title: ALL dasatinib IC90 16x biological replicate A

first: Boyang

address: 500 Main Street

institute: MIT

data_processing:
Basecalls performed using CASAVA v1.7.0
Reads were trimmed to remove adapters and low quality reads using Trimmomatic v0.33
Alignments (to mm9) were performed using TopHat v2.0.12 with the following parameters: --no-novel-juncs --segment-length 20 --read-realign-edit-dist 0. ABL1 was aligned to NM_005157.5 separately using BWA v0.7.10
Differential expression was performed as follows: BAM files sorted and indexed using SAMtools, reads were counted using HTSeq v0.6.1, and differential expression analyses were performed using DESeq R package
Genome_build: mm9
Supplementary_files_format_and_content: expression counts from HTSeq

source_name: Ph+ ALL cells

growth_protocol: Murine derived Ph+ALL cell line containing BCR-ABL1 p185 was cultured in RPMI medium supplemented with 10% FBS, 4 mM L-glutamine, 5 μM β-mercaptoethanol.

extract_protocol:
RNA was extracted using QIAshredder and RNeasy Kit (Qiagen).
Quality of RNA was assessed with BioAnalyzer (Agilent Technologies) and library was prepared with Illumina TruSeq.

treatment_protocol: Cells were plated at 0.5 million cells/mL and treated at desired drug concentrations. Cells were monitored each day. Upon outgrowth (i.e. cell density reaching 4-5 million cells/mL), cells were 1) frozen down, 2) allowed to recover in no-drug medium, or 3) plated again at 0.5 million cells/mL and treated at the next drug dose. For cells in drug-selection condition, medium was changed every week.

tag: treatment

value: dasatinib IC90 16x


title: ALL dasatinib IC90 16x biological replicate C

status: Public on Apr 05 2016

type: SRA

city: Cambridge

last: Zhao

state: MA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus


title: ALL dasatinib IC90 16x biological replicate B


title: ALL (DMSO 16x)

value: DMSO (16x)


title: ALL dasatinib IC90 1x biological replicate A

value: dasatinib IC90 1x


title: LAN6-ATRX-XL-MNase_ChIP

city: New York

first: Emily

last: Bernstein

state: NY

address: 1470 Madison Avenue, 6th floor Rm 302

department: Oncological Sciences

institute: Mount Sinai School of Medicine

library_source: genomic

data_processing:
Basecalls performed using Illumina's Real-Time Analysis (RTA) Software version 1.18.64
Sequence reads were aligned to the GRCh37 (hg19) assembly using Bowtie v1.0.0 with the following parameters: -M 10 -k 1 -n 2 -l 70 --best
Redundant reads were eliminated using the macs2 (v2.1.0) filterdup option with default parameters.
The optimal normalization factor between ChIP and Input samples was calculated with the R NCIS package v1.0.1 using a shift size of 75bp.
Peak calling was performed with macs2 callpeak using the following options: --ratio X --broad --bdg -q 0.0005 --broad-cutoff 0.0005, where X is the normalization factor estimated by NCIS
ChIP/Input fold enrichment pileups were created with the macs2 bdgcmp tool using the -m FE option and converted to bigWig files using the bedGraphToBigWig program (v4) from the UCSC binaries.
All peaks overlapping with the Encode blacklisted regions were eliminated.
Genome_build: GRCh37
Supplementary_files_format_and_content:
- ChIP/Input fold enrichment bigWig file obtained with macs2 bdgcmp, as described.
- Bed file with significant peaks from macs2

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: LAN6 cells were growth in 15cm plates at maximum confluency of ~10x10^6 cells per plate in RPMI + 10%FBS + 1x Penicillin/Streptomycin (gibco). 20 million cells were used per ChIP

extract_protocol:
XL-MNase ChIP: Cross-linked MNase ChIP was performed using the Cell Signaling SimpleChIP Enzymatic Chromatin IP Kit with Magnetic beads (cat. #9003). The vendor’s instructions were followed with some changes. Briefly: 20 million LAN6 cells were cross-linked for 10 minutes at room temperature in complete media, 100mM NaCl, 1mM EDTA pH 8.0, 50mM HEPES pH 8.0, 1% formaldehyde. Glycine was added to a final concentration of 125mM to stop the cross-linked reaction. The cells were washed once with cold PBS. Nuclei were obtained lysing the cells with 4ml of buffer A + DTT + Protease Inhibitor Cocktail (PIC) for 10 minutes at 4°C. Nuclei were washed with 3 ml of ice-cold buffer B + DTT. Nuclei were resuspended in 1ml of ice-cold buffer B + DTT, and digested with 8,000 gel U of Micrococal Nuclease from NEB (cat. #M0247S) at 37°C for 20 minutes. The reaction was stopped adding EDTA for a final concentration of 50nM and incubating on ice for 5 minutes. The nuclei were pelleted, and resuspended in 1ml of ChIP buffer + PIC + PMSF and incubated on ice for 10 min. The nuclei were split in two tubes and lysed by light sonication in a Bioruptor Twin (4 cycles, 20 sec ON/OFF, high power). The chromatin was cleared by centrifugation and a sample taken and processed (see bellow) to measure the concentration of the chromatin. 40ug of chromatin were diluted to 100ng/ul with ChIP buffer. 1% of the diluted chromatin was took as Input and the rest incubated with specific antibodies overnight at 4°C. 40 ul of ChIP-grade Magna ChIP protein A/G magnetic beads from Millipore (cat. #16-663) were added and incubated for 3 hours at 4°C. The beads were washed 3 times with 1ml of ChIP buffer, 1 time with 1ml of ChIP buffer + 350 mM NaCl, 1 time with 1 ml of LiCl buffer (10mM Tris-HCl pH 8.0, 1mM EDTA pH 8.0, 1% sodium deoxycholate, 1% Igepal, 250mM LiCl, not included in the kit) and 1 time with 1ml of TE. The beads and the Input samples were incubated in 100ul of Elution buffer for 30 min in a thermomixer at 65°C, 1200 rpm. The eluted material was incubated for 1 hour at 37°C 1ul of RNAse A (10mg/ml), followed with a 3 hour incubation at 55°C with 3ul of Proteinase K (20mg/ml). The cross-linked was reversed incubating the eluted material for 4-6 hours at 65°C. The DNA was purified using the MinElute PCR purification kit from Qiagen following the kit’s instructions and eluted in 30ul of Qiagen’s elution buffer. The amount and the pattern of the obtained DNA was determined using an Agilent 2100 Bionanalyzer High Sensitivity Kit.
25ng of ChIPed or Input DNA were processed for library preparation from each sample. All enzymes used are from NEB unless stated otherwise. 1. DNA was End Repaired in 50ul reaction containing 40ul of DNA, 5ul T4 DNA ligase buffer with 10mM ATP, 2ul 10mM dNTP, 1ul Klenow DNA pol (1u/ul), 1ul T4 DNA pol and 1ul T4 PNK. The reaction was incubated for 30min at 20C. Products were purified in Qiagen PCR purification column in 35ul. 2. Adding over-hang A to the 3’ end in 50ul reaction containing 34ul DNA, 5ul 10X NEB buffer 2, 10ul 1mM dATP and 1ul Klenow exo-. The reaction was incubated for 30min at 37C. Products were purified in Qiagen PCR Mini elute purification column in 14ul. 3. Adapter ligation in 30ul reaction containing 13ul DNA, 15ul 2X T4 DNA ligase buffer, 1ul of 1:200 dilution of Illumina true seq DNA sample prep kit and 1ul quick T4 DNA ligase. The reaction was incubated for 15min at 25C. Products were purified in Qiagen Mini elute PCR purification column in 15ul. 4. Size selection. Ligated products were loaded onto 2% Agarose gel (1XTAE), and run for 1 hour at 120V. DNA was viewed on low-wave trans illuminator and size selected at the 300-400bp range using the Kb+ invitrogen DNA ladder. Products were purified in Qiagen PCR purification column in 25ul. 5. PCR amplification was done in 50ul reaction containing 25ul 2X master mix (2X Phusion HF, FINZYMES), 2ul PCR primers (illumina) and 23ul DNA. PCR program according to the illumina protocol. Products were purified in Qiagen Mini elute PCR purification column in 15ul. PCR products were then run on an Agilent DNA 1000 chip for quantification and submitted for sequencing on the NextSeq 500 illumina platform.

tag: cell line

tag: protocol

value: XL-Mnase ChIP

tag: fixation

value: 10 mins RT, 1% formaldehyde

tag: phenotype

value: Wild Type

tag: chip antibody

value: ATRX (Abcam, ab97508, 6ug)


title: 36hpf soma

city: Muesnter

first: Katsiaryna

last: Tarbashevich

address: Von-Esmarch Str 56

country: Germany

institute: Institute for Cell Biology

description: processed data file: HT data 36hpf.xls

data_processing:
The reads were filtered and trimmed for low quality reads and then mapped to transcriptome using seqmap for 7hpf samples (bowtie for the 36hpf samples) and generated expression value using rseq.
Differential expression was detected using DEseq package of bioconductor.
Genome_build: Zv8
Supplementary_files_format_and_content: Excel files with Gene Ids and RNA abundance for each sample

organism: Danio rerio

source_name: somaitic cells_36hpf

extract_protocol:
PGCs and somatic cells were FACSed and total RNA was extacted using Arcturus RNA extraction kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: AB

tag: tissue

value: embryo

tag: cell type

value: somatic cell

tag: developmental stage

value: 36 hpf


title: ALL (DMSO 1x)

value: DMSO (1x)


title: ALL parental replicate A


title: ALL dasatinib IC90 1x biological replicate C


title: ALL dasatinib IC90 1x biological replicate B


title: ALL parental replicate B


title: 7hpf soma

description: processed data file: HT data 7hpf.xls

source_name: somaitic cells_7hpf

value: 7 hpf


title: MM1S_DMSO_3

city: Oxford

first: Udo

last: Oppermann

state: Oxfordshire

address: Botnar Research Centre, Nuffield Orthopaedic Centre, Windmill Road

department: Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences

country: United Kingdom

institute: University of Oxford

data_processing:
Libraries were sequenced on the Illumina NextSeq 500 and Basecalling and demultiplexing performed by their standard pipelines
Adaptors and low quality reads were trimmed using Trim_galore version 0.40
Aligned to GRCh37 using Bowtie v 1.1.2 options -m3 -y --best
Peaks called using macs2 v 2.1.0 and the --gapped option
Homer v4.8 used to create tag directories of all samples and produced bedgraph data normalised to 10^7 reads.
Genome_build: GRCh37
Supplementary_files_format_and_content: bedgraph.gz - coveraged data in bedgraph format noramlised to 10e7 reads.  Gapped Peaks file;  is in BED12+3 format which contains both the gapped region and narrow peaks. The 5th column is 10*-log10qvalue, to be more compatible to show grey levels on UCSC browser. Tht 7th is the start of the first narrow peak in the region, and the 8th column is the end. The 9th column should be RGB color key, however, we keep 0 here to use the default color, so change it if you want. The 10th column tells how many blocks including the starting 1bp and ending 1bp of gapped regions. The 11th column shows the length of each blocks, and 12th for the starts of each blocks. 13th: fold-change, 14th: -log10pvalue, 15th: -log10qvalue.

source_name: MM1S Multiple Myeloma cells_DMSO

growth_protocol: Cells were grown under standard conditions in RMPI with 10% FGS and 2mmol glutamine supplemented

extract_protocol:
Cells were fixed in 1% formaldehyde for 8 minutes at room temperature, sonicated on a Bioruptor Pico, incubated for an hour with pre-blocked protein A seppharose beads before being incubated with 1ug of antibody overnight at 4 degrees.  The lysate was allowed to incubate with protein A beads before being washed and subejcted to proteinase K digestion
Libraries were constructed using NEBnext Ultra DNA library prep kit according to manufactures instructions

treatment_protocol: Cells were treated with either KDM5-C70 50uM for 7 days or vehicle control

value: Multiple Myeloma cell line

tag: treated with

value: DMSO (vehicle control)

tag: chip antibody vendor

value: Millpore

tag: chip antibody cat. #

tag: chip antibody lot #


title: 36hpf PGC

description: processed data file: HT data 36hpf.xls

source_name: germ cells_36hpf

value: germ cell


title: Control, rep3 (Paired-end)

city: Los Angeles

first: Yi

last: Xing

state: CA

address: 650 Charles E. Young Dr. South

department: Department of Microbiology, Immunology, & Molecular Genetics

institute: UCLA

description: CTRL

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to Ensembl human transcript (release 72) then hg19 whole genome using tophat v1.4.1 with parameters -a 8 -m 0 -I 300000 -p 8 -g 20 --library-type fr-firststrand -initial-read-mismatches 3 --segment-mismatches 2
Fragments Per Kilobase of exon per Million fragments mapped (FPKM) were calculated using cuffdiff v2.2.0 with uniquely and properly mapped reads.
Genome_build: hg19
Supplementary_files_format_and_content: an excel file includes FPKM values for each Sample …

source_name: Human lung cancer

extract_protocol:
Total RNA were extrated from cells using TRIzol reagent (ThermoFisher 15596) according to the protocol.
cDNA libraries for sequencing were prepared using the Illumina True-seq Stranded mRNA kit and protocol.

value: Lung

tag: genotype

value: CTRL


title: 7hpf PGC

description: processed data file: HT data 7hpf.xls

source_name: germ cells_7hpf


title: Control, rep2 (Paired-end)

description: CTRL


title: RBM47 KD, rep3 (Paired-end)

description: RBM47 KD

value: RBM47 KD


title: RBM47 KD, rep1 (Paired-end)

description: RBM47 KD


title: Control, rep1 (Paired-end)

description: CTRL


title: iTreg_CPI703_H3K27ac

status: Public on Apr 06 2016

first: Barbara

middle: M

last: Bryant

address: 215 First Street

institute: Constellation Pharmaceuticals

data_processing:
50-nucleotide sequence reads were aligned to the hg19 genome using the BWA algorithm with default settings. Only reads that passed Illumina’s purity filter, aligned with no more than 2 mismatches and mapped uniquely to the genome, were used in subsequent analyses.
The aligned read files were sorted and duplicates removed using sort and rmdup functions from samtools version 0.1.18 (Li et al., 2009).
WIG files were generated using IGVTools (version 2.2.2) count function with a window size of 25 nucleotides, an extension of 100 beyond the 50-nucleotide read length, and genome hg19 (Robinson et al., 2011; Thorvaldsdottir et al., 2013). The WIG files were scaled assuming an effective genome length of 2.79B base pairs, so that the mean signal would be 1.0.
Genome_build: hg19
Supplementary_files_format_and_content: WIG files and corresponding TDF files suitable for visualization using the Integrative Genomics Viewer (IGV) available from the Broad Institute.

source_name: Induced regulatory T cells

growth_protocol: Leukopak samples were procured from the Biological Specialty Corporation (Colmar, PA) and peripheral blood mononuclear cells (PBMCs) were isolated by Ficoll (GE Biosciences) density gradient centrifugation. Naive CD4+ CD45RA+ T cells were isolated from PBMCs to a purity > 98% using Miltenyi naive human T cell isolation kits (130-094-131, Miltenyi Biotech). Isolated cells were cultured at 10^6 cells/mL under Treg-polarizing conditions, using Human T-Activator CD3/CD28 Dynabeads® (11132D, Invitrogen), human TGFb at 10 ng/mL and human IL-2 at 10 U/mL (100-B and 202-IL, respectively; R&D Biosystems).

extract_protocol:
For ChIP-seq, cells were pelleted, fixed in 1% formaldehyde for 10 mins, lysed and sonicated. Chromatin samples were precleared with Protein A Dynabeads (Life Technologies), and incubated overnight at 40C with anti-H3K18 Ac (9675, Cell Signaling), anti-H3K27 Ac (ab4729, Abcam), and anti-H3K4 Me3 (Abcam ab8580). Chromatin-antibody complexes were precipitated using Protein A Dynabeads followed by washes in RIPA buffer and Tris/ EDTA. Samples were digested with RNAase A, treated with Proteinase K and 10% SDS, followed by cross-link reversal at 650C. DNA was purified using MinElute PCR purification kits (Qiagen).
DNA libraries for ChIP-seq were prepared using Ovation Ultralow DR Multiplex System kits (0330-32, NuGEN) followed by Illumina sequencing at the MIT BioMicro Center.

treatment_protocol: Naïve human CD4+ T cells were treated with 4 mM CPI703 or DMSO under Treg polarizing conditions (described above) for 4 days.

value: Treg cell

value: anti-H3K27ac (Abcam, catalog# ab4729, lot# GR132150-1)


title: CTRL, rep3 (Paired-end)

description: CTRL


title: H3K36ac_Col_wt_Rep2

city: Uppsala

first: Minerva

middle: Susana

last: Trejo Arellano

state: Uppsala

address: Almas Allé 5

department: Plant Biology

country: Sweden

institute: SLU

description:
Chrosslinked Chromatin
coverageNormSize_H3K36ac_Col_wt.bw

data_processing:
Quality control was done with an in-house R script
Demultiplexing and adapter trimmng was done with reaper (EMBL-EBI)
Clean reads of the replicates were merged and mapped to Arabidopsis TAIR10 genome using Bowtie2
SAM file output from bowtie was converted to BAM format using SAMTOOLS (version 1.4) and imported into R.
Identical reads present more than 25 times were considered as PCR artifacts and filtered out using the filterDuplReads function from package HtSeqTools
ChIP-seq coverage was calculated using the coverage function from R
Normalization of the coverage to identical sequencing depth
Subsequent analysis were performed in R. The used gene models were from TAIR10 gff annotation file
Genome_build: TAIR10
Supplementary_files_format_and_content: BigWig files of coverage

organism: Arabidopsis thaliana

source_name: leaf

growth_protocol: Leaf number six of plants grown for 35 days under short day conditions (8 h light) was harvested at zeitgeber time ZT=7 and used for nuclei isolation.

extract_protocol:
Native Chromatin Immunoprecipitation (N-ChIP) was performed following a slightly modified procedure of (Bernatavichute et al, 2008). Cross-linked chromatin immunoprecipitation (X-ChIP) assays were performed as described (Exner et al, 2009).
Libraries were generated using the Microplex Library Preparation kit (Diagenode) following the manufacturer's protocol using 1 ng of starting material.

tag: ecotype

value: Columbia

value: WT

tag: antibody

value: Anti-H3K36ac 39379 (ActiveMotif)

tag: biological replicate

tag: demultiplexbarcode

value: CTTGTA


title: H3_1

description:
Native Chromatin
H3.bw

value: Anti-H3 MAB3422 (Upstate/Millipore)


title: H3K36ac_1

description:
Native Chromatin
H3K36ac.bw


title: Input_2

description:
Native Chromatin
Input.bw


title: H3K36ac_2

description:
Native Chromatin
H3K36ac.bw


title: H3K36ac_Col_wt_Rep1


title: ESRP KD, rep3 (Paired-end)

description: ESRP KD

tag: cell line

value: ESRP KD


title: ESRP KD, rep1 (Paired-end)

description: ESRP KD


title: ESRP KD, rep2 (Paired-end)

description: ESRP KD


title: CTRL, rep2 (Paired-end)

description: CTRL


title: H3_Col_wt_Rep2

description:
Chrosslinked Chromatin
coverageNormSize_H3_Col_wt.bw

value: Anti-H3 07-690 (Upstate/Millipore)

value: GGCTAC


title: CTRL, rep1 (Paired-end)

description: CTRL


title: Day7, rep3 (Paired-end)

tag: time point

tag: treatment

value: DOX


title: H3_Col_wt_Rep1


title: Day7, rep2 (Paired-end)


title: input_Col_wt_Rep2

description:
Chrosslinked Chromatin
coverageNormSize_input_Col_wt.bw

value: TAGCTT


title: PHTu_3_13

city: Columbia

first: Toshihiko

last: Ezashi

state: MO

address: 240a CS Bond Life Sciences Center

department: Animal Sciences

institute: University of Missouri-Columbia

description: undifferentiated primary trophoblast

data_processing:
The libraries were sequenced as single-end, 50 base read length on an Illumina HiSeq 2500 (Illumina Inc.) with an average read count of 21-28 million reads per sample.
Initial base calling and quality filtering of the mRNA-Seq reads generated with the Illumina analysis pipeline (fastQ format) was performed using the FastxToolkit (http://hannonlab.cshl.edu/fastx_toolkit/) and adapters trimmed using CutAdapt (https://code.google.com/p/cutadapt/).
Reads that mapped to the human mitochondrial genome or to Phix were removed using Bowtie (http://bowtie-bio.sourceforge.net/index.shtml).
Reads were mapped (tophat v2.0.13; http://ccb.jhu.edu/software/tophat/index.shtml) to the reference genome (from Ensembl, v78; http://www.ensembl.org/index.html) Homo_sapiens.GRCh38.dna.primary_assembly.fa using Homo_sapiens.GRCh38.78.gtf as annotation.
Tests for differential expression were made using cuffdiff v2.2.1.
Genome_build: GRCh38
Supplementary_files_format_and_content: Cuffdiff output

source_name: term placenta

growth_protocol: Primary trophoblasts were isolated from third trimester placentas after Trypsin/Dispase/DNaseI digestion followed by purification on a Percoll gradient. Primary trophoblasts were cultured for 9h (undifferentiated) to 48h (differentiated)  in DMEM supplemented with 10% FBS (Fetal Bovine Serum), 20 mM HEPES pH 7.4, and a mixture of penicilin-streptomycin-fungizone. Cells were maintained at 37ºC/5% CO2.

extract_protocol:
Total RNA were prepared using miRNeasy Mini Kit following the manufacturer's instructions
Libraries were constructed following the Illumina’s protocol with reagents supplied in Illumina’s TruSeq mRNA stranded sample preparation kit.

value: placenta

tag: gender

value: male

tag: time in vitro culture

value: 9 h

tag: date of tissue preparation


title: input_Col_wt_Rep1


title: RBM47 KD, rep2 (Paired-end)

description: RBM47 KD

tag: tissue

value: Lung


title: Day6, rep3 (Paired-end)


title: H3K36ac_Col_sdg8_Rep2

description:
Chrosslinked Chromatin
coverageNormSize_H3K36ac_Col_sdg8.bw

value: GATCAG


title: Day7, rep1 (Paired-end)


title: H3K36ac_Col_sdg8_Rep1


title: Day6, rep2 (Paired-end)


title: H3_Col_sdg8_Rep2

description:
Chrosslinked Chromatin
coverageNormSize_H3_Col_sdg8.bw

value: ACTTGA


title: H3_Col_sdg8_Rep1


title: Day6, rep1 (Paired-end)


title: Day5, rep3 (Paired-end)


title: input_Col_sdg8_Rep2

description:
Chrosslinked Chromatin
coverageNormSize_input_Col_sdg8.bw

value: CAGATC


title: Input_1

description:
Native Chromatin
Input.bw

value: Columbia


title: input_Col_sdg8_Rep1


title: Day5, rep1 (Paired-end)


title: Day5, rep2 (Paired-end)


title: Day4, rep1 (Paired-end)


title: H3K36me3_ws_wt_Rep1

description:
Chrosslinked Chromatin
coverageNormSize_H3K36me3_ws_wt.bw

value: Wassilewskija

value: WT

value: Anti-H3K36me3 pAb-058-050 (Diagenode)

value: GCCAAT


title: Day3, rep3 (Paired-end)


title: Day4, rep2 (Paired-end)


title: H3K36me3_ws_wt_Rep2


title: Day3, rep1 (Paired-end)


title: input_ws_wt_Rep2

description:
Chrosslinked Chromatin
coverageNormSize_input_ws_wt.bw

value: TGACCA


title: H3K36me3_ws_gcn5_Rep2

description:
Chrosslinked Chromatin
coverageNormSize_H3K36me3_ws_gcn5.bw

value: TTAGGC


title: input_ws_wt_Rep1


title: H3K36me3_ws_gcn5_Rep1


title: Day2, rep3 (Paired-end)


title: H3_ws_gcn5_Rep2

description:
Chrosslinked Chromatin
coverageNormSize_H3_ws_gcn5.bw

value: Anti-H3 07-690 (Upstate/Millipore)

value: CGATGT


title: H3_ws_wt_Rep2

description:
Chrosslinked Chromatin
coverageNormSize_H3_ws_wt.bw

value: ACAGTG


title: Day2, rep1 (Paired-end)

value: DOX


title: Day1, rep3 (Paired-end)


title: Day2, rep2 (Paired-end)


title: H3_ws_gcn5_Rep1


title: input_ws_gcn5_Rep2

description:
Chrosslinked Chromatin
coverageNormSize_input_ws_gcn5.bw

value: ATCACG


title: Day1, rep1 (Paired-end)


title: Day4, rep3 (Paired-end)


title: H3_ws_wt_Rep1


title: Day3, rep2 (Paired-end)


title: Smyd1 CKO4_RNAseq

city: Houston

first: M. David

last: Stewart

state: TX

address: 4800 Calhoun Rd

institute: University of Houston

data_processing:
Raw reads were aligned to the mouse genome using tophat v2.0.10
Gene expression was calculated using cufflinks v2.1.1 and was expressed as FPKM
Genome_build: mm9
Supplementary_files_format_and_content: expression profiles (fpkm) in txt format

source_name: tibialis anterior muscle

extract_protocol:
Tibialis anterior muscles dissected in PBS and flash frozen in liquid nitrogen.  RNA was extracted using Trizol reagent. Total RNA (100 ng) was depleted of ribosomal RNA using the ScriptSeq Complete Gold kit from Epicentre (Cat. No. SCL24EP).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: muscle (tibialis anterior)

tag: age

value: 6-weeks old

value: Myf6 cre/+; Smyd1 flox/-


title: Smyd1 CKO5_RNAseq


title: Smyd1 CKO6_RNAseq


title: No Dox, rep3 (Paired-end)

description: No Dox (no DOX treatment)

value: Lung

value: No Dox (no DOX treatment)


title: No Dox, rep2 (Paired-end)

description: No Dox (no DOX treatment)


title: Smyd1 CKO3_RNAseq


title: Smyd1 CKO2_RNAseq


title: s2_gDNA 41

city: Waltham

first: Aoife

last: McMahon

state: Massachusetts

address: 415 South St

department: Biology

institute: Brandeis University

description: control

data_processing:
Basecalls performed using CASAVA version 1.7
RNA editing analysis is performed as described in Rodriguez et al, 2012, with some modifications.
In brief, sequencing reads are trimmed with Trimmomatics (Bolger et al., 2014) by 6bp at each end, additional low quality bases from either end are removed and reads with average quality score of 30 or greater are kept.  Reads were aligned to the Drosophila genome (Release 5/dm3) using Genomic DNA reads are aligned using bowtie2 (parameters: --sensitive) to the reference genome (Release 5/dm3) and RNA sequencing reads are aligned using tophat2 (Trapnell et al., 2009) (parameters: -m 1 -p 5 -g 2 -I 50000 --microexon-search --no-coverage-search).   Only events with minimum 20 reads and 10% editing were considered to be an editing events. Code for RNA editing analysis is available here: https://github.com/rosbashlab/TRIBE
The gtf file used throughout the analysis was downloaded from iGenomes (via Illumina, dm3 build).  The editing analysis pipeline used RefSeq annotation of genes, which were downloaded from UCSC genome browser.
CLIP sequence reads were aligned using Novoalign, (novoalign -t 85 -l 23 -s 1 -r None).  Subsequent bioinformatic analysis of CLIP data was performed as described in Moore et al. (2014) and using the CLIPper algorithm (available at https://github.com/YeoLab/clipper) with default settings.
Genome_build: Release 5/dm3
Supplementary_files_format_and_content: RNA editing sites are provided in bedgraph file format, (Chromosome, co-ordinate, co-ordinate, edit %, edit%_number of total reads).  CLIP

organism: Drosophila melanogaster

source_name: s2 cell

extract_protocol: s2 cell mRNA libraries were prepared using Illumina Truseq kits according to manufacturers protocol.  S2 cell nascent RNA libraries were prepared according to Khodor et al. (2011). Neuronal cell sorting libraries were prepared according to Abruzzi et al, 2015.  CLIP libraries were prepared according to Cho et al., 2012)

tag: cell type

value: s2 cell

tag: tribe protein expression


title: No Dox, rep1 (Paired-end)

description: No Dox (no DOX treatment)


title: s2_CLIP_Hrp48-ADARcd-V5 39

description: CLIP performed according to Cho et al., 2012, with some modification. Antibody was mouse monoclonal anti-V5 antibody (Invitrogen, 46-1157).

value: induced


title: Smyd1 CKO1_RNAseq


title: neuron_elav_Hrp48_TRIBE_mRNA 34

description: Fluorescently labelled neurons were isolated from dissected, triturated fly brains by manual sorting using a glass micro-pipette, as described in Abruzzi et al. (2015)

molecule: polyA RNA

source_name: neuron

value: neuron (elav gal4 driver)

value: expressed


title: s2_CLIP_Hrp48 40

description: CLIP performed according to Cho et al., 2012, with some modification. Antibody was a gift from Donald Rio, (Hammond et al., 1997).


title: control4_RNAseq

value: Myf6 cre/+; Smyd1 flox/+


title: neuron_elav_Hrp48_TRIBE_mRNA 33

value: not expressed


title: control5_RNAseq


title: control6_RNAseq


title: input_ws_gcn5_Rep1

value: Wassilewskija


title: Day1, rep2 (Paired-end)


title: neuron_TH_Hrp48_TRIBE_mRNA 32

value: dopaminergic neuron (TH gal4 driver)


title: control2_RNAseq


title: Wild-type 2

city: San Francisco

first: Deepak

last: Srivastava

address: 1650 Owens St

institute: J David Gladstone Institutes

data_processing:
Aligned to mouse genome build "mm9" using the program Tophat 2.0.4, using ENSEMBL annotation. Specific settings: --min-anchor=5 --segment-length=25 --no-coverage-search --segment-mismatches=2 --splice-mismatches=2 --microexon-search --num-threads=6 --mate-inner-dist=50
Per-gene counts and FPKM values provided by "DefinedRegionDifferentialSeq" version 8.6.4, part of the USeq software package (http://useq.sourceforge.net/).
No additional filtering was performed.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM and raw count data, tables in Excel format.

source_name: WT_outflow tract

extract_protocol:
RNA Isolation by Qiagen mini kit
NUGEN

tag: strain background

tag: genotype/variation

value: wild type

value: heart; outflow tracts

tag: barcode

value: CCTTCA

tag: lane

value: lane 1

tag: replicate number

value: Replicate 2


title: Wild-type 3

value: AAGACG

value: lane 2

value: Replicate 3


title: control3_RNAseq

value: muscle (tibialis anterior)

value: 6-weeks old

tag: genotype


title: neuron_pdf_Hrp48_TRIBE_mRNA 30

value: circadian neuron (pdf gal4 driver)


title: neuron_pdf_Hrp48_TRIBE_mRNA 29


title: neuron_TH_Hrp48_TRIBE_mRNA 31


title: control1_RNAseq


title: Mutant 3

source_name: mutant_outflow tract

value: Anterior Heart Field (AHF)-conditional Mef2c Knockout

value: GGATGT


title: s2_Hrp48_mut_TRIBE_mRNA_rep1 27

value: s2 cell

value: induced


title: s2_Hrp48_mut_TRIBE_mRNA_rep2 28


title: Wild-type 4

value: CCTCGG

value: Replicate 4


title: Mutant 2

value: TTCAGC


title: s2_Hrp48_mut_TRIBE_mRNA_rep2 26

value: uninduced


title: s2_ADARcat_domain_mRNA_rep1 21


title: s2_NonA-TRIBE_Nascent_rep1 20

description:
nuclear RNA
Nascent RNA was extracted from S2 cells, according to Khodor et al. (2011) and depleted of ribosomal RNA according to Pennington et al. (2013) and mRNA (two rounds of pA depletion using Invitrogen Dynabeads Oligo dT, according to manufacturer’s protocol).

tag: rna

value: nascent RNA


title: s2_ADARcat_domain_mRNA_rep2 24


title: s2_Hrp48_mut_TRIBE_mRNA_rep1 25


title: s2_NonA-TRIBE_Nascent_rep2 19


title: Mutant 4

value: heart; outflow tracts

value: TTCGCT


title: s2_ADARcat_domain_mRNA_rep1 23


title: neuron_Cha_FMR1_TRIBE_mRNA 38

value: cholinergic neuron (Cha gal4 driver)

value: expressed


title: s2_ADARcat_domain_mRNA_rep2 22


title: Mutant 1

value: GGACCC

value: lane 1

value: Replicate 1


title: neuron_GAD_FMR1_TRIBE_mRNA 36

value: GABAergic neuron (GAD gal4 driver)


title: Wild-type 1

value: wild type

value: AAGGGA


title: s2_NonA-TRIBE_Nascent_rep1 18

value: s2 cell


title: s2_Hrp48-TRIBE_Nascent_rep1 16


title: s2_WT_Nascent_rep1 15


title: s2_NonA-TRIBE_mRNA_rep2 14

value: induced


title: s2_NonA-TRIBE_mRNA_rep1 13


title: neuron_Cha_FMR1_TRIBE_mRNA 37

value: not expressed


title: s2_NonA-TRIBE_mRNA_rep1 11


title: s2_dFMR1-TRIBE_mRNA_rep2 10


title: neuron_GAD_FMR1_TRIBE_mRNA 35


title: s2_Hrp48-TRIBE_mRNA_rep1 5


title: s2_dFMR1-TRIBE_mRNA_rep1 9


title: s2_Hrp48-TRIBE_mRNA_rep2 6


title: s2_dFMR1-TRIBE_mRNA_rep1 7


title: s2_Hrp48-TRIBE_mRNA_rep2 4


title: s2_Hrp48-TRIBE_mRNA_rep1 3


title: s2_WT_mRNA_rep2 2


title: s2_Hrp48-TRIBE_Nascent_rep1 17


title: LAN6-Input_control-Native_ChIP

extract_protocol:
Native ChIP: Native ChIP was performed essentially as described (Hasson et al., Nat Struct Mol. Biol, 2013) with minor changes. Briefly: 20 million cells were gently trypsinized and resuspended in 2 ml of ice-cold buffer I (0.32 M sucrose, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 15 mM Tris, pH 7.5, 0.5 mM DTT, 0.1 mM PMSF and 1:1,000 protease inhibitor cocktail (Sigma)). Ice-cold buffer I supplemented with 0.1% IGEPAL (2 ml) was added, and samples were placed on ice for 8 min. The resulting 4 ml of nuclei was gently layered on top of 8 ml of ice-cold buffer III (1.2 M sucrose, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 15 mM Tris, pH 7.5, 0.5 mM DTT, 0.1 mM PMSF and 1:1,000 protease inhibitor cocktail) and centrifuged at 10,000g for 20 min at 4°C. Pelleted nuclei were resuspended in Native buffer A (0.34 M sucrose, 15 mM HEPES, pH 7.4, 15 mM NaCl, 60 mM KCl, 4 mM MgCl2, 1 mM DTT and 1:1,000 protease inhibitor cocktail (Sigma)) to 400 ng/μl. MNase (Affymetrix) digestion reactions were carried out on chromatin (~100 μg), using ~0.1 U/μg chromatin in Native buffer A supplemented with 3 mM CaCl2 for 10 min at 37 °C. The reaction was quenched with 5 mM EGTA. The chromatin was resuspended in 10 mM EDTA, pH 8.0, 1 mM PMSF and 1:1,000 protease inhibitor cocktail and rotated at 4 °C for 2–4 h. The mixture was adjusted to 500 mM NaCl, allowed to rotate for another 45 min and then centrifuged at 13,500g for 10 min, yielding nucleosomes in the supernatant. Chromatin (40 μg per ChIP) was diluted to 100 ng/μl with Native buffer B (20 mM Tris, pH 8.0, 5 mM EDTA, 500 mM NaCl and 0.2% Tween 20). 1% was took as Input and the rest incubated overnight at 4 °C with specific antibodies. The chromatin was incubated for 3 h at 4 °C with 40 ul of ChIP-grade Magna ChIP protein A/G magnetic beads. The beads were washed three times with Native buffer B and once with Native buffer B without Tween. 100 ul of pK buffer (1x TE, 1mM CaCl2, 50mM NaCl, 0.5% SDS, 0.1ug/ul RNAse A) were added to the Input samples and the beads and incubated in a Thermomixer at 37°C for 1 hour, 2000 rpm. 3ul of Proteinase K were added and incubated for 3h at 56 °C, 2000 rpm. The DNA was purified using the MinElute PCR purification kit from Qiagen following the kit’s instructions, eluted in 30ul of Qiagen’s elution buffer and its concentration determined with an Agilent 2100 Bionanalyzer High Sensitivity Kit.
25ng of ChIPed or Input DNA were processed for library preparation from each sample. All enzymes used are from NEB unless stated otherwise. 1. DNA was End Repaired in 50ul reaction containing 40ul of DNA, 5ul T4 DNA ligase buffer with 10mM ATP, 2ul 10mM dNTP, 1ul Klenow DNA pol (1u/ul), 1ul T4 DNA pol and 1ul T4 PNK. The reaction was incubated for 30min at 20C. Products were purified in Qiagen PCR purification column in 35ul. 2. Adding over-hang A to the 3’ end in 50ul reaction containing 34ul DNA, 5ul 10X NEB buffer 2, 10ul 1mM dATP and 1ul Klenow exo-. The reaction was incubated for 30min at 37C. Products were purified in Qiagen PCR Mini elute purification column in 14ul. 3. Adapter ligation in 30ul reaction containing 13ul DNA, 15ul 2X T4 DNA ligase buffer, 1ul of 1:200 dilution of Illumina true seq DNA sample prep kit and 1ul quick T4 DNA ligase. The reaction was incubated for 15min at 25C. Products were purified in Qiagen Mini elute PCR purification column in 15ul. 4. Size selection. Ligated products were loaded onto 2% Agarose gel (1XTAE), and run for 1 hour at 120V. DNA was viewed on low-wave trans illuminator and size selected at the 300-400bp range using the Kb+ invitrogen DNA ladder. Products were purified in Qiagen PCR purification column in 25ul. 5. PCR amplification was done in 50ul reaction containing 25ul 2X master mix (2X Phusion HF, FINZYMES), 2ul PCR primers (illumina) and 23ul DNA. PCR program according to the illumina protocol. Products were purified in Qiagen Mini elute PCR purification column in 15ul. PCR products were then run on an Agilent DNA 1000 chip for quantification and submitted for sequencing on the Hi-Seq 2500 illumina platform.

tag: cell line

tag: protocol

value: Native ChIP

tag: fixation

tag: phenotype

value: Cas9 overexpressing control

tag: chip antibody


title: s2_WT_mRNA_rep1 1


title: s2_dFMR1-TRIBE_mRNA_rep2 8

value: uninduced


title: K562-H3K9me3-ATRX_KO-Native_ChIP

data_processing:
Basecalls performed using Illumina's Real-Time Analysis (RTA) Software version 1.18.64.
Sequence reads were aligned to the GRCh37 (hg19) assembly using Bowtie v1.0.0 with the following parameters: For 100nt reads: -M 10 -k 1 -n 2 --trim5 5 -l 80 --best. For 50nt reads: -M 10 -k 1 -n 2 --trim5 3 -l 45 --best
Redundant reads were eliminated using the macs2 (v2.1.0) filterdup option with default parameters.
The optimal normalization factor between ChIP and Input samples was calculated with the R NCIS package v1.0.1 using a shift size of 75bp.
Peak calling was performed with macs2 callpeak using the following options: --ratio X --broad --bdg -q 0.0005 --broad-cutoff 0.0005, where X is the normalization factor estimated by NCIS
ChIP/Input fold enrichment pileups were created with the macs2 bdgcmp tool using the -m FE option and converted to bigWig files using the bedGraphToBigWig program (v4) from the UCSC binaries.
A second peak calling was performed using SICER v1.1 using a window of 200bp, allowing gaps of 400pb and filtering for q-values < 1x10^-8.
All peaks overlapping with the Encode blacklisted regions were eliminated.
The final peak list was generated overlaping the macs2 and SICER peaks with the intersectBed program from bedtools v2.17.0. All SICER peaks overlaping at least one macs2 peak were kept
Genome_build: GRCh37
Supplementary_files_format_and_content:
- ChIP/Input fold enrichment bigWig file obtained with macs2 bdgcmp, as described.
- Bed file with significant peaks from macs2 and SICER

growth_protocol: K562 cells were growth in T-75 flasks at maximum confluency of 1x10^6 cells per ml in RPMI + 10%FBS + 1x Antibiotic-Antimycotic (gibco). 40-60 million cells were used per ChIP

extract_protocol:
Native ChIP: Native ChIP was performed essentially as described (Hasson et al., Nat Struct Mol. Biol, 2013) with minor changes. Briefly: 60 million cells were collected and resuspended in 2 ml of ice-cold buffer I (0.32 M sucrose, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 15 mM Tris, pH 7.5, 0.5 mM DTT, 0.1 mM PMSF and 1:1,000 protease inhibitor cocktail (Sigma)). Ice-cold buffer I supplemented with 0.1% IGEPAL (2 ml) was added, and samples were placed on ice for 8 min. The resulting 4 ml of nuclei was gently layered on top of 8 ml of ice-cold buffer III (1.2 M sucrose, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 15 mM Tris, pH 7.5, 0.5 mM DTT, 0.1 mM PMSF and 1:1,000 protease inhibitor cocktail) and centrifuged at 10,000g for 20 min at 4°C. Pelleted nuclei were resuspended in Native buffer A (0.34 M sucrose, 15 mM HEPES, pH 7.4, 15 mM NaCl, 60 mM KCl, 4 mM MgCl2, 1 mM DTT and 1:1,000 protease inhibitor cocktail (Sigma)) to 400 ng/μl. MNase (Affymetrix) digestion reactions were carried out on chromatin (100 μg or more), using 0.1 U/μg chromatin in Native buffer A supplemented with 3 mM CaCl2 for 10 min at 37 °C. The reaction was quenched with 5 mM EGTA. The chromatin was resuspended in 10 mM EDTA, pH 8.0, 1 mM PMSF and 1:1,000 protease inhibitor cocktail and rotated at 4 °C for 2–4 h. The mixture was adjusted to 500 mM NaCl, allowed to rotate for another 45 min and then centrifuged at 13,500g for 10 min, yielding nucleosomes in the supernatant. Chromatin (80 μg per ChIP) was diluted to 100 ng/μl with Native buffer B (20 mM Tris, pH 8.0, 5 mM EDTA, 500 mM NaCl and 0.2% Tween 20). 1% was took as Input and the rest incubated overnight at 4 °C with specific antibodies. The chromatin was incubated for 3 h at 4 °C with 80 ul of ChIP-grade Magna ChIP protein A/G magnetic beads. The beads were washed three times with Native buffer B and once with Native buffer B without Tween. 100 ul of pK buffer (1x TE, 1mM CaCl2, 50mM NaCl, 0.5% SDS, 0.1ug/ul RNAse A) were added to the Input samples and the beads and incubated in a Thermomixer at 37°C for 1 hour, 2000 rpm. 3ul of Proteinase K were added and incubated for 3h at 56 °C, 2000 rpm. The DNA was purified using the MinElute PCR purification kit from Qiagen following the kit’s instructions, eluted in 30ul of Qiagen’s elution buffer and its concentration determined with an Agilent 2100 Bionanalyzer High Sensitivity Kit.
25ng of ChIPed or Input DNA were processed for library preparation from each sample. All enzymes used are from NEB unless stated otherwise. 1. DNA was End Repaired in 50ul reaction containing 40ul of DNA, 5ul T4 DNA ligase buffer with 10mM ATP, 2ul 10mM dNTP, 1ul Klenow DNA pol (1u/ul), 1ul T4 DNA pol and 1ul T4 PNK. The reaction was incubated for 30min at 20C. Products were purified in Qiagen PCR purification column in 35ul. 2. Adding over-hang A to the 3’ end in 50ul reaction containing 34ul DNA, 5ul 10X NEB buffer 2, 10ul 1mM dATP and 1ul Klenow exo-. The reaction was incubated for 30min at 37C. Products were purified in Qiagen PCR Mini elute purification column in 14ul. 3. Adapter ligation in 30ul reaction containing 13ul DNA, 15ul 2X T4 DNA ligase buffer, 1ul of 1:200 dilution of Illumina true seq DNA sample prep kit and 1ul quick T4 DNA ligase. The reaction was incubated for 15min at 25C. Products were purified in Qiagen Mini elute PCR purification column in 15ul. 4. Size selection. Ligated products were loaded onto 2% Agarose gel (1XTAE), and run for 1 hour at 120V. DNA was viewed on low-wave trans illuminator and size selected at the 300-400bp range using the Kb+ invitrogen DNA ladder. Products were purified in Qiagen PCR purification column in 25ul. 5. PCR amplification was done in 50ul reaction containing 25ul 2X master mix (2X Phusion HF, FINZYMES), 2ul PCR primers (illumina) and 23ul DNA. PCR program according to the illumina protocol. Products were purified in Qiagen Mini elute PCR purification column in 15ul. PCR products were then run on an Agilent DNA 1000 chip for quantification and submitted for sequencing on the Hi-Seq 2500 illumina platform.

value: ATRX KO

value: H3K9me3 (Abcam, ab8898, 5ug)


title: K562-H3K9me3-Cas9_control-Native_ChIP


title: K562-Input_control-Native_ChIP

value: Wild Type


title: K562-ATRX_SC-XL-MNase_ChIP

data_processing:
Basecalls performed using  Illumina's Real-Time Analysis (RTA) Software version 1.18.64.
Sequence reads were aligned to the GRCh37 (hg19) assembly using Bowtie v1.0.0 with the following parameters: For 100nt reads: -M 10 -k 1 -n 2 --trim5 5 -l 80 --best. For 50nt reads: -M 10 -k 1 -n 2 --trim5 3 -l 45 --best
Redundant reads were eliminated using the macs2 (v2.1.0) filterdup option with default parameters.
The optimal normalization factor between ChIP and Input samples was calculated with the R NCIS package v1.0.1 using a shift size of 75bp.
Peak calling was performed with macs2 callpeak using the following options: --ratio X --broad --bdg -q 0.0005 --broad-cutoff 0.0005, where X is the normalization factor estimated by NCIS
ChIP/Input fold enrichment pileups were created with the macs2 bdgcmp tool using the -m FE option and converted to bigWig files using the bedGraphToBigWig program (v4) from the UCSC binaries.
A second peak calling was performed using SICER v1.1 using a window of 200bp, allowing gaps of 400pb and filtering for q-values < 1x10^-8.
All peaks overlapping with the Encode blacklisted regions were eliminated.
The final peak list was generated overlaping the macs2 and SICER peaks with the intersectBed program from bedtools v2.17.0. All SICER peaks overlaping at least one macs2 peak were kept
Genome_build: GRCh37
Supplementary_files_format_and_content:
- ChIP/Input fold enrichment bigWig file obtained with macs2 bdgcmp, as described.
- Bed file with significant peaks from macs2 and SICER

extract_protocol:
XL-MNase ChIP: Cross-linked MNase ChIP was performed using the Cell Signaling SimpleChIP Enzymatic Chromatin IP Kit with Magnetic beads (cat. #9003). The vendor’s instructions were followed with some changes. Briefly: 40 million K562 cells were cross-linked for 10 minutes at room temperature in 10ml of PBS, 100mM NaCl, 1mM EDTA pH 8.0, 50mM HEPES pH 8.0, 1% formaldehyde. Glycine was added to a final concentration of 125mM to stop the cross-linked reaction. The cells were washed once with cold PBS. Nuclei were obtained lysing the cells with 4ml of buffer A + DTT + Protease Inhibitor Cocktail (PIC) for 10 minutes at 4°C. Nuclei were washed with 3 ml of ice-cold buffer B + DTT. Nuclei were resuspended in 1ml of ice-cold buffer B + DTT, and digested with 8,000 gel U of Micrococal Nuclease from NEB (cat. #M0247S) at 37°C for 20 minutes. The reaction was stopped adding EDTA for a final concentration of 50nM and incubating on ice for 5 minutes. The nuclei were pelleted, and resuspended in 1ml of ChIP buffer + PIC + PMSF and incubated on ice for 10 min. The nuclei were split in two tubes and lysed by light sonication in a Bioruptor Twin (4 cycles, 20 sec ON/OFF, high power). The chromatin was cleared by centrifugation and a sample taken and processed (see bellow) to measure the concentration of the chromatin. 40-80ug of chromatin were diluted to 100ng/ul with ChIP buffer. 1% of the diluted chromatin was took as Input and the rest incubated with specific antibodies overnight at 4°C. 40-80 ul of ChIP-grade Magna ChIP protein A/G magnetic beads from Millipore (cat. #16-663) were added and incubated for 3 hours at 4°C. The beads were washed 3 times with 1ml of ChIP buffer, 1 time with 1ml of ChIP buffer + 350 mM NaCl, 1 time with 1 ml of LiCl buffer (10mM Tris-HCl pH 8.0, 1mM EDTA pH 8.0, 1% sodium deoxycholate, 1% Igepal, 250mM LiCl, not included in the kit) and 1 time with 1ml of TE. The beads and the Input samples were incubated in 100ul of Elution buffer for 30 min in a thermomixer at 65°C, 1200 rpm. The eluted material was incubated for 1 hour at 37°C 1ul of RNAse A (10mg/ml), followed with a 3 hour incubation at 55°C with 3ul of Proteinase K (20mg/ml). The cross-linked was reversed incubating the eluted material for 4-6 hours at 65°C. The DNA was purified using the MinElute PCR purification kit from Qiagen following the kit’s instructions and eluted in 30ul of Qiagen’s elution buffer. The amount and the pattern of the obtained DNA was determined using an Agilent 2100 Bionanalyzer High Sensitivity Kit.
25ng of ChIPed or Input DNA were processed for library preparation from each sample. All enzymes used are from NEB unless stated otherwise. 1. DNA was End Repaired in 50ul reaction containing 40ul of DNA, 5ul T4 DNA ligase buffer with 10mM ATP, 2ul 10mM dNTP, 1ul Klenow DNA pol (1u/ul), 1ul T4 DNA pol and 1ul T4 PNK. The reaction was incubated for 30min at 20C. Products were purified in Qiagen PCR purification column in 35ul. 2. Adding over-hang A to the 3’ end in 50ul reaction containing 34ul DNA, 5ul 10X NEB buffer 2, 10ul 1mM dATP and 1ul Klenow exo-. The reaction was incubated for 30min at 37C. Products were purified in Qiagen PCR Mini elute purification column in 14ul. 3. Adapter ligation in 30ul reaction containing 13ul DNA, 15ul 2X T4 DNA ligase buffer, 1ul of 1:200 dilution of Illumina true seq DNA sample prep kit and 1ul quick T4 DNA ligase. The reaction was incubated for 15min at 25C. Products were purified in Qiagen Mini elute PCR purification column in 15ul. 4. Size selection. Ligated products were loaded onto 2% Agarose gel (1XTAE), and run for 1 hour at 120V. DNA was viewed on low-wave trans illuminator and size selected at the 300-400bp range using the Kb+ invitrogen DNA ladder. Products were purified in Qiagen PCR purification column in 25ul. 5. PCR amplification was done in 50ul reaction containing 25ul 2X master mix (2X Phusion HF, FINZYMES), 2ul PCR primers (illumina) and 23ul DNA. PCR program according to the illumina protocol. Products were purified in Qiagen Mini elute PCR purification column in 15ul. PCR products were then run on an Agilent DNA 1000 chip for quantification and submitted for sequencing on the Hi-Seq 2500 illumina platform.

value: XL-Mnase ChIP

value: 10 mins RT, 1% formaldehyde

value: ATRX (Santa Cruz, sc-15408 H300, 10ug)


title: Cst6p_ethanol_rep2

status: Public on Apr 04 2016

city: Mölndal

first: David

last: Bergenholm

state: SWEDEN

address: Axgatan 139

institute: Chalmers tekniska högskola

description:
ChIP-exo
Cst6p_ethanol.xlsx

data_processing:
ChIP-exo sequencing reads (R1 reads) were mapped to reference genome assembly with Bowtie2 using default settings to generate SAM files.
SAM files were treated with SAMtools option –q 20 to remove low-quality reads and then converted to sorted BAM files.
BAM files were trimmed 70 bp from 3’ end using trimBam (http://genome.sph.umich.edu/wiki/BamUtil:_trimBam) to increase resolution.
GEM was used to identify peaks and compare biological duplicates. The noise level was calculated from averaged noise throughout each replicate.
Binding events were manually curated in the Integrative Genomics Viewer to remove redundant events and false positive peaks.
Genome_build: R64.2.1  of S. cerevisiae S288C
Supplementary_files_format_and_content: Excel .xlsx file containing summit position and signal-to-noise values of peaks

organism: Saccharomyces cerevisiae

growth_protocol: Cells were cultivated in minimal medium with indicated sole carbon source to OD600 of 1.5 to 1.8 (mid-log phase) at 30°C with vigorous agitation.

extract_protocol:
Formaldehyde with a final concentration of 1% (w/v) and distilled water were added to the culture to cross-link protein-DNA complexes with OD600 of 1.0 and a total volume of 100 ml. Cross-linking was performed for 12 min at room temperature with shaking and quenched by adding 2.5 M glycine to a final concentration of 125 mM. After 5 min, cells were washed twice with 20 ml cold TBS (10 mM Tris-HCl, 150 mM NaCl, pH7.5) and frozen with liquid nitrogen. For ChIP-exo, cells were disrupted with glass beads on FastPrep 24 (MP Biomedicals) and the crude cell lysate was sonicated to shear chromatin on Branson digital sonifier 250 (Branson Ultrasonics). After centrifugation, the supernatant containing chromatin fragments was applied to IgG Sepharose 6 Fast Flow beads (GE Healthcare) for immunoprecipitation at 4°C with gentle rocking overnight. NEBNext End Repair Module, NEBNextdA-Tailing Module, NEBNext Quick Ligation Module, PreCR Repair Mix, Lambda exonuclease and RecJf (all from New England Biolabs) were used for on-bead end repair, 3´-dA DNA tailing, first adaptor ligation, nick filling-in and chromatin trimming, respectively. The first adaptors contain unique 6 bp-index sequences. To elute and reverse cross-link the bound complexes, TE buffer containing 1% SDS was added to the beads and samples were incubated overnight at 65°C. After protease K (Thermo Scientific) digestion and DNA extraction with phenol/chloroform/isoamyl alcohol (Amresco, US), the single-strand DNAs were subjected to primer extension using phi29 DNA polymerase (New England Biolabs). The products were dA-tailed and ligated with the second adapter using the same reagents as in on-bead reactions, and then amplified by PCR for 20-22 cycles using Phusion High-Fidelity DNA Polymerase (New England Biolabs). GeneRead Size Selection Kit (QIAGEN) was used to purify DNA before and after the second dA-tailing, second adapter ligation and PCR.
The DNA samples prepared with ChIP-exo contain adaptors and are ready for direct sequencing with Illumina sequencer. The samples were pooled together in equimolar amounts before sequencing.

value: CST6-TAP constructed from CEN.PK 113-5D by adding a C-terminal CBP-ProtA tag to Cst6p

tag: carbon source

value: 1% (v/v) ethanol


title: s2_NonA-TRIBE_mRNA_rep2 12


title: Cst6p_ethanol_rep1

description:
ChIP-exo
Cst6p_ethanol.xlsx

tag: strain


title: Cst6p_glucose_rep2

description:
ChIP-exo
Cst6p_glucose.xlsx

value: 2% (w/v) glucose


title: Cst6p_glucose_rep1

description:
ChIP-exo
Cst6p_glucose.xlsx


title: OlfactoryBulb_C57BL/6J_spliceJunctions_CaptureSeq

city: Paris

first: Giovanni

last: Bussotti

address: 25-28 Rue du Dr Roux

country: France

institute: Institute Pasteur

description:
biological replicate 1
ERCC: mix2

data_processing:
Illumina Casava1.7 software used for basecalling.
We used TopHat2, (version 2.0.13; --no-coverage-search; --b2-sensitive) to align reads against the mouse genome (GRCm38) and a prebuilt transcriptome index generated using GENCODE annotations (vM4, released on the 3rd December 2014). We used Cufflinks (v2.2.1) to perform Reference Annotation Based Transcript assembly (RAPBT) of reads mapped in each of the 16 CaptureSeq samples. We then merged the individual transcriptome assemblies into a comprehensive assembly using Cuffmerge (v2.2.1). The isoforms count table was generated using Cuffquant followed by Cuffnorm (v2.2.1).
Genome_build: mouse GRCm38
Supplementary_files_format_and_content: .gtf .tsv

source_name: OlfactoryBulb

extract_protocol:
Mouse tissue samples were obtained from adult C57BL/6J mice (AEC Approval Number IMB/030/08/ARC). Mouse brain samples were dissected in ice cold PBS, snap frozen in liquid nitrogen and RNA extracted with TRIzol® (Life Technologies). Non-brain organs were removed and placed in ice cold PBS, where any contaminating tissue was removed and the required organ cut into pieces <30mg and placed in RNAlater® (QIAGEN). RNA was extracted using the TissueRuptor® and RNeasy® Mini purification kit (QIAGEN). Purity of all mouse samples was validated by Nanodrop (Thermo scientific). RNA was DNase treated with Turbo™ DNase (Life Technologies), purified and confirmed DNA-free by PCR for gDNA as previously described (Mercer et al. 2014 ,PMID:24705597). Intact RNA was confirmed by Agilent 2100 Bioanalyzer (Agilent Technologies). Ribo-Zero™ (Epicentre) rRNA depletion was performed on 10 μg of each sample. For non-brain samples 5μg of purified RNA from 2 organ pieces from the same mouse was ribodepleted and then pooled to ensure good coverage across the tissue. Efficient ribodepletion was confirmed by Bioanalyzer (Agilent 2100) Pico chip.
Capture sequencing was performed as previously described (Mercer et al. 2015, PMID:25561518) combining the NimbleGen SeqCap EZ Library SR User’s Guide V3.0 and the NimbleGen Arrays User’s Guide: Sequence Capture Array Delivery v3.2 with the following specifications. RNA sequencing libraries were created using the TruSeq® Stranded mRNA Sample Preparation Kit (Illumina). All samples contained ERCC spike-in mix no1. or no2 at a 1/100 dilution. Test libraries to estimate yield were amplified for 15 cycles as per “Enrich DNA fragments” protocol. Ten cycles of precapture LMPCR was performed for all samples except brain and liver (11 cycles). Capture hybridization were performed as a 4-plex with 250ng of brain or non-brain libraries pooled together. Post-LMPCR was performed for 17 (non-brain samples) or 16 (brain samples) cycles respectively.

tag: tissue

value: OlfactoryBulb

tag: design


title: Testes_C57BL/6J_spliceJunctions_CaptureSeq

description:
biological replicate 1
ERCC: mix2

source_name: Testes

value: Testes


title: Testes_C57BL/6J_lncRNA_CaptureSeq

description:
biological replicate 1
ERCC: mix2


title: Liver_C57BL/6J_spliceJunctions_CaptureSeq

description:
biological replicate 1
ERCC: mix1

source_name: Liver

value: Liver


title: OlfactoryBulb_C57BL/6J_lncRNA_CaptureSeq

description:
biological replicate 1
ERCC: mix2


title: K562-ATRX_Abcam-XL-MNase_ChIP

value: ATRX (Abcam, ab97508, 10ug)


title: Kidney_C57BL/6J_spliceJunctions_CaptureSeq

description:
biological replicate 1
ERCC: mix2

source_name: Kidney

value: Kidney


title: Kidney_C57BL/6J_lncRNA_CaptureSeq

description:
biological replicate 1
ERCC: mix2


title: Sp2_Wdr70del

city: Chengdu

first: Cong

last: Liu

address: Ren Ming Nan Lu 3-17

country: China

institute: Sichuan University

data_processing:
Raw reads of fastq format were firstly processed through in-house perl scripts and clean reads were obtained by removing reads containing adapter, ploy-N and low quality reads from raw data.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two strains was performed using the DESeq R package (1.18.0). Corrected P-value of 0.005 and log2 (Fold change) of 1 were set as the threshold for significantly differential expression.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Schizosaccharomyces pombe

source_name: 907 strain with deleted Wdr70 locus

growth_protocol: All of the strains in cdc25-22 background were grown at 30oC to logrythmic phase and shifted to 35oC for synchronisation.

extract_protocol:
Cells were subjected to total RNA extraction and mRNA purification using poly-T oligo-attached magnetic beads (NEBNext).
Sequencing libraries were generated from purified PolyA+ RNA by NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB) following manufacturer’s protocol.

treatment_protocol: Cells were treated with alkyline reagent (Methyl methanesulfonate) 3.5 hours later for 0.5 hours at 35oC.Two biological samples were collected and mixed for each strains

value: deleted Wdr70 locus

tag: sample type

value: G2 synchronised cells in cdc25-22 background


title: Sp1_Wt

source_name: Wild type yeast strain 907

value: wild type


title: Liver_C57BL/6J_lncRNA_CaptureSeq

description:
biological replicate 1
ERCC: mix1


title: RNA-seq LNCaP rep1

city: Adelaide

first: Joanna

last: Achinger-Kawecka

state: SA

address: AHMS Building, North Terrace

country: Australia

institute: South Australian Immunogenomics Cancer Institute

data_processing:
100bp paired-end reads for LNCaP and PrEC cell lines in biological triplicate were processed using Trim Galore (version 0.11.2) for adapter trimming (parameter settings: --fastqc --paired --retain_unpaired --length 16) (ref1) and STAR (version 2.4.0j)(ref2) for mapping reads to the hg19 human genome build with GENCODE 19 (ref3) used as a reference transcriptome (parameter settings: --quantMode TranscriptomeSAM --outFilterMatchNmin 101).
The reads were aligned to a transcriptome and quantified using RSEM v1.2.7.
Genome_build: hg19
Supplementary_files_format_and_content: LNCaP.TPM.expression.data.tsv: Tab-delimited table showing the expected counts from the RSEM quantification for genes for LNCaP cell line. PrEC.TPM.expression.data.tsv: Tab-delimited table showing the expected counts from the RSEM quantification for genes for PrEC cell line.

source_name: prostate cancer cells LNCaP

growth_protocol: Cell lines were cultured according to manufacturer's instructions.

extract_protocol:
Total RNA was isolated with TRIzol reagent. 500ng of total RNA was spiked with external controls (ERCC RNA spike-in Mix, Thermo Fischer #4456740) and libraries constructed with the Illumina TruSeq Stranded mRNA sample preparation kit (ref. RS-930-1001, Illumina).
Illumina TruSeq Stranded mRNA sample preparation kit

value: prostate

value: LNCaP


title: RNA-seq LNCaP rep2


title: RNA-seq LNCaP rep3


title: RNA-seq PrEC rep1

source_name: normal prostate epithelial cells PrEC

value: PrEC


title: RNA-seq PrEC rep3


title: LAN6-H3K9me3-Native_ChIP

extract_protocol:
Extract Protocol
Native ChIP: Native ChIP was performed essentially as described (Hasson et al., Nat Struct Mol. Biol, 2013) with minor changes. Briefly: 20 million cells were gently trypsinized and resuspended in 2 ml of ice-cold buffer I (0.32 M sucrose, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 15 mM Tris, pH 7.5, 0.5 mM DTT, 0.1 mM PMSF and 1:1,000 protease inhibitor cocktail (Sigma)). Ice-cold buffer I supplemented with 0.1% IGEPAL (2 ml) was added, and samples were placed on ice for 8 min. The resulting 4 ml of nuclei was gently layered on top of 8 ml of ice-cold buffer III (1.2 M sucrose, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 15 mM Tris, pH 7.5, 0.5 mM DTT, 0.1 mM PMSF and 1:1,000 protease inhibitor cocktail) and centrifuged at 10,000g for 20 min at 4°C. Pelleted nuclei were resuspended in Native buffer A (0.34 M sucrose, 15 mM HEPES, pH 7.4, 15 mM NaCl, 60 mM KCl, 4 mM MgCl2, 1 mM DTT and 1:1,000 protease inhibitor cocktail (Sigma)) to 400 ng/μl. MNase (Affymetrix) digestion reactions were carried out on chromatin (~100 μg), using ~0.1 U/μg chromatin in Native buffer A supplemented with 3 mM CaCl2 for 10 min at 37 °C. The reaction was quenched with 5 mM EGTA. The chromatin was resuspended in 10 mM EDTA, pH 8.0, 1 mM PMSF and 1:1,000 protease inhibitor cocktail and rotated at 4 °C for 2–4 h. The mixture was adjusted to 500 mM NaCl, allowed to rotate for another 45 min and then centrifuged at 13,500g for 10 min, yielding nucleosomes in the supernatant. Chromatin (40 μg per ChIP) was diluted to 100 ng/μl with Native buffer B (20 mM Tris, pH 8.0, 5 mM EDTA, 500 mM NaCl and 0.2% Tween 20). 1% was took as Input and the rest incubated overnight at 4 °C with specific antibodies. The chromatin was incubated for 3 h at 4 °C with 40 ul of ChIP-grade Magna ChIP protein A/G magnetic beads. The beads were washed three times with Native buffer B and once with Native buffer B without Tween. 100 ul of pK buffer (1x TE, 1mM CaCl2, 50mM NaCl, 0.5% SDS, 0.1ug/ul RNAse A) were added to the Input samples and the beads and incubated in a Thermomixer at 37°C for 1 hour, 2000 rpm. 3ul of Proteinase K were added and incubated for 3h at 56 °C, 2000 rpm. The DNA was purified using the MinElute PCR purification kit from Qiagen following the kit’s instructions, eluted in 30ul of Qiagen’s elution buffer and its concentration determined with an Agilent 2100 Bionanalyzer High Sensitivity Kit.
25ng of ChIPed or Input DNA were processed for library preparation from each sample. All enzymes used are from NEB unless stated otherwise. 1. DNA was End Repaired in 50ul reaction containing 40ul of DNA, 5ul T4 DNA ligase buffer with 10mM ATP, 2ul 10mM dNTP, 1ul Klenow DNA pol (1u/ul), 1ul T4 DNA pol and 1ul T4 PNK. The reaction was incubated for 30min at 20C. Products were purified in Qiagen PCR purification column in 35ul. 2. Adding over-hang A to the 3’ end in 50ul reaction containing 34ul DNA, 5ul 10X NEB buffer 2, 10ul 1mM dATP and 1ul Klenow exo-. The reaction was incubated for 30min at 37C. Products were purified in Qiagen PCR Mini elute purification column in 14ul. 3. Adapter ligation in 30ul reaction containing 13ul DNA, 15ul 2X T4 DNA ligase buffer, 1ul of 1:200 dilution of Illumina true seq DNA sample prep kit and 1ul quick T4 DNA ligase. The reaction was incubated for 15min at 25C. Products were purified in Qiagen Mini elute PCR purification column in 15ul. 4. Size selection. Ligated products were loaded onto 2% Agarose gel (1XTAE), and run for 1 hour at 120V. DNA was viewed on low-wave trans illuminator and size selected at the 300-400bp range using the Kb+ invitrogen DNA ladder. Products were purified in Qiagen PCR purification column in 25ul. 5. PCR amplification was done in 50ul reaction containing 25ul 2X master mix (2X Phusion HF, FINZYMES), 2ul PCR primers (illumina) and 23ul DNA. PCR program according to the illumina protocol. Products were purified in Qiagen Mini elute PCR purification column in 15ul. PCR products were then run on an Agilent DNA 1000 chip for quantification and submitted for sequencing on the Hi-Seq 2500 illumina platform.

value: Native ChIP

value: ATRX KO

value: H3K9me3 (Abcam, ab8898, 5ug)


title: RNA-seq PrEC rep2


title: Heart_C57BL/6J_lncRNA_CaptureSeq

description:
biological replicate 1
ERCC: mix1

source_name: Heart

value: Heart


title: Cortex_C57BL/6J_spliceJunctions_CaptureSeq

description:
biological replicate 1
ERCC: mix2

source_name: Cortex

value: Cortex


title: HiC LNCaP rep4

data_processing:
Library strategy: Hi-C
All HiC libraries were processed through the NGSane framework v0.5.2, using the "fastqc", "hicup" and "fithicaggregate" modules.
Quality check of sequence libraries was performed with FastQC v0.11.2. Raw fastq files were then pre-processed, mapped with bowtie v1.1.0 and assessed for artifact levels through HiCuP v0.5.2 supplying genome assembly (hg19) and the BglII restriction enzyme cut site. Aligned read files in BAM format were sorted with Samtools v1.2 and duplicates were tagged using MarkDuplicates from Picard tools v1.121. Replicates were pooled using bespoke Python scripts (provided within NGSane) leveraging the sparse matrices formats in the SciPy librarie.
Significant connections were assessed from contact count matrices for multiple resolution (100kb and 1Mb) using a custom adaptation of fit-hi-c (provided within NGSane) supplying iteratively corrected bias offsets calculated through HiCorrector v1.1 as well as genome mappability tracks from ENCODE.
Genome_build: hg19
Supplementary_files_format_and_content: Hi-C data files are normalized/corrected whole genome matrices binned at 100kb/1Mb. The columns follow the fithic output format as follows: column1 chromosome name for contact locus 1; column2 chromosomal position for contact locus 1 (midpoint for given resolution); column3 chromosome name for contact locus 2; column4 chromosomal position for contact locus 2 (midpoint for given resolution); column5 number of contacts (read pairs) mapping between the two loci; column6 p-value; column7 q-value; column8 HiCorrector bias for contact locus 1; column9 HiCorrector bias for contact locus 2; column10 bias adjusted number of contacts. TADs were identified with previously described “Hi-C Domain Caller” pipeline by Ren’s Lab at 40kb resolution.

growth_protocol: Cells were cultured under normal conditions.

extract_protocol:
Cells were cross-linked with formaldehyde, lysed and the nuclei was permeabilized. DNA was then cut with BglII restriction enzyme, the overhangs filled in incorporating a biotinylated base and the free ends were then ligated together. Crosslinks were reversed, the DNA was sheared to 300-500bp and the biotinylated ligation junctions were pulled down with streptavidin beads.
Custom library construction protocol was followed. Briefly, DNA was end-repaired and dA-tailing using the NEBNext DNA Master Mixes kit and the ligation of universal adapter was performed on Streptavidin-bound DNA using the NEBNext Ultra DNA Library Prep kit. After adapter ligation DNA was PCR amplified with indexed Illumina primers for 8-12 cycles and library fragments of at least 200bp were purified using SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq2500 following the manufacturer's protocols.

tag: restriction enzyme

value: BglII


title: HiC LNCaP rep3.2


title: K562-Input_control-XL-MNase_ChIP

value: XL-Mnase ChIP

value: 10 mins RT, 1% formaldehyde

value: Wild Type


title: Cortex_C57BL/6J_lncRNA_CaptureSeq

description:
biological replicate 1
ERCC: mix2


title: HiC LNCaP rep2.2


title: Cerebellum_C57BL/6J_spliceJunctions_CaptureSeq

description:
biological replicate 1
ERCC: mix1

source_name: Cerebellum

value: Cerebellum


title: HiC LNCaP rep1.2


title: Cerebellum_C57BL/6J_lncRNA_CaptureSeq

description:
biological replicate 1
ERCC: mix1


title: Heart_C57BL/6J_spliceJunctions_CaptureSeq

description:
biological replicate 1
ERCC: mix1


title: Brain_C57BL/6J_spliceJunctions_CaptureSeq

description:
biological replicate 1
ERCC: mix1

source_name: Brain

value: Brain


title: HiC LNCaP rep5


title: HiC LNCaP rep3.1


title: HiC LNCaP rep1.1


title: HiC LNCaP rep2.1


title: Brain_C57BL/6J_lncRNA_CaptureSeq

description:
biological replicate 1
ERCC: mix1


title: HiC PrEC rep2


title: HiC PrEC rep1


title: Foxp3Plus_WT_B

city: Freiburg

first: Manching

last: Ku

address: Mathildenstrasse 1

department: Hematology and Oncology

institute: Medical Center - University of Freiburg

description: poly-dT selected mRNA

data_processing:
Basecalling softwares version was HiSeq Control Software 2.2.38 and RTA 1.18.61
BCL files to fastq files conversion and demultiplexing were done using CASAVA v1.8.2
Reads were filtered by quality score using FASTQC (v0.10.1)
Reads were trimmed for Illumina adapters using Trimmomatic (v0.33)
Reads are aligned to reference genome using STAR (v2.4.1a)
Gene expression was quantified using aligned reads to exons of RefSeq transcripts using HOMER (v4.7)
differential gene expression was determined with edgeR (bioconductor version: release 3.1)
Genome_build: mus musculus mm9 (NCBI Build 37)
Supplementary_files_format_and_content: tab-delimited text files include transcript per million (tpm) values for each Sample

source_name: WT Treg cells, CD4+

growth_protocol: Cells are isolated from mouse spleen tissues

extract_protocol:
Nucleospin RNA XS kit (Macherey-Nagel)
mRNA was selected by poly-dT magnetic beads, then RNA was fragmented and reverse-transcribed preserving strand information, and cDNA was end-repaired, adenylated, adapter-ligated and PCR amplified
RNA-Seq (RNA-Seq libraries were sequenced on Illumina HiSeq2500 at single-end 50-bp (base pair), resulting 25-30 million reads per library)

tag: tissue source

value: Spleen

tag: cell type

value: WT Treg cells, CD4+

tag: t cell receptor

value: polyclonal


title: Foxp3minus_WT_A

description: poly-dT selected mRNA

source_name: WT Non-Treg cells, CD4+

value: WT Non-Treg cells, CD4+


title: HiC PrEC rep3

value: prostate


title: Foxp3minus_WT_B

description: poly-dT selected mRNA


title: Foxp3minus_T138_B

description: poly-dT selected mRNA

source_name: NT Non-Treg cells, CD4+

value: NT Non-Treg cells, CD4+

value: monoclonal


title: Foxp3Plus_WT_A

description: poly-dT selected mRNA


title: Foxp3minus_T138_A

description: poly-dT selected mRNA


title: HiC PC3 rep1

source_name: prostate cancer cells PC3


title: Foxp3plus_T138_B

description: poly-dT selected mRNA

source_name: NT Treg cells, CD4+

value: NT Treg cells, CD4+


title: p53fl/fl rep3

first: Yu

address: 6 Wangjiang Road

data_processing:
total RNA from 11B3fl/p53fl;shNf1;shMll3;Vav1-Cre or p53fl/fl;shNf1;shMll3;Vav1-Cre leukemia cells (four lines per cohort), isolated from the bone marrow of moribund mice, was isolated by Trizol extraction (Life Technologies).  After ribogreen quantification (Life Technologies) and quality control on an Agilent BioAnalyzer, 500ng of total RNA (RIN >8) underwent polyA selection and Truseq library preparation according to instruction provided by Illumina (TruSeq™ RNA Sample Prep Kit v2) with 6 cycles of PCR. Samples were barcoded and run on a Hiseq 2500 in a 50bp/50bp Paired end run, using the TruSeq SBS Kit v3 (Illumina).An average of 45 million paired reads were generated per sample. At the most the ribosomal reads represented 0.1% and the percent of mRNA bases was closed to 65% on average. The output from the sequencers (FASTQ files) were mapped to the mouse genome (mm9) using the rnaStar (https://code.google.com/p/rna-star/) aligner, with the 2 pass mapping methods. After mapping, the expression counts of each individual gene were computed using HTSeq (http://www-huber.embl.de/users/anders/HTSeq), followed by normalization and differential expression analysis among samples using the R/Bioconductor package DESeq (http://www-huber.embl.de/users/anders/DESeq). GSEA was performed with Broad’s GSEA algorithm.
Supplementary_files_format_and_content: excel file with p value

source_name: acute myeloid cells

extract_protocol:
11B3fl/p53fl;shNf1;shMll3;Vav1-Cre or p53fl/fl;shNf1;shMll3;Vav1-Cre leukemia cells (four lines per cohort) were isolated from the bone marrow of moribund mice.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotypes

value: acute myeloid cells


title: Anterior_ovariole_Day8_Replicate3

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

data_processing:
We performed single-end 75 bp sequencing on the HiSeq2000 Sequencing System (Illumina, San Diego, CA) according to the manufacturer.  De-multiplexed reads (Chastity > 0.6) FASTQ output was from Illumina CASAVA v.1.8.2. Reads were mapped to FlyBase release 6 version 07 (FlyBase file: dmel-all-chromosome-r6.07.fasta) of the Drosophila melanogaster genome appended with the ERCC sequences (ERCC-00009, ERCC-00014, ERCC-00057, ERCC-00059, ERCC-00099, ERCC-00108, ERCC-00116 were strand-corrected from ERCC_reference.fa, and ERCC-00085 was re-identified as Subpool C; Jiang et al., Genome Research, 2011, PMID 21816910).  We appended the ERCC annotation to the Drosophila melanogaster annotation (dmel-all-r6.07.ERCC.gtf ). Reads were also mapped to the transposable elements dataset from BDGP (BDGP file: FASTA.FORMAT.v.9.4.1) (Kaminker et al; Genome Biol, 2002, PMID 12537573). We used HiSAT (2.0.1-beta) (Kim et al., 2014, Nature methods, PMID 25751142) with parameters (-x indexed_genome_with_ERCC --dta –U) for the mapping, and mapped reads at the gene-level were counted by HTSeq (v0.6.1p1) (--stranded=reverse with dmel_ERCC.gtf) (Anders et al., Bioinformatics, 2015, PMID 25260700). We used SAMtools (v0.1.2) (Li et al., Bioinformatics, 2009, PMID 19505943) to index chromosomes and sort the alignments.
Genome_build: Drosophila melanogaster Release 6
Supplementary_files_format_and_content: There are two supplemental files. The tab-delimited merged.hisat2_htseq_read_count.txt contains the gene-level output, for each library. The dmel_6.07_ERCC.gtf file contains the annotation for the alignment to release 6.07 plus the ERCC spike-ins.

source_name: AO, Day8

growth_protocol: Flies were raised at 25°C under constant light on Drosophila food (Labexpress, Ann Arbor, Michigan) (yeast 15 gm, cornmeal 27 gm, sucrose 43 gm, agar 8 gm, 0.4% propionic acid, 0.15% tegosept and water to 1 L). Virgins were collected based on the presence of meconium (dark spot on their abdomen) and aged at 25°C for 5 to 5.5 days, 6 to 6.5 days, 7 to 7.5 days and 8 to 8.5 days post eclosion.

extract_protocol:
Flies were collected and aged as described above and ovaries were dissected in a glass embryo dish in ice cold Phosphate Buffer Saline (PBS). Ovaries were immediately transferred to fresh ice cold PBS in a new dish.  The ovarioles were teased apart using tungsten needles. Germaria and round previtellogenic egg chambers up to stage 7 were separated from the rest of the ovary using tungsten needles and were immediately transferred to RNAlater (Life Technologies, Carlsbad, CA) on ice. Dissected samples were frozen at -80°C until RNA extraction, and each sample had 30 to 50 ovarioles. Three biological replicates were prepared for each age group. RNA was prepared after all the samples were dissected. Total RNA was isolated using the RNeasy mini kit (Qiagen, Valencia, CA) following manufacturer’s protocol with the following modification. RNAlater solution was removed from the tissue and the tissue was placed in 600 μl Buffer RLT (supplied with the kit). The tissue was then disrupted using five to ten glass beads in a mini-beadbeater (Biospec Products, Bartlesville, OK) for 2 rounds of 30 sec each. After this point we followed the manufacturers protocol exactly. RNA was quantified using Quant-iT Ribogreen RNA assay kit (Invitrogen, Carlsbad, CA) following manufacturers protocol and 200 ng of RNA was used for library preparation.
Libraries were prepared according to Lin et al. (BMC Genomics, 2016, PMID: 26732976) except we used 200 ng total RNA per sample as input.

tag: age (days post eclosion)

tag: Sex

value: female

tag: development stage

value: adult

tag: genotype

value: anterior ovariole


title: Anterior_ovariole_Day8_Replicate2


title: Anterior_ovariole_Day7_Replicate2

source_name: AO, Day7


title: p53fl/fl rep2


title: Anterior_ovariole_Day7_Replicate3


title: p53fl/fl rep1


title: HiC PC3 rep2

value: BglII

tag: cell line


title: p53fl/fl rep4


title: 11B3fl/p53fl rep4


title: 11B3fl/p53fl rep3


title: Anterior_ovariole_Day6_Replicate3

source_name: AO, Day6


title: 11B3fl/p53fl rep2


title: Anterior_ovariole_Day6_Replicate1


title: Anterior_ovariole_Day5_Replicate3

source_name: AO, Day5


title: 11B3fl/p53fl rep1


title: Anterior_ovariole_Day5_Replicate1


title: DK Input DNA

city: Segrate

first: Luca

last: Petiti

state: Milan

address: Via Fratelli Cervi, 93

country: Italy

institute: ITB-CNR

data_processing:
We mapped raw reads against the human reference genome (build hg19) using Bowtie allowing up to 2 or 3 mismatches
Peaks were obtained using MACS2 using default parameters
Genome_build: hg19

source_name: DK

growth_protocol: KP cells were obtained from foreskin biopsies of healthy neonatal donors and expanded by cultivation onto lethally irradiated 3T3-J2 cells in growth FAD medium, a DMEM and Ham’s F12 media mixture (2:1) containing FCS (10%), penicillin-streptomycin (1%), glutamine (2%), insulin(5ug/ml), adenine (24.3ug/ml), hydrocortisone (0.4ug/ml), cholera toxin (50ug/ml), triiodotyronine (2nM). DKs were cultivated in EpiLife serum-free medium (Invitrogen) containing EpiLife defined growth supplements (HKGS, Invitrogen), penicillin-streptomycin (1%) and glutamine (2%).

extract_protocol:
Chromatin preparation and processing was performed starting from pellets of 10e7 KP and DK cells and following the truChIP Chromatin Shering Kit standard protocol (PN520076, Covaris Inc.).
Libraries were prepared according to Illumina's instructions accompanying the standard protocol of Illumina ChIP-seq DNA sample preparation kit (IP-102-1001, Illumina Inc.).

value: Differentiated Keratinocytes


title: Foxp3plus_T138_A

description: poly-dT selected mRNA


title: Anterior_ovariole_Day5_Replicate2


title: Anterior_ovariole_Day6_Replicate2


title: ChIP-Seq analysis of p63 in human differentiated keratinocytes (DK)

tag: chip antibody vendor

value: Santa Cruz Biotechnology

tag: chip antibody catalog #

tag: chip antibody lot number


title: Dma_bisulfite_rep2

city: Gent

first: Jana

last: Asselman

address: Coupure Links 653 (Building F, 2nd floor)

country: Belgium

institute: Ghent University

data_processing:
Basecalling was performed using the Illumina Casava 1.5 software.
Reads containing more than 5% N bases were omitted. The remaining reads were subsequently dynamically trimmed to the longest stretch of bases which had a Phred score higher or equal to 30 using Trim Galore! 0.3.2 software wit h standard settings.
Trimmed reads were transformed into fully bisulfite-converted forward (C->T conversion) and reverse read (G->A conversion of the forward strand) versions, before being mapped to similarly converted versions of the genome (also C->T and G->A converted) using Bowtie2 v.2.1.0 (Langmead and Salzberg 2012) while setting the scoring function as --score_min L,0,-0.6. Non-uniquely mapping reads were discarded.
For each read covering a cytosine site, the methylation state of that site was inferred using the Bismark_methylation_extractor tool from the Bismark 0.9.0 software (Krueger and Andrews 2011) by comparing the uniquely mapped read to the original, non-converted reference genome. Only cytosine sites with a minimum coverage of 5x were further considered.
Genome_build: Dappu1, through DOE JGI Genome Portal
Supplementary_files_format_and_content: Tab-delimited count data files consisting of 5 columns: <chromosome> <start position> <end position> <count methylated> <count unmethylated>. Such files were generated for each cytosine context (CpG, CHG and CHH), each strand (original bottom 'OB'; original top 'OT') and each replicate (ctrl1; ctrl2; ctrl3) separately.

organism: Daphnia magna

source_name: whole body tissue

growth_protocol: 0-24h old juveniles of Daphnia pulex isolate TCO* (Shaw et al. 2009) were grown for 14 days in no-N no-P COMBO medium (Shaw et al. 2007); 0-24h old juveniles of Daphnia magna isolate Xinb3 (Routtu et al. 2010) were grown for 14 days in Adam medium (Routtu et al.). All cultures were kept in controlled conditions at 20 ± 1°C, under white fluorescent lights at a 16h:8h light-dark cycle and at a light intensity of 14 µmoles·m-2·s-1. Daphnids were grown under a density of 20 animals per liter medium and were fed daily 1.5 mg·C·L-1 of an algal Pseudokirchneriella subcapitata:Chlamydomonas reinhardtii mixture in a 3:1 cell count ratio. Medium was renewed every other day.

extract_protocol:
Thirty 14-15 day old daphnids per biological replicate were pooled, shock-frozen in liquid nitrogen and stored at -83°C until DNA extraction. Extraction of the total genomic material was performed using the MasterPure kit (Epicentre, Madison, WI, USA) according to the manufacturer's protocol, including RNase treatment.
Bisulfite library construction and sequencing were performed at BGI-Shenzhen (Shenzhen, Guangdong, China). Briefly, the extracted DNA was fragmented by sonication to a mean size of approximately 300 bp. After blunt ending and 3'-end addition of dA, Illumina methylated adapters (Illumina, San Diego, CA, USA) were added according to the manufacturer's instructions. The bisulfite conversion (C → U) was carried out using the EZ DNA methylation Gold kit (Zymo Research, Irvine, CA, USA) according to manufacturer's instructions.

treatment_protocol: No treatment was applied.

value: whole body

tag: age

value: 14 days

tag: clone

tag: treatment

value: control


title: Dma_bisulfite_rep3

tag: tissue


title: Dma_bisulfite_rep1


title: Anterior_ovariole_Day8_Replicate1


title: Anterior_ovariole_Day7_Replicate1


title: ChIP-Seq analysis of H3K27ac in human human keratinocyte progenitors (KP)

data_processing:
Reads from each sample were mapped in three consecutive steps taking into account from 0 to a maximum of 2 mismatches. After each mapping step the unmapped reads were filtered out and remapped by increasing of one. The results of each mapping step were then pooled together into a single bam file.
sample resulted in a merged BAM file that was then processed by using SAMtools, and converted into a bed file using BEDTools
ChIP-seq peak calling was performed using SICER (Chongzhi Zang et al., 2009) and using  INPUT data (control DNA) to model the background noise.
Genome_build: Hg19
Supplementary_files_format_and_content: The bed files contains the peaks of the histone modification from the analysis of peak calling using SICER.

source_name: KP

extract_protocol:
Chromatin preparation and processing was performed starting from pellets of 10e7 KP and DK cells and following the truChIP Chromatin Shering Kit standard protocol (PN520076, Covaris Inc.).
Libraries were prepared according to Illumina's instructions accompanying  the standard protocol of Illumina ChIP-seq DNA sample preparation kit (IP-102-1001, Illumina Inc.).

tag: sample type

value: keratinocyte progenitors

tag: cell-type

value: KP

tag: chip antibody

value: H3K27ac (Ab4729 anti H3K27ac)


title: ChIP-Seq analysis of H3K27ac in human differentiated keratinocytes (DK)

value: DK


title: control rep2

city: Shanghai

first: Zhen

last: Lin

state: Shanghai

address: 320 Yue Yang Road

department: Shanghai  Institute of Biochemistry and Cell Biology

institute: University of Chinese Academy of Sciences

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed through cut off the top 10 bases, then mapped to GENCODE vM6 reference genome using tophat v2.0.11 with default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Trapnell et al., Nature Protocols, 2012. Using cuffdiff2 v2.2.1 to identify the differentially expressed genes among the control and germ cell RA signaling mutant samples at the standards: p value <0.05, 1.5 fold-difference.
Genome_build: GENCODE vM6/GRCm38
Supplementary_files_format_and_content: tab-delimited text file includes RPKM values for two sample types. two replicates per sample type were combined.

source_name: testis

extract_protocol:
testis were removed, undifferentiated spermatogonia was separated by CD90.2 antibody conjugated beads(Cat#130-049-101) and MACS separation colum(Cat#130-042-201), and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: post natal day 4

value: testis

tag: cell type

value: THY1+ spermatogonia

tag: genotype/variation


title: germ cell RA signaling mutant rep2

value: germ cell RA signaling mutant


title: input (no Ab)

value: none (chromatin processed without incubation with the antibody)


title: Dpu_bisulfite_rep3

organism: Daphnia pulex

value: TCO*


title: germ cell RA signaling mutant rep1


title: ChIP-Seq analysis of H3K4me1 in human keratinocyte progenitors (KP)

value: H3K4me1 (Ab8895 anti-H3K4me1)


title: Dpu_bisulfite_rep1


title: Level 2 promoters in human KP cells

data_processing:
After the sequencing, sequence raw data were generated with processing by GenomeAnalyzer Iix. For CAGE tags mapping to multiple genome locations, a weighting strategy based on the number of CAGE tags within a 200 bp neighbourhood around each candidate mapping location was applied. (Faulkner GJ, et al 2008).
Level-1 promoters (TSSs) were created by summing the weighted number of CAGE tags at each genome position. We required at least one CAGE tag in at least one experimental condition; other mapping positions were discarded. The level-1 promoters were clustered into Level-2 promoters (CAGE-promoters) if they were within 20 bp of each other on the same chromosomal strand. We required that the expression of each level-2 promoter was at least 10 tpm in at least one experimental condition; other promoters were dropped.
Genome_build: Hg19
Supplementary_files_format_and_content: The bed file contains the genomic regions of the level-2 promoters and the TPM levels.

growth_protocol: KP cells were obtained from foreskin biopsies of healthy neonatal donors and expanded by cultivation onto lethally irradiated 3T3-J2 cells in growth FAD medium, a DMEM and Ham’s F12 media mixture (2:1) containing FCS (10%), penicillin-streptomycin (1%), glutamine (2%), insulin(5ug/ml), adenine (24.3ug/ml), hydrocortisone (0.4ug/ml), cholera toxin (50ug/ml), triiodotyronine (2nM).

extract_protocol:
CAGE-seq was performed by DNAFORM Inc. at RIKEN Omics Science Center. The samples were prepared according to the OP-SOLEXA-96CAGE-v.3.0.
The sequencing run and the base call analysis were performed according to the manufacturer's protocol Illumina Sequencing Kit v4.


title: ChIP-Seq analysis of H3K4me3 in human keratinocyte progenitors (KP)

value: H3K4me3 (Ab8580 anti-H3K4me3)


title: control rep1


title: Dpu_bisulfite_rep2


title: Sample136 Wild type preGM

first: Claus

last: Nerlov

address: John Radcliffe Hospital, University of Oxford

department: MRC Molecular Haematology Unit

institute: Weatheral Institute of Molecular Medicine

description: Wild type preGM

data_processing:
Reads were aligned to the murine genome (mm9) using STAR with default parameters.
Non-uniquely mapped reads were discarded. Transcript expression values were quantified using Cufflinks as fragments per kilobase of transcript per million mapped reads (FPKM).
Genome_build: mm9

source_name: Wild type mouse

extract_protocol:
From single sorted cells, cDNA was generated according to C1™ Single-Cell Auto Prep IFC for mRNA Sequencing (Fluidigm) using the Fluidigm C1 system and following manufacturer protocol.
Illumina sequenecing libraries were constructed in 96-well plates using the Illumina Nextera XT DNA Sample Preparation kit according to a protocol supplied by Fluidigm.

treatment_protocol: Cells isolated by FACS from mouse bone marrow

value: Bone marrow

value: C57 BL6

tag: phenotype

value: 7AAD- Lin- Sca1- cKit+ CD41- FcRII/III- CD105- CD150-


title: Sample135 Wild type preGM

description: Wild type preGM


title: Sample132 Wild type preGM

description: Wild type preGM


title: Sample133 Wild type preGM

description: Wild type preGM


title: Sample138 Wild type preGM

description: Wild type preGM


title: MEFs_Bmal1

city: New York

first: Yichi

last: Xu

address: 1275 York Avenue

institute: MSKCC

data_processing:
Raw reads in FASTQ files were mapped on mouse genome (mm9 assembly) by Bowtie0.12.8. Only reads uniquely mapped with no more than two mismatches were considered as valid reads.
Peak calling was implemented by MACS1.4.2 with default parameters and cutoff p < 10e-5.
The signal files (.wig) generated from MACS were normalized to per million total reads.
The normalized signal files were further converted to bigwig as the processed data.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

source_name: mouse embryonic fibroblast cells

growth_protocol: Smc3-flox/flox MEF (mouse embryonic fibroblast) cells was originally derived from European conditional mouse mutagenesis program (White et al., 2013) (http://www.informatics.jax.org/allele/MGI:4434007). MEF cells were cultured with 10% PBS in DMEM (Life technology). The MEFs cells used in ChIP-Seq experiment were not transfected by adenovirus.

extract_protocol:
Bmal1 ChIP in Smc3-flox/flox MEF cells were performed following the protocol by Shimomura et al. with modification. Briefly, 10e7 cells were washed with PBS and cross-linked by 1% formaldehyde for 10 min on a rocker at room temperature. The cross-linking was quenched by 2.5 M Glycine with final concentration of 125 mM. The nuclei was extracted at 4℃ from the homogenate by lysis buffer containing protease inhibitors [50mM Hepes-KOH, pH 7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100], [10mM Tris-HCl, pH 8.0, 200mM NaCl, 1mM EDTA, 0.5 mM EGTA], and [10mM Tris-HCl, pH 8.0, 200mM NaCl, 1mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine]. DNA was fragmented with sonication into 150-300 bp at 4℃. 50 µl DNA fragments were stored in 4℃ as the input DNA. The rest of DNA fragments were incubated on rocker at 4℃ for 6 hr with 1:1 ChIP buffer [20% Triton, NaDOC, NaCl, TE, inhibitor] and 4 µl Bmal1 antibody (sc-8550). Then 15 µl protein A/G agarose beads were added into DNA and incubated on rocker at 4℃ overnight. Co-immunoprecipitated DNA was washed with 1 ml buffers [5% Triton, 1% SDS, 1% NaDOC, 93% TE] twice, [5% Triton, 1% SDS, 1% NaDOC, 6% NaCl, 87% TE] twice, [10% LiCl, 5% NP40, 5% Na-DOC, 80% TE] twice, [10% Triton, 90% TE], and TE. Then DNA was reverse cross-linked at 50℃ for 2 hr with TE 100 µl, 10% SDS 3 µl, and protease K 5 µl. QIAquick PCR Purification Kit (QIAGEN) was used to purified ChIP DNA.
Input and ChIP DNA library were prepared by using Illumina TruSeq ChIP Sample Prep Kit and were subjected to deep sequencing with 100 bp read on HiSeq 2000 at CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai, China.

value: Bmal1 (Santa Cruz, catalog# sc-8550, lot# J1211 )

value: wild type

value: MEF


title: MEFs_input


title: Sample134 Wild type preGM

city: Oxford

description: Wild type preGM


title: Sample128 Wild type preGM

description: Wild type preGM


title: Sample131 Wild type preGM

description: Wild type preGM


title: Sample130 Wild type preGM

description: Wild type preGM


title: Sample127 Wild type preGM

description: Wild type preGM


title: Sample129 Wild type preGM

description: Wild type preGM


title: Sample126 Wild type preGM

description: Wild type preGM


title: Sample139 Wild type preGM

description: Wild type preGM


title: Sample124 Wild type preGM

description: Wild type preGM


title: Sample125 Wild type preGM

description: Wild type preGM


title: M phase TAIL-seq

city: Seoul

first: Jong-Eun

last: Park

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

description:
3' end of RNA
TAIL_M.csv
TAIL-seq

data_processing:
For mRNA-seq and ribosome profiling analysis, FASTQ files were processed using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). The reads were first trimmed to retrieve 26 nt from the 5′ end (fastx_trimmer -l 26), filtered for quality (fastq_quality_filter -q 25 -p 80) and against artifact sequences (fastx_artifacts_filter) and collapsed (fastx_collapse). The processed sequences were first mapped to contaminant filter, which is composed of rDNA repeat units (GenBank accession BK000964.1 for NIH3T3 and U13369.1 for HeLa), PhiX genome (GenBank accession J02482.1), Illumina TruSeq primer sequences and all sequences for 5S and 5.8S rRNAs of respective species (retrieved from Rfam 11.0 of the Wellcome Trust Sanger Institute) using GSNAP with four maximum mismatches. Sequences with any match to the contaminants were removed from the subsequent analysis. The remaining sequences were aligned to hg19 genome using GSNAP allowing one mismatch. All multi-mapped reads were resolved to unique mapped reads using custom algorithm. For transcript annotations, reference annotations for human and mouse were compiled using NCBI RefSeq, RepeatMasker, gtRNAdb, Rfam and miRBase databases (the first three were downloaded from the UCSC Genome Browser on Apr 25, 2013; Rfam version 11; miRBase version 19). The alignments were annotated by intersecting with the compiled annotations using BEDTools (Quinlan and Hall, 2010). To quantify RNA or RPF abundance, annotations with more than 60 mapped reads were selected and normalized using Trimmed Mean of M values (TMM) method implemented in the edgeR Bioconductor package (Robinson et al., 2010). Translation efficiency was calculated by dividing TMM normalized RPF value to that of RNA.
TAIL-seq analysis was performed as previously described (Chang et al., 2014), with a slight modification for poly(A) tail length measurement to include short poly(A)-tailed RNAs. Briefly, genes with more than 50 poly(A)-containing reads were analysed for poly(A) tail length measurement. If poly(A) tail length measured using the previous TAIL-seq algorithm was ≥ 15 nt, the read out value was accepted as the final poly(A) tail length. For reads with poly(A) tail length < 15 nt, they were discarded if the length of untemplated sequence at the 3′ end was < 5 nt. For the remaining reads (poly(A) tail length < 15 nt and untemplated sequence ≥ 5 nt), G and C residues were removed from the untemplated sequence and the number of A residues in the resulting sequence was counted to assign poly(A) tail length.
Genome_build: hg19
Supplementary_files_format_and_content: Count.txt file contains read counts from RNA-seq and ribosome profiling libraries. TAIL_M.csv and TAIL_S.csv contains summary of TAIL-seq results

source_name: HeLa

growth_protocol: HeLa cells were maintained in RPMI (Welgene) supplemented with 10% fetal bovine serum (Welgene).

extract_protocol:
Total RNAs were extracted by TRIzol (Invitrogen)
For TAIL-seq, 90 μg of total RNA extracted by TRIzol (Life Technologies) was DNase-treated and purified (>200 nt) by RNeasy MinElute cleanup column (QIAGEN). rRNAs were depleted by using Ribo-Zero kit (Epicentre) and remaining RNAs were ligated to the biotinylated 3′ adaptor and partially digested by RNaseT1 (Ambion). Fragmented RNAs were pulled-down by streptavidin beads and eluted RNAs were phosphorylated at the 5′ end. RNAs were size fractionated by gel purification (500-1,000 nt), and purified RNAs were ligated to 5′ adaptor, reverse-transcribed and amplified by PCR. PCR products were purified using AMPure XP beads (Beckman), and cDNA libraries were sequenced by Illumina HiSeq 2500 (51 × 251 bp paired end run) with PhiX control library and spike-in mixture with various poly(A) length.

treatment_protocol: For S phase-arrest, cells were arrested by 2 mM thymidine for 18 hr and then released into fresh medium for 9 hr, which was followed by second thymidine block for 17 hr. For M phase-arrest, cells were treated with 2 mM thymidine for 18 hr, released for 4 hr and then treated with 100 ng/mL nocodazole for 10 hr.

value: human cervical cancer cell line


title: Sample137 Wild type preGM

description: Wild type preGM


title: Asynchronous cell ribosome profiling 2

description:
Ribosome protected RNA
Count.txt
ribosome profiling

extract_protocol:
Cells were lysed, treated with RNaseI, purified by spin-column and RNAs were extracted by TRIzol (Invtirgen)
Ribosome profiling libraries were prepared using ARTseq Ribosome Profiling Kit (Epicentre) with some modifications. HeLa cells were grown in two 150 mm dishes, harvested and lysed with lysis buffer. For nuclease digestion, 250 μl of cell lysates were treated with 3 μl of ARTseq nuclease at 4° C for 45 min at RT. Monosomes were purified using MicroSpin S-400 column by centrifuging for 2 min at 600 g. RNAs in the flow-through were purified and depleted of rRNAs using Ribo-Zero kit (Epicentre). rRNA depleted RNA fragments were then radiolabeled, and ~30 nt region was purified using 15% Urea-PAGE. Purified RNAs were treated with Antarctic phosphatase (NEB), 5′ phosphorylated and gel purified to remove free ATP. Resulting RNAs were subjected to 3′ adaptor ligation, and gel purified ligated products were ligated with the 5′ adaptor. Adaptor ligated RNAs were reverse transcribed and amplified to yield final ribosome profiling library. The cDNA libraries were sequenced by Illumina HiSeq (1 × 51 bp single run).


title: Sample122 Wild type preGM

description: Wild type preGM


title: S phase TAIL-seq

description:
3' end of RNA
TAIL_S.csv
TAIL-seq


title: Sample123 Wild type preGM

description: Wild type preGM


title: Sample121 Wild type preGM

description: Wild type preGM


title: Sample118 Wild type preGM

description: Wild type preGM


title: Sample117 Wild type preGM

description: Wild type preGM


title: M phase ribosome profiling replicate 2


title: Sample119 Wild type preGM

description: Wild type preGM


title: Sample120 Wild type preGM

description: Wild type preGM


title: Sample114 Wild type preGM

description: Wild type preGM


title: Asynchronous cell ribosome profiling 1


title: Sample116 Wild type preGM

description: Wild type preGM


title: Sample115 Wild type preGM

description: Wild type preGM


title: M phase ribosome profiling replicate 1


title: S phase ribosome profiling replicate 2


title: Sample110 Wild type preGM

description: Wild type preGM


title: Sample112 Wild type preGM

description: Wild type preGM


title: Sample109 Wild type preGM

description: Wild type preGM


title: Sample111 Wild type preGM

description: Wild type preGM


title: Sample108 Wild type preGM

description: Wild type preGM


title: Sample113 Wild type preGM

description: Wild type preGM


title: S phase ribosome profiling replicate 1


title: Asynchronous cell RNA-seq 2

description:
Total RNA
Count.txt
mRNA seq (oligo-dT)

extract_protocol:
Total RNAs were extracted by TRIzol (Invitrogen)
For oligo-dT enriched mRNA-seq, total RNA extracted by TRIzol (Life Technologies) was treated with DNaseI (Takara) and purified by RNeasy Minelute Cleanup kit (QIAGEN). mRNAs were enriched by oligo dT capture. 5 μg of RNAs were fragmented by incubating in the fragmentation buffer provided by NEBNext Magnesium RNA Fragmentation Module at 95 °C for 6.5 min. Fragmented RNAs were size-selected for 60-80 nt RNAs, dephosphorylated by Antarctic phosphatase (NEB) and 5′ phosphorylated by PNK reaction (Takara). RNAs were then subjected to the library preparation protocol used in ribosome profiling described above. The cDNA libraries were sequenced by Illumina HiSeq (1 × 51 bp single run).


title: Sample107 Wild type preGM

description: Wild type preGM


title: Asynchronous cell RNA-seq 1

description:
Total RNA
Count.txt
mRNA seq (oligo-dT)


title: Sample106 Wild type preGM

description: Wild type preGM


title: M phase ribosome profiling synchronized by shake off


title: Sample104 Wild type preGM

description: Wild type preGM


title: Sample105 Wild type preGM

description: Wild type preGM


title: Sample101 Wild type preGM

description: Wild type preGM


title: M phase RNA-seq oligo-dT enriched replicate 2

description:
Total RNA
Count.txt
mRNA seq (oligo-dT)


title: M phase RNA-seq synchronized by shake off

description:
Total RNA
Count.txt
mRNA seq (oligo-dT)


title: Sample99 Wild type preGM

description: Wild type preGM