title: SJMMMB018135

city: Buffalo

first: Lei

last: Wei

state: NY

address: Elm & Carlton Streets

department: Biostatistics & Bioinformatics

institute: Roswell Park Cancer Institute

data_processing:
Basecalling was performed using Illumina Casava 1.7
FASTQ sequences adapter trimmed (curtadapt) and mapped to the mouse mm9 genome by a pipeline that serially  employs STAR and BWA
Mapped reads were counted with HTSEQ
Genome_build: mm9
Supplementary_files_format_and_content: count files are txt format files that contain raw read counts that map  to  transcripts for each defined gene.

source_name: control G3 MB tumorspheres # 19568

growth_protocol: G3 MB tumorspheres # 19568 were derived from tumors that developed in CD1nu/nu mice implanted with cerebellar granule neuronal progenitors transduced with MSCV retroviruses expressing Myc and the green fluorescent protein (GFP) from an internal ribosomal entry site (IRES) (Myc-IRES-GFP) as previously described (Kawauchi et al, 2012). Briefly, spheres were grown in grown in N2, B27, EGF and FGF supplemented neurobasal medium (“complete tumorsphere medium”).

extract_protocol:
Total RNAs were extracted from tumor chunks using Trizol according to manufacturer’s instruction, and as previously published (Murphy et al., 2013).
Libraries were prepared from ~500 ng total RNA with the TruSeq RNA Library Preparation Kit v2 according to manufacturer’s instructions (Illumina, San Diego CA)

treatment_protocol: Tumorspheres were dissociated and infected six times over a 2-day period in virus collection media supplemented with N2, B27, EGF and FGF containing lentiviral particles encoding empty vector (pCDH-EF1-MCS-T2A-copGFP) or WDR11 (pCDH-EF1-WDR11-T2A-copGFP. The following day, infected tumorspheres were suspended in Matrigel (BD Bioscience, San Jose) at a concentration of 100,000 tumorspheres/5µl Matrigel and transplanted into the cortices of CD1-nu/nu mice, as described previously [19, 49].  When mice became moribund, tumors were isolated and tumor chunks flash frozen and stored at -80 degrees Celsius.

tag: cell description

value: Mouse MB cells

tag: treatment


title: SJMMMB018136

status: Public on Oct 17 2017

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus


title: IAV PR8 YTHDF3-FL PAR-CLIP

city: Durham

first: Bryan

middle: R

last: Cullen

state: NC

address: 213 Research Drive

department: Molecular Genetics & Microbiology

institute: Duke University

description:
Y3-PC
PAR-CLIP of YTHDF3-Flag in IAV infected 293T cells, aligned to the negative strand of IAV
PAR-CLIP of YTHDF3-Flag in IAV infected 293T cells, aligned to the positive strand of IAV
small RNA-seq

data_processing:
Library strategy: PAR-CLIP
CASAVA 1.8.2
fastx toolkit
Bowtie (1)
Aligned to HG19 to remove human reads
Aligned remainder of the reads to theIAV PR8 genome
Genome_build: IAV-PR8 ViralMultiSegProj15521
Supplementary_files_format_and_content: [.bed]  Aligned to the influenza PR8 genome.  All 8 segments of IAV-PR8 were concatenated into a single chromosome which was termed EMK-PR8-MtS-cRNAs-Concat, to facilitate viewing on IGV.

molecule: polyA RNA

organism: Homo sapiens

extract_protocol: All samples were processed with the Illumina Tru-seq small RNA-seq kit

tag: cell line

value: 293T clonally expressing YTHDF3-FL

tag: virus

value: IAV PR8

tag: par-clip antibody

value: anti-Flag, Sigma, Cat No F1804, Lot No SLBQ6349V


title: SJMMMB018134


title: Sample 8 -53371

city: Vienna

first: Heinz

last: Ekker

address: Dr. Bohrgasse 3

country: Austria

institute: VBCF

description: Double thymidine arrest + 1-hour release in S phase; 48 hour depletion with luciferase (Gl2) siRNA.

library_source: genomic

data_processing:
Basecalling performed with RTA 1.18.64.0
Alignment to hg19 using bowtie 0.12.5 with S  -p 6   --trim5 0 --trim3 0   -v 2 --best --strata --tryhard   -m 1 --chunkmbs 256
Filtered out reads mapping to chrMT
Peak calling using BayesPeak 1.18.2 with bin.size=1000
Correlation analysis with IntervalStats 24-Apr-2012 using hg19 as domain set
Peak shuffling with bedtools v2.19.1 bedtools shuffle -chrom -noOverlapping -i $1 -g GRCh37.fa.fai
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bed, peaks

molecule: genomic DNA

source_name: SMC3 (ESCO2-deltaPBMA; control siRNA)

growth_protocol: Cells were grown in DMEM supplemented with 10% FBS, 0.2 mM glutamine, penicillin, and streptomycin.

extract_protocol:
Samples were formaldehyde-crosslinked, lysed, sonicated, precipitated, and reverse crosslinked.
Illumina sample libraries were prepared according to NEB protocol E6040

treatment_protocol: Cells were arrested in G1/S by double thymidine arrest and released for 1 hour in S phase. Transfection with siRNA was done at the first thymidine arrest for a total of 48 hours.

value: HeLa

tag: antibody

value: Anti-SMC3 (A845; JM Peters lab; Sumara et al., 2002)


title: 971673_MB4672F3_S19

source_name: WDR11 Overexpression G3 MB tumorspheres # 19568

value: WDR11 overexpression


title: Sample 9 -53373

source_name: SMC3(ac) (ESCO2-deltaPBMA; control siRNA)

value: Anti-SMC3(ac) (K. Shirahige; Nishiyama et al., 2010)


title: IAV PR8 YTHDF2-FL PAR-CLIP

description:
Y2-PC
PAR-CLIP of YTHDF2-Flag in IAV infected 293T cells, aligned to the negative strand of IAV
PAR-CLIP of YTHDF2-Flag in IAV infected 293T cells, aligned to the positive strand of IAV
small RNA-seq

value: 293T clonally expressing YTHDF2-FL


title: Sample 7 -53379

source_name: BrdU (ESCO2-deltaPBMA; control siRNA)

value: Anti-BrdU (Beckton Dickinson, 347580)


title: IAV PR8 PA-m6A-seq

description:
PA-m6A-seq
PA-m6A-seq in IAV infected 293T cells, aligned to the negative strand of IAV
PA-m6A-seq in IAV infected 293T cells, aligned to the positive strand of IAV
small RNA-seq

data_processing:
Library strategy: PA-m6A-seq
CASAVA 1.8.2
fastx toolkit
Bowtie (1)
Aligned to HG19 to remove human reads
Aligned remainder of the reads to theIAV PR8 genome
Genome_build: IAV-PR8 ViralMultiSegProj15521
Supplementary_files_format_and_content: [.bed]  Aligned to the influenza PR8 genome.  All 8 segments of IAV-PR8 were concatenated into a single chromosome which was termed EMK-PR8-MtS-cRNAs-Concat, to facilitate viewing on IGV.

value: anti-m6A, Synaptic Systems, Cat No 202111, Lot No, 202111/4


title: 971672_MB4671F1_S18


title: IAV PR8 GFP-FL PAR-CLIP

description:
GFP-PC
PAR-CLIP of GFP-Flag in IAV infected 293T cells, aligned to the negative strand of IAV
PAR-CLIP of GFP-Flag in IAV infected 293T cells, aligned to the positive strand of IAV
small RNA-seq

value: 293T clonally expressing GFP-FL


title: Bmal1 CKO 2

city: Cleveland

first: Ernest

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

data_processing:
TrimGalore
Bowtie2
MACS2 peak caller
Genome_build: mm10

source_name: retina

growth_protocol: Pups weaned at P20

extract_protocol:
Retinal chromatin DNA was extracted using a rabbit anti-BMAL1 antibody
Rubicon Genomics ThruPlex® DNA kit

treatment_protocol: No external treatment

tag: strain

tag: tissue

value: retina

tag: genotype/variation

value: Bmal1 CKO


title: Red1-FLAG ChIP at 3h after meiotic induction

city: Suita

first: Masaru

last: Ito

state: Osaka

address: Yamadaoka 3-2

country: Japan

institute: Osaka University

description: Used baseline: WCE at 3h after meiotic induction (SPO11-FLAG cells). Baseline raw file "input.3h.fastq" is deposited to GSE52862 (GSM1277169 - SRA Accession SRX385602)

data_processing:
Sequence reads were filtered and end-trimmed using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). The reads containing tag sequences were removed using tagdust (Lassmann et al. 2009).
The resulting reads were mapped to the S. cerevisiae genome (sacCer2) using bowtie with default settings, except for the option “–n 3” (Langmead et al. 2009).
To calculate DNA enrichment (ChIP/Input), the chromosomes were divided into 10-bp bins. Counting of reads in each bin and normalization were performed using parse2wig with the options “-binsize 10 -F3 47 -flen 150” (Nakato et al. 2013).
Genome_build: sacCer2
Supplementary_files_format_and_content: wig file. Scores represent DNA enrichment (ChIP/Input).

organism: Saccharomyces cerevisiae

source_name: Chromatin immunoprecipitated DNA

growth_protocol: Cells were grown on a YPD plate for 2 days at 30ºC. The cells were grown to a density of 4.0x10e7 cells/ml at 30ºC in presporulation medium (SPS; 0.5% yeast extract, 1% peptone, 0.17% yeast nitrogen base w/o amino acid and ammonium sulfate, 1% potassium acetate, 0.5% ammonium sulfate, usual level of amino acids, 50 mM potassium phthalate, and antifoam, pH 5.5). The cells were suspended in sporulation medium (SPM; 1% potasium acetate, 1/5 levels of amino acids, and polypropylene glycol) to a density of 2x10e7 cells/ml, and incubated at 30ºC for sporulation.

extract_protocol:
The cells were disrupted using Multi-Beads Shocker (YASUI KIKAI, Osaka) with 0.5-mm zirconia beads. Cell lysates were sonicated to obtain average 300 bp of genomic DNA fragments. Whole cell extracts (WCEs) were subjected to immunoprecipitation with anti-FLAG antibody (Wako) coupled to Dynabeads protein A (Invitrogen). A small amount of WCEs was used as input sample. The chromatin immunoprecipitated sample and input sample were incubated overnight at 65ºC, incubated for 2 hours at 50ºC with proteinase K, and DNA was purified using QIAquick Spin Purification Kit (QIAGEN).
Before library preparation, IP DNA and input DNA were fragmented to 150 bp using the covaris model S220. Multiplexed DNA library preparation was performed with the NEBNext ChIP-Seq library prep master mix set for Illumina (P/N E6240S, NEB) and the NEBNext multiplex oligos for Illumina (P/N E7335S, NEB). After 15 cycles of PCR amplification, about 275 bp libraries were obtained. The libraries were sequenced on the MiSeq with the MiSeq Reagent Kit v2 (50-cycles).

treatment_protocol: The cells were fixed in 1% formaldehyde for 10 min at room temperature and then treated with 125 mM glycine for 5 min at room temperature. The cells were washed with ice-cold TBS twice, freezed with liquid nitrogen, and stored at -80ºC.

tag: strain background

tag: culture

value: 3h after transfer to sporulation medium (SPM)


title: IAV PR8 YTHDF1-FL PAR-CLIP

description:
Y1-PC
PAR-CLIP of YTHDF1-Flag in IAV infected 293T cells, aligned to the negative strand of IAV
PAR-CLIP of YTHDF1-Flag in IAV infected 293T cells, aligned to the positive strand of IAV
small RNA-seq

value: 293T clonally expressing YTHDF1-FL


title: 971671_MB4670G3_S17


title: Sample 6 -53370

description: Double thymidine arrest + 1-hour release in S phase; 48 hour depletion with ESCO1 siRNA .

source_name: SMC3(ac) (ESCO2 WT; ESCO1 siRNA)


title: Sample 4 -53378

source_name: BrdU (ESCO2 WT; ESCO1 siRNA)


title: Sample 5 -53368

source_name: SMC3 (ESCO2 WT; ESCO1 siRNA)


title: Bmal1 CKO 1


title: 971670_MB4670F4_S16


title: E13.5_primary_motor_neuron

city: Boston

first: James

middle: Alexander

last: Briggs

state: Massachusetts

address: 200 Longwood Avenue, Harvard Medical School

department: Department of Systems Biology

institute: Harvard Medical School

description:
Sample 6
Timepoint label = 1 in processed data file
E13.5_primary_motor_neuron.filtered_normalized_counts.csv.gz
E13.5_primary_motor_neuron.raw_umifm_counts.csv.gz

data_processing:
The barcode read was first filtered based on presence of two sample barcode components separated by the W1 adaptor sequence (GAGTGATTGCTTGTGACGCCTT), as previously described (Klein et al., Cell 2015).
The cDNA read was then trimmed using Trimomatic (5) (version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20  MINLEN:30).
Barcodes for each read were matched against a list of the pre-determined barcodes, and errors of up to two nucleotides mismatch were corrected. Reads with a barcode separated by more than two nucleotides from the reference list were discarded. The reads were then split into barcode-specific files for mapping and UMI filtering.
The trimmed reads were aligned using Bowtie (version 1.1.1, parameters: -n 1 -l 15 -e 100 -m 200 -best -strata -a) to the mouse transcriptome. The reference transcriptome was built using annotations from ENSEMBL (GRCm38.81) including all annotations with ""Transcript Support Levels"" of 1, 2, or NA (only accepted for protein coding genes).
A custom Python and PySAM script to process mapped reads into counts of UMI-filtered transcripts per gene, as previously described (Zilionis et al., Nature Protocols in press)
Genome_build: GRCm38
Supplementary_files_format_and_content: The raw_umifm_counts files include raw unique molecular identifier (UMI)-filtered counts for all transcriptomes (prior to filtering). The filtered_normalized_counts files have normalized counts for transcriptomes passing all filtering steps. In both cases, columns = cells (with the exception of the first column), rows = genes (with the exception of the first two rows). Column 1 gives the label for each row. Row 1 contains the timepoint label (1 = day 0; 2 = day 5/6; 3 = day 11/12). In raw_umifm_counts files, row 2 contains flag for cell pass filtering (0=fail, 1=pass). In filtered_normalized_counts files, row 2 contains an integer cluster label. Cluster labels follow Briggs, JA and Li, VC et al. For direct_programming, clusterIDs -1:11 = outlier, ESC, NP, EMN, LMN, FN, NN, Gl1, Gl2, Mus, Meso, Endo, respectively. For the standard_protocol, clusterIDs -1:11 = outlier, ESC, NP, PNP, PVNP, MNP, EMN, LMN, Oligo, Astro, Mus, Stro. Rows 3+ contain counts for each gene (gene symbol is in column 1). The SPRING_combined_trajectories file contains a subset of cells from each protocol merged together under the same format except row 1 = Cluster ID, and rows 2+ contain counts for each gene. Data has been total count normalized. The included cells are described in the manuscript and represent the major motor neuron differentiation pathway of both protocols. Cluster 1 = ES; clusters 2-4 = direct_programming (NP, EMN, LMN); clusters 5-10 = standard_protocol (NP, PNP, PVNP, MNP, EMN, LMN).

source_name: Embryo-derived primary motor neurons (Hb9:GFP+)

growth_protocol: ESCs were cultured in standard media (DMEM with LIF + 15% fetal bovine serum) on 0.2% gelatin-coated dishes.

extract_protocol:
Cells were encapsulated using the inDrops platform, into droplets on ice and lysed in the 4nL microfluidic droplets using a final concentration of 0.4% NP-40. Single cell lysates were subject to reverse transcription at 50°C without purification of RNA (as previously described in Klein et al., Cell 2015).
Libraries were prepared as in Zilionis et al., Nature Protocols (2017), with the exception of the first round of libraries, for which the final PCR step was carried out as in Klein et al., Cell 2015.

treatment_protocol: I. CELL CULTURE: Twenty-four hours before starting differentiation, ESCs were trypsinized and seeded onto plates pre-coated with a mix of poly-d-lysine (100 ug/ml) and laminin (50 ug/ml) instead of gelatin for adherence. ESCs were counted by a Beckman Coulter Counter and seeded at a density of approximately 200,000 cells per well of a 6-well dish. At day 0 (ESCs), the media was switched from standard ES media to N2B27 media (Invitrogen). Doxycycline was also added at 3 ug/ml starting to induce expression of the NIL transcription factors. Media was changed daily. For the standard programming protocol, the steps described in Wu et al. were followed strictly. II. MOUSE WORK: The B6.Cg-Tg(Hlxb9-GFP)1Tmj/J mice (JAX# 005029) were bred with C57BL/6J (JAX# 000664) for embryonic motor neurons dissection. All animal protocols were approved the Institutional Animal Care and Use Committee at Boston Children’s Hospital. On gestational day 13 (E13), the female mice were anesthetized and all embryos were collected by caesarian section. Only GFP embryos were used for further dissection. The spinal cords were isolated and their meninges were removed. Each isolated spinal cord was dissociated by trypsin and mechanical trituration. After filtering the cells with 100 μm strainers, the cells were spun down and re-suspended in PBS, and subjected to flow cytometry. Cells were run through a 100 μm nozzle at low pressure (20 p.s.i.) on a BD FACSaria II machine (Becton Dickinson, USA). A neural density filter (2.0 setting) was used to allow visualization of large cells.

tag: cell type

tag: timepoint/stage

tag: # cells (pass filter)

value: B6.Cg-Tg(Hlxb9-GFP)1Tmj/J mice (JAX# 005029) bred with C57BL/6J (JAX# 000664)


title: Sample 2 -53365

source_name: SMC3 (ESCO2 WT; control siRNA)


title: Sample 1 -53377

source_name: BrdU (ESCO2 WT; control siRNA)


title: Sample 10 -53380

source_name: BrdU (ESCO2-deltaPBMA; ESCO1 siRNA)


title: 1% input DNA – Scramble

city: Nice

first: Olivier

last: Croce

address: Faculty of Medicine - Pasteur tower - 28, av. Valombrose

department: Bioinformatics

country: France

institute: IRCAN

data_processing:
Raw fastq files containing reads were trimmed using Trimmomatic V0.36, with default parameters and the “TrueSeq3-SE” set to remove leavings adapters
Reads were aligned using Bowtie on human hg38 release, with default settings
Aligned files (.bam) from different replicates of the same samples were merged with BedTools
The peaks calling software “MACS2” performed peaks identification,taking into account the related “1% input file” in each case.  A 1e-5 p-value cutoff was applied on results.
Peaks were annotated using UCSC table browser tools
Genome_build: hg38
Supplementary_files_format_and_content: bed files with annotations, including for each peak (I)  the first gene found (if any) ; (ii) the first gene found (if any) in a range of +/- 100kb from the peak, (ii) all genes found in a range +-100kb from the peak

source_name: Post-mitotic differentiated muscle cells - MYOTUBES

growth_protocol: For day-to-day maintenance, human myoblasts were seeded in dishes coated with 0.1% pigskin gelatin in 4:1 Dulbecco modified Eagle medium/Medium 199 supplemented with 15% FBS, 0.02M HEPES, 1.4mg/l vitamin B12, 0.03mg/l ZnSO4, 0.055mg/l dexamethasone, 2.5μg/l hepatocyte growth factor and 10μg/l basic fibroblast growth factor. Cultures were maintained in a 5% oxygen environment and passaged at ~60% confluency. Population doublings (PDs) were calculated as PD = ln[(final number of cells)/(initial number of cells)]/In(2).

extract_protocol:
Lysates were clarified from sonicated nuclei and TRF2-DNA complexes were isolated with antibody.
Libraries were prepared according to the standards Illumina's instructions

treatment_protocol: Myogenicity of the cells was verified by myotubes formation following a change to differentiation medium (2% horse serum in 4:1 Dulbecco modified Eagle medium: Medium 199) when 70-90% confluent. Transductions were performed 5 days after complete differentiation.

value: Post-mitotic differentiated muscle cells (myotubes)

tag: origin

value: Muscle biopsy - deltoid

tag: viral transduction

value: sh Scramble

tag: population doublings (from htert removal)

tag: chip antibody


title: 1% input DNA – Empty

value: pWPIR-IRES-GFP


title: 1% input DNA – shTRF2

value: sh TRF2


title: 1% input DNA – TRF2


title: Empty

value: TRF2 (IMGENEX, monoclonal mouse IMG-124A, clone 4A794.15)


title: day12_standard_protocol

description:
Sample 5
Timepoint label = 3 in processed data file
standard_protocol.filtered_normalized_counts.csv.gz
standard_protocol.raw_umifm_counts.csv.gz

source_name: ESC-derived motor neuron cells

value: ESC-derived motor neuron cells

value: Day 12

tag: differentiation protocol

value: standard protocol


title: day6_standard_protocol

description:
Sample 4
Timepoint label = 2 in processed data file
standard_protocol.filtered_normalized_counts.csv.gz
standard_protocol.raw_umifm_counts.csv.gz

value: Day 6


title: TRF2 over-expressed


title: day11_direct_programming

description:
Sample 3
Timepoint label = 3 in processed data file
direct_programming.filtered_normalized_counts.csv.gz
direct_programming.raw_umifm_counts.csv.gz

value: Day 11

value: direct programming


title: TRF2 under-expressed


title: day5_direct_programming

description:
Sample 2
Timepoint label = 2 in processed data file
direct_programming.filtered_normalized_counts.csv.gz
direct_programming.raw_umifm_counts.csv.gz

value: Day 5


title: Scramble


title: WAY-Pax9-WT-422-8

status: Public on Oct 16 2017

city: Salt Lake City

first: Shihai

last: Jia

state: ut

address: 20 South 2030 East, Room 320 BPRB

department: Department of Neurobiology

institute: University of Utah

description: E14 fpkm

data_processing:
Mouse ensembl annotations (build 74) were downloaded and converted to genePred format.  Splice junction sequences were generated using USeq’s (v8.8.8) MakeTranscriptome application using a radius of 46.  The splice junction sequences were added to the mouse chromosome sequences (mm10) and run through novoindex (v2.8) to create the transcriptome index.
Reads were aligned to the transcriptome index described above using Novoalign (v2.08.03), allowing up to 50 alignments for each read.  USeq’s SamTranscriptomeParser application was used to select the best alignment for each read and convert the coordinates of reads aligning to splices back to genomic space.
Read counts for each gene were generated using USeq’s DefinedRegionDifferentialSeq application.  These counts were used in DESeq2 to measure the differential expression between each condition.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: palate shelves

extract_protocol: E13.5 and E14 with or without treatment mouse embryo dissected and put on ice cold PBS, micro-dissect the palate shelves under microscope. Micro-dissected tissues were frozen at -80℃, total RNA was extracted by using RNeasy micro kit from Qiagen.cDNA was made by Illumina TruSeq RNA Sample Prep Kit v2 with oligo(dT) selection.

treatment_protocol: the pregnant Pax9+/- females were treated with WAY-262611 daily injection via tail vein from E10.5 to E14

value: Palate shelf

tag: age

value: embryonic day 14

tag: genotype

tag: treatment


title: CTR-Pax9-mt-393-8

description: E14 fpkm

value: Control


title: WAY-Pax9-mt-422-7

description: E14 fpkm


title: Sample 3 -53367

source_name: SMC3(ac) (ESCO2 WT; control siRNA)

tag: cell line

value: HeLa

tag: antibody

value: Anti-SMC3(ac) (K. Shirahige; Nishiyama et al., 2010)


title: WAY-Pax9-Het-422-1

description: E14 fpkm

tag: strain

tag: tissue


title: CTR-Pax9-Het-393-4

description: E14 fpkm


title: WAY-Pax9-mt-422-4

description: E14 fpkm


title: CTR-Pax9-Het-393-5

description: E14 fpkm


title: WAY-Pax9-WT-318-6

description: E14 fpkm


title: CTR-Pax9-mt-393-6

description: E14 fpkm


title: CC-223 Mouse #268

city: Cincinnati

first: Hala

middle: Elnakat

last: Thomas

state: Ohio

address: 3125 Eden Ave,Vontz bldg, rm 1226, ATTN: Hala Elnakat Thomas

department: Internal Medicine

institute: UNIV OF CINCINNATI

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq in Casava 1.8
fastq seqences were aligned to hg19 using Tophat
number of reads was calculated for each Entrez gene
differential expression analysis was performed using edgeR
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited file with raw counts with genes in rows and samples in columns

source_name: Tumor from a mouse switched to CC-223

growth_protocol: Please refer to the manuscript by Orr-Asman et al for further detailed description. Nude male mice (5-week old) were injected with 2x106 BON-luci cells subcutaneously. Once tumor volumes averaged ~180 mm3, mice were randomized into 2 groups of equal tumor volume for treatment with either placebo or rapamycin. Rapamycin was administered in drinking water at (10 mg/kg body weight (BW) daily). Once the tumors progressed on rapamycin according to a modified RECIST criteria, these mice were divided into 2 cohorts of similar tumor distribution and either maintained on rapamycin or switched to CC-223 for about 17 days. Mice were starved for 3h prior to the time of euthanasia at which point all tumors were harvested and snap-frozen using liquid nitrogen.

extract_protocol: Please refer to the manuscript by Orr-Asman et al for detailed description of the extraction protocol. Briefly, RNA was isolated from each ~50 mg of each tumor sample using the mirVana miRNA Isolation Kit (ThermoFisher) according to the manufacturer protocol. Target RNA enrichment was performed from ~750 ng of RNA by isolation of polyA RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs). PrepX PolyA script was run for automated polyA RNA isolation. RNA-seq library preparation was done using NEBNext Ultra Directional RNA Library Prep Kit (New England BioLabs) with dUTP for cDNA synthesis to maintain strand specificity, indexing via 11 cycles of PCR enrichment and finally cleaning up of the amplified library by AMPure XP beads for QC analysis. The quality and yield of the purified library was analyzed with a Bioanalyzer (Agilent) and a DNA high sensitivity chip; then the concentration was quantified by qPCR using the Kapa Library Quantification kit (Kapabiosystem). Individually indexed and compatible libraries were proportionally pooled (~25x106 million reads per sample) for clustering with a cBot system (Illumina). Libraries at the final concentration of 15 pM were clustered onto a single read flow cell using Illumina TruSeq SR Cluster kit v3, and sequenced to 50 bp using TruSeq SBS kit on an Illumina HiSeq system.

value: BON cells subcutaneously injected into mice

tag: cell source

value: Xenografts of BON cells which were derived from a metastasis of a human pancreatic neuroendocrine tumor

value: Tumor


title: CTR-Pax9-WT-389-5

description: E14 fpkm


title: CC-223 Mouse #263


title: CTR-Pax9-mt-389-2

description: E14 fpkm


title: WAY-Pax9-mt-318-2

description: E14 fpkm


title: CC-223 Mouse #258


title: CC-223 Mouse #251


title: CC-223 Mouse #245


title: CC-223 Mouse #231


title: CC-223 Mouse #236


title: CC-223 Mouse #237


title: CC-223 Mouse #223


title: CC-223 Mouse #213


title: CC-223 Mouse #227


title: Rapamycin Mouse #266

source_name: Tumor from a mouse treated with rapamycin


title: Rapamycin Mouse #261


title: CC-223 Mouse #202


title: CC-223 Mouse #201


title: CC-223 Mouse #212


title: Rapamycin Mouse #259


title: Rapamycin Mouse #247


title: Rapamycin Mouse #244


title: Rapamycin Mouse #229


title: Rapamycin Mouse #235


title: Rapamycin Mouse #207


title: Rapamycin Mouse #206


title: Rapamycin Mouse #226


title: RNA-seq_CR3flp_P4_rep3

city: Research Triangle Park

first: Paul

middle: A

last: Wade

address: 111 TW Alexander Drive

department: Laboratory of Molecular Carcinogenesis

institute: NIEHS

description:
processed data files:
gene_counts_per_sample.RNA-seq_ProgesteroneTreatment.txt
RNA-seq_DEGs.progesterone.txt

data_processing:
Reads were filtered based on a mean base quality score >20.
For RNA-seq analysis, filtered read pairs were mapped against the hg19 reference genome by STAR (version 2.5) with the following parameters: -- outSAMattrIHstart 0 --outFilterType BySJout --alignSJoverhangMin 8 -- outMultimapperOrder Random (other parameters at default settings). Mapped read counts per gene were collected by Subread featureCounts (version 1.5.0-p1). Differentially expressed genes were identified with DESeq2 (v1.10.1) using filtering thresholds of FDR <0.01 and fold change >2.
genome build: hg19
processed data files format and content: bigWig, bed, txt

growth_protocol: Cells were grown on 15 cm plates in high glucose DMEM medium with 10% FBS

extract_protocol: Libraries were prepared according to BIOO SCIENTIFIC instruction. ATAC-seq libraries were prepared by following the original protocol (Buenrostro et al., 2013) with several modifications (as described above)

value: T47D wt/R330fsl cells

tag: passages


title: RNA-seq_CR3flp_Ve_rep3


title: RNA-seq_CR3flp_Ve_rep1


title: RNA-seq_CR3flp_Ve_rep2


title: RNA-seq_T47Dflp_P4_rep2

value: T47D Flp control cells


title: RNA-seq_CR3flp_P4_rep1


title: RNA-seq_T47Dflp_P4_rep3


title: Rapamycin Mouse #253

tag: cell type


title: RNA-seq_T47D_ExoR330fs_rep3

description:
processed data files:
gene_counts_per_sample.RNA-seq.txt
RNA-seq_DEGs.T47Dflp.vs.CR3flp.txt
RNA-seq_DEGs.Vector.vs.ExoR330fs.txt


title: RNA-seq_T47D_ExoR330fs_rep2


title: RNA-seq_T47Dflp_Ve_rep2


title: RNA-seq_T47D_Exo-wtGATA3_rep1


title: RNA-seq_T47D_Exo-wtGATA3_rep3


title: RNA-seq_T47Dflp_Ve_rep3


title: RNA-seq_CR3flp_P4_rep2


title: Rapamycin Mouse #214


title: RNA-seq_T47D_Vector_rep2


title: Rapamycin Mouse #203


title: RNA-seq_T47D_Exo-wtGATA3_rep2


title: RNA-seq_T47D_Vector_rep3


title: RNA-seq_T47Dflp_rep2


title: RNA-seq_CR3flp_rep3


title: RNA-seq_T47Dflp_rep3


title: RNA-seq_CR3flp_rep1


title: RNA-seq_CR3flp_rep2


title: RNA-seq_T47D_rep3


title: RNA-seq_T47D_Vector_rep1


title: RNA-seq_T47D_rep2


title: A549 replicate 2

first: Ann

last: Harris

address: 10900 Euclid Ave

department: Genetics and Genome Sciences

institute: Case Western Reserve University

data_processing:
Single-end reads (50bp) and paired-end reads (100bp) were mapped to the reference human genome (hg19) with ENSEMBL Release 74 of human genome annotation as transcriptome mapping, using TopHat (v2.0.10)
The aligned reads were then processed by Cufflinks (v2.1.1) to assemble expressed genes and transcripts against the UCSC hg19 gene structure annotation, and estimate expression levels for each transcript.
The assembly files for each of the samples were then merged to create a single transcriptome annotation and differentially expressed genes identified by Cuffdiff.
Samples were then normalized and expressed as fragments per kilobase of transcript per million fragments mapped (FPKM) and both a test statistic (p-value) and an adjusted p-value (q-value) were calculated.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each gene and fold difference between non-targeted control and miR-1343 deletion clones

source_name: Lung adenocarcinoma cells

growth_protocol: Cells were grown in DMEM low glucose supplemented with 10% FBS

extract_protocol:
Trizol® (Life Technologies) was used for RNA extraction
RNA libraries were prepared from 2 ug of total RNA using TruSeq™ RNA sample preparation kit v2 as per the manufacturer's low-throughput protocol (Illumina)

treatment_protocol: The pMJ920-Cas9-GFP plasmid (Jinek et al. 2013) and two guide RNAs flanking the miR-1343 locus (blunt cloned into pSCB, Agilent) were transfected into A549 cells at 50% confluence using Lipofectamine 2000 (Life Technologies). Cas9-GFP positive cells were selected by fluorescence activated cell sorting 48 hours after transfection and grown as single clones. miR-1343 locus deletion was confirmed by PCR of genomic DNA isolated from clones. Three individual deletion clones, 3 non-targeted wild type clones, and 3 separate passages of non-clonal A549 cells were grown to similar confluences and lysed in Trizol to be harvested for RNA extraction.

value: A549 cells

value: wild type


title: A549 replicate 3


title: A549 replicate 1


title: miR-1343 deletion clone 12

description:
clones_A549_gene_exp.diff
clones_gene_exp.diff

value: Cas9 + guide RNA transient transfection, followed by FACS of single cells

value: miR-1343 deleted


title: RNA-seq_T47Dflp_P4_rep1


title: RNA-seq_T47Dflp_Ve_rep1


title: RNA-seq_T47D_ExoR330fs_rep1


title: miR-1343 deletion clone 9


title: Non-targeted clone 11

value: miR-1343 wild type


title: RNA-seq_T47Dflp_rep1


title: RNA-seq.CRctrl.rep3

description: Gene_counts_per_sample.Xenograft_CRctrl.txt

data_processing: Reads were filtered based on a mean base quality score >20. Filtered read pairs were mapped against the hg19-mm10 concatenated reference genome by STAR (version 2.5) with the following parameters: -- outSAMattrIHstart 0 --outFilterType BySJout --alignSJoverhangMin 8 -- outMultimapperOrder Random (other parameters at default settings). Mapped read counts per human gene were collected by Subread featureCounts (version 1.5.0-p1). Differentially expressed genes were identified with DESeq2 (v1.10.1) using filtering thresholds of FDR <0.01 and fold change >2.

growth_protocol: Tumors were grown in nude mice (for 7-10 weeks) in the presence of estrogen pellets +/- progesterone pellets.

extract_protocol:
Total RNAs were extracted by QIAzol Reagent and purified by miRNAeasy kit (QIAGEN).
Sequencing libraries were prepared by TruSeq RNA Library Prep Kit (Illumina)

value: T47D CRISPR control (CRctrl) cells


title: RNA-seq.CRctrl.rep1


title: Non-targeted clone 8


title: Non-targeted clone 5


title: RNA-seq.CR3flp.Xenograft.E2plusP4.rep2

value: T47D wt/R330fsl tumors

value: 7 weeks


title: RNA-seq.CR3flp.Xenograft.E2plusP4.rep1


title: miR-1343 deletion clone 4


title: RNA-seq.T47Dflp.Xenograft.E2plusP4.rep1

value: T47D Flp control tumors


title: RNA-seq.T47Dflp.Xenograft.E2plusP4.rep2


title: RNA-seq.CR3flp.Xenograft.E2.rep2

value: 10 weeks


title: RNA-seq.CR3flp.Xenograft.E2.rep1


title: ChIP-seq_PolII_CR3flp_P4_rep2

description:
processed data files:
PolII_ChIP_CR3flp_P4.bigWig

data_processing:
Reads were filtered based on a mean base quality score >20.
For ChIP-seq analysis, reads were mapped to hg19 genome using Bowtie 0.12.8. Duplicate reads were removed using MarkDuplicates.jar from picard-tools-1.107 package. Paired-end reads were converted to a single fragment for metaplot analyses and visualization on the UCSC Genome Browser. After normalization within each data set, bigWig files were generated to visualize the genomic coverage. Peak calling was performed with HOMER v4.1 at default parameters.
genome build: hg19
processed data files format and content: bigWig, bed, txt

treatment_protocol: Cells were treated with a hypotonic buffer, and lysed with Tris-HCl pH 8.0 based buffer with appropriate concentration of SDS. Chromatin fragmentation was performed by sonication with Covaris. DNA was precipitated with antibody against each target protein.

value: anti-PolII serum (Wade lab)


title: input ExoR330fs-1

description:
processed data files:
input_ExoR330fs.bigWig

value: T47D ExoR330fs


title: ChIP-seq_PolII_T47Dflp_Ve_rep1

description:
processed data files:
PolII_ChIP_T47Dflp_Vehicle.bigWig


title: ChIP-seq_PolII_T47Dflp_P4_rep2

description:
processed data files:
PolII_ChIP_T47Dflp_P4.bigWig


title: ChIP-seq_PolII_T47Dflp_Ve_rep2


title: ChIP-seq_PolII_CR3flp_Ve_rep1

description:
processed data files:
PolII_ChIP_CR3flp_Vehicle.bigWig


title: RNA-seq.T47Dflp.Xenograft.E2.rep1


title: ChIP-seq_PolII_CR3flp_P4_rep1


title: Female Rep5

city: Boulder

first: Leslie

last: Leinwand

state: CO

address: 596 UCB

department: MCDB

institute: University of Colorado at Boulder

data_processing:
Illumina Casava1.8.2 and software used for basecalling and demultiplexing
Fastq quality control via Fastqc; Command = fastqc <.fastq>
Trimmed adapter sequences with trimmomatic version 0.32; Command = Trimmomatic-0.32/trimmomatic-0.32.jar PE -phred33, TruSeq3-PE.fa:2:30:10:8:True
Alignment to reference transcriptome via Tophat2 version 2.0.12; Command = Tophat2 -p 16  --b2-very-sensitive --microexon-search --no-mixed  --library-type fr-firststrand -G rn6_rn5Mito.gtf
Gene counts obtained via Htseq-count version 0.6.1; Command =htseq-count -f bam -s reverse -m intersection-nonempty -t exon -i gene_id
Differential expression analysis via DESeq version v1.10.1 method=c("pooled"))
Genome_build: rn6
Supplementary_files_format_and_content: DESeq formated differential expressed gene file. Tab-delimited;id, baseMean, baseMeanA (represents males), baseMeanB (represents females), foldChange, log2FoldChange, pval, padj

organism: Rattus norvegicus

source_name: Adult rat ventriuclar myocytes

growth_protocol: primary adult rat ventricular myocytes were isolated from the animal using a langendorff apparatus. Cells were plated on 10cm dishes in spring horn media for 45 minutes prior to being flash frozen and then used for total RNA isolation

extract_protocol:
Total RNA was isolated using the miRNeasy mini kit (Qiagen, Valencia, CA) according to the manufacturers protocol with the on-column DNase digestion. RNA concentration was determined using the Qubit RNA BR Assay (Invitrogen, Carlsbad, CA) and RNA integrity was analyzed with the Agilent Bioanalyzer (Agilent, Santa Clara, CA) with all of the RNA samples used for sequencing having a RNA integrity number (RIN) of at least 9.
Ribo-zero gold depleted paired-end sequencing libraries were then constructed from 650ng total RNA using the TruSeq Stranded Total RNA Sample Kit (Illumina, San Diego, CA) according to the manufacturers protocol.

treatment_protocol: No treatment

value: Sprague Dawley

value: Adult rat ventriuclar myocytes

value: 3-4 months

value: wild-type

tag: Sex

value: female


title: input ExoR330fs-2


title: Female Rep4


title: RNA-seq.CR3flp.Xenograft.E2.rep3


title: Female Rep2


title: Female Rep3


title: ChIP-seq_Ty1-Exo330fs_rep2

description:
processed data files:
R330fs_ChIP.bigWig
R330fs_ChIP.bed

value: anti-Ty1 (Menafra et al., 2014)


title: Female Rep1


title: ChIP-seq_Ty1-Exo330fs_rep1


title: RNA-seq.CRctrl.rep2


title: ChIP-seq_PolII_CR3flp_Ve_rep2

value: T47D wt/R330fsl cells


title: ChIP-seq_PolII_T47Dflp_P4_rep1

value: T47D Flp control cells


title: Male Rep5

value: male


title: input_CR3flp_P4_rep2

description:
processed data files:
input_CR3flp_P4.bigWig


title: Male Rep4


title: input_CR3flp_P4_rep1


title: input_CR3flp_Ve_rep2

description:
processed data files:
input_CR3flp_Vehicle.bigWig


title: input_T47Dflp_Ve_rep1

description:
processed data files:
input_T47Dflp_Vehicle.bigWig


title: Male Rep3


title: input_T47Dflp_P4_rep1

description:
processed data files:
input_T47Dflp_P4.bigWig


title: Male Rep1


title: Male Rep6


title: ChIP-seq_PR_CR3flp_P4_rep1

description:
processed data files:
PR_ChIP_CR3flp_P4.bigWig
PR_ChIP_CR3flp_P4.bed

value: anti-PR (Santa Cruz, H-190)


title: ChIP-seq_PR_CR3flp_P4_rep2


title: input_T47Dflp_P4_rep2


title: SEP3-AGe1C6-R2

city: Berlin

first: Jose

middle: M.

last: Muino

address: Max-Dohrn-Str. 8-10

country: Germany

institute: German Federal Institute for Risk Assessment

data_processing:
Basecalls performed using CASAVA version 1.8
Read that did not pass the filter quality of CASAVA 1.8 were removed
Reads that mapped to the PhiX174 genome allowing one misatche were removed (using Soapv2 )
Barcodes at the beginning and at the end of the sequence read were used (no mistmach allowed) to obtain the different libraries provided. Barcoded were eliminated from the sequence read
Genome_build: Not applicable- SELEX reads are not aligned to reference genome
Supplementary_files_format_and_content: Relative affinities were calculated for all possible 12-mer sequence. Tables providing information of sequence of the 12-mer, relative affinity, and standard deviation of the relative affinity estimation are included in the submission

molecule: other

organism: synthetic construct

source_name: synthetic Oligos

extract_protocol:
The dsDNA libraries were made from the ssDNA sequences by single-cycle PCR amplification with a complementary primer essentially as described before (Jolma et al., 2010). The dsDNA libraries contained 20 random nucleotide fragment flanked by specific barcodes that allowed for later characterization when multiplexed in high-throughput sequencing. Protein dimers were synthesized using TNT SP6 Quick Coupled Transcription/Translation System (Promega) following the manufacturer’s instructions in a total volume of 20 µl and equimolar expression plasmid concentrations. The binding reaction mix was prepared essentially as described previously for EMSA experiments (Egea-Cortines et al., 1999; Smaczniak et al., 2012b) and contained 20 µl of in vitro-synthesized proteins and 50-100 ng of dsDNA library in a total volume of 120 µl. The binding reaction was incubated on ice for 1 h followed by 1 h immunoprecipitation with protein specific antibodies (affinity-purified peptide antibodies, Eurogentec) coupled to magnetic beads (MyOne, Invitrogen) in a thermomixer at 4 °C with constant mixing at 700 rpm. Magnetic beads with attached antibodies where prepared in advance according to manufacturer’s instructions (MyOne, Invitrogen) with purified antibodies resuspended in 1X PBS (~1 mg/ml); 20 µg of antibodies and 0.5 mg of beads were used for a single binding reaction. After immunopreciptiation, beads were washed 5 times with 150 µl of binding buffer without salmon-sperm DNA and bound DNA was eluted with 50 µl 1X TE in a thermomixer at 90 °C with full mixing speed. Afterwards, magnetic beads were immobilized and the supernatant was transferred to a 1.5-ml tube. DNA fragments were amplified with 10 to 15 cycles of PCR with SELEX round-specific primers (Jolma et al., 2010) and the total amplicon was used in the subsequent SELEX round. The amplification efficiency was checked on the agarose gel by comparing to a known concentration of a standard probe. Samples for sequencing, after amplification, were cut out from agarose gel and purified using MinElute Gel Extraction Kit (Qiagen).
Each SELEX library was quantified by Qubit and processed by BioAnalyser. The same rounds of SELEX were multiplexed by mixing in equimolar amounts and diluted to 10 nM. Such multiplexed libraries were processed following Illumina's "Denature and Dilute Libraries Guide" with 40% PhiX control. Samples were sequences on GAII or HiSeq2000.

value: Custom made, peptide specific antibody, anti-SEP3 (Eurogentec), HPLC-purified

tag: round of selex enrichment


title: input_CR3flp_Ve_rep1


title: SEP3-AGe1C6-R1


title: ChIP-seq_PR_CR3flp_Ve_rep2

description:
processed data files:
PR_ChIP_CR3flp_Vehicle.bigWig
PR_ChIP_CR3flp_Vehicle.bed


title: SEP3-AGe1C6-R0


title: ChIP-seq_PR_T47Dflp_P4_rep2

description:
processed data files:
PR_ChIP_T47Dflp_P4.bigWig
PR_ChIP_T47Dflp_P4.bed


title: SEP3-AGe1C6-R3


title: ChIP-seq_PR_T47Dflp_P4_rep1


title: ChIP-seq_PR_CR3flp_Ve_rep1


title: SEP3-SEP3e1B7-R2


title: ChIP-seq_PR_T47Dflp_Ve_rep2

description:
processed data files:
PR_ChIP_T47Dflp_Vehicle.bigWig
PR_ChIP_T47Dflp_Vehicle.bed


title: Male Rep2


title: SEP3-SEP3e1B7-R1


title: SEP3-SEP3e1B7-R0


title: RNA-seq_T47D_rep1

description:
processed data files:
gene_counts_per_sample.RNA-seq.txt
RNA-seq_DEGs.T47Dflp.vs.CR3flp.txt
RNA-seq_DEGs.Vector.vs.ExoR330fs.txt


title: ChIP-seq_PR_T47Dflp_Ve_rep1


title: input_T47Dflp_Ve_rep2


title: input_CR3_rep2

description:
processed data files:
input_CR3flp.NormalizedTo40millionReadCounts.bigWig


title: SEP3-AP1e1C12-R3


title: input_CR3_rep1


title: input_T47Dflp_rep2

description:
processed data files:
input_T47Dflp.NormalizedTo40millionReadCounts.bigWig


title: SEP3-AP1e1C12-R1


title: SEP3-AP1e1C12-R2


title: 4-OHT rep1

first: Matthias

last: Wirth

address: Hindenburgdamm 30

institute: Charité Berlin

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie2 Galaxy Version 2.2.6.2
Reads were calculated using htseq-count (Galaxy Version 0.6.1galaxy3) and normalized using DESeq2 (Galaxy Version 2.11.39)
Genome_build: mm10
Supplementary_files_format_and_content:  [mtor.txt] a table of htseq-count, [mtor_normalizedcounts.txt] a table of DeSeq2-normalized counts

source_name: Pancreatic ductal adenocarcinoma

extract_protocol:
RNA was isolated using the standard Qiagen RNeasy protocol. Illumina TruSeq RNA Sample Prep Kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: pancreas

value: Pancreatic ductal adenocarcinoma cell line

value: Pdx1-Flp, FSF-KRasG12D/+, Rosa26-CreERT2/tdEG, Mtor-D/D


title: input_T47Dflp_rep1


title: EtOH rep2

value: Pdx1-Flp, FSF-KRasG12D/+, Rosa26-CreERT2/tdEG, Mtor-lox/lox


title: EtOH rep1


title: SEP3-AP1e1C12-R0


title: SEP3-SEP3e1B7-R3


title: SEP3-AGe1C1-R3


title: NB naïve #3

city: Lyon

first: joel

last: lachuer

address: 8 avenue rockefeller

institute: university Lyon1

data_processing:
Basecalls performed using CASAVA version 1.8.2
Data demultiplexing performed using CASAVA version 1.8.2
Alignment to reference genome performed using TopHat 2.0.6 including Bowtie 2.0.2
gene expression performed using Cufflinks 2.0.2
Genome_build: Human Genome: hg19 (GRCh37, Fev 2009) from UCSC
Supplementary_files_format_and_content: Cufflinks used gene annotation file to calculate overall normalized gene expression in terms of FPKM (Fragments Per Kilobases of exon per Million mapped reads ).

source_name: IGR-N91 neuroblastoma cells

growth_protocol: IGR-N91::GFP cells were cultured in DMEM supplemented with 10% Fetal Bovine Serum, 25 U/mL Penicillin Streptomycin, 2.5 μg/mL Amphotericin B. Cells were grafted in chick embryos and harvested 50 hours later and were immediately frozen.

extract_protocol:
total RNA were extracted from cultured cells using RNeasy microkit (Qiagen), quantified and qualified using bioanalyzer 2100 (Agilent)
ribosomal RNA depletion has been performed using Ribo-Zero™ Gold Kit (Epicentre) and rRNA quantified and qualified on bioanalyzer 2100 (Agilent)
index of multiplexing are : GGACCC (P1); CCTCGG (P2); TTCGCT (P3); ACACGA(T1bis); GTGTTA (T2); TGTGAA (T3)
500 pg of depleted RNA have been preamplified with the Ovation RNAseq system Kit (Nugen) and the libraries were done from 100 ng of ds-cDNA with the Ovation ultralow library system kit (Nugen)

value: IGR-N91 neuroblastoma cells


title: SEP3-AGe1C1-R2


title: ChIP-seq_C-GATA3_CR3flp_rep2

description:
processed data files:
WT_GATA3_ChIP_CR3flp.bigWig
WT_GATA3_ChIP_CR3flp.bed

value: anti-GATA3 C-terminus (ThermoFisher, PA5-20892)


title: NB naïve #2


title: NB naïve #1


title: ChIP-seq_C-GATA3_T47Dflp_rep2

description:
processed data files:
WT_GATA3_ChIP_T47Dflp.bigWig
WT_GATA3_ChIP_T47Dflp.bed


title: ChIP-seq_C-GATA3_CR3flp_rep1


title: SEP3-AGe1C1-R0


title: NB tumor masses #3


title: RNA-seq.T47Dflp.Xenograft.E2.rep2

description: Gene_counts_per_sample.Xenograft_CRctrl.txt

value: T47D Flp control tumors

value: 10 weeks


title: 4-OHT rep2


title: ChIP-seq_C-GATA3_T47Dflp_rep1


title: ChIP-seq_FOXA1_CR3flp_rep2

description:
processed data files:
FOXA1_ChIP_CR3flp.bigWig
FOXA1_ChIP_CR3flp.bed

value: anti-FOXA1 (abcam, ab5089)


title: NB tumor masses #2


title: SEP3-AGe1C1-R1


title: ChIP-seq_FOXA1_CR3flp_rep1


title: NB tumor masses #1


title: treated rep2

city: Tuxedo

first: Chunyuan

last: Jin

address: 57 Old Forge Rd

institute: New York University School of Medicine

data_processing:
FASTQ files assessed for quality by FastQC (v0.10.0)
Single-end reads were mapped to the human genome using STAR (v2.5.2)
Transcript assembly and abundance was determined using Cufflinks (v2.0.2) with hg19 genes reference annotation
RNA-seq reads were counted using GFOLD (v1.0.8)
Genome_build: GRCH37/hg19
Supplementary_files_format_and_content: gtf

source_name: BEAS-2B cell line

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

treatment_protocol: BEAS-2B cells were treated with or without 100 microM for 48 hours

value: lung

tag: tumor stage

value: immortalized

tag: expsoure

value: yes


title: ChIP-seq_FOXA1_T47Dflp_rep1

description:
processed data files:
FOXA1_ChIP_T47Dflp.bigWig
FOXA1_ChIP_T47Dflp.bed


title: untreated rep1

value: no


title: untreated rep2


title: treated rep1


title: ChIP-seq_N-GATA3_CR3flp_rep2

description:
processed data files:
Total_GATA3_ChIP_CR3flp.bigWig
Total_GATA3_ChIP_CR3flp.bed

value: T47D wt/R330fsl cells

value: anti-GATA3 (Cell Signaling, D13C9)


title: ChIP-seq_N-GATA3_T47Dflp_rep2

description:
processed data files:
Total_GATA3_ChIP_T47Dflp.bigWig
Total_GATA3_ChIP_T47Dflp.bed

value: T47D Flp control cells


title: SEP3-AGe2-R2

value: Custom made, peptide specific antibody, anti-AG (Eurogentec), HPLC-purified


title: SEP3-AGe2-R3


title: ChIP-seq_N-GATA3_T47Dflp_rep1


title: ChIP-seq_N-GATA3_CR3flp_rep1


title: ChIP-seq_ERalpha_CR3flp_rep2

description:
processed data files:
ERalpha_ChIP_CR3flp.bigWig
ERalpha_ChIP_CR3flp.bed

value: anti-ERalpha (Santa Cruz, HC-20)


title: SEP3-AGe2-R1


title: ChIP-seq_ERalpha_T47Dflp_rep2

description:
processed data files:
ERalpha_ChIP_T47Dflp.bigWig
ERalpha_ChIP_T47Dflp.bed


title: ChIP-seq_ERalpha_T47Dflp_rep1


title: ChIP-seq_ERalpha_CR3flp_rep1


title: ATAC-seq_CR3flp_rep3

description:
processed data files:
ATAC_CR3flp.bigWig

data_processing:
Reads were filtered based on a mean base quality score >20.
For ATAC-seq data processing, we performed Trim Galore! to remove adapter sequence contamination. Reads were mapped to hg19 genome using Bowtie 0.12.8. The offset parameters suggested by Buenrostro et al (Nat. Methods, 2013) were applied to each mapped read.  Unique reads (non- duplicate reads) were used for the subsequent analysis.
genome build: hg19
processed data files format and content: bigWig, bed, txt

treatment_protocol: Cells were treated with CSK buffer (10 mM PIPES pH 6.8, 100 mM NaCl, 300 mM sucrose, 3 mM MgCl2, 0.1% Triton X-100), and then chromatin tagmentation was performed by Tn5 transposase (2.5 µl in 25 µl total reaction, Nextera DNA Library Preparation Kit from Illumina).


title: AP1-AP1e2-R3

value: Custom made, peptide specific antibody, anti-AP1 (Eurogentec), HPLC-purified


title: ATAC-seq_CR3flp_rep2


title: ATAC-seq_CR3flp_rep1


title: ChIP-seq_FOXA1_T47Dflp_rep2


title: AP1-AP1e2-R2


title: AP1-AP1e2-R1


title: AG-AGe2-R2


title: SEP3-AGe2-R0


title: AG-AGe2-R3


title: AG-AGe2-R1


title: AP1-AP1e2-R0


title: ATAC-seq_T47Dflp_rep1

description:
processed data files:
ATAC_T47Dflp.bigWig


title: AG-AGe2-R0


title: KOViNKT_LCMV

status: Public on Oct 15 2017

city: Rehovot

first: Ester

last: Feldmesser

state: Rehovot

address: POB 25

department: Life Science Core Facilities

country: Israel

institute: Weizmann Institute

data_processing:
bcl files were converted into fastq by bcl2fastq v2.17.1.14
Adapters and low quality bases were removed from the raw reads using cutadapt
The remaining reads were mapped to the Mus musculus genome (mm10) using STAR v2.4.2a with the option "alignEndsType EndToEnd".
Gene expression levels were calculated by counting uniquely mapped reads with htseq-count using the mm10 Refseq 3’UTR GTF annotations.
 Duplicate reads were filtered if they mapped to the same gene and had identical UMIs.
Normalization and differential expression analysis was performed using the DESeq2 R-package (Bioconductor, https://bioconductor.org/packages/release/bioc/html/DESeq2.html). Differentially expressed genes were defined as genes that had a significant adjusted p value of less than 0.05 and at least 2-fold change.
Genome_build: mm10

source_name: Liver

extract_protocol:
Liver was homogenized in 750 µl Trizol reagent (Invitrogen) and vortexed after adding 150 µl chloroform and incubated for 5 min at room temperature, followed by centrifugation for 15 min at 20,000 g. 300 µl from the upper phase was transferred to a new microtube and after the addition of 70% ethanol (1:1 vol), transferred to an RNeasy column (RNeasy mini kit, Qiagen). RNA was purified following DNase I digestion on the column according to manufacturer’s instructions
For library preparation, 6.1 µl of total RNA (5 ng/µl) was used for the MARS-seq  protocol (Jaitin et al. 2014 Science.343:776-9). RNA-seq libraries were sequenced using Illumina NextSeq 500
3' end-RNA-seq (DGE)

value: liver

value: CerS2 -/-

value: WT iNKT cell transfer + infection with LCMV


title: KOIViNKT_LCMV


title: H3D_H3H_rep1

city: Shanghai

first: Jin

middle: Qiu

last: Zhou

address: 320 Yueyang Road

department: Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences

country: China

institute: Chinese Academy of Sciences

data_processing:
Illumina Casava1.8.2 software used for basecalling.
The raw paired-end reads contained the adapter sequences, which the P7 adapter (read1) is 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC', the P5 adapter (read2) is 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT'.we using FASTX Toolkit (version 0.0.13) to remove the adapter sequences. After trimmed the reads, we using tophat (v2.0.11) only mapping the reads to the transcriptomeof sacCer3 (Apr. 2011) with the default parameter.
For the mapped reads, we then extracted the reads which have the “NH:i:1” field. In order to reduce the PCR duplicates’ bias, in here, we only keep at most 3 records at the same position.
The aligned reads were analyzed using the Cuffdiff2 (v2.2.1) to determine the RPKM (Reads Per Kilobase of transcript per Million mapped reads) value in each sample. Genes with a change greater than or equal to 2 fold and p value <= 0.001 were regarded as differentially expressed genes.

growth_protocol: Sample 1-8 were grown in YPD to mid-log phase and then shifted to medium containing 0.05% glucose for one-hour induction. Sample 9-12 were grown in YPD to OD600=0.8.

extract_protocol:
Total RNA from yeast cells was isolated by RNeasy midi kit (Qiagen).The mRNA was purified from total RNA by Dynal oligo(dT) beads (Invitrogen).
The first and second strand cDNA was synthesized by SuperScript III CellsDirect™ cDNA Synthesis Kit (Invitrogen) and SuperScript® Double-Stranded cDNA Synthesis Kit (Invitrogen), respectively; the resulting double strand cDNAs were followed by DNA repair and end-polishing (blunt-end) with End-It DNA End-Repair Kit (Epicentre), purified with QIAquick PCR Purification Kit(Qiagen), and dA-tailed utilizing the 3´-5´ exo-Klenow Fragment (NEB),the resulting purified fragments were ligated to adaptor oligo mix (Illumine) using Quick T4 DNA ligase (NEB). The 200-500 bp ligation products were recovered from a 2% (w/v) agarose gel using Qiagen gel extraction kit. Then followed by a PCR amplification with Solexa primers using KAPA HiFiTMHotStart kit. The 250-400 bp amplified products were purified again from a 2% agarose gel and used directly for high throughput sequencing.

value: histone H3 mutant H3A110D/H3L130H

tag: replicate

value: Replication 1

tag: growth medium

value: grow in YPD to OD600=0.8


title: KOIIiNKT_LCMV


title: KOV_LCMV

value: infection with LCMV


title: ATAC-seq_T47Dflp_rep3


title: ATAC-seq_T47Dflp_rep2


title: WT_rep2

value: Wild type

value: Replication 2


title: WT_rep1


title: KOII_LCMV


title: KOIV_LCMV


title: WTIV_LCMV

value: CerS2 +/+


title: KO878

value: untreated


title: set1D_1_rep1

value: histone H3 mutant H3A110D/H3L130H with SET1 knockout

value: glucose starvation for 1 hr(s)


title: set1D_1_rep2


title: Dlx5-/- 3

city: Los Angeles

first: Hideki

last: Sugii

state: CA

address: 2250 Alcazar Street CSA103

department: craniofacial molecular biology

institute: University of Southern California

data_processing:
A total of 200 million single-end reads with 75 cycles were performed on Illumina Next Seq 500 equipment for six samples.
Raw sequencing reads were first trimmed from both ends with Quality Score method (bases with quality score Phred less than 20 were trimmed from both ends, and trimmed reads shorter than 25 nt were excluded from downstream analyses)
Trimmed reads were then mapped to the mouse genome mm10 using STAR 2.4.1d with default parameter settings
Gencode M12 annotation was used to quantify the aligned reads to genes/transcripts using Partek E/M method.
read counts per gene/transcript in all samples were normalized using Upper Quartile normalization and analyzed for differential expression using Partek Gene Specific Analysis method (genes/transcripts with less than 10 reads in any sample among a data set were excluded).
Genome_build: mm 10
Supplementary_files_format_and_content: .txt file with normalized gene counts

source_name: soft palate

extract_protocol:
Cut off the posterior one-third of the palate and extract RNA using Rneasy Mini Kit (Cat No./ID: 74104)
cDNA library preparation and sequencing were performed at the USC Molecular Genomics Core. For preparing cDNA library, we used the Illumina TruSeq mRNA library prepration kit.

tag: Stage

value: soft palate


title: Dlx5-/- 2


title: Dlx5-/- 1


title: H3D_H3H_1_rep2


title: WT923

tag: age


title: WTII_LCMV

tag: genotype


title: Control 3


title: Control 2


title: H3D_H3H_rep2

value: histone H3 mutant H3A110D/H3L131H


title: Control 1


title: set1D_0_rep2

value: glucose starvation for 0 hr(s)


title: set1D_0_rep1


title: sgKif3a, biological rep2

first: Xuesong

last: Zhao

address: 450 Brookline Ave

department: Cancer Biology

institute: Dana-Farber Cancer Institute

description:
CRISPR knockout
sgKif3a_2

data_processing:
Illumina software used for basecalling.
STAR aligner was used to map sequenced reads to the mm9 genome assembly and to quantify gene level expression. Comparative analysis was performed by DESeq2.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include raw counts of sequencing reads

source_name: SMB21 cell line

growth_protocol: Cells were cultured as neurospheres at 37°C in a humidified incubator with 5% CO2 in DMEM/F12 media (2% B27, 1% Pen/Strep).

extract_protocol:
RNA was isolated from cells using RNeasy Kit (Qiagen).
Libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kits from 500ng of purified total RNA according to the manufacturer’s protocol. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according to manufacturer’s protocol. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on a single Illumina NextSeq500 run with single-end 75bp reads by the Dana-Farber Cancer Institute Molecular Biology Core Facilities.

treatment_protocol: Targeted knockout of Ofd1, or Kif3a was achieved using lentiCRISPR vector system. 2 weeks after viral infection, cells were collected for RNA extraction

tag: strain background

value: Ptch1tm1Mps/J (JAX003081)

value: Adult

value: medulloblastoma cell line

tag: genotype background

value: Ptch mutant

tag: genotype/variation


title: sgKif3a, biological rep1

description:
CRISPR knockout
sgKif3a_1

tag: cell line


title: H3D_H3H_0_rep2

value: histone H3 mutant H3A110D/H3L130H


title: H3D_H3H_0_rep1

value: Replication 1


title: WTV_LCMV

tag: strain

tag: tissue

value: liver

tag: treatment


title: WT939


title: sgOfd1, biological rep2

description:
CRISPR knockout
sgOfd1_2

tag: cell type


title: sgGFP, biological rep2

description:
CRISPR knockout
sgGFP_2

value: CRISPR-GFP


title: sgOfd1, biological rep1

description:
CRISPR knockout
sgOfd1_1


title: H3D_H3H_1_rep1


title: sgOfd1, biological rep3

description:
CRISPR knockout
sgOfd1_3


title: Ofd1_R14, biological rep2

source_name: Ofd1mutant clone identified from transposon screen

treatment_protocol: 24 hours with or without Sonidegib treatment


title: Ofd1_R14, biological rep1


title: Ofd1_R16


title: Ofd1_R25


title: Sufu_R1

source_name: Sufu mutant clone identified from transposon screen

value: Sufu mutant


title: sgGFP, biological rep1

description:
CRISPR knockout
sgGFP_1


title: Parental, biological rep3

source_name: untreated parental SMB21 cells

value: parental


title: Parental, biological rep1


title: Parental, biological rep2


title: H3DK4R_H3HK4R_1_rep2

description: processed data file: normalized_abundance_H3DK4R_H3HK4R_0_1.txt

data_processing:
Illumina Casava1.8.2 software used for basecalling.
For the raw sequence data, we trimmed the top 15 bp, using tophat (v2.0.11) only mapping the reads to the transcriptome of sacCer3 (Apr. 2011) with the default parameter.
For the mapped reads, we then extracted the reads which have the “NH:i:1” field. In order to reduce the PCR duplicates’ bias, in here, we only keep 1 record at the same position.
The aligned reads were analyzed using the Cuffdiff2 (v2.2.1) to determine the RPKM (Reads PerKilobase of transcript per Millionmapped reads) value in each sample. Besides, we also calculate the average RPKM value of the sample put two replicates together.
Genome_build: sacCer3 (Apr. 2011)
Supplementary_files_format_and_content: text file with RPKM values for each replicate and average RPKM of two replicates.

growth_protocol: samples were grown in YPD to mid-log phase and then shifted to medium containing 0.05% glucose for one-hour induction.

value: histone H3 mutant H3A110DK4R/H3L130HK4R

tag: replicate number

value: Replication 2

tag: starvation duration

value: glucose starvation for 1 hr


title: H3DK4R_H3HK4R_0_rep2


title: H3D_H3HK4R_1_rep2

description: processed data file: normalized_abundance_H3D_H3HK4R_0_1.txt

value: histone H3 mutant H3A110D/H3L130HK4R


title: H3DK4R_H3HK4R_1_rep1


title: Sufu_R13


title: H3DK4R_H3HK4R_0_rep1


title: H3D_H3HK4R_1_rep1


title: Parental_LDE, biological rep1

source_name: parental SMB21 24 hrs with Sonidegib treatment


title: H3D_H3HK4R_0_rep2


title: H3D_H3HK4R_0_rep1


title: Mo(cIgG/LPS).rep3

city: Suzhou

first: Xiao-Ming

last: Gao

address: 199 Ren’ai Road

department: Institute of Biology and Medical Sciences, School of Biology and Basic Medical Sciences,

institute: Soochow University

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were mapped to human reference genome hg19 using BWA/Bowtie2 tool
Genes expression level is quantified by RSEM package.The differentially expression was indentified by EBSeq package.
Peak calling was done for individual samples using macs (version 1.4.2 20120305).
Genome_build: hg19
Supplementary_files_format_and_content: wig files were generated using Extended tag pileup from MACS (version 1.4.2 20120305) for every 10 bp

source_name: Human blood monocytes

growth_protocol: Freshly isolated CD14+ human blood monocytes were cultured for 24 hrs in R10 medium in microtiter tissue culture plates pre-coated with IVIG (cIgG), or without (RPMI), at 37°C and 5% CO2.

extract_protocol:
For ChIP-seq, purified monocytes (1×10^7 cells/mL) were pre-incubated either with cell culture medium, or cIgG (10 μg/mL) for 24 hrs. Then, cells were cross-linked with 1% formaldehyde (Sigma-Aldrich) at room temperature for 10 min. Chromatin was fragmented to 200-500 bp with Bioruptor (Diagenode; 20×30 sec cycles, low power at 4°C), cleared at 14,000 rpm at 4°C for 20 min and immunoprecipitated with 1 μg αH3K4me3 Ab (#07-473, Merck Millpore) or αH3K27ac Ab (#07-449, Merck Millpore) and 40 μL of protein A/G plus magnetic beads (Merck Millpore) per reaction at 4°C overnight. Then, the ChIPed DNA was purified with MinElute PCR purification kits (Qiagen). The quality of DNA shearing and library preparation was verified by Bioanalyzer (Agilent Tech).For RNA-seq, purified monocytes (5×10^6 cells/mL) were seeded on 60 mm dishes. Monocytes were pre-incubated either with cell culture medium (RPMI), or cIgG (10 μg/ml) for 24 hrs. In parallel, these monocytes were stimulated with LPS (10ng/ml) or not for 2 hrs. After wash-out, cells were harvested and processed into RNA extraction.
Total RNA was polyA enriched, fragmented and converted into a library of Illumina-compatible sequencing templated with Illumina mRNA-seq sample preparation kit according to the manufacturer’s instructions. The cDNA library was size-fractionated in a 1% agarose gel. 200-250 bp fragments were isolated and amplified by PCR with Illumina primers PE1 and PE2 for 15 cycles. The integrity and quality of total RNA and size-selected libraries was evaluated with Bioanalyzer 2100 (Agilent Tech).

treatment_protocol: Freshly fractionated monocytes from 3 unrelated healthy donors were cultured for 24 hrs in RPMI-10 medium for preparation of Mo(RPMI) and Mo(cIgG), then half of these cultures were washed and given a 2 hrs LPS (10 ng/mL) stimulation, resulting in additional groups of Mo(RPMI/LPS) and Mo(cIgG/LPS), respectively.

value: Peripheral blood

value: After cIgG priming for 24 hrs, additional  10 ng/mL LPS expousre for 2 hrs


title: Mo(cIgG/LPS).rep1

value: After cIgG priming for 24 hrs,additional  10 ng/mL LPS expousre for 2 hrs


title: Mo(RPMI/LPS).rep3

value: After RPMI for 24 hrs, additional 10 ng/mL LPS expousre for 2 hrs


title: Mo(RPMI/LPS).rep2


title: Mo(cIgG).rep3

value: cIgG priming for 24 hrs


title: Mo(cIgG).rep2


title: H3DK4R_H3H_1_rep2

description: processed data file: normalized_abundance_H3DK4R_H3H_0_1.txt

value: histone H3 mutant H3A110DK4R/H3L130H


title: H3DK4R_H3H_0_rep2

value: glucose starvation for 0 hr(s)


title: Mo(RPMI/LPS).rep1


title: H3DK4R_H3H_1_rep1


title: Mo(cIgG).rep1


title: Mo(RPMI).rep3

value: RPMI for 24 hrs


title: Mo(RPMI).rep1


title: input DNA_ChIPSeq_Mo(RPMI)


title: H3D_H3H_1_rep2

description: processed data file: normalized_abundance_H3D_H3H_0_1.txt

value: histone H3 mutant H3A110D/H3L130H


title: Parental_LDE, biological rep2

value: Ptch1tm1Mps/J (JAX003081)

value: Adult

value: medulloblastoma cell line

value: Ptch mutant


title: Mo(RPMI).rep2


title: H3D_H3H_1_rep1

value: Replication 1


title: Mo(cIgG/LPS).rep2


title: H3K4me3_ChIPSeq_Mo(cIgG)

value: H3K4me3(#07-473, Merck Millpore)


title: H3D_H3H_0_rep1


title: H3K4me3_ChIPSeq_Mo(RPMI)

value: RPMI culture for 24 hrs


title: H3DK4R_H3H_0_rep1


title: Embryo_E9 [P455]

city: Geneva

first: Jozsef

last: Zakany

state: Geneva

address: 30, quai Ernest Ansermet

department: Genetics and Evolution

country: Switzerland

institute: University of Geneva

description: extra-embryonic, head, cervical and heart tissues avoided

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Demultiplexed RNA-seq reads were mapped onto the public available GRCm38 (mm10) genome. The RNA-seq data were aligned using TopHat release 2.1.1 (Kim et al., 2013). TopHat output files were processed with SAMTools (Li et al., 2009) and bedTools (Quinlan, 2014) to extract the read coverage along the genome. For visualization and comparison across samples, the read coverage was divided by the number of millions of mapped reads in each sample.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph of the forward or reverse strand RNAseq read coverage (before normalization by the total read counts)

source_name: Trunk and limbs, thoracic-to-tailbud

extract_protocol:
Trunk from the anterior limit of the forelimb bud to the tailbud were isolated, aiming to exclude all extra-embryonic, head, cervical and heart tissues. Isolates were stored in RNAlater at -80°C. Extraction was performed using the RNAeasy micro kit (Qiagen) according to manufacturer's instructions. On-column DNase I treatment was performed during 20 min at room temperature to ensure pure, DNA-free RNA sample.
TruSeq Stranded Total RNA with Ribo-Zero kit from Illumina was used for the library preparation with 200 ng of total RNA as input. Library molarity and quality was assessed with  Qubit and Tapestation using a DNA High sensitivity chip (Agilent Technologies).
RNA-seq. The 4 libraries were pooled and loaded at 8 pM for clustering on a Paired-end Illumina Flow cell. Reads of 100 bases were generated using the TruSeq SBS HS v3 chemistry on an Illumina HiSeq 2500 sequencer. The preparation of libraries and sequencing were performed by the genomic platform of the University of Geneva.

tag: tissues

value: trunk and limbs

value: Del(CpG114) homozygous


title: Embryo_E9 [P456]

value: wild type


title: Embryo_E9 [P445]


title: VSG Colon

status: Public on Oct 14 2017

city: South San Francisco

first: Joshua

last: Lichtman

address: 333 Oyster Point Boulevard

department: Translational Science

institute: NGM Biopharmaceuticals

data_processing:
Assembled against the mouse genome using GSNAP/CUFFLINKS
Annotated using CUFFCOMPARE
Genome_build: mm10

source_name: Colon Tissue

growth_protocol: Seventeen week old male C57BL/6J mice were maintained on high-fat diet for 13 weeks and then fasted overnight prior to the surgery

extract_protocol:
TRIzol
TruSeq RNA Preparation Kit

treatment_protocol: VSG and sham surgeries were performed under isoflurane anesthesia as described previously (Wilson-Pérez et al., 2013). Briefly, using sterile 7 French polyethylene tubing to size the gastric pouch remnant from the esophagus to the pylorus, the lateral 80% of the stomach was excised. Then, using a 6-0 PDS suture, the stomach was closed at the edge of the sizing using a single interrupted suture through both layers of stomach wall.  The remaining stomach pouch has a lumen diameter sized to 6 French and approximating 20% of the original stomach area. The sham procedure involved the opening of the peritoneal cavity and applying a gentle pressure using a pair of hemostats at a location that is approximately 2/3 cranial to the greater curvature, along a vertical line between the esophageal sphincter and the pylorus. Mice consumed Osmolite 1 Cal liquid diet (Abbott Laboratories, Abbott Park, IL) for the first 3 postoperative days and were gradually reintroduced to high-fat diet on day 3. The surgery survival rate was 100%.

value: Colon

value: VSG


title: input DNA_ChIPSeq_Mo(cIgG)

value: Peripheral blood

value: cIgG priming for 24 hrs


title: Embryo_E9 [P443]


title: VSG Duodenum

source_name: Duodenum Tissue

value: Duodenum


title: VSG Jejunum

source_name: Jejunum Tissue

value: Jejunum


title: VSG Stomach

source_name: Stomach tissue

value: Stomach


title: Sham Colon

value: Sham


title: Sham Stomach


title: Sham Duodenum


title: Sham Jejunum


title: P20 testicular m6a IP: IP: YTHDC2 +/+; sample 2

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

description:
immunopurified RNA
processed data file:
GEO_YTHDC2_m6a_IP.txt.gz

data_processing:
For analysis of m6A-RNASeq and total RNAseq the reads were sorted into individual libraries based on the barcodes and mapped to the mouse genome (mm10 assembly). The software used for processing the data (genomic coordinates etc) from the raw data files are in-house tools developed by the Sachidanandam lab (Olson et al., 2008). Only reads perfectly matching the genome were kept for further analysis using R (R Core Team, 2017) and Bioconductor (Huber et al., 2015). Differential expression analysis was performed using DESeq2 bioconductor package (Love et al., 2014)
genome build: mm10
processed data files format and content: The files for mouse testicular and ovarian samples contain the comparison of transcript abundances calculated by DESeq2.

source_name: testes

growth_protocol: To get the Ythdc2 knock-out mice, endogenous Ythdc2 locus of the C57BL/6J mouse embryos was targeted with two guide RNAs (gRNAs) that direct the DNA endonuclease Cas9 to create a 152 bp deletion that removes all of the exon 7 (Line #2). Additionally, a 181 nt single-stranded DNA (ssDNA) repair template (IDT) that carries a triple-stop codon (and 80 nt homology arms on each side of triple-stop codon) was co-injected into single-cell mouse embryos. This resulted in a knock-in line that has the triple-stop codon cassette introduced into the exon 7, truncating the coding sequence within the RNA helicase domain (Line #1).

extract_protocol:
For RNA Bind-n-Seq experiment  randomized 21 nt single-stranded RNAs carrying a central m6A moiety were mixed with Ni-NTA agarose beads alone or bound to 6xHis-SUMO-YTH domain (of hYTHDC2). RNA bound to the beads was phenol chloroform extracted.
For m6a IP experiment testicular RNA was isolated using the Trizol reagent and polyA+ transcripts were purified, fragmented and the fragments were immunopurified using anti-m6A antibody. Total testicular and ovarian RNAs were isolated using the Trizol reagent.
Sequencing libraries  of RNA Bind-n-Seq and m6a IP experiments were prepared using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (Cat No:E7300) according to manufacturer instructions and sequenced on Illumina 2000 HiSeq platform (EMBL Heidelberg Gene core facility). Sequencing libraries of total testicular and ovarian RNAs were prepared by TruSeq Stranded Total RNA kit with Ribo-Zero Gold and sequenced on the Illumina HiSeq 4000 sequencer (iGE3 Genomics Platform, University of Geneva)

tag: purification

value: IP with m6A rabbit polyclonal antibody (Synaptic Systems, catalog no. 202003)

tag: background strain

value: testes

value: YTHDC2 +/+


title: P20 testicular m6a IP: IP: YTHDC2 +/+; sample 1


title: P12 testicular m6a IP: IP: YTHDC2 +/-; sample 2

value: YTHDC2 +/-


title: P8 testicular m6a IP: IP: YTHDC2 +/+; sample 1


title: H3D_H3H_0_rep2

value: histone H3 mutant H3A110D/H3L130H

value: Replication 2

value: glucose starvation for 0 hr(s)


title: P20 testicular m6a IP: input: YTHDC2 +/+; sample 1

value: input of m6A IP


title: P20 testicular m6a IP: input: YTHDC2 +/+; sample 2


title: P12 testicular m6a IP: input: YTHDC2 +/-; sample 1


title: P8 testicular m6a IP: input: YTHDC2 +/+; sample 1


title: P12 testicular m6a IP: input: YTHDC2 +/-; sample 2


title: e10-5-L26-11-ventral

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

country: United Kingdom

institute: IGMM MRC Human Genetics Unit

data_processing:
Genome build: mm10
Expression levels were quantified with CUFFLINKS v2.2.1 using the –b, -u, --library-type fr-unstranded, --total-hits-norm, -- min-frags-per-transfrag 10, no-faux-reads, -G options.
Supplementary file format and content: Mean RPKM values across each set of independent samples representing a developmental stage were quantified by CUFFLINKS, and the mean values reported as a tab-delimited text file (.xlsx file submitted to GUDMAP).

source_name: Ventral cloacal cells isolated by LCM from sample e10-5-L26-11

extract_protocol:
Immediately following Laser micro-dissection, the collection tubes were capped and vortexed.  After addition of 300 μl RLT buffer to each tissue sample (total 350 μl), the RNA was prepared using the RNeasy Micro Kit (Qiagen #74004) as per instructions.  An on column DNase digestion was included in RNA preparation.
Total RNA was processed for library construction by Cofactor Genomics (St. Louis, MO) according to the following procedure: 700-1000pg of RNA was amplified using the Ovation RNA-Seq System v2 system (NuGEN, San Carlos, CA). Double-stranded cDNA was sheared to the desired size (175-200bp) using the Covaris S2 (Covaris, Woburn, MA). Indexed adaptors (Illumina truseq barcodes 1-8 ) were ligated to 500ng cDNA.  Ligation reactions were incubated at 20oC for 15 minutes, and the adaptor-ligated DNA was then size-selected (175-200bp) on a 2% SizeSelect™ E-Gel (Invitrogen, Carlsbad, CA) and amplified by PCR. PCR cycling conditions used were: 45 seconds at 98oC; (15 seconds @ 98oC, anneal for 30 seconds at 60oC, extend for 30 seconds at 72oC) – repeat 7X; 60 seconds at 72oC.  Library quality, quantity and insert size range was assessed with an Agilent Bioanalyzer.

treatment_protocol: Embryos were harvested from CD1 mice and placed in ice cold PBS and dissected to remove anterior structures.  Posterior portions were then embedded in OCT on dry ice, flash frozen in iso-pentane and subsequently stored at -80 °C.  10μm sections were placed on MembraneSlide 1.0 PEN microscope slides (Zeiss #415190-9401-000) and immediately placed on dry ice.  Sections were then washed in 95%, 75%, 50% ethanol for 30 second intervals.  Sections were then stained in 1% (w/v) cresyl violet acetate prepared in 50% ethanol for 30 seconds.  Subsequent to staining, sections were dehydrated using 50%, 75%, 95%, and 2 X100% ethanol washes, 30 seconds each, then washed in Xylene for 5 minutes.  Stained slides were then placed on dry ice and tissues were excised no later than 2-3 hours after staining. The dorsal and ventral portions of the cloaca from E10.5 embryos and urethra and hindgut from E13.5 embryos were excised using the Zeiss PALM MicroBeam system and catapulted into 0.65 ml microfuge collection tube (Corning #3208) caps containing 50 ul of RLT buffer (Qiagen) containing β-mercaptoethanol.  As many sections as possible were collected per sample.

value: wild type

value: cloaca

tag: Sex

value: male

tag: pooled sample

value: no


title: e10-5-L26-11-dorsal

source_name: Dorsal cloacal cells isolated by LCM from sample e10-5-L26-11

tag: age


title: VSG Ileum

source_name: Ileum Tissue

value: Ileum

value: VSG


title: e10-5-L26-2-ventral

source_name: Ventral cloacal cells isolated by LCM from sample e10-5-L26-2

tag: genotype


title: e10-5-L26-9-dorsal

source_name: Dorsal cloacal cells isolated by LCM from sample e10-5-L26-9

treatment_protocol: Embryos were harvested from CD1 mice and placed in ice cold PBS and dissected to remove anterior structures.  Posterior portions were then embedded in OCT on dry ice, flash frozen in iso-pentane and subsequently stored at -80 °C.  10μm sections were placed on MembraneSlide 1.0 PEN microscope slides (Zeiss 415190-9401-000) and immediately placed on dry ice.  Sections were then washed in 95%, 75%, 50% ethanol for 30 second intervals.  Sections were then stained in 1% (w/v) cresyl violet acetate prepared in 50% ethanol for 30 seconds.  Subsequent to staining, sections were dehydrated using 50%, 75%, 95%, and 2 X100% ethanol washes, 30 seconds each, then washed in Xylene for 5 minutes.  Stained slides were then placed on dry ice and tissues were excised no later than 2-3 hours after staining. The dorsal and ventral portions of the cloaca from E10.5 embryos and urethra and hindgut from E13.5 embryos were excised using the Zeiss PALM MicroBeam system and catapulted into 0.65 ml microfuge collection tube (Corning 3208) caps containing 50 ul of RLT buffer (Qiagen) containing β-mercaptoethanol.  As many sections as possible were collected per sample.


title: e10-5-L26-9-ventral

source_name: Ventral cloacal cells isolated by LCM  from sample e10-5-L26-9


title: e10-5-L26-2-dorsal

source_name: Dorsal cloacal cells isolated by LCM from sample e10-5-L26-2


title: P0 ovarian total RNA sequencing: YTHDC2 -/-; sample 2

description:
processed data file:
GEO_YTHDC2_P0_ovary.txt.gz

data_processing:
For RNA Bind-n-Seq experiment the reads were sorted into individual libraries based on the barcodes and the 3′ adapter sequences were removed using cutadapt . Only reads of final length of 21 nucleotides with A at 10th position were kept for further analysis using R (R Core Team, 2017) and Bioconductor (Huber et al., 2015). Frequencies of individual nucleotides were calculated for each position as well as enrichment vs. the bead control. MEME - Motif discovery tool (Bailey and Elkan, 1994)  was used to search for a motif in a collection of 9-mers (read positions 6-14) centred around the  m6A at position 10.
For analysis of m6A-RNASeq and total RNAseq the reads were sorted into individual libraries based on the barcodes and mapped to the mouse genome (mm10 assembly). The software used for processing the data (genomic coordinates etc) from the raw data files are in-house tools developed by the Sachidanandam lab (Olson et al., 2008). Only reads perfectly matching the genome were kept for further analysis using R (R Core Team, 2017) and Bioconductor (Huber et al., 2015). Differential expression analysis was performed using DESeq2 bioconductor package (Love et al., 2014)
Genome_build: mm10 (mouse testicular samples)
Supplementary_files_format_and_content: The files for mouse testicular and ovarian samples contain the comparison of transcript abundances calculated by DESeq2.

source_name: ovary

extract_protocol:
For RNA Bind-n-Seq experiment  randomized 21 nt single-stranded RNAs carrying a central m6A moiety were mixed with Ni-NTA agarose beads alone or bound to 6xHis-SUMO-YTH domain (of hYTHDC2). RNA bound to the beads was phenol chloroform extracted.  For m6a IP experiment testicular RNA was isolated using the Trizol reagent and polyA+ transcripts were purified, fragmented and the fragments were immunopurified using anti-m6A antibody.  Total testicular and ovarian RNAs were isolated using the Trizol reagent.
Sequencing libraries  of RNA Bind-n-Seq and m6a IP experiments were prepared using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (Cat No:E7300) according to manufacturer instructions and sequenced on Illumina 2000 HiSeq platform (EMBL Heidelberg Gene core facility). Sequencing libraries of total testicular and ovarian RNAs were prepared by TruSeq Stranded Total RNA kit with Ribo-Zero Gold and sequenced on the Illumina HiSeq 4000 sequencer (iGE3 Genomics Platform, University of Geneva)

value: ovary

value: YTHDC2 -/-


title: e10-5-L10-6-dorsal

source_name: Dorsal cloacal cells isolated by LCM from sample e10-5-L10-6


title: e10-5-L10-6-ventral

source_name: Ventral cloacal cells isolated by LCM from sample e10-5-L10-6


title: Sham Ileum

value: Sham


title: L13_5_HG

source_name: Dorsal cloacal cells isolated by LCM from sample L13_5_HG

value: rectum epithelium,hindgut epithelium


title: P0 ovarian total RNA sequencing: YTHDC2 +/-; sample 2


title: Ammonia50_3

city: Beijing

first: Bao

last: Yi

address: No.2 Yuanmingyuan West Road

department: Institute of Animal Sciences

institute: Chinese Academy of Agricultural Sciences

data_processing:
Basecalls performed using CASAVA version 1.7
The adaptor sequences were removed and data were Q20, Q30 filtered
Fragments Per Kilobase of transcript per Million mapped fragments (FPKM) was calculated using bowtie2 and HTSeq
Genome_build: Gallus_gallus-4.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Gallus gallus

source_name: Breast muscle

extract_protocol:
Total RNA of breast muscle was isolated with TRIzol reagent (Invitrogen) according to the manufacturer's instructions. mRNA was extracted from total RNA using oligo (dT) magnetic beads (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Arbor Acres

value: 42-day old

value: breast muscle

tag: ammonia concentration

value: 50 ± 3 ppm


title: Ammonia50_2


title: P12 testicular m6a IP: IP: YTHDC2 +/-; sample 1

value: IP with m6A rabbit polyclonal antibody (Synaptic Systems, catalog no. 202003)

value: testes

value: YTHDC2 +/-


title: L13_13_HG

source_name: Dorsal cloacal cells isolated by LCM from sample L13_13_HG

value: wild type


title: L12_11_HG

source_name: Dorsal cloacal cells isolated by LCM from sample L12_11_HG


title: Ammonia50_1


title: P0 ovarian total RNA sequencing: YTHDC2 -/-; sample 1


title: L12_5_HG

source_name: Dorsal cloacal cells isolated by LCM from sample L12_5_HG


title: P8 testicular total RNA sequencing: YTHDC2 +/+; sample 1

description:
processed data file:
GEO_YTHDC2_P8_testis.txt.gz

value: YTHDC2 +/+


title: L13_13_urethra

source_name: Ventral cloacal cells isolated by LCM from sample L13_13_urethra

value: epithelium of pelvic urethra, pelvic urethra, rest of epithelium of pelvic urethra

value: male


title: L13_5_urethra

source_name: Ventral cloacal cells isolated by LCM from sample L13_5_urethra

value: no


title: L12_5_urethra

source_name: Ventral cloacal cells isolated by LCM from sample L12_5_urethra


title: P8 testicular total RNA sequencing: YTHDC2 -/-; sample 2

source_name: testes


title: P8 testicular total RNA sequencing: YTHDC2 -/-; sample 1


title: L12_11_urethra

source_name: Ventral cloacal cells isolated by LCM from sample L12_11_urethra


title: P8 testicular total RNA sequencing: YTHDC2 +/-; sample 1


title: P12 testicular total RNA sequencing: YTHDC2 -/-; sample 3

description:
processed data file:
GEO_YTHDC2_P12_testis.txt.gz


title: PL-VTA_vTRAP_Input_rep2

city: New York

first: Alexander

last: Nectow

state: New York

address: 630 W 168th St., Physicians and Surgeons

department: Medicine

institute: Columbia University

data_processing:
Reads were aligned to the mouse reference genome (version mm10) using STAR v2.3 aligner with default parameters. Alignment results were evaluated through RNA-SeQC v1.17 to ensure that all the samples had a consistent alignment rate, and no obvious 5’ or 3’ bias. Aligned reads were then summarized through featureCounts with the Ensemble gene model (Mus_musculus.GRCm38.75.gtf) at the gene level. Uniquely mapped reads that overlapped with an exon (feature) by at least 1bp were counted and then the counts of all annotated Ensemble gene exons (meta features) were summed into a single number. Only protein coding genes were used for downstream analysis.
DESeq2 was applied to normalized counts to estimate fold change between the Input and IP samples using the negative binomial distribution. For each brain region, the average expression level for each gene was first estimated; fold of change and significance of the fold of change were then calculated taking into account the variation of gene expression across all samples. Adjusted p-value of less than 0.05 was used to determine significantly enriched genes.
Genome_build: mm10
Supplementary_files_format_and_content: CSV files, DESeq2 output on all genes for each sample. Includes Ensembl ID,baseMean, log2FoldChange (IP/Input), lfcSE, stat, pvalue, padj, genesymbol

source_name: vTRAP Input from PL

extract_protocol:
RNA was isolated using previously established protocols (Nectow et al., 2017). Briefly, GFPL10-positive polysomes were immunoprecipitated using anti-GFP magnetic beads, followed by RNA purification using Agilent Nanoprep.
Libraries were prepared with the SMARTer Ultra Low RNA for Illumina sequencing kit (Clontech), followed by Nextera XT DNA sample preparation kit (Illumina).

treatment_protocol: AAV-IV-GFPL10 was injected presynaptically in the PL; CAV-Cre was injected postsynaptically in the NAc, BLA, or VTA.

tag: rna

value: Total (Input)

tag: projection target

value: VTA


title: P12 testicular total RNA sequencing: YTHDC2 +/-; sample 2


title: PL-VTA_vTRAP_IP_rep2

source_name: vTRAP IP from PL-VTA neurons

tag: strain

value: TRAP IP


title: PL-VTA_vTRAP_Input_rep1


title: P12 testicular total RNA sequencing: YTHDC2 +/-; sample 1

tag: tissue


title: P12 testicular total RNA sequencing: YTHDC2 +/-; sample 3


title: P12 testicular total RNA sequencing: YTHDC2 -/-; sample 1

value: YTHDC2 -/-


title: PL-BLA_vTRAP_IP_rep3

source_name: vTRAP IP from PL-BLA neurons

value: BLA


title: PL-BLA_vTRAP_IP_rep2


title: P0 ovarian total RNA sequencing: YTHDC2 +/-; sample 1

value: ovary


title: PL-BLA_vTRAP_Input_rep2


title: PL-BLA_vTRAP_Input_rep3


title: PL-BLA_vTRAP_IP_rep1


title: P12 testicular total RNA sequencing: YTHDC2 -/-; sample 2


title: PL-NAc_vTRAP_Input_rep3

value: NAc


title: PL-BLA_vTRAP_Input_rep1


title: PL-VTA_vTRAP_IP_rep1


title: 5.3 hpf, unfractionated

city: Warsaw

first: Cecilia

middle: Lanny

last: Winata

state: Mazovia

address: 4 Ks. Trojdena

country: Poland

institute: International Institute of Molecular and Cell Biology in Warsaw

description: rRNA-depleted RNA

data_processing:
Basecalling was performed by Illumina RTA 1.18.61. Files were translated into demultiplexed FASTQ files by Illumina bcl2fastq2 2.16.10.
For the RNA-Seq data analysis sequencing reads were aligned to the GRCz10 zebrafish genome using STAR v2.4.2a (Dobin et al. 2012).
For the novel transcript discovery sequencing reads were trimmed using cutadapt 1.9.1 (-e 0.1; -q 20; -O 3; -m 20; -a  AGATCGGAAGAGC). Subsequently the reads were aligned to the GRCz10 zebrafish genome using GSNAP version 2015-12-31 (--filter-chastity=both; --max-mismatches=5; --novelsplicing=1). Transcriptome was assembled using cufflinks 2.2.1 (--multi-read-correct; --library-type fr-secondstrand) with Ensembl release 83 genome annotation. Cuffcompare was run to compare and annotate the newly assembled transcripts.
Transcript level abundances were generated using Salmon 0.6.0 algorithm (Patro et al., 2015). The abundances were summarized to gene level and imported to DESeq2 using tximport 1.0.2. Subsequently data was normalized to library size using DESeq2 „median ratio method” (Anders and Huber 2010).
Genome_build: GRCz10
Supplementary_files_format_and_content: Salmon's quantification files, tab-delimited text files, contain abundance measurements for each sample. normalizedCounts.txt tab-delimited text file contains counts for all the samples, normalized using DESeq2.

organism: Danio rerio

source_name: whole zebrafish embryo

growth_protocol: Zebrafish embryos were maintained according to standard protocol (Westerfield et al., 2000) and staged according to standard morphological criteria (Kimmel et al., 1995).

extract_protocol:
rRNA-depletion was performed using RiboZero Magnetic Gold Kit (Epicentre), unfractionated, polysome-associated and non associated RNA were subsequently isolated using Qiagen RNAeasy kit (Qiagen, USA).
Sequencing library was constructed using Stranded RNA-seq libraries were generated using ScriptSeq v2 RNA Library Preparation Kit (Illumina, USA).

value: wild-type (AB)

tag: developmental stage

value: 5.3 hpf

value: whole embryo


title: PL-NAc_vTRAP_IP_rep3

source_name: vTRAP IP from PL-NAc neurons


title: 128-cell, unfractionated

description: rRNA-depleted RNA


title: 3.5 hpf, unfractionated

description: rRNA-depleted RNA

value: 3.5 hpf


title: PL-NAc_vTRAP_IP_rep2


title: 16-cell, unfractionated

description: rRNA-depleted RNA


title: egg, unfractionated

description: rRNA-depleted RNA

value: Egg


title: 1-cell, unfractionated

description: rRNA-depleted RNA


title: PL-NAc_vTRAP_Input_rep1


title: PL-NAc_vTRAP_IP_rep1


title: 5.3 hpf, polysome-unbound

description: rRNA-depleted RNA


title: hESC line H9 cells after 72 hours of BMP4 treatment, biological replicate 2

city: Neuherberg

first: Dmitry

last: Shaposhnikov

address: Ingolstädter Landstraße 1

institute: Helmholtz Center Munich

data_processing:
FASTQ generation was done automatically in Illumina BaseSpace application
Reads were aligned to human genome h38 using STAR aligner 2.4.2a with default parameters
Gene count table was generated using featureCounts software from Rsubread package 1.20.0
Normalized gene count table was generated using DEseq2 1.15.3
Genome_build: h38
Supplementary_files_format_and_content: csv file containing normalized gene counts for all samples

source_name: human embryonic stem cells

growth_protocol: H9 cell line was grown on Geltrex-coated plates in mTESR1 medium

extract_protocol:
RNA was extracted using Qiagen RNeasy Mini kit according to manufacturer's instructions
Total RNA libraries were prepared from 1 µg of total RNA using Illumina TruSeq Stranded Total RNA LT kit according to manufacturer's instructions.

treatment_protocol: For trophoblast differentiation, cells were seeded at 100% confluency on Matrigel-coated plates containing KSR-based differentiation medium and 50 ng/ml BMP4. During the time course, medium was changed every 24 hours.

tag: cell line

tag: time point

value: 72 hours


title: hESC line H9 cells after 72 hours of BMP4 treatment, biological replicate 1


title: S2 cell rep2

city: Taipei

first: Jia-Ming

last: Chang

address: NO.64, Sec. 2, ZhiNan Rd., Wenshan District

department: Department of Computer Science

country: Taiwan

institute: National Chengchi University

data_processing:
Hi-C data was processed using an in-house pipeline based on TADbit. First, quality of the reads was checked using the quality_plot() function in TADbit, which is similar to the tests performed by the FastQC program with adaptations for Hi-C datasets. Next, the reads are mapped following a fragment-based strategy as implemented in TADbit where each side of the sequenced read was mapped in full length to the reference genome (dm3). After this step, if a read was not uniquely mapped, we assumed the read was chimeric due to ligation of several DNA fragments. We next searched for ligation sites, discarding those reads in which no ligation site was found. Remaining reads were split as often as ligation sites were found. Individual split read fragments were then mapped independently. Next, we used the TADbit filtering module to remove non-informative contacts and to create contact matrices. From the resulting contact matrices, low quality bins (those presenting low contacts numbers) were removed as implemented in TADbit’s filter_columns() function. Next, the matrices were normalized using the ICE algorithm. The normalization iterations stopped when the biases were diverting less than 10% of the previous values or a max of 10 iterations. Finally, all matrices were corrected to achieve an average content of one interaction per cell. All parameters in TADbit were kept at default values.
Genome_build: dm3
Supplementary_files_format_and_content: *.dat: TAB separated values file containing the ICE-normalized Hi-C matrix at 50kb for  corresponding chromosome arm
Supplementary_files_format_and_content: *.png: Plot of the matrix in correspinding mat file using TADbit’s function hic_map()

organism: Drosophila melanogaster

growth_protocol: Drosophila S2 cells were obtained from the Drosophila Genomics Resource Center. S2 cells were grown in serum-supplemented (10%) Schneider’s S2 medium at 25 °C. In two of the replicates, cells were subjected to a control RNAi treatment against GFP as follows. S2 cells were transfected with dsRNA against  GFP by bathing in 10cm culture dishes (petri dish).Two dishes were used in each experiment. 9 x10^6 cells per dish were resuspended in 6 mL of serum free medium and incubated with 60 μg dsRNA at RT for 45 min, before addition of 12 mL complete media with 15% FBS to each well. The cells were harvested 3 days later. This procedure is described in "Gonzalez, I., Mateos-Langerak, J., Thomas, A., Cheutin, T. & Cavalli, G. Identification of regulators of the three-dimensional polycomb organization by a microscopy-based genome-wide RNAi screen. Mol Cell 54, 485-499,  (2014)".

extract_protocol:
S2 cells were scraped, transferred to 50 mL Falcon tubes and the volume adjusted to 25 mL with Schneider medium. Formaldehyde was added to a final concentration of 2% and the cells were fixed for 10 min at 25°C. The fixation was quenched with 25 mL 2 M glycine and placing on ice. Cells were centifuged, washed in cold PBS, then counted by haemocytomety. 2x10^7 cell aliquots were resuspended in 5 mL nuclear permeabilisation buffer (15 mM HEPES pH 7.6, 60 mM KCl, 15 mM NaCl, 4 mM MgCl2, 0.1% Triton-X100, 0.5 mM DTT, protease inhibitor cocktail (Roche)) and left on ice for 30 min. Nuclei were centrifuged then resuspended in 300 µl 1.25 x Dpn II buffer (New England Biolabs) plus 0.3% SDS and incubated for 1 hr at 37°C, 1000 rpm on a shaker. Triton-X100 was added to a final concentration of 2% and the nuclei were incubated for a further 1 hr at 37°C, 1000 rpm, before overnight digestion with 1500 U Dpn II (New England Biolabs) at 37°C, 1000 rpm. The restriction enzyme was inactivated by incubation for 20 min at 65°C, 1000 rpm with SDS at a final concentration of 1.3%, before dilution of the chromatin in 10 ml 1x T4 DNA ligase buffer (New England Biolabs) plus 1% Triton-X100 and incubation for 1 hr at 37°C, 750 rpm. The chromatin was ligated for 4 hr at 25°C, 750 rpm with 40,000 U T4 DNA ligase (New England Biolabs) then crosslinks were reversed overnight at 65°C, 750 rpm in the presence of 150 µg/ml proteinase K. The 3C DNA was then purified by 1 hr treatment with 40 µg/ml RNase A at 37°C, 750 rpm, phenol extraction, phenol/chloroform extraction and ethanol precipitation. The DNA was quantified with the Qubit dsDNA assay (Invitrogen). Aliquots of 5 µg 3C DNA were sonicated in a Bioruptor (Diagenode) in 50 µl volumes in sonication buffer (50 mM Tris-HCl, pH 8, 10 mM EDTA, 1% SDS) to obtain a smear between 500-1500 bp. The sonicated 3C DNA was then purified by phenol/chloroform extraction and ethanol precipitation and quantified with the Qubit dsDNA assay (Invitrogen).
Libraries for paired-end sequencing were made from 500 ng aliquots of sonicated 3C DNA using Illumina reagents and protocols, with size selection for products of ~800 bp.

value: S2 cell


title: S2 cell rep3


title: 16-cell, polysome-unbound

description: rRNA-depleted RNA


title: S2 cell rep1


title: 3.5 hpf, polysome-unbound

description: rRNA-depleted RNA


title: RNA Bind-N-Seq: YTH purification ; sample 4

description:
processed data file:
GEO_bind_n_seq.txt.gz

data_processing:
Library strategy: RNA Bind-N-Seq
For RNA Bind-n-Seq experiment the reads were sorted into individual libraries based on the barcodes and the 3′ adapter sequences were removed using cutadapt . Only reads of final length of 21 nucleotides with A at 10th position were kept for further analysis using R (R Core Team, 2017) and Bioconductor (Huber et al., 2015). Frequencies of individual nucleotides were calculated for each position as well as enrichment vs. the bead control. MEME - Motif discovery tool (Bailey and Elkan, 1994)  was used to search for a motif in a collection of 9-mers (read positions 6-14) centred around the  m6A at position 10.
genome build: N/A
processed data files format and content: The files for RNA Bind-n-Seq experiment contains the comparison of frequencies of 9mers centered on m6A.

source_name: random 21 nt ssRNAs with a central m6A moiety (N10-m6A-N10)

value: Ni-NTA beads + 6xHis-SUMO-YTH domain (of hYTHDC2)


title: PL-NAc_vTRAP_Input_rep2


title: RNA Bind-N-Seq: YTH purification ; sample 3


title: hESC line H9 cells after 24 hours of BMP4 treatment, biological replicate 1

value: 24 hours


title: hESC line H9 cells after 24 hours of BMP4 treatment, biological replicate 2


title: RNA Bind-N-Seq: YTH purification ; sample 2


title: egg, polysome-unbound

description: rRNA-depleted RNA


title: RNA Bind-N-Seq: YTH purification ; sample 1


title: hESC line H9 cells after 16 hours of BMP4 treatment, biological replicate 1

value: 16 hours


title: 1-cell, polysome-unbound

description: rRNA-depleted RNA


title: hESC line H9 cells after 16 hours of BMP4 treatment, biological replicate 2


title: RNA Bind-N-Seq: Bead control for YTH purification; sample 4

value: Ni-NTA beads


title: hESC line H9 cells after 8 hours of BMP4 treatment, biological replicate 2

value: 8 hours


title: 128-cell, polysome-bound

description: rRNA-depleted RNA


title: RNA Bind-N-Seq: Bead control for YTH purification; sample 3


title: 16-cell, polysme-bound

description: rRNA-depleted RNA


title: 1-cell, polysome-bound

description: rRNA-depleted RNA


title: RNA Bind-N-Seq: Bead control for YTH purification; sample 2


title: hESC line H9 cells after 48 hours of BMP4 treatment, biological replicate 2

value: 48 hours


title: hESC line H9 cells after 48 hours of BMP4 treatment, biological replicate 1


title: undifferentiated hESC line H9 cells, biological replicate 2

value: 0 hour (undifferentiated)


title: undifferentiated hESC line H9 cells, biological replicate 1


title: hESC line H9 cells after 8 hours of BMP4 treatment, biological replicate 1


title: egg, polysome-bound

description: rRNA-depleted RNA