title: PolII ChIP-seq, Epididymal white adipose tissue

data_processing:
All the ChIP-seq libraries were sequenced by the Functional Genomics Core at the University of Pennsylvania using HiSeq 2000.
ChIP-seq reads were aligned to mouse genome (mm9) using Bowtie with options, ‘-k 1 -m 1 --best --strata’. All redundant reads were discarded except one per genomic position.
BigWig files for RPM-normalized stack-height profiles were generated using Homer and bedGraphToBigWig command.
Genome_build: mm9
Supplementary_files_format_and_content: RPM-normalized bigWig files

source_name: Epididymal white adipose tissue

growth_protocol: C57BL/6J male mice were maintained in a 12 hour dark /light cycle, and sacrificed at 5 pm between 10 and 12 weeks of age for tissue collection.

extract_protocol:
Interscapular BAT and epididymal WAT were isolated and processed separately for each sacrificed mouse. The tissues were immediately minced, crosslinked in 1 % formaldehyde/PBS, and stored at -80 C. For each fat pad, material from 3-4 mice was used for sequencing. To prepare ChIP extracts, frozen crosslinked tissue was thawed and suspended ChIP buffer (50 mM HEPES/NaOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-Deoxycholate and Complete protease inhibitor) supplemented with 0.1% SDS. Samples were incubated at 4 C for 10 min, and subjected to microtip probe sonication under conditions optimized for IP efficiency. Extracts were cleared of insoluble lipid by microfuge centrifugation at full speed followed by extract transfer to a new tube. The process was repeated until minimal lipid accumulated at the top of the extract after centrifugation.
ChIP-Seq libraries were produced and sequenced according to Illumina protocols. Libraries were multiplexed for sequencing.

treatment_protocol: Male mice were delivered from the vendor at seven weeks of age. After arrival, placed on a normal chow diet and allowed to acclimate for 3-5 weeks.

value: Epididymal white adipose tissue

value: PolII (Santa Cruz sc-899, sc-9001)


title: Prdm16 ChIP-seq, WT BAT, rep1

status: Public on Feb 10 2015

type: SRA

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

country: USA

institute: Cincinnati Children's Hospital Medical Center

library_source: genomic

data_processing:
All the ChIP-seq libraries were sequenced by the Functional Genomics Core at the University of Pennsylvania using HiSeq 2000 or Illumina Genome Analyzer IIx.
ChIP-seq reads were aligned to mouse genome (mm9) using Bowtie with options, ‘-k 1 -m 1 --best --strata’. All redundant reads were discarded except one per genomic position. Peak-calling for PRDM16 and MED1 was performed using Homer. After initial calling, all peaks were resized to 200 bp, and a 1 RPM cut-off was applied. PRDM16 binding sites were more rigorously defined as follows. After initial peak-calling, replicates were compared to check reproducibility then pooled. Final peak-calling was performed for a pooled WT sample using a pooled KO sample as a background control. Any genomic regions that overlapped with ENCODE blacklist regions were eliminated.
BigWig files for RPM-normalized stack-height profiles were generated using Homer and bedGraphToBigWig command.
Genome_build: mm9
Supplementary_files_format_and_content: RPM-normalized bigWig files

molecule: genomic DNA

organism: Mus musculus

source_name: Wildtype BAT

growth_protocol: C57BL6 male mice were maintained in a 12 hour dark /light cycle. Mice used for PRDM16 ChIP seq were sacrificed at 8 weeks of age. Mice used for Pol2, Med1 and H3K27ac were sacrificed at 9 months of age or older for tissue collection.

extract_protocol:
Interscapular BAT was isolated and processed for each sacrificed mouse. The tissues were immediately minced, crosslinked in 1 % formaldehyde/PBS. MED1 ChIPs were performed using EGS as an additional crosslinker. For each fat pad, material from 3-4 mice was used for sequencing. To prepare ChIP extracts, crosslinked tissue was suspended in a ChIP buffer containing 20mM Tris, 0.1% SDS, 1% Triton-100, 150 mM NaCl, 1 mM EDTA, protease inhibitors. Samples were incubated at 4 C for 10 min, and subjected to microtip probe sonication under conditions optimized for IP efficiency. Extracts were cleared of insoluble lipid by microfuge centrifugation at full speed followed by extract transfer to a new tube. The process was repeated until minimal lipid accumulated at the top of the extract after centrifugation.
ChIP-Seq libraries were produced and sequenced according to Illumina protocols. Libraries were multiplexed for sequencing.

tag: strain

value: Prdm16(fl/fl) C57Bl6

tag: tissue

value: Brown adipose tissue

tag: antibody

value: Made in Lab (Harms et al. 2014. Cell Metab.)


title: FLP-IN_R495X_FUS-RNAi_1

city: La Jolla

first: Xiang-Dong

last: Fu

state: CA

address: 9500 Gilman Drive, Room 231

department: CMM

institute: UC San Diego

description: R495X + FUS-RNAi

library_source: transcriptomic

data_processing:
The sequenced 40 bases were mapped to the oligo pool sequences with Bowtie by allowing 1 mismatch in each of the donor and acceptor sequences.
Genome_build: hg18
Supplementary_files_format_and_content: The processed files contain both the genomic location (the first 6 columns) and counts for 2 isoforms (last 2 columns) of each alternative splicing event.

molecule: total RNA

organism: Homo sapiens

source_name: HeLa

growth_protocol: DMEM with 10% FBS for HeLa cells. DMEM with 20% FBS and 1x NEAA for primary fibroblasts.

extract_protocol:
Total RNA was extracted from cells using Trizol reagent (Life technologies).
RASL library was constructed according to Li H, et al protocol published Current Protocols in Molecular Biology.

treatment_protocol: Transgene expression was induced by 4μg/ml tetracycline. siRNA was transfected using Lipofectmine RNAiMAX (Life technologies)

tag: cell type

value: human cervical cancer patient imortalized

tag: strategy

value: RASL-seq

tag: cell line

value: HeLa

tag: sample type

value: R495X + FUS-RNAi


title: FLP-IN_P525L_FUS-RNAi_3

description: P525L + FUS-RNAi

value: P525L + FUS-RNAi


title: FLP-IN_P525L_FUS-RNAi_1

description: P525L + FUS-RNAi


title: FLP-IN_WT-FUS_FUS-RNAi_2

description: wt-FUS + FUS-RNAi

value: wt-FUS + FUS-RNAi


title: FLP-IN_WT-FUS_FUS-RNAi_3

description: wt-FUS + FUS-RNAi


title: H3K27ac ChIP-seq, Epididymal white adipose tissue

value: H3K27ac (Abcam ab4729)


title: H3K27ac ChIP-seq, Brown adipose tissue

source_name: Brown adipose tissue


title: FLP-IN_WT-FUS_FUS-RNAi_1

description: wt-FUS + FUS-RNAi


title: FLP-IN_FUS-RNAi_3

description: FLP-IN HeLa parental + FUS-RNAi

value: FLP-IN HeLa parental + FUS-RNAi


title: FLP-IN_FUS-RNAi_2

description: FLP-IN HeLa parental + FUS-RNAi


title: FLP-IN_parental_3

description: FLP-IN HeLa parental

value: FLP-IN HeLa parental


title: FLP-IN_parental_2

description: FLP-IN HeLa parental


title: FLP-IN_parental_1

description: FLP-IN HeLa parental


title: FLP-IN_FUS-RNAi_1

description: FLP-IN HeLa parental + FUS-RNAi


title: FLP-IN_R514G_FUS-RNAi_3

description: R514G + FUS-RNAi

value: R514G + FUS-RNAi


title: L76

city: East Lansing

first: Rance

last: Nault

state: United States

address: 1355 Bogue St. B403

department: Department of Pharmacology and Toxicology

institute: Michigan State University

description: Mice dosed every 4 days for 28 days

data_processing:
Quality Control: FASTQC v0.11.2
Removal of adaptors and low-complexity reads: FASTX v0.0.14
Alignment: TopHat v1.4.1
Conversion to SAM format: SAMTools v0.1.19
Abundance measurement: HTSeq v0.6.1
Count transformation: DESeq
Normalization and analysis: Transformed counts were normalized using a semi-parametric approach (Eckel et al., 2004) and analyzed using an empirical Bayes method (Eckel et al., 2005).
Genome_build: GRCm38 release 74
Supplementary_files_format_and_content: Tab-delimited text files represent the number of aligned reads to each gene

source_name: Liver

extract_protocol:
Livers were homogenized in TRIzol (Invitrogen, Carlsbad, CA) using a mixer mill 300 tissue homogenizer (Retsch, Germany). Total RNA was isolated according to manufacturers instructions with an additional phenol:chloroform extraction and resuspended in RNA storage solution (Ambion Inc., Austin, TX). RNA was quantified and examined for purity and quality by nanodrop, Qubit, Bioanalyzer and visualization on a denaturing gel.
Libraries were were prepared using the Illumina TrueSeq RNA sample preparation kit according to manufacturers instructions. Library sizes were confirmed using Caliper GX and quantified by the Kapa biosystems qPCR according to manufacturers instructions

treatment_protocol: Female ovariectomized C57BL/6 mice were gavaged daily with sesame oil vehicle, 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 ug/kg TCDD every  4 days for 28 days.

value: Liver

tag: gender

value: Female

tag: treatment

value: TCDD

tag: dose

value: ug/kg


title: AMB061

city: Durham

first: Jenny

last: Tung

state: NC

address: 125 Science Drive

institute: Duke University

data_processing:
Illumina Casava software was used for basecalling
Reads were mapped to the baboon genome using bwa 0.5.9, with a seed length of 25 bases, max edit distance of 2 mismatches in the seed, read trimming QS threshold of 20, and default maximum edit distance
reads that mapped to putative exon boundaries were identified using the program jfinder
Only reads that uniquely mapped to exons with a mapping QS >= 10 were retained for downstream analysis
RPKM were calculated for each gene, quantile normalized across individuals, and transformed to a standard normal for each gene
Genome_build: Panu2.0
Supplementary_files_format_and_content: countdata.txt includes counts (unnormalized) for each gene-individual combination; processeddata.txt includes normalized and transformed RPKM values for each gene-individual combination (to a standard normal)

molecule: polyA RNA

organism: Papio cynocephalus

source_name: whole blood

growth_protocol: natural population

extract_protocol:
PaxGene RNA extraction followed by DynaI bead poly-A mRNA purification
Illumina RNA-seq

tag: Sex

value: M

tag: age

value: whole blood


title: AMB060

value: F


title: L80

description: Mice dosed every 4 days for 28 days


title: AMB063


title: FLP-IN_R495X_FUS-RNAi_3

description: R495X + FUS-RNAi

value: human cervical cancer patient imortalized


title: L79

description: Mice dosed every 4 days for 28 days


title: AMB062


title: L74

description: Mice dosed every 4 days for 28 days


title: L72

description: Mice dosed every 4 days for 28 days


title: AMB059


title: AMB058


title: AMB057


title: PolII ChIP-seq, Brown adipose tissue

value: Brown adipose tissue

value: PolII (Santa Cruz sc-899, sc-9001)


title: L71

description: Mice dosed every 4 days for 28 days


title: AMB056


title: AMB055


title: L70

description: Mice dosed every 4 days for 28 days


title: L64

description: Mice dosed every 4 days for 28 days


title: L66

description: Mice dosed every 4 days for 28 days


title: L68

description: Mice dosed every 4 days for 28 days


title: L63

description: Mice dosed every 4 days for 28 days


title: AMB054


title: AMB052


title: AMB053


title: AMB050


title: AMB051


title: L75

description: Mice dosed every 4 days for 28 days


title: AMB049


title: AMB048


title: L58

description: Mice dosed every 4 days for 28 days


title: L56

description: Mice dosed every 4 days for 28 days


title: L54

description: Mice dosed every 4 days for 28 days


title: AMB047


title: L55

description: Mice dosed every 4 days for 28 days


title: L53

description: Mice dosed every 4 days for 28 days


title: AMB044


title: AMB045


title: L51

description: Mice dosed every 4 days for 28 days


title: AMB043


title: AMB046


title: AMB042


title: L48

description: Mice dosed every 4 days for 28 days


title: AMB041


title: L46

description: Mice dosed every 4 days for 28 days


title: L60

description: Mice dosed every 4 days for 28 days


title: L59

description: Mice dosed every 4 days for 28 days


title: AMB040


title: L44

description: Mice dosed every 4 days for 28 days


title: AMB039


title: L45

description: Mice dosed every 4 days for 28 days


title: L40

description: Mice dosed every 4 days for 28 days


title: AMB038


title: L39

description: Mice dosed every 4 days for 28 days


title: L38

description: Mice dosed every 4 days for 28 days


title: AMB037


title: AMB036


title: L37

description: Mice dosed every 4 days for 28 days


title: L36

description: Mice dosed every 4 days for 28 days


title: AMB034


title: AMB033


title: L32

description: Mice dosed every 4 days for 28 days


title: L47

description: Mice dosed every 4 days for 28 days


title: L29

description: Mice dosed every 4 days for 28 days


title: AMB032


title: L30

description: Mice dosed every 4 days for 28 days


title: L28

description: Mice dosed every 4 days for 28 days


title: AMB030


title: AMB029


title: L27

description: Mice dosed every 4 days for 28 days


title: AMB025


title: AMB026


title: L23

description: Mice dosed every 4 days for 28 days


title: L24

description: Mice dosed every 4 days for 28 days


title: AMB027


title: AMB035


title: L21

description: Mice dosed every 4 days for 28 days


title: AMB024


title: L18

description: Mice dosed every 4 days for 28 days


title: L8

description: Mice dosed every 4 days for 28 days

value: Vehicle


title: AMB023


title: L22

description: Mice dosed every 4 days for 28 days


title: L4

description: Mice dosed every 4 days for 28 days


title: AMB020


title: AMB031


title: L3

description: Mice dosed every 4 days for 28 days


title: L7

description: Mice dosed every 4 days for 28 days


title: AMB022


title: AMB018


title: L2

description: Mice dosed every 4 days for 28 days


title: AMB019


title: AMB015


title: AMB017


title: AMB014


title: AMB013


title: AMB012


title: AMB011


title: AMB021


title: AMB010


title: cord_sci_day8_run2

city: Melbourne

first: Norman

last: Saunders

state: VIC

address: Grattan Street, Parkville

department: Pharmacology and Therapeutics

country: Australia

institute: University of Melbourne

data_processing:
Short reads were mapped to the Ensembl Monodelphis domestica genome, version 69, using Bowtie2 with the local alignment setting
Mapped reads were counted using HTSeq using the default "union" setting and counts for non-protein-coding and mitochondrial genes removed.
EdgeR v2.6.12 was used to test for significant differences in gene expression with age and injury, and for differences in response to injury at each age .  The model design included factors accounting for age, run, and an interaction between age and injury. Genes with a Benjamini-Hochberg   false discovery rate of less than 0.05 were considered significant.
Genome_build: Monodelphis domestica, Ensembl version 69
Supplementary_files_format_and_content: The counts were generated as above.

organism: Monodelphis domestica

source_name: Spinal cord

growth_protocol: Monodelphis domestica were obtained from a colony based at the University of Melbourne Medical Sciences Animal House Facility, Melbourne, Australia. Procedures were performed according to National Health and Medical Research Council guidelines, with the approval of the University of Melbourne Animal Ethics Committee (Ethics #0707108). Pups of both sexes were used. Day of birth was designated as postnatal day zero, P0 (see Wheaton et al., 2011, 2013).

extract_protocol:
The cords were separated into two segments, the upper (rostral to the injury) and lower (caudal to the injury) divided at T10, or corresponding segments from control animal spinal cords. Samples were stored at -80°C until used. Rostral segments of the cords were used in the present study. For morphological studies spinal cords were dissected out, fixed in Bouin’s fixative and paraffin embedded as described previously (Noor et al, 2011, 2013). Total RNA was extracted from individual samples of rostral spinal cord using the RNeasy Mini Kit, Qiashredder columns and gDNA removal columns (Qiagen, Valencia, CA, USA) according to standard supplier protocol. Total RNA samples were quantifies using a NanoDrop ND-100 UV-VIS spectrophotometer (Thermo Scientific, Wilmington, DE, USA) and quality checked on an RNA chip using and Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA). Only samples with an RNA Integrity Number close to 2 were kept for further sequencing experiments.
A cDNA library was prepared from 10µg of total RNA using the mRNA-Seq Sample Preparation Kit (Illumina, San Diego, CA, USA) according to standard manufacturer protocol. Quality of the library was verified using a DNA 1000 chip using the Agilent 2100 Bioanalyzer (Agilent) and quantified by fluorimetry. The library was subjected to 100bp single end read cycles of sequencing on an Illumina Genome Analyzer IIx (Illumina) as per manufacturer protocol. Cluster generation was performed on a c-Bot (Illumina) with a single read cluster generation kit. Sequencing was performed using a 36 cycle sequencing kit v4. In total 16 separate sequencing lanes were run on the platform. Two separate runs were conducted from separately collected samples, which were: rostral spinal cords from P8 control, P7+24h injury, P29 controls and P28+24h injury

treatment_protocol: At P7, Monodelphis pups are still attached to the mothers’ teats (Saunders et al 1989). The female adult Monodelphis were anaesthetized with 2–3% isofluorane; the same anaesthetic was administered to the P7 pups via a small facemask during the surgical procedure. Pups at P28 are no longer attached to the mother and were separately anaesthetized with isofluorane throughout the surgical procedure (Fry et al 2003;Wheaton et al, 2011).  Complete spinal cord transection was performed at thoracic level 10 (T10) using sharp sterilized fine scissors. Skin was closed using surgical grade glue (Vetbond, 3M, St. Paul, MN, USA). Animals were returned to their cages and allowed to recover for 24 hours (+24h) post injury. At the end of the experimental period, control and injured animals were terminally anaesthetized with an overdose of isofluorane and spinal cords were dissected out.

value: post-natal day 8

value: injured; day 8

value: spinal cord


title: cord_sci_day8_run1


title: cord_control_day8_run2

value: control; day 8


title: cord_control_day29_run1

value: post-natal day 29

value: control; day 29


title: AMB009


title: cord_sci_day29_run1

value: injured;day 29


title: AMB016


title: RRBS_shDnmt3a

city: Torino

first: Francesco

last: Neri

state: Italy

address: Via Nizza 52

country: Italy

institute: University of Torino

description: DNA was treated with EpiTect Bisulfite Kits (Qiagen)

data_processing:
Basecalls performed using CASAVA version 1.8
Nucleotide positions with a quality score behind 20 (Phred33 scale) were trimmed using the fastx_trimmer tool from the FASTX Toolkit
Reads were subjected to adapter clipping using the fastx_clipper tool from the FASTX Toolkit, and reads shorter than 35nt were discarded
Reads for RRBS_E14 were aligned to the mouse genome assembly using Bismark v0.10.1 using the default parameters
Methylation status was peformed using Methylation Extractor tool of Bismark.
Genome_build: mm9
Supplementary_files_format_and_content: bed file of RRBS were performed using custom perl script.

source_name: ESC E14

extract_protocol:
Genomic DNA was extracted using DNeasy Blood and Tissue kit (Qiagen).
The genomic DNA was digested O/N with MspI (New England Biolabs). Libraries were generated with Illumina TruSeq DNA Sample Prep Kit following manufacturer instructions, bisulfite converted using EpiTect Bisulfite Kits (Qiagen)  and sequenced on Illumina HiScanSQ Platform.

value: shRNA Dnmt3a

value: embryonic stem cells

tag: developmental stage


title: RRBS_shDnmt1a

value: shRNA Dnmt1


title: AMB007

value: M


title: RRBS_shTet1/2

value: shRNA Tet1 and Tet2


title: RRBS_shCtr

value: shRNA control


title: AMB004

value: whole blood


title: WKY KO rep1

city: London

first: Jacques

last: Behmoaras

address: Du Cane road

department: Centre for Complement and Inflammation Research (CCIR),

country: United Kingdom

institute: Imperial College

description: WKY KO macrophages rep1

data_processing:
fastq files were mapped using Tophat2
Mapped files were summarised to count level using 'union' model from Htseq
Genome_build: rn4
Supplementary_files_format_and_content: text file containing raw count data

organism: Rattus norvegicus

source_name: macrophages

extract_protocol:
Total RNA was extracted from rat (Wild type Wistar-Kyoto strain, n=3; Cyp2j4-/-, n=3) and mice (commercially outbred mice; n=4) bone marrow derived macrophages (BMDMs) and human monocytes-derived macrophages (n=3 healthy donors) using Trizol (Invitrogen) according to manufacturer's instructions with an additional purification step by on-column DNase treatment using the RNase-free DNase Kit (Qiagen) to ensure elimination of any genomic DNA.
The integrity and quantity of total RNA was determined using a NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific) and Agilent 2100 Bioanalyzer (Agilent Technologies). 1μg of total RNA from each species was used to generate RNA-seq libraries using TruSeq RNA sample preparation kit (Illumina) according to the manufacturer's instructions. Briefly, RNA was purified and fragmented using poly-T oligo-attached magnetic beads using two rounds of purification followed by the first and second cDNA strand synthesis.

value: wistar kyoto

tag: genotype/variation

value: Cyp2j4 kO


title: RRBS_shDnmt3a/b

value: shRNA Dnmt3a and Dnmt3b


title: RRMAB-Seq_shTdg

description:
DNA was treated with M.SssI and EpiTect Bisulfite Kits (Qiagen)
library strategy: MAB-Seq and RRMAB-Seq

data_processing:
Basecalls performed using CASAVA version 1.8
Nucleotide positions with a quality score behind 20 (Phred33 scale) were trimmed using the fastx_trimmer tool from the FASTX Toolkit
Reads were subjected to adapter clipping using the fastx_clipper tool from the FASTX Toolkit, and reads shorter than 35nt were discarded
Reads were aligned to the mouse genome assembly using Bismark v0.10.1 using the default parameters
Methylation status was peformed using Methylation Extractor tool of Bismark.
The 5fcaC sites were determined by using a binomial test for each cytosine = pbinom(x, N, p) where N is the sequencing depth at the C residue, p is the fail-rate of the M.SssI treatment, as estimated on E. coli genome, and x is the number of times that the C residue was sequenced as T. Only the cytosines with a coverage > 10 and a p-value < 0.01 were considered for further analysis.
Genome_build: mm9
Supplementary_files_format_and_content: bed files with percentage of fcaC

extract_protocol:
Genomic DNA was extracted using DNeasy Blood and Tissue kit (Qiagen).
1 μg of mESC genomic DNA (plus 1 ng of E. coli DH10B genomic DNA) was incubated with 4U of M.SssI CpG Methyltransferase (NEB), supplemented with 160 μM final S-Adenosyl methionine for 2 h at 37°C. The incubation was repeated 3 times to maximize CpG methylation. For whole-genome MAB-Seq, methylated DNA was sheared using a Bioruptor® Twin (Diagenode) for 2 runs of 15 cycles [30 s “ON,” 30 s “OFF”] at high power setting. For Reduced Representation MAB-Seq (RRMAB-Seq), methylated DNA was digested for 4h at 37°C with 200U of MspI restriction endonuclease (NEB).
Fragmented/digested DNA was then end-repaired, dA-tailed, and ligated to methylated adapters, using the Illumina TruSeq DNA Sample Prep Kit, following manufacturer instructions. Adapter-ligated DNA, was treated for additional 3 cycles with M.SssI enzyme to methylate the unmodified cytosines introduced by the end-repair step. DNA was loaded on an EGel Size select 2% agarose pre-cast gel (Invitrogen), and a fraction corresponding to fragments ranging from 180bp to 350bp was recovered. Purified DNA was then subjected to bisulfite conversion using the EpiTect Bisulfite Kit (Qiagen). Bisulfite-converted DNA was finally enriched by 15 cycles of PCR using Pfu Turbo Cx HotStart Taq (Agilent).

value: shRNA Tdg


title: RRBS_shDnmt3b

value: shRNA Dnmt3b


title: WKY KO rep3

description: WKY KO macrophages rep3


title: RRMAB-Seq_shCtr


title: AMB006


title: cord_sci_day29_run2

value: spinal cord


title: WKY KO rep2

description: WKY KO macrophages rep2


title: cord_control_day8_run1

value: post-natal day 8

value: control; day 8


title: WKY control rep3

description: WKY control macrophages rep3

value: wild type


title: AMB003


title: MAB-Seq

data_processing:
Basecalls performed using CASAVA version 1.8
Nucleotide positions with a quality score behind 20 (Phred33 scale) were trimmed using the fastx_trimmer tool from the FASTX Toolkit
Reads were subjected to adapter clipping using the fastx_clipper tool from the FASTX Toolkit, and reads shorter than 35nt were discarded
Reads were aligned to the mouse genome assembly using Bismark v0.10.1 using the default parameters
Methylation status was peformed using Methylation Extractor tool of Bismark.
The 5fcaC sites were determined by using a binomial test for each cytosine = pbinom(x, N, p) where N is the sequencing depth at the C residue, p is the fail-rate of the M.SssI treatment, as estimated on E. coli genome, and x is the number of times that the C residue was sequenced as T. Only the cytosines with a coverage > 50 and a p-value < 0.001 were considered for further analysis.
Genome_build: mm9
Supplementary_files_format_and_content: bed files with percentage of fcaC

value: wt


title: AMB008

value: F


title: MAB-Seq_rep2

value: embryonic stem cells


title: WKY control rep2

description: WKY control macrophages rep2


title: AMB001


title: ChIP-Seq_BioMock

data_processing:
Basecalls performed using CASAVA version 1.8
Nucleotide positions with a quality score behind 20 (Phred33 scale) were trimmed using the fastx_trimmer tool from the FASTX Toolkit
Reads were subjected to adapter clipping using the fastx_clipper tool from the FASTX Toolkit, and reads shorter than 35nt were discarded
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie v0.12.7 using the following parameters : -q --max /dev/null -v 1  -S --sam-nohead -m 1
Data were filtered using the following specifications: duplicate reads were filtered out
Peaks were called using MACS v1.4.1 with the following setting: --gsize=mm --nolambda --bw=300
Genome_build: mm9
Supplementary_files_format_and_content: bed file of BioTdg peaks

extract_protocol:
DNA was treated with EpiTect Bisulfite Kits (Qiagen)
Chromatin from fixed cells was extracted with 1% SDS buffer and sonicated for 20' prior immunoprecipiattion step (detailed description is in Material and Methods)
Library were perfomed using NEBNext ChIP-Seq Library Prep Master Mix Set (NEB), following manufacturer instructions

tag: ChIP

value: BirA cells (mock)


title: Head fold 5

status: Public on Feb 09 2015

city: Cambridge

first: Evangelia

last: Diamanti

address: Wellcome Trust / MRC Building, Hills Road

department: Haematology

institute: University of Cambridge

data_processing:
RNA-seq reads aligned to mm10 using STAR (version 2.3.0) with parameters --outFilterMultimapScoreRange 1 --outSAMstrandField intronMotif --genomeLoad NoSharedMemory --outStd SAM.
SAM files converted to BAM format and then sorted using samtools (version 0.1.18).
Read counts for features were calculated using HTSeq (version 0.6.1).
Genome_build: mm10
Supplementary_files_format_and_content: HTSeq counts/spreadsheet.

source_name: Flk1+ mesoderm

extract_protocol:
Timed matings were set up and embryos were staged according to morphologic criteria. Suspensions of embryo cells were prepared as described previously (Tanaka et al 2012 PNAS) and single cell suspensions were stained with Flk-1-APC (AVAS12; BD Bioscience). Cells were sorted into 2 μl of lysis buffer (0.2 % (v/v) Triton X-100 and 2 U/μl RNase inhibitor (Clontech)) and stored at -80 °C.
RNAseq was carried out using the Smart-seq2 protocol according to Picelli et al 2014 Nature Protocols and sequenced on an Illumina HiSeq 2500.

value: E7.75 embryo


title: ChIP-Seq_BioTdg

value: Bio-Tdg cells


title: AMB002


title: Head fold 4


title: Head fold 3


title: Head fold 2


title: AMB005

value: M


title: Head fold 1


title: WKY control rep1

description: WKY control macrophages rep1


title: SF3_LPS_rep3

city: Denver

first: Scott

last: Alper

state: CO

address: 1400 Jackson St.

department: Integrated Center for Genes Environment & Health

institute: National Jewish Health

data_processing:
Basecalling, barcode demultiplexing and adapter trimming by Ion Torrent Suite 3.6
Mapping with GSNAP 2013-11-27 using SNP137 (after removal of reads <30 nt).
Counting reads per gene using htseq-count (from HTSeq version 0.5.4p) and Ensembl annotation (downloaded from UCSC table browser July 29, 2013)
Counting reads per (partial) exon using scripts from DEXSeq version 1.6.0 (and libraries from HTSeq version 0.5.4p)
Genome_build: mm10
Supplementary_files_format_and_content: htseq-genecounts_uniq.txt: reads per gene for each gene and sample (consolidated from htseq-count output); *DEXSeq-counts.txt files: reads per (partial) exon (for DEXSeq).

growth_protocol: RAW264.7 cells were maintained in DMEM supplemented with 10% FBS

extract_protocol:
Total RNA was harvested with the RNAeasy kit (Qiagen).  PolyA RNA was then isolated using the Dynabeads mRNA Direct Purification kit (Life Technologies).
polyA-RNA-seq library construction was prepared using the Ion Total RNA-Seq kit v2, for next generation sequencing using an Ion Proton platform (Life Technologies).

treatment_protocol: siRNAs were transfected using the Amaxa nucleofector shuttle; 24 hours later, cells were treated with LPS for 4 hours

value: RAW 264.7 macrophages

value: BALB/c

tag: lps addition

value: 20 ng/ml for 4 h

tag: sirna

value: targeting SF3A1 for 24 h


title: Neural Plate 5

tag: strain

value: E7.5 embryo


title: SF3_LPS_rep1


title: Neural Plate 2


title: Neural Plate 4


title: Neural Plate 3


title: SF3_Ctrl_rep3


title: 24_LPS_rep2

value: nontargeting for 24 h


title: SF3_Ctrl_rep1


title: 24_LPS_rep3


title: Primitive Streak 5

value: E7.0 embryo


title: Primitive Streak 2


title: Primitive Streak 4


title: Ezh2-KO-CD62Llo rep3

city: SAN FRANCISCO

first: GAURAV

last: CHOPRA

address: 513 PARNASSUS AVE, HSW 1102

department: DIABETES CENTER

institute: UNIVERSITY OF CALIFORNIA - SAN FRANCISCO (UCSF)

data_processing:
Illumina Casava v.1.8.2 software used for basecalling and the FastQC program (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) was used for a quality check of the sequencing run.
RNA-Seq raw data was mapped by Tophat to mm10.
Read counting, final transcriptome assembly and differential gene expression analysis were done using Cufflinks v2.1.1 using significance cutoff = 0.05 as described in Trapnell, C. et al. Nature protocols 7, 562-78 (2012).
Ezh2-HET-CD62Lhi rep3 was removed from final transcriptome assembly using Cuffmerge and differential expression analysis due to low read counts.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files with FPKM values for each sample is provided as well as the combined FPKM values for all samples is given as a supplementary file (see corresponding KO and Het FPKM columns). Gene symbol, chromosomal location, TSS ID and FPKM values, etc. are shown.

source_name: Spleen and LN Tregs

extract_protocol:
RNA was isolated by TRIzol homogenization and extraction (Invitrogen) following manufacturer's protocol from sorted Tregs from Spleen and Lymph Node (LN).
RNA libraries were prepared for sequencing using standard Illumina protocols. Illumina TruSeq 2 kit, poly A selection protocol was used for library construction.

tag: tissue

value: Spleen and LN

value: CD62Llo Tregs from Foxp3YFP-Cre/Foxp3WT;Ezh2fl/fl

value: female


title: 24_Ctrl_rep1


title: Ezh2-KO-CD62Lhi rep2

value: CD62Lhi Tregs from Foxp3YFP-Cre/Foxp3WT;Ezh2fl/fl


title: 24_LPS_rep1


title: SF3_Ctrl_rep2


title: 24_Ctrl_rep3


title: Primitive Streak 1


title: 24_Ctrl_rep2


title: Ezh2-HET-CD62Llo rep3

value: CD62Llo Tregs from Foxp3YFP-Cre/Foxp3WT;Ezh2fl/+


title: Ezh2-HET-CD62Llo rep2


title: Ezh2-HET-CD62Lhi rep3

description: Removed from final analysis due to low read counts

value: CD62Lhi Tregs from Foxp3YFP-Cre/Foxp3WT;Ezh2fl/+


title: Ezh2-KO-CD62Llo rep2


title: PSG7 rep2

city: Buenos Aires

first: Natalia

last: Macchiaroli

address: Paraguay 2155, 13th floor

country: Argentina

institute: IMPaM

data_processing:
Base-calling performed with Illumina Casava 1.8 software.
small RNA-seq reads were trimmed for adaptor sequence and low quality reads were discarded. Then  reads were mapped to E. multilocularis genome assembly v4 using bowtie (mapper module of miRDeep2 software package) with parameters -c -j -l 18 -m –p.
miRNA prediction was performed with the core algorithm of miRDeep2 software package using as input all metazoan mature miRNAs and hairpins along with mapped reads from the previous step.
Data were filtered using the following criteria: i) miRDeep2 score ≥ 4 ii) significant randfold p-value < 0.05 iii) mature reads in more than one library iv) presence of star strand v) rRNAs, tRNAs and CDS were removed.
Genome_build: Echinococcus multilocularis genome assembly version 4
Supplementary_files_format_and_content: tab-delimited text file include raw miRNA counts for each sample

organism: Echinococcus canadensis

source_name: Fertile hydatid cyst from the liver of naturally infected swine

extract_protocol:
Protoscoleces and cyst walls were carefully recovered from fertile hydatid cysts obtained from the livers of naturally infected swine and sheep. Samples were frozen in liquid nitrogen and stored at -80ºC until RNA extraction. RNA enriched in small RNAs (<200 nt) was purified from protoscoleces and cyst walls using mirVana miRNA Isolation Kit (Ambion) according to the manufacturer’s instructions.
Libraries were prepared for sequencing using a NEBNext Small RNA Library Prep Set for Illumina (NEB) following the instruction’s manual with 1.5 μg of RNA enriched in small RNAs (<200 nt) as starting material.

tag: genotype

value: protoscoleces

tag: extracted molecule

value: small RNAs (<200 nt)


title: PSG7 rep1


title: Ezh2-HET-CD62Lhi rep1

tag: cell type


title: Ezh2-KO-CD62Llo rep1


title: CWG7 rep1

value: cyst wall


title: PSG1 rep2

organism: Echinococcus granulosus

source_name: Fertile hydatid cyst from the liver of naturally infected sheep


title: Ezh2-KO-CD62Lhi rep3


title: SF3_LPS_rep2


title: krps299SM1640h1

city: Ann Arbor

first: Mats

last: Ljungman

state: Michigan

address: NCRC, B520 Room 1346 2800 Plymouth Rd.

institute: University of Michigan

description:
Bru-Seq
molecule: bru-labeled RNA

data_processing:
Illumina Casava v1.8.2 software used for basecalling.
Reads were mapped to the Human ribosomal DNA complete repeating unit (U13369.1) using bowtie v.0.12.8 and parameters -n 3 -k 1 -m 1
Reads that did not map to the ribosomal DNA were mapped to the hg19 genome using TopHat v1.4.1 and parameters –min-isoform-fraction 0, --max-multihits 1, --no-closure-search, --no-coverage-search, --bowtie-n, --initial-read-mismatches 3
A coverage determination was then made for every base in the genome using Bedtools v.2.16.2 such that a base covered by one read was recorded as having a coverage of 1/read_length
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: The columns of the abundance measurement files indicate: (1) chromosome; (2) start; (3) end; (4) name; (5) score; (6) strand; (7) gene length; (8) feature type – exon, intron, etc; (9) number of introns and exons; (10) feautre length; (11) hits count; (12) density – count/length; (13) RPKM - count/(length/1E3)/(mapped read count/1E6)

source_name: Karpas 299

growth_protocol: Karpas 299 were grown in RPMI 1640 (Mediatech, Herndon, VA, USA) medium. The generation of the CD30L+ Chinese hamster ovary (CHO) cells has been previously described (Wright et al. 2007). CHO cells and CD30L+ CHO cells were cultured in F-12 nutrient medium (Gibco, Carlsbad, CA, USA). All cells were maintained at 37C in an atmosphere of 5% CO2 and cultured in media supplemented with 10% FBS and 2 mL L-glutamine.

extract_protocol:
Total RNA was isolated by using TRIzol reagent (Invitrogen), and Bru-labeled RNA was isolated from the total RNA by incubation with anti-BrdU antibodies (BD Biosciences) conjugated to magnetic beads (Dynabeads, Goat anti-Mouse IgG; Invitrogen) under gentle agitation at room temperature for 1 h. For more detail, see Paulsen et. al 2013
Bru-labeled RNA was mixed with first strand buffer and random primers and fragmented by heating at 85 ̊C for 10 minutes. The first strand cDNA was then  synthesized, in the presence of Actinomycin D to result in strand specific reads (only applicable to certain samples as indicated in sample table above). After purifying the first strand cDNA using AMPure RNAclean beads (Beckman Coulter), the second strand cDNA was synthesized. The resulting cDNA was purified with AMPure XP beads, after which the Illumina TruSeq RNA Sample Prep Kit was used to repair the cDNA ends, adenylate and ligate adaptors to the cDNA. The samples were then run on a 3% agarose gel and size-selected by excising gel slices in the 300bp region. These gel slices were purified using the QIAEX II Gel Extraction Kit (Qiagen) and then the Illumina TruSeq Kit PCR reagents were used to enrich the DNA fragments. After a final purification using AMPure XP beads, the quality and concentration of the DNA libraries were determined using an Agilent Bioanalyzer.

treatment_protocol: For drug treatment, drug (DMSO or SM-164) was added to cells for 3 hours. For receptor activation, As described previously (Wright et al., 2007) Karpas 299 cells were exposed for 3 hours to either CHO cells (negative control) or CD30L+ CHO cells and were collected with gentle pipetting. Labeling occurred during the last 30 minutes of the drug treatment or receptor activation treatment. RNA was extracted immediately after.

tag: cell line

value: Karpas 299

value: Test

tag: treatment type

value: Drug

tag: drug treatment

tag: receptor activation

tag: treatment time

value: 3 hours

tag: labeling agent

value: Bromouridine

tag: labeling time

value: 30 minutes


title: PSG1 rep1

tag: developmental stage


title: krps299DMSO0h1

description:
Bru-Seq
molecule: bru-labeled RNA

tag: sample type

value: Control

value: DMSO


title: Drosha -/- rep3 RNA-seq

city: Volos

first: Artemis

last: Hatzigeorgiou

address: 37 Glavani – 28th October Str

department: Department of Electrical and Computer Engineering

country: Greece

institute: University of Thessaly

data_processing:
Base call (.bcl) files for each cycle of sequencing were generated by Illumina Real Time Analysis (RTA) software and de-multiplexed to FASTQ files.
Quality control has been performed with FastQC in order to detect any possible adapter sequences or PCR primers. This has been accomplished by utilizing the algorithms of minion and trim galore.
GSNAP has been utilized in order to align the reads to the reference genome based on Ensembl GRCm38 resulting in 19 million uniquely mapped reads for the Drosha +/+ samples and  27.1 million uniquely mapped reads for the Drosha -/- samples.
HOMER software suite has been utilized to produce genome coverage files (bedGraph format) for each sample.
Genome_build: mm10
Supplementary_files_format_and_content: Genome coverage of each sample in bedGraph format.

source_name: Embryonic stem cells

growth_protocol: Mouse ES cells of WT or Drosha-null genotype were cultured on gelatinized plates free of feeder cells.

extract_protocol:
Total RNA was extracted by miRNeasy Mini Kit (Qiagen).
2 µg of total RNA was converted to poly(A)+ RNA using oligo-dT coated magnetic beads (Invitrogen).  Poly(A)+ RNA was converted to strand specific Illumina sequencing libraries with 8 bp barcodes using Epicenter ScriptSeq V1 RNA-Seq library preparation kit (Epicenter, Illumina Inc).  RNA-Seq libraries were hybridized to a single-end flow cell and individual fragments were clonally amplified by bridge amplification on the Illumina cBot.  Upon completion of clustering, the flow cell was loaded on the HiSeq 2000 (Illumina Inc) and sequenced using Illumina’s SBS chemistry.

value: Drosha -/-


title: Ezh2-HET-CD62Llo rep1

value: Spleen and LN

tag: gender


title: si-/Negtive control-Rep2_4899

city: Charlottesville

first: Fujun

last: Qin

state: VA

address: 345 Crispell Dr.

department: Pathology

institute: University of Virginia

description:
4899
3899 and 4899 are two runs from the same control sample.
5236, 3899 and 4899 come from the same sample but were sequenced at different lengths and by different companies (5236, 50 bp; 3899/4899, 101 bp)

data_processing:
5236 and 5237 are  analyzed by cufflinks.
SOAPfuse was used for analyzing the RNA sequencing data after combining the data for 5236, 3899 and 4899 for the si_control and 5237, 3900, and 4900 for the siCTCF sample.
Genome_build: hg19
Supplementary_files_format_and_content: txt file with FPKM for 5236 and 5237 by cufflinks, fusion genes from the SOAPfuse result using the combined data.

source_name: LNCaP cells

growth_protocol: LNCaP cells are cultured in phenol free RPMI 1640 with 10% FBS.

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

treatment_protocol: Cells are treated with siRNA CTCF and siRNA negative control for 3 days.

value: LNCaP

tag: treatment


title: corrected R14del-CMs (clone L2GC2)

city: NEW YORK

first: FRANCESCA

last: STILLITANO

state: NY

address: 1470 Madison Avenue

department: CARDIOVASCULAR RESEARCH

institute: Mount Sinai School of Medicine

data_processing:
Library strategy: Exome-Seq
Paired end exom-seq reads were aligned to the hg19 genome assembly using Bowtie2 version 2.1 with default configurations
After conversion into bam files same sample files were merged using samtools version 0.1.7_x86_64-linux
Picard-tools version 1.110 was used to coordinate sort the merged files, to mark duplicates, to add read groups and to create BamIndexes
GenomeAnalysisTK version 3.1-1 was used for local realignement under consideration of the known indels specified in the files 1000G_phase1.indels.hg19.sites.vcf Mills_and_1000G_gold_standard.indels.hg19.sites.vcf (downloaded from Broad Institute website) and default configurations
Base Quality Scores were recalibrated using GenomeAnalysisTK version 3.1-1 under consideration of known SNPs specified in dbsnp_138.hg19.vcf (downloaded from Broad Institute website) and default configurations
Variants were called using the GenomeAnalysisTK version 3.1-1 HaplotypeCaller
GenomeAnalysis TK version 3.1-1 was used for variant (indel) recalibration with the following configurations:
Variant Recalibrator: -nt 8 --maxGaussians 4 -resource:mills,known=false,training=true,truth=true,prior=12.0 /Data/reference_genomes/hg19_broad/Variation/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 /Data/reference_genomes/hg19_broad/Variation/dbsnp_138.hg19.vcf -an QD -an FS -an ReadPosRankSum -an MQRankSum -mode INDEL
ApplyRecalibration: --ts_filter_level 99.5 -mode INDEL
GenomeAnalysis TK version 3.1-1 was used for variant (SNP) recalibration with the following configurations:
Variant Recalibrator: -nt 8 -resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.hg19.sites.vcf -resource:omni,known=false,training=true,truth=true,prior=12.0 1000G_omni2.5.hg19.vcf -resource:1000G,known=false,training=true,truth=false,prior=10.0 1000G_phase1.snps.high_confidence.hg19.sites.vcf  -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_138.hg19.vcf -an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -mode SNP
ApplyRecalibration: -nt 8 -o francesca_recalibrated_snps_recalibrated_indels.vcf --ts_filter_level 99.5 -mode SNP
Genome_build: hg19
Supplementary_files_format_and_content: vcf data (will be submitted to dbVar or dbSNP)

source_name: Cardiomyocytes derived from PLN-R41del iPSC cells infected with AAV6-EGFP-miR-PLN

extract_protocol:
Genomic DNA samples were assessed for quantity by Qubit fluorometry (Life Technologies, Grand Island, NY) and for quality by the 2100 Bioanalyzer system (Agilent). Initial shearing of 0.5–1 µg genomic DNA to an average of 200-300 bp fragments was performed using the Covaris E210 focused acoustic energy system (Covaris). Whole genome libraries were prepared using the NEBNext DNA Library Prep kit according to the standard manufacturer's protocol (New England Biolabs). Illumina compatible paired-end adapters were used and the adapter-ligated DNA fragments was amplified by ligation-mediated PCR (KAPA Biosystems) using a reverse PCR primer containing a six nucleotide barcode that allowed for multiples samples to be pooled and sequenced in the same run. The library was enriched for human exomic sequences using the SeqCap EZ Human Exome Library v3.0 capture system (Roche NimbleGen).
The libraries were sequenced with a 100bp paired-end protocol on the Illumina HiSeq 2500 according to the manufacturer's protocol (Illumina)

value: iPS-derived cardiomyocytes

tag: differentiation stage

value: Day 30 post-differentiation


title: Neural Plate 1

tag: strain

tag: age

value: E7.5 embryo


title: Drosha -/- rep2 RNA-seq

tag: genotype


title: AMB028

tag: Sex

value: M

tag: tissue

value: whole blood


title: siCTCF-Rep1_3900

description:
3900
3900 and 4900 are two runs from the same siCTCF sample.
5237, 3900 and 4900 come from the same sample but were sequenced at different lengths and by different companies (5237, 50 bp; 3900/4900, 101 bp)

tag: cell line

value: siCTCF/lane 3


title: Drosha -/- rep1 RNA-seq


title: si-/Negtive control-Rep1_3899

description:
3899
3899 and 4899 are two runs from the same control sample.
5236, 3899 and 4899 come from the same sample but were sequenced at different lengths and by different companies (5236, 50 bp; 3899/4899, 101 bp)

value: control/lane 3


title: Ezh2-HET-CD62Lhi rep2

tag: cell type

value: CD62Lhi Tregs from Foxp3YFP-Cre/Foxp3WT;Ezh2fl/+

value: female


title: R14del-CMs AAV6-PLN miRNA

data_processing:
Read alignment with Star under default configurations
Gene raw read counts were determined with Htseq under default conditions
Genome_build: hg19

extract_protocol:
Cardiomyocytes derived from PLN-R41del iPSC cells were infected with AAV6-EGFP-miR-PLN or AAV6-EGFP-miR-luc as a negative control at an MOI of 1e4. One week after infection, total RNA was extracted using Zymo columns and 2 micrograms were used to generate an RNAseq sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: krps299pre3hCD30L0h2

description:
Bru-Seq
molecule: bru-labeled RNA

value: Karpas 299

value: Test

tag: treatment type

value: Receptor Activation

tag: drug treatment

value: CD30L+ CHO cells

value: 3 hours


title: Primitive Streak 3

value: E7.0 embryo


title: Drosha +/+ rep2 RNA-seq

value: wild type


title: CWG7 rep2

value: cyst wall

tag: extracted molecule

value: small RNAs (<200 nt)


title: Ezh2-KO-CD62Lhi rep1

value: Spleen and LN

value: CD62Lhi Tregs from Foxp3YFP-Cre/Foxp3WT;Ezh2fl/fl


title: krps2990h2

description:
Bru-Seq
molecule: bru-labeled RNA

value: Control

tag: receptor activation

value: CHO cells (negative control)

tag: treatment time

tag: labeling agent

value: Bromouridine

value: 30 minutes


title: Drosha +/+ rep1 RNA-seq


title: siCTCF-Rep2_4900

description:
4900
3900 and 4900 are two runs from the same siCTCF sample.
5237, 3900 and 4900 come from the same sample but were sequenced at different lengths and by different companies (5237, 50 bp; 3900/4900, 101 bp)

value: LNCaP

value: siCTCF/lane 4


title: corrected R14del-CMs (clone L2GC1)

source_name: Cardiomyocytes derived from PLN-R41del iPSC cells infected with AAV6-EGFP-miR-luc

value: iPS-derived cardiomyocytes

value: Day 30 post-differentiation


title: lncap_AR_DHT_control2

status: Public on Feb 08 2015

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

country: Japan

institute: Tokyo Metropolitan Institute of Gerontology

description: ChIP by AR antibody (santacruz H-280) after treating cells with siControl

data_processing:
Basecalls performed using CASAVA-1.8.2 for generating BED file
ChIP-seq reads were aligned to the hg18 genome assembly using Bowtie version 0.12.8 with parameters -a --best --strata -m 1 -v 2.
Generate alignments in the SAM format given single-end reads. Convert SAM to BAM files using samtools view command. samtools version is 0.1.16.
Signal scores in bed files were calculated using Model-based analysis of ChIP-seq (MACS; P-value < 10xE-4 or -5)
Basecalls performed using CASAVA version 1.7 for generating BAR file
ChIP-seq reads were aligned to the hg18 genome assembly using Illumina
Signal scores in bar files were calculated using in-house program described at Mol Cell Biol. 2009 Jul;29(13):3544-55. Shortly , rates of ChIP counts / control counts in 300bps window were used.
Genome_build: hg18
Supplementary_files_format_and_content: peak files can be visualized by Integrative genomic viewer ver 2.2 (IGV ver 2.2)
Supplementary_files_format_and_content: Bar files can be visualized by integrative genome browser (IGB) downloaded from Affymetrix.

source_name: prostate cancer cells

growth_protocol: LNCaP cells were cultures in RPMI 1640 containing 10% FBS. Before hormone treatment, cells were incubated in Phenol red-free RPMI 1640 containing 2.5% charcoal/dextran treated FBS for three days.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
The Chromatin immunoprecipitated DNA fragments (approx.10 ng in 30 µl water) are end repaired by using T4 DNA polymerase, Klenow DNA polymerase and T4 polynucleotide kinase in the presence of dNTPs. And an ‘A’ base is added to the 3’end of the blunt phosphorylated DNA fragments, using the polymerase activity of Klenow fragment. Then, adaptors (Adaptor oligo mix, Illumina) are ligated to the ends of the DNA fragments. The resulting DNA fragments are purified by MinElute column (QIAGEN).  300 ~ 500 bp DNA fragments are purified by using E-Gel SizeSelect agarose Gels (Invitrogen) according to manufacturer’s instruction.  Size selected adaptor-modified DNA fragments are amplified by 18 cycles of PCR using Phusion polymerase and PCR primer 1.1 and 2.1 (Illumina). The resulting PCR products are purified by MinElute column (QIAGEN).  The size and amount of DNA fragments (libraries) are validated by Bioanalyzer (Agilent).

treatment_protocol: In some samples, cells were transfected with siRNA for 48 h. LNCaP cells were treated with vehicle or DHT 10 nM or R1881 10 nM for 24 h or 1h.

value: LNCaP cells

value: DHT 10 nM treatment

tag: chip antibody

value: AR


title: lncap_DHT_EZH2

description: ChIP by EZH2 antibody (BD bioscience 612666)


title: lncap_Input2

description: input DNA of LNCaP

value: input


title: R14del-CMs

source_name: Cardiomyocytes derived from PLN-R41del iPSC cells


title: R14del-CMs (clone L2)


title: Drosha +/+ rep3 RNA-seq

value: wild type


title: siCTCF_5237

description:
5237
5237, 3900 and 4900 come from the same sample but were sequenced at different lengths and by different companies (5237, 50 bp; 3900/4900, 101 bp)

value: siCTCF


title: lncap_AR_DHT_Control


title: lncap_AR_DHT_siFOXP1

description: ChIP by AR antibody (santacruz H-280) after treating cells with siFOXP1


title: lncap_AR_DHT_siRUNX1

description: ChIP by AR antibody (santacruz H-280) after treating cells with siRUNX1


title: lncap_DHT_RUNX1

description: ChIP by RUNX1 antibody (Abcam ab23980)


title: si-/Negtive control_5236

description:
5236
5236, 3899 and 4899 come from the same sample but were sequenced at different lengths and by different companies (5236, 50 bp; 3899/4899, 101 bp)

value: control


title: lncap_vehicle_K36me3

description: ChIP by K36me3 antibody (Abcam ab9050)

value: ethanol (Vehicle) treatment


title: lncap_vehicle_RUNX1

description: ChIP by RUNX1 antibody (Abcam ab23980)


title: lncap_R1881_K36me3

description: ChIP by K36me3 antibody (Abcam ab9050)


title: lncap_R1881_K4me3

description: ChIP by K4me3 antibody (Millipore #17-614)


title: lncap_R1881_K4me1

description: ChIP by K4me1 (Abcam ab8895)


title: lncap_input

description: input DNA of LNCaP

value: Input


title: lncap_R1881_K27me3

description: ChIP by K27me3 antibody (Abcam ab6002)


title: lncap_DHT_FOXP1

description: ChIP by FOXP1 antibody (Antibody produced in our laboratory)


title: input_1 for BCL6 and E2A

city: San Francisco

first: Huimin

last: Geng

address: 513 Parnassus Ave., MSB HSW 1201

department: Department of Laboratory Medicine

institute: UCSF

data_processing:
Counts: Raw image data were converted into base calls via the Illumina pipeline CASAVA version 1.8 with default parameters. All 51-bp-long paired-end reads were mapped to the reference human genome sequence, hg18, using BWA aligner (Li H. and Durbin R. (2009) Bioinformatics, 25:1754-60) with the default parameters. Only reads mapping uniquely to the genome with not more than 2 mismatches were retained for downstream analysis.
Peaks: Peak detection was performed with the ChIPseeqer program (Giannopoulou and Elemento, BMC Bioinformatics 2011, 12:277) and annotated to genes and/or promoters based on hg18 refseq genes downloaded from the UCSC Genome Browser
Genome_build: human hg18 build
Supplementary_files_format_and_content: bigwig and bigbed formats
Genome Build:
ICN12_input.bigWIG: hg18

source_name: ICN12 cells

growth_protocol: Leukemia cells from bone marrow biopsy of patients with pre-B ALL (ICN12) were xenografted into sublethally irradiated NOD/SCID mice via tail vein injection. After passaging, leukemia cells were harvested and cultured on OP9 stroma cells in Alpha Minimum Essential medium (Alpha-MEM, Invitrogen, Carlsbad, CA) without ribonucleotides and deoxyribonucleotides, supplemented with 20% fetal bovine serum, 2 mmol/l L-glutamine, 1 mmol/l sodium pyruvate, 100 IU/ml penicillin and 100 μg/ml streptomycin.

extract_protocol: Genomic DNA-fragment libraries were prepared using the Illumina ChIP-seq Library preparation Kit following the manufacture’s instructions (Illumina, CA). Briefly 10ng of purified ChIP DNA was end repaired by conversion of overhangs into phosphorylated blunt ends with the use of T4 DNA polymerase and E. coli DNA polymerase I Klenow fragment. Illumina single-end adapters were ligated to the ends of the DNA fragments. Ligation products were purified on a 2% agarose gel with a size selection of 200-300bp. Fifteen PCR cycles were performed with Illumina genomic DNA primers that anneal to the ends of the adapters. The purified PCR-amplified fragment libraries were quantified with the use of the PicoGreen dsDNA Quantitation Assay with the Qubit Fluorometer (Invitrogen, CA). The size range of libraries was validated on the Agilent Technologies 2100 Bioanalyzer with the High Sensitivity DNA Kit (Agilent, CA).

treatment_protocol: ICN12 cells were fixed with 1% formaldehyde, lysed and sonicated to generate fragments less than 500bp. Sonicated lysates were incubated with antibodies overnight and after increasing stringency washes immunocomplexes were recovered and DNA was isolated.

value: primary pre-B acute lymphomablastic leukemia

tag: chip antibody host, amount, catelog number and provider

value: Rabbit, 2ug, 2729, Cell Signaling


title: lncap_vehicle_K27me3

description: ChIP by K27me3 antibody (Abcam ab6002)

tag: treatment


title: lncap_vehicle_K4me1

description: ChIP by K4me1 (Abcam ab8895)


title: R14del-CMs AAV6-Luc miRNA

tag: differentiation stage


title: input_2 for PBX1 and p300

data_processing:
Counts: Raw image data were converted into base calls via the Illumina pipeline CASAVA version 1.8 with default parameters. All 51-bp-long paired-end reads were mapped to the reference human genome sequence, hg18, using BWA aligner (Li H. and Durbin R. (2009) Bioinformatics, 25:1754-60) with the default parameters. Only reads mapping uniquely to the genome with not more than 2 mismatches were retained for downstream analysis.
Peaks: Peak detection was performed with the ChIPseeqer program (Giannopoulou and Elemento, BMC Bioinformatics 2011, 12:277) and annotated to genes and/or promoters based on hg18 refseq genes downloaded from the UCSC Genome Browser
Genome_build: human hg18 build
Supplementary_files_format_and_content: bigwig and bigbed formats
Genome Build:
ICN12_input_08022013.bigwig: hg18


title: lncap_AR_vehicle

description: ChIP by AR antibody (santacruz H-280)


title: lncap_vehicle_AcH3

description: ChIP by AcH3 antibody (Millipore #06-599)


title: BCL6

data_processing:
Counts: Raw image data were converted into base calls via the Illumina pipeline CASAVA version 1.8 with default parameters. All 51-bp-long paired-end reads were mapped to the reference human genome sequence, hg18, using BWA aligner (Li H. and Durbin R. (2009) Bioinformatics, 25:1754-60) with the default parameters. Only reads mapping uniquely to the genome with not more than 2 mismatches were retained for downstream analysis.
Peaks: Peak detection was performed with the ChIPseeqer program (Giannopoulou and Elemento, BMC Bioinformatics 2011, 12:277) and annotated to genes and/or promoters based on hg18 refseq genes downloaded from the UCSC Genome Browser
Genome_build: human hg18 build
Supplementary_files_format_and_content: bigwig and bigbed formats
Genome Build:
ICN12_BCL6.bigWIG: hg18
ICN12_BCL6_target_1.bigBED: hg18

value: Rabbit, 2ug, 4242, Cell Signaling


title: lncap_vehicle_FOXP1


title: KOCCl4 14

status: Public on Feb 07 2015

city: Beijing

first: Xu

middle: Zhao

last: Gao

state: Beijing

address: The Summer Palace Road No. 5

department: College of Biological Sciences

country: China

institute: Peking University

description:
Primary hepatocytes were prepared by collagenase perfusion at Yale Liver Center. Hepatocytes were washed twice with FACS buffer (2mM EDTA, 2% FBS in PBS), stained with 7-Aminoactinomycin D (7AAD) or propidium iodide, and analyzed on BD Accuri or LSRII, or sorted on MoFlo cytometers. Samples were gated on live hepatocytes based on forward and side scatter and live dye exclusion.
processed data file: WT-KOCCl.txt,KO-KOCCl.txt,GFPh-KOCCl.txt,GFPl-KOCCl.txt,WTCCl-KOCCl.txt,

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Mus_musculus whole genome using tophat with parameters -p -r -G -o genome C1_R1_1.fq
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks.The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Mus_musculus.GRCm38.72.cdna.all
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Hepatocyte

extract_protocol:
Total RNA was isolated with Trizol reagent as recommended by the manufacturer.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Animals were maintained at the Yale Animal Resources Center. All animal experiments were performed with approval by the Institutional Animal Care and Use Committee of Yale University. Liver damage was induced by i.p. injection of CCl4 (Sigma, 1ul/g, diluted 1:10 with peanut oil).

value: Sorted Hepatocytes

value: 1-2 months old

tag: genotype/variation


title: KOCCl4 13

tag: age


title: lncap_vehicle_K4me3


title: WTCCl4 12

description:
Primary hepatocytes were prepared by collagenase perfusion at Yale Liver Center. Hepatocytes were washed twice with FACS buffer (2mM EDTA, 2% FBS in PBS), stained with 7-Aminoactinomycin D (7AAD) or propidium iodide, and analyzed on BD Accuri or LSRII, or sorted on MoFlo cytometers. Samples were gated on live hepatocytes based on forward and side scatter and live dye exclusion.
processed data file: WT-WTCCl.txt,KO-WTCCl.txt,GFPh-WTCCl.txt,GFPl-WTCCl.txt,


title: YapKO 10

description:
Primary hepatocytes were prepared by collagenase perfusion at Yale Liver Center. Hepatocytes were washed twice with FACS buffer (2mM EDTA, 2% FBS in PBS), stained with 7-Aminoactinomycin D (7AAD) or propidium iodide, and analyzed on BD Accuri or LSRII, or sorted on MoFlo cytometers. Samples were gated on live hepatocytes based on forward and side scatter and live dye exclusion.
processed data file: WT-KO.txt


title: p300

data_processing:
Counts: Raw image data were converted into base calls via the Illumina pipeline CASAVA version 1.8 with default parameters. All 51-bp-long paired-end reads were mapped to the reference human genome sequence, hg18, using BWA aligner (Li H. and Durbin R. (2009) Bioinformatics, 25:1754-60) with the default parameters. Only reads mapping uniquely to the genome with not more than 2 mismatches were retained for downstream analysis.
Peaks: Peak detection was performed with the ChIPseeqer program (Giannopoulou and Elemento, BMC Bioinformatics 2011, 12:277) and annotated to genes and/or promoters based on hg18 refseq genes downloaded from the UCSC Genome Browser
Genome_build: human hg18 build
Supplementary_files_format_and_content: bigwig and bigbed formats
Genome Build:
ICN12_p300_08022013.bigwig: hg18
ICN12_p300_08022013_target_ChIPseeqer_1.bigBED: hg18

value: Rabbit, 2ug, sc-585, Santa Cruz


title: WTCCl4 11


title: PlGFPh 5

description:
Primary hepatocytes were prepared by collagenase perfusion at Yale Liver Center. Hepatocytes were washed twice with FACS buffer (2mM EDTA, 2% FBS in PBS), stained with 7-Aminoactinomycin D (7AAD) or propidium iodide, and analyzed on BD Accuri or LSRII, or sorted on MoFlo cytometers. Samples were gated on live hepatocytes based on forward and side scatter and live dye exclusion.
processed data file: WT-GFPh.txt,KO-GFPh.txt,


title: lncap_R1881_AcH3


title: E2A

data_processing:
Counts: Raw image data were converted into base calls via the Illumina pipeline CASAVA version 1.8 with default parameters. All 51-bp-long paired-end reads were mapped to the reference human genome sequence, hg18, using BWA aligner (Li H. and Durbin R. (2009) Bioinformatics, 25:1754-60) with the default parameters. Only reads mapping uniquely to the genome with not more than 2 mismatches were retained for downstream analysis.
Peaks: Peak detection was performed with the ChIPseeqer program (Giannopoulou and Elemento, BMC Bioinformatics 2011, 12:277) and annotated to genes and/or promoters based on hg18 refseq genes downloaded from the UCSC Genome Browser
Genome_build: human hg18 build
Supplementary_files_format_and_content: bigwig and bigbed formats
Genome Build:
ICN12_E2A.bigWIG: hg18
ICN12_E2A_target_1.bigBED: hg18

value: Rabbit, 2ug, sc-888, Santa Cruz


title: HiCCl4 16

description:
Primary hepatocytes were prepared by collagenase perfusion at Yale Liver Center. Hepatocytes were washed twice with FACS buffer (2mM EDTA, 2% FBS in PBS), stained with 7-Aminoactinomycin D (7AAD) or propidium iodide, and analyzed on BD Accuri or LSRII, or sorted on MoFlo cytometers. Samples were gated on live hepatocytes based on forward and side scatter and live dye exclusion.
processed data file: WT-CClH.txt,KO-CClH.txt,GFPh-CClH.txt,GFPl-CClH.txt,WTCCl-CClH.txt,KOCCl-CClH.txt,CClH-CClL.txt


title: lncap_R1881_24h_AR

description: ChIP by AR antibody (santacruz H-280)


title: LoCCl4 15

description:
Primary hepatocytes were prepared by collagenase perfusion at Yale Liver Center. Hepatocytes were washed twice with FACS buffer (2mM EDTA, 2% FBS in PBS), stained with 7-Aminoactinomycin D (7AAD) or propidium iodide, and analyzed on BD Accuri or LSRII, or sorted on MoFlo cytometers. Samples were gated on live hepatocytes based on forward and side scatter and live dye exclusion.
processed data file: WT-CClL.txt,KO-CClL.txt,GFPh-CClL.txt,GFPl-CClL.txt,WTCCl-CClL.txt,KOCCl-CClL.txt,CClH-CClL.txt


title: WT 1

description: Primary hepatocytes were prepared by collagenase perfusion at Yale Liver Center. Hepatocytes were washed twice with FACS buffer (2mM EDTA, 2% FBS in PBS), stained with 7-Aminoactinomycin D (7AAD) or propidium iodide, and analyzed on BD Accuri or LSRII, or sorted on MoFlo cytometers. Samples were gated on live hepatocytes based on forward and side scatter and live dye exclusion.

value: wild type/BL6


title: WT 9


title: NR

city: Mumbai

first: T

middle: R

last: Ganapathi

state: Maharashtra

address: Trombay

department: Nuclear Agriculture & Biotechnology Division

country: India

institute: Bhabha Atomic Research Centre, Mumbai

description: small RNA

data_processing:
The Illumina raw reads were filtered for high quality reads using Genotypic proprietary tool
DSAP web suite was used for adaptor removal, clustering of tags,  classification of non-coding small RNAs and miRNAs based on sequencing homology search against the Rfam and miRBase databases
Genome_build: Musa acuminata subsp. malaccensis strain Doubled-haploid Pahang (DH Pahang),whole genome shotgun sequencing project GenBank: CAIC00000000.1
Supplementary_files_format_and_content: Normalized abundance measurements

organism: Musa AAB Group

source_name: Leaves

extract_protocol:
Total RNA isolated using Concert Plant RNA reagent (Invitrogen) was processed using mirVana small RNA isolation kit (Ambion) to isolate small RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: Rasthali

tag: group

value: AAB

tag: subgroup

value: Silk

value: leaf


title: GN

description: small RNA

organism: Musa acuminata AAA Group

value: Grand Naine

value: AAA

value: Cavendish

tag: tissue


title: CClGFPl 8


title: CClGFPh 7


title: PhGFPl 4

description:
Primary hepatocytes were prepared by collagenase perfusion at Yale Liver Center. Hepatocytes were washed twice with FACS buffer (2mM EDTA, 2% FBS in PBS), stained with 7-Aminoactinomycin D (7AAD) or propidium iodide, and analyzed on BD Accuri or LSRII, or sorted on MoFlo cytometers. Samples were gated on live hepatocytes based on forward and side scatter and live dye exclusion.
processed data file: WT-GFPl.txt,KO-GFPl.txt,GFPh-GFPl.txt,


title: PBX1

data_processing:
Counts: Raw image data were converted into base calls via the Illumina pipeline CASAVA version 1.8 with default parameters. All 51-bp-long paired-end reads were mapped to the reference human genome sequence, hg18, using BWA aligner (Li H. and Durbin R. (2009) Bioinformatics, 25:1754-60) with the default parameters. Only reads mapping uniquely to the genome with not more than 2 mismatches were retained for downstream analysis.
Peaks: Peak detection was performed with the ChIPseeqer program (Giannopoulou and Elemento, BMC Bioinformatics 2011, 12:277) and annotated to genes and/or promoters based on hg18 refseq genes downloaded from the UCSC Genome Browser
Genome_build: human hg18 build
Supplementary_files_format_and_content: bigwig and bigbed formats
Genome Build:
ICN12_PBX1_08022013.bigwig: hg18
ICN12_PBX1_08022013_target_ChIPseeqer_1.bigBED: hg18

tag: cell type

value: Rabbit, 2ug, developed by the Roeder Laboratory


title: HCT116-H3K9me3 Rep2

status: Public on Feb 06 2015

city: Los Angeles

first: Fides

middle: D

last: Lay

address: 615 Charles E Young Drive South, BSRB 457

department: MCDB

institute: UCLA

data_processing:
Sequencing reads were mapped using bwa and reads were filtered to remove non-unique reads and PCR duplicates
Reads were extended by each library's mean fragment size as estimated by HOMER's v4.3's makeTaqDirectory
Each data was normalized using the default setting of Wiggler and mean wiggler value was calculated for each genomic position
Z-score transformation was performed using the wiggler value
The ENCODE HCT116 input sample GSM945855 was used in the analysis of all HCT116 Rep2 ChIP-seq experiments.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated and scores represent z-scores

source_name: HCT116 cells

growth_protocol: HCT116 and DKO1 cells were cultured in McCoy5A media supplemented with 10% FBS and penicillin/streptomycin at 37C/5%CO2

extract_protocol:
Cells were fixed and nuclei were sonicated. Histone-DNA complexes were isolated with target antibody. For NOMe-seq samples, freshly isolated nuclei were treated with M.CviPI
Libraries were prepared according to Illumina's recommendation from 20ng ChIP'ed DNA and indexed prior to sequencing on HiSeq2000 using 50SR cycles for ChIP-seq and 75PE for NOMe-seq samples

tag: cell line

value: colon cancer

tag: genotype

value: wildtype

tag: Sex

value: male

tag: antibody manufacturer

value: Abcam

tag: antibody catalog number


title: PlGFPl 6

value: Sorted Hepatocytes


title: PhGFPh 3

value: 1-2 months old


title: DKO1-H3K9me3 Rep2

data_processing:
Sequencing reads were mapped using bwa and reads were filtered to remove non-unique reads and PCR duplicates
Reads were extended by each library's mean fragment size as estimated by HOMER's v4.3's makeTaqDirectory
Each data was normalized using the default setting of Wiggler and mean wiggler value was calculated for each genomic position
Z-score transformation was performed using the wiggler value
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated and scores represent z-scores

source_name: DKO1 cells

value: DNMT3B & DNM1 KO


title: HCT116-H3K27me3 Rep2

value: Active Motif


title: YapKO 2


title: HCT116-H3K36me3 Rep2


title: HCT116-H3K36me3

extract_protocol:
Cells were fixed and nuclei were sonicated. Histone-DNA complexes were isolated with target antibody.
Libraries were prepared according to Illumina's recommendation from 20ng ChIP'ed DNA and indexed prior to sequencing on HiSeq2000 using 50SR cycles

value: colon cancer cell line

value: anti-H3K36me3 (Abcam #9050)


title: DKO1-H3K9me3

value: colon cancer cell line; DNMT3B & DNM1 KO

value: anti-H3K9me3 (Abcam #ab8898)


title: DKO1-H3K27ac Rep2


title: CrePos (Isl1 fl/fl)-3

first: Vasanth

last: Vedantham

address: 505 Parnassus Avenue, M1176D

department: Medicine-Cardiology

institute: University of California, San Francisco

data_processing:
Short read assembly was performed using TopHat v2.0.6 against mm8 build of the genome.
Gene counts were determined using Rsamtools and sample normalization was performed using edgeR.
Differential expression was performed using edgeR.
Genome_build: mm8
Supplementary_files_format_and_content: text-tab delimited with rows as genes and columns as samples; contains normalized counts as output by edgeR

source_name: heart - sinoatrial node

growth_protocol: Genetically modified mice were maintained on a mixed background.

extract_protocol:
Total RNA was prepared from regions of interest isolated with laser capture using the PicoPure Kit (Arcturus) according to manufacturers instructions.
RNA-seq libraries were prepared with the Ovation RNA-Seq System V2 kit (NuGEN) according to manufacturers instructions.  Briefly, total RNA is reverse-transcribed using a combination of random hexamers and a poly-T chimeric primer, followed by second strand synthesis using DNA polymerase. The cDNA was then amplified using single primer isothermal amplification (SPIA). Libraries from the SPIA amplified cDNA were made using the Ultralow DR library kit  (NuGEN) according to manufacturers instructions.  The RNA-seq libraries were analyzed by Bioanalyzer (Agilent) and quantified by QPCR (KAPA).

treatment_protocol: Embryos or hearts were removed intact, washed with cold PBS, and immediately embedded in OCT and stored at -20 °C until sectioning. Tissue was sectioned at a thickness of 8 microns onto membrane-coated slides (MembraneSlide NF 1.0 PEN, Zeiss Microscopy, Gottingen, Germany). For laser capture, slides were thawed to room temperature until evaporation of moisture (approximately 1 minute), placed on the microscope stage of a PALM Micro-Beam inverted microscope with LCM capability (Zeiss). The sinus node tissue and right atrial tissue were identified visually and outlined manually with the microscope user interface (Online Video 2).  Laser power and catapult energy were optimized prior to the experiment and varied from experiment-to-experiment. After each experiment, sections were stained with DAPI and anti-Hcn4, mounted, and visualized to confirm accurate dissection of the region of interest.

tag: strain background

value: mixed

tag: developmental stage

value: Embryonic Day 12.5

value: Hcn4-GFP;Isl1 fl/fl;CAG-Cre/Esr1

tag: injected with

value: Tamoxifen at embryonic day 10.5

value: heart; sinoatrial node


title: P14-RA-3

source_name: heart - right atrium

value: Postnatal Day 14

value: heart; right atrium


title: P14-SAN-1


title: P14-RA-2


title: CrePos (Isl1 fl/fl)-1


title: DKO1-H3K36me3

value: male

tag: chip antibody


title: CrePos (Isl1 fl/fl)-2 (Outlier)


title: P14-RA-1


title: P14-SAN-3


title: CreNeg (Isl1 fl/fl)-4

value: Hcn4-GFP;Isl1 fl/fl


title: P4-SAN-3

value: Postnatal Day 4


title: P4-SAN-2


title: CreNeg (Isl1 fl/fl)-3


title: P4-SAN-1


title: CreNeg (Isl1 fl/fl)-1


title: P4-RA-3


title: P14-SAN-2


title: CreNeg (Isl1 fl/fl)-2


title: HCT116-H3K9me3


title: P4-RA-1


title: E14.5-SAN-3

value: Embryonic Day 14.5


title: P4-RA-2


title: E14.5-RA-3


title: E14.5-SAN-1


title: E14.5-SAN-2


title: K562-400mM-GCH and HCG

data_processing:
Library strategy: WGBS/whole-genome NOMe-seq
genomic alignment for paired-end reads were done using MAQ with the -c bisulfite mode
Low quality reads and improperly paired reads were filtered out
Methylation calling of CpG and GpC was done using Bis-SNP (Liu et al 2011)
Genome_build: hg19
Supplementary_files_format_and_content: Methylation value of CG and GC sites were extacted and bigwig files were generated

growth_protocol: K562 cells were cultured in McCoy5A media supplemented with 10% FBS and penicillin/streptomycin at 37C/5%CO2

extract_protocol:
Cells were trypsinized and washed with PBS. Nuclei were isolated and treated with 300 U of M.CvIPI, a GpC methyltransferase which can methylate accessible GpC sites without affecting CpG information (Kelly et al 2012)
WGBS libraries were prepared based on previously described (Berman et al 2012) and according to Illumina's recommendation.


title: E14.5-RA-1


title: E14.5-RA-2


title: DKO1-Input Rep2

value: colon cancer

value: DNMT3B & DNM1 KO

value: none (input)


title: DKO1-H3K4me1 Rep2

value: Active Motif


title: K562-10mM-GCH and HCG


title: HCT116-H3K4me1 Rep2

value: wildtype


title: HCT116-H3K4me3 Rep2


title: DKO1-H3K4me3 Rep2


title: DKO1-H3K27me3 Rep2


title: DKO1-H2A.Z Rep2

value: Abcam


title: DKO1-HCG/GCH-Rep2

data_processing:
genomic alignment for paired-end reads were done using MAQ with the -c bisulfite mode
Low quality reads and improperly paired reads were filtered out
Methylation calling of CpG and GpC was done using Bis-SNP (Liu et al 2011)
Genome_build: hg19
Supplementary_files_format_and_content: Methylation value of CG and GC sites were extacted and bigwig files were generated


title: DKO1-NOMe-seq

description: library strategy: NOMe-seq


title: DKO1-Input

value: colon cancer cell line; DNMT3B & DNM1 KO


title: HCT116-NOMe-seq

description: library strategy: NOMe-seq


title: DKO1-H3K27ac

value: anti-H3K27ac (Active Motif #39135)


title: DKO1-H3K27me3

value: anti-H3K27me3 (Active Motif #39155)


title: HCT116-HCG/GCH-Rep2


title: DKO1-H3K4me1

value: anti-H3K4me1 (Active Motif #39297)


title: HCT116-Input

value: colon cancer cell line


title: DKO1-H3K4me3

value: anti-H3K4me3 (Active Motif #39915)


title: DKO1-H2A.Z

value: anti-H2A.Z (Abcam #ab4174)


title: DNA_CTL

city: University Park

first: David

middle: Asher

last: Galbraith

state: Pennsylvania

address: 19a Chemical Ecology Lab

institute: Penn State University

description: AntiviralDNAmethylationResponse.txt

data_processing:
Transcriptome sequencing reads were preprocessed using Illumina HCS 1.1 software.
We removed adaptor sequences, reads composed of more than 5% unknown nucleotides, and reads with more than 20% of the base qualities under 10.
The transcriptome sequencing reads were aligned to the most recent honey bee genome assembly (Amel_4.5) using Tophat.
The data was normalized using a trimmed mean of M-values (TMM) method.
The DESeq package in R statistical program was used to identify significantly differentially expressed genes.
The trimmed bisulfite-converted DNA reads in both control and treated group are aligned to honey bee genome Amel_4.5 using BSMAP. Ambiguously mapped reads were filtered with parameter -u and potential PCR duplications were removed by parameter -r
To avoid erroneous annotation, we restricted our analyses to genes that fit the following criteria: 1) mapped by RNA-seq data, 2) have orthologs in D. melanogaster, and 3) with corresponding assembly in the previous assembly 2.0. Following this filtering step, we examined a total of 12,446 genes.
Methylated CpG sites are determined by the binomial test. The error rate (non-conversion rate and sequencing error) is estimated from the sequencing result of the unmethylated λ phage mixed in our sample. Error rates estimated from these were 0.0041 and 0.0037 from control and treatment groups, respectively. P-values were subsequently corrected for multiple testing, and sites with adjusted p-value < 0.1 were considered methylated.
Genome_build: Amel_4.5
Supplementary_files_format_and_content: Tab-delimited text files include read counts for each RNA samples and fractional methylation levels for DNA samples

organism: Apis mellifera

source_name: pool of 9 eviscerated abdomen with attached fat bodies

extract_protocol:
Eviscerated abdomens with attached fat bodies from individual bees were dissected in ice-cold RNAlater® (Qiagen, Valencia, CA) and excess RNAlater® was removed from the samples.  RNA was isolated using TRIzol® Reagent (Invitrogen, Carlsbad, CA). Samples were then treated with TURBO™ DNase (Ambion, Austin, TX) to remove DNA contamination. DNA was isolated from the fat bodies from a second set of bees using a Gentra® Puregene® kit (Qiagen, Valencia, CA).  DNA quality was assessed by electrophoresis, using 1% Agarose gel, and the concentration was determined using a Qubit® 2.0 Fluorometer (Invitrogen, Carlsbad, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Individual workers were fed extracts of virus-infected bees (which contained IAPV, DWV, BQCV, KBV and SBV; bees were obtained from D. Cox-Foster, Penn State) in a 50%-sucrose solution while control bees were fed a 50%-sucrose control (4 µL/bee)

value: Eviscerated abdomen with attached fat bodies

value: Adults (<48 hours post emergence)

tag: treatment

value: Control


title: HCT116-H3K27me3

value: male


title: HCT116-H2A.Z Rep2

value: colon cancer


title: DNA_TMT

description: AntiviralDNAmethylationResponse.txt

value: IAPV treated


title: HCT116-H3K4me1


title: HCT116-H3K4me3


title: CTL1

description: AntiviralTranscriptomicResponseReadCounts.txt

source_name: pool of 3 eviscerated abdomen with attached fat bodies


title: HCT116-H2A.Z


title: TMT3


title: TMT2


title: CTL2


title: 12hr_2

status: Public on Feb 05 2015

city: New Haven

first: Mei

last: Zhong

address: 10 Amistad Street

department: Stem Cell Center

institute: Yale University

description: processed data file: HDMYZ processed data.xlsx

data_processing:
Illumina Casava1.8.1 software used for basecalling.
Sequence reads were processed by miRDeep2 package, with the following modifications. First, to remove adaptor sequence, we removed both the main adaptor sequence present in the sequencing reads, as well as the second most abundant adaptor variant. In addition, we did not restrict the size of small RNAs during adaptor removal. Second, we used miRBase v18 for mapping the reads. Third, for quantifying miRNA and isoform frequency, we limited reads to more or equal to 15 bases in length with zero mis-match during mapping.
The total number of reads that were mapped to known mature miRNAs was used to normalize read frequencies for each miRNA or each miRNA isoform.
Genome_build: miRBase v18
Supplementary_files_format_and_content: The processed date file is in excel format. Each row in the excel file indicates a miRNA isoform, each column indicates a kind of information for miRNA isoforms. The first column "Category" indicates the turnover pattern of miRNA isoforms. If left blank, indicates a slow turnover miRNA; "1" means a ultra-fast turnover miRNA whose level goes down more than 75% after 12 hours of ActD treatment; "2" means a fast turnover miRNA whose level goes down more than 50% after 12 hours of ActD treatment. The second column "Precursor" shows the miRNA precursor name for each miRNA isoform. The third column "Mature miRNA region" shows the arm of the hairpin that mature miRNA mapped to. The fourth column " Isoform sequence" shows the sequence for each miRNA isoform. The fifth to sixteenth column shows the normalized read frequency for each sample. The seventeenth column shows the turnover percentage at 4 hour compared with 0 hour.  The eighteenth column shows the turnover percentage at 12 hour compared with 0 hour. The ninteenth column shows the p value comparing 0 hour samples with 12 hour samples.  The twentieth column shows the p value comparing 0 hour samples with 4 hour samples. The twenty-first column shows the p value comparing 0 hour samples with 4 and 12 hour samples. The twenty-second column "Detectable" shows the detectability of each miRNA isoform: "1" indicates the average of normalized read frequency for 0 hour is larger than 5X10E-6.

growth_protocol: HDMYZ cells were cultured in RPMI with 10% FBS and 1% Penicillin-Streptomycin.

extract_protocol:
HDMYZ cells were collected with Trizol reagent (Invitrogen) following manufacturer's protocol. Small RNAs of 15-40 bases were gel-purified from 10 ug total RNA
The TruSeq Small RNA Sample Prep Kit (Part# RS-200-0012) is used following TruSeq Small RNA Sample Preparation Guide. The protocol takes advantage of the natural structure common to most known microRNA molecules. Most of the mature miRNA/piRNA have a 5’ phosphate and a 3’ hydroxyl group as they were created. The RNA 3’ adaptor is specifically modified to target small RNAs that have a 3’ hydroxyl group. The adapters are ligated to each end of the RNA molecule and an RT reaction is used to create single stranded cDNA. The cDNA is then PCR amplified using a common primer and a primer containing one of 48 index sequences. The introduction of the index sequence at the PCR step separates the indexes from the RNA ligation reaction. This design allows for the indexes to be read using a second read and significantly reduces bias compared to designs which include the index within the first read. After amplification the cDNA construct are further gel purified and the final library are validated by an Agilent Technologies 2100 Bioanalyzer using a DNA‐1000 chip. The multiplexed samples can be pooled in equimolar amounts. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq 2000 following the manufacturer's protocols.
TruSeq Small RNA Library

treatment_protocol: HDMYZ cells were treated with 4ug/ml ActD for 0, 1, 4 and 12 hours.

value: HDMYZ

value: human hodgkin's lymphoma cell line

tag: treated with

value: 4ug/ml ActinomycinD

tag: time post treatment

value: 12 hours


title: 1hr_3

value: 1 hour


title: TMT1


title: nrpe1-11_MethylC-Seq

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: treated with bisulfite

data_processing:
Reads were mapped to TAIR10 using BRAT-BW v2.0.1 with parameters -m 2 -i 0 -a 1000
Copy-duplicates were remove using remove-dupl command of BRAT-BW
acgt-count command of BRAT-BW was used to count mapped Cs and Ts at each cytosine of forward and reverse strands of the reference
Genome_build: TAIR10
Supplementary_files_format_and_content: The wig files give methylation level for all Cs(three contexts) with depth >= 4. Methylation level of each cytosine base was calculated according to number of converted and unconverted C mapped at that position (converted_C / ( converted_C+ unconverted_C ) ).

organism: Arabidopsis thaliana

source_name: Seedlings

extract_protocol: Genomic DNA was extracted from 14-d-old seedlings and sent to BGI (Shenzhen, China) for bisulfite treatment, library preparation, and sequencing. Bisulfite sequencing libraries were prepared using standard Illumina protocols.

tag: genotype/variation

value: nrpe1-11 mutant


title: 12hr_3


title: nrpd1-3_MethylC-Seq

description: treated with bisulfite

value: nrpd1-3 mutant


title: 4hr_3

value: 4 hours


title: 12hr_1


title: HCT116-H3K27ac

value: colon cancer cell line

value: anti-H3K27ac (Active Motif #39135)


title: MCF7-WT-miR-222

data_processing:
Illumina Casava1.8.1 software used for basecalling.
Sequence reads were processed by miRDeep2 package, with the following modifications. First, to remove adaptor sequence, we removed both the main adaptor sequence present in the sequencing reads, as well as the second most abundant adaptor variant. In addition, we did not restrict the size of small RNAs during adaptor removal. Second, we used miRBase v21 for mapping the reads. Third, for quantifying miRNA and isoform frequency, we limited reads to more or equal to 15 bases in length with zero mis-match during mapping.
The total number of reads that were mapped to known mature miRNAs was used to normalize read frequencies for each miRNA or each miRNA isoform.
Genome_build: miRBase v21
Supplementary_files_format_and_content: The processed date file is in excel format. Each row in the excel file indicates a miRNA isoform, each column indicates a kind of information for miRNA isoforms. The first column "Hairpin" indicates the hairpin that the isoform matched to. The second column "Read Sequence" shows the sequence of the miRNA isoform. The third column "Read Length" shows the length of the reads. The fourth column "Read region" indicates the region on the hairpin that the reads belong to. The fifth column "MCF7-WT-miR-222" indicates the number of reads from MCF7-WT-miR-222 sample. The sixth column "MCF7-mut-miR-222" indicates the number of reads from MCF7-mut-miR-222 sample.

source_name: MCF7, human breast cancer cell line

growth_protocol: MCF7 cells were cultured in DMEM with 10% FBS and 1% Penicillin-Streptomycin.

extract_protocol:
MCF7 cells were collected with Trizol reagent (Invitrogen) following manufacturer's protocol. Small RNAs of 15-40 bases were gel-purified from 5 ug total RNA
Small RNAs of 15-40 bases were gel-purified from 5 ug total RNA with 10% acrylamide gel (American Bioanalytical AB13021). Purified small RNA was subjected to library preparation, similar to Illumina protocol with modification. Briefly, pre-adenylated primer was made following a published protocol (Chen, Y.-R., Zheng, Y., Liu, B., Zhong, S., Giovannoni, J. and Fei, Z. (2012) A cost-effective method for Illumina small RNA-Seq library preparation using T4 RNA ligase 1 adenylated adapters. Plant Methods, 8, 41.) using /5Phos/TGGAATTCTCGGGTGCCAAGG/3ddC/. Small RNA was ligated to the pre-adenylated primer with truncated T4 RNA ligase 2 (NEB M0242S). The 35-55 bases product was purified with 10% acrylamide gel and further went through a 5’ ligation reaction with primer: dGdTdTdCdAdGdAdGdTdTdCdTdAdCdA GUCCGACGAUC (Dharmacon) with T4 RNA ligase 1 (Fermentas EL0021). The 60-80 bases product was purified with 10% acrylamide gel and reverse transcribed with M-MLV reverse transcriptase (Invitrogen 28025-013) using primer: GCCTTGGCACCCGAGAATTCCA. The RT product was PCR amplified for 18 cycles with Phusion DNA polymerase (NEB M0530) using a universal primer: AATGATACGGCGACCACCGAGATCTACACGTT-CAGAGTTCTACAGTCCGA and a specific primer for each sample. 130-150nt small RNA libraries were purified with 8% acrylamide gel. Barcoded small RNA libraries were sequenced on a HiSeq2000 (Illumina).
TruSeq Small RNA Library

tag: mir-222 overexpression

value: wild-type


title: MCF7-mut-miR-222

value: mutant


title: 1hr_1


title: CTL3

value: Eviscerated abdomen with attached fat bodies

value: Adults (<48 hours post emergence)


title: 0hr_2

value: none (0h control)

value: 0 hour


title: 4hr_1


title: 0hr_1


title: 0hr_3


title: ChIP-seq-IgG

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing:
Aligned using /usr/local/bin/bowtie with configuration -p 4 --best -k 1 -m 1 --sam -l 40
mm9
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1

source_name: Embryonic stem cells

growth_protocol: V6.5 (C57BL/6-129) murine ES cells were grown under typical ES conditions on irradiated mouse embryonic fibroblasts (MEFs). For location analysis, cells were grown for two passages off of MEFs, on gelatinized tissue-culture plates.

extract_protocol:
Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
Lysates were clarified from sonicated chromatin fraction and target bound fragments were isolated with antibody

value: IgG

tag: antibody manu.

value: Upstate

tag: antibody catalog

tag: system

value: Stem Cell


title: ChIP-seq-H3K9me3

tag: cell type

value: Abcam


title: ChIP-seq-input

tag: antibody manu.:

tag: antibody catalog:


title: ChIP-seq-H3K27me3


title: ChIP-seq-H3K36me3


title: 1hr_2

tag: cell line

value: HDMYZ

value: human hodgkin's lymphoma cell line

value: 4ug/ml ActinomycinD


title: ChIP-seq-H3K79me2


title: 4hr_2


title: ros1-13_MethylC-Seq

description: treated with bisulfite

data_processing:
Reads were mapped to TAIR10 using BRAT-BW v2.0.1 with parameters -m 2 -i 0 -a 1000
Copy-duplicates were remove using remove-dupl command of BRAT-BW
acgt-count command of BRAT-BW was used to count mapped Cs and Ts at each cytosine of forward and reverse strands of the reference
Genome_build: TAIR10
Supplementary_files_format_and_content: The wig files give methylation level for all Cs(three contexts) with depth >= 4. Methylation level of each cytosine base was calculated according to number of converted and unconverted C mapped at that position ( unconverted_C / ( converted_C+ unconverted_C ) ).

growth_protocol: Plants were grown at 23°C in a growth chamber with 16 h of light and 8 h of darkness on 1/2 MS medium with 1% glucose.

extract_protocol:
The genomic DNA was extracted from 1 gram of 14-day-old seedlings using the Plant DNeasy Maxi Kit from Qiagen. And 5 µg of gDNA was used for library construction using Illumina’s standard DNA methylation analyses protocol and the TruSeq DNA sample preparation kit. The samples were sequenced in the Genomics Core Facilities of the Shanghai Center for Plant Stress Biology, SIBS, CAS (Shanghai, China) with Illumina HiSeq2500.
5 µg of gDNA was used for library construction using Illumina’s standard DNA methylation analyses protocol and the TruSeq DNA sample preparation kit. The samples were sequenced in the Genomics Core Facilities of the Shanghai Center for Plant Stress Biology, SIBS, CAS (Shanghai, China) with Illumina HiSeq2500.

tag: tissue

value: Seedlings


title: ChIP-seq-H3K4me3


title: nrpd1-12_MethylC-Seq

description: treated with bisulfite

value: nrpd1-12 mutant


title: ChIP-seq-H3K27ac


title: 1B4 CAP-

city: North Shore City

first: Paul

last: Rainey

address: The Station Crescent

department: NZIAS

country: New Zealand

institute: Massey University

data_processing:
Reference alignment was performed with SOAP2.
Per gene coverage was determined.
Deseq was applied on the per gene coverage data
Genome_build: ASM922v1
Supplementary_files_format_and_content: File normalized_mean_coverage.txt (linked as supplementary file to Series record) a tab-delimited text file that contains normalized mean coverage per gene for each of the four samples done by DEseq.
Supplementary_files_format_and_content: Excel files (linked as supplementary files to Series record) containing a list of the genes identified by mRNA-seq as having statistically significantly (Adjusted p-value <0.01) different mRNA levels in genotype 1 and genotype 2 (numbered in the order listed above). Each list is split into two worksheets: (a) genotype1_higher, and (b) genotype2_higher. Within each worksheet, entries are organised in order of statistical significance (lowest to highest adjusted p-value) and subsequently by Fold Change. Column A is “Locus” (the nth gene in the SBW25 genome; note that while this correlates with pflu number, it is not necessarily the same); column B is “Gene Name” (assigned name or pflu number); column C is “Product” (protein product of the gene); column D is “EC Number” (enzyme catalogue number, where available); column E is “Colour in SBW25 Genome” (colours 1-15 each indicate a distinct functional class of gene product); columns F and G are “Genotype1 BaseMean” and “Genotype2 BaseMean” respectively (BaseMean is the normalized mean expression level of 2 replicates of the relevant genotype); column H is “Fold Change” (calculated by dividing the BaseMean of each genotype as indicated); column I is “p-value” (calculated by assuming a binomially distributed read coverage analogous to Fisher’s exact test (Anders and Huber, 2010; Robinson and Smyth, 2008)); column J is “Adjusted p-value” (the p-value adjusted for multiple testing with the Benjamini-Hochberg procedure (controls for false discovery rate) (Anders and Huber, 2010))"

organism: Pseudomonas [fluorescens] SBW25

source_name: bacterial culture

growth_protocol: Single colonies of P. fluorescens SBW25, 1A4 or 1B4 were inoculated into 6 ml of KB broth and incubated overnight at 28°C with shaking.  These pre-cultures were then diluted 1:1000 into 20 ml fresh KB broth (filter-sterilised) and incubated at 28°C with shaking for ~24 hours.

extract_protocol:
RNA extraction and purification was performed using a RiboPureTM Bacteria Kit (Ambion®) and the concentration and purity of RNA was determined spectrophotometrically using a BioPhotometer (Eppendorf). Two RNA preparations for each strain were pooled; yields of total RNA ranged from 11.6-24.7 μg.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To harvest total RNA from SBW25 and 1A4, 100 μl of bacteria (~1.5-1.9 ×109 cells) were mixed with 900 μl of KB broth, pelleted by centrifugation at 3,500 ×g, and re-suspended in 1 ml of RNAlater® RNA stabilization solution (Ambion®).  The differing density of capsulated and non-capsulated cells enabled a crude separation of types from cultures of 1B4 by low-speed centrifugation. Following centrifugation of 1B4 at 3500 ×g, Cap- cells formed a pellet at the bottom of the tube while Cap+ cells remained in suspension. Successful fractionation was confirmed by microscopy. Cap+ cells were subsequently pelleted by centrifugation at 24,652 ×g for 5 minutes and Cap+ and Cap- cell pellets were resuspended independently in 1 ml RNAlater®.

tag: strain

value: evolved strain 1B4

tag: phenotype

value: CAP-


title: 1B4 CAP+

value: CAP+


title: pGC1::SOC1-GFP/phot1 phot2_rep3

status: Public on Feb 04 2015

city: Nagoya

first: Norihito

last: Nakamichi

state: Aichi

address: Furo-cho, Chikusa

department: Institute of Transformative Bio-Molecules

institute: Nagoya University

data_processing:
Base calling and Mapping were done by Torrent Suite (Lifetechnologies).
Bam to Bed conversion was done by GenomicAlignments R package.
Genome_build: Arabidopsis TAIR10 transcripts

source_name: pGC1::SOC1-GFP/phot1 phot2

extract_protocol:
Total RNA was isolated by NucleoSpin RNA Plant kit (Takara).
From total RNA of 4 µg, poly-A containing RNA was enriched by Dynabeads mRNA DIRECT Micro Purification Kit (Lifetechnologies, CA). mRNA was then used to generate an RNA sequencing library using an Ion Total RNA-Seq Kit v2 (Lifetechnologies).Ion 318 Chip v2 was used for sequencing with Ion PGM system.

tag: accession background

tag: genotype/varation

value: pGC1::SOC1-GFP in in phot1 phot2 double mutant

value: Epidermis including guard cells

tag: age

value: 3 weeks after germination


title: Col-0_MethylC-Seq

description: treated with bisulfite

data_processing:
Reads were mapped to TAIR10 using BRAT-BW v2.0.1 with parameters -m 2 -i 0 -a 1000
Copy-duplicates were remove using remove-dupl command of BRAT-BW
acgt-count command of BRAT-BW was used to count mapped Cs and Ts at each cytosine of forward and reverse strands of the reference
Genome_build: TAIR10
Supplementary_files_format_and_content: The wig files give methylation level for all Cs(three contexts) with depth >= 4. Methylation level of each cytosine base was calculated according to number of converted and unconverted C mapped at that position (unconverted_C / ( converted_C+ unconverted_C ) ).

tag: genotype

value: WT

tag: cultivar

value: seedling


title: SBW25

value: wildtype (SBW25)


title: 1A4

value: evolved strain 1A4 (immediate ancestor)


title: phot1 phot2_rep2

source_name: phot1 phot2

value: phot1 phot2 double mutant


title: pGC1::SOC1-GFP/phot1 phot2_rep1