title: 16cell_5-6

description: 16-cell stage embryo 5 cell 6


title: 16cell_5-4

status: Public on Jan 10 2014

type: SRA

city: Stockholm

first: Daniel

last: Ramsköld

address: Nobels väg 3

country: Sweden

institute: Karolinska Institutet

description: 16-cell stage embryo 5 cell 4

library_source: transcriptomic

data_processing:
For expression values, we aligned reads using bowtie 0.12.7, option --best, against the genome and transcriptome (Ensembl, version 16 May 2011) with the genotype of both strains, in mm9 coordinates
Non-uniquely mapped reads were removed
Rpkmforgenes (available at http://sandberg.cmb.ki.se/rnaseq/), options -readcount -fulltranscript -mRNAnorm -rmnameoverlap -u, was used to generate RPKM values and read counts. We used a file with unique positions from Storvall et al. 2013 PLOS ONE.
For allelic ratios, we aligned using gsnap version 2012-07-20, with tolerance for known SNP positions
We used samtools mpileup to extract allelic counts
Genome_build: mm9
Supplementary_files_format_and_content: gene expression values (tab-delimited text)

molecule: polyA RNA

organism: Mus musculus

source_name: 16-cell stage blastomere

extract_protocol:
We used lysis buffer of the kit 'SMARTer Ultra Low Input RNA for Illumina Sequencing' from Clontech
We used the kit 'SMARTer Ultra Low Input RNA for Illumina Sequencing' from Clontech

tag: strain

value: CAST/EiJ(mother) x C57BL/6J(father)

tag: cross

value: first generation cross

tag: developmental stage

value: 16-cell stage blastomere


title: 16cell_5-13

description: 16-cell stage embryo 5 cell 13


title: 16cell_5-2

description: 16-cell stage embryo 5 cell 2


title: 16cell_5-12

description: 16-cell stage embryo 5 cell 12


title: 16cell_5-3

description: 16-cell stage embryo 5 cell 3


title: 16cell_5-10

description: 16-cell stage embryo 5 cell 10


title: 16cell_4-9

description: 16-cell stage embryo 4 cell 9


title: 16cell_5-1

description: 16-cell stage embryo 5 cell 1


title: 16cell_4-7

description: 16-cell stage embryo 4 cell 7


title: 8cell_8-4

description: 8-cell stage embryo 8 cell 4

source_name: 8-cell stage blastomere

value: 8-cell stage blastomere


title: 16cell_4-10

description: 16-cell stage embryo 4 cell 10


title: 16cell_4-1

description: 16-cell stage embryo 4 cell 1


title: 16cell_4-8

description: 16-cell stage embryo 4 cell 8


title: 16cell_4-6

description: 16-cell stage embryo 4 cell 6


title: 16cell_4-11

description: 16-cell stage embryo 4 cell 11


title: 16cell_6-12

description: 16-cell stage embryo 6 cell 12


title: 16cell_4-3

description: 16-cell stage embryo 4 cell 3


title: 16cell_4-2

description: 16-cell stage embryo 4 cell 2


title: 16cell_1-8

description: 16-cell stage embryo 1 cell 8


title: 16cell_5-8

description: 16-cell stage embryo 5 cell 8


title: 16cell_5-7

description: 16-cell stage embryo 5 cell 7


title: 16cell_1-9

description: 16-cell stage embryo 1 cell 9


title: 16cell_1-7

description: 16-cell stage embryo 1 cell 7


title: 16cell_5-11

description: 16-cell stage embryo 5 cell 11


title: 16cell_1-3

description: 16-cell stage embryo 1 cell 3


title: 16cell_1-6

description: 16-cell stage embryo 1 cell 6


title: 16cell_1-15

description: 16-cell stage embryo 1 cell 15


title: 16cell_4-5

description: 16-cell stage embryo 4 cell 5


title: 16cell_1-13

description: 16-cell stage embryo 1 cell 13


title: 16cell_1-4

description: 16-cell stage embryo 1 cell 4


title: 16cell_1-14

description: 16-cell stage embryo 1 cell 14


title: 16cell_1-11

description: 16-cell stage embryo 1 cell 11


title: PDAT_11-12_A

city: East Lansing

first: Kevin

middle: M

last: Carr

state: MI

address: Plant Biology Lab, 612 Wilson Rd., Rm. S-20 A

department: Research Technology Support Facility

country: USA

institute: Michigan State University

description: CL37 line with the castor PDAT gene (RcPDAT1a) expressed in seeds (van Erp, H., Bates, P. D., Burgal, J., Shockey, J., and Browse, J. (2011) Plant Physiol. 155, 683-693)

data_processing:
Basecalls were performed by Illumina Real Time Analysis software v 1.13.48. Demultiplexing and FASTQ conversion by Illumian BCL2Fastq v1.8.2
Reads were trimmed of Illumina adapter and low quality bases with Trimmomatic v0.22
Reads were mapped to the  Arabidopsis thalian genome, vTAIR10 using TopHat (v2.0.3). Only reads aligning to annotated genes were accepted.
Raw counts of reads aligning to each gene within each sample were determined with htseq-count (v0.5.4p3). Output is reported in processed data files.
Normalized expression (FPKM) was determined using Cufflinks (v2.0.1). Output is reported in supplementary matrix file, averaged FPKM across all biological replicates per condition.
Genome_build: TAIR10
Supplementary_files_format_and_content: Count files are tab delimited text output by htseq-count reporting TAIR10 gene ID, raw count. Supplementary matrix file is tab delimited text output by cufflinks reporting TAIR10 gene ID, short gene name, gene locus (<chr#>:<start>-<stop>), normalized (FPKM) expression values for each plant line/developmental stage, average of three biological replicates each.

molecule: total RNA

organism: Arabidopsis thaliana

growth_protocol: All plant lines were grown randomized across a growth chamber under constant ~100-170 μE light, ~22° C and ~60% humidity.

extract_protocol:
Developing siliques of 7-8, 9-10, or 11-12 DAF were collected from a single shoot of ~50 plants of each plant line, frozen in liquid nitrogen and developing seeds removed by (Bates, P., Jewell, J., and Browse, J. (2013) Plant Methods 9, 9). Approximately 100 mg of frozen seed samples (three biological replicates for each plant line/ developmental stage) were ground to a fine power,  RNA extracted Suzuki, Y., Kawazu, T., and Koyama, H. (2004) BioTechniques 37, 542-544 , and DNA removed (DNA-Free RNA Kit, Zymo Research).
Libraries were constructed using the Illumina TruSeq mRNA Library Preparation Kit v2

tag: tissue

value: Seeds

tag: age (days after flowering)

tag: genotype/variation

value: PDAT


title: 16cell_1-12

description: 16-cell stage embryo 1 cell 12


title: 16cell_4-4

description: 16-cell stage embryo 4 cell 4


title: PDAT_11-12_B


title: PDAT_7-8_B


title: 16cell_1-10

description: 16-cell stage embryo 1 cell 10


title: PDAT_7-8_C


title: PDAT_9-10_A


title: PDAT_9-10_B


title: PDAT_7-8_A


title: PDAT_9-10_C


title: Taf7 (ptr6, SPAC13F5.02c)

city: New York

first: Michael

middle: Christopher

last: Keogh

state: New York

address: 1300 Morris Park Avenue

department: Department of Cell Biology

institute: Albert Einstein College of Medicine

description: Job J10378 Index #10 (Ritu22). Multiplex Barcode: ATGAGTCT (Single-end read). Flowcell ID / Lane: D0JT6ACXX / lane_3_PM_I10

library_source: genomic

data_processing:
WASP pipeline (J10288: 3.0.39 [rev. 4526]; J10377 [3.0.47 (rev. 5500])
Peak Finder (MACS 1.4.1)
Aligner (bowtie 0.12.7)
BEDTools-Version-2.10.1
Genome_build: Schizosaccharomyces pombe (Sanger Center Release pombe090511)
Supplementary_files_format_and_content: Bed files

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: Fission yeast

growth_protocol: ChIP analyses (from asynchronous or cell-cycle synchronized populations) were as previously (Kim et al (2009) NSMB 16:1286). Synchronization cultures were G2-arrested at the non-permissive temperature for cdc25-22 (36.5oC, 4.5 hrs) before release at 24.5oC. Aliquots were collected at 25-minute intervals and fixed either with formaldehyde (2% final) for ChIP (50 ml), or in ethanol (70% v/v) for cell-septation analysis (500 μl).

extract_protocol:
Essentially as in: Keogh et al (2004) Methods Mol Biol 257:1-16.
Input or ChIP samples were converted to barcoded libraries by adaptor addition as previously (Quail et al (2008) Nat Methods 5:1005). In brief each sample was quantified, end-repaired (End-It kit, Epicenter Biotechnologies), an A-overhang added, and ligated to one of a set of 12 barcode-specific adaptor primers. The resulting libraries were size selected (600 ± 50 bp), amplified by 18 cycles of PCR, purified with SPRI beads (Agencourt AMPure XP; Fisher Scientific), quantified on a high-sensitivity DNA chip by 2100 bio-analyzer (Agilent Technologies, Inc.), mixed at equivalent concentrations, and multiplexed at 12 samples per Illumina HiSeq 2000 lane.

tag: strain number

tag: cell cycle stage

value: Aynchronous population

tag: chip-antibody

value: Rabbit Polyclonal anti-ptr6 (RTK7-8) (Mitsuzawa et al (2001) JBC 276:17117)


title: 16cell_1-5

description: 16-cell stage embryo 1 cell 5


title: INPUT (Replicate 2)

description: Job J10378 Index #5 (Ritu17). Multiplex Barcode: TCGATTCT (Single-end read). Flowcell ID / Lane: D0JT6ACXX / lane_3_PM_I5

value: h-, ade6-M210 ura3-D18 leu1-32 his3-D1 Nrc1.HA3::KanMX6


title: 16cell_1-2

description: 16-cell stage embryo 1 cell 2


title: Cut3.FLAG5, T125 (G1/S) [SPBC146.03c]

description: Job J10377 Index #8 (Ritu8). Multiplex Barcode: GATTGTGT (Single-end read). Flowcell ID / Lane: D0JT6ACXX / lane_2_P0_I8

value: h?, cdc25-22, Cut3.FLAG5::HphMX6, Nrc1.HA3::KanMX6

value: Synchronous, estimated G1/S

value: Mouse Monoclonal anti-FLAG M2


title: Cut3.FLAG5, T100 (Anaphase) [SPBC146.03c]

description: Job J10377 Index #7 (Ritu7). Multiplex Barcode: CTAGGCAT (Single-end read). Flowcell ID / Lane: D0JT6ACXX / lane_2_P0_I7

value: Synchronous, estimated Anaphase


title: Cut3.FLAG5, T75 (Metaphase) [SPBC146.03c]

description: Job J10377 Index #6 (Ritu6). Multiplex Barcode: AGTCACAT (Single-end read). Flowcell ID / Lane: D0JT6ACXX / lane_2_P0_I6

value: Synchronous, estimated Metaphase


title: PDAT_11-12_C


title: Cut3.FLAG5, T0 (G2/M) [SPBC146.03c]

description: Job J10377 Index #5 (Ritu5). Multiplex Barcode: TCGATTCT (Single-end read). Flowcell ID / Lane: D0JT6ACXX / lane_2_P0_I5

value: Synchronous, estimated G2/M


title: Nrc1.HA3, T125 (G1/S) [SPAC631.02]

description: Job J10377 Index #4 (Ritu4). Multiplex Barcode: GTCATGAT (Single-end read). Flowcell ID / Lane: D0JT6ACXX / lane_2_P0_I4

value: Mouse Monoclonal anti-HA (12CA5)


title: H3-K36Me3 (Replicate 2)

description: Job J10288 Index #12 (K36Me3-2). Multiplex Barcode: GCAGTTCT (Paired-end reads). Flowcell ID / Lane: AC04JJABXX / lane_3_PM_I12

value: Rabbit Polyclonal anti-Histone H3-K36Me3 (Abcam ab9050)


title: H3-K9Me2

description: Job J10288 Index #9 (K9Me2). Multiplex Barcode: TGCTCTAT (Paired-end reads). Flowcell ID / Lane: AC04JJABXX / lane_3_PM_I9

value: Rabbit Polyclonal anti-Histone H3-K9Me2 (Active Motif 39137)


title: H3-K36Me3 (Replicate 1)

description: Job J10288 Index #8 (K36Me3-1). Multiplex Barcode: GATTGTGT (Paired-end reads). Flowcell ID / Lane: AC04JJABXX / lane_3_PM_I8


title: Nrc1.HA3, T0 (G2/M) [SPAC631.02]

description: Job J10377 Index #1 (Ritu1). Multiplex Barcode: TATGACGT (Single-end read). Flowcell ID / Lane: D0JT6ACXX / lane_2_P0_I1


title: Nrc1.HA3, T100 (Anaphase) [SPAC631.02]

description: Job J10377 Index #3 (Ritu3). Multiplex Barcode: CGGTACAT (Single-end read). Flowcell ID / Lane: D0JT6ACXX / lane_2_P0_I3


title: H3-K4Me3 (Replicate 2)

description: Job J10288 Index #11 (K4Me3-2). Multiplex Barcode: CATCATGT (Paired-end reads). Flowcell ID / Lane: AC04JJABXX / lane_3_PM_I11

value: Rabbit Polyclonal anti-Histone H3-K4Me3 (Mark Bedford, Ab8678)


title: H3-K4Me3 (Replicate 1)

description: Job J10288 Index #7 (K4Me3-1). Multiplex Barcode: CTAGGCAT (Paired-end reads). Flowcell ID / Lane: AC04JJABXX / lane_3_PM_I7


title: TBP (TATA-Binding Protein, SPAC29E6.08)

description: Job J10288 Index #2 (TBP). Multiplex Barcode: ACATCTCT (Paired-end reads). Flowcell ID / Lane: AC04JJABXX / lane_3_PM_I2

value: Rabbit Polyclonal anti-TBP (Huang et al (2000) JBC 275:31480)


title: RNAseq_rhesusESC_pAplus

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

country: China

institute: Fudan University

data_processing:
Basecalling using Illumina Casava1.8.2 software.
combine three technical replicates RNAseq_mouseESC_pAminus_1.txt, RNAseq_mouseESC_pAminus_2.txt, RNAseq_mouseESC_pAminus_3.txt to RNAseq_mouseESC_pAminus.txt for further analysis
combine three technical replicates RNAseq_mouseESC_pAplus_1.txt, RNAseq_mouseESC_pAplus_2.txt, RNAseq_mouseESC_pAplus_3.txt to RNAseq_mouseESC_pAplus.txt for further analysis
Map to mouse genome mm9 or rhesus genome rheMac3 using Tophat (v 2.0.8)
Bam to Bedgraph using genomeCoverageBed
Bedgraph to bigwig using UCSC bedGraphToBigWig
For visualization, Bigwig files were generated using UCSC bedGraphToBigWig from Bedgraph files, which were generated using genomeCoverageBed from Tophat generated .bam. A UCSC browser session with uploaded Bigwig (.bw) track files is used for visualizing gene expression, etc.
Genome_build: mm9 for mouse samples or for rheMac3 rhesus samples
Supplementary_files_format_and_content: bigwig file (UCSC bigwig in an indexed binary format. http://genome.ucsc.edu/goldenPath/help/bigWig.html)

organism: Macaca mulatta

source_name: embryonic stem cells

growth_protocol: hES cells were maintained on plates coated with Matrigel (BD Biosciences) in either defined mTeSR medium (StemCell Technologies Inc.) or conditioned medium (CM) with irradiated mouse embryo fibroblasts supplemented with 4 ng/mL human Basic Fibroblast Growth Factor (bFGF)

extract_protocol:
Total RNAs were prepared using Trizol Reagent and treatment with DNase I. 20μg of total RNAs were separated into polyadenylated and nonpolyadenylated fraction by oligo(dT) magnetic beads (Invitrogen). Ribosomal RNAs were further depleted in nonpolyadenylated fractionby using RiboMinus kit (Invitrogen) o get the poly(A)-/ribo- RNA population. Poly(A)-/ribo- RNAs were further incubated with 5U of RNase R (Epicentre) for 3h at 37℃ and then were subjected to Trizol extraction (Invitrogen).
An aliquot of poly(A)-/ribo- enriched and RNase R digested RNA was used for library preparation with Illumina TruSeq Stranded Total RNA HT Sample Prep Kit (P/N 15031048), and then subjected to 1x100 deep sequencing with Illumina HiSeq 2000

tag: cell type

value: embryonic stem cells

tag: chromosome

value: diploid

tag: passages


title: Flower 3

status: Public on Jan 09 2014

city: New Delhi

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

country: India

institute: Jawaharlal Nehru University

data_processing:
Illumina 1.3 pipeline used for basecalling
Low-quality reads and reads containg adaptor/primer contamination were filtered using NGS QC Toolkit v2.3
Reads per kilobase per million (RPKM) value was calculated for all the genes in each tissue sample
Genome_build: Chickpea transcriptome v1.0 (http://www.nipgr.res.in/ctdb.html)
Supplementary_files_format_and_content: tab delimited text files include RPKM values for each sample

organism: Cicer arietinum

source_name: Mature plant

growth_protocol: Seedlings were grown in a culture room and mature plants were grown in field

extract_protocol:
Tissue samples were collected and frozen in liquid nitrogen. Total RNA was isolated using TRI reagent from Sigma
Libraries were prepared using mRNA-Seq Sample Prep kit (Illumina) according to the manufacture’s protocol

tag: genotype

value: Mature plant

value: Flower 3


title: Flower bud 2

value: Flower bud 2


title: Flower bud 4

value: Flower bud 4


title: RNAseq_rhesusESC_pAminus


title: Flower 4

value: Flower 4


title: Flower 1

value: Flower 1


title: Nrc1.HA3 (SPAC631.02)

description: Job J10378 Index #7 (Ritu19). Multiplex Barcode: CTAGGCAT (Single-end read). Flowcell ID / Lane: D0JT6ACXX / lane_3_PM_I7

value: h-, ade6-M210 ura3-D18 leu1-32 his3-D1 Nrc1.HA3::KanMX6

value: Aynchronous population


title: Flower bud 1

value: Flower bud 1


title: Flower bud 3

value: Flower bud 3


title: Flower 2

value: Flower 2


title: Germinating seedling

source_name: Seedling

value: Seedling

value: Germinating seedling


title: Shoot apical meristem

source_name: 20-day-old plants

value: 20-day-old plants

value: Shoot apical meristem


title: 3rd stage of potato tuberization (PT3)

first: Amar

last: Kumar

state: Delhi

address: Chatra Marg

department: Botany

institute: University of Delhi

description:
Sample 7
small RNA profiling

data_processing:
Illumina Casava1.7 software used for basecalling.
The removal of poor quality sequences and trimming of adaptor sequences from the raw sequence data was carried out using the UEA sRNA workbench 2.4- Plant version sequence file pre-processing (http://srna-tools.cmp.uea.ac.uk/) . Sequences, smaller than 16 nt and larger than 30 nt were also removed. High quality trimmed sequences (16-30 nt in length, reads with no N, no more than 4 bases with quality score <10 and no more than 6 bases with quality score <13) were mapped onto plant t/rRNAs sequences from “Rfam” (excepted miRNAs), Arabidopsis tRNAs from “The Genomic tRNA Database”, and plant t/rRNA sequences from “EMBL” release 95. The matched sequences were removed from downstream analysis. UEA sRNA toolkit-Plant version filter pipeline (http://srna-tools.cmp.uea.ac.uk/) was also used to remove any t/rRNA matchouts .
The unique reads were submitted to the UEA sRNA toolkit-Plant version miRCat pipeline (http://srna-tools.cmp.uea.ac.uk/)  and default criteria were used to predict potato-specific and conserved miRNAs in potato. The read were aligned to the potato reference genome (PGSC DM assembly version 3) (http://potatogenomics.plantbiology.msu.edu/) with no mismatch.
Genome_build: PGSC DM assembly version 3
Supplementary_files_format_and_content: The .txt files report abundance measurements.

organism: Solanum tuberosum

source_name: 3rd stage of potato tuberization (PT3)

growth_protocol: The plantlets of Solanum tuberosum (cv. Kufri Chandramukhi) were raised in vitro on MS medium  and maintained under the 16hr light/8 hr dark photoperiod conditions at 22°C. The leaves, stem and root were collected from 45 days old whole in vitro grown potato plantlets and immediately frozen in liquid nitrogen, subsequently stored at -80°C until used. These in vitro grown plantlets were then potted and grown under natural field conditions, during the period of November-January, in the net house at the Department of Botany, University of Delhi, India. Mature plants started to tuberize after 35 days and tissues from the four early developmental stages of tuberization were harvested, according to size, from these naturalized plants, frozen in liquid nitrogen and stored at -80°C until used.

extract_protocol:
Total RNA was isolated from the above mentioned tissues (0.2 grams each) using TRI reagent (Sigma, USA) as per the manufacturer’s instructions. The quality and quantity of RNA isolates was verified on denaturing agarose gel and by optical density (OD) measurement respectively.
Small RNA libraries for each tissue type were prepared independently using an Illumina Small RNA sample prep kit (Illumina, U.S.A), according to manufacturer’s instructions. Briefly, small RNAs (20-40 nt) were separated on 15% denaturing polyacrylamide gel and purified. Next, small RNAs were ligated with the 5’ and 3’adapters sequentially, eluted and gel purified. The 5’and 3’ligated small RNAs were reverse transcribed using SuperScript II Reverse Transcriptase (Invitrogen, U.S.A) and PCR amplified with Phusion DNA Polymerase. The quality and quantity of cDNA library was assessed using Agilent Bioanalyzer (Agilent Technologies, U.S.A). Small RNA library preparation and their high-throughput sequencing was performed using an Illumina Genome Analyzer IIx (Illumina, U.S.A) at DBT-funded High Throughput Sequencing Facility at University of Delhi South Campus, India.

tag: cultivar

value: Kufri Chandramukhi

value: Potato tuber 3rd stage (PT3)

tag: age

value: 45 days old


title: 2nd stage of potato tuberization (PT2)

description:
Sample 6
small RNA profiling

source_name: 2nd stage of potato tuberization (PT2)

value: Potato tuber 2nd stage (PT2)


title: Young leaves

value: Mature plant

value: Young leaves


title: Nrc1.HA3, T75 (Metaphase) [SPAC631.02]

description: Job J10377 Index #2 (Ritu2). Multiplex Barcode: ACATCTCT (Single-end read). Flowcell ID / Lane: D0JT6ACXX / lane_2_P0_I2

value: h?, cdc25-22, Cut3.FLAG5::HphMX6, Nrc1.HA3::KanMX6

value: Synchronous, estimated Metaphase

value: Mouse Monoclonal anti-HA (12CA5)


title: 1st stage of potato tuberization (PT1)

description:
Sample 5
small RNA profiling

source_name: 1st stage of potato tuberization (PT1)

value: Potato tuber 1st stage (PT1)


title: 0 stage of potato tuberization (PT0)

description:
Sample 4
small RNA profiling

source_name: 0 stage of potato tuberization (PT0)

value: Potato tuber 0 stage (PT0)


title: Root(R)

description:
Sample 3
small RNA profiling

source_name: Root(R)

value: Root(R)


title: Stem(S)

description:
Sample 2
small RNA profiling

source_name: Stem(S)

value: Stem(S)


title: Leaf(L)

description:
Sample 1
small RNA profiling

source_name: Leaf(L)

value: Leaf(L)


title: Cka1.HA3 (SPAC21C11.11)

description: Job J10378 Index #9 (Ritu21). Multiplex Barcode: TGCTCTAT (Single-end read). Flowcell ID / Lane: D0JT6ACXX / lane_3_PM_I9

value: h-, ade6-M210 ura3-D18 leu1-32 his3-D1 Cka1.HA3::KanMX6

value: Aynchronous population


title: E14 5-hmC ChIP-seq

city: Urbana

first: Chieh-Chun

last: Chen

state: Illinois

address: 1206 West Gregory Drive

department: Bioengineering

institute: University of illinois

data_processing:
mouse_5hmC.bed; genome build: mm9
Sequence reads were obtained and mapped to mouse genomes (mm9) using Bowtie. Only reads with one or fewer mismatches and uniquely mapped onto the genome were retained.

source_name: E14 embryonic stem cells

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

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

treatment_protocol: No treatment on E14 cells

tag: chip antibody

value: E14 embryonic stem cells

tag: chip antibody manufacturer

value: Active Motif

tag: chip antibody catalog #


title: E14 MeDIP-seq

data_processing:
mouse_MeDIP.bed; genome build: mm9
Sequence reads were obtained and mapped to mouse genomes (mm9) using Bowtie. Only reads with one or fewer mismatches and uniquely mapped onto the genome were retained.

tag: strain

value: Eurogentec


title: E14 H2A.Z ChIP-seq

data_processing:
mouse_H2AZ.bed; genome build: mm9
Sequence reads were obtained and mapped to mouse genomes (mm9) using Bowtie. Only reads with one or fewer mismatches and uniquely mapped onto the genome were retained.

value: Abcam


title: Mouse Adult Stomach 2

city: Reno

first: Nicole

last: Ortogero

state: Nevada

address: 1664 N. Virginia St

department: Physiology and Cell Biology

institute: University of Nevada, Reno

description:
flash frozen
st2

data_processing:
tMAP (Torrent Server LifeTechnologies) aligned to mm9
reads <15nt removed
reads aligned to miRNAs removed
reads aligned to piRNA clusters classified as pilRNAs
Genome_build: mm9
Processed Numbers: Counts

source_name: Stomach

extract_protocol:
Small RNA was collected using miRvana kit (life Technologies)
LifeTechnologies RNA-seq kit v2 (PGM sequencing)
A 200bp Ion Torrent sequencing kit was used allowing for up to 200bp resolution

treatment_protocol: Tissue was collected and flash frozen

value: Adult


title: E14 MRE-seq

data_processing:
mouse_MRE.bed; genome build: mm9
Sequence reads were obtained and mapped to mouse genomes (mm9) using Bowtie. Only reads with one or fewer mismatches and uniquely mapped onto the genome were retained.


title: Mouse Adult Stomach 1

description:
flash frozen
st1


title: INPUT (Replicate 1)

description: Job J10288 Index #1 (Input). Multiplex Barcode: TATGACGT (Paired-end reads). Flowcell ID / Lane: AC04JJABXX / lane_3_PM_I1


title: ESC_IgG

city: Copenhagen N

first: Marianne

middle: Terndrup

last: Pedersen

address: Ole Maaloes Vej 5

department: University of Copenhagen

country: Denmark

institute: BRIC

data_processing:
No filtering of the raw reads were performed prior to alignment.
Raw sequence reads were mapped to the mouse genome using the the BOWTIE tool (version 0.12.7) with default parameters except:  -S -m 1
BedGraph files were generated by extending each aligned read to 250 bp in the 3' direction & removing all duplicates, before finally converting to bedGraph format using the UCSC command line tool “bedItemOverlapCount”
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph: BedGraph files were generated by extending each aligned read in the 3' direction to 250 bp & removing all duplicates, before finally converting to bedGraph format using the UCSC command line tool “bedItemOverlapCount”

source_name: Conditional Jmjd2c knockout ESCs

growth_protocol: ESCs were cultured in serum-free '2i' medium on 0.2% gelatin coated plates.

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed using formaldehyde crosslinked chromatin sonicated to an average size of 200-600 bp and the indicated antibodies.
5-10 ng of DNA was processed using NEBNext and Illumina ChIP seq kits according to the manufacturer's instructions. In brief, DNA was adaptor-ligated, subjected to gel size selection, amplified and analyzed by Solexa/Illumina high-throughput sequencing.

treatment_protocol: ESCs were cultured in the absence or presence of 500 nM OHT for 96 h.

value: Conditional Jmjd2c knockout ESCs

tag: treatment

value: IgG


title: MEF_OHT_H3K36me3

description: pool of four sequencing runs (read lengths 42 and 96)

data_processing:
No filtering of the raw reads were performed prior to alignment.
Raw sequence reads were mapped to the mouse genome using the the BOWTIE tool (version 0.12.7) with default parameters except:  “-S -m 1” OR “-S -m 1 –solexa1.3-quals”
BedGraph files were generated by extending each aligned read to 250 bp in the 3' direction & removing all duplicates, before finally converting to bedGraph format using the UCSC command line tool “bedItemOverlapCount”
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph: BedGraph files were generated by extending each aligned read in the 3' direction to 250 bp & removing all duplicates, before finally converting to bedGraph format using the UCSC command line tool “bedItemOverlapCount”

source_name: mouse embryonic fibroblasts

growth_protocol: Early passage MEFs were cultured in D-MEM (GIBCO) supplemented with 10% FBS (Hyclone).

treatment_protocol: MEFs were grown in the absence or presence of 500 nM OHT for 72h prior to harvesting.

value: conditional Jmjd2c knockout MEFs

value: OHT


title: E14 H3K27ac ChIP-seq

data_processing:
mouse_H3K27ac.bed; genome build: mm9
Sequence reads were obtained and mapped to mouse genomes (mm9) using Bowtie. Only reads with one or fewer mismatches and uniquely mapped onto the genome were retained.

value: Millipore


title: MEF_H3K36me3


title: MEF_OHT_H3K9me3


title: ESC_Jmjd2c


title: ESC_OHT_Jmjd2c


title: MEF_H3K9me3


title: KYSE150_shJMJD2C_H3K9me3

data_processing:
No filtering of the raw reads were performed prior to alignment.
Raw sequence reads were mapped to the human genome using the the BOWTIE tool (version 0.12.7) with default parameters except:  “-S -m 1” OR “-S -m 1 –solexa1.3-quals”
BedGraph files were generated by extending each aligned read to 250 bp in the 3' direction & removing all duplicates, before finally converting to bedGraph format using the UCSC command line tool “bedItemOverlapCount”
Genome_build: hg18
Supplementary_files_format_and_content: bedgraph: BedGraph files were generated by extending each aligned read in the 3' direction to 250 bp & removing all duplicates, before finally converting to bedGraph format using the UCSC command line tool “bedItemOverlapCount”

organism: Homo sapiens

growth_protocol: KYSE150 cells were cultured in D-MEM/F-12 1:1 (Invitrogen) supplemented with 10% FBS (Hyclone).

treatment_protocol: KYSE150 cells were transfected with the indicated pRetrosuper shRNA constructs using Fugene 6 (Roche Diagnostics) according to manufacturer's instructions and selected 24h after transfection with 2 μg/ml puromycin for 72 h prior to harvesting.

tag: cell line


title: KYSE150_IgG

value: shCtrl

value: IgG ctrl


title: KYSE150_shCtrl_H3K36me3


title: KYSE150_shCtrl_H3K9me3


title: KYSE150_shJMJD2C_H3K36me3


title: H3K4ME3_leo1_delta_FM392_Rep_1

city: Kansas City

first: Malcolm

last: Cook

email: mec@stowers.org, malcolm.cook@gmail.com

state: MO

address: 1000 E 50th Street

department: Big Data AI

institute: Stowers Institute For Medical Research

data_processing:
Base-calling was done with Casava v1.8.2 using default settings for quality filtering.
Unique ChIP-seq alignments were produced in by Bowtie v1.0.0 (Langmead et al. 2009) allowing up to 2 mismatches (parameters -v 2 –m 1)
Alignments were extended to 150bp  and normalized to total tag count (reads/million) (producing the bigWig files)
Genome_build: Saccharomyces Genome Database (SGD) SacCer_Apr2011 as imported by UCSC sacCer3
Supplementary_files_format_and_content: bigWig files are all extended read coverage normalized as reads/million

organism: Saccharomyces cerevisiae

growth_protocol: Chromatin immunoprecipitations (ChIPs) were performed with cell lysates prepared from exponentially growing yeast strains to OD600nm of 1.0 and the cells were cross-linked by formaldehyde treatment.

extract_protocol: We followed the modified ChIP protocol described previously (Wood et al., 2005) and used anti-trimethylated H3K4 antibodies for immunoprecipitation.; anti-trimethylated H3K4 was developed by our lab. 10 ng of DNA prepared from each ChIP was amplified using LMPCR and subjected to single read sequencing on a HiSeq2000 instrument.

treatment_protocol: leo1 deleted in the FM392 strain

value: (rb) α-H3K4me3 (#528; Ali Shilatifard)


title: H3K4ME3_WT_FM392_Rep_1

treatment_protocol: wild-type


title: H3K4ME3_leo1_delta_FM392_Rep_2


title: H3K4ME3_WT_FM392_Rep_2


title: H3K4ME3_Full_length_Set1_Rep_2

treatment_protocol: Full-length Set1 integrated into the BY4741 strain


title: Input_for_Full_length_Set1_Rep1

treatment_protocol: Full length Set1 integrated into a strain with a TAP tag on Bre2

value: input


title: H3K4ME3_chd1_delta_FM392_Rep_2

treatment_protocol: chd1 deleted in the FM392 strain


title: H3K4ME3_aa762-1080_Set1_Rep_1

treatment_protocol: Flag tagged and trunctaed version of Set1 integrated into a strain deleted for Shg1 and a TAP-tag on Bre2


title: H3K4ME3_chd1_delta_FM392_Rep_1


title: H3K4ME3_aa762-1080_Set1_Rep_2

treatment_protocol: Set1 deleted for first 761 amino acids was integrated into the BY4741 strain


title: Input_Set1_aa762-1080_Rep_1


title: MEF_IgG


title: MEF_Jmjd2c


title: KYSE150_shCtrl_H3K4me3


title: KYSE150_shJMJD2C_JMJD2C


title: KYSE150_shCtrl_JMJD2C


title: MEF_OHT_Jmjd2c


title: Wild type ChIP (cohesin)

status: Public on Jan 08 2014

city: Edinburgh

first: Alastair

middle: Robert

last: Kerr

state: Midlothian

address: 2.21 Michael Swann Building, Kings Buildings, Mayfield Road

department: Wellcome Centre for Cell Biology

country: United Kingdom

institute: University of Edinburgh

data_processing:
Cassava 1.8.2
Mapping: BWA Version: 0.6.1-r104  to sacCer3  with argument -t 20
Format conversion and removal of duplicate reads: samtools Version: 0.1.16 (r963:234)
RPM scaling, bedgraph creation and bed intersections: bedtools v2.16.2
bedgraph to bigwig conversion: wigToBigWig v 4 (UCSC utilities)
scripts from https://github.com/AlastairKerr/Marston2013/
Genome_build: sacCer3
Supplementary_files_format_and_content: bedGraph
Supplementary_files_format_and_content: Dedup = optical duplicates removed,   all = no optical duplicates removed,  WT = Wild Type, Mut = sgo1delta

organism: Saccharomyces cerevisiae W303

growth_protocol: Cells were arrested in mitosis by treatment with nocodazole for 3h.

extract_protocol:
Anti-HA ChIP was performed and both input and IP samples were sequenced. NEBNext ChIP-Seq kit (manual attached) with an E-gel selection of desired fragment size in the finished library.
Made by Bianka Baying (EMBL)

treatment_protocol: Samples were fixed in formaldehyde for 2h before harvesting.

tag: ChIP

value: anti-HA 12CA5

tag: antibody vendor

value: Roche

tag: antibody catalog number

tag: antibody lot


title: Wild type input (cohesin)


title: sgo1D ChIP (condensin)

value: sgo1D BRN1-6HA


title: sgo1D input (condensin)


title: sgo1D input (cohesin)

value: sgo1D SCC1-6HA


title: Wild type input (condensin)


title: Wild type ChIP (condensin)


title: Control HGB_17

city: Bethesda

first: Nirmala

last: Akula

state: Maryland

address: Building 35, Room 1A-205

department: Human Genetics Branch

institute: National Institute of Mental Health/National Institutes of Health

description:
HGB11-22_geneLevel_HTSeqCountData.txt
HGB11-22_transcriptLevel_eXpressCountData.txt

data_processing:
The raw data was mapped to human genome build 19 using Tophat
The counts of each gene from Ensemble were obtained using HTSeq and analyzed with DESeq
Transcript level analyses were performe using eXpress and DESeq was used to analyze this data. Ensemble.gtf file was used for this analysis.
HGB_5 was excluded in the processed data because it had a low RNA integrity number
Genome_build: n/a
Supplementary_files_format_and_content: abundance

source_name: postmortem brain

extract_protocol:
Total RNA was extracted from the dorsolateral prefrontal cortex (Brodmann area 46) of post-mortem brain tissue of 11 BD cases and 11 healthy controls
Illumina RNA sequencing protocol was followed

tag: tissue

value: dorsolateral prefrontal cortex

tag: disease state

value: Control


title: Control HGB_21


title: Control HGB_19


title: BD HGB_16

value: BD


title: Control HGB_20


title: Control HGB_22


title: Control HGB_18


title: BD HGB_15


title: BD HGB_14


title: H3K4ME3_Full_length_Set1_Rep_1


title: BD HGB_13


title: BD HGB_11


title: sgo1D ChIP (cohesin)


title: R-11268-RNA-Seq-rep3 control

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
RNA-Seq RPKM data were generated using Bowtie version 0.12.7 and Tophat version 1.4.1 (flags = -g 1). Gene expression values were calculated using Cufflinks version 1.1.0 (flags = -F 0, -b, -N)
For each gene, a generalized Poisson linear mixed model was fitted under the full model with the library size as the offset as described in the methods section. The fitted values from this gene-specific model (also called the conditional mean of the observations) were then used as the reported expression values for different conditions.
Genome_build: Gm1.01

organism: Glycine max

growth_protocol: Seeds were surface sterilized [30% bleach, rinsed several times with sterile, double-distillated H2O (ddiH2O)], planted in soil-less medium (SogeMix “SM-2”-general purpose growing medium), and germinated in growth chambers (190 μmol PAR m-2s-1, 230C, 60% R.H., and 16 h photoperiod).

extract_protocol: Total RNA was purified from 0.5 g of leaves by using Trizol Reagent (Invitrogen, Carlsbad, CA), according to the manufacturer’s instructions, and subsequently purified using chloroform extraction. RNA-Seq libraries were constructed using the Illumina TruSeq Kit v2 (Illumina, San Diego, CA) according to the manufacturer’s guidelines.

treatment_protocol: Trifoliolate leaves from three-week-old plants were detached and then vacuumed infiltrated with ddiH2O for 2 min. Water-infiltrated trifoliolate leaves from five different plants of each genotype were pooled and cut into approximately 1 cm2 slices. An equal amount of leaf slices (~30 slices) from each treatment were transferred into two different Petri dishes and then floated overnight on autoclaved ddiH2O. Water was removed from both Petri dishes and replaced with 5 ml of MAMP solution [1 μM flagellin 22 (flg22; Genescript) and 50 μg of crab shell chitin (referred to as chitin in this study; Sigma-Aldrich)], or 5 ml of mock solution [autoclaved ddiH2O plus equivalent amount of dimethyl sulfoxide (DMSO; Fisher Scientific). DMSO was included since it was contained in the solution used to dissolve the flg22 peptide]. After a 30 min treatment, mock- and MAMP-treated leaf slices were harvested into different tubes and immediately frozen in liquid nitrogen. Samples were stored at -80 until use. All procedures described above were performed under dark conditions.

tag: ecotype

value: Trifoliolate leaves

value: 3 week

value: 190 mmol PAR m-2s-1, 230C, 60% R.H., 16 h photoperiod, and 5 ml of mock solution [autoclaved ddiH2O plus equivalent amount of dimethyl sulfoxide (DMSO; Fisher Scientific)


title: LDX-RNA-Seq-rep3 control

source_name: Trifoliolate leaves from three-week-old plants

value: LDX


title: R-11268-RNA-Seq-rep2 control


title: LDX-RNA-Seq-rep2 control


title: R-11268-RNA-Seq-rep1 control


title: LDX-RNA-Seq-rep1 control


title: R-11272-RNA-Seq-rep1 control


title: R-11272-RNA-Seq-rep3 control


title: R-11272-RNA-Seq-rep2 control


title: LD-RNA-Seq-rep3 control

value: LD


title: LD-RNA-Seq-rep2 control


title: R-11268-RNA-Seq-rep3_treated

source_name: Trifoliolate leaves from three-week-old plants treated with MAMPs

value: 190 mmol PAR m-2s-1, 230C, 60% R.H., 16 h photoperiod, and 5 ml of MAMP solution [1 uM flagellin 22 (flg22; Genescript) and 50 ug of crab shell chitin (referred to as chitin in this study; Sigma-Aldrich)]


title: R-11272-RNA-Seq-rep2_treated


title: R-11272-RNA-Seq-rep1_treated


title: LD-RNA-Seq-rep1 control


title: LDX-RNA-Seq-rep3_treated


title: R-11272-RNA-Seq-rep3_treated


title: BD HGB_12


title: LD-RNA-Seq-rep2_treated


title: LD-RNA-Seq-rep1_treated


title: R-11268-RNA-Seq-rep1_treated


title: Liver_lipoicacid_fed_rep4

city: Lincoln

first: Jean-Jack

middle: M.

last: Riethoven

state: NE

address: 1901 Vine Street

department: Beadle Center for Biotechnology

institute: University of Nebraska-Lincoln

description: Liver tissue,  lipoic acid fed, biological replicate 4

data_processing:
Basecalls performed using CASAVA version 1.8.2
RNA-Seq reads were aligned to the Rattus norvegicus genome assembly (RGSC 3.4) using tophat version 0.12.8 with default parameters.
Digital gene expression files were generated using cuffdiff version v2.0.2 (3522) with default parameters, and results were further annotated and summarised via in-house perl scripts.
Genome_build: RGSC 3.4
Supplementary_files_format_and_content: Tab delimited files containing FPKM gene-level values for each sample, as well as a cuffdiff generated and further annotated tab-delimited files containing fold-changes and q-values of AL versus AP and LL versus LP.

organism: Rattus norvegicus

source_name: liver

growth_protocol: Eight obese male Zucker rats (ZDF/GmiCrl-fa/fa, 7-week old) were purchased from Charles River Laboratories (Wilmington, MA)

extract_protocol:
At the end of the trial, rats (11 weeks of age) were anesthetized with inhalant isoflurane and samples of liver and epididymal fat were quickly removed, frozen in liquid N2, and stored at –80°C. Total RNA was isolated from materials by using TRIzol Reagent (Invitrogen cat#: P/N 15596-018), followed by further purification by Qiagen RNeasy Mini Kit (P/N 74104). RNA qualities were assessed using an Agilent BioAnalyzer 2100 system (Agilent Technologies).
RNA libraries were prepared from 4ug total RNA using the Illumina TruSeq RNA Sample Prep Kit-V2 set A (RS-122-2002 ) according to the manufacturer’s instructions. Libraries were analyzed and measured by gel electrophoresis and Nanodrop 1000 Spectrophotometer to a concentration of 10nM each.

treatment_protocol: Rats were acclimated for two weeks in individual cages in a controlled environment (ambient temperature 22 ± 2 C, 12:12-h light–dark cycle) with free access to food (Purina 5008, 26.8% calories from protein, 16.7% from fat, 56.4% from carbohydrates; Dyets, Bethlehem, PA) and water. At 9 weeks of age, the rats were randomly assigned to one of two treatments (Purina 5008+LA or Purina 5008 pair-feeding) for 2 weeks (n = 4 replicates). Throughout the trial, animals were given 2-day feeding rations between 1 and 3 pm and provided MilliQ water to drink

value: liver

tag: genotype/variation

value: Zucker (ZDF/GmiCrl-fa/fa)

tag: diet

value: R-a-lipoic acid


title: Liver_lipoicacid_fed_rep3

description: Liver tissue,  lipoic acid fed, biological replicate 3


title: LDX-RNA-Seq-rep2_treated

tag: genotype


title: LD-RNA-Seq-rep3_treated

tag: age


title: Liver_lipoicacid_fed_rep2

description: Liver tissue,  lipoic acid fed, biological replicate 2


title: Liver_lipoicacid_fed_rep1

description: Liver tissue, lipoic acid fed, biological replicate 1


title: Liver_pairfed_rep4

description: Liver tissue, pair fed, biological replicate 4

value: pairfed


title: Liver_pairfed_rep2

description: Liver tissue, pair fed, biological replicate 2


title: Liver_pairfed_rep1

description: Liver tissue, pair fed, biological replicate 1


title: Liver_pairfed_rep3

description: Liver tissue, pair fed, biological replicate 3


title: Adipose_lipoicacid_fed_rep3

description: Adipose tissue,  lipoic acid fed, biological replicate 3

source_name: epididymal fat

value: epididymal fat


title: Adipose_lipoicacid_fed_rep4

description: Adipose tissue,  lipoic acid fed, biological replicate 4


title: Adipose_lipoicacid_fed_rep2

description: Adipose tissue,  lipoic acid fed, biological replicate 2


title: R-11268-RNA-Seq-rep2_treated


title: LDX-RNA-Seq-rep1_treated


title: Adipose_pairfed_rep4

description: Adipose tissue, pair fed, biological replicate 4


title: Adipose_pairfed_rep3

description: Adipose tissue, pair fed, biological replicate 3


title: Adipose_pairfed_rep2

description: Adipose tissue, pair fed, biological replicate 2


title: Adipose_pairfed_rep1

description: Adipose tissue, pair fed, biological replicate 1


title: CEBPa_macrophages _ChIPSeq

city: Birmingham

first: Salam

middle: Adli

last: Assi

address: IBR

department: Institute for Cancer and Genomic Sciences

institute: University of Birmingham

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using BWA
reads tags density were obtained using bedtools and samtools
peaks were called using MACS 1.4
Genome_build: mm9
Supplementary_files_format_and_content: bigwig file was generated using bedtools and samtools

source_name: CEBPa from macrophages cells

extract_protocol:
Primary macrophages were differentiated from isolated bone marrow in IMDM medium supplemented with IL-3 and CSF1 and ChIP assays were performed with rabbit antibodies against C/EBPa (sc-61X, Santa Cruz).
DNA from in vivo treated cells was run on an agarose gel and fragments in the range of 100-600 bp were excised and isolated. This DNA was used to prepare the libraries, according to Illumina's sample preparation protocol

tag: strain background

tag: cell type

value: bone Marrow derived Macrophages

tag: chip antibody

value: C/EBPalpha

tag: chip antibody vendor

value: Santa Cruz biotechnology

tag: chip antibody cat. #


title: PARP1.T5_ChIPseq

city: Barcelona

first: Miguel

last: Beato

address: Aiguader 88

country: Spain

institute: CRG

description: ChIP-seq

data_processing:
Basecalls performed using Illumina pipeline version 1.4.0
ChIP-Seq Single-end reads were processed by aligning to the reference human genome (GRCh37/hg19) using Bowtie v1.0.0
ChIP-seq signals were summed in windows of 10 Kb
Genome_build: hg19
Supplementary_files_format_and_content: TXT file with read counts all over the genome of all ChIP-seq samples

source_name: Breast cancer cell line

growth_protocol: Cells were routinely grown in RPMI 1640 medium supplemented with 10% FBS, 2 mM L-glutamine, 100 U/ml penicillin, and 100 mg/ml streptomycin

extract_protocol:
After hormone treatment, the medium was replaced by medium containing 1% formaldehyde and incubated 10 min at 37ºC for cross-linking. The reaction was stop by adding 125 mM glycine and incubated 5 min at room temperature. Cells were washed twice with cold PBS, and collected. Preparation of chromatin and ChIP experiments were performed as previously described (Strutt et al, Methods Mol Biol. 1999; 119:455-567). Immunoprecipitated DNA was purified by phenol:chloroform followed by ethanol precipitation
It was performed using the NEBNext DNA sample prep Reagents set 1

treatment_protocol: For the experiments, cells were plated in RPMI medium without phenol red supplemented with 10% dextran-coated charcoal-treated FBS and 48 hr later medium was replaced by fresh medium without serum. After 1 day in serum-free conditions, cells were incubated with R5020 (10 nM) for different times between 0 and 30 minutes

tag: time

value: 5 min

tag: cell line

tag: treatment

value: progestin


title: Control HGB_9

description:
HGB1-10_geneLevel_HTSeqCountData.txt
HGB1-10_transcriptLevel_eXpressCountData.txt

value: dorsolateral prefrontal cortex

value: Control


title: Control HGB_10


title: CDK2.T5_ChIPseq

description: ChIP-seq


title: CDK2.T30_ChIPseq

description: ChIP-seq

value: 30 min


title: CDK2.T0_ChIPseq

description: ChIP-seq

value: 0 min


title: Control HGB_8


title: BD HGB_4

value: BD


title: PARP1.T0_ChIPseq

description: ChIP-seq


title: BD HGB_5


title: Control HGB_6


title: Control HGB_7


title: BD HGB_1


title: BD HGB_3


title: Adipose_lipoicacid_fed_rep1

description: Adipose tissue, lipoic acid fed, biological replicate 1


title: Subject10 WNV

city: New Haven

first: Ruth

last: Montgomery

state: CT

address: 300 Cedar St.

department: Internal Medicine

institute: Yale University School of Medicine

data_processing:
Using the fastq files, all sequencing reads were mapped back to human genome (hg19) using TopHat (v1.1.4).
Cufflinks (v0.9.3) was used to assemble the mapped reads against the ENSEMBL (release 57) gene structure annotation, and estimate expression levels for each transcript.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample.

source_name: macrophages, WNV

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated using Ficoll-Hypaque (GE Healthcare, NJ) and suspended in RPMI-1640 containing L-Glutamine supplemented with 20% (v/v) human serum (Lonza, MD), 100 U/ml penicillin and 100 µg/ml streptomycin (Invitrogen, CA). Cells were plated at 2x10e7 cells/10-cm tissue culture dish. Non-adherent cells were washed away after 2 h, and adherent monocytes were incubated 6-8 days to mature into macrophages.

extract_protocol: mRNA was fragmented into 150-300bp fragments by incubation in RNA Fragmentation Reagent (Ambion, TX) at 70°C for 5 minutes. The fragmented mRNA was purified away from the fragmentation buffer by Agencourt RNAClean beads (Beckman Coulter, MA) following the manufacturer's instructions. The purified, fragmented mRNA was converted into double-stranded cDNA using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen, CA) by priming with random hexamers.

treatment_protocol: Virulent WNV (CT-2741) was passaged once in Vero cells (ATCC CCL-81) and viral PFU were quantified by plaque assays. Cells were infected with WNV (multiplicity of infection, MOI = 1) for 24 h.

value: monocyte-derived macrophages

value: West Nile virus (WNV)

tag: donor identifier


title: Subject9 Mock

source_name: macrophages, mock

value: mock


title: Subject10 Mock


title: PARP1.T30_ChIPseq

description: ChIP-seq


title: Subject7 Mock


title: Subject7 WNV


title: Subject5 WNV


title: Subject5 Mock


title: Subject4 WNV


title: Subject3 WNV


title: Subject8 Mock


title: Subject3 Mock


title: Subject2 Mock


title: Subject4 Mock


title: Subject1 Mock


title: BD HGB_2


title: Subject1 WNV


title: Subject6 Mock


title: Subject2 WNV


title: Stimulated MATa Biological Replicate 3

status: Public on Jan 07 2014

city: Ithaca

first: Lori

middle: B

last: Huberman

state: NY

address: 236 Tower Rd.

department: Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science

institute: Cornell University

data_processing:
Illumina's  CASAVA software, version 1.8.2, (using function configureBclToFastq.pl)  with default parameters
Sequenced reads were trimmed for adaptor sequence and mapped to S288C reference genome r64 using tophat v1.1.4 with the command: tophat -o my_tophat --library-type fr-unstranded -G genome.gtf --no-novel-juncs genome filename.fastq
Fragments Per Kilobase of exon per Million fragments mapped (FPKM) were calculated using Cufflinks v0.9.3 with the command: cufflinks -o my_cufflinks -L s5 -G genes.gtf -r genome.fa  -N --library-type fr-unstranded accepted_hits.bam
Genome_build: S288C reference genome r64
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: yeast cells

growth_protocol: Cells were grown to log phase in YPD + 0.1% BSA at 30C.  10 mL of the culture was harvested by spinning at 4C, washed in 1 mL RNase-free ice-cold water, pelleted, and flash frozen in dry ice to generate unstimulated samples.

extract_protocol:
RNA was extracted using hot acid phenol as described in Collart, M. A., and S. Oliviero, 2001 Preparation of yeast RNA. Current protocols in molecular biology 13.12. 1-13.12. 5
RNA libraries were prepared for sequencing using standard Illumina protocols.  All samples were multiplexed in a single lane using standard Illumina adapter barcodes.  The Illumina adapter barcode numbers are listed in this spreadsheet under "characteristics: Illumina Adapater Barcode"

treatment_protocol: To generage stimulated samples, 10nM α-factor was added to the remaining culture, incubated for 2 hours at 30C, and harvested in the same manner.

tag: strain

tag: +/- α-factor

tag: illumina adapter barcode


title: Stimulated MATa Biological Replicate 2


title: Stimulated MATa Biological Replicate 1


title: Unstimulated MATa Biological Replicate 3


title: Subject8 WNV


title: Unstimulated MATa Biological Replicate 2


title: Subject9 WNV


title: Input DNA

city: Zurich

first: Valentina

last: Boeva

address: Universitatstrasse 6

department: Computer Science

country: Switzerland

institute: ETH Zurich

data_processing:
The sequencing reads were aligned to the hg19 human genome using Bowtie 0.12.8 (Langmead et al., 2009) with the following options: “-C -k 1 -y --col-keepends”.
Regions enriched in H3K27me3 mark were called using  CCAT (Xu et al., 2010) and HMCan (Ashoor et al., "HMCan – a tool to detect chromatin modifications in cancer samples using ChIP-seq data", submitted).
Genome_build: hg19
Supplementary_files_format_and_content: bed files with peaks predicted by HMCan and CCAT

source_name: human bladder cancer cell line CL1207 derived from a muscle-invasive bladder cancer

growth_protocol: The human bladder cancer cell line CL1207 was derived from a muscle-invasive bladder cancer (De Boer et al., 1997). CL1207 was cultured in Dulbecco’s modified Eagle medium F-12 Glutamax medium (Invitrogen, Cergy Pontoise, France) supplemented with 10% fetal bovine serum (Lonza Verviers, Verviers, Belgium). One confluent 75 cm2 dish of CL1207 were used for one ChIP-seq experiment.

extract_protocol:
CL1207 chromatin was extracted from cell nuclei and sheared enzymatically using an Active Motif kit (Active Motif, Rixensart, Belgium). An extract of the original chromatin was kept as an internal standard (input DNA) for both duplicates. 5x105 cells were immunoprecipitated per ChIP assay with 4 μg of rabbit polyclonal antibodies against trimethyl histone H3 lysine 27 (Upstate Biotechnology, Santa Cruz, CA) and  Dynabeads® Protein A (Invitrogen, Cergy Pontoise, France) in dilution buffer containing 1% Triton X-100, 150 mM NaCl, 2 mM EDTA, 20 mM Tris–HCl at pH 8.0, and protease inhibitors. Six ChIP assays in the same experimental conditions were necessary to perform one ChIP-Seq experiment, so the total of 3x106 cells for each of the duplicates.
The SOLiD System 2.0 workflow for the Lower Input/Lower Complexity DNA fragment library preparation kit was used following the manufacturers’ instructions (Applied Biosystems) starting with 50 and 58 ng of ChIP or input DNA, respectively.

tag: disease state

value: bladder cancer

tag: antibody


title: Unstimulated MATa Biological Replicate 1


title: ChIP-seq for trimethylation of Lysine 27 of histone 3 (H3K27me3)

tag: antibody vendor

value: Upstate Biotechnology


title: Stimulated MATα-playing-a Biological Replicate 2


title: Subject6 WNV


title: Stimulated MATα-playing-a Biological Replicate 3


title: Unstimulated MATα-playing-a Biological Replicate 3


title: Unstimulated MATα-playing-a Biological Replicate 2


title: Unstimulated MATα-playing-a Biological Replicate 1


title: Rhesus(10y)_CBC

city: Shang Hai

first: zs

last: li

address: No. 320, Yueyang Road

institute: Partner Institute of Computational Biology

data_processing:
Image files were preprocessed by illumina software, which generates qseq files
qseq files were converted into fastq files by perl scripts, and only the ones passing illumina quality controls were retained
Reads were mapped onto  reference genome panTro2 and rheMac2 by Tophat(1.0.1.0)
mapped reads with more than three mismatches, multiple location mapping filtered out using perl script
sequencing information for each exonic genome sites were extracted by SAMtools (0.1.18)
Processed data files contain the counts of 'A' and 'G' base nucleotides with high sequencing quality (Phred quality score supplied by Illumina sequencing platform >20) for each predicted editing site (DARNED sites) used for analysis of each sample.
Genome_build: Pan_troglodytes-2.1 (http://www.ncbi.nlm.nih.gov/assembly/GCF_000001515.3/) for Pan troglodytes,
Genome_build: Mmul_051212 (http://www.ncbi.nlm.nih.gov/assembly/GCF_000002255.2/) for Macaca mulatta
Supplementary_files_format_and_content: Tab delimited file, counts of 'G' and 'A' base nucleotides for each DARNED sites used;
Supplementary_files_format_and_content: first column: the genomic coordinates
Supplementary_files_format_and_content: second column: counts of 'A' base nucleotides with high sequencing quality
Supplementary_files_format_and_content: third column: counts of 'G' base nucleotides with high sequencing quality

source_name: Rhesus_10y_Cerebellar cortex

extract_protocol:
RNA was isolated using Trizol reagent (Invitrogen, Carlsbad, CA). Oligo(dT) selection was performed twice using Oligotex mRNA Midi Kit (Qiagen). After selection, 100 ng mRNA was first fragmented by addition of 5 X fragmentation buffer (200 mM Tris acetate, pH 8.2, 500 mM potassium acetate, and 150 mM magnesium acetate) with heating at 94 °C for 2 min 30 s in a thermo-cycler. The fragments were then transferred to ice and run over a Sephadex-G50 column (USA Scientific) to remove the fragmentation ions.
Sequencing libraries were prepared according to the paired-end non-strand-specific sample preparation protocol of Illumina(http://www.illumina.com)

value: postnatal 10 years

tag: tissue

value: Cerebellar cortex


title: Rhesus(1d)_CBC

source_name: Rhesus_1d_Cerebellar cortex

tag: age

value: postnatal 1 day


title: Rhesus(1d)_PFC

source_name: Rhesus_1d_prefrontal cortex

value: prefrontal cortex


title: Rhesus(10y)_PFC

source_name: Rhesus_10y_prefrontal cortex


title: chimpanzee(12y)_PFC

organism: Pan troglodytes

source_name: chimpanzee_12y_prefrontal cortex

value: postnatal 12 years


title: chimpanzee(12y)_CBC

source_name: chimpanzee_12y_Cerebellar cortex


title: Naïve 3, 17M

city: Malaga

first: James

last: Perkins

address: Pl. Hosp. Civil

department: Hospital Civil

institute: Hospital Carlos Haya

data_processing:
Initial processing – Sequenced reads were trimmed for adaptor sequence and low quality reads removed (those that did not pass the Illumina quality filter)
Normalisation – the DESeq method was used for library size normalisation (estimateSizeFactors(), estimateDispersions()), as described in pmid:20979621 and the DESeq vignette (http://www.bioconductor.org/packages/devel/bioc/vignettes/DESeq/inst/doc/DESeq.pdf)
Gene Counting – expression was calculated by counting all reads aligning to the known exons of a given gene, according to Ensembl (version 74). Exons for a given gene that overlap with exons from another gene (on the same strand or on opposite strand) were removed
Alignment – fastq files (with low quality reads removed) were aligned to the Rat genome (version Rn5) using bowtie, with parameters -m 1 -v 1 -p 8 --best, that is, allowing for 1 mismatch and discarding ambiguous reads
Genome_build: Rn5, downloaded from UCSC
Supplementary_files_format_and_content: Tables of normalised counts: matrix with genes (Ensemble gene id) as rows and samples as columns. Separate tables are provided for the different sequencing depths

source_name: Dorsal root ganglia, L5

extract_protocol:
Extraction performed using miRNEasy kit (QIAGEN). RNA concentration measured using the NanoDrop 1000 Spectrophotometer (Thermo Scientific, Wilmington, DE, USA
cDNA libraries were prepared using the TruSeqTM RNA Sample Preparation Kit (Illumina), low throughput protocol. 200 ng of total RNA were subjected to poly(A) enrichment using poly(T)-attached magnetic beads. Poly(A)-enriched RNA was subsequently used for reverse transcription and library preparation according to Illumina’s instructions

treatment_protocol: Spinal nerve transection (SNT) of the L5 spinal nerve was performed. Dorsal root ganglia (DRG) were harvested 7 days after surgery fresh dissection

value: Dorsal root ganglia, L5

value: Wistar

value: SNT or naïve:Naïve

tag: sequencing depth

value: 17M reads


title: chimpanzee(7d)_PFC

source_name: chimpanzee_7d_prefrontal cortex

value: postnatal 7 days


title: chimpanzee(7d)_CBC

source_name: chimpanzee_7d_Cerebellar cortex


title: SNT 2, 17M

value: SNT or naïve:SNT


title: SNT 1, 17M


title: SNT 3, 17M


title: Naïve 1, 17M


title: Stimulated MATα-playing-a Biological Replicate 1


title: Naïve 1, 25M

value: 25M reads


title: SNT 1, 25M


title: Naïve 3, 25M


title: SNT 2, 25M


title: SNT 3, 25M


title: Naïve 3, 50M

value: 50M reads


title: SNT 2, 50M


title: SNT 1, 50M


title: SNT 3, 50M


title: Naïve 2, 50M


title: Naïve 1, 50M


title: Control_Rep5

city: Chicago

first: Jie

last: Zhou

state: ILLINOIS

address: 900 East 57th Street, KCBD 10100

institute: University of Chicago IGSB

data_processing:
Alignment was performed with Tophat v1.4.0 using default settings.
The alignment files were subsampled to different levels of sequencing depth using the DownsampleSam program in software package picard v1.61.
The subsampled alignment files were overlapped with hg18 GTF files from UCSC using coverageBed in the package BEDTools v2.16.2 to generate read counts for each gene/transcript.
The read counts file (count.matrix.byGene.round1.txt) were then used as input for RNA-seq differential expression calling programs such as edgeR, and differential expression/expression abundance and log fold changes are calculated by edgeR v3.2.3
Genome_build: hg18
Supplementary_files_format_and_content: Read count matrix for the abusolute count of number of reads on each gene of hg18 human genome. Columns are different samples at different level of subsampling, rows are different genes.

source_name: MCF7 cell line

growth_protocol: MCF7 breast cancer cells (ATCC HTB-22) were maintained in Dulbecco's modified Eagles's medium (DMEM), 10% fetal bovine serum (FBS), and antibiotics at 37oC in a 5% CO2 humidified atmosphere.

extract_protocol:
Standard protocol of Qiagen RNeasy mini kit.
Standard protocol of TrueSeq mRNA sample prep kit.

treatment_protocol: Cells were hormone-deprived  in phenol-free DMEM with 10% charcoal-stripped FBS 3 days before treatment with 10nM E2.  mRNAs were collected 24hrs after treatment with Qiagen RNeasy mini kit.

value: Control ethanol 24h

tag: cell type


title: Naïve 2, 25M


title: Naïve 2, 17M


title: Control_Rep4


title: Villi_jejunum

city: Utrecht

first: Michal

last: Mokry

address: Lundlaan 6

country: Netherlands

institute: Wilhelmina Children's Hospital, University Medical Center Utrecht

data_processing:
Sequencing reads were mapped against the reference genome (mm9) using BWA
Reads per 1000 base pairs of transcript per million reads sequenced (RPKM) values were calculated for all RefSeq annotated genes
Genome_build: mm9
Supplementary_files_format_and_content: *.rna files were generated using Cisgenome “rnaseq_countgeneread” command

source_name: mouse jejunum

extract_protocol:
Freshly isolated villi, crypts or organoids (cultured for 12 weeks) were used for mRNA sequencing. Total RNA was isolated using Trizol LS reagent (Invitrogen). Total RNA was purified using the Poly(A)Purist MAG Kit (Life Technologies) and subsequently re-purified using the mRNA-ONLY Eukaryotic mRNA Isolation Kit (Epicentre) to obtain full length mRNA.
Sequencing libraries were constructed using the SOLiD® Total RNA-Seq Kit (Life technologies) and sequenced on a SOLiD 4 sequencer to produce 50-bp long reads.

value: intestinal villi

tag: origin

value: jejunum


title: Villi_duodenum

source_name: mouse duodenum

value: duodenum


title: Organoid_ileum

source_name: mouse ileum

growth_protocol: Murine organoids were generated from isolated small intestinal crypts and maintained in culture as described previously. Sato T, Vries RG, Snippert HJ, et al. Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche. Nature. May 14 2009;459(7244):262-265

value: intestine derived cultured organoids

value: ileum


title: E2_Rep7

value: 10nM E2 treatment for 24h


title: Organoid_jejunum


title: Control_Rep7


title: ZT20 CRY1 ChIP Seq

city: Chapel Hill

first: Rui

last: Ye

state: NC

address: 120 Mason Farm road, Genetic medicine building, suite 3010

department: Biochemistry and Biophysics

institute: UNC Chapel Hill

data_processing:
Basecalls performed using CASAVA version 1.8
The reads were aligned to the mm9 mouse reference genome using Bowtie accepting up to 4 reportable alignments and two mismatches per read. In cases where more than a single alignment was possible, only the one with the highest mapping quality was reported using bowtie’s "--best" option.
Genome_build: mm9
Supplementary_files_format_and_content: To generate ChIP-seq signal tracks, reads were extended in-silico to 150bp, and the number of reads overlapping with each base in the genome was counted and divided by the chromosome-wide average of per-base read coverage. The average signal over 50bp windows was calculated and viewed using the UCSC genome browser.

source_name: Liver

growth_protocol: Male C57BL/6J at 12-14 weeks of age were housed in LD12:12 conditions.

extract_protocol:
livers from mice were immediately homogenized and cross-linked in PBS buffer including 1% formaldehyde (5 ml per liver), and the homogenate was incubated for 15 min at 25 °C. Cross-linking reactions were stopped by the addition of 21 ml of ice-cold nuclei buffer (2.2 M sucrose, 125 mM glycine, 10 mM HEPES pH 7.6, 15 mM KCl, 2 mM EDTA, 0.15 mM spermine, 0.5 mM spermidine, 0.5 mM DTT, 0.5 mM PMSF and 10% glycerol). The homogenate was layered on top of 10 ml of cold nuclei buffer and centrifuged for 90 min at 24,000 rpm (100,000g) at 4 °C in a Beckmann SW27 rotor. The nuclei were washed with wash buffer (20 mM Tris, pH 7.5, 150 mM NaCl, 2 mM EDTA) and stored at  -80 °C. Cross-linked nuclei were then subjected to ChIP analysis.
For ChIP-seq, ChIP DNA was ligated to single-end sequencing adapters and amplified. DNA fragments of 300-800 bp in size were purified and sequenced (50 base) on an Illumina Hi-seq2000 instrument (Illumina, California, USA).

tag: chip antibody

tag: chip antibody manufacturer

value: Lab made

value: 12-14 weeks

tag: gender

value: male


title: Control_Rep1


title: Organoid_duodenum


title: Control_Rep6


title: ZT8 BMAL1 ChIP Seq-2

value: Bethyl lab A302-616A


title: E2_Rep5


title: Crypt_ileum_2

value: intestinal crypt


title: Crypt_ileum_1


title: E2_Rep6


title: ZT8 BMAL1 ChIP Seq-1


title: E2_Rep4


title: ZT8 CLOCK ChIP Seq-2

value: CLOCK

value: Bethyl lab A302-618A


title: ZT8 CLOCK ChIP Seq-1


title: E2_Rep3


title: E2_Rep2


title: Crypt_jejunum_1


title: Crypt_jejunum_2


title: Villi_ileum


title: E2_Rep1


title: Crypt_duodenum_2


title: KRas;Atg5fl/+

city: Vienna

first: Shuan

last: Rao

address: Dr. Bohrgasse 7

country: Austria

institute: IMBA

data_processing:
50-bp single-end Illumina mRNA sequencing reads were aligned using Tophat v2.0.6 and bowtie v0.12.9.
aligned reads were counted with HTSeq
FPKM estimation was performed with Cufflinks (v2.1.1) and differential expression analysis with DESeq (v1.10.1)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample (Standard output cufflinks)

extract_protocol:
Total RNA was purified using RNAeasy mini Kit (Qiagen). Twice poly-T selected RNA was isolated from 10ug of total RNA and dUTP-containing cDNA was generated.
Illumina Truseq Protocol

value: lung

value: pneumocytes

tag: genotype/variation


title: Control_Rep3

tag: treatment


title: KRas;Atg5fl/fl


title: Villi_Input

status: Public on Jan 06 2014

city: Boston

first: Fugen

last: Li

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

description: Input DNA for villus cells

data_processing:
Basecalls performed using CASAVA version 1.7
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie version 0.12.7 with default settings. Only uniquely aligned tags were retained
Peaks were called using MACS2 with the following settings: Q value <= 0.01, shiftsize = 146 for histone marks and shiftsize = 100 forATOH1 ChIP and DNaseI hypersensitive fragments
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files were converted from wig files generated using unique reads from MACS2

source_name: Intestinal villus cells

extract_protocol: Fresh intestinal crypt epithelial cells were collected by removing villi manually and incubating crypts in 5 mM EDTA for 50 min at 4°C. Lgr5+ intestinal stem cells were purified from Lgr5-eGFP-Cre mice using flow cytometry for GFP. Crypt secretory progenitors (Sec-Pro) were enriched by treating mice with the Notch inhibitor Dibenzazepine or by deleting Rbpj, and mature goblet cells (GOB) were isolated from Rbpj-/- mouse villi.  Enterocyte progenitors (Ent-Pro) and mature enterocytes (ENT) were isolated from Atoh1-/- mouse (which lacks all secretory cells) crypts and villi, respectively. Cells were fixed in 1% formaldehyde for 25 min at room temperature and lysed. Chromatin was sheared by sonication. DNA was amplified using ThruPLEX-FD kit (Rubicon Genomics).


title: Lgr5+ISC_Input

description: Input DNA for Lgr5+ cells

source_name: Lgr5+ intestinal stem cells


title: Sec-Pro_Atoh1

description: ATOH1 ChIP-seq

source_name: Intestinal crypt secretory progenitors

tag: antibodies

value: FLAG (Sigma F3165)


title: Sec-Pro_DHS

description: DNase-seq

tag: strain


title: Ent-Pro_H3K27ac

source_name: Intestinal crypt enterocyte progenitors

value: H3K27ac (Abcam ab4729)


title: Ent-Pro_DHS

description: DNase-seq


title: Sec-Pro_H3K27ac


title: ENT_H3K4me2

description: H3K4me2 ChIP-seq

source_name: Intestinal villus enterocytes

value: H3K4me2 (Millipore 07-030)


title: GOB_H3K4me2

description: H3K4me2 ChIP-seq

source_name: Intestinal villus goblet cells


title: Ent-Pro_H3K4me2_rep1

description: H3K4me2 ChIP-seq


title: Sec-Pro_Rbpj-/-_H3K4me2

description: H3K4me2 ChIP-seq


title: Ent-Pro_H3K4me2_rep2

description: H3K4me2 ChIP-seq


title: Sec-Pro_DBZ_H3K4me2

description: H3K4me2 ChIP-seq


title: Lgr5+ISC_H3K4me2

description: H3K4me2 ChIP-seq


title: H2AZ_BM8_ZT14

city: College Station

first: Jerome

middle: S

last: Menet

state: TX

address: 301 Old Main Drive, Building 1530, ILSB

department: Dept of Biology

institute: Texas A&M University

description: Mnase-digested chromatin

data_processing:
Basecalls performed using CASAVA v1.7
Reads were aligned to the mm9 genome assembly using bowtie with the following criteria: –p 6 –q –a –-best –m 1
Uniquely mapped reads (51nt) were extended to 147nt to represent a full mononucleosome
H2AZ ChIP-Seq signal (MNase signal) was retrieved at genomic location of interest, and further normalized to sequencing depth
Genome_build: mm9
Supplementary_files_format_and_content: Table_GEO_H2AZsignal_at_CB3217peaks.txt contains average H2AZ ChIPseq signal at CLK:BMAL1 DNA binding sites; peak location of CLK:BMAL1 binding sites are in the file Table_GEO_CB3217_GenomicLocation_AllPeaks.txt

extract_protocol:
Adult mouse liver were collected at 6 different time of the day (mouse held under LD12:12, time points every 4hrs starting at ZT2)
Mouse liver were crosslinked with 1% formaldehyde for 10min, and nuclei were purified using standard sucrose cushion protocol.
Nuclei were resuspended, flash frozen in liquid nitrogen and stored at -80C.
Nuclei were thawed on ice, pelleted down and chromatin was digested with micrococcal nuclease.
Mnase digestion was performed for 15min using 30,000 gel unit per reaction
Following chromatin digestion with Mnase, H2AZ-containing nucleosome were imunoprecipitated using an anti-H2AZ antibody.
Immunoprecipitated chromatin (mononucleosome fraction) was purified and used for generating illumina libraries
Illumina libraries were generated using standard protocol: end repair, add A, adapter ligation, amplification, gel purification.

treatment_protocol: Mouse were exposed to a 12h light: 12h dark cycle (LD12:12) for at least 2 weeks before the experiment

value: Liver

value: Adult (3-6months)

value: rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008016


title: H2AZ_BM8_ZT06

description: Mnase-digested chromatin

value: rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008014


title: H2AZ_BM8_ZT22

description: Mnase-digested chromatin

value: rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008018


title: H2AZ_BM8_ZT10

description: Mnase-digested chromatin

value: rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008015


title: H2AZ_BM8_ZT18

description: Mnase-digested chromatin

value: rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008017


title: Control_Rep2

value: Control ethanol 24h


title: H2AZ_BM8_ZT02

description: Mnase-digested chromatin

value: rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008013


title: H2AZ_WT26_ZT22

description: Mnase-digested chromatin

value: rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008012


title: Crypt_duodenum_1

value: intestinal crypt

value: duodenum


title: H2AZ_WT26_ZT14

description: Mnase-digested chromatin

value: rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008010


title: H2AZ_WT26_ZT18

description: Mnase-digested chromatin

value: rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008011


title: H2AZ_WT26_ZT06

description: Mnase-digested chromatin

value: rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008008


title: MSB1, AGO-2 PAR-CLIP

city: Durham

first: Oren

last: Parnas

address: 430 CARL, Research Dr.

department: MGM

institute: Duke university

description:
Small RNA-seq
AGO2, PAR-CLIP

data_processing:
Library strategy: PAR-CLIP
Mapping Reads: The reads were stripped of the 3' adapter sequence and 5' barcode ATCACG using the FASTX toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Reads that were less than 15 nt in length or contained an ambiguous nucleotide were discarded. The remaining reads were aligned to the chicken (Gallus_gallus-4.0 ENSEMBLE),MDV-1 (GenBank accession no. AF243438.1) or MDV-2 (Gen-  Bank accession no. AB049735.1) genomes with up to 3 mismatches allowed, by the Bowtie algorithm (Langmead et al., 2009). Mapped locations were only reported for those with the minimum number of observed mismatches for each read. The location that a read mapped, relative to a known transcript, was determined based on the ENSEMBL.
Defining microRNA interaction sites by PARalyzer: Overlapping reads were grouped together for further analysis. A group must have contained ≥15 reads with conversions at two or more locations. Separate kernel density estimates were calculated across all positions based on read counts both with and without T to C conversions, as long as there was a minimum read depth of 15 at a position to ensure a robust density estimate. Clusters (txt) were defined as regions for which the conversion density was greater than the non-conversion density for at least 15 consecutive nucleotides, and extended until the group read depth fell below 5. Following filtering (see supplemental methods in PMID 22291592), clusters were scored by a cross-linking index (CLI) = log2(1+T to C conversion events for all reads within a cluster). PARalyzer is available athttp://www.genome.duke.edu/labs/ohler/research/PARalyzer .
Genome_build: chicken (Gallus_gallus-4.0 ENSEMBLE), MDV-1 (GenBank accession no. AF243438.1) or MDV-2 (GenBank accession no. AB049735.1)
Supplementary_files_format_and_content: TXT file that contains list of clusters

organism: Gallus gallus

source_name: MSB1 cells

extract_protocol:
The pellets of cells crosslinked with UV 365 nm were resuspended in NP40 lysis buffer and incubated on ice for 10 min. The cell lysate was cleared by centrifugation at 13,000g.
The recovered RNA was carried through a cDNA library preparation protocol originally described for cloning of small regulatory RNAs (Hafner et al., 2008 (PMID 18158127))

tag: cell line

value: T-cell line MSB1

value: Transformed chicken T cells persistently infected with MDV-1 and MDV-2

tag: ip antibody

value: pan-Ago antibody (Abcam, AB 57113)


title: H2AZ_WT25_ZT14

description: Mnase-digested chromatin

value: Liver

value: Adult (3-6months)

value: rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008004


title: H2AZ_WT25_ZT22

description: Mnase-digested chromatin

value: rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008006


title: H2AZ_WT25_ZT18

description: Mnase-digested chromatin

value: rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008005


title: H2AZ_WT26_ZT10

description: Mnase-digested chromatin

value: rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008009


title: H2AZ_WT25_ZT02

description: Mnase-digested chromatin

value: rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008001


title: CLK_Input_Sonicated_WT30_ZT22

data_processing:
Basecalls performed using CASAVA v1.7
Reads were aligned to the mm9 genome assembly using bowtie with the following criteria: –p 6 –q –a –-best –m 1
Uniquely mapped reads (51nt) were extended to 147nt to represent a full mononucleosome
CLK ChIP-Seq signal was retrieved at genomic location of interest, and further normalized to sequencing depth
Genome_build: mm9
Supplementary_files_format_and_content: Table_GEO_CLK_ChIPseqSignal_MNase_vs_Sonication.txt contains average CLK ChIPseq signal at CLK:BMAL1 DNA binding sites; peak location of CLK:BMAL1 binding sites are in the file Table_GEO_CB3217_GenomicLocation_AllPeaks.txt

extract_protocol:
Adult mouse liver were collected at 6 different time of the day (mouse held under LD12:12, time points every 4hrs starting at ZT2)
Mouse liver were crosslinked with 1% formaldehyde for 10min, and nuclei were purified using standard sucrose cushion protocol.
Nuclei were resuspended, flash frozen in liquid nitrogen and stored at -80C.
Nuclei were thawed on ice, pelleted down and chromatin either was digested with micrococcal nuclease or sonicated using Bioruptor.
Mnase digestion was performed for 15min using 30,000 gel unit per reaction
Following chromatin shearing, chromatin was imunoprecipitated using an anti-CLK antibody.
Immunoprecipitated chromatin and inpur fraction was purified and used for generating illumina libraries
Illumina libraries were generated using standard protocol: end repair, add A, adapter ligation, amplification, gel purification.

value: none, input


title: CLK_Input_Sonicated_WT30_ZT06


title: CLK_Input_Sonicated_WT29_ZT06


title: CLK_ChIP_Sonicated_WT30_ZT22

value: goat polyclonal anti-CLK, S-19; sc-6927; lot E3112


title: H2AZ_WT25_ZT10

description: Mnase-digested chromatin

value: rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008003


title: Crypt_Input

description: Input DNA for crypt cells

source_name: Intestinal crypt cells


title: CLK_Input_Sonicated_WT29_ZT22


title: CLK_Input_Sonicated_WT28_ZT22


title: CLK_ChIP_Sonicated_WT28_ZT06


title: CLK_ChIP_Sonicated_WT29_ZT06


title: CLK_ChIP_MNase_WT29_ZT06


title: CLK_ChIP_Sonicated_WT30_ZT06


title: CLK_ChIP_MNase_WT29_ZT22


title: CLK_ChIP_MNase_WT28_ZT22


title: CLK_ChIP_Sonicated_WT29_ZT22


title: H2AZ_WT26_ZT02

description: Mnase-digested chromatin

value: rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008007


title: H2AZ_BM5_ZT22


title: CLK_ChIP_MNase_WT30_ZT06


title: H2AZ_WT25_ZT06

description: Mnase-digested chromatin

value: rabbit polyclonal anti-H2AZ antibody from Active Motif, #39113 , lot 01008002


title: CLK_Input_Sonicated_WT28_ZT06


title: H2AZ_WT12_ZT22


title: H2AZ_BM5_ZT10


title: H2AZ_BM5_ZT02


title: H2AZ_BM5_ZT14


title: H2AZ_WT12_ZT18


title: H2AZ_BM5_ZT18


title: H2AZ_WT12_ZT14


title: H2AZ_WT12_ZT10


title: CLK_ChIP_Sonicated_WT28_ZT22


title: H2AZ_WT11_ZT14


title: CLK_ChIP_MNase_WT30_ZT22


title: CLK_ChIP_MNase_WT28_ZT06


title: Mnase_BM10_ZT14

description: Mnase-digested chromatin

data_processing:
Basecalls performed using CASAVA v1.7
Reads were aligned to the mm9 genome assembly using bowtie with the following criteria: –p 6 –q –a –-best –m 1
Uniquely mapped reads (51nt) were extended to 147nt to represent a full mononucleosome
MNase signal was retrieved at genomic location of interest, and further normalized to sequencing depth
Genome_build: mm9
Supplementary_files_format_and_content: Table_GEO_MNase_signal_at_CB3217peaks_ALL.txt contains average nucleosome signal at CLK:BMAL1 DNA binding sites; peak location of CLK:BMAL1 binding sites are in the file Table_GEO_CB3217_GenomicLocation_AllPeaks.txt

extract_protocol:
Adult mouse liver were collected at 6 different time of the day (mouse held under LD12:12, time points every 4hrs starting at ZT2)
Mouse liver were crosslinked with 1% formaldehyde for 10min, and nuclei were purified using standard sucrose cushion protocol.
Nuclei were resuspended, flash frozen in liquid nitrogen and stored at -80C.
Nuclei were thawed on ice, pelleted down and used for micrococcal nuclease diggestion.
Mnase digestion was performed for 15min using 30,000 gel unit per reaction
DNA was extracted (size ~150nt)  and about 50ng of purified DNA was used for generating Illumina libraries
Illumina libraries were generated using standard protocol: end repair, add A, adapter ligation, amplification, gel purification.


title: Mnase_BM10_ZT18

description: Mnase-digested chromatin


title: H2AZ_WT11_ZT06


title: Mnase_BM10_ZT10

description: Mnase-digested chromatin


title: H2AZ_WT11_ZT10


title: Mnase_BM9_ZT22

description: Mnase-digested chromatin


title: H2AZ_WT11_ZT02


title: Mnase_BM9_ZT18

description: Mnase-digested chromatin


title: Mnase_BM10_ZT02

description: Mnase-digested chromatin


title: H2AZ_WT11_ZT18


title: H2AZ_BM5_ZT06


title: Mnase_BM9_ZT14

description: Mnase-digested chromatin


title: Mnase_BM9_ZT10

description: Mnase-digested chromatin


title: Mnase_BM9_ZT06

description: Mnase-digested chromatin


title: Mnase_BM10_ZT22

description: Mnase-digested chromatin


title: Mnase_BM8_ZT14

description: Mnase-digested chromatin


title: Mnase_BM9_ZT02

description: Mnase-digested chromatin


title: Mnase_BM8_ZT10

description: Mnase-digested chromatin


title: H2AZ_WT12_ZT02


title: H2AZ_WT12_ZT06


title: Mnase_BM10_ZT06

description: Mnase-digested chromatin


title: H2AZ_WT11_ZT22


title: Mnase_BM5_ZT22

description: Mnase-digested chromatin


title: Mnase_BM8_ZT06

description: Mnase-digested chromatin


title: Mnase_BM5_ZT18

description: Mnase-digested chromatin


title: Mnase_BM5_ZT14

description: Mnase-digested chromatin


title: Mnase_BM5_ZT02

description: Mnase-digested chromatin


title: Mnase_WT27_ZT22

description: Mnase-digested chromatin


title: Mnase_BM5_ZT06

description: Mnase-digested chromatin


title: Mnase_WT27_ZT14

description: Mnase-digested chromatin


title: Mnase_WT27_ZT10

description: Mnase-digested chromatin


title: Mnase_BM5_ZT10

description: Mnase-digested chromatin


title: Mnase_WT26_ZT10

description: Mnase-digested chromatin


title: Mnase_WT26_ZT14

description: Mnase-digested chromatin


title: Mnase_WT26_ZT06

description: Mnase-digested chromatin


title: Mnase_BM8_ZT18

description: Mnase-digested chromatin


title: Mnase_WT12_ZT22

description: Mnase-digested chromatin


title: Mnase_WT12_ZT14

description: Mnase-digested chromatin


title: Mnase_WT12_ZT18

description: Mnase-digested chromatin


title: Mnase_WT26_ZT02

description: Mnase-digested chromatin


title: Mnase_WT12_ZT10

description: Mnase-digested chromatin


title: Mnase_WT11_ZT22

description: Mnase-digested chromatin


title: Mnase_WT27_ZT06

description: Mnase-digested chromatin


title: Mnase_WT12_ZT06

description: Mnase-digested chromatin


title: Mnase_WT26_ZT18

description: Mnase-digested chromatin


title: Mnase_WT12_ZT02

description: Mnase-digested chromatin


title: Mnase_WT11_ZT10

description: Mnase-digested chromatin


title: Mnase_WT11_ZT02

description: Mnase-digested chromatin


title: Mnase_WT27_ZT18

description: Mnase-digested chromatin


title: Mnase_WT11_ZT06

description: Mnase-digested chromatin


title: Mnase_WT27_ZT02

description: Mnase-digested chromatin


title: Mnase_WT11_ZT14

description: Mnase-digested chromatin


title: Mnase_BM8_ZT02

description: Mnase-digested chromatin


title: Mettl14 knockdown 4

city: Cambridge

first: Yue

state: Massachusetts

address: 32 Vassar Street, 32-D528

institute: Massachusetts Institute of Technology

data_processing:
The Genome Analyzer Pipeline Software (currently Casava v1.8.2) is used to perform the early data analysis of a sequencing run, which does the image analysis, base calling, and alignment.
Reads containing non-determinant nucleotides (`N') were filtered out using fastx_clipper from FASTX-Toolkit (0.0.13). Bases lower than a defined Phred quality threshold (default: 20) at the 3' end were trimmed off from each read using cutadapt (1.1). Next, known Illumina primers and adaptor sequences were clipped off from each read by cutadapt. Finally, filtered reads were aligned against a custom contaminant list using Bowtie (0.12.7) to further filter contaminant (aligned) reads mapped to mitochondria genome, ribosomal, actin RNA or phi X genome.
Alignment to the mouse genome build mm10 was performed using TopHat (v2.0.6) with the following options: --max-multihits 1 (obtain uniquely mapped reads); --b2-very-sensitive (maximize alignment sensitive); --GTF provided with RefSeq gene annotation downloaded from UCSC Genome Browser for mm10 (May 13, 2012) to improve detection of splicing junctions.
To account for PCR artefacts, only reads aligned to the distinct genome coordinates were retained. This post-alignment filtering was achieved using samtools rmdup from Samtools (0.1.18) and MarkDuplicates from Picard (1.74). As a result, the final processed alignments in each library comprises of distinct reads each mapped to a unique location in the mm10 reference genome.
To identify strand-specific reads-enriched regions or peaks in m6A-IP relative to the control library, we applied MACS to reads on “+” and “-” strands separately (Zhang et al., 2008).  MACS was run with default options except for --nomodel, --shiftsize=25, and --gsize ‘mm’ to turn off fragment size estimation (only applicable to double-stranded DNA), to make window size as 25 bp (which was chosen empirically to obtain peaks of median size around 200 nt), and to base peak calling on mouse reference genome size, respectively.  The strand-specific peaks from MACS were then pooled for each library.  The pooled peaks from m6A-IP libraries were subject to a stringent cutoff requiring each peak to have false discover rate (FDR estimated by MACS) < 0.1.
The fold-enrichment calculated from MACS for each filtered peaks were scaled by the corresponding fold-change of ActB gene (in terms of RPKM) to control for differential base-line expression between IP libraries.
Finally, we compared peaks from wildtype (control) with peaks from knockdown (treatment) to obtain "treatmentOnly", "controlOnly", "common" peaks. The "common" peaks are the peaks overlapped between control and knockdown peaks. For the common peaks, we compared their scaled fold-enrichments computed above to obtain "fold_enrichment_scaled_diff", which is the fold-change of treatment over control. Thus, negative (positive) fold_enrichment_scaled_diff indicates the common peak has higher (lower) enrichment in control than in treatment.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited file containing the peaks statistics as described above and the genes overlapped by the peaks

source_name: Mettl14 knockdown

growth_protocol: Mouse ES cells were maintained on feeder layers of irradiated mouse embryonic fibroblasts (MEFs) in DMEM (Invitrogen) supplemented with 15% fetal bovine serum (FBS, Hyclone), 2 mM L-glutamine, 0.1 mM non-essential amino acids (Gibco), 0.1 mM β-mercaptoethanol (Sigma) and 500 units/ml leukemia inhibiting factor (LIF, Chemicon).

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen). RNA was treated with RNAse free DNAse I (Roche) to deplete DNA contamination. PolyA RNA was purified using GenEluteª mRNA Miniprep Kit (Sigma Aldrich) per manufacturer's instruction. PolyA RNA was fragmented using RNA fragmentation kit (Ambion). Two _g fragmented RNA was saved as input. Two hundred _g fragmented RNA was incubated with 3 _g anti-m6A antibody (Synaptic Systems) in RIP buffer (150mM NaCl, 10mM Tris, 0.1% NP40) for 2 hrs at 4 oC, followed by the addition of washed protein A/G magnetic beads (Millipore) and incubation at 4 oC for additional 2 hrs. Beads were washed 6 times in RIP buffer and incubated with 50 _l IP buffer containing 0.5mg/mL to elute RNA. IP'ed RNA was extracted with phenol/chloroform.
The Scriptseq v.2 RNA-seq Library Preparation method was performed on 40 ng of RNA for each sample. We followed the protocol given in the Scriptseq v.2 RNA-seq Library Preparation manual (Epicentre, an Illumina company), except DNA Clean & Concentratorª-5 - PCR/DNA clean columns (Zymo Research) were used to isolate the cDNA prior to PCR step. 15 cycles of PCR were performed on the cDNA and the resulting DNA products were purified on 2% E-Gel¨ EX Agarose Gels (Invitrogen). The products were visualized using a blue light transluminator and selected regions of the gel were excised corresponding to 200-400 bp products. The gel slices were dissolved in agarose dissolving buffer and the DNA was isolated on DNA Clean & Concentratorª-5 - PCR/DNA clean columns. The isolated DNA products were then analyzed and quantitated on an Agilent Bioanalyzer 2100.  Samples were pooled and loaded into one lane of a HiSeq2000 v3 flowcell (Illumina) and sequenced for 100 bases with separate 7 base indexing read.

treatment_protocol: Lentiviral constructs including shRNA were purchased from Sigma. To produce lentivirus, lentiviral constructs and packaging constructs were transfected into 293ft cells by calcium phosphate reagent (Clontech). About 36 hours after transfection, viral supernatants were collected and supplemented with 6 μg/μl polybrene (Millipore). ES cells were incubated with virus-containing medium for 12 h. 3 days after infection, 2 μg/ml puromycin (Sigma) were added to medium for stable cell lines selection.

value: Mettl14 knockdown

value: anti-m6A antibody


title: Mettl3 knockdown 4

source_name: Mettl3 knockdown

value: Mettl3 knockdown


title: Mettl3 knockdown 3


title: Scramble control 4

source_name: Scramble control

value: Scramble control


title: Mettl14 knockdown 3


title: Scramble control 2


title: Mettl3 knockdown 1


title: Mettl14 knockdown 2


title: Scramble control 1


title: Mettl3 knockdown 2


title: Mettl14 knockdown 1


title: P.falciparum_3D7_18h_HiSeq_non-crosslinked_control

city: Riverside

first: Karine

last: Le Roch

address: 900 University Ave

institute: University of California, Riverside

description: Sample 4

data_processing:
All raw paired-end reads were trimmed to 40 bp and each end was mapped separately to whole human genome (hg19) using BWA v0.5.9 with default parameters allowing an edit distance of at most 3 in order to filter the human DNA contamination in samples. All pairs with at least one of the ends mapped to the human genome (without checking quality or uniqueness) were eliminated from further consideration. Remaining paired-end reads were used for further analysis of Plasmodium genome architecture (trimmedAndFiltered files).
Each end of the paired-end reads in trimmedAndFiltered fastq files was mapped separately to Plasmodium falciparum 3D7 (PlasmoDB v9.0) genome using BWA v0.5.9 with default parameters. The alignment results were post-processed further to extract the reads that mapped (i) uniquely to one location in the reference genome, (ii) with an alignment quality score of at least 30 (which corresponds to a 1 in 1000 chance that the mapping is incorrect), and (iii) with an edit distance of at most 2. The paired-end reads with both ends mapping to the Plasmodium genome were kept for further analysis. Potential PCR duplicates (i.e., pairs of read-pairs with identical genomic coordinates) were identified and only one copy of each such group of reads were retained.
Each paired-end read was assigned to a pair of restriction enzyme fragments (restriction enzyme used is MboI with cut site |GATC) that are listed by their start coordinates in MboI-cutSites.txt file. The mapping coordinates of the reads were used to identify the nearest MboI restriction site to do the assignment of read pairs to restriction fragment pairs. At this native resolution of one restriction fragment (1RE) the number of times each fragment pair is linked were calculated as the number of observed paired-end reads that link the two fragments. These numbers were listed in rawContactCounts-1RE files for each of the three crosslinked as well as the not crosslinked control library.
For 3D modeling and other downstream analysis the Plasmodium genome was partitioned into non-overlapping 10 kb windows and each restriction fragment was assigned to the 10 kb window that covers the majority of the bases in that fragment. For each pair of such 10 kb windows, the contact count was calculated as the total number of times a pair of restriction fragments, one from each 10 kb window, were linked by a paired-end read. These numbers were listed in rawContactCounts-10kb files for each of the three crosslinked as well as the not crosslinked control library.
The 10 kb aggregated raw contact count matrices were normalized in two steps. First, all 10 kb windows were ranked by their percentage of intrachromosomal interactions with zero counts, and the top 2% of this list were filtered out from further analysis removing regions of low mappability. Second, an iterative correction and eigenvector decomposition (ICE) method (Imakaev et al, Nature Methods 2012) was applied which attempts to eliminate systematic biases in Hi-C data. This method generates normalized contact counts from each raw contact count which are listed for as normalizedContactCounts-10kb files for the three crosslinked libraries. Control library was not subjected to normalization.
Genome_build: Plasmodium falciparum 3D7 (PlasmoDB v9.0)
Supplementary_files_format_and_content: trimmedAndFiltered are in fastq format. Other files are text files that contain fields listed in their header lines.

organism: Plasmodium falciparum 3D7

source_name: Erythrocytic cycle

growth_protocol: P. falciparum strain 3D7 was maintained in human O+ erythrocytes in 5% haematocrit according to a previously described protocol (Trager et al., Science 1976).

extract_protocol:
P. falciparum cultures were crosslinked for 25 minutes at 37C in 1.25% formaldehyde. The reaction was quenched for 15 min at 37C, followed by extensive washes to remove cellular debris. We then applied an adapted Hi-C method referred to as tethered conformation capture. Briefly, proteins were first biotinylated and the DNA was digested using the restriction enzyme MboI. Fragments were captured on streptavidin-coated beads, ligated under dilute conditions and subsequently sequenced using the Illumina HiSeq 2000 platform, generating 50 bp paired-end reads.
Libraries were generated using the NEBNext ChIP-Seq Library Preparation kit (NEB) according to the manufacturer’s instructions, with the following modifications for the high AT-content of the P. falciparum genome: libraries were amplified for a total of 11 PCR cycles (3 cycles of [15s at 98°C, 30s at 55°C, 30s at 62°C] followed by 8 cycles of [15s at 98°C, 30s at 63°C, 30s at 72°C]).

treatment_protocol: Cultures were synchronized twice at ring stage with 5% D-sorbitol treatments performed eight hours apart. Parasites were harvested 48 hours after the first sorbitol treatment (0h; ring stage), and then 18 hours (early trophozoite stage) and 36 hours (late schizont stage) thereafter. The developmental stage of the parasites was verified by microscopy using Giemsa-stained blood smears prior to harvesting.

tag: developmental stage

value: 18 hpi; early trophozoite stage


title: P.falciparum_3D7_0h_HiSeq

description: Sample 1

value: 0hpi; ring stage


title: Mnase_WT11_ZT18

description: Mnase-digested chromatin

value: Liver

value: Adult (3-6months)


title: P.falciparum_3D7_36h_HiSeq

description: Sample 3

value: 36 hpi; late schizont stage


title: Scramble control 3

tag: antibody


title: Mnase_WT26_ZT22

description: Mnase-digested chromatin


title: P.falciparum_3D7_18h_HiSeq

description: Sample 2