title: ChIPseq Input from the pooled controls

city: Milano

first: Giuseppe

last: Testa

address: Via Adamello, 16

institute: European Institute of Oncology & University of Milano, Italy

description: ChIPseq Input from the pooled controls

data_processing:
Base calling and primary read filtering were performed according to Illumina protocols.
Reads were trimmed for potential adapter contamination using scythe 0.981 (min 4 nucleotides)
Trimmed reads were aligned to the GRCh38 genome using bowtie 1.0 (-v 2 -m 1).
Peaks were called using MACS 2.0.9 with default settings for YY1, and with the 'broad' option for H3K27ac and H3K27me3.
Genome_build: GRCh38
Supplementary_files_format_and_content: Peak calls (encodePeak format)

growth_protocol: LCL were cultured in RPMI 1640, FBS 15%, HEPES 1%, L-Glutamine 1%, Penicillin-Streptomycin 1%. All LCL samples were tested for mycoplasma.

extract_protocol:
Chromatin immunoprecipitation was performed as previously described (Frank et al., 2001) with some modification. Briefly, LCL were centrifuged at 150g for 5 minutes, an average of 150 x 106 LCLs were re-suspended in formaldehyde 1% in PBS for cross-linking. To stop the cross-linking reaction glycine was added to the final concentration 125 mM. Cells were re-suspended using ChIP SDS buffer (0.5% SDS, 5 mM EDTA, NaCl 100mM and 50 mM Tris-HCl at pH 8.1). Pellets were collected by centrifuging at 400g for 30 min and re-suspended in IP buffer (0.5% SDS, 5 mM EDTA, NaCl 100mM and 50 mM Tris-HCl at pH 8.6, Triton X-100 1,5%). To obtain a bulk of 300 bp DNA fragments, cells were sonicated using the Branson digital sonifier (Emerson Industrial Automation). Chromatin was quantified using Bradford protein assay (Bio-Rad). To immuno-precipitate YY1, 1 mg of total proteins was incubated with YY1 antibodies (sc-1703 or sc-281, Santa-Cruz Biotechnologies). For H3K27Ac chromatin immunoprecipitation, 100µg of proteins were immuno-precipitated using the antibody ab4729 (Abcam). Chromatin was incubated overnight with antibody at 4°C. G-Sepharose 4B (Thermo Fisher) beads were incubated with chromatin and antibodies mix for 4 hours at 4°C and followed by washes using low and high salt buffers (1% Triton X-100, 0.1% SDS, 150mM or 500mM NaCl , 2mM EDTA, 20 mM Tris-HCl ph8). Decross-linking was performed at 65°C for 3 hours. DNA was collected with QIAquick PCR Purification Kit (Qiagen).
Libraries were prepared as already described (Blecher-Gonen et al., 2013) with adaptations for the automated system Biomek FX.

value: Immortalized lymphoblastoid cell line (LC)

value: control

tag: chip target


title: ChIPseq Input from the pooled mutated samples

status: Public on May 19 2017

type: SRA

country: Italy

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell type

tag: genotype/variation

tag: chip antibody


title: YY1 (2) ChIPseq in HEP14_0080 LCLs

description: YY1 (2) ChIPseq in HEP14_0080 LCLs with YY1 mutation (p.Leu366Pro)

value: YY1-mutated (p.Leu366Pro)

value: YY1, (H-414)X sc-1703X lot#A1414 rabbit polyclonal


title: YY1 (2) ChIPseq in HEP14_0079 LCLs

description: YY1 (2) ChIPseq in HEP14_0079 LCLs with YY1 heterozygous deletion

value: YY1 hemizygous deletion


title: no antibody-rep1

city: Shanghai

first: Hong

last: Cheng

address: 320 YueYang Road

department: Shanghai Institute of Biochemistry and Cell Biology

country: China

institute: Shanghai Institutes for Biological Sciences

library_source: transcriptomic

data_processing:
For iCLIP-seq,the reads containing parts of the 3’ Solexa primer were trimmed from the 3’ end using fastx-toolkit.  These iCLIP reads after random barcode evaluation and barcode removed, were mapped to the human genome (hg19) using bowtie2, allowing 0-2 mismatches.  Only uniquely mapped reads were used for further analysis.  The first nucleotide in the genome upstream of a mapping cDNA tag was defined as ‘cross-link nucleotide’.  The clustered binding sites were identified though the strategy described in (König J, et al.Nat Struct Mol Biol. 2010,17(7):909-15. ).  We performed the evaluation of cluster binding site with the recommended default parameters (FDR < 0.05 and cluster sites within a window of 10 nts).  Only the cluster binding sites and the cluster cDNA tag were used in further analyses.
RNA-seq reads were cleaned and mapped the human genome (hg19 version) TopHat2.0. Reads mapping to multiple independent genomic locations were assigned to the most abundant biotype of the locations. Genome annotations from RefSeq and ENSEMBL were downloaded from the UCSC genome browser website, and supplemented with published datasets.
Genome_build: hg19
Supplementary_files_format_and_content: bed or xlsl

molecule: total RNA

source_name: uterine cervix

growth_protocol: HeLa cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum (Biochrom)

extract_protocol:
HeLa cells were irradiated with UV light at 300 mJ/cm2.  After cell lysis, RNAs were partially fragmented using 0.5 U/ml of RNase I, followed by immunoprecipitaions with or without (no antibody control) 10 μg of the ALYREF antibody immobilized on protein A Dynabeads (Life Technologies).  After extensive washing, immunoprecipitated RNAs were ligated at the 3’ ends to a RNA adapter and radioactively labeled by T4 polynucleotide kinase (Fermentas).  The protein-RNA complexes were then transferred to a nitrocellulose membrane.  Then, fragmented RNAs were purified from nitrocellulose membrane by PK treatment and phenol / chloroform extranction.
For iCLIP cDNA library preparation, fragmented RNAs, which were ligated with a RNA adapter (3' linker)  at the 3’ ends , reverse-transcribed with a primer containing a barcode (iCLIP RT primer).  The resulting cDNAs were purified by PAGE, circularized by single-stranded DNA ligase (Epicentre), linearized by restriction enzyme cleavage, and amplified and add P5/P3 adaptors by PCRs with (P3 and P5 solexa primer).
iCLIP-seq

treatment_protocol: Ctrl or indicated siRNAs were transfected with RNAimax (invitrogen)

tag: cell line

value: HeLa cell

tag: tissue

value: uterine cervix


title: YY1 (2) ChIPseq in CTRL3_JD LCLs

description: YY1 (2) ChIPseq in CTRL3_JD LCLs (unaffected control)


title: YY1 (2) ChIPseq in CTRL1_AB LCLs

description: YY1 (2) ChIPseq in CTRL1_AB LCLs (unaffected control)


title: YY1 (2) ChIPseq in CTRL2_BH LCLs

description: YY1 (2) ChIPseq in CTRL2_BH LCLs (unaffected control)


title: YY1 (1) ChIPseq in HEP14_0079 LCLs

description: YY1 (1) ChIPseq in HEP14_0079 LCLs with YY1 heterozygous deletion

value: YY1, (c-20)X sc-281X lot#F1614 rabbit polyclonal


title: YY1 (1) ChIPseq in HEP14_0080 LCLs

description: YY1 (1) ChIPseq in HEP14_0080 LCLs with YY1 mutation (p.Leu366Pro)


title: H3K27me3 ChIPseq in HEP14_0080 LCLs

description: H3K27me3 ChIPseq in HEP14_0080 LCLs with YY1 mutation (p.Leu366Pro)

value: H3K27me3, Cell Signaling C36B11 lot:11, ref 04/2016 9733BF rabbit monoclonal


title: YY1 (1) ChIPseq in HEP14_00120 LCLs

description: YY1 (1) ChIPseq in HEP14_00120 LCLs with YY1 mutation (p.Lys179* undergoing non-sense mediated decay)

value: YY1-mutated (p.Lys179*)


title: H3K27me3 ChIPseq in HEP14_00120 LCLs

description: H3K27me3 ChIPseq in HEP14_00120 LCLs with YY1 mutation (p.Lys179* undergoing non-sense mediated decay)


title: YY1 (1) ChIPseq in CTRL2_BH LCLs

description: YY1 (1) ChIPseq in CTRL2_BH LCLs (unaffected control)


title: H3K27me3 ChIPseq in CTRL4_PK LCLs

description: H3K27me3 ChIPseq in CTRL4_PK LCLs (unaffected control)


title: H3K27me3 ChIPseq in CTRL5_JL LCLs

description: H3K27me3 ChIPseq in CTRL5_JL LCLs (unaffected control)


title: YY1 (2) ChIPseq in HEP14_00120 LCLs

description: YY1 (2) ChIPseq in HEP14_00120 LCLs with YY1 mutation (p.Lys179* undergoing non-sense mediated decay)


title: YY1 (1) ChIPseq in CTRL4_PK LCLs

description: YY1 (1) ChIPseq in CTRL4_PK LCLs (unaffected control)


title: YY1 (1) ChIPseq in CTRL1_AB LCLs

description: YY1 (1) ChIPseq in CTRL1_AB LCLs (unaffected control)


title: H3K27me3 ChIPseq in CTRL3_JD LCLs

description: H3K27me3 ChIPseq in CTRL3_JD LCLs (unaffected control)


title: YY1 (1) ChIPseq in CTRL5_JL LCLs

description: YY1 (1) ChIPseq in CTRL5_JL LCLs (unaffected control)


title: YY1 (2) ChIPseq in HEP10_01008 LCLs

description: YY1 (2) ChIPseq in HEP10_01008 LCLs with YY1 mutation (p.Asp380Tyr)

value: YY1-mutated (p.Asp380Tyr)


title: H3K27me3 ChIPseq in HEP10_01008 LCLs

description: H3K27me3 ChIPseq in HEP10_01008 LCLs with YY1 mutation (p.Asp380Tyr)


title: H3K27me3 ChIPseq in HEP14_0079 LCLs

description: H3K27me3 ChIPseq in HEP14_0079 LCLs with YY1 heterozygous deletion


title: H3K27me3 ChIPseq in CTRL1_AB LCLs

description: H3K27me3 ChIPseq in CTRL1_AB LCLs (unaffected control)


title: YY1 (2) ChIPseq in CTRL4_PK LCLs

description: YY1 (2) ChIPseq in CTRL4_PK LCLs (unaffected control)


title: YY1 (1) ChIPseq in CTRL3_JD LCLs

description: YY1 (1) ChIPseq in CTRL3_JD LCLs (unaffected control)


title: dpdr-1_rhamnose_4h_3

city: Freising

first: Nils

last: Thieme

state: Bavaria

address: Hans-Carl-von-Carlowitz-Platz 2

department: Holzforschung München

country: Germany

institute: Technische Universität München

data_processing:
Basecalls performed using casava 1.8.2 and 1.8.4 and quality filtered using bbduk and fastxtoolkit
reads were mapped with Tophat v2.0.4 and Bowtie2.0.0 to Neurospora crassa OR74A Broad v12 genome and provided with Neurospora crassa OR74A Broad v12 transcripts.gtf
fragments per kilobase of transcript per million mapped reads (FPKMS) were calculated with Cufflinks v2.0.2 with parameters --max-bundle-frags=10000000 --compatible-hits-norm -u -g (providing Neurospora crassa OR74A Broad v12 transcripts.gtf)
rawcounts with htseq 0.6.0 with parameters  --stranded=no -m intersection-strict
Genome_build: Neurospora crassa OR74A Broad v12 assembly
Supplementary_files_format_and_content: Rawcounts and normalized counts in FPKMs

organism: Neurospora crassa

growth_protocol: Conidia obtained from 10-day-old pregrown cultures was used to inoculate 3 ml of 1x Vogel’s salts plus 2% (w/v) sucrose at 1x106 cells/mL in 24 deep well plates. The bottoms of the wells for each plate were initially scratched with a sharp needle to allow adherence and formation of mycelial mat. After 16 hours of growth, mycelia were washed three times in 1 x Vogel’s salts without added carbon and transferred to 1 x Vogel’s salts with their respective new carbon source (either 2% sucrose, 1% pectin, 2 mM L-rhamnose or no carbon source).

extract_protocol:
After 4 hours of induction, mycelia were harvested over Whatman #1 filter paper and subsequently flash frozen in liquid nitrogen for storage at -80˚C. RNA was  prepared using the TRIzol reagent (Invitrogen).
Stranded cDNA libraries were generated using the Illumina Truseq Stranded RNA LT kit. mRNA was purified from 1 ug of total RNA using magnetic beads containing poly-T oligos. The purified mRNA was fragmented and reverse transcribed using random hexamers and SSII (Invitrogen) followed by second strand synthesis. The fragmented cDNA was treated with an end-pair, A-tailing, adapter ligation, and 10 cycles of PCR. The prepared library was then quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit and run on a Roche LightCycler 480 real-time PCR instrument. The quantified library was then then multiplexed with other libraries, and the pool of libraries was then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate a clustered flowcell for sequencing. Sequencing of the flowcell was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit, v3, following a 2x100 indexed run recipe.

tag: strain

tag: age

value: 10 dpi

value: hyphal biomass

tag: treatment

value: induced for 4 hrs on 2 mM L-rhamnose


title: OX_12hr_rep3

city: NEW YORK

first: Nam-Hai

last: Chua

state: New York

address: 1230 York Avenue

country: USA

institute: The Rockefeller University

description: ELENA1 over-expressing plants with elf18 treatment, replicate 3 (OX_12hr_rep3)

data_processing:
Strand-specific RNA-seq reads were mapped to the Arabidopsis genome (TAIR10) using TopHat (version 2.0.8) with parameters “--library-type=fr-firststrand -i 40 -I 5000 -g 1 --segment-length=20”.
The mapped reads were assembled using Cufflinks (v2.1.1) with parameters “--library-type=fr-firststrand -I 5000 --min-intron-length=40” and with TAIR10 annotation as the reference.
The assembled transcripts of each ssRNA-seq sample were merged and annotated using Cuffcompare (v2.1.1) with TAIR10 annotation as the reference.
The expression levels of each gene were then calculated by the fragments per kilobase of exons per million fragments mapped (FPKM) using Cuffdiff with parameter “--library-type=fr-firststrand”.
A 2-fold variance in FPKM, a P value less than 0.05, and an adjusted P value less than 0.1 were used as cutoffs to define differentially expressed genes. The P value and adjusted P value were calculated using DESeq2.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited files include FPKM values and raw read counts of 21,407 protein coding genes

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: OX, 12hr, 2-week-old Arabidopsis seedlings

growth_protocol: Plants of all genotypes were grown on 0.6% agar media containing 0.5x Murashige and Skoog (MS) salts (MP Biomedicals), 1% sucrose (Fisher) and 0.5 g/L MES hydrate (Sigma) in a growth room at 22 oC under 16 h light/8 h dark with white fluorescent light (~100 μmolom-2os-1).

extract_protocol:
Total RNA was extracted from Arabidopsis 2-week old seedlings using TRIzol reagent (Ambion), treated with TURBO DNase (Ambion) and purified using RNeasy mini spin column (Qiagen). The quality of purified RNA was assessed using an Agilent 2100 Bioanalyzer.
cDNA libraries for ssRNA-seq were prepared using the Illumina TruSeq Stranded mRNA Sample Preparation Kit according to the low sample protocol guidelines. The quality and size of each sample library was assessed using an Agilent High Sensitivity D1K ScreenTape System. The average sizes of the enriched cDNA fragments were between 272 and 300 bp. The three biological replicates for each condition (negative control, 1 h_elf18, 6 h_elf18, and 12 h_elf18) were pooled into one well, and sequenced on an Illumina NextSeq High Output SR 75 with 75-cycle single reads per multiplexed sample.

treatment_protocol: For elf18 (EZBiolab) treatment, 2-week-old seedlings grown on MS solid medium were transferred to MS liquid medium (pH 5.7) with 1% sucrose and 5 μM elf18 or flg22, and incubated under the same condition and then seedlings were harvested at each time point after peptide application.

tag: developmental stage

value: 2-week-old seedlings

tag: genotype

value: ELENA1 over-expressing plants

tag: ecotype

value: elf

tag: time

value: 12 hr


title: H3K27Ac ChIPseq in HEP14_0080 LCLs

description: H3K27Ac ChIPseq in HEP14_0080 LCLs with YY1 mutation (p.Leu366Pro)

value: Immortalized lymphoblastoid cell line (LC)

value: H3K27Ac, Abcam ab4729


title: OX_6hr_rep3

description: ELENA1 over-expressing plants with elf18 treatment, replicate 3 (OX_6hr_rep3)

source_name: OX, 6hr, 2-week-old Arabidopsis seedlings

value: 6 hr


title: H3K27Ac ChIPseq in HEP14_0079 LCLs

description: H3K27Ac ChIPseq in HEP14_0079 LCLs with YY1 heterozygous deletion

value: YY1 hemizygous deletion


title: OX_6hr_rep2

description: ELENA1 over-expressing plants with elf18 treatment, replicate 2 (OX_6hr_rep2)


title: YY1 (2) ChIPseq in CTRL5_JL LCLs

description: YY1 (2) ChIPseq in CTRL5_JL LCLs (unaffected control)

value: control

value: YY1, (H-414)X sc-1703X lot#A1414 rabbit polyclonal


title: YY1 (1) ChIPseq in HEP10_01008 LCLs

description: YY1 (1) ChIPseq in HEP10_01008 LCLs with YY1 mutation (p.Asp380Tyr)

value: YY1, (c-20)X sc-281X lot#F1614 rabbit polyclonal


title: OX_1hr_rep1

description: ELENA1 over-expressing plants with elf18 treatment, replicate 1 (OX_1hr_rep1)

source_name: OX, 1hr, 2-week-old Arabidopsis seedlings

value: 1 hr


title: H3K27Ac ChIPseq in HEP14_00120 LCLs

description: H3K27Ac ChIPseq in HEP14_00120 LCLs with YY1 mutation (p.Lys179* undergoing non-sense mediated decay)

value: YY1-mutated (p.Lys179*)


title: OX_1hr_rep2

description: ELENA1 over-expressing plants with elf18 treatment, replicate 2 (OX_1hr_rep2)


title: OX_1hr_rep3

description: ELENA1 over-expressing plants with elf18 treatment, replicate 3 (OX_1hr_rep3)


title: H3K27Ac ChIPseq in HEP10_01008 LCLs

description: H3K27Ac ChIPseq in HEP10_01008 LCLs with YY1 mutation (p.Asp380Tyr)

value: YY1-mutated (p.Asp380Tyr)


title: OX_0hr_rep3

description: ELENA1 over-expressing plants without elf18 treatment, replicate 3 (OX_0hr_rep3)

source_name: OX, 0hr, 2-week-old Arabidopsis seedlings

value: Without elf18 treatment

value: 0 hr


title: OX_0hr_rep1

description: ELENA1 over-expressing plants without elf18 treatment, replicate 1 (OX_0hr_rep1)


title: ALYREF-rep2

value: HeLa cell

value: uterine cervix


title: OX_12hr_rep1

description: ELENA1 over-expressing plants with elf18 treatment, replicate 1 (OX_12hr_rep1)

value: 2-week-old seedlings

value: ELENA1 over-expressing plants


title: WT_12hr_rep2

description: Wild type plants with elf18 treatment, replicate 2 (WT_12hr_rep2)

source_name: WT, 12hr, 2-week-old Arabidopsis seedlings

value: Wild type

value: elf

value: 12 hr


title: WT_12hr_rep1

description: Wild type plants with elf18 treatment, replicate 1 (WT_12hr_rep1)


title: OX_0hr_rep2

description: ELENA1 over-expressing plants without elf18 treatment, replicate 2 (OX_0hr_rep2)


title: H3K27Ac ChIPseq in CTRL5_JL LCLs

description: H3K27Ac ChIPseq in CTRL5_JL LCLs (unaffected control)

value: Immortalized lymphoblastoid cell line (LC)

value: H3K27Ac, Abcam ab4729


title: WT_12hr_rep3

description: Wild type plants with elf18 treatment, replicate 3 (WT_12hr_rep3)


title: OX_12hr_rep2

description: ELENA1 over-expressing plants with elf18 treatment, replicate 2 (OX_12hr_rep2)


title: WT_6hr_rep2

description: Wild type plants with elf18 treatment, replicate 2 (WT_6hr_rep2)

source_name: WT, 6hr, 2-week-old Arabidopsis seedlings

value: 6 hr


title: WT_6hr_rep3

description: Wild type plants with elf18 treatment, replicate 3 (WT_6hr_rep3)


title: H3K27Ac ChIPseq in CTRL3_JD LCLs

description: H3K27Ac ChIPseq in CTRL3_JD LCLs (unaffected control)

value: control


title: WT_1hr_rep3

description: Wild type plants with elf18 treatment, replicate 3 (WT_1hr_rep3)

source_name: WT, 1hr, 2-week-old Arabidopsis seedlings


title: H3K27Ac ChIPseq in CTRL2_BH LCLs

description: H3K27Ac ChIPseq in CTRL2_BH LCLs (unaffected control)


title: WT_6hr_rep1

description: Wild type plants with elf18 treatment, replicate 1 (WT_6hr_rep1)


title: OX_6hr_rep1

description: ELENA1 over-expressing plants with elf18 treatment, replicate 1 (OX_6hr_rep1)


title: H3K27me3 ChIPseq in CTRL2_BH LCLs

description: H3K27me3 ChIPseq in CTRL2_BH LCLs (unaffected control)

value: H3K27me3, Cell Signaling C36B11 lot:11, ref 04/2016 9733BF rabbit monoclonal


title: HEP14_0120_rnaseq_2

description:
HEP14_0120 (YY1-mutated p.Lys179*) LCL RNAseq (batch 2)
V548M_B_S13868

data_processing:
Base calling and primary read filtering were performed according to Illumina protocols.
RNAseq quantification was performed directly from the reads using Salmon 6.1 (quasi), using default parameters and indexes based on the GChr38 RefSeq annotation complemented with ERCC spike-ins.
Genome_build: GChr38
Supplementary_files_format_and_content: Matrix of gene-level expected fragment counts

source_name: LC_YY1-mutated (p.Lys179*)

extract_protocol:
RNA was extracted using the RNeasy Micro Plus kit (Qiagen) according to the manufacturer's protocol. Concentration and RNA quality was assessed by the NanoDrop (NanoDrop Technologies). Prior RNAseq library construction RNA fragmentation was assessed by 2100 Bioanalyzer (Agilent Technologies). Only samples with RIN > 9 were accepted for library preparation. ERCC spike-in were added to total RNA.
RNAseq libraries were prepared according to Illumina protocols for Truseq stranded and RiboZero-depleted libraries.

tag: genotype/variataion

tag: batch

tag: molecule subtype

value: Total RNA (Ribozero-depleted)


title: WT_0hr_rep2

description: Wild type plants without elf18 treatment, replicate 2 (WT_0hr_rep2)

source_name: WT, 0hr, 2-week-old Arabidopsis seedlings


title: WT_0hr_rep3

description: Wild type plants without elf18 treatment, replicate 3 (WT_0hr_rep3)


title: H3K27Ac ChIPseq in CTRL1_AB LCLs

description: H3K27Ac ChIPseq in CTRL1_AB LCLs (unaffected control)


title: WT_1hr_rep1

description: Wild type plants with elf18 treatment, replicate 1 (WT_1hr_rep1)

value: 1 hr


title: H3K27Ac ChIPseq in CTRL4_PK LCLs

description: H3K27Ac ChIPseq in CTRL4_PK LCLs (unaffected control)


title: SH-SY5Y_H3K4me3

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

data_processing:
Peaks were called using the RSEG algorithm using the following arguments (rseg-diff -d k41.hg19.bed  -m 2 -v -i 20 -c human.hg19.size.bed -o )
Genome_build: hg19
Supplementary_files_format_and_content: bed files: rseg-diff ouput files.

source_name: Neuroblatoma cell line

extract_protocol: Cultured cells were fixed with 1% formaldehyde. Nuclei were isolated and the DNA was sheared to 200 to 300 bp fragments. Histon-bound DNA was precipitated using antibodies H3K27Ac (#4729, Abcam) and H3K4me3 (#04-745, Millipore).  De-crosslinked DNA was purified using Qiagen PCR purification kit (Qiagen) and quantified with Quant-IT Picogreen (Invitrogen). The DNA was used to generate sequencing libraries according to the manufactures procedure (Life Technologies): The DNA was end-polished, dA-tailed and adaptors with barcodes were ligated. The fragments were amplified (8 cycles) and quantified with a Bioanalyzer (Agilent). The libraries were prepped with the 5500W Flowchip v2 kit  (Life Technologies) and sequenced on the SOLiD Wildfire (Illumina) resulting in 50 bp reads. Alternatively, the libraries were sequenced using the HiSeq PE cluster kit v4 (Illumina) with the HiSeq2500 (Illumina) resulting in 125 bp reads.

value: Neuroblatoma cell line

tag: growth medium

value: DMEM 10% FCS

value: H3K4me3 (#04-745, Millipore)


title: SH-EP2_H3K4me3


title: SH-SY5Y_input


title: 700-ADN_H3K27ac

source_name: Neuroblatoma TIC line

value: Neuroblatoma TIC line

value: neural stem cell medium


title: 691-ADN_H3K4me3


title: SH-EP2_H3K27ac


title: 691-MES_H3K4me3


title: SH-EP2_input


title: SH-SY5Y_H3K27ac


title: WT_1hr_rep2

description: Wild type plants with elf18 treatment, replicate 2 (WT_1hr_rep2)

value: 2-week-old seedlings


title: CTRL3_JD_rnaseq_2

description: CTRL3_JD LCL RNAseq (batch 2)


title: HEP14_0080_rnaseq_2

description:
HEP14_0080 (YY1-mutated p.Leu366Pro) LCL RNAseq (batch 2)
MZ_226_S13869

source_name: LC_YY1-mutated (p.Leu366Pro)

value: YY1-mutated (p.Leu366Pro)


title: 700-ADN_H3K4me3


title: 691-MES_H3K27ac


title: WT_0hr_rep1

description: Wild type plants without elf18 treatment, replicate 1 (WT_0hr_rep1)

value: Wild type

value: Without elf18 treatment

value: 0 hr


title: CTRL5_JL_rnaseq_2

description:
CTRL5_JL LCL RNAseq (batch 2)
LCL_JL_S13865

value: Immortalized lymphoblastoid cell line (LC)


title: CTRL2_BH_rnaseq_2

description: CTRL2_BH LCL RNAseq (batch 2)


title: 691-ADN_input


title: CTRL1_AB_rnaseq_2

description: CTRL1_AB LCL RNAseq (batch 2)


title: 691-ADN_H3K27ac


title: CTRL6_MD_rnaseq_2

description:
CTRL6_MD LCL RNAseq (batch 2)
LCL_MD_S13867


title: 711-ADN_H3K27ac


title: 700-ADN_input


title: 753-ADN_H3K4me3


title: HEP14_0120_rnaseq_1

description:
HEP14_0120 (YY1-mutated p.Lys179*) LCL RNAseq (batch 1)
LCL_HEP-10120_S13860

value: YY1-mutated (p.Lys179*)


title: HEP14_0079_rnaseq_2

description: HEP14_0079 (YY1 hemizygous deletion) LCL RNAseq (batch 2)

source_name: LC_YY1 hemizygous deletion

value: YY1 hemizygous deletion


title: 753-ADN_input


title: HEP10_1008_rnaseq_2

description: HEP10_1008 (YY1 mutated p.Asp380Tyr) LCL RNAseq (batch 2)

source_name: LC_YY1-mutated (p.Asp380Tyr)

value: YY1-mutated (p.Asp380Tyr)


title: 753-ADN_H3K27ac


title: HEP14_0080_rnaseq_1

description:
HEP14_0080 (YY1-mutated p.Leu366Pro) LCL RNAseq (batch 1)
LCL_HEP-1008_S13861


title: 711-ADN_input


title: 711-ADN_H3K4me3


title: HEP14_0079_rnaseq_1

description:
HEP14_0079 (YY1 hemizygous deletion) LCL RNAseq (batch 1)
LCL_HEP-10080_S13859


title: HEP10_1008_rnaseq_1

description:
HEP10_1008 (YY1 mutated p.Asp380Tyr) LCL RNAseq (batch 1)
LCL_HEP-10079_S13858


title: 691-MES_input


title: Tet TKO, mRNA, sample 1

city: Mannheim

first: Francesca

last: Tuorto

address: Ludolf-Krehl-Str. 13-17

department: Division of Biochemistry  Mannheim Institute for Innate Immunoscience (MI3)

institute: Deutsches Krebsforschungszentrum

data_processing:
Library strategy: RNA Bisulfite-seq
Reads were trimmed with a quality cutoff of 30 for each base (corresponding to a confidence level of 99.9%) and aligned using BSMAP (Xi and Li 2009), which allows C-T base modifications without flagging them as mismatches.
We used 3% mismatch rate, and full sequence usage in BSMAP (parameters: -s 12 -v 0.03 -g 0 -w 1000 -S 0 -p 1 -V 1 -I 1 -n 0 -r 2 -u -m 15 -x 1000).
Resulting aligned reads were kept only if their length was 25 nt or more, if they aligned uniquely, and if both forward and reverse pairs were located at the same positions.
Reads containing more than 3 adjacent non-converted cytosines (rRNA and mRNA), or more than 6 adjacent non-converted cytosines (tRNA) were interpreted as non-converted reads resulting from RNA folding or bound proteins and were thus discarded. The presence of Nsun2- and Dnmt2-dependent methylation at C38, C48 and C49 in some tRNAs made it necessary to raise this threshold from 3 to 6 in tRNAs. (2.) Mismatches apart from C/T, occurring consistently at a specific position indicate the existence of a distinct subset of reads (as caused by RNA editing or single-nucleotide polymorphisms). If such a subset additionally correlates with the presence or absence of a converted cytosine, we discarded the mismatched subsets of reads to avoid confounding errors (upon significance of a Fisher exact test between reads with converted cytosines or not, compared to reads with a mismatch or not, Bonferroni-adjustment for multiple testing, significance cutoff α=0.05). We permitted an exception for tRNA(Val), which is known to be subject to RNA editing at position 34
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include non-conversion ratio at each cytosine

organism: Mus musculus

source_name: embryonic stem cells

growth_protocol: ESCs were grown on a primary MEF feeder layer in standard culture medium: knock-out DMEM (Gibco), 15% heat inactivated fetal calf serum (Hyclone), 1% non-essential amino acids (Gibco), 1% penicillin/streptomycin (Gibco), 2nM L-glutamine (Gibco), 0.1mM _-mercaptoethanol, 500 U/mL ESGRO (ESG1106, Merck Millipore).

extract_protocol:
RNA extraction was performed according to the Invitrogen TRIzol RNA isolation protocol (Ambion). The nucleic acid concentrations and purity were analyzed on the NanoDrop ND-1000 Spectrophotometer. RNA integrity was measured on a Bioanalyzer (Agilent) or TapeStation (Agilent). Samples were stored at -80 °C.
Poly(A)+ RNA was isolated from 500 µg total RNA by two rounds of purification using polyA Spin mRNA Isolation kit (New England Biolabs). Poly(A)+ RNA were further processed with the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs). This was carried out as described in the manual. 3 min of fragmentation at 94 °C has been established to lead to a peak at approximately 250 nt, appropriate for the final 100 bp paired-end sequencing. The fragmented RNA was precipitated using ethanol with 20 μg GlycoBlue at -80 °C for at least 10 min.   TURBO DNase (Ambion) was applied to each sample according to the protocol in a total volume of 20 μl. This volume was immediately applied to the EZ RNA Methylation Kit (Zymo Research), following the manufacturer’s manual. As a final step before library preparation, a stepwise RNA end repair was carried out using T4 polynucleotide kinase (TaKaRa). 3’-Dephosphorylation and 5’-phosphorylation (using 10 mM dATP) were carried out at 37°C for 20 min each. RNA was further purified by a phenol/chloroform extraction and ethanol precipitation.  Library preparation was done according to the NEBNext Small RNA Library Prep Set protocol. Following adaptor ligation and cDNA synthesis, cDNA was amplified with 12 cycles of PCR and purified using the QIAquick PCR Purification Kit (Qiagen). The libraries were further size selected on a 6% polyacrylamide gel. Compatible barcodes were selected and samples were pooled in equimolar ratios on multiple lanes on an Illumina HiSeq 2000 platform. A 100 bp paired-end sequencing approach was used.

treatment_protocol: The feeder cells were removed by serial passaging as follows: MEFs and ESCs were harvested and the feeder was allowed to attach to the dishes for 40- 60 min at 37 °C. All cells that had not attached were re-plated into second dishes for an additional 40-60 min. The supernatants (non-attached cells) were then spun down and pellets were snap-frozen in liquid nitrogen. This allowed harvest of pure ESCs without any MEF contaminants, as MEFs attach significantly faster. The purity of the harvest was very high, which was ultimately confirmed by genotyping of Dnmt2-/-  ESCs using PCR.

tag: background


title: D2R

extract_protocol:
RNA extraction was performed according to the Invitrogen TRIzol RNA isolation protocol (Ambion). The nucleic acid concentrations and purity were analyzed on the NanoDrop ND-1000 Spectrophotometer. RNA integrity was measured on a Bioanalyzer (Agilent) or TapeStation (Agilent). Samples were stored at -80 °C.
30 µg of total RNA was fractionated into a long (<200 nt) and a small RNA fraction (<200 nt) by a modified protocol for small RNA cloning (W. Gu and D. Conte) using mirVana Isolation Kit buffers. Briefly, 400 μl of Lysis/Binding Buffer was mixed with 48μl of Homogenate Additive and 80 µl of total RNA. The mix was incubated at RT for exactly 5 min. 1/3rd volume of Ethanol was added and mixed by inversion. This was incubated at RT for exactly 20 min to increase yield. 10 μg GlycoBlue was added and spun at 21 °C and 2,500 x g for 8 min to pellet the long fraction. The supernatant containing the small fraction was carefully transferred to a fresh tube and precipitated with isopropanol and 15 μg GlycoBlue at -80 °C for at least 10 min. rRNA depletion was carried out on the small fraction and on the half amount of the long fractions according to the RiboMinus Eukaryote System v2 (Ambion) protocol. The other half amount of the long fraction was further processed and sequenced as Ribo+ sample. rRNA-depleted samples were concentrated using ethanol precipiptation. The long fractions were further processed with the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs). This was carried out as described in the manual. 3 min of fragmentation at 94 °C has been established to lead to a peak at approximately 250 nt, appropriate for the final 100 bp paired-end sequencing. The fragmented RNA was precipitated using ethanol with 20 μg GlycoBlue at -80 °C for at least 10 min.   TURBO DNase (Ambion) was applied to each sample according to the protocol in a total volume of 20 μl. This volume was immediately applied to the EZ RNA Methylation Kit (Zymo Research), following the manufacturer’s manual. As a final step before library preparation, a stepwise RNA end repair was carried out using T4 polynucleotide kinase (TaKaRa). 3’-Dephosphorylation and 5’-phosphorylation (using 10 mM dATP) were carried out at 37°C for 20 min each. RNA was further purified by a phenol/chloroform extraction and ethanol precipitation.  Library preparation was done according to the NEBNext Small RNA Library Prep Set protocol. Following adaptor ligation and cDNA synthesis, cDNA was amplified with 12 cycles of PCR and purified using the QIAquick PCR Purification Kit (Qiagen). The libraries were further size selected on a 6% polyacrylamide gel. Compatible barcodes were selected and samples were pooled in equimolar ratios on multiple lanes on an Illumina HiSeq 2000 platform. A 100 bp paired-end sequencing approach was used.

tag: fraction

value: long RNA fraction (>200 nt


title: Tet TKO, mRNA, sample 2


title: CTRL4_PK_rnaseq_1

description:
CTRL4_PK LCL RNAseq (batch 1)
LCL_PK_S13866

tag: cell type

value: control

value: Total RNA (Ribozero-depleted)


title: CTRL3_JD_rnaseq_1

description:
CTRL3_JD LCL RNAseq (batch 1)
LCL_JD_S13864


title: D1R

value: long RNA fraction (>200 nt)


title: CTRL2_BH_rnaseq_1

description:
CTRL2_BH LCL RNAseq (batch 1)
LCL_BH_S13863


title: D2L

value: long RNA fraction (>200 nt) Ribo-


title: D3L


title: D1L


title: zebrafish mpeg1:mCherry +, 72 hpf [EH_R]

city: Boston

first: Leonard

last: Zon

state: MA

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

description: cells that were mCherry + only

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using cutadapt, then mapped to UCSC danRer7 whole genome using Tophat 2.0.11 without novel splicing form calls
Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts
Genome_build: danRer7
Supplementary_files_format_and_content: excel files include RPKM values for each Sample

organism: Danio rerio

source_name: mpeg1:mCherry; mpx:EGFP transgenic zebrafish embryos (wild-type)

growth_protocol: Transgenic zebrafish (mpeg1:mCherry and mpx:EGFP) were crossed together and embryos were grown under standard conditions at 28C in E3 buffer until 72 hpf.  Embryos positive for both transgenes were homogenized, filtered, and sorted using FACS into PBS, collecting >50,000 GFP (+) cells, >50,000 mCherry (+) cells and >50,000 GFP/mCherry (-) cells

extract_protocol:
Total RNA was collected using Trizol LS and GenElute LPA carrier per manufacturer instructions
Libraries were prepared using Ribogone kit (Clontech) and the SMARTer Universal Low input RNA Kit (Clontech; input was 50 ng total RNA for each sample) and sequenced on the Illumina Hiseq 2500

treatment_protocol: No treatments

tag: genotype/variation

value: mpeg1:mCherry; mpx:EGFP transgenic (wild-type)

value: zebrafish embryos

tag: cell population

value: mpeg1:mCherry +


title: CTRL1_AB_rnaseq_1

description:
CTRL1_AB LCL RNAseq (batch 1)
LCL_AB_S13862


title: D3S

value: small RNA fraction (<200 nt) Ribo-


title: Spermatocytes from 7-month Zmym3 KO mice

city: Beijing

first: Chunsheng

last: Han

state: Beijing

address: 1-5 Beichen West Road, Chaoyang District

department: Institute of Zoology

institute: Chinese Academy of Sciences

data_processing:
The sequencing reads were mapped to the mouse genome (UCSC mm9) by TopHat (v2.0.6).
The expression level of mRNAs was represented by FPKM calculated by Cufflinks (v2.0.2).
The differentially expressed genes were identified with Cuffdiff.
Genome_build: UCSC mm9
Supplementary_files_format_and_content: The expression level of mRNAs.

source_name: testes

extract_protocol:
Total RNA from mouse testis cells and mSSCs was extracted using Trizol. The RNA libraries were constructed by Illumina library preparation protocols. High-throughput sequencing was performed on HiSeq4000/HiSeq X 10.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Zmym3 WT and KO SSC were cultured on laminin-coated dishes.  c-KIT+ cells were induced from both WT and KO SSCs by 100 nM RA 36 h after RA treatment. For collecting the spermatocytes, the testes were firstly digested into single cells. The cells were firstly FACS sorted to collect tetraploid cells which were further sorted into two populations based on their forward scatter (FSC) and side scatter (SSC) features. The population of larger sizes consisted mainly of pachytene spermatocytes of about 80% purity based on the co-immunostaining of SYCP3 and rH2AX were collected.

tag: gender

value: male

tag: development stage

value: knockout type


title: zebrafish double negative, 72 hpf [EH_N]

description: cells that were neither mCherry + nor GFP +

growth_protocol: Transgenic zebrafish (mpeg1:mCherry and mpx:EGFP) were crossed together and embryos were grown under standard conditions at 28C in E3 buffer until 72 hpf. Embryos positive for both transgenes were homogenized, filtered, and sorted using FACS into PBS, collecting >50,000 GFP (+) cells, >50,000 mCherry (+) cells and >50,000 GFP/mCherry (-) cells

value: double negative


title: zebrafish mpx:EGFP +, 72 hpf [EH_G]

description: cells that were EGFP + only

value: mpx:EGFP +


title: Wt2R

value: wild type


title: Spermatocytes from 5-month Zmym3 KO mice

tag: strain


title: D1S


title: Spermatocytes from 7-month Zmym3 WT mice


title: Wt1R


title: Spermatocytes from 5-month Zmym3 WT mice


title: Wt3L


title: Tet TKO, mRNA, sample 3


title: Wt2L


title: Wt1L


title: Sp9-KO rep3

city: shanghai

first: Zhidong

last: Liu

address: Mingdao Building, 138 Yi Xue Yuan Road

institute: fudan university

data_processing:
Illumina Casava1.8.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome（version:GRCm38.p4）using TopHat（version:2.0.9).
Cufflinks v2.1.1 was used to count the read numbers mapped to each gene
To identify most differentially expressed genes, we ranked genes according to their size and sequencing coverage normalized FPKM (fragments per kilo base of exon per million). The log2 fold changes of gene FPKM between two genotypes were tested statistically to determine whether an individual gene expression was altered significantly or not.
Genome_build: ensembl GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values and the fragments count of each gene for each sample.

source_name: MGE

extract_protocol:
Total RNA was extracted using mir VanaTM miRNA Isolation kit (Cat# AM1561, Ambion),following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The medial ganglionic eminence from E12.5 wild type littermate controls and Sp9 null mutant mice were dissected in ice-cold HBSS.These tissues were flash frozen in the nitrogen and then stored into -80 oC

value: mixed genetic background of C57BL/6J, 129S6, and CD1

tag: tissue

value: embryonic brain

value: embryonic 12.5


title: Wt3S


title: Sp9-KO rep2

tag: developmental stage


title: D2S

tag: genotype


title: Sp9-KO rep1


title: WT rep3


title: Wt2S


title: WT rep2


title: Wt1S


title: WT rep1


title: WT-K3

first: Jen

last: Sheen

address: 185 Cambridge st. CPZN7620

department: Molecular Biology

institute: Massachusetts General Hospital

description:
wild type KCL
processed data file(s): WT-N_WT-K.txt

data_processing:
51 nucleotide reads from single-end sequncing in fastq files were aligned to the Arabidopsis genome, TAIR10, with the Tophat aligner.
htseq-count from the HTSeq python library was used to determine numbers of reads per gene
Differential experssion between treatment conditions was determined in R with DESeq2. The baseMean is an average of normalized count values, divided by size factors, taken over all samples.
Genome_build: TAIR10
Supplementary_files_format_and_content: [.txt] files contain HTSeq count data and the output of DESeq2 analysis

source_name: seedlings

growth_protocol: For RNA-Seq analysis, 10 seedlings were germinated in one well of 6-well tissue culture plate with 1 ml of ammonium succinate medium, which contained basal medium (10 mM KH2PO4/KH2PO4 pH 5.5, 1 mM MgSO4, 1 mM CaCl2, 0.1 mM FeSO4-EDTA, 50 µM H3BO4, 12 µM MnSO4·H2O, 1 µM ZnCl2, 1 µM CuSO4·5H2O, 0.2 µM Na2MoO4·2H2O, 1 g/L MES, and 0.5 % sucrose, pH 5.8) and 2.5 mM ammonium succinate as the sole nitrogen source. Plates were sealed with the parafilm and placed on the shaker at 70 rpm under constant light (45mE) at 23 °C for 7 days.

extract_protocol:
Approximately 10 seedlings were pooled and total RNA was isolated using Trizol reagent (Invitrogen).
Total RNA (0.5 ug) was used for making the library. The library was prepared using Illumina TruSeq RNA sample Prep Kit v2 according to the manufacture's  guidelines with 9 different barcodes (triplicate samples). The libraries were sequenced for 50 cycles on an Illumina HiSeq 2500 rapid mode using two lanes of a flow cell.

treatment_protocol: Before nitrate induction, seedlings were washed three times with 1 ml basal medium. Seedlings were treated in 1 ml of medium with different concentration (0.5 mM or 10 mM) of KCl or KNO3 for 15 min. Seedlings were then harvested for RNA extraction. In order to block CPK10 (M141G) kinase activity, seedlings were pre-treated with 10 µM 3MBiPin the basal medium for 2 min and then treated with 0.5 mM or 10 mM KCl or KNO3 for 15 min.

tag: age

tag: treatment

value: 10 mM KCl

value: seedling


title: icpk-N3

description:
inducible cpk10,30,32 triple mutant expressing CPK10(M141G)-DHA KNO3
processed data file(s): CPK-N_WT-N.txt

value: icpk mutant

value: 10 mM KNO3


title: WT-N3

description:
wild type KNO3
processed data file(s): WT-N_WT-K.txt, CPK-N_WT-N.txt


title: WT-N1


title: icpk-N1


title: icpk-N2


title: WT-K1


title: WT-N2


title: WT-K2


title: ChIP Aly-HA from Aly-HA; kmg KD rep2

status: Public on May 18 2017

city: Ithaca

first: Jongmin

middle: J

last: Kim

state: NY

address: 930 Campus Road

department: Biomedical Sciences

institute: Cornell University

data_processing:
fastq files were generated using bcl2fastq (v2.17.1.14) from Illumina
Trimming: all raw sequencing data were quality and adapter trimmed by using a wrapper script TrimGalore that combines Cutadapt (ver. 1.8.1) and FastQC (ver. 0.11.4) with adapter overlap stringency of 1 and Phred quality score cutoff of 20.
Mapping: trimmed fastq files were mapped to the Drosophila melanogaster genome (release 6.07 downloaded from Flybase) using the Burrows-Wheeler Aligner (bwa aln, ver. 0.7.10) with default parameters assuming sequencing error rate lower than 2%.
Post mapping: the bam files generated by mapping were further filtered to exclude unmapped reads (-F 0x04), and reads mapped with low confidence (-q 1) using SAMtools (ver. 1.2). Filtered bam files were sorted and indexed by using SAMtools.
Peak calling: genomic regions enriched after chromatin immunoprecipitation with respective proteins (peaks) were identified using MACS2 (ver. 2.1.0) without building a shifting model (--nomodel) since it is possible that Kmg, dMi-2 and Aly bind to broad regions of DNA.
Read counts calculation and visualization: to obtain read counts corresponding to genomic positions, bedgraph files were generated from BAM files using the BEDTools genomecov while normalizing all the samples to have the equivalent of 1 million mapped reads using the '-scale' option. For visualization in genome browsers (i.e. Integrative Genomic Viewer), bedgraph files were converted into bigwig files using the bedGraphToBigWig program.
Genome_build: dm6 (release 6.07 downloaded from the Flybase)
Supplementary_files_format_and_content: Bigwig files which can visualize read abundances in genome browsers

organism: Drosophila melanogaster

source_name: Testis

growth_protocol: Crosses and experimental flies were grown on cornmeal and molasses media at 30 °C

extract_protocol:
85 pairs of testes were dissected at a time in PBS. Dissected testes were fixed in 1% formaldehyde in PBS at room temperature for 8 minutes in rotating test tubes. The reaction was stopped by adding 2.5M glycine to the testes in 1% formaldedhyde to a final concentration of 125mM glycine and incubating at 4°C for 5 minutes. Then the fixed testes were washed in PBS three times and snap frozen in liquid nitrogen, and stored in -80°C. Eight such batches (680 pairs altogether) were used per condition. After accumulating enough samples, each batch of 85 pairs of frozen, fixed testes were thawed and homogenized using a plastic pestle, and resuspended in 130uL of sonication buffer (10mM Tris pH 8.0, 1mM EDTA, 0.1% SDS). The testis lysates were transferred to Covaris sonication miniTubes (Covaris, microTUBE AFA Fiber Pre-Slit Snap-Cap 6x16mm), and sonicated for 10 minutes each in the Covaris E220 Focused-ultrasonicator (Treatment Time: 600 sec; Acoustic Duty Factor: 2 %; Peak Incident Power: 105 W; Cycles Per Burst: 200) to a final DNA size distribution maximum between 300-500bp. After sonication, lysates from all 680 pairs of testes for the same genotype were pooled together and centrifuged at 4ºC for 5 minutes to clear debris. About 40 µL (~4%) of supernatant was saved to check fragment size and also to use as an input sample. 1/3 volume of 3X IP buffer was then added to sonicated testes lysates to achieve a final buffer composition of (20mM Tris pH 8.0, 135mM NaCl, 10% glycerol, 1% NonidetP-40, 5mM EDTA, 0.03% SDS, 1mM PMSF, 1x Complete protease inhibitor (Roche, Cat# 11697498001)). Testis lysates in IP buffer were incubated with Protein A magnetic beads conjugated with antibodies against Kmg, HA (for Aly) or dMi-2, prepared as described above for protein immunoprecipitation. After overnight incubation, magenetic beads were washed two times with IP buffer (without SDS), two times with high salt wash buffer (same as the IP buffer but with 270mM NaCl), two times with NaDOC buffer (10mM Tris, pH 8.0, 250mM LiCl, 0.5% Nonidet P-40, 1mM EDTA, 0.5% NaDOC), and finally one time with TE NaCl (10mM Tris pH 8.0, 1mM EDTA, 50mM NaCl), then eluted with 200µl elution buffer (50mM Tris pH 8.0, 10mM EDTA, 1% SDS, 1mM PMSF, 1x Complete protease inhibitor (Roche, Cat# 11697498001)) twice by incubating at 70ºC with occasional mixing every five minutes for 30 minutes. Immunoprecipitated protein-chromatin complexes were treated with RNase A for 30 minutes at 37ºC, then with proteinase K for three hours at 55 ºC, then de-crosslinked by incubating at 65ºC for >12 hours. DNA was extracted from de-crosslinked eluates by phenol:chloroform:isoamyl alcohol (25:24:1) based phase separation followed by ethanol/sodium acetate precipitation. Precipitated DNA was resuspended in 15 µl of 10mM Tris, pH 8.0. The concentration of purified DNA was measured by Qubit (dsDNA HS Assay kit, Thermo Fisher Scientific, Cat#: Q32851).
Because the amount of immunoprecipiated DNA was very low (~1ng), sequencing libraries were generated without a purification step until the final PCR amplification by using a kit utilizing stem-loop adapters (Rubicon genomics, ThruPLEX DNA-Seq 12S kit) based on the manufacturer’s instructions.
All ChIP-Seq libraries were sequenced by NextSeq High Output mode with 75bp single end, except one replicate of the Kmg ChIP-Seq, which was sequenced with NextSeq Mid Output mode with 75bp paired end. Between 4 to 8 libraries were pooled into one sequencing lane, on average yielding over 40 million reads per sample (17 ~ 81 million). All sequencing was performed by the Stanford Functional Genomics Facility (SFGF).

value: alyP-Aly-HA; UAS-RNAi-kmg (VDRC# 107395); bam-gal4, UAS-dicer2

value: 0~1 day post eclosion


title: Input for ChIP Aly-HA from Aly-HA rep2

value: alyP-Aly-HA; UAS-RNAi-kmg (VDRC# 107395); TM6b


title: Input for ChIP Aly-HA from Aly-HA; kmg KD rep2


title: ChIP Aly-HA from Aly-HA; kmg KD rep1


title: ChIP Aly-HA from w1118 rep1 (negative control, no transgene)


title: Input for ChIP Aly-HA from Aly-HA; kmg KD rep1


title: Input for ChIP Aly-HA from Aly-HA rep1


title: Input for ChIP Aly-HA from w1118 rep1 (negative control, no transgene)


title: ChIP dMi-2 from wild-type rep2


title: ChIP dMi-2 from kmg KD rep2

value: UAS-RNAi-kmg (VDRC# 107395); bam-gal4, UAS-dicer2


title: Input for ChIP dMi-2 from kmg KD rep2


title: Input for ChIP dMi-2 from wild-type rep2


title: ChIP dMi-2 from kmg KD rep1


title: ChIP dMi-2 from wild-type rep1


title: ChIP Kmg from wild-type rep2


title: Input for ChIP dMi-2 from kmg KD rep1


title: ChIP Kmg from kmg KD rep2


title: Input for ChIP Kmg from kmg KD rep2


title: Input for ChIP Kmg from wild-type rep2


title: ChIP Kmg from kmg KD rep1


title: ChIP Aly-HA from Aly-HA rep2


title: Input for ChIP Kmg from kmg KD rep1


title: dMi-2 KD testis rep2

description: polyA RNA purified from total RNA by oligodT beads

data_processing:
fastq files were generated using bcl2fastq (v2.17.1.14) from Illumina
Trimming: all raw sequencing data were quality and adapter trimmed by using a wrapper script TrimGalore that combines Cutadapt (ver. 1.8.1) and FastQC (ver. 0.11.4) with adapter overlap stringency of 1 and Phred quality score cutoff of 20.
Mapping: trimmed fastq files were mapped using a splice-aware aligner, Tophat (ver. 2.0.9), utilizing Bowtie2 (ver. 2.1.0) to the Drosophila melanogaster genome (release 6.07) while supplying trancript annotation obtained from the Ensembl database (Drosophila_melanogaster.BDGP6.82.chr.gff3). Default parameters were used, except the library type was specified as ‘fr-firststrand’ since only the first strand was retained by dUTP method in library preparation.
Post mapping: the bam files generated by mapping were further filtered to exclude unmapped reads (-F 0x04), and reads mapped with low confidence (-q 1) using SAMtools (ver. 1.2) (48). Filtered bam files were sorted and indexed by using SAMtools.
Read counts calculation and visualization: to obtain read counts corresponding to genomic positions, bedgraph files were generated from bam files using the BEDTools genomecov (50) while normalizing all the samples to have the equivalent of 1 million mapped reads using '-scale' and '-split' options. Given the sequencing library is made with dUTP method, Bam files were divided and re-merged to obtain strand specific read counts. Bedgraph files were converted into bigwig files using the bedGraphToBigWig program.
Genome_build: dm6 (release 6.07 downloaded from the Flybase)
Supplementary_files_format_and_content: Bigwig files which can visualize strand specific read abundances in genome browsers

extract_protocol:
kmg ctrl, kmg KD, dMi-2 ctrl, and dMi-2 KD testes without accessory glands were dissected in PBS for 30 minutes and immediately frozen in liquid nitrogen before transferred to -80°C. Wild-type heads were manually decapitated from the body and frozen and stored as in testes preparation. Total RNA was extracted using TRIzol (Invitrogen).  RNA was further purified by RNeasy mini column (Qiagen) to minimize residual salts. RNA quality was assessed by checking rRNA integrity using Bioanalyzer. ~30ug of total RNA was used to purify polyA RNA by using Poly(A)Purist MAG Kit (Thermo Fisher, Cat#AM1922).
100ng of purified mRNA was used to make a strand-specific sequencing library by dUTP incorporation method using KAPA Stranded RNA-Seq Library Preparation Kit Illumina® Platforms (KAPA Biosystems, Cat#: KK8400) following manufacturer’s instructions.
All RNA-Seq libraries were sequenced by NextSeq Mid Output mode 150bp paired end. Between 3 to 4 samples were pooled in a single lane, yielding on average 48 million reads per sample (34 to 65 million). All sequencing was performed by the Stanford Functional Genomics Facility (SFGF).

value: UAS-RNAi-dMi-2 (VDRC# 107204); bam-gal4, UAS-dicer2


title: dMi-2 ctrl testis (no driver) rep2

value: UAS-RNAi-dMi-2 (VDRC# 107204); TM6b


title: dMi-2 KD testis rep1


title: ChIP Aly-HA from Aly-HA rep1


title: ChIP Kmg from wild-type rep1


title: dMi-2 ctrl testis (no driver) rep1


title: kmg KD testis rep2


title: Input for ChIP Kmg from wild-type rep1


title: Input for ChIP dMi-2 from wild-type rep1


title: wild-type head rep2

source_name: Head


title: wild-type head rep1


title: kmg KD testis rep1


title: LC1_RNA_seq

city: Nanjing

last: Shen

address: Weigang No.1

institute: Nanjing Agriculture University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to NCBI goat genome annotation release version 101 using bowtie v1.2.0 with default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Cufflinks v2.2.1.The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: NCBI goat genome annotation release version 101
Supplementary_files_format_and_content: *txt: Tab-delimited text files include RPKM values.

organism: Capra hircus

source_name: rumen epithelia cells, LC

extract_protocol:
Rumen epithelium were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.

value: rumen epithelium

value: 4 months

value: LC diet


title: kmg ctrl testis (no driver) rep1

value: UAS-RNAi-kmg (VDRC# 107395); TM6b


title: kmg ctrl testis (no driver) rep2


title: LC2_RNA_seq


title: MC2_RNA_seq

source_name: rumen epithelia cells, MC

value: MC diet


title: MC1_RNA_seq


title: HC1_RNA_seq

source_name: rumen epithelia cells, HC

value: HC diet


title: MC3_RNA_seq


title: LC3_RNA_seq


title: HC3_RNA_seq


title: HC2_RNA_seq


title: prp43 damp/htz1 double mutant

city: Los Angeles

first: Stephen

last: Douglass

state: CA

address: 5128 TLSB Terasaki Life Sciences Building, 610 Charles Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

data_processing:
Illumina CASAVA used for basecalling
Reads demultiplexed requiring exact barcode match
Paired-end reads merged
Unfiltered reads aligned using STAR v2.4.0
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, the number of reads falling in the exons of each transcript were counted and normalized by the size of the transcript and library.
Genome_build: saccer3
Supplementary_files_format_and_content: The processed data file is RPKM measurements for each gene in each sample

organism: Saccharomyces cerevisiae

source_name: BY4741/2_prp43 damp/htz1 double mutant

growth_protocol: Cells were grown up to midlog phase (OD600 between 0.4-0.7) in YPDextrose.

extract_protocol:
RNA was extracted using hot phenol extraction, treated with Roche Dnase
Library was constructed using TRUseq V2 kit (Illumina)

tag: strain background

tag: genotype background

value: his-leu-ura-

tag: ploidy

value: Haploid

value: prp43 damp/htz1 double mutant

value: rRNA-depleted RNA


title: Wildtype replicate 3

value: Wildtype

tag: molecule subtype


title: prp43 damp allele

source_name: BY4741/2_prp43 damp allele

value: prp43 damp allele


title: htz1 deletion replicate 2

source_name: BY4741/2_htz1 deletion

value: htz1 deletion


title: xrn1 deletion replicate 2

source_name: BY4741/2_xrn1 deletion

value: xrn1 deletion


title: upf1 deletion replicate 2

source_name: BY4741/2_upf1 deletion

value: upf1 deletion


title: htz1/upf11 double mutant deletion

source_name: BY4741/2_htz1/upf11 double mutant deletion

value: htz1/upf11 double mutant deletion


title: htz1/xrn1 double mutant deletion

source_name: BY4741/2_htz1/xrn1 double mutant deletion

value: htz1/xrn1 double mutant deletion


title: swr1/upf1 double mutant deletion

source_name: BY4741/2_swr1/upf1 double mutant deletion

value: swr1/upf1 double mutant deletion


title: KP-4 BRD4 1 (Experiment #3)

city: Glasgow

first: Kevin

middle: M

last: Ryan

address: Garscube Estate, Switchback Road

country: United Kingdom

institute: Cancer Research UK Beatson Institute

data_processing:
bcl2fastq v2.15.0.4
TopHat v2.0.10
htseq-count  version 0.5.4p3
DESeq2_1.6.3
Genome_build: GRCh37
Supplementary_files_format_and_content: comma seperated values (csv). gene_id,count

source_name: KP-4 Cell Line

growth_protocol: KP-4 cells (Obtained from RIKEN) were cultured in IMDM (Thermo Fisher Scientific, Cat#: 21980065) supplemented with 20% FBS (Thermo Fisher Scientific, Cat#: 10270106) and Penicillin-Streptomycin (Thermo Fisher Scientific, Cat#: 15140122) in a humidified atmosphere with 5% CO2.

extract_protocol:
Total RNA was isolated and purified using RNeasy mini kit (QIAGEN, Cat#: 74104).
Libraries for cluster generation and DNA sequencing were prepared following an adapted method from (Fisher et al., Genome Biol 12, R1 (2011)) using Illumina TruSeq RNA Sample Prep Kit v2. Quality and quantity of the DNA libraries were assessed on an Agilent 2100 Bioanalyser and Qubit (Thermo Fisher Scientific), respectively.

treatment_protocol: KP-4 cells were reverse-transfected with 20 nM of control (labeled as CON 3, Dharmacon, Cat#: D-001810-03-20), BRD4 #1 (labeled as BRD4 1, Ambion, ID: s23901) or BRD4 #2 (labeled as BRD4 4, Ambion, ID: s23903) siRNA using Lipofectamine RNAiMAX reagent (Thermo Fisher Scientific, Cat#: 13778150) for 72 hrs.

value: Pancreatic Adenocarcinoma Cell Line

tag: sirna transfection

value: BRD4 #1 (labeled as BRD4 1) siRNA

tag: experiment number


title: swr1/xrn1 double mutant deletion

source_name: BY4741/2_swr1/xrn1 double mutant deletion

value: swr1/xrn1 double mutant deletion


title: KP-4 BRD4 4 (Experiment #3)

tag: cell type

value: BRD4 #2 (labeled as BRD4 4) siRNA


title: htz1 deletion replicate 1

tag: genotype/variation


title: swr1 deletion

source_name: BY4741/2_swr1 deletion

value: swr1 deletion


title: KP-4 BRD4 4 (Experiment #2)


title: KP-4 BRD4 4 (Experiment #1)


title: KP-4 BRD4 1 (Experiment #2)


title: KP-4 BRD4 1 (Experiment #1)


title: KP-4 CON 3 (Experiment #1)

value: Control (labeled as CON 3) siRNA


title: xrn1 deletion replicate 1

value: his-leu-ura-

value: Haploid


title: upf1 deletion replicate 1

value: rRNA-depleted RNA


title: J-37

first: Konrad

last: Hochedlinger

address: 185 Cambridge St.

data_processing:
Quality Control: PICARD, Version: 1.100, CollectRnaSeqMetrics
Alignment: STAR version 2.3.0
Alignment manipulation: Samtools 0.1.18.0
Feature Counting: HTSeq version 0.6.0. Parameters: unstranded=TRUE, quality thresh=10, feature file=ftp://ftp.ensembl.org/pub/release-79/gtf/mus_musculus/Mus_musculus.GRCm38.79.gtf.gz
Differential Expression: R library edgeR, version 3.8.6
Genome_build: mm10
Supplementary_files_format_and_content: Excel spreadsheet (TPM_Table.xlsx) provides transcript per million (TPM) values for all genes, all samples.

source_name: Embryonic stem cells

growth_protocol: The cells were cultured for additional 3-4 days and fed every two days with fresh 2i-LIF medium until picking. Outgrowth from the culture was picked, trypsinized, and re-plated onto MEF feeders containing KO DMEM (Invitrogen) supplemented with 15% FBS (Hyclone), 1 mM L- glutamine, 100 uM non-essential amino acids, and 0.1 mM beta-mercaptoethanol, and LIF.

extract_protocol:
Undifferentiated EGCs/ESCs were sorted for SSEA1+ to control for the homogeneity of cells before RNA extraction. The quality and quantity of total input mRNA was determined on an Agilent BioAnalyzer 2100 using Agilent RNA 6000 Nano kit.
One microgram of total RNA from each sample was then used as input for library preparation using Illumina TruSeq RNA Sample Prep Kit, following manufacturer’s instructions.
Each paired-end library was prepared with an adaptor with unique index sequence. The size profile and quantity of resulting libraries were than determined on the BioAnalyzer 2100 with Agilent High Sensitivity DNA kit. These libraries were then pooled together at equal molar concentration and sequenced on an Illumina HiSeq 2000.

tag: passage

value: Embryonic stem cells


title: J-35


title: Sample 59_Mettl3_H5_37_input

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description:
processed data file:
DGCR8_Mettl3_heatshock_ChIPseq_5kb_windows.tab.txt

data_processing:
library strategy: Samples 1-35: Ribo-Zero RNA-seq
Basecalling was performed using RTA v. 1.13.48.
Reads were aligned to the mm10 genome assembly using the qAlign function from the QuasR R package (v. 3.2) with default settings. This calls the Bowtie aligner with the parameters “ -m 1 –best –strata".
Gene expression for RNA-seq data was quantified using Feb. 2014 Ensembl gene annotations. The qCount function in the QuasR package was used to count reads overlapping all annotated exons for each gene.
ChIP-seq data was quantified by counting reads overlapping with 5-kb bins tiled across the genome.
Genome_build: mm10
Supplementary_files_format_and_content: Count tables: Tab-delimited file. First column contains either gene names (Ensembl identifiers) or a genomic range in the format chromosome:start-end. For gene-based count tables, the "width" column indicates the length of the gene body. Following columns contain raw counts of reads overlapping each gene or range for each sample. BigWig: wiggle files were generated in R using the qExportWig function from the QuasR package. Scores represent coverage of read 5' ends in 50-bp bins.

growth_protocol: All samples: Mouse embryonic stem cells were cultured on gelatin-coated dishes in mES medium (DMEM (Gibco 21969-035), supplemented with 15% fetal bovine serum (Gibco), 1x non-essential amino acids (Gibco), 1mM sodium pyruvate (Gibco), 2 mM L-glutamine (Gibco), 0.1mM 2-mercaptoethanol (Sigma), 50mg/ml penicillin, 80mg/ml streptomycin and LIF conditioned medium) at 37°C in 5% CO2.

extract_protocol:
Samples 1-35: total RNA was extracted from mESCs with the Absolutely RNA Microprep Kit (Stratagene). RNA was subjected to ribosomal RNA depletion using Ribozero removal kit (Illumina) followed by library construction using ScriptSeq V2 library preparation kit (Illumina)
Samples 36-59 Genomic DNA was extracted using Phenol/Chloroform followed by  EtOH precipitation in the presence of sodium acetate and molecular biology grade glycogen
Samples 1-35: ScriptSeq v2 RNA-Seq Library Preparation Kit. Samples were treated with a ribosomal depletion kit
Samples 36-41:Illumina ChIP-Seq prep kit starting from 5ng purified ChIP DNA or respective input.
Samples 42-59 :ChIP-seq library preparation kit from NEB. Starting with 10ng purified ChIP DNA or resepective input.

treatment_protocol:
Samples 2,4,6,8,10,12,14,16,18,20,22 were treated with 0.5μM 4-hydroxytamoxifen for varying number of hours (see sample name for durations of treatment)
Samples 27,28,29,33,34,35,52,54,56 were incubated for 42 degrees C for 1 hour prior to RNA extraction or cross-linking, repsectively

value: 129xC57Bl6 hybrid line

value: Rosa26:BirA, METTL3 FLAG/Avi

value: embryonic stem (ES) cells


title: Wildtype replicate 1

value: Wildtype


title: J-34


title: Sample 58_Mettl3_H4_37_input


title: J-32


title: Sample 56_Mettl3_H5_HS_IP


title: Sample 54_Mettl3_H4_HS_IP


title: KP-4 CON 3 (Experiment #3)


title: J-31


title: Sample 53_Mettl3_H4_37_IP

value: Rosa26:BirA, DGCR8 FLAG/Avi


title: J-30


title: KP-4 CON 3 (Experiment #2)


title: Sample 50_DGCR8_WT_input

description:
processed data file:
DGCR8_Mettl3KO_ChIPseq_5kb_windows.tab.txt

treatment_protocol:
Samples 3,4,7,8,11,12,15,16,19,20,23 were treated with 0.5μM 4-hydroxytamoxifen for varying number of hours (see sample name for durations of treatment)
Samples 27,28,29,33,34,35 were incubated for 42 degrees C for 1 hour prior to cross-linking


title: Sample 51_DGCR8_37_IP


title: J-29

source_name: Embryonic germ cells

value: Embryonic germ cells


title: Sample 49_DGCR8_Mettl3-KO_IP

value: Rosa26:BirA, DGCR8 FLAG/Avi, METTL3KO


title: Sample 47_mettl3_clone2_input

description:
processed data file:
Mettl3_ChIPseq_5kb_windows.tab.txt


title: Sample 48_DGCR8_WT_IP


title: Sample 46_mettl3_clone2_rep2_IP


title: J-26


title: J-27


title: J-25


title: Sample 45_mettl3_clone2_rep1_IP


title: Sample 44_mettl3_clone1_input


title: Sample 57_DGCR8_37_input


title: J-24


title: Sample 40_Drosha_DSG_IP

description:
processed data file:
MP_ChIPseq_5kb_windows.tab.txt

value: Rosa26:BirA, DROSHA FLAG/Avi


title: Sample 55_Mettl3_H5_37_IP


title: J-23


title: Sample 39_Dicer_DSG_IP

value: Rosa26:BirA, DICER FLAG/Avi


title: Sample 38_DGCR8_input


title: J-17


title: CTRL4_PK_rnaseq_2

description: CTRL4_PK LCL RNAseq (batch 2)

value: Immortalized lymphoblastoid cell line (LC)

tag: genotype/variataion

value: control

tag: batch

value: Total RNA (Ribozero-depleted)


title: Sample 37_DGCR8_DSG_IP


title: Sample 52_DGCR8_HS_IP


title: Sample 36_DGCR8_FA_IP


title: Sample 34_Mettl3KO_1d2_HS

description:
processed data file:
Mettl3KO_heatshock_RNAseq_exon_expr.tab.txt


title: J-15


title: Sample 33_parental_2_HS


title: Sample 32_Mettl3KO_2c4d


title: HAN

city: beijing

first: zhengqin

last: rong

address: Chaoqian Rd,Changping Science Park of Zhongguancun Science Park

institute: hornortech

description: Small RNA

data_processing:
3' adapter was removed with mirdeep2
Supplementary_files_format_and_content: fasta file with raw counts of small RNA sequences

organism: Ovis aries

extract_protocol:
libraries were prepared according to a version of Illumina's mRNA-Seq protocol adapted for small sample inputs
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Kazakh

tag: estrous status

value: HAN (non-estrous group)

value: Hypothalamus

tag: diet

value: low nutrition


title: Sample 29_Mettl3KO_3xU_HS


title: HEN

description: Small RNA

value: HEN (estrous group)

tag: tissue

value: high nutrition


title: Sample 28_Mettl3KO_1d1_HS

value: 129xC57Bl6 hybrid line


title: Sample 30_parental_2

value: embryonic stem (ES) cells


title: Sample 43_mettl3_clone1_rep2_IP

value: Rosa26:BirA, METTL3 FLAG/Avi


title: Sample 42_mettl3_clone1_rep1_IP


title: Sample 31_Mettl3KO_1d2


title: Sample 27_parental_1_HS

value: Rosa26:BirA, DGCR8 FLAG/Avi


title: Sample 26_Mettl3KO_3xU


title: Sample 25_Mettl3KO_1d1


title: Sample 41_parental_input_1


title: Sample 24_parental_1


title: Sample 23_Drosha_96h_ctrl_rep2

description:
processed data file:
DGCR8KO_DroshaKO_RNAseq_exon_expr.tab.txt

value: Drosha Flox/Flox

tag: treated with

value: 0.5μM 4-hydroxytamoxifen for 96hrs


title: Sample 22_Drosha_96h_4oht_rep1


title: Sample 20_Drosha_48h_4oht_rep2

value: 0.5μM 4-hydroxytamoxifen for 48hrs


title: Sample 21_Drosha_96h_ctrl_rep1


title: Sample 35_Mettl3KO_2c4d_HS

value: Rosa26:BirA, DGCR8 FLAG/Avi, METTL3KO


title: J-16

value: Embryonic germ cells


title: Sample 18_Drosha_48h_4oht_rep1


title: Sample 15_Drosha_24h_ctrl_rep2

value: 0.5μM 4-hydroxytamoxifen for 24hrs


title: Sample 19_Drosha_48h_ctrl_rep2


title: Sample 17_Drosha_48h_ctrl_rep1


title: Sample 16_Drosha_24h_4oht_rep2


title: Sample 14_Drosha_24h_4oht_rep1


title: Sample 12_DGCR8_96h_4oht_rep2

value: Rosa26:CRE, DGCR8 Flox/Flox


title: Sample 13_Drosha_24h_ctrl_rep1


title: Sample 11_DGCR8_96h_ctrl_rep2


title: Sample 9_DGCR8_96h_ctrl_rep1


title: Sample 8_DGCR8_48h_4oht_rep2


title: Sample 7_DGCR8_48h_ctrl_rep2


title: Sample 5_DGCR8_48h_ctrl_rep1


title: Sample 6_DGCR8_48h_4oht_rep1


title: Sample 4_DGCR8_24h_4oht_rep2


title: Sample 2_DGCR8_24h_4oht_rep1


title: Sample 1_DGCR8_24h_ctrl_rep1


title: Sample 3_DGCR8_24h_ctrl_rep2


title: Control_LKS.SLAM_2

city: New York City

first: Balvir

last: Kunar

address: 1300 York Ave

department: Regenerative Medicine; Physiology, Biophysics, & Systems Biology

institute: Weill Cornell Medical College

data_processing:
Base calling and sequencing reads de-multiplexing were performed using bcl2fastq v2.17.
Sequencing reads were checked for quality (FastQC v0.11.5), and trimmed/filtered using Trimmomatic v0.36.
Read alignment to the transcriptome sequence reference of the UCSC mm10 genome build were performed using TopHat2 v2.1.0.
Mapped reads were assembled into transcripts, and abundance measures (FPKM values) quantified using Cufflinks v2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: Single tab-delimited data-matrix with GENE_ID, GENE_DESCRIPTION, and SAMPLE_NAMES. All numerical inputs represent FPKM values.

source_name: hematopoietic stem cell

extract_protocol:
At least 100 ng of total RNA from both freshly harvested and cultured cells was isolated (phenol-chloroform separation of TRIzol LS) and purified using Qiagen’s RNeasy Mini Kit.
RNA library preps were prepared and multiplexed using Illumina’s TruSeq RNA Library Preparation Kit v2 (non-stranded and poly-A selection) and 10 nM of cDNA was used as input for high-throughput sequencing via Illumina’s HiSeq 2500 producing 51 bp paired-end reads.

treatment_protocol: All cell populations were purified via FACS. Purity mask was applied.

value: bone marrow

value: hematopoietic stem cell

tag: genotype

value: wild type

tag: co-culture status

value: freshly isolated from tissue


title: rEC_T.Cd8+_Secondary_2

source_name: lymphocyte

value: blood

value: lymphocyte

value: derived


title: rEC_T.Cd8+


title: Adherent_FGRS.KLS_Day28_1

value: with HUVEC


title: Control_LKS.SLAM_1


title: Adherent_FGRS.KLS_Day28_2


title: Adherent_FGRS.KLS_Day28_3


title: rEC_LKS.SLAM_47G1_Primary


title: rEC_T.Cd8+_Secondary_1


title: LEGSKO+BSO Fibers 4

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

description:
JW24
Severely glutathione deficient
Processed data file: countsTable.txt

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq in Casava 1.8.
Fastq sequences were aligned to mm10 using Tophat.
Number of read counts was calculated for each Entrez gene.
Differential expression analysis was performed using DESeq.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: countsTable.txt: Tab-delimited text file includes raw counts with genes in rows and samples in columns.

source_name: BSO-treated LEGSKO lens cortical fiber cells

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

tag: strain/background

value: LEGSKO

value: Lens

value: Cortical fiber cells

tag: treatment

value: Buthionine sulfoximine (BSO)


title: Control_Cd3+Cd8+_1


title: rEC_T.Cd4+_Secondary

source_name: t cell

value: t cell


title: rEC_T.Cd4+


title: rEC_LKS.SLAM_Secondary


title: Control_Cd3+Cd8+_3


title: LEGSKO+BSO Fibers 3

description:
JW23
Severely glutathione deficient
Processed data file: countsTable.txt


title: Sample 10_DGCR8_96h_4oht_rep1

tag: strain background

value: 129xC57Bl6 hybrid line

value: embryonic stem (ES) cells


title: Control_Cd3+Cd4+_2


title: LEGSKO+BSO Fibers 1

description:
JW21
Severely glutathione deficient
Processed data file: countsTable.txt


title: Control_Cd3+Cd4+_1


title: rEC_B220++_Secondary

source_name: b cell

value: b cell


title: LEGSKO+BSO Epithelia 4

description:
JW20
Severely glutathione deficient
Processed data file: countsTable.txt

source_name: BSO-treated LEGSKO lens epithelia

value: Epithelia


title: rEC_B220+_47G1_Primary


title: LEGSKO+BSO Epithelia 3

description:
JW19
Severely glutathione deficient
Processed data file: countsTable.txt


title: LEGSKO+BSO Epithelia 2

description:
JW18
Severely glutathione deficient
Processed data file: countsTable.txt


title: LEGSKO+BSO Epithelia 1

description:
JW17
Severely glutathione deficient
Processed data file: countsTable.txt


title: B220+_Clonal_47G1_Primary


title: Control_Cd3+Cd8+_2


title: Control_B220+_3


title: LEGSKO Fibers 4

description:
JW16
Mildly glutathione deficient
Processed data file: countsTable.txt

source_name: LEGSKO lens cortical fiber cells


title: LEGSKO Fibers 1

description:
JW13
Mildly glutathione deficient
Processed data file: countsTable.txt


title: Control_B220+_2


title: LEGSKO Epithelia 2

description:
JW10
Mildly glutathione deficient
Processed data file: countsTable.txt

source_name: LEGSKO lens epithelia


title: LEGSKO Fibers 2

description:
JW14
Mildly glutathione deficient
Processed data file: countsTable.txt


title: Control_B220+_1


title: LEGSKO+BSO Fibers 2

description:
JW22
Severely glutathione deficient
Processed data file: countsTable.txt


title: LEGSKO Epithelia 1

description:
JW9
Mildly glutathione deficient
Processed data file: countsTable.txt


title: LEGSKO Fibers 3

description:
JW15
Mildly glutathione deficient
Processed data file: countsTable.txt


title: rEC-LKS-SLAM_1

source_name: long-term hematopoietic stem cell

value: bone marrow

value: long-term hematopoietic stem cell


title: rEC_Gr1+Cd11b+_1

source_name: myeloid-lineage cell

value: myeloid-lineage cell


title: LEGSKO Epithelia 4

description:
JW12
Mildly glutathione deficient
Processed data file: countsTable.txt


title: Control_Gr1+Cd11b+_1

value: wild type

value: freshly isolated from tissue


title: rEC_Gr1+Cd11b+_2

value: blood


title: WT Fibers 4

description:
JW8
Processed data file: countsTable.txt

source_name: Wild-type lens cortical fiber cells

value: WT


title: Control_LKS.SLAM_3


title: Control_Gr1+Cd11b+_2


title: MK2_RNA_Rep2

city: Buffalo

first: Satrajit

last: Sinha

address: 701 Ellicott Street

department: Department of Biochemistry

institute: State University of New York at Buffalo

data_processing:
Reads were mapped to the Mus musculus genome (mm10 build) with TopHat2 (v2.0.13),using Bowtie2 (v2.2.6) as the underlying aligner.
Reads aligning to the UCSC mm10 build were quantified with featureCounts (v1.5.0) , which disregarded any read/read pair that aligned to more than one location, or more than one gene at a single location.
DESeq2 (v1.10.1) was used to normalize the read counts and derive FPKM values.
Genome_build: mm10
Supplementary_files_format_and_content: featureCounts output containing gene-level read count summaries for each RNA-Seq sample

source_name: Mouse keratinocyte cell-line 2

extract_protocol:
RNA was extracted from mouse keratinocyte cells (MK1 and MK2) using the Direct-zol RNA Mini-Prep kit.
Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.

tag: cell line

value: keratinocyte


title: rEC_B220+

value: derived


title: MK2_RNA_Rep1


title: WT Fibers 3

description:
JW7
Processed data file: countsTable.txt

value: Lens


title: WT Epithelia 4

description:
JW4
Processed data file: countsTable.txt

source_name: Wild-type lens epithelia


title: WT Fibers 1

description:
JW5
Processed data file: countsTable.txt

value: Cortical fiber cells


title: MK1_RNA_Rep1

source_name: Mouse keratinocyte cell-line 1


title: MK2-input

description:
Input ChIP DNA
UCSC/IGV track generated by merging MK1-Input and MK2-Input
processed data file: Mouse_Input.bigWig

data_processing:
Raw sequencing reads were mapped to the Mus musculus genome (mm10 build) using Bowtie v1.1.1 with the following parameters: m = 1 (i.e. removes all those alignments with more than one match).
Pooled data files were generated using replicates with merge function in samtools v1.1
Genome_build: mm10
Supplementary_files_format_and_content: Bed and bigWig file for p63 ChIP-Seq.bigWig files for Histone ChIP-Seq

extract_protocol:
Chromatin was extracted from mouse keratinocyte cells (MK1 and MK2) using a low SDS shearing kit (Diagenode: C01020010). Lysates were sonicated with a Bioruptor for 30-40 min. Ips were carried out with Indirect ChIP protocol using 4A4 antibody for p63 and histone antibodies from Diagenode.
Libraries were prepared using ThruPLEX DNA-seq kits from Rubicon Genomics. The samples were then 50 bp single-end sequenced on an Illumina HiSeq 2500.


title: WT Epithelia 3

description:
JW3
Processed data file: countsTable.txt


title: LEGSKO Epithelia 3

description:
JW11
Mildly glutathione deficient
Processed data file: countsTable.txt

value: LEGSKO


title: WT Epithelia 1

description:
JW1
Processed data file: countsTable.txt


title: WT Epithelia 2

description:
JW2
Processed data file: countsTable.txt


title: MK2-H3K27ac

description:
H3K27ac ChIP DNA
UCSC/IGV track generated by merging MK1-H3K27ac and MK2-H3K27ac
processed data file: Mouse_H3K27ac.bigWig


title: MK1-H3K27ac


title: MK1-H3K4me3

description:
H3K4me3 ChIP DNA
UCSC/IGV track generated by merging MK1-H3K4me3 and MK2-H3K4me3
processed data file: Mouse_H3K4me3.bigWig


title: MK2-H3K4me1

description:
H3K4me1 ChIP DNA
UCSC/IGV track generated by merging MK1-H3K4me1 and MK2-H3K4me1
processed data file: Mouse_H3K4me1.bigWig


title: MK1-H3K4me1


title: MK2-p63(4A4)

description:
p63 ChIP DNA
UCSC/IGV track generated by merging MK1-p63 and MK2-p63
processed data file: Mouse_p63.bed, Mouse_p63.bigWig


title: 6h ribosome footprint data

city: San Francisco

first: Arun

middle: P.

last: Wiita

address: 185 Berry St., Suite 290

department: Laboratory Medicine

institute: University of California, San Francisco

description: ribosome-protected mRNA

data_processing:
Stranded alignment with Bowtie 0.12.8 to hg19 canonical transcripts allowing up to 2 mismatches
Read counting using in-house C++ scripts based on bowtie alignments, with counting only based on coding sequence of canonical splice isoform per UCSC annotation
Genome_build: hg19
Supplementary_files_format_and_content: Excel spreadsheet with raw read counts and RPKM for all reads mapping to canonical coding sequence of hg19-annotated transcripts.  Only genes with >128 raw reads mapping to the coding sequence in all samples are included.

source_name: MM1.S cells

extract_protocol:
mRNA-seq and ribosome footprint samples were prepared by the method of Ingolia et al. Cell (2011) 147:789.
mRNA-seq and ribosome footprint sequencing libraries were prepared by the method of Ingolia et al. Cell (2011) 147:789.
mRNA-seq, ribosome profiling

treatment_protocol: Cells were treated with 0.5 nM bortezomib

tag: drug treatment

value: 0.5 nM bortezomib

tag: cell lline


title: 0h ribosome footprint data

description: ribosome-protected mRNA

value: untreated


title: 24h ribosome footprint data

description: ribosome-protected mRNA


title: 36h ribosome footprint data

description: ribosome-protected mRNA


title: MK1-p63(4A4)

description:
p63 ChIP DNA
Processed file (bed) generated by running IDR on MK1-p63 and MK2-p63
processed data file: Mouse_p63.bed, Mouse_p63.bigWig

tag: cell type


title: 12h ribosome footprint data

description: ribosome-protected mRNA


title: WT Fibers 2

description:
JW6
Processed data file: countsTable.txt

tag: genotype/variation


title: MK1_RNA_Rep2


title: 48h ribosome footprint data

description: ribosome-protected mRNA


title: 48h mRNA-seq data

description: poly(A) mRNA


title: siMETT16 m6A IP_rep3

city: Dallas

first: Nicholas

middle: K

last: Conrad

state: TX

address: 6000 Harry Hines Blvd

department: Microbiology

institute: UT Southwestern Medical Center

description: peaks.xls

data_processing:
Library strategy: m6A-seq
Raw reads were aligned to the human reference genome hg38 using the bwa (v 0.7.9a-r786) aligner with default settings. Only uniquely mapped reads were kept for further analysis
For each pair, the reads were connected from the start of read1 to the end of read2 and the whole region was used for gene coverage in a strand-specific fashion.
Peak calling and filtering using inhouse script
Input samples were used for calculating gene expression level (FPKM) using StringTie (v1.1.2)
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited text file with FPKM of input samples
Supplementary_files_format_and_content: tab delimited text file with location of peaks and gene annotation

source_name: Embryonic Kidney

growth_protocol: HEK293A-TOA cells were cultured in DMEM media (Sigma) and supplemented with 10% Tet-Free FBS (Atlanta Biologicals), penicillin-streptomycin, and 2mM L-glutamate.

extract_protocol:
RNA was harvested with TriReagent, poly-A selected using using manufacturer’s protocol of Sera-Mag Oligo (dT)-Coated Magnetic particles. RNA was fragmented, and then selected using the anti-m6A antibody.
Librariers were prepared using the Kapa Stranded mRNA-Seq Kit for the  Illumina pllatform

treatment_protocol: HEK293A-TOA cells were transfected with 30nM siRNA (Thermo Fisher) using RNAiMax transfection reagent (Thermo Fisher) according to the manufacturer’s instructions. Twenty-four hours following transfection, ∼100% confluent cells were diluted to new plates to allow the cells to divide for an additional 72 hours (total 96 hour knockdown).

tag: passages

tag: transfection

tag: antibody

value: Synaptic Systems anti-m6A Cat#202003


title: 36h mRNA-seq data

description: poly(A) mRNA


title: siMETT16 m6A IP_rep2

description: peaks.xls


title: siCtrl m6A IP_rep3

description: peaks.xls

value: siCtrl


title: 24h mRNA-seq data

description: poly(A) mRNA


title: siMETT16 m6A IP_rep1

description: peaks.xls


title: UV_III_9

city: Antwerpen

first: Gerrit

last: Beemster

state: Antwerpen

address: Groenenborgerlaan 171

department: Biology

country: Belgium

institute: University of Antwerp

data_processing:
Trimming of Illumina adapters (CLC Genomics Workbench v.6 )
Quality control for individual samples (CLC Genomics Workbench v.6 )
Mapping against the reference genome (CLC Genomics Workbench v.6 )
Calculation of expression values using unique matches (CLC Genomics Workbench v.6)
Normalisation by scaling 10.000.000 reads per sample
Genome_build: Zea mays (cv B73) sequence (RefGen V3; http://www.maizegdb.org)

organism: Zea mays

source_name: UV_zone 3

growth_protocol: Maize (Zea Mays) plants from the B73 inbred were used in filed experiments during the summer 2013 in Rosario, Argentina (32º latitude),

extract_protocol:
Total RNA was isolated from the first three10-mm leaf segments from the basal 30 mm of leaf 4 three days after leaf emergement, during steady-state growth, from each treatment. The TRIzol reagent (Invitrogen) was used as described in the manufacturer’s protocol. Then, 0.5 to 1.0 mg of total RNA was incubated with RNase-free DNase I (1 unit/mL) following the protocol provided by the manufacturer to remove possible genomic DNA.
Prior to library preparation the RNA quality and integrity was assessed by using a gel cartridge on a QIAxcel platform (Qiagen, Hilden, Germany). Library preparation was done using the TruSeq® Stranded mRNA sample preparation 96 rcx kit (Illumina™) following the low sample protocol according to Illumina™ guidelines. Briefly, approximately 2.5 µg of total RNA was diluted and purified using RNA purification beads targeting the poly-A tail of the mRNA and subsequently was fragmented by means of the enzymes provided in the kit. After the cDNA synthesis adenylation of 3’ ends and ligation of the adaptors were employed. Adaptors were ligated in 12-plex formations, allowing the pooling of 12 samples after the PCR enrichment of the library. Subsequently, the library was quantified using PicoGreen® dye (Life Technologies™) as described in the manufacturer’s protocol. In order to accurately quantify the concentration in nM of our pools, the Kapa SYBR® FAST universal qPCR kit (Kapa Biosystems™) for Illumina™ sequencing was used to quantify the number of the amplifiable molecules in the pools and the Bioanalyzer® (Agilent Technologies™) to determine the average fragment size of our pools. These measurements allowed optimizing the flow cell clustering and proceed with the Run. The illumina HiSeq 1500 was used in the high throughput mode together with the TruSeq® SBS Kit to sequence the samples in a 25 cycle pair-end run. Following the analysis of these runs, rapid run was performed on the samples having yielded below 5 million reads. The rapid runs were performed on the same pools as in the first sequencing round. Data from these rapid runs were added to the high throughput data.
Groups of 12 samples were pooled at equal concentrations to create eight pools for each of the lanes of the flow cell

treatment_protocol: UV treatments were done using different plastic filters to screen UV-B. Solar UV-B radiation was removed to produce the minus UV-B (Control) treatment using PE filters (100 mm clear PE plastic, Tap Plastics, Mountain View, CA). This PE filter absorbs UV-B without significantly affecting UV-A or visible radiation. To control for differences in wind or humidity under plastic sheeting, CA sheeting was used (100 mm extra clear CA plastic, Tap Plastics); the CA sheeting transmits most radiation from sunlight and is designated as the full UV treatment. For this experiment, 1 x 2 m of each plastic was draped over 0.5 x 1.4-m wooden frames that were erected outdoors; the excess plastic was stapled to the sides of the frames to reduce shading. The North and South sides were left open to allow air to circulate. However, 50-cm-long curtains with the same plastic were made on the east and west sides to avoid early morning and late afternoon UV exposure. The frames were maintained about 30 cm above the plant canopy during the experiments. Measurements of incoming UV-B radiation were recorded at noon using a UV-B/UV-A radiometer (UV203 A+B radiometer, Macam Photometrics, Ltd, Livingston, UK). The average UV-A radiation was 8 W/m2 in both groups and the average UV-B radiation was 0.35 W/m2 in the control group and 1.5 W/m2 in the UV-B exposed group. The experiment was repeated three times during the summer of 2013.

tag: cultivar

value: B73 inbred

tag: exposed to

value: UV-B radiation

value: Zone 3 (2-3cm from base of the leaf)

tag: replicate

value: Biological replicate 3


title: MK1-input


title: 6h mRNA-seq data

description: poly(A) mRNA


title: siCtrl m6A IP_rep2

description: peaks.xls


title: UV_II_9

source_name: UV_zone 2

tag: tissue

value: Zone 2 (1-2cm from base of the leaf)


title: MK2-H3K4me3


title: siCtrl m6A IP_rep1

description: peaks.xls


title: siMETTL16 input_rep3


title: siMETTL16 input_rep2


title: UV_II_8

value: Biological replicate 2


title: siMETTL16 input_rep1


title: siCtrl input_rep1


title: UV_III_7

value: Biological replicate 1


title: UV_I_9

source_name: UV_zone 1

value: Zone 1 (0-1cm from base of the leaf)


title: UV_III_8


title: UV_II_7


title: siCtrl input_rep2


title: siCtrl input_rep3


title: C_III_7

source_name: control_zone 3

value: none (Control)


title: W303_SET2KO_rep3

city: Portsmouth

first: Samuel

last: Robson

address: St Michael's Building

department: School of Pharmacy & Biomedical Science

institute: University of Portsmouth

description:
truseq barcode: CTTGTA
Total RNA (ribodepleted)

data_processing:
Demultiplexing: Multiplexed reads were split based on their NEXTFlex barcodes using Basespace v1.3.0.9.
Adapter Trimming: Reads were trimmed to remove the adapter sequence from the 3' of reads by Basespace.
Quality Control: Read quality was assessed using FastQC v0.11.3
Mapping: Trimmed reads were mapped to the sacCer3 genome using tophat v2.1.0 with parameters --segment-length 38 --no-coverage-search --max-multihits 20 --report-secondary-alignments --read-mismatches 2.
Filtering: Mapped reads were filtered to remove reads mapping to more than one unique genomic locus (multihits) by keeping only reads with flag NH:i:1 in the output bam file from tophat. Reads were further filtered to remove reads with mapping quality less than 20 using samtools v1.2.
Coverage: Genome coverage bedgraph files were generated using genomeCoverageBed from the bedtools suite of tools (v2.24.0). Coverage files were converted to bigwig format using bedGraphToBigWig v4.
Normalization: Normalized coverage bedgraph files were generated for visualization purposes by scaling the genome coverage bedgraph counts by the total number of mapped reads (in 10s of millions).
Differential Expression Analysis: Downstream analyses were conducted using the statistical programming language R (v3.2.3) and bioconductor packages (v3.2). Transcriptome annotation was taken from Ensembl (EF4.74), supplemented with non-coding sequences as previously described (Tuck and Tollervey 2013). Read counts within transcriptional units were generated using summarizeOverlaps() from the GenomicAlignments package with parameters mode = "Union", singleEnd = TRUE, inter.feature = TRUE, ignore.strand = TRUE, fragments = FALSE. Differential expression analysis of SET2 KO samples against WT samples was performed using DESeq2. DESeq2 output for each transcript, along with raw read counts and normalized RPKM (reads per kilobase mapped) values, are provided in supplementary file SET2_KO_DESeq2_output.txt. Genes showing significant changes in expression in SET2 KO samples were identified based on a fold change greater than 1.5 (up or down) and an adjusted p value (Benjamini and Hochberg) less than 0.05.
Genome_build: sacCer3
Supplementary_files_format_and_content: Bigwig files give coverage scores across the whole sacCer3 genome at each base position. Normalized and non-normalized coverage files are provided for each sample. The SET2_KO_DESeq2_output.txt file provides differential expression results from DESeq2 for all transcripts tested, along with the raw read counts and RPKM (reads per kilobase mapped) normalized counts within each transcript region.

source_name: Whole cell

growth_protocol: WT and SET2 KO cells were grown in YPDA to OD(660)=0.6.

extract_protocol:
Independent samples of total RNA were prepared from three WT and three SET2 KO colonies by hot phenol extraction. RNA was further subjected to DNAse I treatment (E1009-A, Zymo Research) and Ribo-zero treatment (RZY1324, Illumina) following manufacturer instructions. Quantity and purity of RNA was measured using Agilent High sensitivity RNA screen Tape System (Agilent Technologies, cat:5067-5579) and Qubit (Molecular Probes, Invitrogene).
200ng of rRNA depleted total RNA was used to prepare libraries for sequencing on Illumina platforms using the NEXTflex RNA-Seq Kit (Bioo scientific, cat: 5129-02) following manufacturer instructions. Samples were barcoded using NEXTflex Illumina DNA barcodes matching Illumina barcodes 7-12. Barcoded samples were combined together at uniform molarity to create a single pool, which was sequenced in a single end 76 bp run on an Illumina NextSeq machine.

value: set2::His3 knockout (SET2 KO)


title: C_II_7

source_name: control_zone 2


title: 12h mRNA-seq data

description: poly(A) mRNA


title: C_I_7

source_name: control_zone 1


title: W303_SET2KO_rep2

description:
truseq barcode: GGCTAC
Total RNA (ribodepleted)


title: C_II_4


title: W303_WT_rep3

description:
truseq barcode: GATCAG
Total RNA (ribodepleted)

value: WT


title: C_III_4


title: W303_SET2KO_rep1

description:
truseq barcode: TAGCTT
Total RNA (ribodepleted)


title: 0h mRNA-seq data

description: poly(A) mRNA


title: C_III_3


title: Patient 1 (III-4)

status: Public on May 17 2017

city: Portland

first: Zheng

last: Xia

state: Oregon

address: 3181 SW Sam Jackson Park Rd

department: Department of Biomedical Engineering

institute: Oregon Health & Science University

data_processing:
TopHat 2.0.11 is used to align reads to reference genome. The tophat parameters are: -g 5 -r 100 -r 100 --mate-std-dev 150, others are default.
Then use wiggles to convert into wig file
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph

source_name: Patient, cultured primary skin fibroblast

growth_protocol: DMEM, 10% FBS, penicillin, streptomycin

extract_protocol:
Trizol extraction, DNAseI treatment, Phenol/Chloroform extraction
We used Epicenter’s ScriptSeq V2 to prepare the libraries for all 4 samples.
We performed 101-nt pair-end RNA sequencing.

treatment_protocol: Asynchronously growing cells (80% confluency)

value: cultured primary skin fibroblast

tag: individual

value: Patient 1 (III-4)


title: Patient 2 (III-2)

value: Patient 2 (III-2)


title: W303_WT_rep2

description:
truseq barcode: ACTTGA
Total RNA (ribodepleted)


title: C_I_3


title: W303_WT_rep1

description:
truseq barcode: CAGATC
Total RNA (ribodepleted)


title: Control 2

source_name: Control, cultured primary skin fibroblast

value: aged matched, healthy Control 2

value: control


title: ATAC_ML35_1

city: New York

first: Andrea

last: Schietinger

address: 1275 York Avenue

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

description: mouse splenocytes

data_processing:
Library strategy: ATAC-Seq
Base trimming and quality filtering using TrimGalore! v0.4.0, powered by CutAdapt v1.8.1 and FastQC v0.11.3 using paired and fastqc options
Alignment using Bowtie2 v2.2.5 using default parameter settings
conversion to bam, uniq, sort bam using SAMtools v0.1.18
peak calling using macs2 callpeak v2.1.0.20140616 on merged replicates per sample type, using p-value cutoff of 1e-2, no model, keep-dup=all, call-summits
IDR per sample to find reproducible peaks, create atlas of reproducible ATAC-seq peaks for both mouse and human
Counting of reads aligning to atlas peak regions using the summarizeOverlaps function of the R package GenomicAlignments v1.2.2 and GenomicRanges v1.18.4
Library-size normalized read counts per atlas peak were calculated using DESeq2 v1.6.3
Genome_build: mm10 for mus musculus data and hg38 for human samples
Supplementary_files_format_and_content: tab-delimited text file - columns: chromosome, peak start, peak end, gene symbol, gene refseq ID, peak type, DESeq2 size-factor normalized read count for peak

source_name: Sort-purified (CD8/Thy1.1) memory TCR SV40-I CD8 T cells isolated D35 from established tumors (with listeria immunization) replicate#1

extract_protocol:
CD8 T cells were FACS-sorted into FCS containing tubes and after sort 10% DMSO were added, mixed and stored at -80°C until all samples were collected. Profiling of Chromatin was performed by ATAC-seq. Cells were thawed and washed in cold PBS and lysed.
After cell lysis, transposition happened at 42ºC for 45 min. After purification of the DNA with the MinElute PCR purification kit (Qiagen), material was amplified for 5 cycles. Additional PCR cycles were evaluated by real time PCR. Final product was cleaned by Ampure Beads at a 1.5x ratio. Libraries were sequenced on a Hiseq 2500 1T in a 50bp/50bp Paired end run, using the TruSeq SBS Kit v3 (Illumina).  An average of 47x106 paired reads were generated per sample.

tag: cd8 t cell status

value: TCR SV40-I transgenic CD8 T cells

tag: disease state

value: established hepatocellular carcinoma


title: ATAC_ML14_noLM_1

source_name: Sort-purified (CD8/Thy1.1) memory TCR SV40-I CD8 T cells isolated D14 from established tumors (without listeria immunization) replicate#1


title: ATAC_ML14_noLM_3

source_name: Sort-purified (CD8/Thy1.1) memory TCR SV40-I CD8 T cells isolated D14 from established tumors (without listeria immunization) replicate#3


title: ATAC_ML7_noLM_2

source_name: Sort-purified (CD8/Thy1.1) memory TCR SV40-I CD8 T cells isolated D7 from established tumors (without listeria immunization) replicate#2


title: ATAC_ML35_2

description: mouse splenocytes

source_name: Sort-purified (CD8/Thy1.1) memory TCR SV40-I CD8 T cells isolated D35 from established tumors (with listeria immunization) replicate#2


title: ATAC_L60_2

description: mouse splenocytes

source_name: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D60 from early malignant lesions replicate#2

value: early malignant liver lesions


title: Control 1

value: aged matched, healthy Control 1


title: ATAC_L35_1

description: mouse splenocytes

source_name: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D35 from early malignant lesions replicate#1


title: ATAC_ML14_1

description: mouse splenocytes

source_name: Sort-purified (CD8/Thy1.1) memory TCR SV40-I CD8 T cells isolated D14 from established tumors (with listeria immunization) replicate#1


title: ATAC_ML7_noLM_3

source_name: Sort-purified (CD8/Thy1.1) memory TCR SV40-I CD8 T cells isolated D7 from established tumors (without listeria immunization) replicate#3


title: ATAC_ML7_3

description: mouse splenocytes

source_name: Sort-purified (CD8/Thy1.1) memory TCR SV40-I CD8 T cells isolated D7 from established tumors (with listeria immunization) replicate#3


title: C_I_4

value: B73 inbred


title: ATAC_L28_3

description: mouse splenocytes

source_name: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D28 from early malignant lesions replicate#3


title: ATAC_ML7_noLM_1

source_name: Sort-purified (CD8/Thy1.1) memory TCR SV40-I CD8 T cells isolated D7 from established tumors (without listeria immunization) replicate#1


title: ATAC_ML35_3

description: mouse splenocytes

source_name: Sort-purified (CD8/Thy1.1) memory TCR SV40-I CD8 T cells isolated D35 from established tumors (with listeria immunization) replicate#3


title: ATAC_ML7_1

description: mouse splenocytes

source_name: Sort-purified (CD8/Thy1.1) memory TCR SV40-I CD8 T cells isolated D7 from established tumors (with listeria immunization) replicate#1


title: ATAC_L60_1

description: mouse splenocytes

source_name: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D60 from early malignant lesions replicate#1


title: ATAC_ML14_2

description: mouse splenocytes

source_name: Sort-purified (CD8/Thy1.1) memory TCR SV40-I CD8 T cells isolated D14 from established tumors (with listeria immunization) replicate#2


title: ATAC_L28_1

description: mouse splenocytes

source_name: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D28 from early malignant lesions replicate#1


title: ATAC_L35_2

description: mouse splenocytes

source_name: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D35 from early malignant lesions replicate#2


title: ATAC_L35_3

description: mouse splenocytes

source_name: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D35 from early malignant lesions replicate#3


title: ATAC_ML7_2

description: mouse splenocytes

source_name: Sort-purified (CD8/Thy1.1) memory TCR SV40-I CD8 T cells isolated D7 from established tumors (with listeria immunization) replicate#2


title: ATAC_L21_3

description: mouse splenocytes

source_name: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D21 from early malignant lesions replicate#3


title: ATAC_L21_1

description: mouse splenocytes

source_name: Sort-purified (CD8/Thy1.1) TCR SV40-I CD8 T cells isolated D21 from early malignant lesions replicate#1


title: ATAC_ML14_noLM_2

source_name: Sort-purified (CD8/Thy1.1) memory TCR SV40-I CD8 T cells isolated D14 from established tumors (without listeria immunization) replicate#2