: 2131273_TimePoint5_BoneMarrow


title: 2130101_TimePoint4_BoneMarrow


title: Caf1RIP_sol_wild_type 1


title: Caf1_exoChIP_wild_type 1


title: 2130104_TimePoint4_BoneMarrow


title: PolII_RIP_caf1*ccr4*dcr1Δ

value: RNA-PolII bound RNA


title: Caf1RIP_sol_untagged 1


title: 2130102_TimePoint3_BoneMarrow


title: PolII_RIP_caf1*ccr4*dcr1Δ 2


title: 2130105_TimePoint5_BoneMarrow


title: PolII_RIP_dcr1Δ 2


title: PolII_RIP_caf1Δdcr1Δ 2


title: 2130106_TimePoint3_BoneMarrow


title: 2130110_TimePoint3_BoneMarrow


title: 2130109_TimePoint4_BoneMarrow


title: 2131266_TimePoint3_BoneMarrow


title: PolII_RIP_wild_type 2


title: 2131280_TimePoint2_BoneMarrow


title: Caf1_exoChIP_untagged 1

value: background DNA


title: PolII_RIP_mock 1


title: 2131277_TimePoint2_BoneMarrow


title: 2130112_TimePoint4_BoneMarrow


title: PolII_RIP_caf1Δdcr1Δ 1


title: 2131270_TimePoint2_BoneMarrow


title: 2130107_TimePoint2_BoneMarrow


title: PolII_RIP_wild_type 1


title: p(A)RNA_dcr1Δ

molecule: polyA RNA

extract_protocol:
RNA libraries were prepared with NEBnext Ultra Directional RNA Library Prep Kit for Illumina (NEB); DNA library construction with NEBNext Ultra II DNA Library Prep Kit for Illumina kit (NEB). siRNA library: ligation of 3’ adapter (5'-App CTG TAG GCA CCA TCA AT/ddC/-3') and 5’ adapter (5'-GUU CAG AGU UCU ACA GUC CGA CGA UC-3'), reverse transcription, PCR of cDNA with Illumina P5 5' primer and barcoded llumina P7 3' primer.
Total RNA was isolated applying the hot phenol method. The extracted nucleic acids were treated with DNAse I for 2 h at 37°C. DNAse was removed by a second phenol-chloroform-isoamylalcohol extraction and ethanol precipitation. Poly-adenylated RNA was extracted from total RNA with oligo d(T)25 magnetic beads (NEB)

value: p(A) RNA


title: 2131268_TimePoint2_BoneMarrow


title: p(A)RNA_caf1Δdcr1Δ


title: 2131275_TimePoint1_BoneMarrow


title: p(A)RNA_caf1Δ


title: RNA_clr4Δ

extract_protocol:
RNA libraries were prepared with NEBnext Ultra Directional RNA Library Prep Kit for Illumina (NEB); DNA library construction with NEBNext Ultra II DNA Library Prep Kit for Illumina kit (NEB). siRNA library: ligation of 3’ adapter (5'-App CTG TAG GCA CCA TCA AT/ddC/-3') and 5’ adapter (5'-GUU CAG AGU UCU ACA GUC CGA CGA UC-3'), reverse transcription, PCR of cDNA with Illumina P5 5' primer and barcoded llumina P7 3' primer.
Total RNA was isolated applying the hot phenol method. The extracted nucleic acids were treated with DNAse I for 2 h at 37°C. DNAse was removed by a second phenol-chloroform-isoamylalcohol extraction and ethanol precipitation. 1 µg total RNA was degraded with Terminator nuclease (Epicentre) in buffer A at 30°C for 2 h.

value: total RNA


title: 2131272_TimePoint1_BoneMarrow


title: Bmal1_control_CT0_rep2

extract_protocol:
Livers of all mice were quickly dissected and snap-frozen in liquid nitrogen and stored at −80 °C. Total RNA was extracted from each liver sample using Trizol.
The RNA samples were converted into Illumina sequencing libraries by using Illumina TruSeq RNA Sample Prep Kit v2 as per manufacturer’s protocol.

value: liver

value: 8 weeks


title: 2131278_TimePoint1_BoneMarrow


title: p(A)RNA_wild_type


title: MPB1574P2

organism: Mus musculus musculus

value: MPBxMBS

value: female


title: RNA_caf1Δdcr1Δ


title: MPB1574P1


title: RNA_wild_type


title: K3D, UV, 72h/30 mJ/cm2 (time/dose)_ChIP-seq

status: Public on Apr 11 2017

city: New York

first: Liang

last: Liu

state: NY

address: 1150 St. Nicholas Avenue

institute: Columbia University

data_processing:
For Chip-Seq, reads generated by Illumina sequencing were mapped to the NCBI/build37.2 genome using the BWA algorithm.  ChIP-Seq tags were extended at their 3’-ends to 200bp. The genome was divided into 32-nt bins to estimate the density of extended tags in each bin along the genome. The model-based analysis of ChIP-Seq (MACS) algorithm was used for peak calling to identify chromatin regions with H3K27Ac tags compared to the input control. Genes were annotated if peaks were within 10 kb of start or end of a nearby gene.
genome build: NCBI/build37.2
processed data files format and content: bigwig files contain genome wide chip-seq signals for a histone mark (H3K27Ac) that could be visualized in UCSC or IGV.

source_name: neonatal foreskin

growth_protocol: Primary human keratinocytes were isolated from neonatal foreskins and were cultured in 154CF medium supplemented with human keratinocyte growth supplement (Life Technologies, Grand Island, NY)

extract_protocol:
Cells were fixed with 1% (final concentration) freshly prepared formaldehyde at 37°C for 15 min. The fixation was stopped by incubation in 125 mM (final concentration) glycine solution for 5 min at RT. Cells were washed with PBS containing proteinase inhibitor cocktail (1x final concentration), scraped and collected as cell pellets in Eppendorf tubes.
ChIP assays and sequencing were performed by Active Motif using the H3K27ac HistonePath™ Kit following standard protocols (Active Motif, Carlsbad, CA)

treatment_protocol: Cells were irradiated in approximately 0.5 ml PBS in each 10 cm dish with 30 mJ/cm2 UV. Control and irradiated cells were collected at 4 or 72 hours after UV radiation.

value: neonatal foreskin

value: Cultured primary keratinocytes

tag: treatment

value: UVR

tag: uv dose (time/dose)

tag: chip antibody

value: H3K27ac HistonePath™ Kit (Active Motif)


title: K4H, UV, 4h/30 mJ/cm2 (time/dose)_ChIP-seq

tag: tissue


title: K0 Control_ChIP-seq

value: no UVR


title: MBS1852P8

value: whole placenta

value: MBSxMPB


title: IgG_TH17(23)_ChIPSeq

city: Onna-son,Kunigami-gun

first: Hiroki

last: Ishikawa

address: 1919-1 Tancha

country: Japan

institute: Okinawa Institute of Science and Technology Graduate University

data_processing:
Basecalls performed using RTA2
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie1.1.2 with optional parameters “-a --strata --best -m 1 -v 2”
peaks were called using Homer v4.8 with the default setting
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated using Homer v4.8

source_name: in vitro-generated TH17 cells

growth_protocol: CD4+ T cells from single cell suspensions of murine spleens and lymph nodes were enriched using a MACS magnetic cell sorting system with anti-CD4 microbeads (Miltenyi). Then naive CD4+ T cells (CD4+CD25-CD62LhiCD44lo) were sorted by FACS AriaII or AriaIII (BD). Cells were activated with plate bound anti-CD3 antibody (Biolegend) and soluble anti-CD28 antibody (Biolegend) in IMDM media (Invitrogen) supplemented with 10% Fetal calf serum (FCS) (Invitrogen) containing the following cytokines and antibodies: IL-6 (20 ng/mL) and TGF-β (3 ng/mL) for TH17(β); IL-6 (20 ng/mL), IL-1β (20 ng/mL) and IL-23 (40 ng/mL) for TH17(23) differentiation.

extract_protocol:
ChIP was performed using a SimpleChIP Plus Enzymatic Chromatin IP Kit (Cell signaling) with some modifications. Briefly, activated T cells (10^6/ChIP-Seq or 1-3 x 10^5/ChIP-PCR) were cross-linked in culture medium containing 1% formaldehyde at room temperature for 10 min, and the reaction was stopped by adding glycine solution. THen cells were lysed, and nuclei were collected and treated with micrococcal nuclease (0.0125 μl/ml) for 20 min at 37°C. After stopping the reaction by adding 0.05M EGTA, samples were sonicated with several pulses to disrupt nuclear membranes, and then the supernatant containing chromatin was collected after centrifugation. Chromatin solutions were incubated with 2 μg of antibodies overnight at  4°C with rotation, followed by incubation with Protein G magnetic beads for 2 hr at 4°C. Beads were washed, and the chromatin was eluted. Cross-links were reverted according to kit instructions.
Libraries were prepared using KAPA Hyper Prep Kit (KAPA Biosystems) protocols for blunt-ending, polyA extension, and adapter ligation. Post ligation clean-up by Agencort AMPure XP (Beckman Coulter) was performed at a 1.8X DNA ratio to purify ligated DNA, which was then PCR-amplified and purified using AMPure XP at a 1.2X DNA ratio to remove excess adapter-dimer and to preserve small fragments. Size selection was performed with a 2% agarose gel cassette of Blue Pippin (Sage Science) for target insert size between 30 and 180bp. Library quantification was performed by droplet digital PCR (BioRad). All libraries were pooled and loaded on to cBot (50 µL of 200 pM) for cluster generation, and then sequenced on an Illumina HiSeq4000 at a target sequencing depth of 10 million uniquely aligned reads.

value: JUNBFl/Fl

value: IgG


title: 2130098_TimePoint1_BoneMarrow

tag: gender

value: Male

value: Plasmodium cynomolgi strain B


title: IgG_TH17(beta)_ChIPSeq

tag: genotype


title: BATF_TH17(beta)_ChIPSeq

tag: cell type

value: BATF


title: MBS1852P5

extract_protocol:
Using a Qiagen DNA extraction kit, DNA was extracted and purified for all whole placental, labyrinthine, and junctional zone samples. Samples were sent to the Beijing Genomics Institute for bisulfite conversion and sequencing.
BGI library construction protocols for WGBS samples

tag: strain


title: IRF4_TH17(23)_ChIPSeq


title: JunB_TH17(23)_ChIPSeq

value: JUNB


title: IRF4_TH17(beta)_ChIPSeq


title: Promoter 4 Biological rep 2 Expression

city: Scarborough

first: Guillaume

middle: J

last: Filion

state: Ontario

address: 1265 Military Trail

department: Biological Sciences

country: Canada

institute: UTSC

description: Promoter 4

data_processing:
Mapping.  Reads from the inverse PCR were trimmed in order to isolate the barcode and the sequence at the insertion point. In the forward read, barcodes were identified as the nucleotides preceding the NlaIII site (CATG), and in the reverse read, the Drosophila sequence flanking the transposon was identified as the nucleotides following the plasmid sequence TGTATGTAAACTTCCGACTTCAACTGTA (allowing up to 5 errors). After trimming, reverse reads were mapped to the genome of Drosophila melanogaster (dm3/Release5) with GEM version 1.376 (beta) with options -m3 --unique-mapping, giving a candidate insertion point for the associated barcode on the forward read. Barcode sequences were clustered using Starcode (Bioinformatics 2015 31:1913-9. doi: 10.1093/bioinformatics/btv053) with default parameters and each sequence was replaced by the centroid of the cluster. Since the same barcodes may be associated to different insertion points, we used a voting scheme to associate barcodes to a unique location. We kept locations representing over 10% of the read counts for a given barcode. If all those locations were within a 10 bp genomic window, the most frequent location was attributed as the unique location of the barcode. Otherwise, the barcode was discarded for being duplicated or unmapped.    Reporter expression.  Reads from the RT-PCR and genomic PCR, barcodes were identified with the NlaIII site and clustered with Starcode as above. Barcodes were then matched with their location (or discarded if unmatched). Spikes were identified as reads containing the sequence CATGATTACCCTGTTATC (allowing up to 2 errors) and the corresponding barcodes were extracted and clustered as above. The mean number of read counts per spike was computed and half of this value was added to the read count of each barcode (i.e. we added a pseudo count corresponding to half a molecule). Corrected values were normalized to the total read count of the experiment and summed over replicates. The normalized expression of a reporter was defined as the log2 ratio of the RT-PCR score and genomic PCR score computed above.
Genome_build: dm3/Release5
Supplementary_files_format_and_content: text file with barcode, chr, strand,  position,  normalized expression,   promoter,   rep

organism: Drosophila melanogaster

growth_protocol: Kc167 cells were maintained in Schneider’s Drosophila medium (Gibco). Transfections were performed by electroporating 20 million cells with 20 ug of plasmid DNA and 10 ug barcoded pT2-promoter-GFP (plasmid libraries at 1 ug/ul with a complexity higher than 10E6), 5 ug pC-sleeping beauty (Addgene plasmid #65487) and 5 ug LNGFR expression plasmid at 250 V and 1000 uF. The cells were counted, pelleted at 300 g for 5 minutes, resuspended and electroporated in 750 uL of  medium in Biorad cuvettes (0.4 cm) in a GenePulser II Electroporation system (Biorad). Immediately after electroporation 700 ul of the electroporated cell suspension were transferred to 25 cm2 flasks containing 5 mL of fresh medium, leaving the top layer of dead cells that forms in the cuvette. 24 hours after electroporation the expression of the Sleeping Beauty 100X transposase and of LNGFR were induced by two heat shocks at 37 °C of two hours each, with at least four hours recovery between them. The next day, two more heat shocks were given in the same conditions. At day three after electroporation, LNGFR positive cells were selected using MACSelect LNGFR micro beads (Miltenyi biotech) and pools of 10.000, 20.000 or 50.000 cells were plated in 25 cm2 flasks containing 5 mL and grown for 2 weeks transferring to a 75 cm2 when the culture reached a density of 10 million cells/mL.

extract_protocol:
Reporter expression: RNA was extracted using Trizol (Life Technologies). 100 ug of total RNA were taken for polyA+ selection (Oligotex mRNA mini Kit Qiagen). Reverse transcription (ThermoScript, Life Technologies) was performed on 2 ug mRNA using a primer (ACACTCTTTCCCTACACGACGCTCTTCCGATCT) specific of the barcoded reporter transcripts. In order to add the Illumina adaptors and indexes needed for single-end sequencing, 2 ul of cDNA or 500 ug of genomic DNA (normalization control) were amplified by PCR (98 °C for 1 min // 98 °C for 15 sec / 68 °C for 30 sec / 72 °C for 1 min // – 25 cycles / 72 °C for 3 min) with primers AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT and CAAGCAGAAGACGGCATACGAGAT [index] GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGC. Approximately 5000 molecules of the oligonucleotide GCACGCCTTCAAGACCCCCATCGCCTTCGCCAGATCTCGAGCTTAGGGATAACAGGGTAATCATGNNNNNNNNNNNNNNNNNNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT were added to the template mixture of the PCR above. This oligonucleotide is a target for the primer pair above, and it contains a barcode of 20 nucleotides making every molecule unique. This allows to infer the read count corresponding to a single molecule of template.
High-Seq Single-end sequencing 1 * 50bp

tag: cell line


title: JunB_TH17(beta)_ChIPSeq


title: Promoter 4 Biological rep 2 Normalization

description: Promoter 4

data_processing:
Library strategy: DNA-Seq
Mapping.  Reads from the inverse PCR were trimmed in order to isolate the barcode and the sequence at the insertion point. In the forward read, barcodes were identified as the nucleotides preceding the NlaIII site (CATG), and in the reverse read, the Drosophila sequence flanking the transposon was identified as the nucleotides following the plasmid sequence TGTATGTAAACTTCCGACTTCAACTGTA (allowing up to 5 errors). After trimming, reverse reads were mapped to the genome of Drosophila melanogaster (dm3/Release5) with GEM version 1.376 (beta) with options -m3 --unique-mapping, giving a candidate insertion point for the associated barcode on the forward read. Barcode sequences were clustered using Starcode (Bioinformatics 2015 31:1913-9. doi: 10.1093/bioinformatics/btv053) with default parameters and each sequence was replaced by the centroid of the cluster. Since the same barcodes may be associated to different insertion points, we used a voting scheme to associate barcodes to a unique location. We kept locations representing over 10% of the read counts for a given barcode. If all those locations were within a 10 bp genomic window, the most frequent location was attributed as the unique location of the barcode. Otherwise, the barcode was discarded for being duplicated or unmapped.    Reporter expression.  Reads from the RT-PCR and genomic PCR, barcodes were identified with the NlaIII site and clustered with Starcode as above. Barcodes were then matched with their location (or discarded if unmatched). Spikes were identified as reads containing the sequence CATGATTACCCTGTTATC (allowing up to 2 errors) and the corresponding barcodes were extracted and clustered as above. The mean number of read counts per spike was computed and half of this value was added to the read count of each barcode (i.e. we added a pseudo count corresponding to half a molecule). Corrected values were normalized to the total read count of the experiment and summed over replicates. The normalized expression of a reporter was defined as the log2 ratio of the RT-PCR score and genomic PCR score computed above.
Genome_build: dm3/Release5
Supplementary_files_format_and_content: text file with barcode, chr, strand,  position,  normalized expression,   promoter,   rep

extract_protocol:
Inverse PCR: The genomic DNA from Kc167 cells was isolated with DNeasy kit (Qiagen) and 3 ug were digested with NlaIII restriction enzyme (NEB) for 2 hours at 37 °C followed by 20 minutes heat inactivation at 65 °C. The reaction was diluted to a final volume of 1.8 mL in T4 ligase buffer (Thermoscientific) to favor self-ligation events, and ligation was carried out with 20 U T4 ligase at 16 °C overnight. After ligation samples were ethanol precipitated, pellets were redissolved in water and column purified (QIAquick PCR purification kit) and eluted in 100ul EB buffer. Non circularized templates were eliminated by 2h digestion at 37 °C with Plasmid-safe DNAse (Epicentre), the enzyme was inactivated by heating 30 minutes at 70 °C and the sample was column purified (QIAquick PCR purification kit). The backbone of the TRIP reporters contains a I-CeuI site outside the transposable cassette, taking advantage of this, non integrated plasmids were destroyed by 2 h digestion at 37 °C with I-CeuI restriction enzyme (NEB) in a total volume of 100 ul followed by 20 minutes heat inactivation at 65 °C. All enzymatic reactions were carried out in the recommended manufacturer's buffer. PCR was performed in two rounds. In the first round (98 °C for 1 min // 98 °C for 15 sec / 60 °C for 30 sec / 72 °C for 1 min // – 25 cycles / 72 °C for 3 min) gDNA flanking insertions and barcode was amplified using primers GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCTAAGGTGTATGTAAACTTCCGACTTCAACTG and AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT annealing to the transposon and to the Illumina PE1.0 sequence present in the integrated construct. In the second round (98 °C for 1 min // 98 °C for 15 sec / 60 °C for 30 sec / 72 °C for 1 min // – 10 cycles / 72 °C for 3 min) Illumina adaptors for paired-end sequencing and indexes were incorporated with primers AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT and CAAGCAGAAGACGGCATACGAGA [index]  GGTGACTGGAGTTC.
Using the same primers and conditions of the cDNA indexing PCR, another amplification was done on the gDNA in order to amplify all the barcodes present in our cell population and normalize for barcode abundance.
High-Seq Single-end sequencing 1 * 50bp


title: Promoter 4 Biological rep 1 Mapping

description: Promoter 4

extract_protocol:
Inverse PCR: The genomic DNA from Kc167 cells was isolated with DNeasy kit (Qiagen) and 3 ug were digested with NlaIII restriction enzyme (NEB) for 2 hours at 37 °C followed by 20 minutes heat inactivation at 65 °C. The reaction was diluted to a final volume of 1.8 mL in T4 ligase buffer (Thermoscientific) to favor self-ligation events, and ligation was carried out with 20 U T4 ligase at 16 °C overnight. After ligation samples were ethanol precipitated, pellets were redissolved in water and column purified (QIAquick PCR purification kit) and eluted in 100ul EB buffer. Non circularized templates were eliminated by 2h digestion at 37 °C with Plasmid-safe DNAse (Epicentre), the enzyme was inactivated by heating 30 minutes at 70 °C and the sample was column purified (QIAquick PCR purification kit). The backbone of the TRIP reporters contains a I-CeuI site outside the transposable cassette, taking advantage of this, non integrated plasmids were destroyed by 2 h digestion at 37 °C with I-CeuI restriction enzyme (NEB) in a total volume of 100 ul followed by 20 minutes heat inactivation at 65 °C. All enzymatic reactions were carried out in the recommended manufacturer's buffer. PCR was performed in two rounds. In the first round (98 °C for 1 min // 98 °C for 15 sec / 60 °C for 30 sec / 72 °C for 1 min // – 25 cycles / 72 °C for 3 min) gDNA flanking insertions and barcode was amplified using primers GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCTAAGGTGTATGTAAACTTCCGACTTCAACTG and AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT annealing to the transposon and to the Illumina PE1.0 sequence present in the integrated construct. In the second round (98 °C for 1 min // 98 °C for 15 sec / 60 °C for 30 sec / 72 °C for 1 min // – 10 cycles / 72 °C for 3 min) Illumina adaptors for paired-end sequencing and indexes were incorporated with primers AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT and CAAGCAGAAGACGGCATACGAGA [index]  GGTGACTGGAGTTC.
High-Seq Paired-end Sequencing 2*100bp


title: Promoter 4 Biological rep 1 Expression

description: Promoter 4


title: Wapl ChIP (Peters Lab ID: 22604)

city: Vienna

first: Roman

middle: R

last: Stocsits

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP - Research Institute of Molecular Pathology

description: Peters Lab ID: 22604

data_processing:
Basecalling software: Illumina RTA
Alignment: TopHat 1.3.1. for samples 85, 86, 89, 90, 93, 94 (RNA-Seq), reads are mapped uniquely to genome with 0 to 2 errors
Alignment: TopHat 1.4.1. for all other RNA-Seq samples, reads are mapped uniquely to genome with 0 to 2 errors
Alignment: Bowtie 0.12.5 and 1.0.0 for ChIP-Seq and GRO-Seq data, reads are trimmed and mapped uniquely to genome with 0 to 2 errors
ChIP-Seq MACS peak calling version 1.4.2
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using MACS 1.4.2 with output switches [-w -S] and represent genomic distribution of the factors as described in the paper.
Supplementary_files_format_and_content: RPKM and TPM values are generated according to standard formulas after read counting using 'bedtools coverage' and 'htseq-count' methods resp. as described.

source_name: mouse embryonic fibroblasts (E13.5d)

growth_protocol: Quiescent, non-proliferating MEFs were used in all experiments.

extract_protocol:
ChIP-Seq: Cells were cross-linked and scrapped of the plate. The DNA was fragmented and the protein of interest was immunoprecipitated with indicated antibodies; GRO-Seq: Nuclei were isolated and global run-on was preformed in the presence of BrU analog. RNA was fragmented and isolated by a BrU immunoprecipitation. Adaptors were ligated to the 5' and 3' ends and the library was prepared for Illumina sequencing by a qPCR amplification step; RNA-Seq: Total RNA was extracted from MEFs via the RNA Easy Plus kit and PolyA containing mRNAs were isolated using Dynabeads. The mRNA was fragmented and reversely transcribed with Superscript III followed by second strand synthesis.
RNA and ChIP libraries were prepared for sequencing using standard Illumina protocols; GRO-Seq: see extract protocol

treatment_protocol: The deletion of the Smc3 and Wapl gene was induced in quiescent MEFs by activating an inducible Cre recombinase with 4'-hydroxytamoxifen; The deletion of the Ctcf gene alone or in the combination with the Wapl gene was induced by the expression Cre recombinase from an adenovirus.

value: Mouse embryonic fibroblasts

value: wild-type

value: resting

value: Wapl (Peters laboratory ID A960)


title: Promoter 4 Biological rep 2 Mapping

description: Promoter 4


title: Scc1 ChIP (Peters Lab ID: 27715)

description:
Peters Lab ID: 27715
processed data file: 27715.wig

data_processing:
Basecalling software: Illumina RTA
Alignment: Bowtie 0.12.5 and 1.0.0 for ChIP-Seq and GRO-Seq data, reads are trimmed and mapped uniquely to genome with 0 to 2 errors
ChIP-Seq MACS peak calling version 1.4.2
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using MACS 1.4.2 with output switches [-w -S] and represent genomic distribution of the factors as described in the paper.

value: Ctcf(fl/fl)

value: 4h Adeno-Cre and 10d resting

value: Scc1 (Abcam AB992)


title: 2131269_TimePoint1_BoneMarrow


title: Promoter 3 Biological rep 1 Expression

description: Promoter 3


title: Promoter 3 Biological rep 2 Expression

description: Promoter 3


title: Promoter 4 Biological rep 1 Normalization

description: Promoter 4


title: Promoter 3 Biological rep 2 Normalization

description: Promoter 3


title: Ctcf Wapl MEFs (Peters Lab ID: 32720)

description:
Peters Lab ID: 32720
processed data file: TPM_GRO-Seq_Ctcf-Wapal-dKO.sort.txt

value: Ctcf(fl/fl) Wapl(fl/fl)

value: 4h Adeno-Cre and 10d resting + 3.5h DRB + 1d no DRB

tag: assayed molecule

value: BrU containing RNA


title: Promoter 3 Biological rep 1 Mapping

description: Promoter 3


title: Ctcf Wapl MEFs (Peters Lab ID: 32718)

description:
Peters Lab ID: 32718
processed data file: TPM_GRO-Seq_Ctcf-Wapal-dKO.sort.txt

value: 4h Adeno-Cre and 10d resting + 3.5h DRB


title: BATF_TH17(23)_ChIPSeq

value: JUNBFl/Fl


title: Promoter 3 Biological rep 1 Normalization

description: Promoter 3


title: S5_mRNA_seq

city: ShenZhen

first: Zhoufang

last: Li

address: No 1088,xueyuan Rd., Xili, Nanshan District,Shenzhen,Guangdong,China

department: Department of Biology

country: China

institute: SUSTech

description: total mRNA

data_processing:
Analysis of DNA sequence data (v1.var). 5′ ends of sequencing reads of samples S3-S6 (by WGA4) were trimmed by 32 bp by Bowtie software (Bowtie parameter: -5 32), because they contained the amplification primers. Reads were aligned to the mouse genome (GRCm38/mm10 version, downloaded from the UCSC Genome Browser) with Bowtie (version 2.1.0) with parameters -I 200 -X 300. Next the samtools mpileup function was used to prepare consensus genotype files (subcommand: mpileup2cns) for variant detection. Variants were called by VarScan with default parameters. In the default settings of VarScan, at least eight reads are needed to cover a base to call a variant, and the P-value threshold of calling a variant was 0.01.
Analysis of RNA sequence data (fpkm_tracking). RNA sequence data were aligned to the mouse genome (GRCm38/mm10 version) using Tophat (version 2.0.10) with default parameters. The gene expression level was calculated as an FPKM value by Cufflinks, and given an Ensembl gene annotation gtf file. The file (GRCm38/mm10) was downloaded from the Ensembl Genome Browser and only protein-coding and lincRNA genes were selected.
Genome_build: mm10

source_name: mouse secondary oocytes

extract_protocol:
Sample collection and preparation. Metaphase II (MII) oocytes were collected from superovulated sexually mature female Kunming mice. The mouse oviducts were dissected and placed in M2 media, and extracted the cumulus cell complex. Then we removed the cumulus cells around the oocytes by treatment with hyaluronidase (sigma), washed the oocytes by pipetting them 4-6 times with M2 media, and collected the oocytes under a stereomicroscope by mouth pipetting. The oocytes were treated by microinjection system (Eppendorf). Next we transferred the oocytes to a drop of M2 media under mineral oil (Sigma) in a 3.5-cm dish, partially removed zone pellucida by laser-assisted biopsy, and collected the first body and nucleus by a micropipette in 0.2 mL PCR tube with 5 μL Nuclease-free distilled water (InvitrogenTM), respectively. Then we collected cytoplasm (oocytes without nucleus or first body) in a 0.2 mL PCR tube with 5 μL lysis buffer. The nucleus, first bodies and cytoplasm were stored at -80℃ until required for library preparation. Negative controls were either Nuclease-free water or lysis buffer alone.
Single cell DNA amplification. We amplified the genomic DNA from single isolated nucleus. Out of six different samples, two samples were amplified by REPLI-g Single Cell Kit (Qiagen, Cat no.150345) based on multiple displacement amplification (MDA) method. In short, single nucleus was lysed and denatured at 65oC for 10 minutes, then the DNA amplification was starting with the random hexamer primers binding to the template in the reaction tube by a high fidelity f29 DNA polymerase and incubating at 30oC for 8 hours. The reactions were then inactivated at 65oC for 3 minutes and stored in -80oC for holding. The other four samples were amplified by GenomePlex single cell amplification kit (Sigma-Aldrich, Cat no. WGA4-50RXN). In short, we first lysed the nucleus and digested the proteins by protease K at 50 °C for 1 hour. The genomic DNA was fragmented into 200-400bp at 99 °C for 4 minutes . Random primers linked with common adaptors were annealed to the fragmented DNA template using the following incubation setting: 16 °C, 20 minutes, 24 °C, 20 minutes, 37 °C, 20 minutes, 75 °C, 5 minutes, and 4 °C hold. Then, the mixture were amplified with an initial denaturation at 95 °C, 3 minutes, and 25 cycles of 94 °C, 30 seconds and 65 °C, 5 minutes. The amplified products were purified using the Qiagen PCR purification reagents. The sequencing libraries were constructed by BGI-Shenzhen and sequenced using the Illumina HiSeq 2000 sequencing platform.
Exome-seq. We used SureSelectQXT exome enrichment kit (Agilent technologies Inc., Germany) to capture and enrich the exome regions from the sequencing library of single cell whole genomic DNA. In short, we mixed the sequencing library from single nucleus with SureSelect exome probes, which were tagged with magnetic labelling, and incubated at 65oC for 24 hours (optimal, 72hours), allowing the probe hybridized to the library thoroughly. Then the purified sequences were further amplified by PCR and purified. After quantity assessment by bioanalyzer, they were sequenced on the illumina HiSeq 2000 sequencing platform (illumina co., CA, USA).
Single cell RNA amplification. Single cell transcriptome of the enucleated cytoplasm was amplified by SMARTer ultra low RNA kit (Clontech, Cat. no. 634936) as the manual instructed. Briefly, we first synthesized the first strand cDNA from single enucleated cytoplasm using modified oligo(dT) (SMART CDS primer) and then tailed several additional nucleotides to the 3’end of the first strand cDNA due to the enzyme’s terminal transferases activity. Common adaptor (SMARTer II A oligonucleotide) were linked to the 3’end of the first strand cDNA. The resulting full-length single strand cDNAs started with poly T and ended with a common adaptor. Then full transcriptome of the enucleated cytoplasm was amplified by universal primers (by common adaptor and oligod(T) ) and ready for sequencing library construction. The sequencing libraries were constructed by BGI-Shenzhen and sequenced using the Illumina HiSeq 2000 sequencing platform.

value: mouse secondary oocytes


title: Promoter 2 Biological rep 2  Mapping

description: Promoter 2


title: S4_mRNA_seq

description: total mRNA


title: Promoter 3 Biological rep 2 Mapping

description: Promoter 3


title: Ctcf Wapl MEFs - 1 (Peters Lab ID: 28018)

description:
Peters Lab ID: 28018
processed data file: RPKM_serum_stimulation.txt

data_processing:
Basecalling software: Illumina RTA
Alignment: TopHat 1.3.1. for samples 85, 86, 89, 90, 93, 94 (RNA-Seq), reads are mapped uniquely to genome with 0 to 2 errors
Alignment: TopHat 1.4.1. for all other RNA-Seq samples, reads are mapped uniquely to genome with 0 to 2 errors
Alignment: Alignment: Bowtie 0.12.5 and 1.0.0 for ChIP-Seq and GRO-Seq data, reads are trimmed and mapped uniquely to genome with 0 to 2 errors
ChIP-Seq MACS peak calling version 1.4.2
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using MACS 1.4.2 with output switches [-w -S] and represent genomic distribution of the factors as described in the paper.
Supplementary_files_format_and_content: RPKM and TPM values are generated according to standard formulas after read counting using 'bedtools coverage' and 'htseq-count' methods resp. as described.

value: Ctcf(fl/fl) Wapl(fl/fl); clone 3

value: mRNA


title: Ctcf Wapl MEFs - 2 (Peters Lab ID: 30256)

description:
Peters Lab ID: 30256
processed data file: RPKM_values_RNA-seq.txt

value: Ctcf(fl/fl) Wapl(fl/fl); clone 4


title: S3_mRNA_seq

description: total mRNA


title: S2_mRNA_seq

description: total mRNA


title: S1_mRNA_seq

description: total mRNA


title: Promoter 2 Biological rep 2 Technical 2 Expression

description: Promoter 2


title: S6_exome_seq

description: exome DNA

data_processing:
Library strategy: exome-seq
Analysis of DNA sequence data (v1.var). 5′ ends of sequencing reads of samples S3-S6 (by WGA4) were trimmed by 32 bp by Bowtie software (Bowtie parameter: -5 32), because they contained the amplification primers. Reads were aligned to the mouse genome (GRCm38/mm10 version, downloaded from the UCSC Genome Browser) with Bowtie (version 2.1.0) with parameters -I 200 -X 300. Next the samtools mpileup function was used to prepare consensus genotype files (subcommand: mpileup2cns) for variant detection. Variants were called by VarScan with default parameters. In the default settings of VarScan, at least eight reads are needed to cover a base to call a variant, and the P-value threshold of calling a variant was 0.01.
Analysis of RNA sequence data (fpkm_tracking). RNA sequence data were aligned to the mouse genome (GRCm38/mm10 version) using Tophat (version 2.0.10) with default parameters. The gene expression level was calculated as an FPKM value by Cufflinks, and given an Ensembl gene annotation gtf file. The file (GRCm38/mm10) was downloaded from the Ensembl Genome Browser and only protein-coding and lincRNA genes were selected.
Genome_build: mm10


title: Ctcf Wapl MEFs - 2 (Peters Lab ID: 30255)

description:
Peters Lab ID: 30255
processed data file: RPKM_values_RNA-seq.txt

value: 10d resting


title: Promoter 2 Biological rep 2 Technical 2 Normalization

description: Promoter 2


title: Promoter 2 Biological rep 2 Technical 1 Expression

description: Promoter 2


title: S1_exome_seq

description: exome DNA


title: Ctcf Wapl MEFs - 1 (Peters Lab ID: 28014)

description:
Peters Lab ID: 28014
processed data file: RPKM_serum_stimulation.txt

value: Mouse embryonic fibroblasts


title: S3_exome_seq

description: exome DNA


title: S4_exome_seq

description: exome DNA


title: S2_exome_seq

description: exome DNA


title: Ctcf Wapl MEFs - 2  (Peters Lab ID: 30252)

description:
Peters Lab ID: 30252
processed data file: TPM_GRO-Seq_Ctcf-Wapal-dKO.sort.txt

data_processing:
Library strategy: GRO-Seq
Basecalling software: Illumina RTA
Alignment: TopHat 1.3.1. for samples 85, 86, 89, 90, 93, 94 (RNA-Seq), reads are mapped uniquely to genome with 0 to 2 errors
Alignment: TopHat 1.4.1. for all other RNA-Seq samples, reads are mapped uniquely to genome with 0 to 2 errors
Alignment: Alignment: Bowtie 0.12.5 and 1.0.0 for ChIP-Seq and GRO-Seq data, reads are trimmed and mapped uniquely to genome with 0 to 2 errors
ChIP-Seq MACS peak calling version 1.4.2
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using MACS 1.4.2 with output switches [-w -S] and represent genomic distribution of the factors as described in the paper.
Supplementary_files_format_and_content: RPKM and TPM values are generated according to standard formulas after read counting using 'bedtools coverage' and 'htseq-count' methods resp. as described.

value: Ctcf(fl/fl) Wapl(fl/fl); clone 2


title: Promoter 2 Biological rep 2 Technical 1 Normalization

description: Promoter 2


title: S6_mRNA_seq

description: total mRNA


title: S5_exome_seq

description: exome DNA


title: Ctcf MEFs - 2 (Peters Lab ID: 12536)

description:
Peters Lab ID: 12536
processed data file: RPKM_values_RNA-seq.txt

value: Ctcf(fl/fl); clone 2


title: Promoter 2 Biological rep 1  Mapping

description: Promoter 2


title: Ctcf MEFs - 1 (Peters Lab ID: 11649)

description:
Peters Lab ID: 11649
processed data file: RPKM_values_RNA-seq.txt

value: Ctcf(fl/fl); clone 1


title: Promoter 2 Biological rep 1 Technical 2 Expression

description: Promoter 2


title: Ctcf MEFs - 2 (Peters Lab ID: 12535)

description:
Peters Lab ID: 12535
processed data file: RPKM_values_RNA-seq.txt


title: Ctcf MEFs - 1 (Peters Lab ID: 11647)

description:
Peters Lab ID: 11647
processed data file: RPKM_values_RNA-seq.txt


title: wild-type MEFs - 4 (Peters Lab ID: 12532)

description:
Peters Lab ID: 12532
processed data file: RPKM_values_RNA-seq.txt

value: Rosa26(CreER/+); clone 3

value: 2-3d 4'hydroxytamoxifen and 10d resting


title: Ctcf Wapl MEFs - 1 (Peters Lab ID: 30251)

description:
Peters Lab ID: 30251
processed data file: TPM_GRO-Seq_Ctcf-Wapal-dKO.sort.txt

value: Ctcf(fl/fl) Wapl(fl/fl); clone 1

value: 4h Adeno-Cre and 10d resting


title: wild-type MEFs - 4 (Peters Lab ID: 12531)

description:
Peters Lab ID: 12531
processed data file: RPKM_values_RNA-seq.txt


title: wild-type MEFs - 3 (Peters Lab ID: 12530)

description:
Peters Lab ID: 12530
processed data file: RPKM_values_RNA-seq.txt

value: Rosa26(CreER/+); clone 2


title: Ctcf Wapl MEFs - 1 (Peters Lab ID: 28013)

description:
Peters Lab ID: 28013
processed data file: RPKM_values_RNA-seq.txt


title: Promoter 2 Biological rep 1 Technical 2 Normalization

description: Promoter 2


title: Ctcf Wapl MEFs - 1 (Peters Lab ID: 30250)

description:
Peters Lab ID: 30250
processed data file: TPM_GRO-Seq_Ctcf-Wapal-dKO.sort.txt

value: BrU containing RNA


title: Ctcf Wapl MEFs - 2 (Peters Lab ID: 30253)

description:
Peters Lab ID: 30253
processed data file: TPM_GRO-Seq_Ctcf-Wapal-dKO.sort.txt


title: Promoter 2 Biological rep 1 Technical 1 Expression

description: Promoter 2


title: wild-type MEFs - 2 (Peters Lab ID: 12528)

description:
Peters Lab ID: 12528
processed data file: RPKM_values_RNA-seq.txt

value: wild-type; clone 3


title: Promoter 2 Biological rep 1 Technical 1 Normalization

description: Promoter 2


title: wild-type MEFs - 2 (Peters Lab ID: 20108)

description:
Peters Lab ID: 20108
processed data file: TPM_GRO-Seq_wildtype.sort.txt

value: wild-type; clone 1


title: Promoter 1 Biological rep 2 Expression

description: Promoter 1


title: wild-type MEFs - 2 (Peters Lab ID: 20107)

description:
Peters Lab ID: 20107
processed data file: TPM_GRO-Seq_wildtype.sort.txt


title: wild-type MEFs - 1 (Peters Lab ID: 17594)

description:
Peters Lab ID: 17594
processed data file: TPM_GRO-Seq_wildtype.sort.txt

value: Rosa26(CreER/+); clone 1


title: wild-type MEFs - 1  (Peters Lab ID: 12525)

description:
Peters Lab ID: 12525
processed data file: RPKM_values_RNA-seq.txt

value: wild-type; clone 2


title: Promoter 1 Biological rep 2 Mapping

description: Promoter 1


title: wild-type MEFs - 1  (Peters Lab ID: 17593)

description:
Peters Lab ID: 17593
processed data file: TPM_GRO-Seq_wildtype.sort.txt


title: CTCF ChIP (Peters Lab ID: 19593)

description:
Peters Lab ID: 19593
processed data file: 19593.wig

value: Ctcf(fl/fl)

value: CTCF (Upstate 07-729)


title: CTCF ChIP (Peters Lab ID: 27722)

description:
Peters Lab ID: 27722
processed data file: 9149+27722.wig

value: Rosa26(CreER/+) Wapl(fl/-)


title: CTCF ChIP (Peters Lab ID: 12156)

description:
Peters Lab ID: 12156
processed data file: 12156+27721.wig

value: Mouse embryonic fibroblasts

value: Rosa26(CreER/+) Smc3(fl/-)


title: Scc1 ChIP (Peters Lab ID: 20320)

description:
Peters Lab ID: 20320
processed data file: 20096+20320+27717.wig

value: Scc1 (Abcam AB992)


title: CTCF ChIP (Peters Lab ID: 27721)

description:
Peters Lab ID: 27721
processed data file: 12156+27721.wig


title: Promoter 1 Biological rep 1 Expression

description: Promoter 1


title: wild-type MEFs - 1 (Peters Lab ID: 12526)

description:
Peters Lab ID: 12526
processed data file: RPKM_values_RNA-seq.txt

value: mRNA


title: Scc1 ChIP (Peters Lab ID: 20319)

description:
Peters Lab ID: 20319
processed data file: 20095+20319+27716.wig


title: Scc1 ChIP (Peters Lab ID: 20096)

description:
Peters Lab ID: 20096
processed data file: 20096+20320+27717.wig


title: wild-type MEFs - 3 (Peters Lab ID: 12529)

description:
Peters Lab ID: 12529
processed data file: RPKM_values_RNA-seq.txt

value: 10d resting


title: H3K4ac9 ChIP (Peters Lab ID: 18874)

description:
Peters Lab ID: 18874
processed data file: 16830+18874.wig

value: 2-3d 4'hydroxytamoxifen and 10d resting

value: H3K9ac (Millipore 07-352)


title: Scc1 ChIP (Peters Lab ID: 20095)

description:
Peters Lab ID: 20095
processed data file: 20095+20319+27716.wig


title: Scc1 ChIP (Peters Lab ID: 20094)

description:
Peters Lab ID: 20094
processed data file: 20094+20106.wig

value: 4h Adeno-Cre and 10d resting


title: CTCF ChIP (Peters Lab ID: 27719)

description:
Peters Lab ID: 27719
processed data file: 9147+27719.wig

value: wild-type


title: Promoter 1 Biological rep 1 Mapping

description: Promoter 1


title: Promoter 1 Biological rep 2 Normalization

description: Promoter 1


title: wild-type MEFs - 2 (Peters Lab ID: 12527)

description:
Peters Lab ID: 12527
processed data file: RPKM_values_RNA-seq.txt


title: Scc1 ChIP (Peters Lab ID: 20093)

description:
Peters Lab ID: 20093
processed data file: 20093+20105.wig


title: H3K4ac9 ChIP (Peters Lab ID: 16830)

description:
Peters Lab ID: 16830
processed data file: 16830+18874.wig


title: Stag1 ChIP (Peters Lab ID: 19589)

description:
Peters Lab ID: 19589
processed data file: 19589+20318+26235.wig

value: Stag1 (Peters laboratory ID A823)


title: Promoter 0 Biological rep 2  Expression

description: Promoter 0


title: Nipbl ChIP (Peters Lab ID: 22603)

description:
Peters Lab ID: 22603
processed data file: 22603.wig

value: resting

value: Nipbl (Sanova A301-779A)


title: Stag1 ChIP (Peters Lab ID: 20318)

description:
Peters Lab ID: 20318
processed data file: 19589+20318+26235.wig


title: Promoter 1 Biological rep 1 Normalization

description: Promoter 1


title: Stag1 ChIP (Peters Lab ID: 19587)

description:
Peters Lab ID: 19587
processed data file: 14551+19587+26233.wig

treatment_protocol: The deletion of the Smc3 and Wapal gene was induced in quiescent MEFs by activating an inducible Cre recombinase with 4'-hydroxytamoxifen; The deletion of the Ctcf gene alone or in the combination with the Wapal gene was induced by the expression Cre recombinase from an adenovirus.


title: Stag1 ChIP (Peters Lab ID: 19588)

description:
Peters Lab ID: 19588
processed data file: 19588+26234+27235.wig


title: H3K4ac9 ChIP (Peters Lab ID: 16824)

description:
Peters Lab ID: 16824
processed data file: 16824+18873.wig


title: H3K4ac9 ChIP (Peters Lab ID: 16822)

description:
Peters Lab ID: 16822
processed data file: 16822+18872.wig


title: Promoter 0 Biological rep 2 Technical 1 Normalization

description: Promoter 0


title: Promoter 0 Biological rep 2 Technical 2 Normalization

description: Promoter 0


title: Promoter 0 Biological rep 2  Mapping

description: Promoter 0


title: H3K4ac9 ChIP (Peters Lab ID: 18872)

description:
Peters Lab ID: 18872
processed data file: 16822+18872.wig


title: Promoter 0 Biological rep 1  Expression

description: Promoter 0


title: H3K4ac9 ChIP (Peters Lab ID: 18871)

description:
Peters Lab ID: 18871
processed data file: 16818+18871.wig


title: Promoter 0 Biological rep 1 Technical 2 Normalization

description: Promoter 0


title: H3K4me2 ChIP (Peters Lab ID: 18870)

description:
Peters Lab ID: 18870
processed data file: 16828+18870.wig

value: H3K4me2 (Millipore 07-030)


title: H3K4ac9 ChIP (Peters Lab ID: 16818)

description:
Peters Lab ID: 16818
processed data file: 16818+18871.wig


title: H3K4me2 ChIP (Peters Lab ID: 16828)

description:
Peters Lab ID: 16828
processed data file: 16828+18870.wig


title: H3K4me2 ChIP (Peters Lab ID: 18869)

description:
Peters Lab ID: 18869
processed data file: 16826+18869.wig


title: Promoter 0 Biological rep 1 Technical 1 Normalization

description: Promoter 0


title: H3K4me2 ChIP (Peters Lab ID: 16826)

description:
Peters Lab ID: 16826
processed data file: 16826+18869.wig


title: WT_starvation2

city: Ames

first: Yanhai

last: Yin

state: IA

address: 1035D Roy J. Carver Co-Lab

department: Genetic Development and Cell Biology

institute: Iowa State University

description: Sample name: 56

data_processing:
Quality Control
Alignment using GSNAP
Differential expression using DESeq2
Genome_build: TAIR10
Supplementary_files_format_and_content: comma seperated files including RPM values and statistical significance for each sample calculated using DESeq2

source_name: leaf tissue

extract_protocol:
RNA was then extracted using Trizol, followed by DNAse digestion and RNA cleanup using Qiagen RNeasy kit. Purified RNA was subject to quality control on an Agilent 2100 Bioanalyzer.
Library preparation and RNA sequencing were performed by BGI Americas using an Illumina HiSeq 2000 with 50bp single-end reads and ~30 million reads per sample.

value: leaf

value: WT

value: Starvation

tag: replication


title: WT_starvation1

description: Sample name: 55


title: Promoter 0 Biological rep 1  Mapping

description: Promoter 0


title: WT_dehydration3

description: Sample name: 6

value: Dehydration


title: H3K4me2 ChIP (Peters Lab ID: 16820)

description:
Peters Lab ID: 16820
processed data file: 16820+18868.wig

value: Mouse embryonic fibroblasts

value: Ctcf(fl/fl)


title: H3K4ac9 ChIP (Peters Lab ID: 18873)

description:
Peters Lab ID: 18873
processed data file: 16824+18873.wig

value: Rosa26(CreER/+) Smc3(fl/-)


title: WT_dehydration2

description: Sample name: 4


title: H3K4me2 ChIP (Peters Lab ID: 18867)

description:
Peters Lab ID: 18867
processed data file: 16816+18867.wig


title: H3K4me2 ChIP (Peters Lab ID: 16816)

description:
Peters Lab ID: 16816
processed data file: 16816+18867.wig


title: H3K4me2 ChIP (Peters Lab ID: 18868)

description:
Peters Lab ID: 18868
processed data file: 16820+18868.wig


title: WT_control3

description: Sample name: 5

value: Control


title: WT_dehydration1

description: Sample name: 2


title: Scc1 ChIP (Peters Lab ID: 32724)

description:
Peters Lab ID: 32724
processed data file: 32724.wig

value: Ctcf(fl/fl) Wapl(fl/fl)

value: 4h Adeno-Cre, 10d resting, 3.5h DRB and washout for 1 day

value: Scc1 (Abcam AB992)


title: WT_control1

description: Sample name: 1


title: WT_control2

description: Sample name: 3


title: 6_dehydration3

description: Sample name: 54


title: Scc1 ChIP (Peters Lab ID: 32722)

description:
Peters Lab ID: 32722
processed data file: 32722.wig

value: 4h Adeno-Cre, 10d resting and 3.5h DRB


title: Scc1 ChIP (Peters Lab ID: 32721)

description:
Peters Lab ID: 32721
processed data file: 32721.wig

value: 4h Adeno-Cre and 10d resting


title: 6_control3

description: Sample name: 53


title: Scc1 ChIP (Peters Lab ID: 29079)

description:
Peters Lab ID: 29079
processed data file: 29079.wig


title: Scc1 ChIP (Peters Lab ID: 29077)

description:
Peters Lab ID: 29077
processed data file: 29077.wig

value: 4h Adeno-Cre and 6d resting


title: Scc1 ChIP (Peters Lab ID: 29078)

description:
Peters Lab ID: 29078
processed data file: 29078.wig

value: 4h Adeno-Cre and 8d resting


title: 6_dehydration1

description: Sample name: 50


title: 6_control2

description: Sample name: 51


title: 6_control1

description: Sample name: 49


title: Scc1 ChIP (Peters Lab ID: 29076)

description:
Peters Lab ID: 29076
processed data file: 29076.wig

value: 4h Adeno-Cre and 4d resting


title: Scc1 ChIP (Peters Lab ID: 29075)

description:
Peters Lab ID: 29075
processed data file: 29075.wig

value: 4h Adeno-Cre and 2d resting


title: 54t_dehydration2

description: Sample name: 40

value: leaf


title: Scc1 ChIP (Peters Lab ID: 29074)

description:
Peters Lab ID: 29074
processed data file: 29074.wig

value: timepoint 0d


title: Scc1 ChIP (Peters Lab ID: 29072)

description:
Peters Lab ID: 29072
processed data file: 29072.wig

value: 4h Adeno-Cre, 10d resting and 2.5h actinomycin D


title: Scc1 ChIP (Peters Lab ID: 29073)

description:
Peters Lab ID: 29073
processed data file: 29073.wig

value: 4h Adeno-Cre, 10d resting and 5h actinomycin D


title: 54t_control3

description: Sample name: 41


title: 54t_dehydration3

description: Sample name: 42

value: Dehydration


title: 54t_dehydration1-2

description: Sample name: 38


title: 54t_control2

description: Sample name: 39


title: Scc1 ChIP (Peters Lab ID: 32723)

description:
Peters Lab ID: 32723
processed data file: 32723.wig

value: Mouse embryonic fibroblasts

value: 4h Adeno-Cre, 10d resting, 3.5h DRB and washout for 30 min


title: 6_dehydration2

description: Sample name: 52


title: Scc1 ChIP (Peters Lab ID: 26238)

description:
Peters Lab ID: 26238
processed data file: 26238+27718.wig


title: Scc1 ChIP (Peters Lab ID: 29071)

description:
Peters Lab ID: 29071
processed data file: 29071.wig

value: 4h Adeno-Cre, 10d resting and 6h 20% serum


title: oe_dehydration1

description: Sample name: 32


title: oe_dehydration2

description: Sample name: 34


title: Scc1 ChIP (Peters Lab ID: 27718)

description:
Peters Lab ID: 27718
processed data file: 26238+27718.wig

value: Ctcf(fl/fl) Wapl(fl/fl)


title: Scc1 ChIP (Peters Lab ID: 27716)

description:
Peters Lab ID: 27716
processed data file: 20095+20319+27716.wig

value: Rosa26(CreER/+) Smc3(fl/-)

value: 2-3d 4'hydroxytamoxifen and 10d resting


title: oe_control3

description: Sample name: 35

value: Control


title: Scc1 ChIP (Peters Lab ID: 20106)

description:
Peters Lab ID: 20106
processed data file: 20094+20106.wig

value: Ctcf(fl/fl)

value: 4h Adeno-Cre and 10d resting

value: Scc1 (Abcam AB992)


title: Scc1 ChIP (Peters Lab ID: 27717)

description:
Peters Lab ID: 27717
processed data file: 20096+20320+27717.wig

value: Rosa26(CreER/+) Wapl(fl/-)


title: oe_control1

description: Sample name: 31


title: oe_control2

description: Sample name: 33


title: Stag1 ChIP (Peters Lab ID: 27237)

description:
Peters Lab ID: 27237
processed data file: 26236+27237.wig

value: Stag1 (Peters laboratory ID A823)


title: 53t_dehydration3

description: Sample name: 48

value: leaf


title: 53t_dehydration2

description: Sample name: 46


title: Stag1 ChIP (Peters Lab ID: 26236)

description:
Peters Lab ID: 26236
processed data file: 26236+27237.wig


title: Scc1 ChIP (Peters Lab ID: 20105)

description:
Peters Lab ID: 20105
processed data file: 20093+20105.wig

value: wild-type

value: 10d resting


title: Stag1 ChIP (Peters Lab ID: 26235)

description:
Peters Lab ID: 26235
processed data file: 19589+20318+26235.wig


title: 53t_dehydration1

description: Sample name: 44


title: Stag1 ChIP (Peters Lab ID: 27235)

description:
Peters Lab ID: 27235
processed data file: 19588+26234+27235.wig


title: oe_dehydration3

description: Sample name: 36


title: 53t_control3

description: Sample name: 47


title: 54t_control1

description: Sample name: 37


title: Stag1 ChIP (Peters Lab ID: 26234)

description:
Peters Lab ID: 26234
processed data file: 19588+26234+27235.wig


title: 53t_control1

description: Sample name: 43


title: Stag1 ChIP (Peters Lab ID: 26233)

description:
Peters Lab ID: 26233
processed data file: 14551+19587+26233.wig


title: 53t_control2

description: Sample name: 45


title: Stag1 ChIP (Peters Lab ID: 14954)

description:
Peters Lab ID: 14954
processed data file: 14549+14954.wig


title: Stag1 ChIP (Peters Lab ID: 14551)

description:
Peters Lab ID: 14551
processed data file: 14551+19587+26233.wig


title: bri1_starvation2

description: Sample name: 62

value: Starvation


title: bri1_starvation1

description: Sample name: 61


title: bri1_dehydration3

description: Sample name: 24

value: Dehydration


title: bri_dehydration2

description: Sample name: 22


title: bri1_control3

description: Sample name: 23


title: bri1_control2

description: Sample name: 21


title: bri1_dehydration1

description: Sample name: 20


title: Stag1 ChIP (Peters Lab ID: 14549)

description:
Peters Lab ID: 14549
processed data file: 14549+14954.wig

value: Mouse embryonic fibroblasts


title: bri1_control1

description: Sample name: 19


title: DSK2 RNAi_starvation2

description: Sample name: 60

value: DSK2 RNAi


title: K326_ShootApex_ZT18_R2

first: Kieron

middle: David

last: Edwards

state: Cambridgeshire

address: GR&D Cambridge, 210 Cambridge Science Park

department: Plant Biotechnology

institute: British American Tobacco

data_processing:
Basecalls performed using HiSeq Control Software 2.2.38
Deconvolution of multiplexed reads was carried out using Casava 1.9.4
Data were filtered and multiplex adaptors trimmed from reads using fastq-mcf  1.04.803 with the following configurations: -q 30 -l 50 -P 30
Reads were aligned to Nitab4.5 gene models and quantified using rsem 1.2.7 and bowtie 1.1.0
Genome_build: nitab45_transcripts.fasta
Supplementary_files_format_and_content: tab-delimited text files including gene model, TPM and FPKM were produced for each sample

organism: Nicotiana tabacum

growth_protocol: Plants were grown under long day conditions (18h light, 6h dark) at 23 degrees.

extract_protocol:
Total RNA was extracted using QIAzol followed by clean up, including on-column DNase treatment, using Qiagen RNeasy spin columns. RNA was QC'd using Bioanalyzer RNAnano protocol. RNA with RIN>=8.0 was used in library preparation
Random primed cDNA-libraries were prepared at GATC Biotech (Konstanz, Germany) using propritary methods

treatment_protocol: Tissue was harvested at ZT0, 6, 12 and 18

tag: cultivar

value: ShootApex

tag: timepoint

tag: age (days)

tag: photoperiod

tag: replicate


title: K326_ShootApex_ZT18_R1


title: DSK2 RNAi_starvation1

description: Sample name: 59


title: K326_ShootApex_ZT18_R3


title: DSK2 RNAi_dehydration3

description: Sample name: 18


title: K326_Shoot_ZT18_R1

value: Shoot


title: DSK2 RNAi_dehydration1

description: Sample name: 14


title: K326_Root_ZT18_R3

value: Root


title: DSK2 RNAi_control3

description: Sample name: 17


title: DSK2 RNAi_control2

description: Sample name: 15


title: K326_ShootApex_ZT12_R3


title: bes1_starvation2

description: Sample name: 64


title: K326_ShootApex_ZT12_R2


title: K326_Root_ZT18_R1


title: DSK2 RNAi_control1

description: Sample name: 13


title: bes1_starvation1

description: Sample name: 63


title: bes1_dehydration2

description: Sample name: 28


title: K326_Shoot_ZT12_R3


title: bes1_dehydration3

description: Sample name: 30


title: K326_ShootApex_ZT12_R1


title: K326_Shoot_ZT12_R2


title: K326_Shoot_ZT12_R1


title: bes1_control3

description: Sample name: 29


title: bes1_control2

description: Sample name: 27


title: DSK2 RNAi_dehydration2

description: Sample name: 16


title: K326_Shoot_ZT18_R2


title: K326_Shoot_ZT18_R3


title: K326_Root_ZT12_R3


title: bes1_control1

description: Sample name: 25


title: K326_Root_ZT12_R1


title: K326_Root_ZT18_R2


title: atg7-2_starvation2

description: Sample name: 58


title: K326_ShootApex_ZT6_R3


title: Sjogren's syndrome

city: Nashville

first: Charles

middle: F

last: Spurlock III

state: Tennessee

address: 1161 21st Avenue South

department: Medicine

institute: Vanderbilt University School of Medicine

data_processing:
Illumina Casava1.9 software used for basecalling.
Quality control to filter out bad samples and reads
Alignment to human genome (hg19) using Tophat 2
Read count quantification using HTSeq
Genome_build: hg19
Supplementary_files_format_and_content: text file, FPKM table

source_name: peripheral whole blood draw

extract_protocol:
Peripheral whole blood was collected into PaxGene tubes. RNA was isolated per the manufacturer's supplied protocol.
Total RNA isolated from PaxGene tubes was purified with the RNeasy MinElute Cleanup kit (Qiagen) using an on-column DNAse treatment to ensure absence of genomic DNA contamination according to the manufacturer’s supplied protocol.
Libraries were constructed using the Illumina TruSeq Stranded mRNA kit (Cat. No. RS-122-2101) following the manufacturer's supplied protocol.

tag: type

value: Sjogren's syndrome


title: atg7-2_starvation1

description: Sample name: 57

tag: treatment


title: Psoriatic arthritis

value: Psoriatic arthritis


title: K326_ShootApex_ZT6_R2


title: Psoriasis

value: Psoriasis


title: K326_ShootApex_ZT6_R1


title: Systemic lupus erythematosus

value: Systemic lupus erythematosus


title: atg7-2_dehydration2

description: Sample name: 10


title: K326_Shoot_ZT6_R3


title: atg7-2_dehydration1

description: Sample name: 8


title: K326_Shoot_ZT6_R1


title: atg7-2_control2

description: Sample name: 9

value: Control


title: K326_Root_ZT12_R2


title: atg7-2_control3

description: Sample name: 11


title: K326_Root_ZT6_R3


title: RA+MTX (receiving methotrexate)

value: RA+MTX (receiving methotrexate)


title: MS-NAÏVE

value: MS-NAIVE


title: MS-EST

value: MS-EST


title: atg7-2_control1

description: Sample name: 7

value: leaf