title: fetal 1

city: stanford

first: chunjiang

last: he

address: 265 campus drive

institute: stanford university

description: Sample 4

data_processing:
Reads were then mapped to human genome (Hg19) using TOPHAT
HTSeq-count was used to quantify the read counts within each gene. RPKM (reads per kilobase per million mapped reads) for each sample was then calculated using a custom Perl script
Genome_build: hg19
Supplementary_files_format_and_content: txt files including counts was generated from HTSeq-count

source_name: fetal_heart tissues

growth_protocol: heart tissues are acquired from donors

extract_protocol:
RNA was isolated using miRNeasy kit (Qiagen) following the manufacture's protocol, 100ng of total RNA was converted to cDNA and amplified using NuGen V2 RNA-Seq kit (NuGen, San Carlos, CA)
Sonication of cDNA was performed to produce an average fragment size of 280 bps and Illumina sequencing adapters were ligated to 500ng of cDNA using NEBNext® mRNA Library Prep Reagent Set (New England Biolabs, Ipswich, MA)

treatment_protocol: DNAse treatment was performed using RNase-free DNase kit (Qiagen)

tag: developmental stage

value: fetal

tag: tissue

value: heart


title: fetal 2

status: Public on Feb 10 2016

type: SRA

country: USA

description: Sample 5

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens


title: T12-3716A

city: Gaithersburg

first: Dong

last: Shen

state: MD

address: MedImmune Way

department: Translational Science

institute: Medimmune

data_processing:
Illumina
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Human genome reference hg19  via Bowtie
Data were normalized using DESeq in R.
Genome_build: hg19
Supplementary_files_format_and_content: TSV file with normalized read counts for each sample.

source_name: tumor

extract_protocol:
Tumor and normal samples  were removed, flash frozen on dry ice, and RNA was harvested.  1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease status

value: small cell lung cancer


title: T11-4067A


title: T10-5656A


title: B12-814A


title: B12-738A


title: B12-703A


title: B12-1662A


title: B12-1353A


title: B12-2013A


title: B11-4430A


title: B11-283A


title: B11-2810A


title: B11-4A


title: HeLa mRNA IP replicate B

city: Tel-Hashomer

first: Sharon

last: Moshitch-Moshkovitz

address: Laboratory wing

department: Cancer Research Center

country: Israel

institute: Sheba Medical Center

data_processing:
Library strategy: M1A-seq
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence,  then mapped to mm10 or hg19 whole genome using tophat version 2.0.12 with parameters - -M -p 3 --no-novel-juncs -g 5
Enriched intervals were identified using MACS2,in IP over input. FC>=2, FDR<=0.05
Peak middle was determined for peaks that appeared in both replicates.
For PARSseq samples reads were trimmed using cutadapt and aligned to the human transcriptome (knownCanonical transcripts from UCSC) using bowtie2 (--local).
Only uniquely aligned reads were used for downstream analysis
For each position in the transcriptome number of read start at each base were counted. For this step only reads with more than 5 nts matching the transcript at the start of the read were counted
PARS-scores were calculted for each position in the transcriptome as described in Wan et al. 2014.
Genome_build: hg19 for human, mm10 for mouse
Supplementary_files_format_and_content: Peak lists include peak middle coordinates for each cell type

source_name: HeLa cell line

extract_protocol:
Total RNA of the indicated cell types was extracted using 5PRIME RNA purification kit. Where indicated mRNA enriched RNA was purified by oligo dT selection.
Fragmentation was carried out using Ambion fragmentation reagents in 70ºc.Competitive elution was carried out using free m1A nucleoside  (330 microMolar m1A in 10 mM Tris pH 7.4 ,375 mM NaCl 0.1% NP-40.
Immunoprecipitation was done using MBL anti-m1A antibody D345-3 mAb.Dimmroth rearrangement was performed by heating the samples to either 50ºC or 60ºC for 1H under pH 10.4 conditions.
Libraries were prepared according to NEB's instructions accompanying the NEBNext® Ultra™ RNA Library Prep Kit for Illumina (Cat# 7530).

tag: cell line

value: HeLa


title: B11-1085A


title: B10-5295A


title: B10-6017A


title: B10-5210A


title: B10-5716A


title: B10-6122A


title: B10-5656A


title: B10-5116A


title: B10-5346A


title: B10-5484A


title: B10-4161A


title: B10-3851A


title: B10-3514A


title: B10-363A


title: B10-2275A


title: B10-3353A


title: B10-4914A


title: B10-183A


title: DMSO (control)

city: Los Angeles

first: Ascia

last: Eskin

state: California

address: 695 Charles Young Drive South  Gonda 5554

department: Human Genetics

institute: UCLA

data_processing:
Illumina Casava software used for basecalling.
Reads were aligned to mm9 genome using TopHat v2.0.6 with parameters  -G (using Ensembl NCBIM37 GTF) and --no-novel-juncs.
Transcripts were assembled using Cufflinks v2.0.2. Cuffdiff was used to compare the treated sample to the control, using Ensembl NCBIM37 GTF
Genome_build: mm9
Supplementary_files_format_and_content: Cuffdiff result files include FPKM values for each Sample, as well as q-value and fold change.

organism: Mus musculus

source_name: DMSO, liver

growth_protocol: Isolated heptocytes treated with William E media, FBS, insulin and Dexamethasone

extract_protocol:
RNA was isolated from cells using TRIZOL followed by RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.
RNA sequencing libraries, starting with 500 ng total RNA, were constructed with the TruSeq RNA Sample Prep Kits from Illumina on RNA isolated from primary hepatocytes

treatment_protocol: 1μM GW3965 or DMSO

tag: stain

tag: cell type

value: primary hepatocytes

tag: agent

value: control


title: B10-1708A


title: NTg-6327

first: Jacqueline

middle: Gire

last: O'Rourke

state: CA

address: 8700 Beverly Blvd

institute: Cedars Sinai Medical Center

data_processing:
fastq reads were alignd to the mouse genome (mm9) with tophat v2.0.8b with parameters -G --no-novel-juncs
bam files were annotated in using Partek software to generate RPKM numbers for each Refseq annotated gene
Genome_build: mm10 (brain) and mm9 (spinal cord)

source_name: spinal cord

growth_protocol: Mouse brains and spinal cords were collected at 6 month

extract_protocol:
Brain and spinal cords were flash frozen on dry ice, and RNA was harvested using Trizol. Total RNA isolated using the PureLink™ RNA Mini Kit (Catalog # 12183018A) and 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Iontorrent (brain) or Illumina (spinal cord) protocols.  RNA sequencing libraries were constructed with the TruSeq RNA Sample Prep Kits v2 from Illumina. 12 RNA samples were indexed with different adapters and pooled for sequencing.

tag: strain

value: lumbar spinal cord

tag: genotype

value: nontransgenic (NTg)


title: NTg-6326


title: B10-144A


title: B10-158A


title: B09-450A


title: NTg-6323


title: F08-6321


title: NTg-6322


title: B08-4579TA


title: B08-4497TA


title: B08-4286TA


title: F08-6318


title: F08-6319


title: GW (LXR Ligand)

source_name: GW, liver

value: GW


title: F08-6320


title: F112-6325


title: F112-6316


title: F112-6324


title: B08-3699TA


title: B08-3758TA


title: B08-3483TA


title: B08-3503TA


title: F112-6317


title: mouse embryonic fibroblasts input replicate B

data_processing:
Library strategy: M1A-seq
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence,  then mapped to hg19 whole genome or S.pombe genome version ASM294v2.29 or S.cerevisea genome version S288C. Aligment was done using tophat version 2.0.12 with parameters - -M -p 3 --no-novel-juncs -g 5 and the relevant gff transcriptome annotation
Enriched intervals were identified using MACS2,in IP over input. FC>=2, FDR<=0.05
Peak middle was determined for peaks that appeared in both replicates.if no replicates were avialable FC>=4 was taken.
For PARSseq samples reads were trimmed using cutadapt and aligned to the human transcriptome (knownCanonical transcripts from UCSC) using bowtie2 (--local).
Only uniquely aligned reads were used for downstream analysis
For each position in the transcriptome number of read start at each base were counted. For this step only reads with more than 5 nts matching the transcript at the start of the read were counted
PARS-scores were calculted for each position in the transcriptome as described in Wan et al. 2014.
Genome_build: hg19 for human ,S.pombe genome version ASM294v2.29 , S.cereviseae genome version S288C
Supplementary_files_format_and_content: Peak lists in excel format include peak middle coordinates for each cell type

source_name: mEFS

growth_protocol: in the Glucose starvation experiments cells were grown on glucose free medium for 4 hours before harvest. In S.Pombe Cells were grown in either EMM-N medium for 4 hours or in malt mating medium for 5 hours

extract_protocol:
Total RNA of the indicated cell types was extracted using 5PRIME RNA purification kit. Where indicated mRNA enriched RNA was purified by oligo dT selection.
Fragmentation was carried out using Ambion fragmentation reagents in 70ºc.Competetive elution was carried out using free m1A nucleoside  (330 microMolar m1A in 10 mM Tris pH 7.4 ,375 mM NaCl 0.1% NP-40.
Immunoprecipitation was done using MBL anti-m1A antibody D345-3 mAb.Dimmroth rearrangment was performed by heating the samples to either 50ºC or 60ºC for 1H under pH 10.4 conditions.
Libraries were prepared according to NEB's instructions accompanying the NEBNext® Ultra™ RNA Library Prep Kit for Illumina (Cat# 7530).

treatment_protocol: in the heat shock experiments cells were incubated at 43 degrees celsius for 4 hours prior to harvesting.

value: mEFS


title: B08-3256TA


title: mouse embronic stem cells input replicate A

source_name: mESCs

value: mESCs


title: mouse embryonic fibroblasts IP replicate B


title: B07-3747A


title: mouse embronic stem cells IP replicate A


title: 9A


title: 8A


title: B08-4454TA


title: mouse liver total RNA input replicate B

source_name: Mouse liver

value: liver


title: mouse embryonic fibroblasts IP replicate A


title: 7A


title: 6A


title: B08-4386TA


title: mouse liver total RNA IP replicate B


title: 5A


title: 3A


title: 36A


title: mouse liver total RNA input replicate A


title: 4A


title: mouse liver total RNA IP replicate A


title: 33A


title: 29A


title: 32A


title: 34A


title: 27A


title: B08-3085A


title: 31A


title: 26A


title: mouse embryonic fibroblasts input replicate A


title: 21A


title: 20A


title: 22A


title: 25A


title: 18A


title: 23A


title: 17A


title: 12A


title: 13A


title: 15A


title: 14A


title: 16A


title: N08-4497A

source_name: normal

value: healthy


title: N08-3503A


title: N08-3758A


title: B08-4579NA


title: 28A


title: B08-3483NA


title: Plant at 27°C, biological rep 2

city: Nottingham

first: Venkata Suresh

last: Bonthala

address: Wollaton Road

department: School of Computer Science

country: United Kingdom

institute: University of Nottingham

description:
Gene expression data from fully expanded single leaflet under 27°C
Bambara_27_2

data_processing:
As there was no genome, the SOLiD reads were aligned to the contigs from the Roche 454 assembly that were at least 50bp in length. In this context “contigs” are like exons. The alignment was performed using LifeScope version 2.5.1.
The number of reads that aligned to each “Isogroup” (i.e. gene) were calculated by summing the read count for each of the contigs that belonged to each Isogroup
The raw read counts were normalized and These are the Reads per KB per million reads (RPKMs) and are normalized by number of reads and Isogroup length.
Genome_build: 454 Bambara Transcriptome; isogroups.fa
Supplementary_files_format_and_content: RPKMs were calculated for each of the samples

organism: Vigna subterranea

source_name: leaflet at 27°C after 3 days

growth_protocol: Two plants of Bambara groundnut genotype S19-3 were grown in controlled environment growth rooms at Sutton Bonington Campus, University of Nottingham under a 12 hour photoperiod and at a constant temperature of 27°C. A single, fully-expanded leaflet was sampled from each of the three plants growing at 27°C, snap frozen in liquid nitrogen and stored at -80°C. Plants were given a further 3 days at 27°C to recover from sampling before being moved to a controlled environment room at 23°C. On the fifth day at 23°C a single fully-expanded leaflet was sampled and stored, as described above. After 3 further days plants were moved to 18°C, and then five days later were sampled again.

extract_protocol:
For extraction of total RNA, 100 mg ground leaf tissue was processed, as per manufacturer’s instructions, using a RNeasy Plant Mini Kit (Qiagen).
As per ABI SOLiD sequencer manufacturer's instructions

value: Fully-expanded leaflet

tag: growth temperature

value: at 27°C after 3 days


title: B08-4386NA


title: 30A


title: WT SP1 EMM-N medium 4h IP 2

organism: Schizosaccharomyces pombe

source_name: Schizosaccharomyces pombe cells


title: WT SP1 vegetative IP 2


title: B08-3758NA


title: WT SP1 vegetative Input 2


title: WT SP1 EMM-N medium 4h input

data_processing:
Library strategy: m1A-seq
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence,  then mapped to hg19 whole genome or S.pombe genome version ASM294v2.29 or S.cerevisea genome version S288C. Aligment was done using tophat version 2.0.12 with parameters - -M -p 3 --no-novel-juncs -g 5 and the relevant gff transcriptome annotation
Enriched intervals were identified using MACS2,in IP over input. FC>=2, FDR<=0.05
Peak middle was determined for peaks that appeared in both replicates.if no replicates were avialable FC>=4 was taken.
For PARSseq samples reads were trimmed using cutadapt and aligned to the human transcriptome (knownCanonical transcripts from UCSC) using bowtie2 (--local).
Only uniquely aligned reads were used for downstream analysis
For each position in the transcriptome number of read start at each base were counted. For this step only reads with more than 5 nts matching the transcript at the start of the read were counted
PARS-scores were calculted for each position in the transcriptome as described in Wan et al. 2014.
Genome_build: hg19 for human ,S.pombe genome version ASM294v2.29 , S.cervisea genome version S288C
Supplementary_files_format_and_content: Peak lists in excel format include peak middle coordinates for each cell type


title: WT SP1 EMM-N medium 4h input 2


title: Plant at 23°C, biological rep 2

description:
Gene expression data from fully expanded single leaflet under 23°C
Bambara_23_2

source_name: leaves at 23°C after 3 days

value: at 23°C after 3 days


title: WT SP1 vegetative IP


title: Saccharomyces_cerevisiae input 2

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae cells


title: 11A


title: WT SP1 vegetative Input


title: Saccharomyces_cerevisiae IP


title: Saccharomyces_cerevisiae IP 2


title: Plant at 27°C, biological rep 1

description:
Gene expression data from fully expanded single leaflet under 27°C
Bambara_27_1


title: RNA-seq, rRNA depleted using RiboMinus

city: San Francisco

first: David

middle: Eric

last: Weinberg

address: 600 16th Street, GH S572F

institute: University of California, San Francisco

data_processing:
Raw read files were stripped of adaptor and randomized barcode sequences.
Reads originating from ribosomal RNAs were pre-filtered by mapping to an index of yeast rRNA sequences with bowtie2.
Filtered reads were mapped to the yeast genome and spliced transcript models using tophat2, discarding any reads mapping to tRNA genes or other noncoding RNA genes.
For each annotated coding sequence, counts of the number of uniquely mapped reads on the sense strand whose 5'-most mapped base occupied every position from 50 nt upstream of the start codon to 50 nt downstream of the stop codon were calculated.
Genome_build: sacCer3
Supplementary_files_format_and_content: The processed data file contains abundance measurements for all genes

molecule: cytoplasmic RNA

growth_protocol: Yeast were grown in YPD to mid-log phase in accordance with standard protocols.

extract_protocol:
RNA-seq: Cytoplasmically-enriched RNA was extracted; depleted of rRNA using Dynabeads, RiboMinus, or Ribo-Zero; randomly fragmented by partial alkaline hydrolysis; and then size-selected RNA fragments were used for library preparation. Ribosome profiling: Cells were harvested and extracts were perpared and processed as described for S. pombe samples in Subtelny et al., 2014 (GSE52809).
Libraries were constructed exactly as described in Subtelny et al., 2014 (GSE52809).


title: Plant at 18°C, biological rep 1

description:
Gene expression data from fully expanded single leaflet under 18°C
Bambara_18_1

source_name: leaves at 18°C after 3 days

value: at 18°C after 3 days


title: RNA-seq, poly(A) selected using Dynabeads oligo(dT)


title: Plant at 23°C, biological rep 1

description:
Gene expression data from fully expanded single leaflet under 23°C
Bambara_23_1


title: RNA-seq, unselected (total) RNA


title: Large 12 (small RNA seq)

status: Public on Feb 09 2016

city: Kansas City

first: Lane

middle: K

last: Christenson

address: 3901 Rainbow Blvd

institute: University of Kansas Medical Center

data_processing:
The three groups of follicles (small, medium and large) were analyzed in biological triplicates giving nine samples in total.  After 3' adapter removal, the read sequences were mapped using the bwa software (v 0.7.5a, [30]) to the bovine genome (assembly UMD3.1) and annotated for overlapped regions with the Ensemble gene annotation file for bovine (release 70) and miRBase (release 21).
Genome_build: Bos_taurus_UMD_3.1/bosTau6
Supplementary_files_format_and_content: data.txt

organism: Bos taurus

source_name: > 9 mm follicular fluid extracellular vesicles

growth_protocol: ovarian tissues were collected from cows

extract_protocol:
total RNA isolated via trizol
Extracellular vesicle RNA (ranging from 1.8 ng – 100 ng) was used to initiate the TruSeq Small RNA library preparation protocol (Illumina #RS200-0012 kit A).  The EV RNA was ligated with 3’ and 5’ RNA adapters followed by a modified reverse transcription reaction and modified PCR amplification. Due to low starting RNA quantities, the reverse transcription of the RNA adapter ligated samples was modified by performing two duplicate reactions containing 6 μl of the 3’/5’ RNA ligated RNA. The 12.5 μl yield of each duplicate reverse transcription reaction was then pooled to obtain 25 μl of homogeneous cDNA.  The subsequent PCR amplification, with index adapter incorporation, was modified by replacing 8.5 μl of ultra-pure water in the PCR master mix with 8.5 μl of the reverse transcribed and pooled cDNA (21 μl cDNA total).  The modified PCR reaction was performed with 15 cycles of amplification.  Size selection and purification of the cDNA library construct was conducted using 3 % marker H gel cassettes on the Pippin Prep size fractionation system (Sage Science).  The Agilent 2100 Bioanalyzer was used with the High Sensitivity DNA kit (Agilent #5067-4626) or the DNA1000 kit (Agilent #5067-1504) to validate the purified libraries.  Libraries were quantified on the Illumina ECO Real Time PCR System using KAPA SYBR Universal Library Quant kit – Illumina (KAPA Biosystems KK4824).  Following quantification, libraries were adjusted to a 2 nM concentration and pooled for multiplexed sequencing.  Libraries are denatured and diluted to the appropriate pM concentration (based on qPCR results) followed by clonal clustering onto the sequencing flow cell using the TruSeq Rapid Single Read (SR) Cluster Kit-HS (Illumina GD402-4001).  The clonal clustering procedure was performed using the automated Illumina cBOT Cluster Station.  The clustered flow cell was sequenced on the Illumina HiSeq 2500 Sequencing System in Rapid Read mode with a 1x50 cycle read and index read using the TruSeq Rapid SBS kit-HS (Illumina FC402-4002).  Following collection, sequence data was converted from .bcl file format to FASTQ files and de-multiplexed into individual sequences for further downstream analysis.

treatment_protocol: follicles were measured and fluid was aspirated, follicles that were 3-5 mm, 6-9 mm and >9 mm were pooled on a given collection day.

value: ovary

tag: follicle size

value: Large

tag: rna source

value: EVs from follicular fluid


title: Large 10 (small RNA seq)


title: Medium 8 (small RNA seq)

source_name: 6-9 mm follicular fluid extracellular vesicles

value: Medium


title: PE_small_a_2

city: Edinburgh

first: Olga

middle: Anna

last: Puchta

address: Crewe Road

department: MRC Human Genetics Unit IGMM

institute: University of Edinburgh

library_source: genomic

data_processing:
(PE) candidate barcode sequences were extracted from between flanking sequences using blastall;
(PE) next we used bedtools programs and bowtie2 and samtools to map all reads with each barcode to wild type U3 to identify  the consensus U3 sequence corresponding to each random barcode
(PE) to create a final 'filtered list' we discarded all barcodes for which we found any mutation in U3 present in between 20-79% of reads, or the linker sequence between U3 and the barcode was mutated or U3 sequence was not totally covered by reads
(E1-5) we used blast and bedtools to localise and remove the flanking sequences from reads and we counted unique barcodes;
(E1-5) next we recovered barcode sequences that could be uniquely matched to exactly one of the barcode sequences from the filtered list, allowing at most two sequencing errors per barcode
Supplementary_files_format_and_content: processed data files are in the custom format
Supplementary_files_format_and_content: column
Supplementary_files_format_and_content: 1 - barcode
Supplementary_files_format_and_content: 2 - sequence of U3 variant assigned to given barcode
Supplementary_files_format_and_content: 3 up to 9 - number of reads for given barcode in subsequent-time points of the experiment

molecule: other

growth_protocol: Cells were grown at 30C (E1 and E3-5) or 37C (E2) and 230 RPM in liquid medium supplemented with 2% glucose in competition experiments (E1-3 and E5) or 2% galactose in control conditions (E2)

extract_protocol:
Yeast cells collected at each time point were treated with zymolyase to remove the cell wall, and plasmid DNA was isolated from remaining spheroplasts using Qiagen MAXIprep
Illumina / Ion Torrent adapters were added in a 25-cycles PCR reaction

treatment_protocol: ~500 000 000 cells were transferred into fresh medium every 12 hours

tag: sample type

value: U3 snoRNA mutated variants


title: PE_small_a_1


title: PE_small_b_1


title: WT SP1 EMM-N medium 4h IP


title: PE_big_b_2


title: Medium 5 (small RNA seq)


title: Small 4 (small RNA seq)

source_name: 3-5 mm follicular fluid extracellular vesicles

value: Small


title: Saccharomyces_cerevisiae input


title: Small 2 (small RNA seq)


title: PE_big_a_2


title: Plant at 18°C, biological rep 2

description:
Gene expression data from fully expanded single leaflet under 18°C
Bambara_18_2


title: E5_D0.75

organism: synthetic construct

value: 20nt random barcode (seqID)


title: E5_D0.25


title: PE_big_a_1


title: E5_G0


title: embryo R1

city: State College

first: Michael

middle: J

last: Axtell

state: PA

address: University Park

department: Department of Biology

institute: Penn State University

data_processing:
cutadapt was used to remove the 3' adapter (--discard-untrimmed -m 15) and to discard reads containing the 5' adapter
Low quality reads were removed with FASTX-Toolkit (-q 20 -p 85 -Q 33 -v)
Reads were aligned to the maize genome with ShortStack 3.3
Genome_build: (AGPv3)
Supplementary_files_format_and_content: Tab-delimited text files contain two columns: the first column is the sequence of the unique, non-redundant sRNA read, the second column is its total raw abundance

organism: Zea mays

source_name: embryo

extract_protocol:
For each tissue, samples from three-four plants were pooled together, flash-frozen in liquid nitrogen and stored at -80°C. Total RNA was extracted from frozen tissue with Trizol and small RNA extracted with PAGE gel.
The sRNA libraries were produced using the TruSeQ® small RNA Sample Preparation Kit (Illumina) and sequenced on an Illumina HiSeq 2500 platform

tag: treatment

value: control, greenhouse conditions

tag: sampling time point

value: mix of kernels of different DAP:21-27 DAP

tag: biological replicate


title: PE_small_b_2


title: pollen R3

source_name: mature pollen

value: mature pollen, collected before 9AM


title: E4_G4.25


title: E4_G3.25


title: Large 11 (small RNA seq)


title: E4_G2.25


title: Medium 6 (small RNA seq)


title: PE_big_b_1


title: E4_G1.25


title: E3_D2.25


title: pollen R1


title: E3_D4.25


title: E3_D0.75


title: Small 1 (small RNA seq)


title: wrapped leaf R3

source_name: leaf number 6, wrapped

value: V5 developmental stage


title: E3_D3.25


title: E3_D1.25


title: E4_G0


title: wrapped leaf R1


title: wrapped leaf R2


title: E3_D0.25


title: E3_G0


title: E5_D1.25


title: expanded leaf R3

source_name: leaf number 5, expanded


title: E2_D6.25


title: E2_D5.25


title: pollen R2


title: E2_D4.25


title: E2_D3.25


title: E2_G0


title: expanded leaf R1


title: expanded leaf R2


title: E2_D1.25


title: HeLa Ribosome footprints_replicate2

city: Guangzhou

first: Gong

last: Zhang

address: Huang-Pu Avenue West 601

department: Institute of Life and Health Engineering

country: China

institute: Jinan University

description:
Ribosome footprints (mRNA fragments covered by ribosomes)
Protocol: directional library construction

data_processing:
Basecalling and basic quality filtering was performed in Illumina HiSeq-2500 by default settings.
Reads were truncated at the first nucleotide whose Phred score is less than 10.
Reads shorter than 18nt are discarded
Mapping reference sequence: RefSeq-RNA (accessed from UCSC genome browser on Jan 21. 2013)
For RFP dataset: reads were mapped to RefSeq-RNA using FANSe2 -S10 -E2 -U1
Genes were quantified using rpkM method
Genome_build: hg19
Supplementary_files_format_and_content: text file with rpkM of all quantified genes in Ribosome footprints_replicate2

source_name: HeLa cells

extract_protocol:
RFP extraction protocol: see Ingolia et al. Nature Protocols
RFP: NEBNext small RNA library construction kit

value: HeLa


title: E4_G0.25


title: H1299 RFP

description: ribosome footprints

data_processing:
the adapter sequences were removed from all reads
Reads were truncated at their first nucleotides, whose Phred quality scores were less than 10. Reads shorter than 18 nt were then discarded.
The rest high quality reads were aligned to the RefSeq-RNA reference sequence using FANSe2 algorithm (http://bioinformatics.jnu.edu.cn/software/fanse2/) with the parameters –L60 –E2 –U1 –S10.
Genome_build: hg19
Supplementary_files_format_and_content: rpkm

source_name: H1299 cells

extract_protocol:
Ribosome profiling
NEBNext small RNA library preparation


title: A549 RFP

description: ribosome footprints

source_name: A549 cells


title: E2_D2.25


title: HBE RFP

description: ribosome footprints

source_name: HBE cells

value: HBE


title: input_DNA_d22_pooled

city: St. Louis

first: Paul

last: Cliften

address: 4320 Forest Park Parkway

department: Genetics

institute: Washington University

description: pooled inputs for samples 1-6

data_processing:
Basecalls performed using CASAVA 1.8
ChIP-seq reads were aligned to the mm10 genome assembly using novoalign version V2.08.02 with harclipping (-H) and adapter stripping (-a)
peaks were called using MACS  version 1.4.2 (20120305) using a pooled input control
Genome_build: mm10
Supplementary_files_format_and_content: Bed files: The bed files contain the called peaks, the 5th column is the standard MACS -10*log10pvalue; txt files: contain the peaks with additional information, such as position of peak summit, number of tags in peak region, fold enrichment and FDR

molecule: genomic DNA

source_name: regenerating liver harvested 12 h after PH

extract_protocol: As described in Huang et al., Identification of an epigenetic signature of early mouse liver regeneration that is disrupted by Zn-HDAC inhibition, Epigenetics, 2015. PubMed: 25482284

treatment_protocol: Mice were subjected to partial hepatectomy (PH) with liver tissue harvested 12 h after surgery as previously described.

tag: gender

value: male

tag: age

value: 2-3 months

value: liver

value: dextrose (22.5% in vehicle)

tag: chip antibody


title: input_DNA_pbs_pooled

description: pooled inoput for samples 7-12

tag: tissue


title: Ac-H3K9_pbs_5_ChIPSeq

description: Sample 11

value: AcH3K9 (abcam, ab10812)


title: Ac-H3K9_pbs_6_ChIPSeq

description: Sample 12


title: Ac-H3K9_d22_6_ChIPSeq

description: Sample 6

value: vehicle (1/2 strength PBS)


title: Ac-H3K9_d22_5_ChIPSeq

description: Sample 5


title: Ac-H3K9_d22_2_ChIPSeq

description: Sample 2


title: Ac-H3K9_pbs_1_ChIPSeq

description: Sample 7


title: Ac-H3K9_pbs_2_ChIPSeq

description: Sample 8


title: Ac-H3K9_d22_4_ChIPSeq

description: Sample 4


title: Ac-H3K9_pbs_4_ChIPSeq

description: Sample 10


title: Ac-H3K9_d22_1_ChIPSeq

description: Sample 1


title: Ac-H3K9_d22_3_ChIPSeq

description: Sample 3


title: X.M.C,  0.5% 8min

city: West Haven

first: Matthew

middle: D

last: Simon

state: CT

address: 600 West Campus Dr. MIC312

department: Molecular Biophysics & Biochemistry

institute: Yale University Chemical Biology Instiute

description:
Xist Targeted Structure Seq Analysis
Targeted_Structure_Seq_Xist_higher_DMS.wig

data_processing:
Basecalls performed using CASAVA.
Alignment was performed with bowtie2. The sequences were aligned to Xist RNA (GenBank Accession # NR_001463).
For each base, paired end reads corresponding to RT events that either proceeded through the base or where stopped immediately before the base were counted. These counts where used to estimate the probability of termination. The estimated probability of DMS modification for A and C bases was calculated by subtracting the probability of termination of the untreated from the treated sample corresponding to each primer set. These data were then combined across the entire RNA for all regions with sufficinet sequencing depth.
Alignment to RNA sequences Mus musculus 18S rRNA (NR_003278.3) or Mus musculus Xist (NR_001463).
Supplementary_files_format_and_content: Using data from samples treated with DMS, the probability of DMS modification is indicated for each base in either 18S rRNA or Xist. The value representing the final estimated percent probability of DMS modification at each A or C base. Regions without sufficient data to estimate the probability are indicated with values of -0.01.

source_name: Female MEF cells

growth_protocol: Cells were cultured in 150mm dishes with DMEM (high glucose) including 10% FBS, 2 mM glutamine, 100 U penicillin, 0.1 mg/ml streptomycin at 37 °C , 5% CO2.

extract_protocol:
Cells were collected in the same buffer using Cell Lifter (Corning) and were centrifuged at 1000g for 5 min at 4 °C. For probing of 18S rRNA, total RNA was extracted using TRIzol (Life Technologies) according to the manufacturer’s instruction. For probing of Xist, ~ 5×107 cells were lysed in 1 ml ice-cold RIPA buffer (50mM Tris HCl, pH 8.0, 150mM NaCl, 1% NP40, 0.5% sodium deoxycholate, 0.1% SDS, 1mM EDTA) supplemented with 100U SUPERasin (Invitrogen). The insoluble fraction enriched with Xist RNA was collected by centrifugation at 3000g for 1 min at 4°C, dissolved in hot TRIzol (65 °C) and the RNA was purified using standard procedures.
TRIzol purified RNA was treated with TURBO DNase (Life Technologies) and was purified using RNeasy Mini Kit (Qiagen). For reverse transcription, a 12 µl solution of 1-2 μg RNA in water was annealed with pre-mixed gene-specific RT-primers (10 pmol primer total) by incubating at 70°C for 5 min., 4°C for 2 min. To this mixture, 3 μl 5X first-strand buffer (250 mM Tris-HCl, pH 8.3, 375 mM KCl, 15 mM MgCl2, 0.1 M DTT) was added and the solution incubated at 55°C for 10 min. While incubating at 55°C, 5 µl RT pre-mix (1 µl 5xFS buffer, 1 µl 10 mM dNTPs, 1 µl 100 mM DTT, 0.5 µl Superscript III (Invitrogen), 0.2 µl RNaseOut (Invitrogen), 1.3 µl H2O) was added and kept at 55 °C 20 min for first strand cDNA synthesis. Reverse transcription was stopped by heating to 85°C for 5 min. For 18S rRNA probing, a mixture of three 18S-specific RT primers was used for reverse transcription. For Xist studies, 87 Xist-specific primers were divided and used in nine RT reactions, which were pooled later to make 3 sequencing libraries. Each RT primer includes a 5’ adaptor sequence (5’- CAGACGTGTGCTCT-3’) to facilitate library construction. Sequencing libraries were constructed using Illumina TruSeq adaptor sequences. Prior to linker ligation, 1 μl RNase H (New England Biolabs) and 0.5 μl RNase A was added to the RT reaction and incubated at 37 °C for 1h to degrade RNA and purified using Ampure Xp beads (Beckman Coulter) following the supplemental protocol for miRNA enrichment by manufacturer with modifications. Briefly, RT product was mixed with 1 volume Ampure Xp beads, 3 volumes 2.5M NaCl, 20% PEG8000, and 1 volume isopropanol and incubated at room temperature for 15 minutes. Ampure Xp beads were captured by magnets for 15 minutes, rinsed 3 times with freshly made 80% ethanol, air-dried for 5 min, and eluted in 15 µl H2O. Purified cDNA was ligated to a 3’-adaptor (/5Phos/NNNAGATCGGAAGAGCGTCGTGTAG/3Bio/) using CircLigase (Epicentre)  by mixing 6.8 μl cDNA with 0.2 μl 100 μM 3’-adaptor, 10×buffer (0.5 M MOPS pH 7.5, 0.1 M KCl, 50 mM MgCl2, and 10 mM DTT), 1 µl 50 mM MnCl2, 1 μl 1 mM ATP and 8 μl 50% PEG8000. The mixture was incubated at 65 °C for 2h, and then at 85 °C for 15 min. to inactivate CircLigase. Ligation products were recovered by Ampure XP beads and subjected to sequential PCR as follows. cDNA was first amplified using forward and reverse primers matching 5’- and 3’- adaptor sequences (5’-CAGACGTGTGCTCTTCCGATC-3’; 5’-CTACACGACGCTCTTCCGATCT-3’) and Phusion polymerase (98°C, 20 sec; 64°C, 20 sec; 72°C, 90 sec, for 4-8 cycles)(New England Biolabs). PCR products were mixed with 1.8x volume Ampure XP beads to enrich PCR products >100 bp. Illumina TruSeq forward primer and indexed reverse primers were used for 4-8 rounds of PCR (98°C, 20 sec; 64°C, 20 sec; 72°C, 90 sec) and the final PCR product was recovered by Ampure XP beads using 1:1.8 sample:beads ratio. Multiplexed sequencing libraries were mixed and subjected to 2x75 paired end sequencing.

treatment_protocol: Immediately before treatment, DMS was diluted to 25% in absolute ethanol, and was further diluted in PBS to desired concentration (0.4%-2% final).  Immediately prior to treatment, cells were rinsed once with PBS and were incubated in 15 ml DMS solution (or with a buffer control) at room temperature for indicated time (4-8 minutes). The DMS reaction was quenched by removing DMS solution and immediate rinsing the cells three times with 25 ml of 50 mM Tris pH 7.5, 100 mM NaCl, 3 mM MgCl2, 40 mM β-mercaptoethanol.

value: MEF

tag: rt-primer set

value: Xist RT primer set C

tag: dms treatment

value: 0.5% v/v DMS 8 min


title: X.M.A, 0.5% 8min

tag: cell type

value: Xist RT primer set A


title: X.M.B,  0.5% 8min

value: Xist RT primer set B


title: X.M.B, 0.4% 4min

description:
Xist Targeted Structure Seq Analysis
Targeted_Structure_Seq_Xist_lower_DMS.wig

value: F1:129S1/CastEiJ x 129S8

value: 0.4% v/v DMS 4 min


title: X.M.C, untreated

description: Xist Targeted Structure Seq Analysis

value: F1:129S1/CastEiJ x 129S6

value: Untreated


title: X.M.C, 0.4% 4min

value: F1:129S1/CastEiJ x 129S9


title: X.M.A, 0.4% 4min

value: F1:129S1/CastEiJ x 129S7


title: X.M.B, untreated

description: Xist Targeted Structure Seq Analysis

value: F1:129S1/CastEiJ x 129S5


title: 18S 0.75% DMS 8min

description:
18S rRNA Targeted Structure Seq Analysis
Targeted_Structure_Seq_18S_rRNA_intermediate_DMS.wig

value: F1:129S1/CastEiJ x 129S2

value: 18S RT primers

value: 0.75% DMS 8min


title: X.M.A, untreated

description: Xist Targeted Structure Seq Analysis

value: F1:129S1/CastEiJ x 129S4


title: 18S 2% DMS 4min

description:
18S rRNA Targeted Structure Seq Analysis
Targeted_Structure_Seq_18S_rRNA_higher_DMS.wig

value: F1:129S1/CastEiJ x 129S3

value: 2% DMS 4 min


title: 18S untreated

description: 18S rRNA Targeted Structure Seq Analysis

value: MEF

value: F1:129S1/CastEiJ x 129S1


title: E1_D3.25

value: 20nt random barcode (seqID)


title: E1_D4.25


title: 18S 0.4% DMS 8min

description:
18S rRNA Targeted Structure Seq Analysis
Targeted_Structure_Seq_18S_rRNA_lower_DMS.wig

value: 0.4% DMS 8 min


title: E1_D2.25


title: E1_D1.25


title: E1_G0


title: rhizophore_rep1

city: Shanghai

first: Lin

last: XU

address: 300 Fenglin Road

department: Chinese Academy of Sciences

institute: Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences

description: sample 2

data_processing:
tophat alignment
cufflinks analysis
Genome_build: LDJE00000000
Supplementary_files_format_and_content: gff3

organism: Selaginella kraussiana

source_name: rhizophore tissue

growth_protocol: selaginella kraussiana was grown at 26 ºC with a 16-h light (~ 5000 Lux, cool white fluorescent lamp) and 8-h dark photoperiod in the greenhouse or plant chamber.

extract_protocol: RNA extraction using Trizol protocols

value: rhizophore


title: seedling_rep1

description: sample 3

source_name: seedling tissue

value: seedling


title: HeLa RNC-mRNA

description:
random fragmentation
translating mRNA (polyA+)

data_processing:
Basecalling and basic quality filtering was performed in Illumina HiSeq-2000 by default settings.
Reads were truncated at the first nucleotide whose Phred score is less than 10.
Reads shorter than 18nt are discarded
Mapping reference sequence: RefSeq-RNA (accessed from UCSC genome browser on Jan 21. 2013)
For mRNA and RNC-mRNA datasets: reads were mapped to RefSeq-RNA using FANSe2 -S10 -E4 -U0
For RFP dataset: reads were mapped to RefSeq-RNA using FANSe2 -S10 -E2 -U1
Genes were quantified using rpkM method
Genome_build: hg19
Supplementary_files_format_and_content: HeLa rpkM all.txt
Supplementary_files_format_and_content: Content: rpkM of all quantified genes in all three datasets

extract_protocol:
RNC-mRNA extraction protocol: see PMID: 23519614
RNC-mRNA: NEBNext mRNA library construction kit

tag: cell line

value: HeLa


title: MSCs T3

city: Charlottesville

first: Fujun

last: Qin

state: VA

address: 345 Crispell Dr.

department: Pathology

institute: University of Virginia

data_processing:
all samples FPKM are analyzed by cufflinks.
SOAPfuse was used for analyzing fusion genes from the RNA sequencing data.
Genome_build: hg19
Supplementary_files_format_and_content: FPKMs for all samples by cufflinks; fusion genes from SOAPfuse

source_name: Mesenchymal stem cell

growth_protocol: Mesenchymal Stem Cells (MSC) cells were maintained in MEM alpha medium with 20% fetal bovine serum (FBS). The Alveolar Rhabdomyosarcoma (ARMS) cell line RH30 was cultured in RPMI1640 medium with 10% FBS.

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

treatment_protocol: To induce muscle differentiation, MSC cells were plated on 0.5% gelatin coated plates and fed with DMEM containing 10% FBS, 0.1μM dethamethasone and 50μM hydrocortisone.

value: mesenchymal stem cells


title: HeLa Ribosome footprints

description:
directional library construction
Ribosome footprints (mRNA fragments covered by ribosomes)


title: RH30

source_name: Alveolar rhabdomyosarcoma cell line

value: alveolar rhabdomyosarcoma


title: leaf_rep1

description: sample 1

source_name: leaf tissue

value: leaf


title: MSCs T4


title: MSCs T2


title: smallRNA_RNAi_RET1_B1

status: Public on Feb 08 2016

city: boston

first: Ruslan

last: Afasizhev

state: MA

address: 72 East Concord Street, Evans, Room 426

department: Department of Molecular & Cell Biology

institute: Boston University

description: RNAi target RET1

data_processing:
Base calling was performed by CASAVA-1.8.2.
Stranded precursor RNA-Seq samples were barcode-separated and adaptor sequence 5′ TGGAATTCTCGGGTGCCAAGG3′ was removed using Trim-galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with the following parameters (-s 3 –e 0.3).
To eliminate contamination from nuclear transcriptome, we removed the precursor reads that mapped to nuclear genome by BWA as described before.
We use custom script and cd-hits to assemble the reference
We use FeaturCounts to count the abudance of each transcripts.
Genome_build: mito_P6_reference_20140917.fa.gz
Supplementary_files_format_and_content: tab deliminated FeatureCounts output

organism: Trypanosoma brucei

source_name: mitochondrial

growth_protocol: Procyclic T. brucei (strain 29-13 (Wirtz et al., 1999)) were grown in SDM-79 media supplemented with appropriate antibiotics. Suspension cultures were maintained with mild aeration at 27C.

extract_protocol:
Mitochondrial fraction was isolated as described except omitting the Percoll density gradient (Pelletier et al., 2007). Mitochondrial pellets were extracted into 25 mM HEPES (pH 7.6), 125 mM KCl, 12 mM MgCl2 and 1.2 % Nonidet P-40 (NP-40) and fractionated on 10%-30% glycerol gradient.
RNA was excised from areas corresponding to 35 to 75 nucleotides (nt), eluted, and processed with a ScriptMiner small RNA-Seq library preparation kit (Epicentre) to generate Illumina-compatible libraries.Single-ended 75-nt stranded sequencing and raw data extraction were performed at the University of California (UC) Irvine Genomics High-Throughput Facility.

tag: strain

tag: Stage

value: procyclic

tag: genotype/variation

tag: molecule subtype

value: mitochondrial RNA


title: smallRNA_RNAi_GRBC_B1

description: RNAi target GRBC


title: smallRNA_RNAi_CN_B1

description: RNAi target control


title: precursor_RNAi_DSS1_B3

tag: RNAi target

value: mitochondrial small RNA precursor


title: precursor_RNAi_RET1_B3


title: precursor_RNAi_RET1_B1


title: precursor_RNAi_DSS1_B1


title: precursor_RNAi_CN_B3


title: RET2_RAP_without_terminator

tag: clip antibody

value: TAP-tagged protein, affnity puldown with IgG-coated magentic beads.


title: precursor_RNAi_RET1_B2


title: precursor_RNAi_CN_B1


title: RET2_RAP_with_terminator


title: HeLa mRNA

description:
random fragmentation
polyA+ mRNA

extract_protocol:
mRNA extraction: standard Trizol protocol
mRNA: NEBNext mRNA library construction kit


title: GRBC_RAP_without_terminator


title: GRBC_CLIP_control2


title: GRBC_RAP_with_terminator


title: GRBC_CLIP_control1


title: precursor_RNAi_DSS1_B2


title: smallRNA_RNAi_MP18_24_B1

description: RNAi target MP18/24


title: GRBC_CLIP_replicate1


title: RET1_CLIP_replicate2

value: RET1 antibody


title: RET1_CLIP_replicate1


title: RET1_CLIP_control1


title: mito_small_RNA_without_terminator


title: Ac-H3K9_pbs_3_ChIPSeq

description: Sample 9

value: male

value: 2-3 months

value: liver

tag: treatment

value: dextrose (22.5% in vehicle)

value: AcH3K9 (abcam, ab10812)


title: 482N1 shArntl2 #2 rep1

city: Stanford

first: Jennifer

last: Brady

address: 269 Campus Drive

institute: Stanford University

description: 482N1 with shArntl2 #2

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using TopHat.
Aligned RNA-seq reads were assembled into transcripts using the Cufflinks assembler (version 0.9.3). Annotated transcripts were obtained from the UCSC genome browser (http://genome.ucsc.edu) and the Ensembl database; the category of transcripts was described at http://vega.sanger.ac.uk/info/about/gene_and_transcript_types.html. (FPKM).category of transcripts was described at http://vega.sanger.ac.uk/info/about/gene_and_transcript_types.html.
Transcript abundances were measured in Fragments Per Kilobase of exon per Million fragments mapped (FPKM). To address the common issue in the assembly that a read may align to multiple isoforms of the same gene or multiple transcripts within the same genetic locus, maximum likelihood estimation was performed by Cufflinks based on a numerical optimization algorithm for calculating FPKM.
The program Cuffdiff was used to define differential expression.
Genome_build: mm10
Supplementary_files_format_and_content: A single tab-delimited text file, including FPKM values for each Sample

source_name: 482N1 lymph node metastasis-derived cell line

growth_protocol: Cells were grown in high glucose DMEM, supplemented with Glutamine, Sodium Pyruvate, Pen/Strep, 2ug/mL puromycin and 10% FBS

extract_protocol:
Total RNA was extracted using the Qiagen RNEasy Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tumor genotype

value: Kras G12D, p53 null


title: 482N1 shArntl2 #2 rep2

description: 482N1 with shArntl2 #2

value: 482N1 lymph node metastasis-derived cell line


title: precursor_RNAi_CN_B2


title: GH8

city: Chicago

first: Joanna

last: Burdette

state: IL

address: 900 S. Ashland Ave

institute: University of Illinois at Chicago

data_processing:
Adapters were removed and reads were removed that had either more than 5% unknown bases, or more than 50% of the reads had a phred score less than 10
The remaining reads were aligned to mm10 (UCSC) with TopHat v2.0.8b with parameters -p 12 -G genes.gtf
Differential expression was performed with cuffdiff v2.1.1 using parameters -p 12 -b genome.fa.  FPKM values were extracted from the cuffdiff results.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: oviduct epithelial cell line

growth_protocol: Cells were maintained in alpha-modified Eagle's medium (Mediatech) supplemented with 10% v/v fetal bovine serum, 2 mM l-glutamine (Life Technologies), 1 ug/mL epithelial growth factor(Roche), 5 ug/mL insulin (Roche), 5 ug/mL transferrin (Roche), 1 mg/mL gentamycin (Roche) and 100 U/mL penicillin (Roche) and 50 ug/mL streptomycin (Roche) and 18.2 ng/mL 17-betaestradiol.

extract_protocol:
Following treatment, RNA was harvested and isolated using Qiashredder column and Qiagen RNAeasy spin columns with on column DNAse digestion (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 48 hours prior to treatment, cell were passaged and plated in "stripped media" consisting of phenol red free α-modified Eagle’s medium (Life Technologies, Carlsbad, CA) supplemented with 10% v/v charcoal stripped fetal bovine serum (FBS) (Life Technologies) (Oakely 1987), 1 mg/mL gentamycin, 2 mM L-glutamine, 100 U/mL penicillin and 50 μg/mL streptomycin. Twenty-four hours prior to treatment, cell were washed with 1X PBS and the sripped media was replenished. Cells were treated with DMSO solvent control (0.1%), 1 nM 17-betaestradiol or 100 nM 4-hydroxytamoxifen (in DMSO) for 24 hours.

value: FVB

tag: replicate


title: GH9


title: GH7

value: Solvent


title: GH6


title: GH4


title: GH5


title: GRBC_CLIP_replicate2


title: GH2


title: GH3


title: MSCs T1

value: mesenchymal stem cells


title: DEL-R

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

data_processing:
STAR_2.4.0a versus mm10 paired-end mapping.
FeatureCounts transcripts quantification (subread-1.4.6-p1-Linux-x86_64) with "--primary -g gene_name -p -s 1 -M " options and Mus_musculus.GRCm38.77 Ensembl GTF annotation file.
Kallisto v0.42.3 transcripts quantification with Ensembl release 79 GTF file.
Genome_build: mm10
Supplementary_files_format_and_content: featurecounts_table.txt: raw counts from featureCounts (subread-1.4.6-p1-Linux-x86_64) with "--primary -g gene_name -p -s 1 -M " options and Mus_musculus.GRCm38.77 Ensembl GTF annotation file. Kallisto_estcounts_table.txt: estimate counts produce with kallisto v0.42.3 with Ensembl release 79 GTF file. Kallisto_tpm_table.txt: transcript counts per million produce with kallisto v0.42.3 with Ensembl release 79 GTF file. BigWig files has been generated using samtools to discriminate expression strand for paired-end reads then genomeCoverageBed and bedGraphToBigWig from bedtools 2 suite.

source_name: delta2leftPAL mice

extract_protocol:
Total RNA was extracted using miRNeasy kit (Qiagen) from either freshly purified splenic B cells, obtained after gradient separation using Lympholyte Mammal (Cedarlane) followed by CD43 negative selection (Miltenyi Biotec), or from purified splenic B cells stimulated in vitro (one million cells per ml) for 48 hours in RMPI 1640 medium (Lonza) supplemented with 10% fetal calf serum (Lonza) and with 5µg/mL LPS (Cayla Invivogen), separated on a Lympholyte Mammal gradient. For each genotype (wt, deltaleftPAL, deltaIRIS), RNA sample was prepared from a pool of equivalent numbers of purified B cells from 4 animals
1 µg of total RNA were depleted from ribosomal RNA, ligated, reverse transcribed and amplified (14 cycles) with the reagents from the truseq stranded total RNA kit (illumina). Libraries were quantified with the Bioanalyzer DNA 1000 Kit (Agilent). 4nM of libraries were then diluted and denatured according to the Illumina recommendations.  Paired-end 150-bp reads were sequenced on an Illumina Nextseq 500 sequencer.

value: B-cell splenocytes

tag: passages

value: Freshly isolated cells

tag: genotype

value: Deletion of the hs3a-IRIS-hs1,2 genomic fragment of the IgH locus


title: IRIS-R

source_name: deltaIRIS mice

value: Deletion of the IRIS genomic fragment of the IgH locus


title: 3882-NA AD

status: Public on Feb 06 2016

city: Seattle

first: John

last: Lee

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology Division

institute: Fred Hutchinson Cancer Research Center

data_processing:
Illumina CASAVA 1.8 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Reads were mapped to UCSC hg19 using MapSplice software.
Gene expression was quantified using RSEM and quantile normalized.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include normalized RSEM quantification for each sample.

source_name: Prostate adenocarcinoma

growth_protocol: Tumors were grown in NSG mice for 6-10 weeks prior to harvest.

extract_protocol:
Tumors were embedded and frozen in OCT freezing compound. Frozen sections were mounted on laser capture microdissection slides and stained with the Arcturus Histogene Frozen Section Staining Kit. Laser capture microdissection of tumor regions was performed on a Leica Microsystems LMD7000. RNA was isolated with the Arcturus PicoPure RNA Isolation Kit.
cDNA libraries were prepared from Illumina RNA using the TruSeq RNA Sample Prep Kit v2 per manufacturer's protocol.

value: Prostate

tag: disease state

value: adenocarcinoma


title: DEL-S

value: Freshly isolated cells cultured for 2 days with 5 micrograms/ml LPS


title: 482N1 shArntl2 #1 rep2

description: 482N1 with shArntl2 #1


title: 482N1 shLuciferase rep2

description: 482N1 with shLuciferase


title: 3051-NA NE

source_name: NEPC

tag: tissue

value: neuroendocrine prostate cancer


title: 482N1 shLuciferase rep1

description: 482N1 with shLuciferase


title: GH1


title: 3882-NA NE


title: IRIS-S


title: 3051-NA AD


title: mito_small_RNA_terminator

value: procyclic

value: mitochondrial RNA


title: 3045-NA AD


title: 3045-NA NE


title: TW09308 transcriptome from starvation growth_2

city: East Lansing

first: Benli

last: Chai

state: Michigan

address: 567 Wilson Road Rm 2225 A

department: Center for Microbial Ecology

institute: Michigan State University

description:
Processed data: raw_count.txt, normalized_count.txt, panGeneMap.txt, Gene_annotations.txt
TW09308_starv_2

data_processing:
Quality trimming of 3' end at Read Segment Quality Control Indicator.
Map RNA-Seq reads to reference genomes using Bowtie  (Langmead et al., 2009) with alignment parameters (-n 2-e 70-l 28 –best)
Summarize the read count to each annotated gene
Remove non-protein coding counts
Differential expression analysis with DESeq (Anders and Huber 2010)  with the default setting
Genome_build: NC_011741 (E.coli strain IAI1), NC_000913.2 (E.coli strain MG1655), TW09308 (E.coli strain TW09308), and TW11588 (E.coli strain TW11588)
Supplementary_files_format_and_content: All in tab-delimited ASCII format. raw_count.txt (pre-normalized read count), normalized_count.txt,  panGeneMap.txt (geneID map between the strains and pangene ID), Gene_annotations.txt (annotation of genes)

organism: Escherichia coli

source_name: TW09308 starvation

growth_protocol: A minimal growth medium as described in the study by Ihssen and Egli (2004) was used for all experiments. Bacterial stock cultures were streaked onto agar plates and incubated overnight. One colony was then transferred into 20 ml minimal medium, grown at 37 °C (250 r.p.m.) over night culture (ONC) and served as the inoculum for experiments. For continuous culture experiments we designed and constructed 500 ml bioreactors according to the study by Huwiler et al., (2012) that were half-filled with medium (0.5 g glucose per l) and incubated at 37 °C in a temperature controlled water bath. Before continuous cultivation (dilution rate=0.25), 1–2 ml of the ONC was transferred and grown in batch-mode until reactors became visibly turbid. Subsequently, cells were grown to steady-state (defined as constant optical density over time) and harvested for experimentation. For starvation experiments the medium flow was stopped during steady-state and bacteria were collected after 4 h. To avoid gene-expression signatures of stationary cells from the ONC, batch cultures (1000 ml Erlenmeyer flasks containing 100 ml of pre-warmed medium (1 g glucose per l); 37 °C; 250 r.p.m.)) were inoculated with 5 ml of an exponentially growing pre-culture that derived from the ONC.

extract_protocol:
Harvested cells (4 × 6 ml) were immediately combined with 6 ml RNAlater (Life Technologies, Grand Island, NY, USA), centrifuged for 15 min at 12 000 r.p.m., washed with 1 ml RNAlater (3 min at 15 000 r.p.m.), re-suspended in 0.5 ml RNAlater and stored at −20 °C. For RNA extraction the RiboPure-Bacteria Kit (Life Technologies) was used according to the manufacturer’s instructions. To achieve high RNA yields several reactions for each sample were done in parallel and pooled at the end of the procedure. An additional DNase treatment step with TURBO DNase (Life Technologies) was included to assure no genomic DNA contamination. Messenger RNA was enriched using the RiboMinus Bacteria Kit (Life Technologies) according to the manufacturer’s instructions.
RNA quality was confirmed with the Bioanalyzer system (Agilent Technologies, Santa Clara, CA, USA) and sequencing (50 cycles, pooling eight bar-coded samples per lane) was performed on the Illumina HiSeq platform (Illumina, San Diego, CA, USA) at the Research Technology Support Facility (RTSF) at Michigan State University.

tag: growth protocol

value: Bacteria liquid culture

value: starvation growth


title: TW09308 transcriptome from batch growth_2

description:
Processed data: raw_count.txt, normalized_count.txt, panGeneMap.txt, Gene_annotations.txt
TW09308b2

source_name: TW09308 batch

value: batch growth


title: TW11588 transcriptome from batch growth_2

description:
Processed data: raw_count.txt, normalized_count.txt, panGeneMap.txt, Gene_annotations.txt
TW11588b2

source_name: TW11588 batch


title: TW09308 transcriptome from chemostat growth_2

description:
Processed data: raw_count.txt, normalized_count.txt, panGeneMap.txt, Gene_annotations.txt
TW09308CC2

source_name: TW09308 chemostat

value: chemostat growth


title: TW11588 transcriptome from chemostat growth_2

description:
Processed data: raw_count.txt, normalized_count.txt, panGeneMap.txt, Gene_annotations.txt
TW11588CC2

source_name: TW11588 chemostat


title: TRAMP tumor: Control

city: Cincinnati

first: Vladimir

last: Kalinichenko

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Base calling, alignment, filtering as well as quality control were performed by the CCHMC DNA Sequencing and Genotyping Core.
Data values were given as expressed FKPM for each transcript with appropriate gene ID.
FKPM values were normalized to internal housekeeping genes and then to each group to determine relative abundance
Genes with values lower than FKPM were considered not expressed highly enough for further analysis and not included in gene ontology.

source_name: TRAMP tumor

extract_protocol:
mRNA was isolated using Qiagen RNeasy Mini Kit
Libraries were prepared and quality controlled by the Cincinnati Children's Hosptial Medical Center DNA Sequencing and Genotyping Core Facilities and Staff

value: TRAMP tumor

value: prostate cancer


title: IAI1 transcriptome from starvation growth_2

description:
Processed data: raw_count.txt, normalized_count.txt, panGeneMap.txt, Gene_annotations.txt
IAI1_starv_2

source_name: IAI1 starvation


title: TRAMP tumor: Foxf1 Over Expression


title: IAI1 transcriptome from batch growth_2

description:
Processed data: raw_count.txt, normalized_count.txt, panGeneMap.txt, Gene_annotations.txt
IAI1b2

source_name: IAI1 batch


title: IAI1 transcriptome from chemostat growth_2

description:
Processed data: raw_count.txt, normalized_count.txt, panGeneMap.txt, Gene_annotations.txt
IAI1CC2

source_name: IAI1 chemostat


title: TW09308 transcriptome from starvation growth_1

description:
Processed data: raw_count.txt, normalized_count.txt, panGeneMap.txt, Gene_annotations.txt
TW09308_starv_1


title: MG1655 transcriptome from batch growth_2

description:
Processed data: raw_count.txt, normalized_count.txt, panGeneMap.txt, Gene_annotations.txt
MG1655b2

source_name: MG1655 batch


title: TW09308 transcriptome from batch growth_1

description:
Processed data: raw_count.txt, normalized_count.txt, panGeneMap.txt, Gene_annotations.txt
TW09308b1


title: TW11588 transcriptome from starvation growth_1

description:
Processed data: raw_count.txt, normalized_count.txt, panGeneMap.txt, Gene_annotations.txt
TW11588_starv_1

source_name: TW11588 starvation


title: TW09308 transcriptome from chemostat growth_1

description:
Processed data: raw_count.txt, normalized_count.txt, panGeneMap.txt, Gene_annotations.txt
TW09308CC1


title: stem_rep1

description: sample 4

source_name: stem tissue

value: stem


title: TW11588 transcriptome from batch growth_1

description:
Processed data: raw_count.txt, normalized_count.txt, panGeneMap.txt, Gene_annotations.txt
TW11588b1


title: MG1655 transcriptome from chemostat growth_2

description:
Processed data: raw_count.txt, normalized_count.txt, panGeneMap.txt, Gene_annotations.txt
MG1655CC2

source_name: MG1655 chemostat


title: IAI1 transcriptome from starvation growth_1

description:
Processed data: raw_count.txt, normalized_count.txt, panGeneMap.txt, Gene_annotations.txt
IAI1_starv_1


title: IAI1 transcriptome from batch growth_1

description:
Processed data: raw_count.txt, normalized_count.txt, panGeneMap.txt, Gene_annotations.txt
IAI1b1


title: smallRNA_RNAi_DSS1_B1

description: RNAi target DSS1

source_name: mitochondrial


title: IAI1 transcriptome from chemostat growth_1

description:
Processed data: raw_count.txt, normalized_count.txt, panGeneMap.txt, Gene_annotations.txt
IAI1CC1


title: MG1655 transcriptome from starvation growth_1

description:
Processed data: raw_count.txt, normalized_count.txt, panGeneMap.txt, Gene_annotations.txt
MG1655_starv_1

source_name: MG1655 starvation


title: MG1655 transcriptome from batch growth_1

description:
Processed data: raw_count.txt, normalized_count.txt, panGeneMap.txt, Gene_annotations.txt
MG1655b1


title: 8 WAP

city: Beibei

first: Huafang

last: Wan

state: Chongqing

address: Tiansheng

institute: Southwest University

data_processing:
The clean reads were screened from raw sequencing reads by removing reads containing adapter, ploy-N and low quality reads.
The clean reads were aligned to the B. napus reference genome using the TopHat program.
The expression levels of all genes from the B. napus reference annotation were quantified using htseq-count 0.6.1p2.
RNA-Seq raw counts were normalized by the DESeq normalization
Time-series differential expression analysis was carried out using the maSigPro package. The p-values were corrected for multiple comparisons by the Benjamini & Hochberg false discovery rate procedure. We set Q = 0.05 and rsq = 0.7 to get significant genes, and we set k = 8 to classify significant genes.
Genome_build: Brassica_napus_v4.1.chromosomes.fa
Supplementary_files_format_and_content: tab-delimited text files including normalized expression values for each gene in all samples

organism: Brassica napus

source_name: Brassica napus

growth_protocol: B. napus were planted in southwest China

extract_protocol:
The total RNA from the four samples were extracted and purified using the RNAprep pure Plant Kit (DP 432, TIANGEN BIOTECH (BEIJING) CO., LTD) according to the manufacturer’s protocol. RNA purity was checked with NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). The concentration was measured with Qubit® RNA Assay Kit and Qubit® 2.0 Fluorometer (Life Technologies, CA, USA). The integrity was assessed using the Agilent 2100 Bioanalyzer and RNA Nano 6000 kit (Agilent Technologies, CA, USA).
cDNA libraries for samples from the four time points of seed development were constructed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) according to the manufacturer’s protocol. Library quality was assessed using the Agilent 2100 Bioanalyzer. The library preparations were sequenced and 100-bp paired-end reads were generated by an Illumina Hiseq 2000 platform.

treatment_protocol: B. napus seeds were harvested at 2, 4, 6 and 8 WAP. After being dissected from the siliques, these seeds were frozen in liquid nitrogen immediately and then stored at -80°C.

tag: developmental stage (weeks after pollination)

value: 8 WAP

value: seeds


title: 2 WAP

value: 2 WAP


title: 6 WAP

value: 6 WAP


title: MS_3

city: Parkville

first: Andrew

middle: David

last: Fox

state: VIC

address: 30 Royal Parade

department: MS Division

country: Australia

institute: The Florey Institute of Neuroscience and Mental Health

description: Binder_Mertk_Rnaseq.txt, Column "MS_3"

data_processing:
Read mapping with "Subread" software package, specifically the "subjunc" tool in this package which maps either single-end or paired-end RNA-seq reads to a reference genome (not a reference transcriptome - hence it can identify both known and novel exon-exon junctions). Parameter in commandline call: "subjunc -Q -H -T 7 -n 10 -I 16"
Sorting (Picard), merging (samtools) and duplicate marking (Picard)
Used "featurecounts" utility tool within the "Subread" package to count the number of reads mapping to each gene/transcript model annotated in the human GENCODE v19 database. All parameters were default and multimapping reads were excluded.
Genome_build: GRCh37 (NCBI build 37 / UCSC hg19)
Supplementary_files_format_and_content: Tab delimited text. First line gives the column names for the data fields (columns). Remaining lines are the transcript abundance data, one line for each human gene (identified by Ensembl gene ID), followed by metadata fields and number of reads that mapped to that gene for each sample.

source_name: Purified human monocytes

extract_protocol:
Monocytes purified from human blood using MACS. Total RNA isolated from purified monocytes using Qiagen RNeasy columns, followed by isolation of mRNA using Ambion ployA purist kit.
Library prepared using Illumina mRNA library preparation kit

tag: disease

value: Multiple Sclerosis

tag: mertk haplotype

value: Homozyg. MS Risk


title: TW11588 transcriptome from chemostat growth_1

description:
Processed data: raw_count.txt, normalized_count.txt, panGeneMap.txt, Gene_annotations.txt
TW11588CC1

tag: strain


title: MS_2

description: Binder_Mertk_Rnaseq.txt, Column "MS_2"


title: MS_4

description: Binder_Mertk_Rnaseq.txt, Column "MS_4"


title: MS_1

description: Binder_Mertk_Rnaseq.txt, Column "MS_1"


title: MS_5

description: Binder_Mertk_Rnaseq.txt, Column "MS_5"


title: 482N1 shArntl2 #1 rep1

description: 482N1 with shArntl2 #1

source_name: 482N1 lymph node metastasis-derived cell line

value: Kras G12D, p53 null

tag: cell line


title: HC_1

description: Binder_Mertk_Rnaseq.txt, Column "HC_1"

value: healthy control

value: Homozyg. MS non-risk


title: 4 WAP

value: 4 WAP


title: Input.mESC+UTX+RA.2014_05_29

status: Public on Feb 05 2016

city: Houston

first: Alin

last: Tomoiaga

address: 6670 Bertner Ave

institute: Houston Methodist Research Institute

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 3.2 with the following configuration: -a -m 1 --best --strata -X 1000
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: wig files were generated using the dregion function in DANPOS2 with the following configuration: -c 10000000 --frsz 200 --extend 200

source_name: embryoid bodies, WT, RA, input

growth_protocol: ES cells were grown on gelatin in an undifferentiated state (ES medium (+LIF)).

extract_protocol:
Briefly, cells were grown to log phase and fixed with 1% formaldehyde for 10 min at room temperature. The fixed cells were sonicated directly. Exactly 10% of the chromatin was used for the extraction of input DNA. For ChIP, 4 μg of antibodies, including anti-H3K4me3 or anti-H3K27me3 antibodies, was bound to protein A or protein G magnetic beads depending on the antibody origin.
The ChIP-Seq libraries were constructed using the TruSeq DNA sample prep kit v2 (Illumina) according to the manufacturer's protocol.

treatment_protocol: ESCs were trypsinized, transferred onto 10-cm petri dishes, and cultured in ESC media without LIF for 5 days to induce embryoid bodies (EBs). EBs were transferred onto gelatin-coated tissue culture dishes, cultured in ESC media without LIF, and treated with the indicated RA concentrations for 5 days to induce cellular differentiation.

tag: cell type

value: embryonic stem cells (ESCs)

tag: genotype/variation

value: Wild type (UTX +/Y)

value: Retinoic acid (RA)

tag: chip antibody


title: M_HU-BRPF3

city: Lausanne

first: Eric

middle: R

last: Paquet

state: Vaud

address: Station 15  CH - 1015

department: Life sciences

country: Switzerland

institute: EPFL

description: BRPF1/2 ChIP-seq in RKO cells

data_processing:
Raw sequences were mapped using Bowtie version 0.12.8 on build hg18 or hg19 of the human genome . BPRF1/2 and input data were previously deposited under accession numbers GSE47190 and GSE33221 (Avvakumov et al. 2012; Lalonde et al. 2013). Read alignments in sam format were converted to bam files using samtools [PMID : 19261174]. Samtools was then successively applied to remove duplicated reads, sort, and index bam files. Peak calling was performed using MACS version 1.4.0 by comparing AS-Brpf3, HU-Brpf3 and M-Brpf3 to M-HU IgG and Brpf1/2 to the signal from the input[PMID : 18798982]. We identified intersection between two sets of significant peaks in hg19 coordinates using bedtools “intersect” function [PMID : 20110278]. In case where we needed to compare hg18 and hg19 peaks, we used the liftover tool from the UCSC genome browser to convert hg18 into hg19 coordinates [PMID 12045153]. The ORC1 ChIP-seq data used for comparison was obtained from Dellino et al. Genome Res 2013 (GSE37583). We used the Bioconductor package VennDiagram [PMID:21269502] to display the overlaps between the different experiments and IGV for ChIP-seq signal visualization in genomic context [PMID:22517427].
genome build: hg19
processed data files format and content: bw, bed

source_name: human colon carcinoma

growth_protocol: DMEM, 10% FBS

extract_protocol:
Lysates were clarified from sonicated nuclei and DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions . Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation library fragments of ~200-500 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel and DNA was PCR amplified with Illumina primers for 18 cycles. Amplicons were purified with Qiagen QIA Quick MinElute PCR purification kit and libraries were sequenced on the HiSeq2000 following the manufacturer's protocols.

treatment_protocol: no treatment (AS), synchronisation: mimosin 0.5mM 22h (M), cells released 3h and HU 3mM treated 1h30 (M+HU)

value: RKO

tag: synchronisation

value: mimosine 0.5mM for 22h, cells released 3h and HU-3mM treated for 1h30

value: homemade rabbit BRPF3 (from X-J Yang, McGill univ)


title: MCF-7 NAF-1(-) Rep 3

city: Denton

first: Rajeev

middle: K.

last: Azad

state: Texas

address: 1155 Union Circle #305220

institute: University of North Texas

data_processing:
Used Tophat and Bowtie for read alignment onto human reference genome and Cufflinks for obtaining the FPKMs and assessment of significance of fold change
Genome_build: NCBI build 37.2
Supplementary_files_format_and_content: Excel file; FPKMs for empty vector control and NAF-1 suppressed breast cancer cell lines MCF-7

source_name: NAF-1 suppressed

growth_protocol: Cells were grown in culture in complete DMEM liquid medium supplemented with 10% FBS, 2 mM glutamine, 100 U/ml penicillin, 100 ug/ml streptomycin and 0.25 ug/ml amphotericin B.  Cells were maintained in petri dishes in an incubator at 37 degrees C and 5% CO2.

extract_protocol:
Cells were grown to 80% confluence, medium was discarded and cells were washed with 1x PBS.  Cells were collected directly from plates and RNA was extracted using the Qiagen RNeasy Mini Kit (Cat.# 74104) according to manufacturers instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: NAF-1(-) cells were generated through Lipofectamine transfection using a 29-mer pGFP-V-RS plasmid from OriGene Technologies, previously described in Sohn et al. (2013). EV (empty vector) was the scrambled sequence negative control. Cells were grown under puromycin selection and stable knockdown lines were obtained by FACS, selecting for GFP.

value: breast cancer


title: UT_IP_rep2

city: Hangzhou

first: Xushen

last: Xiong

state: Zhejiang

address: Wenyi Road West

department: Medical Center

institute: Zhejiang University

description: supplementary file: Starve2.macs_peaks.txt

data_processing:
Tirm_galore[version 0.3.7, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/] was used to remove or trim adaptor contained reads and low quality reads, requiring the minimum length of trimmed reads to be 20 bases. Artificial sequences, two bases added during library construction at the 5 prime of reads, were also removed
Remained reads were mapped to the human transcriptome (downloaded from UCSC genome tables) using hisat [Kim D, Langmead B and Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nature Methods 2015]
Only proper paired mapped reads were used for subsequently analysis. Peak calling was done by MACS2.(https://github.com/taoliu/MACS/)
Genome_build: hg19

molecule: polyA RNA

source_name: HEK293T (untreat control)

growth_protocol: cells was maintained in DMEM with 10% FBS and penicillin/streptomycin.

extract_protocol:
total RNA was isolated from cell lines by Trizol(invitrogen).40 ug mRNA was enriched from 2.5 mg total RNA with size selection using Megaclear kit (invitrogen) followed by two rounds of polyA selection using Dynabeads Oligo(dT)25 (invitrogen).
Libraries were prepared by library preparation modules (New England Biolabs) according to manufacturer's instructions with slight modifications. AMV reverse transcriptase was used for reverse transcription with low dNTP concentration (0.2mM).The following steps are done according to manufacturer's instructions.

value: wild type

value: human embryonic kindey cells

tag: enrichment

value: Immunoprecipitation with anti-m1A antibody

tag: treatment


title: M-BRPF3

description: BRPF1/2 ChIP-seq in RKO cells

value: mimosine 0.5mM for 22h


title: M_HU-IgG

description: Control IgG ChIP-seq in RKO cells

value: homemade rabbit IgG


title: MCF-7 NAF-1(-) Rep 1


title: MCF-7 EV Rep 1

source_name: Control


title: HC_2

description: Binder_Mertk_Rnaseq.txt, Column "HC_2"


title: MCF-7 EV Rep 2


title: MCF-7 EV Rep 3


title: Input.mESC+UTX-RA.2014_05_29

source_name: embryoid bodies, WT, no RA, input

value: Normal


title: RET1_CLIP_control2

tag: Stage

value: procyclic

tag: clip antibody

value: RET1 antibody

tag: molecule subtype

value: mitochondrial RNA


title: AS-BRPF3

description: BRPF1/2 ChIP-seq in RKO cells

value: untreated cells, normal growth conditions


title: MCF-7 NAF-1(-) Rep 2


title: Input.mESC-UTX+RA.2014_05_29

source_name: embryoid bodies, UTX depleted, RA, input

value: embryonic stem cells (ESCs)

value: UTX knockout (UTX -/Y)


title: HC_3

description: Binder_Mertk_Rnaseq.txt, Column "HC_3"

value: healthy control

value: Homozyg. MS non-risk


title: Input.mESC-UTX-RA.2014_05_29

source_name: embryoid bodies, UTX depleted, no RA, input


title: UT_Input_rep1

description: supplementary file: Starve1.macs_peaks.txt

tag: genotype


title: Input.mESC+UTX+RA.2014_05_25

value: Wild type (UTX +/Y)

value: Retinoic acid (RA)


title: Input.mESC+UTX-RA.2014_05_25


title: Input.mESC-UTX+RA.2014_05_25


title: UT_Input_rep2


title: Input.mESC-UTX-RA.2014_05_25


title: Starve_IP_rep2

source_name: HEK293T (Starvation treatment)

treatment_protocol: Cells were washed with PBS twice and cultured with DMEM medium without FBS 16 hours.

value: starvation


title: MG1655 transcriptome from chemostat growth_1

description:
Processed data: raw_count.txt, normalized_count.txt, panGeneMap.txt, Gene_annotations.txt
MG1655CC1

value: Bacteria liquid culture

value: chemostat growth


title: TW11588 transcriptome from starvation growth_2

description:
Processed data: raw_count.txt, normalized_count.txt, panGeneMap.txt, Gene_annotations.txt
TW11588_starv_2

source_name: TW11588 starvation

value: starvation growth


title: Input.mESC+UTX-RA.2014_02_01


title: Input.mESC+UTX+RA.2014_02_01


title: Input.mESC-UTX+RA.2014_02_01


title: Starve_IP_rep1

value: wild type

value: human embryonic kindey cells

value: Immunoprecipitation with anti-m1A antibody


title: Input.mESC-UTX-RA.2014_02_01

value: Normal


title: H3K4me3.mESC+UTX+RA.2014_05_29

source_name: embryoid bodies, WT, RA, H3K4me3 ChIP


title: Starve_Input_rep1


title: H3K4me3.mESC-UTX-RA.2014_05_29

source_name: embryoid bodies, UTX depleted, no RA, H3K4me3 ChIP


title: Starve_Input_rep2


title: UT_IP_rep1


title: H3K4me3.mESC+UTX+RA.2014_05_25


title: H3K4me3.mESC+UTX-RA.2014_05_29

source_name: embryoid bodies, WT, no RA, H3K4me3 ChIP


title: H2O2_IP_rep2

description: supplementary file: H2O2_2.macs_peaks.txt

source_name: HEK293T (H2O2 treatment)

treatment_protocol: Cells were incubated with Hydrogen peroxide (50 uM) for 30min


title: H3K4me3.mESC-UTX-RA.2014_05_25


title: H2O2_IP_rep1

description: supplementary file: H2O2_1.macs_peaks.txt


title: H3K4me3.mESC+UTX-RA.2014_05_25


title: H3K4me3.mESC+UTX+RA.2014_02_01


title: H3K4me3.mESC-UTX+RA.2014_05_25

source_name: embryoid bodies, UTX depleted, RA, H3K4me3 ChIP


title: H3K4me3.mESC+UTX-RA.2014_02_01


title: H3K4me3.mESC-UTX-RA.2014_02_01


title: H2O2_Input_rep1


title: KO_Demethyl_rep2

description: supplementary file: KO2.normed.win10.txt

source_name: ALKBH3 KO HEK293T

value: ALKBH3 Knockout

value: ALKBH3 KO HEK293T

value: Immunoprecipitation with anti-m1A antibody followed by demethylase treatment


title: H3K27me3.mESC+UTX-RA.2014_05_29

source_name: embryoid bodies, WT, no RA, H3K27me3 ChIP

value: embryonic stem cells (ESCs)


title: H3K27me3.mESC+UTX+RA.2014_05_29

source_name: embryoid bodies, WT, RA, H3K27me3 ChIP


title: KO_Demethyl_rep1

description: supplementary file: KO1.normed.win10.txt


title: H3K27me3.mESC-UTX+RA.2014_05_29

source_name: embryoid bodies, UTX depleted, RA, H3K27me3 ChIP

value: UTX knockout (UTX -/Y)


title: H3K4me3.mESC-UTX+RA.2014_05_29


title: H3K27me3.mESC-UTX-RA.2014_05_29

source_name: embryoid bodies, UTX depleted, no RA, H3K27me3 ChIP


title: KO_IP_rep2

description: supplementary file: KO2.macs_peaks.txt


title: H3K27me3.mESC+UTX-RA.2014_05_25


title: H3K27me3.mESC+UTX+RA.2014_05_25


title: H3K27me3.mESC-UTX+RA.2014_05_25


title: H3K27me3.mESC-UTX-RA.2014_05_25


title: H3K27me3.mESC+UTX-RA.2014_02_01


title: H3K4me3.mESC-UTX+RA.2014_02_01


title: H2O2_Input_rep2


title: WT_Demethyl_rep1

description: supplementary file: WT1.normed.win10.txt


title: KO_IP_rep1

description: supplementary file: KO1.macs_peaks.txt


title: H3K27me3.mESC+UTX+RA.2014_02_01


title: KO_Input_rep1

description: supplementary file: KO1.macs_peaks.txt


title: KO_Input_rep2

description: supplementary file: KO2.macs_peaks.txt


title: WT_IP_rep2

description: supplementary file: WT2.macs_peaks.txt


title: H3K27me3.mESC-UTX+RA.2014_02_01


title: WT_IP_rep1

description: supplementary file: WT1.macs_peaks.txt


title: WT_HFSC

city: Boulder

first: Li

last: Wang

state: CO

address: 347 UCB

institute: University of Colorado, Boulder

description:
Genomic DNA of region that accessible to Tn5 transposase
ATAC-seq, protocol as described in Buenrostro et al., Nat Methods, 2013

data_processing:
Library strategy: ATAC-seq
Libraries are sequenced by Illumina HiSeq 2000
Raw reads are alligned to mouse genome version mm10 though bowtie2
Peak calling were performed using MACS2 on individual sequence data and pooled by mergeBed in Bedtools
Genome_build: mm10
Supplementary_files_format_and_content: peaks.bed

source_name: hair follicle stem cells

extract_protocol:
Back skin is dissected and treated with Collagenase and Trypsin to achieve single cell suspension. Stem cells are purified through FACS by antibody staining and gating of H2BGFP(+), Sca-1(-), CD34(+) and CD49f(+) cells.
Illumina Nextera DNA Library Prep Kit

tag: age

value: postnatal day 30

value: K14-H2BGFP, Foxc1 fl/fl

tag: gender

value: female


title: KO_HFSC resequenced

value: K14-H2BGFP, K14Cre, Foxc1 fl/fl


title: WT_HFSC resequenced


title: KO_HFSC


title: P47_KO_HFSC_3

description: processed data file: P47_HTseq_count.txt

data_processing:
Libraries are sequenced by Illumina HiSeq 2000 and 2500.
Raw reads are alligned to mouse genome version mm10 though Tophat 2.
Gene count data are generated using Htseq count function.
Genome_build: mm10
Supplementary_files_format_and_content: column names are sample names, and sample names are gene symbols.

extract_protocol:
Back skin is dissected and treated with Collagenase and Trypsin to achieve single cell suspension. Stem cells are purified through FACS by antibody staining and gating of H2BGFP(+), Sca-1(-), CD34(+) and CD49f(+) cells.
NEBNext® Ultra™ Directional RNA Library Prep Kit

value: postnatal day 47

value: hair follicle stem cells (HFSC)

value: Oligo(dT) selected RNA


title: P47_KO_HFSC_1


title: P31_KO_HFSC

description: processed data file: P30_HTseq_count.txt

value: postnatal day 31


title: P47_KO_HFSC_2

value: male


title: P43_KO_HFSC_5


title: WT_Input_rep2

description: supplementary file: WT2.macs_peaks.txt

value: wild type

value: human embryonic kindey cells


title: WT_Input_rep1

description: supplementary file: WT1.macs_peaks.txt


title: H3K27me3.mESC-UTX-RA.2014_02_01

value: Normal


title: WT_Demethyl_rep2

description: supplementary file: WT2.normed.win10.txt


title: UMSCC47 DEKsh

first: Susanne

last: Wells

state: Ohio

address: 3333 Burnet Ave.

data_processing:
Samples were sequenced at the CCHMC DNA core, on an Illumina HiSeq2500 and is based on the TopHat/Cufflinks pipeline. Refence annotation is based on UCSC known genes table.
BAM files from RNA-Seq were imported into GeneSpring NGS software (v12.6) and aligned to hg19/GRCh37 reference genome. Reference annotations produced by Emsembl. Aligned reads were filtered on base quality >=30.
Aligned read couts quantified and used to compute RPKMS. Normalized using DESeq algorithm and threshold set to 1. Filtrations removes all genes with fewer than 3 reads in each sample.
Fold change was calculated as DEKsh/NTsh with a cut-off of 1.4 fold change.
Genome_build: hg19
Supplementary_files_format_and_content: TXT files containing UMSCC1 and UMSCC47 normalized values, gene symbols, and Emsembl IDS

source_name: HPV+ RNA-Seq Knockdown

growth_protocol: Cells lines are grown in complete DMEM (UMSCC47) or complete DMEM supplemented with 1% hydrocortisone (UMSCC1).

extract_protocol:
RNA was extracted with the Zymo RNA mini-prep kit. This included a Dnase digestion.  Final RNA was aliquoted and submitted for quality control and RNA-Sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: At 30% confluency wells were infected with shRNA for NTsh or DEKsh and selected with puromycin. After selection, cells were plated and pellets collected at similar cell numbers for RNA extraction.

tag: diagnosis

value: Head and Neck Squamous Cell Carcinoma

tag: dek status

value: DEK Knockdown

tag: hpv status

value: HPV+


title: UMSCC1 DEKsh

source_name: HPV- RNA-Seq Knockdown

value: HPV-


title: UMSCC1 NTsh

source_name: HPV- RNA-Seq Control

value: Control


title: UMSCC47 NTsh

source_name: HPV+ RNA-Seq Control


title: P29_KO_HFSC

value: postnatal day 29


title: maize tassel R1 drought rep 1

status: Public on Feb 04 2016

city: Newark

first: Shawn

last: Thatcher

state: DE

address: 15 Innovation Way

institute: University of Delaware

data_processing:
Illumina Casava software used for basecalling.
Tophat2 was used to map reads to genome and maize transcriptome (version 5a)
Cufflinks was used to discover novel transcripts
Cuffdiff was used to quantify known and novel transcripts
Genome_build: Maize genome version 5a
Supplementary_files_format_and_content: Tab-delimited FPKM expression

source_name: maize tassel R1 drought

growth_protocol: B73 maize plants were grown in a field in Woodland, CA in 2012. Plots were designed utilizing a randomized complete block design, with four biological replicates. Drought stress was applied by withholding water after stage V8.

extract_protocol:
Total RNA was isolated from frozen maize leaf tissues via Qiagen RNeasy kit for total RNA isolation (Qiagen, Valencia, California USA).
Standard Illumina

tag: developmental stage

tag: growth condition

value: drought-stressed

tag: tissue

value: tassel


title: maize tassel R1 drought rep 3


title: maize tassel R1 drought rep 2


title: maize tassel V16 drought rep 3

source_name: maize tassel V16 drought


title: maize tassel R1 drought rep 4


title: maize tassel V16 drought rep 4


title: maize tassel V16 drought rep 1


title: maize tassel V14 drought rep 2

source_name: maize tassel V14 drought


title: maize tassel V14 drought rep 4


title: maize tassel V14 drought rep 1


title: maize tassel V16 drought rep 2


title: maize tassel V12 drought rep 2

source_name: maize tassel V12 drought


title: maize tassel V12 drought rep 1


title: maize tassel V14 drought rep 3


title: maize tassel V12 drought rep 3


title: MG1655 transcriptome from starvation growth_2

description:
Processed data: raw_count.txt, normalized_count.txt, panGeneMap.txt, Gene_annotations.txt
MG1655_starv_2

source_name: MG1655 starvation

tag: strain

tag: growth protocol

value: Bacteria liquid culture

value: starvation growth


title: maize tassel R1 rep 2

source_name: maize tassel R1

value: well-watered


title: maize tassel R1 rep 3


title: maize tassel R1 rep 1


title: maize tassel V16 rep 3

source_name: maize tassel V16


title: maize tassel V16 rep 1


title: Cwalk library from 1pg of 3C template amplified with Phi29 (ns_k562_V)

city: Rehovot

first: Pedro

last: Olivares-Chauvet

address: 234 Hertzl Street

department: Department of Computer Science and Applied Mathematics/Department of Biological Regulation

institute: Weizmann Institute of Science

description: processed data file:  k562.cadj.annot.gz

data_processing:
Cwalks were assembled using the cwalk pipeline with default parameters
3-way 4C maps were generated using UMI4C pipeline with a few modifications for filtering out fendchains of size three.
reads were mapped using bowtie2 with --reorder --local for cwalks and --reorder --end-to-end for 4C
Genome_build: hg19 and mm9
Supplementary_files_format_and_content: [Cwalk] cadj.annot: annotated adjacency; tab separated text file with adjacency information, linked to cwalks, annotated by the epigenomic features of TADs who are visited by the cwalk; 38 fields  [chr1]: chromosome of side 1  [start1]: chrosomal coordinate of side 1  [chr2]: chromosome of side 2  [start2]: chromosomal coordinate of side 2  [comp]: component (cwalk) id  [amp_i]: phi29 amplification well id  [fid1]: restriction fragment id of side 1  [fid2]: restriction fragment id of side 2  [span1]: span of component 1  [span2]: span of component 2  [seq_batch]: sequencing batch  [n]: number of hops  [trans_n]: number of trans interfaces  [cmer_doms.dist.x]: distance to closest TAD for side 1  [cmer_doms.id.x]: id of domain hosting side 1  [cmer_doms.k4me3.x]: signal of k4me3 in domain side 1  [cmer_doms.size.x]: size of domain side 1  [cmer_doms.tor.x]: time of replication for domain side 1  [cmer_doms.mode.x]: classification of active or inactive for domain side 1  [cmer_doms.dist.y]: distance to closest TAD for side 2  [cmer_doms.id.y]: id of domain hosting side 2  [cmer_doms.k4me3.y]: signal of k4me3 in domain side 2  [cmer_doms.size.y]: size of domain side 2  [cmer_doms.tor.y]: time of replication for domain side 2  [cmer_doms.mode.y]: classification of active or inactive for domain side 2  [dom_n]: number of domains visited by cwalk  [tss_1]: distance to the closest tss from side 1  [k4me3_1]: distance to the closest peak of k4me3 from side 1   [k27me3_1]: distance to the closest peak of k27me3 from side 1  [actenh_1]: distance to the closest active enhancer from side 1  [ctcf_1]: distance to the closest ctcf from side 1  [border_1]: distance to the closest domain border for side 1  [tss_2]: distance to the closest tss from side 2  [k4me3_2]: distance to the closest peak of k4me3 from side 2   [k27me3_2]: distance to the closest peak of k27me3 from side 2  [actenh_2]: distance to the closest active enhancer from side 2  [ctcf_2]: distance to the closest ctcf from side 2  [border_2]: distance to the closest domain border for side 2
Supplementary_files_format_and_content: [3-way 4C]  tadj file: triplet adjacency file ; 6 fields   [chr1]: chromosome side 1  [chr2]: chromosome side 2  [start1]: coordinate side 1  [start2]: coordinate side 2  [mol]: number of different molecules supporting this triplet  [bait]: bait name

source_name: K-562 cells

extract_protocol:
Between 25 to 50 x 10e7 cells were used to perform in-nucleus ligation 3C; biotin fill-in was omitted. Briefly, adherent cells (mES) were incubated in the presence of trypsin (Biological Industries 03-053-1) for 8-10 minutes max at 37°C and passed through a cell strainer after harvesting to ensure a single-cell suspension. Cells (including K562 from now on) were washed 1x with phosphate-buffered saline (PBS) and resuspended PBS/FBS 10% and cross-linked in formaldehyde final concentration of 2% for 5 minutes at room temperature. After quenching with 0.125 M glycine and wash with PBS, cells were incubated in permeabilization buffer (10 mM Tris–HCl pH 8, 10 mM NaCl, 0.2 % NP-40 alternative (CALBIOCHEM 492016), Protease Inhibitor Cocktail (P8340 Sigma)) for 60 minutes at 4°C while slowly mixing. Cells were split into 5 M cell aliquots and washed 2x with cold PBS. After the second wash, cell pellets were then flash frozen on liquid nitrogen. Pellets were resuspended on 175.5 µl H2O and 24.5 µl DpnII RE buffer 10x. After addition of 3 µl of 20% SDS (final concentration of 0.3%), cells were incubated for 60 minutes at 37°C while agitating (750 RPM). Triton X-100 20% was added to a final concentration of 1.8% and incubated for 60 min at 37°C. Aliquots were then digested with 15 µl HC DpnII (NEB 50,000 U/ml) ON. Cells were centrifuged for 5 minutes at 600 g and washed 1x with PBS. Incubation of pellets for 20 minutes at 65°C was performed in order to heat-inactivate any DpnII residue. In-nucleus ligation was then performed incubating cells on ligation mix (415 µl H2O, 5 µl BSA (10mg/ml NEB) and 5 µl T4 ligation enzyme NEB (2x106 U/ml)) ON at 16°C.  Cross-link was reversed by incubating aliquots with 10 mg/ml proteinase K (Roche) at 65°C ON followed by the addition of 15 µl of RNase A (Roche) for 45 minutes at 37°C. DNA was purified with AmpureXP SPRI beads 1x (Beckman Coulter; A63881) with two elution rounds of 100 µl each with the aim of size selecting for the high molecular weight portion of the sample.
C-walks. Serial dilutions (1:10) of 3C template were performed to reach a final concentration of 10 pg/µl stock template. REPLI-g single cell kit (Qiagen 150343) protocol for purified genomic DNA was used under the recommendation of the manufacturers with a few modifications. To avoid contamination, all operations before the amplification step were performed under strict hygienic conditions (TC hood), thorough DNA decontamination with DNAZap (ThermoFisher) and UV irradiation of laboratory utensils. A single C-walk amplification reaction consisted of ~1 picogram of 3C material. Typically for 100 reactions, 10 µl of 10 pg/µl stock were mixed into 16.56 µl of sterile TE buffer and denatured at RT for 3 minutes by mixing with buffer D1 (5.83 µl DLB buffer + 20.83 scH2O; both from REPLI-g sc kit). Denaturation of DNA was stopped by addition of 50 µl buffer N1 (7.5 µl Stop solution + 42.5 µl scH2O; both REPLI-g sc kit) and stored on ice. A final Master Mix was prepared by mixing 400 µl of reaction buffer (290 µl Reaction Buffer + 90 µl scH2O + 20 µl Phi29 DNA polymerase; from REPLI-g sc kit). Alternatively, the enzyme can be substituted with NEB Phi29 (M0269S) using the same volume. An aliquot of 5 µl of the Master Mix was taken as negative control. Master Mix and DNA template were then mixed and kept on ice. Aliquots of 5 µl from the Master Mix were split into single wells on 96-well plates and incubated for 2 hours and 50 minutes at 30°C followed by a heat inactivation step of 3 minutes at 65°C. Additional 45 µl of H2O were added to each well after spinning down for a few seconds. The amplified material was cleaned with SPRI beads (2.5x) and resuspended in 100 µl. Phi29-amplified material (300-700 ng per library) was sonicated in Bioruptor (program: 11 cycles of 5s on, 90s off) in 0.1 ml Bioruptor Microtubes (C30010015) to reach a DNA fragment size between 900-1,500 bp, peaking at 1,200 bp. The sonicated DNA (42.5 µl) was then subjected to end-repair reaction (5µl 10x end-repair buffer + 2.5 µl end-repair mix (NEB E6050L)) at 20°C for 30 minutes. The DNA was cleaned with SPRI beads (2.2x) and eluted in 38µl EB. A-tailing reaction was performed with 5 µl NEB buffer 2, 4 µl Klenow (NEB M0212M) and 10 µl dATP 10nM for 30 minutes at 37°C, cleaned with AmpureXP beads (2.2x) and eluted in 30 µl EB. DNA template was ligated with 5 µl Illumina indexed adapters 0.75 µM, 5 µl T4 quick ligase (NEB M2200) and 40 µl 10x ligase buffer for 15 minutes at 25°C. Ligated template was then cleaned with SPRI beads (1.3x) and eluted in 41 µl. Each indexed template was PCR amplified on a final volume of 50 µl with the following reagents: 1 µl dNTPs (10 mM), 2 µl Illumina enrichment primer I and II mix 10mM, 1 µl Pfu ultra II Fusion HS DNA polymerase (Promega 600670), 5 µl Pfu ultra II Fusion buffer (Promega 600670) and 200 ng of Phi29-amplified material. PCR program: 2 minutes 95°C, 14 cycles of 30s 95°C, 30s 55°C, 60s 72°C, final extension of 10 minutes 72°C. Following the PCR reaction, products were cleaned with SPRI beads (1x) and quantified. Libraries were pooled in groups of 8 in equal quantities and ran on a 1% agarose gel, not loading more than 1000 ng per lane. Gel was excised selecting for an 800-1200 bp band. DNA was purified using minelute gel extraction kit (QIAGEN). Samples were then pooled all together and paired-end sequenced using the Illumina platform.
3way 4C.  5-10 µg of 3C template was taken to a volume of 200 µl Elution Buffer (EB, 10mM Tris-HCl, pH 8) and was sonicated at 4°C using Bioruptor; program: 5 cycles of 25s on, 60s off. The sonicated material was inspected by running 10 µl on agarose gel to assure size distribution of 700-900 bp. The sonicated DNA was subjected to end-repair reaction: 20µl 10x end-repair buffer and 10µl end-repair mix (NEB E6050L) were added to the mix and incubated at 20°C for 30 minutes. The DNA was cleaned by SPRI (2.2x) beads and eluted in 76 µl EB. A-tailing reaction was performed with 10 µl NEB buffer 2, 4 µl Klenow (NEB M0212M), and 10 µl dATP 10 nM. Following A-tailing, the 5’ ends of the DNA were dephosphorylated with 2 µl of Alkaline Phosphatase (NEB M0290S) at 50°C for 60 minutes, and the DNA was cleaned with SPRI beads (2x), then eluted in 67 µl EB. The DNA template was ligated in 1,000 ng aliquots with 5 µl Illumina indexed adapters 15 µM (final concentration 0.4 µM), 10 µl quick ligase mix and 80 µl 10x buffer (NEB M2200). To release the non-ligated strand of the adapter, the DNA was denatured at 95°C for 3 minutes, moved immediately to ice and cleaned with SPRI beads (1x) to select for the UMI-4C DNA template . Two nested PCR reactions were used for UMI-4C library construction. The PCR reactions were performed in 50 µl volume with the following reagents: 10 µl GoTaq Flexi buffer (Promega M792A), 3 µl MgCl 25mM (Promega A3511), 25 µM dNTPs, 2 µl bait primer pool 100 µM (final concentration of each bait varies depending on the pool size), 2 µl Illumina enrichment primer II 10 mM (0.4 mM final concentration), 1 µl GoTaq (Promega M3008) and 200 ng UMI-4C DNA template. PCR program: 2 minutes 95°C, 20 cycles of 30s 95°C, 30s 56°C, 60s 72°C, final extension of 5 minutes 72°C. Following the PCR reaction, products were cleaned with SPRI beads (1x). The second PCR reaction was identical to the first with the only difference on the primer pool. Second primer targets a nested sequence of the 4C bait and is attached with the Illumina I adapter. The program for the second PCR reaction was the same but performed for only 18 cycles.The amplified DNA was cleaned with SPRI beads (0.7x) and the size distribution was inspected using Tapestation D1000 (Agilent Technologies). Typically, libraries had a size distribution around 800-1000 bps. The libraries were then pooled to 10 nM and were multiplexed with other libraries for paired-end sequencin

tag: cell line

tag: cell type

value: Lymphoblastoid leukemia

tag: lineage

value: Hematopoietic

tag: library

value: C-walks


title: maize tassel V14 rep 3

source_name: maize tassel V14


title: maize tassel V14 rep 2


title: maize tassel V14 rep 1


title: maize tassel V14 rep 4


title: maize tassel V12 rep 4

source_name: maize tassel V12


title: maize tassel V12 rep 3


title: maize leaf R1 drought rep 4

source_name: maize leaf R1 drought

value: leaf


title: maize ear V16 drought rep 3

source_name: maize ear V16 drought

value: ear


title: maize ear R1 drought rep 4

source_name: maize ear R1 drought


title: maize ear R1 drought rep 3


title: maize ear R1 drought rep 2


title: maize tassel V12 rep 1


title: maize ear R1 drought rep 1


title: maize leaf V16 drought rep 4

source_name: maize leaf V16 drought


title: maize ear V16 drought rep 1


title: maize ear V16 drought rep 4


title: maize leaf R1 drought rep 1


title: maize tassel V12 rep 2


title: maize ear V16 drought rep 2


title: maize tassel V16 rep 4


title: maize leaf V16 drought rep 3


title: maize tassel V16 rep 2


title: maize leaf V16 drought rep 2


title: maize ear V14 drought rep 4

source_name: maize ear V14 drought


title: maize ear V14 drought rep 3


title: maize ear V14 drought rep 1


title: maize ear V14 drought rep 2


title: maize leaf V16 drought rep 1


title: maize leaf V14 drought rep 4

source_name: maize leaf V14 drought


title: maize leaf V14 drought rep 2


title: maize leaf V14 drought rep 1


title: maize ear V12 drought rep 4

source_name: maize ear V12 drought


title: maize leaf R1 drought rep 2


title: maize leaf R1 drought rep 3


title: maize ear V12 drought rep 2


title: maize leaf V12 drought rep 4

source_name: maize leaf V12 drought


title: maize leaf V12 drought rep 1


title: maize leaf V12 drought rep 3


title: maize ear R1 rep 2

source_name: maize ear R1


title: maize ear R1 rep 4


title: maize leaf V12 drought rep 2


title: maize ear R1 rep 3


title: maize ear V16 rep 4

source_name: maize ear V16


title: maize ear R1 rep 1


title: maize leaf R1 rep 4

source_name: maize leaf R1


title: maize leaf R1 rep 2


title: maize ear V16 rep 3


title: maize leaf R1 rep 1


title: maize leaf V14 drought rep 3


title: maize ear V16 rep 1


title: maize ear V16 rep 2


title: maize leaf V16 rep 3

source_name: maize leaf V16


title: maize leaf V16 rep 4


title: maize leaf V16 rep 2


title: maize ear V14 rep 2

source_name: maize ear V14


title: maize ear V14 rep 3


title: maize ear V12 drought rep 3


title: maize leaf V16 rep 1


title: maize ear V14 rep 4


title: maize leaf V14 rep 4

source_name: maize leaf V14


title: maize ear V14 rep 1


title: maize leaf R1 rep 3


title: maize leaf V14 rep 2


title: maize leaf V14 rep 1


title: maize ear V12 rep 4

source_name: maize ear V12


title: maize ear V12 drought rep 1


title: maize leaf V14 rep 3


title: maize ear V12 rep 3


title: maize leaf V12 rep 1

source_name: maize leaf V12


title: maize ear V12 rep 2


title: maize leaf V12 rep 2


title: maize leaf V12 rep 3