title: Stomach_MS091_051

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

institute: Kyoto University, Graduate school of medicine

description: cDNAs amiplified from 1 ng total RNA extracted from cells using SC3-seq technology

data_processing:
All the reads were surveyed and the adaptor or the poly-A sequences were trimmed by cutadapt-1.3 with options "-c -m 30 -a CTCGAGGGCGCGCCGGATCCATATACGCCTTGGCCGTACAGCAG -g CTCGAGGGCGCGCCGGATCCATATACGCCTTGGCCGTACAGCAG -a AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA". The trimmed reads with less than 30 bp were discarded.
Untrimmed and trimmed reads of 30 bp or longer were mapped onto the macfas5.0 genome and the ERCC spike-in RNA sequences with tophat-1.4.1/bowtie1.0.1 with the “—no-coverage-search” option.
Mapped reads on the genome and the ERCC were separated, and the reads on the genome were converted into the expression levels by cufflinks-2.2.0 using the “—compatible-hits-norm”, “—no-length-correction” and “—library-type fr-secondstrand” options and reference gene annotations with extended TTSs. We also set the cufflinks option “—max-mle-iterations” to 50,000, because default iterations (5,000) resulted in “FAILED” when estimating the expression levels of some genes. For the reference gene annotations used in cufflinks, we extended the TTSs of the reference genes up to 10 kb downstream to correctly estimate the expression levels of genes whose transcripts are longer than the reference toward the 3 prime.
Genome_build: Macaca_fascicularis_5.0
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample

organism: Macaca fascicularis

source_name: Stomach

growth_protocol:
Somatic cells derived from the liver and stomach of a female Cm fetus were cultured by somatic cell medium consisting Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% FBS, 10 mg/l insulin, 5.5 mg/l transferrin, 6.7 ug/l selenium, 40 ng/ml hepatocyte growth factor (Peprotech, Rocky Hill, NJ, USA), 20 ng/ml epidermal growth factor (Peprotech), penicillin, and streptomycin.
Prime state Cm ESCs and Cm iPSCs (ESC and iPSC: PSC) were maintained under a feeder-free condition on recombinant LAMININ511 (rLN511E8) (iMatrix-511, Nippi, Tokyo, Japan)-coated cell culture plates. Cells were cultured in bFGF/KSR medium consisting of 78% Dulbecco’s modified Eagle’s medium/Ham’s F-12 (DMEM/F12) supplemented with 15% KSR, 2 mM GlutaMax (Invitrogen Life Sciences), 1% nonessential amino acids, 0.1 mM b-mercaptoethanol, and 4 ng/ml human recombinant bFGF (Wako, Osaka, Japan).
Naive-like state Cm PSCs were maintained under a feeder-free condition on recombinant LAMININ511 (rLN511E8) (iMatrix-511, Nippi, Tokyo, Japan)-coated cell culture plates. To convert prime state Cm PSCs into a Naive-like state, PiggyBac (PB) vectors carrying Dox-inducible hKLF2 or hNANOG coupled to Venus were cotransfected with a PB-EOS-GFP/puroR reporter, which has an rtTA expression construct (Takashima et al., 2015), and pCAG-PBase using an NEPA21 electroporator (Nepa Gene Co., Ltd., Chiba, Japan). To confirm the chimeric contribution of ESCs into mouse or rabbit embryos as interspecific chimeras, cell lines transfected with PB-CAG-Su9DsRediN were established concurrently. One day after transfection, G418 (200ug/ml) and puromycin (250 ng/ml) were added to the selection in the presence of 1uM Dox. Two weeks after selection, transfectants were dissociated with trypsin digestion and replated and cultured in Naive conversion medium (K5cLD) consisting of 38% DMEM/F12 and Neurobasal Medium supplemented with 20% KSR, 1% N2 supplement, 2% B27 supplement, 2 mM GlutaMax, 1% nonessential amino acids (Invitrogen Life Sciences), 0.1 mM b-mercaptoethanol, 1% penicillin-streptomycin, and a five-chemical mix (5c): 5 M Gö6983, 10uM forskolin (Sigma-Aldrich, St. Louis, MO, USA), 5 uM kenpaullone, 3 uM CHIR99021 (Stemgent Inc., Cambridge, MA, USA), 0.5 uM SB590885(Wako). Additionally, cell lines were maintained in the presence of 0.1% recombinant human LIF (L in media abbreviations; Wako) and 1uM Dox (D in media abbreviations; TaKaRa, Bio Inc., Shiga, Japan).
Differentiated Cm PSCs were maintained under a feeder-free condition on recombinant LAMININ511 (rLN511E8) (iMatrix-511, Nippi, Tokyo, Japan)-coated cell culture plates. To convert Naive-like state Cm PSCs into a differentiated state, K5cLD-maintained Naive-like PSCs were cultured 5c medium consisting of 38% DMEM/F12 and Neurobasal Medium supplemented with 20% KSR, 1% N2 supplement, 2% B27 supplement, 2 mM GlutaMax, 1% nonessential amino acids, 0.1 mM -mercaptoethanol, 1% penicillin-streptomycin, and a five-chemical mix (5c): 5 uM Gö6983, 10 uM forskolin (Sigma-Aldrich), 5 uM kenpaullone, 3 uM CHIR99021 (Stemgent), 0.5 uM SB590885(Wako).

extract_protocol:
Total RNA was extracted from Cm somatic cells, prime state Cm PSCs, Naive-like state Cm PSCs, and differentiated Cm PSCs by using an RNeasy Mini Kit (QIAGEN, Hilden, Germany) according to the manufacturer’s instructions. Synthesis and amplification of cDNAs using 1 ng of purified total RNA, and construction of cDNA libraries for RNA sequencing (ABI SOLiD 5500XL system; Life Technologies) were performed as described in (Nakamura et al., 2015).
cDNA synthesis and amplification from isolated RNAs/single cells were perfomed essentially as reported in [Kurimoto, K.et.al., Nucleic Acids Research, 34(5), e42.]. Library constructions for Nextseq500 were performed as reported in [Ishikura et al. submitted].

value: Stomach

tag: cell status

value: Somatic

tag: culture condition

value: somatic cell medium


title: MCF-7 mock replicate 1 IR 6h

status: Public on Apr 20 2017

type: SRA

city: Berlin

first: Markus

last: Landthaler

address: Hannoversche Str. 28

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrueck Center

library_source: transcriptomic

data_processing:
Basecalls were performed using CASAVA 1.8.2 or bcl2fastq v2.16.0.10. Demultiplexing and adapter removal of raw reads were performed using Flexbar (v2.5) utilizing Illumina RPI index barcodes. Reads were simultaneously filtered for quality (cutoff Phred+ 10) and length (cutoff 18 nucleotides).
We used Tophat2 (v2.1.0) (Kim et al., 2013) to align reads to the common reference composed of human genome (version hg19) and 92 sequences corresponding to synthetic RNAs in the ERCC Spike in Control (Thermo Fisher). Reads were counted in Gencode v19 exons and ERCC spike-in sequences using HTSeq-count (Anders et al., 2015). Pairwise differential expression analyses were performed by DESeq2 (Love et al., 2014) using default parameters. Normalization of read counts was performed using size factors obtained from ERCC spike-in read counts from HTSeq-count output. Transcripts with p adjusted value lower than 0.10 were considered differentially expressed.
We quantified pre-mRNA and mRNA levels by RSEM (v.1.2.20) (Li and Dewey, 2011) using bowtie (v.1.1.2) (Langmead et al., 2009) as read alignment program. We first prepared a custom annotation file by adding whole gene loci as “transcript” category in the Gencode v19 annotation GTF file (i.e. all rows with the “gene” category were modified to “transcript”). Bowtie/RSEM index was then obtained by rsem-prepare-reference program using default settings with the modified GTF file. Pre-mRNA abundance metrics (expected counts, TPM and FPKM) were considered only for genes with more than one exon and were derived from reads that mapped to the entire gene locus only (ENSG* id*s in the transcript_id column of *.isoform.expression files). For mRNA abundance we computed the sum of metrics for all annotated transcripts within the annotated gene.
Genome_build: hg19
Supplementary_files_format_and_content: txt files (HTSeq-count read counts; RSEM read counts, TPMs and FPKMs)

molecule: polyA RNA

organism: Homo sapiens

source_name: MCF-7 mock IR 6h

growth_protocol: MCF-7 Flp-In cells were cultured in high glucose Dulbeco’s modified Eagle’s medium (DMEM, Thermo Fisher), supplemented with 10% (v/v) fetal bovine serum, 2 mM L-glutamine, 100 U/ml penicillin/streptomycin (all from Gibco).

extract_protocol:
Cells were harvested at different time periods after irradiation (0h, 1h, 2h and 6h) by removing the media and adding 1ml Trizol (Thermo Fisher) per well. RNA was then extracted by miRNAeasy kit (Qiagen) according to manufacturer's protocol. Next, 2 µg of total RNA were treated with 0.4 U Turbo DNase (Thermo Fisher) for 30 min at 37 ºC, phenol-chlorotorm extracted, ethanol-precipitated and resuspended in water.
Equal amounts of total RNA (1 µg) and 2 µl of 1:100 dilution of ERCC Spike-in Control Mix 1 (Thermo Fisher) were mixed, adjusted to 50 µl final volume with water, and input into the Truseq unstranded mRNA kit v2 (Illumina) using 2 rounds of oligo-dT enrichment. Manufacturer's instructions were followed in all subsequent steps. cDNA libraries from different samples were multiplexed using Illumina RPI oligonucleotides and sequenced by multiplexing 6 samples per lane on a HiSeq 2000 instrument using 1x101+7 cycles.
Illumina Truseq RNA v2 kit (unstranded)

treatment_protocol: MCF-7 Flp-in cells were reverse-transfected in a 6-well format using 2 different siRNAs (1 and 3). We plated 0.5 ml Optimem per well, followed by the addition of 60 pmol siRNA and 5 µl Lipofectamine RNAimax. After a 15-20 min incubation, 2.5x105 cells in 2.5 ml of supplemented DMEM (final volume was thus 3 ml per well) were added, incubated for 48 hours and irradiated (10Gy).

tag: cell line

tag: cell type

value: breast carcinoma epithelial cell line

tag: transfected with

value: mock

tag: time point

value: 1h post irradiation

tag: barcode

value: CCGTCC


title: S6_Dif_MS091_048

country: Japan

molecule: total RNA

source_name: induced pluripotent stem cells

value: Stomach-derived iPSC

value: Differentiated


title: MCF-7 mock replicate 1 IR 0h

source_name: MCF-7 mock IR 0h

value: AGTCAA


title: L3_Dif_MS091_046

value: Liver-derived iPSC


title: AV macrophage, Transcriptome 13

city: Boston

first: Matthias

last: Nahrendorf

state: MA

address: 185 Cambridge St.

department: Center for Systems Biology

country: USA

institute: Massachusetts General Hospital

data_processing:
transcriptome mapping: STAR version 2.3.0 using the Ensembl 67 release exon/splice-junction annotations
feature counting: HTSeq v.0.6.0 with unstranded count parameter. The 76 samples with the most reads (260K to 6.3M, median 2.1M) weres selected for further analysis.
selection of detected genes: clean.counts() routine within SCDE (Single Cell Differential Expression)
quantification of overdispersion: pagoda.varnorm() routine within SCDE. 9235 total genes were retained for further analysis.
Genome_build: mm9
Supplementary_files_format_and_content: MHa10.cpm.txt

organism: Mus musculus

source_name: AV node macrophage

extract_protocol:
AV node macrophages were FACS-purified from whole AV node tissue as described above. Single macrophages were then captured using the Fluidigm C1 microfluidic chip designed for 5- to 10-µm cells according to the manufacturer’s protocol. A concentration of 1.8x105 cells per ml was used for chip loading. After cell capture, chips were examined visually to identify empty chambers, which were excluded from later analysis. Cell lysis and cDNA synthesis were performed on-chip with Clontech SMARTer Ultra Low RNA kit for the Fluidigm C1 system. Amplified cDNA was validated and quantified on an Agilent Bioanalyzer with the High Sensitivity DNA chip.
Illumina libraries were constructed in 96-well plates using the Illumina Nextera XT DNA Sample Preparation kit according to a modified protocol supplied by Fluidigm. Constructed libraries were validated and quantified with the Agilent High Sensitivity DNA chip, and subsequently normalized and pooled to equal concentrations. The pooled libraries were quantified by qPCR using KAPA Library Quantification kit (Kapa Biosystems).

treatment_protocol: For AV node harvest, C57BL6/J mice were perfused through the left ventricle with 10 ml of ice-cold PBS. Hearts were then excised and subjected to AV node microdissection. In detail, the triangle of Koch, which contains the AV node, was excised by using the following landmarks: ostium of the coronary sinus, tendon of Todaro and septal leaflet of the tricuspid valve. After harvest, AV nodes were minced into small pieces and subjected to enzymatic digestion with 450 U/ml collagenase I, 125 U/ml collagenase XI, 60 U/ml DNase I, and 60 U/ml hyaluronidase (all Sigma) for 20 minutes at 37°C under agitation. Tissues were then triturated and cells filtered through a 40-μm nylon mesh (BD Falcon), washed and centrifuged to obtain single-cell suspensions. To purify macrophages from AV node tissue, digested samples were stained with hematopoietic lineage markers, CD11b, CD45, F4/80 and Ly6C, and macrophages were FACS-sorted using a FACSAria II cell sorter (BD Biosystems). DAPI was used as a cell viability marker. AV node macrophages were identified as (B220/CD49b/CD90.2/CD103/Ly6G/NK1.1/Ter119)low (CD45/CD11b)high Ly6Clow/int F4/80high.

tag: strain

value: AV node macrophage

tag: genotype

value: WT


title: Liver_MS091_050

source_name: Liver

value: Liver


title: S12_Dif_MS091_049


title: TRSK_Dif_MS091_044

source_name: Embryonic stem cells

value: ESC

value: TRSK


title: MCF-7 4SU UV, no IR replicate 2

data_processing:
Basecalls were performed using CASAVA 1.8.2. Demultiplexing and adapter removal of raw reads were performed using Flexbar (v2.5) utilizing Illumina RPI index barcodes. Reads were simultaneously filtered for quality (cutoff Phred+ 10) and length (cutoff 18 nucleotides).
We quantified mRNA levels by RSEM (v.1.2.20) (Li and Dewey, 2011) using bowtie (v.1.1.2) (Langmead et al., 2009) as read alignment program. Pairwise differential expression analyses were performed by DESeq2 (Love et al., 2014) using default parameters and read counts obtained from RSEM output. Transcripts with p adjusted value lower than 0.10 were considered differentially expressed.
Genome_build: hg19
Supplementary_files_format_and_content: txt files (read counts from RSEM ouputs)

source_name: MCF-7 4SU UV_no IR

growth_protocol: MCF-7 cells were cultured in high glucose Dulbeco’s modified Eagle’s medium (DMEM, Thermo Fisher), supplemented with 10% (v/v) fetal bovine serum, 2 mM L-glutamine, 100 U/ml penicillin/streptomycin (all from Gibco).

extract_protocol:
RNA was extracted by adding Trizol LS (Thermo Fisher) and following the miRNAeasy kit (Qiagen) protocol. Next, 2 µg of total RNA were treated with 0.4 U Turbo DNase (Thermo Fisher) for 30 min at 37 ºC, phenol-chlorotorm extracted, ethanol-precipitated and resuspended in water.
Equal amounts of total RNA (1 µg) were adjusted to 50 µl final volume with water, and input into the Truseq unstranded mRNA kit v2 (Illumina) using 2 rounds of oligo-dT enrichment. Manufacturer's instructions were followed in all subsequent steps. cDNA libraries from different samples were multiplexed using Illumina RPI oligonucleotides and sequenced on a HiSeq 2000 instrument using 1x101+7 cycles.
Illumina Truseq RNA v2 kit (unstranded)

treatment_protocol: Cells were treated with 200 µM 4SU for 16h, IR-exposed (10 Gy) or left untreated. One hour after IR exposure, all cell culture plates were irradiated with UV light at 365 nm (0.2 J/cm2) on ice and harvested immediately. We next lysed the cell pellets obtained in lysis/binding buffer (1% lithium dodecylsulphate, 100 mM Tris pH 7.5, 10 mM EDTA, 500 mM LiCl, 5 mM DTT, Complete Mini EDTA-free protease inhibitor (Roche)), and passed them 4 times through a 23G needle, followed by 2 passes through a 26G needle. Input lysates were (0.25 ml) stored at -80 C until further processing.

tag: exposed to

value: none (control)

tag: irradiated with

value: UV light at 365 nm (0.2 J/cm2)

value: CGATGT


title: L6_Dif_MS091_047


title: MCF-7 4SU, UV, IR replicate 1

source_name: MCF-7 4SU_UV_IR

value: 10 Gy irradition

value: GTGAAA


title: PAR-CLIP DDX54 wild-type control replicate1

description:
binding sites, T-C transitions
parclip_DDX54_C1

data_processing:
Basecalls were performed using CASAVA 1.8.2 and bcl2fastq v2.16.0.10. Demultiplexing and adapter removal of raw reads were performed using Flexbar (v2.5) utilizing Illumina RPI index barcodes. Reads were simultaneously filtered for quality (cutoff Phred+ 10) and length (cutoff 18 nucleotides). For PAR-CLIP libraries, reads were collapsed using collapsed_reads.pl script (S. Mackowiak, (Jens, 2016; Lebedeva et al., 2011)) and trimmed to remove 2 nucleotides from both 3’ and 5’ ends of reads using fastx_trimmer (FASTX Toolkit, v0.0.14) and re-filtered for length (minimum 18 nt).
We used the previously published computational PAR-CLIP pipeline (v0.97a) (Jens, 2016; Lebedeva et al., 2011). Briefly, reads were aligned to hg19 and a set of RefSeq pre-mRNA sequences with BWA 0.5.8c. Unique alignments were converted to a pileup and read clusters scored for characteristic conversions and read variability with a custom script. After stringent-false positive filtering (using antisense clusters as a decoy database) remaining clusters were output as bed files. See Lebedeva et al. 2011 Mol Cell 43, 340–352 for details. T-C transitions were extracted using Samtools (v.0.1.19) and a custom perl script (Schueler et al., 2014).
Genome_build: hg19
Supplementary_files_format_and_content: bed files (binding sites and T-C transitions)

source_name: PAR-CLIP DDX54 wild-type control

growth_protocol: MCF-7 cells expressing FLAG/HA-tagged DDX54 WT and DDX54-D247N were grown in standard DMEM to 80% confluency. For a typical experiment, 15 15-cm dishes were used.

extract_protocol:
Cell pellets were lysed in approximately 3 cell pellet volumes (5 ml) of high salt NP-40 lysis buffer (50 mM Tris pH 7.5, 500 mM NaCl, 1% (v/v) NP-40, 1 mM DTT, complete EDTA-free protease inhibitor cocktail (Roche)), incubated for 30 minutes on ice followed by 10-second sonication at 80% amplitude.
Immunoprecipitation (IP), small RNA cloning and cDNA library generation were performed as previously described (Hafner et al., 2010; Hafner et al., 2012) with the following minor modifications. Briefly, the first and second RNase T1 treatments were performed at 1 U/µl for 10 min at 22 °C and at 2 U/µl in 80 µl of IP wash buffer (50 mM HEPES, pH 7.5, 300 mM KCl, 0.05% (v/v) IGEPAL CA-630, 0.5 mM DTT) for 7 min at 22 °C, respectively. Crosslinked protein-RNA complexes were resolved by SDS-PAGE using Novex 3-8% gradient Tris-acetate gels (Thermo Fischer). Proteins and protein-RNA complexes were transferred to a nitrocellulose membrane (Whatman) and exposed to phosphorimager screen. 32P-RNA-FLAG/HA-DDX54 complex migrating at approximately 115 kDa was excised and proteinase K (Roche) digested (4 mg/ml for 1 h at 55 °C).  After phenol-chloroform extraction and precipitation, RNA was ligated to 3’ adaptor (see Oligonucleotides) and gel purified. Two RNA size ranges per each sample (corresponding to 22-35 and 50-100 nucleotides of unligated fragments) were excised, 5’adaptor ligated, reverse transcribed and PCR-amplified to obtain cDNA libraries. cDNA libraries were amplified using Phusion High-Fidelity DNA polymerase (Thermo Fischer) and different barcode containing reverse PCR primers (see Oligonucleotides) followed by gel purification using QIAquick gel extraction kit (Qiagen). Clustering and amplification of cDNA libraries was performed according to manufacturer's instruction. Massively parallel sequencing was carried out on HiSeq2000 Illumina instrument using 1x51+7 cycle and 1x101+7 cycle runs.
small RNA cloning (Hafner et al, 2012)

treatment_protocol: Cells were incubated with 200µM 4SU (ChemGenes) for 16 h, IR-exposed (10 Gy), UV-crosslinked at 365 nm (0.2 J/cm2), harvested and stored at -80 °C.

value: breast carcinoma epithelial cell line

tag: genotype/variation

value: expressing FLAG/HA-tagged DDX54 WT

tag: antibody

value: anti-FLAG

tag: molecule subtype

value: UV 365nm DDX54-crosslinked RNA (PAR-CLIP)

value: ATCACG


title: MCF-7 4SU siDDX54 replicate 2 IR 2h

data_processing:
Basecalls were performed using CASAVA 1.8.2 and bcl2fastq v2.16.0.10. Demultiplexing and adapter removal of raw reads were performed using Flexbar (v2.5) utilizing Illumina RPI index barcodes. Reads were simultaneously filtered for quality (cutoff Phred+ 10) and length (cutoff 18 nucleotides).
For 4SU-seq experiments we quantified pre-mRNA and mRNA levels by RSEM (v.1.2.20) (Li and Dewey, 2011) using bowtie (v.1.1.2) (Langmead et al., 2009) as read alignment program. We first prepared a custom annotation file by adding whole gene loci as “transcript” category in the Gencode v19 annotation GTF file (i.e. all rows with the “gene” category were modified to “transcript”). Bowtie/RSEM index was then obtained by rsem-prepare-reference program using default settings with the modified GTF file. Pre-mRNA abundance metrics (expected counts, TPM and FPKM) were considered only for genes with more than one exon and were derived from reads that mapped to the entire gene locus only (ENSG* id*s in the transcript_id column of *.isoform.expression files). For mRNA abundance we computed the sum of metrics for all annotated transcripts within the annotated gene. To perform differential expression analysis we used DESeq2 (Love et al., 2014) using default parameters. Normalization of read counts was performed using DESeq2 size factors obtained from D.melanogaster exon read counts from HTSeq-count outputs (see above). Transcripts with p adjusted value lower than 0.01 were considered differentially expressed.
To obtain percent intron retention scores, reads from each sample were first separately mapped to the human genome (version hg19) and D.melanogaster genome (BDGP6) using Tophat2 (v2.1.0). To manipulate the alignment BAM/SAM files we used Samtools (v0.1.19) (Li et al., 2009). A custom perl script (E. Wyler) was used to intersect human and D.melanogaster alignment bam files and remove the reads that aligned to both genomes. Next, human genome uniquely mapped reads were extracted from the remaining reads by filtering for the NH:i:1 attribute in the BAM/SAM file. Next, we performed an intron-centric analysis by using junction and spliced read counts in all non-overlapping Refseq introns and their upstream or downstream exons as decribed previously (Braunschweig et al., 2014). Specifically, we used Samtools, Bedtools (v2.25.0) (Quinlan and Hall, 2010) and custom Unix scripts to count unspliced reads in introns (I), 5' and 3' exon-intron junctions (E1I and IE2, respectively) and spliced reads in exon-exon junctions (E1E2). Briefly, we demanded a minimum overlap of 8 nucleotides over any given junction for a read to be counted. Read counts were then normalized using DESeq2 size factors obtained from D.melanogaster exon read counts from HTSeq-count outputs (see above). Per-intron PIR scores were computed as follows: PIR=100x average(E1I, IE2)/(E1E2 + average(E1I, IE2)), where E1I,IE2 and E1E2 were normalized read counts for the junctions described above. We only considered PIR scores for introns with sufficient read evidence by demanding an empirical criterion of median(EI1, IE2, I) + E1E2 to be higher than 10, as previously used in (Braunschweig et al., 2014). In addition, a between-replicate mean PIR score was only computed for introns where the computation of PIR score was possible for both replicates.
To obtain synthesis, degradation and processing rates we used the default parameters of iNSPEcT Bioconductor package (de Pretis et al., 2015) by inputting the FPKM values from RSEM outputs obtained as described above.
Genome_build: hg19, dm3
Supplementary_files_format_and_content: txt files (RSEM read counts, TPMs and FPKMs; HTSeq-count read counts)

source_name: MCF-7 4SU siDDX54 IR 2h

extract_protocol:
Total RNA was extracted using miRNA easy kit (Qiagen) using manufacturer's instruction. Total RNA (60 µg) was treated with 12 U Turbo DNase (Thermo Fisher) in 350 µl reaction volumes for 30 min at 37ºC. To remove the enzyme, RNA was phenol-chloroform extracted, followed by isopropanol precipitation and resuspension in water. We next performed 4SU biotinylation as previously described (Gregersen et al., 2014a; Radle et al., 2013) with minor modifications. Briefly, 4SU biotinylation reactions were carried out at room temperature for 3 h in 250 µl reaction volumes containing 10 mM Tris pH 7.5, 5 mM EDTA, 50 µg MCF-7 total RNA, 250ng S2 cell RNA (200:1 ratio) and 100 µg EZ-Link biotin-HPDP (Thermo Fisher). Afterwards, RNA was phenol/chloroform extracted in phase-lock tubes, isopropanol precipitated and resuspended in 100 µl of water. RNA was next denatured at 65ºC for 10 min, cooled on ice and incubated for 15 min at room temperature with 150 µl streptavidin-conjugated magnetic beads (µMACS, Miltenyi Biotec). To isolate 4SU containing RNA, the mixtures were applied to µColumns, washed 3 times in washing buffer (100 mM Tris-HCl, pH 7.4, 10 mM EDTA, 1 M NaCl, 0.1% Tween20) and eluted twice in 100µl of 0.1M DTT. Cleanup was performed by RNAeasy MinElute kit (Qiagen) with elution in 14 µl of water. Typical yields were in the range of 25 - 50 ng.
Unstranded Truseq mRNA kit v2 was used according to the manufacturer's instruction to prepare cDNA libraries using 10 µl of starting 4SU-enriched RNA. Clustering and amplification of cDNA libraries was performed according to manufacturer's instruction. Massively parallel sequencing was carried out on HiSeq2000 Illumina instrument using 1x101+7 cycles.
Illumina Truseq RNA v2 kit (unstranded)

treatment_protocol: MCF-7 Flp-in cells were reverse-transfected in a 10-cm dish format using 2 different siRNAs (1 and 3). We plated 2 ml of Optimem (Thermo Fisher), followed by the addition of 240 pmol siRNA and 20 µl Lipofectamine RNAimax. After a 20-min incubation, 1.5x10^6 cells were plated in 10 ml of supplemented DMEM (final volume was 12 ml per dish), incubated for 48 hours and irradiated (10 Gy). 4SU was added to the final concentration of 500 µM 20 min before harvesting at different time periods post irradiation (0h, 1h and 2h) in 1ml of Trizol (Thermo Fisher). To obtain spike-in control 4SU-labeled total RNA from D.melanogaster, S2 cells were labeled for 16h with 200 µM 4SU.

value: 2h post irradiation

value: 4SU+ RNA

value: GCCAAT


title: RNA-seq, adult Fto KO mice, hippocampus, replicate 2

city: Atlanta

first: Feiran

last: Zhang

state: GA

address: 615 Michael St NE

department: Human Genetics

institute: Emory University

description: Poly(A)+ RNA

data_processing:
For m6A-IP-seq, reads were first aligned to mouse genome (mm9) by Bowtie v2.2.3, using the local, sensitive and non-deterministic mode.
m6A peaks were identified by HOMER findPeaks, using the factor mode and additional settings (peak size = 100 nt; fragment length = 100 nt; maximum distance used to stitch peaks together = 50; fold change threshold = 3; local fold change = disabled; size of region to search for control tags = 1x peak size; p-value threshold = 0.0001; and false-discovery rate (FDR) threshold = 0.001).
High-confidence peaks found in both biological replicates were annotated by HOMER annotatePeaks.pl.
The annotation of boundary genes were corrected using a Python script.
Tiled data files (TDF) for the Integrative Genomics Viewer (IGV) were generated by igvtools.
The genome-wide coverage data were normalized by 1,000,000/total read count, and were visualized by IGV.
In addition, reads from input samples were also aligned to mouse transcriptome annotations and genome assembly (mm9) using TopHat v2.0.13.
FPKM values were calculated by Cufflinks v2.2.1.
In addition, for RNA-seq, SR125 reads were first aligned to mouse transcriptome annotations and genome assembly (mm9) using TopHat v2.1.1.
FPKM values were calculated by Cufflinks v2.2.1.
Genome_build: mm9
Supplementary_files_format_and_content: For m6A-IP-seq, peak files with quantitative data and tag density files are included. In addition, for RNA-seq, gene expression values are in Cufflinks-normalized fpkm_tracking format.

source_name: Hippocampus

extract_protocol:
Total RNA was extracted from fresh hippocampi by using TRIzol Reagent (Invitrogen).
RNA-seq libraries were generated from 1 μg of total RNA from duplicated samples per condition. The input libraries for m6A-IP were generated from about 50 ng of poly(A)+ RNA fragments from duplicated samples per condition. The m6A-IP libraries were generated from all immunoprecipitated and eluted fragments of poly(A)+ RNA from duplicated samples per condition.The TruSeq LT RNA Library Preparation Kit v2 (Illumina) was used and the manufacturer’s protocol was followed. An Agilent 2100 BioAnalyzer and DNA1000 kit were used to quantify amplified cDNA and to control the quality of the libraries.

value: Fto knock-out

tag: age

value: 8-12 weeks

tag: treatment of rna sample

value: Poly(A) selection

tag: biological replicate no.


title: MCF-7 4SU UV, no IR replicate 1

value: CTTGTA


title: PAR-CLIP DDX54 wild-type actinomycin D treated

description:
binding sites, T-C transitions
parclip_DDX54_actD2

value: actinomycin D

value: ACAGTG


title: MCF-7 4SU, UV, IR replicate 2

value: UV light at 365 nm (0.2 J/cm2)

value: TGACCA


title: CMK9_Dif_MS091_045

value: ESC

tag: cell status

value: Differentiated


title: L3_Naive-like_MS091_039

value: Liver-derived iPSC

value: Naive-like

tag: culture condition


title: PAR-CLIP DDX54 wild-type IR 10Gy replicate2

description:
binding sites, T-C transitions
parclip_DDX54_IR2

source_name: PAR-CLIP DDX54 wild-type IR 10Gy

tag: cell line

value: breast carcinoma epithelial cell line

value: expressing FLAG/HA-tagged DDX54 WT

value: 10 Gy irradition

value: anti-FLAG

value: UV 365nm DDX54-crosslinked RNA (PAR-CLIP)


title: PAR-CLIP DDX54 wild-type IR 10Gy replicate1

description:
binding sites, T-C transitions
parclip_DDX54_IR1

tag: cell type

value: CGATGT


title: CMK6_Dif_MS091_043


title: S12_Naive-like_MS091_042

value: Stomach-derived iPSC


title: RNA-seq, adult WT mice, hippocampus, replicate 1

description: Poly(A)+ RNA

value: Wild-type

value: 8-12 weeks

value: Poly(A) selection


title: PAR-CLIP DDX54 wild-type control replicate2

description:
binding sites, T-C transitions
parclip_DDX54_C2

value: none (control)

value: TTAGGC


title: CMK6_Naive-like_MS091_036


title: MCF-7 4SU siDDX54 replicate 1 IR 1h

source_name: MCF-7 4SU siDDX54 IR 1h

tag: transfected with

value: 1h post irradiation

value: 4SU+ RNA


title: TRSK_Naive-like_MS091_037

value: ESC

value: TRSK


title: L6_Naive-like_MS091_040

value: Liver-derived iPSC

value: Naive-like


title: S6_Naive-like_MS091_041


title: RNA-seq, adult Fto KO mice, hippocampus, replicate 1

description: Poly(A)+ RNA

value: Fto knock-out


title: RNA-seq, adult WT mice, hippocampus, replicate 2

description: Poly(A)+ RNA


title: MCF-7 4SU mock replicate 2 IR 2h

source_name: MCF-7 4SU mock IR 2h

value: breast carcinoma epithelial cell line

value: mock

tag: time point

value: 2h post irradiation

value: CTTGTA


title: MCF-7 4SU siDDX54 replicate 2 IR 0h

source_name: MCF-7 4SU siDDX54 IR 0h

value: 0h post irradiation

tag: barcode


title: MCF-7 4SU siDDX54 replicate 1 IR 2h

value: ACAGTG


title: MCF-7 4SU siDDX54 replicate 2 IR 1h

value: TGACCA


title: S12_Prime_MS091_035

value: Stomach-derived iPSC

value: Prime

value: bFGF/KSR


title: MCF-7 4SU siDDX54 replicate 1 IR 0h

value: CAGATC


title: RNA-seq, 6-week-old WT mice, hippocampus, input, replicate 2

description: Poly(A)+ RNA

value: Wild-type

value: 6 weeks

value: Poly(A) selection


title: RNA-seq, 6-week-old WT mice, hippocampus, m6A-IP-1

description: Poly(A)+ RNA

value: Poly(A) selection; m6A immunoprecipitation


title: RNA-seq, 6-week-old WT mice, hippocampus, m6A-IP-2

description: Poly(A)+ RNA


title: S6_Prime_MS091_034


title: ume6∆snf2∆

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: Processed data files are RPKM values are splicing effieciencies calculated from STAR alignments

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown up to midlog phase (OD600 between 0.5-0.6) 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: strain

value: ume6:KanMX ; snf2-delta:NatMX

tag: ploidy

value: haploid

value: his-ura-leu-


title: CMK9_Prime_MS091_033

value: ESC


title: ume6∆


title: L6_Prime_MS091_032

value: Liver-derived iPSC


title: CMK9_Naive-like_MS091_038

value: Naive-like


title: MCF-7 4SU mock replicate 2 IR 1h

source_name: MCF-7 4SU mock IR 1h

value: breast carcinoma epithelial cell line

value: mock

value: 1h post irradiation

value: 4SU+ RNA

value: GCCAAT


title: RNA-seq, 6-week-old WT mice, hippocampus, input, replicate 1

description: Poly(A)+ RNA

tag: genotype


title: MCF-7 4SU mock replicate 2 IR 0h

source_name: MCF-7 4SU mock IR 0h

value: 0h post irradiation

value: TGACCA


title: RNA-seq, 2-week-old WT mice, hippocampus, m6A-IP, replicate 2

description: Poly(A)+ RNA

value: Wild-type

value: 2 weeks


title: snf2∆

tag: genotype/variation


title: MCF-7 4SU mock replicate 1 IR 2h

value: 2h post irradiation

value: CAGATC


title: WT

value: wild type


title: RNA-seq, 2-week-old WT mice, hippocampus, m6A-IP, replicate 1

description: Poly(A)+ RNA

value: Poly(A) selection; m6A immunoprecipitation


title: MCF-7 4SU mock replicate 1 IR 1h

value: ACAGTG


title: RNA-seq, 2-week-old WT mice, hippocampus, input, replicate 2

description: Poly(A)+ RNA

value: Poly(A) selection


title: L3_Prime_MS091_030

value: Liver-derived iPSC

value: Prime

value: bFGF/KSR


title: MCF-7 4SU mock replicate 1 IR 0h

value: breast carcinoma epithelial cell line

value: mock

value: CGATGT


title: CMK6_Prime_MS091_029

value: ESC


title: TRSK_Prime_MS091_031

value: TRSK


title: AML blast 7421

status: Public on Apr 19 2017

city: New York

first: Jacob

middle: Lowell

last: Glass

state: NY

address: 1275 York Avenue

institute: Memorial Sloan Kettering Cancer Center

library_source: genomic

data_processing:
Casava 1.7 for base calling
Adapter trimming with FAR 2.15
Alignment with Bowtie 0.12.7
Methylation calling with Bismark 0.5.4
Genome_build: hg19
Supplementary_files_format_and_content: Files are in text format with the following 7 columns: chrBase, chr, base, strand, coverage, freqC, freqT. 'chrBase' is a concatenation of chromosome and base position for easy indexing. 'chr' is the chromosome, 'base' is the base position, 'coverage' ranges from 10-400. 'freqC' is the 'C' frequency representing the % of methylated bases and 'freqT' is the 'T' frequency, representing unmethylated bases.

molecule: genomic DNA

source_name: AML blast cells

extract_protocol: Enhanced reduced representation of bisulfite sequencing (PMC4354670): High molecular weight genomic DNA was digested with MspI restriction enzyme, subjected to end repair and adenylation followed by ligation to cytosine methylated paired-end Illumina adaptors. Fragments of 150-400 bp were isolated by size selection and subjected to bisulfite conversion and PCR amplification using paired-end Illumina primers.  Libraries were sequenced using an Illumina HiSeq2000 per manufacturer’s recommended protocol for 50bp single end read reads

tag: diagnosis

value: acute myeloid leukemia (AML)

value: blast

tag: gender

value: male

tag: fab

tag: cytogenetics

value: NN

value: Neg

tag: other

tag: normal karyotype

value: Pos

tag: flt3 itd

tag: flt3 tkd

tag: nras

tag: kras

tag: cebpa

tag: kit

tag: dnmt3a amino acid mutation

tag: evi1 overexpression


title: RNA-seq, 2-week-old WT mice, hippocampus, input, replicate 1

description: Poly(A)+ RNA

value: Wild-type

tag: age

value: 2 weeks

tag: treatment of rna sample

tag: biological replicate no.


title: AML blast 7420

tag: diagnosis

tag: cell type


title: AML blast 7418

tag: gender

tag: fab


title: AML blast 7411

value: female

tag: cytogenetics

tag: other


title: AML blast 7407

tag: normal karyotype

tag: flt3 itd


title: AML blast 7408

tag: flt3 tkd

tag: nras


title: AML blast 7412

tag: kras

tag: cebpa


title: AML blast 7328

tag: kit

tag: dnmt3a amino acid mutation


title: AML blast 7322

tag: age

value: Other

tag: evi1 overexpression


title: AML blast 7402


title: AML blast 7324


title: AML blast 7319


title: AML blast 7318


title: AML blast 7308


title: AML blast 7316


title: AML blast 7301


title: AML blast 7273


title: AML blast 7312

value: RAEB MDS

value: Complex


title: AML blast 7180


title: AML blast 7178


title: AML blast 7168


title: AML blast 7172


title: AML blast 7145

value: failure


title: AML blast 7143


title: AML blast 7176


title: AML blast 7188


title: AML blast 7131


title: AML blast 7122


title: AML blast 7079


title: AML blast 7118


title: AML blast 7074


title: AML blast 7076

value: Sil


title: AML blast 7067


title: AML blast 7059


title: AML blast 7062


title: AML blast 7313

value: -5/7(q), complex


title: AML blast 7051


title: AML blast 7052


title: AML blast 7058


title: AML blast 6945


title: AML blast 7150


title: AML blast 6887


title: AML blast 6882


title: AML blast 7142

value: DM


title: AML blast 7139


title: AML blast 6456


title: AML blast 6463


title: AML blast 7115

value: t(8;21), complex


title: AML blast 6379

value: acute myeloid leukemia (AML)


title: AML blast 7114

value: blast


title: AML blast 7081

value: male


title: AML blast 6881


title: AML blast 6375


title: AML blast 7070

value: NN


title: AML blast 6364

value: Neg


title: AML blast 6243

value: Pos


title: AML blast 6239


title: AML blast 6374


title: AML blast 5352


title: AML blast 6947


title: AML blast 5286


title: AML blast 5287


title: AML blast 5282


title: AML blast 4340


title: AML blast 5358


title: AML blast 4337


title: AML blast 4335


title: AML blast 4334


title: AML blast 3331


title: AML blast 3330


title: AML blast 3328


title: AML blast 3316


title: AML blast 2748


title: AML blast 3314


title: AML blast 2753


title: AML blast 2666


title: AML blast 2549


title: AML blast 2327


title: AML blast 2545


title: AML blast 6237


title: AML blast 5289


title: AML blast 2276


title: AML blast 2299


title: AML blast 2306


title: AML blast 2301


title: AML blast 2273


title: AML blast 2254


title: AML blast 2253


title: AML blast 2260


title: AML blast 2250


title: AML blast 2246


title: AML blast 2248


title: AML blast 2245


title: AML blast 2240


title: AML blast 2238


title: AML blast 2668


title: AML blast 2236


title: AML blast 2235


title: AML blast 2234


title: AML blast 2210


title: AML blast 2208


title: AML blast 2204


title: AML blast 2190


title: AML blast 2186


title: AML blast 2206


title: AML blast 2230


title: AML blast 2268


title: AML blast 2189


title: AML blast 2185


title: AML blast 2179


title: AML blast 1316


title: AML blast 1448


title: AML blast 2242


title: AML blast 2195


title: Testis_3W-T-rep2

city: Beijing

first: Bao-Fa

last: Sun

address: Da-Tun Road

country: China

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

description:
3-week-old Mouse testis
normal tissue cells

data_processing:
Reads were aligned to the hg19 or mm10 genome assembly using TopHat v2.0.9
For each sample, reads counts of all genes were computed using HTSeq v0.5.3p9
Genome_build: hg19 or mm10
Supplementary_files_format_and_content: all-samples-reads-count.xls

source_name: 3-week-old Mouse testis

extract_protocol:
RNA was isolated from siCTRL, siNSUN2 and ALYREF-RIP HeLa cells, and mutiple mouse tissues  using the TRIzol (Invitrogen) reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100
Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 (Illumina) or HiSeq2500 in paired-read mode, creating reads with a length of 101 or 125 bp

tag: strain

value: 3 week

tag: tissue

value: testis


title: Testis_4W-T-rep1

description:
4-week-old Mouse testis
normal tissue cells

source_name: 4-week-old Mouse testis

value: 4 week


title: Testis_4W-T-rep2


title: Testis_3W-T-rep1


title: AML blast 2170

tag: diagnosis

tag: cell type


title: AML blast 322

tag: gender

value: female

tag: fab

value: Other


title: Liver_8W-T-rep2

description:
8-week-old Mouse liver
normal tissue cells

source_name: 8-week-old Mouse liver

value: 8 week

value: liver


title: Liver_8W-T-rep1


title: AML blast 2197

tag: cytogenetics

tag: other


title: Brain_8W-T-rep2

description:
8-week-old Mouse brain
normal tissue cells

source_name: 8-week-old Mouse brain

value: brain


title: Kidney_8W-T-rep2

description:
8-week-old Mouse kidney
normal tissue cells

source_name: 8-week-old Mouse kidney

value: kidney


title: AML blast 2200

tag: normal karyotype

tag: flt3 itd


title: Brain_8W-T-rep1


title: Muscle_8W-T-rep2

description:
8-week-old Mouse muscle
normal tissue cells

source_name: 8-week-old Mouse muscle

value: muscle


title: Heart_8W-T-rep1

description:
8-week-old Mouse heart
normal tissue cells

source_name: 8-week-old Mouse heart

value: heart


title: Muscle_8W-T-rep1


title: Heart_8W-T-rep2


title: AML blast 5360

value: acute myeloid leukemia (AML)

tag: flt3 tkd

tag: nras

value: Sil


title: Small-Intestine_8W-T-rep2

description:
8-week-old Mouse small intestine
normal tissue cells

source_name: 8-week-old Mouse small intestine

value: male

value: small intestine


title: Small-Intestine_8W-T-rep1


title: BY4741_saturated_RNAseq_rep2

city: Stanford

first: Seungsoo

last: Kim

address: 265 Campus Dr

department: Chemical and Systems Biology

institute: Stanford University

data_processing:
Hi-C
Basecalls were converted to FASTQ using bcl2fastq 2.17
Sequencing reads were quality-trimmed (cutadapt -q 20) trimmed of adapter sequences and then trimmed up to the ligation junction (if present), excluding read pairs in which either read was shorter than 20 bp after trimming.
Reads were independently mapped using bowtie2 2.2.3 using the parameter set --very-sensitive. For interspecific hybrids, reads were mapped to a combined reference containing both species references, where if secondary mappings were present the best alignment must have a score ≥ 10 greater than the next best alignment. For intraspecific S. cerevisiae hybrids, reads were mapped separately to both strain references, keeping only read pairs mapping to both—perfectly to one reference and with ≥ 2 mutations including ≥ 1 substitution to the other. In both cases, only read pairs in which both reads mapped with MAPQ ≥ 30 were used.
PCR duplicates (with identical fragment start and end positions) were removed, as were read pairs mapping within 1 kb of each other or in the same restriction fragment, which represent either unligated or invalid ligation products.
The genome was then binned into 32 kb fragments (except the last fragment of each chromosome), and the number of read pairs mapping to each 32 kb genomic bin was counted based on the position of the restriction sites that were ligated together. Due to gaps in the reference genomes of S. uvarum, some repetitive sequences were only represented once and therefore artifactually mapped uniquely; therefore, reads mapping to annotated repetitive sequences were masked from further analysis. Similarly, gaps in the S. paradoxus reference led to mismapping of reads to the corresponding S. cerevisiae sequence; therefore, for S. cerevisiae x S. paradoxus libraries we masked regions in the S. cerevisiae genome where > 1 read from a S. paradoxus Hi-C library mapped, and vice versa. We took a similar approach to mask regions of the Y12 and DBVPG6044 references that were prone to mismapping, as estimated by haploid Y12 and DBVPG6044 Hi-C libraries. For knock-in experiments, the HAS1pr-TDA1pr region was masked to account for its altered genomic location. The resulting matrices were then normalized by excluding the diagonal (interactions within the same genomic bin), filtering out rows/columns with an average of less than 1 read per bin, and then multiplying each entry by the total number of read pairs divided by the column and row sums.
Genome_build: Saccharomyces cerevisiae R64.2.1 from SGD and Saccharomyces cerevisiae and Saccharomyces uvarum (bayanus var. uvarum) from saccharomycessensustricto.org, with minor modifications; Y12 and DBVPG6044 references generated by Pacbio sequencing
Supplementary_files_format_and_content: tab-delimited text files ending in "matrix.txt" include the raw read counts and normalized interaction frequencies for each pair of 32 kb genomic bins; those ending in "rowsums.txt" include the raw sums across each row of these matrices. BED files include either the genomic regions included in each matrix bin or those masked from the matrices.
ChIP-seq
Basecalls were converted to FASTQ using bcl2fastq 2.17
Sequencing reads were quality-trimmed (cutadapt -q 20), trimmed of adapter sequences, excluding read pairs in which either read was shorter than 28 bp after trimming.
Reads were mapped using bowtie2 2.2.3 using the parameter set --very-sensitive -X 2000
PCR duplicates (with identical fragment start and end positions) were removed.
Coverage across the genome was calculated using bedtools genomecov, using only read pairs with a minimum MAPQ score of 30.
Genome_build: sacCer3
Supplementary_files_format_and_content: bedgraph files of fragment coverage across the genome
RNA-seq
Basecalls were converted to FASTQ using bcl2fastq 2.17
Sequencing reads were quality-trimmed (cutadapt -q 20), trimmed of adapter sequences, excluding read pairs in which either read was shorter than 28 bp after trimming.
Reads were mapped using bowtie2 2.2.3 using the parameter set --very-sensitive -X 500
The number of read pairs with a minimum MAPQ score of 30 that overlap each gene uniquely were counted using HTSeq-count.
Genome_build: sacCer3
Supplementary_files_format_and_content: sacCer3_genes.gff are the gene annotations used; tab-delimited text files ending in "counts.txt" include the number of read pairs mapping to each gene.

source_name: Cells

growth_protocol: Cells were grown overnight in YPD (for exponential growth and saturated samples) or YP + 2% galactose (for galactose samples) at 30˚C, then diluted to OD600 = 0.1-0.125 in 50 ml medium, and then grown to OD600 = 0.5-0.6, pelleted and stored at -80˚C.

extract_protocol:
RNA was purified using acid phenol extraction, and then treated with the DNA-free DNase kit (Thermo).
RNA-seq libraries were then prepared using the TruSeq RNA Library Prep Kit v2 (Illumina), with 6 cycles of amplification.

tag: growth conditions

value: saturated

tag: growth medium

value: YPD

tag: growth phase

tag: growth temperature


title: BY4741_galactose_RNAseq_rep3

value: galactose

value: YP+galactose

value: exponential


title: BY4741_saturated_RNAseq_rep1


title: BY4741_galactose_RNAseq_rep2


title: DamIDseq-DamPiwi_rep1

city: Moscow

first: Sergei

last: Ryazansky

address: Kurchatov sq., 2

department: Department of Molecular Genetics of Cell

country: Russia

institute: Institute of Molecular Genetics

data_processing:
Library strategy: DamID-seq
Two biological replicates of Dam-only or Dam-Piwi DamID-seq reads were adapter clipped, mapped to the dm3 genomic assembly by bowtie2 (Langmead 2012) and counted by ‘HTSeq-count’ software (Anders et al, 2015) on the GATC-GATC fragments or the ~300-bp genomic bins. The resulted counts of Dam-Piwi samples were converted to RPM, normalized to the Dam-only samples counts and log2-transformed. The domain calling was performed with the 2-state HMM algorithm.
genome build: dm3
processed data files format and content: Genomic profiles of RPM-normalized counts binned in ~300 bp intervals.

organism: Drosophila melanogaster

source_name: ovaries

growth_protocol: Flies were grown according to standard protocols.

extract_protocol: 160-200 ovaries from 0-4 days old females were manually dissected using dissection needles in PBS at 4°C. Isolation of genomic DNA was performed by DNeasy Blood and Tissue kit (Qiagen), following the protocol for cultured cells. DNA was concentrated by centrifugation in 0.5 ml Amicon-Ultra columns (Millipore) for 10 min at 18000 × g and its concentration was measured using a NanoDrop spectrophotometer. For the selective amplification of methylated GATC-GATC fragments, genomic DNA was first digested by DpnI, followed by ligation of adaptors, DpnII digestion and PCR-amplification as described previously (Vogel et al. 2007) with a minor modification: ~0.5 µg instead of 2.5 µg of genomic DNA was used as an input. We applied 14 cycles of PCR (1 min at 94°C, 1 min at 65°C, 2 min at 68°C) for Dam-only DNA samples and 19 cycles of PCR for Dam-Piwi DNA samples. Adaptors were removed by DpnII digestion for 2 h at 37°C. The amplified methylated DNA fragments were purified using QIAquick PCR Purification kit (Qiagen), concentrated by centrifugation in 0.5 ml Amicon-Ultra columns (Millipore) for 10 min at 18000 × g, and quantified on a NanoDrop spectrophotometer. 0.5 µg of Dam-only and Dam-Piwi DNA samples (each in two biological replicates) were subjected to next generation sequencing (NGS) on Illumina HiSeq 2500 resulting in ~30 million 101-nt single-end reads per sample.

value: ovaries

value: female

tag: treatment

value: not treated

tag: replicate number

value: F1 [pUAST-loxP-stop-loxP-Dam-Piwi] x [Mos1-Cre]


title: DamIDseq-DamPiwi_rep2

tag: tissue

tag: strain


title: DamIDseq-Dam_rep2

value: F1 [pUAST-loxP-stop-loxP-Dam] x [Mos1-Cre]


title: DamIDseq-Dam_rep1


title: BY4741_galactose_RNAseq_rep1


title: BY4741_glucose_RNAseq_rep2


title: RIPseq-Piwi_ActD

data_processing:
RIP-seq: Sequencing reads with clipped adapter were subjected to the TopHat Cufflink software.
genome build: dm3
processed data files format and content: Tab-delimited files include the frequencies of clipped read occurrences in each library.

source_name: OSC cells

growth_protocol: OSC cells were grown according to standard protocols.

extract_protocol:
RIP-seq: 1 × 10^8 cells per sample were incubated in lysis buffer (50 mM Tris-HCl pH 7.4, 150 mM NaCl, 2 mM MgOAc, 1 mM DTT, 1% Triton-X100, 0.1% NP-40, 1 mM EDTA, 2 × Complete Protease inhibitor cocktail (Sigma-Aldrich), 100 U/ml RNaseOUT™ Ribonuclease Inhibitor (Thermo Fisher Scientific)). Samples were cleared by centrifugation at 16000 × g for 5 min at 4°C and extracts were incubated with rabbit polyclonal anti-Piwi antibodies (kindly provided by R. Pillai), immobilized on the Protein G Dynabeads (Thermo Fisher Scientific), for 3 h at 4°C with rotation. In parallel, RNA-immunoprecipitation was carried out in the absence of the antibody (‘mock’ sample). After incubation, the beads were washed five times with lysis buffer. Precipitated RNA was isolated by treatment of the beads with 0.7 mg/ml proteinase K for 2 h at room temperature, followed by phenol/chloroform extraction and ethanol precipitation. For protein elution, approximately one fifth of the beads per sample after RNA-immunoprecipitation were incubated for 10 min at 70°C in SDS-sample buffer, and then loaded onto SDS-PAGE gels for further Western-blot analysis. Equal amounts of Piwi were detected in the actinomycin D-treated and control RIP extracts and no Piwi signal was observed in the ‘mock’ sample.
RIP-seq: The precipitated RNA was chemically fragmented, converted into cDNA using random hexamer priming, prepared for NGS by TruSeq RNA library preparation kit (Illumina) and sequenced on Illumina HiSeq 2000 resulting in ~18-19 million 51-nt single-end reads obtained per sample.

treatment_protocol: RIP-seq: Piwi RIP was performed from OSCs treated for 1h with actinomycin D (1 μg/ml) or from control untreated cells. The effectiveness of transcriptional repression after actinomycin D treatment was checked by Click-iT® RNA Alexa Fluor® 594 Imaging Kit (Thermo Fisher Scientific) that enables detection of global nascent RNA transcription.

tag: cell line

value: OSC

value: Actinomycin D

tag: antibody

value: Ab-Piwi


title: RIPseq-Piwi_mock

value: mock


title: Kidney_8W-T-rep1

tag: gender

tag: age

value: 8 week

value: kidney


title: BY4741_glucose_RNAseq_rep3


title: RIPseq-Piwi_control


title: BY4741_glucose_RNAseq_rep1


title: MeDIP-seq WT rep2

city: Shanghai

first: Qicheng

last: Ni

address: 197 Ruijin 2nd Road

institute: Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
Reads were aligned to reference mouse genome (mm10) by Bowtie2 v2.2.5 after QC and further pre-procession.
Peaks were called by MACS v0.14.2, and DMRs (Differential methylation region) were analyzed by MEDIPS v1.12.0 R Bioconductor package.
DMRs were calculated using a window size of 500bp, extend by 100bp, increasing in 500bp increments, a minimum number of 10 reads in a window was required prior to inclusion in the DMRs.
Additionally, DMRs were filtered out if it has no overlap with peaks called by MACS.
Genome_build: mm9
Supplementary_files_format_and_content: Peaks were called by MACS v0.14.2; methylation peaks and its location

source_name: islets

growth_protocol: Mice were injected with Collagenase P (Roche) solution into the common hepatic bile duct to perfuse the pancreas. Pancreas were then removed and digested at 37°C. Islets were handpicked after several purification steps under a microscope.

extract_protocol:
Genomic DNA from freshly isolated islets were extracted using DNeasy Blood Tissue Kit (Qiagen, GmBH, Germany).
MeDIP was performed using a MagMedIP kit (Diagenode, Denville, NJ, USA) as previously described69. Libraries were prepared following the manufacture’s instruction and were sequenced by Illumina HiSeq 2500 with 50 cycles.

tag: strain background

tag: genotype/variation

value: WT; Raptor lox/lox

value: 8 weeks

value: pancreas-islets


title: MeDIP-seq WT rep1


title: Glc/Ac Ac Specialist_ac

city: La Jolla

first: Troy

middle: E

last: Sandberg

address: 9500 Gilman Dr

department: Bioengineering

institute: UCSD

data_processing:
Read quality was examined with FastQC and reads were trimmed with FASTX Trimmer as necessary.
RNAseq reads were aligned to the E. coli genome using bowtie2.
FPKM values were calculated with cufflinks.
Sample normalization was performed with cuffnorm.
Differential expression levels were quantified via cuffdiff.
Genome_build: NC_000913.3
Supplementary_files_format_and_content: *txt: Tab-delimited text files present per-gene FPKM values.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: whole cells, acetate

growth_protocol: Cells were grown under conditions of aerobic, exponential phase growth on M9 minimal medium containing either 4 g/L glucose, 4 g/L xylose, 4 g/L acetate, or 0.2% (v/v) glycerol.

extract_protocol:
Cells were harvested using the Qiagen RNA-protect bacteria reagent according to the manufacturer’s specifications. Prior to RNA extraction, pelleted cells were stored at -80°C, then thawed and incubated with lysozyme, SuperaseIn, protease K, and 20% sodium dodecyl sulfate for 20 min at 37°C. Total RNA was isolated and purified using Qiagen’s RNeasy mini kit column according to the manufacturer’s specifications. Ribosomal RNA (rRNA) was removed using Epicentre’s Ribo-Zero rRNA removal kit for Gram-negative bacteria.
A KAPA Stranded RNA-Seq Kit was used to generate paired-end, strand-specific RNA sequencing libraries.

tag: growth carbon source

value: acetate

value: Glc/Ac Ac Specialist


title: MeDIP-seq KO rep1

value: Raptor lox/lox; RipCre


title: Testis_4W-BS-rep2

description:
bisulfite treated mRNA
4-week-old Mouse testis
Mouse_m5C_sites_information.xls

data_processing:
Raw Reads were stripped of adaptor sequence and removed low quality bases using Trimmomatic, clean reads were aligned to the hg19 or mm10 genome assembly using bismark
The m5C sites were called by bismark.
Genome_build: hg19 or mm10
Supplementary_files_format_and_content: Human_m5C_sites_information.xls, m5C_sites_in_ALYREF-RIP.xls, Mouse_m5C_sites_information.xls

extract_protocol:
mRNAs of siCTRL, siNSUN2 and ALYREF-RIP HeLa cells, and multiple mouse tissues were purified using oligo (dT)-conjugated magnetic beads followed by RiboMinus treatement.
Bisulfite treated mRNAs were reverse transcribed to cDNA using ACT random hexamer primers. The cDNAs were subjected to libraries construction using KAPA Stranded mRNA-Seq Kit (KAPA)

value: male

value: 4 week

value: testis


title: Glc/Ac Glc Specialist_ac

value: Glc/Ac Glc Specialist


title: Testis_4W-BS-rep1


title: Ac3_ac


title: Ac2_ac


title: Testis_3W-BS-rep2

description:
bisulfite treated mRNA
3-week-old Mouse testis
Mouse_m5C_sites_information.xls

value: 3 week


title: BY4741_saturated_RNAseq_rep3

value: saturated

value: YPD


title: Testis_3W-BS-rep1


title: Liver_8W-BS-rep1

description:
bisulfite treated mRNA
8-week-old Mouse liver
Mouse_m5C_sites_information.xls

value: liver


title: WT_ac

value: wild-type


title: Kidney_8W-BS-rep2

description:
bisulfite treated mRNA
8-week-old Mouse kidney
Mouse_m5C_sites_information.xls

value: 8 week


title: Kidney_8W-BS-rep1

value: kidney


title: Xyl3_xyl

source_name: whole cells, xylose

value: xylose


title: Glc/Xyl Generalist_xyl

value: Glc/Xyl Generalist


title: Liver_8W-BS-rep2


title: Xyl2_xyl


title: Brain_8W-BS-rep2

description:
bisulfite treated mRNA
8-week-old Mouse brain
Mouse_m5C_sites_information.xls

value: brain


title: MeDIP-seq KO rep2

value: 8 weeks

value: pancreas-islets


title: Glc/Gly Generalist_gly

source_name: whole cells, glycerol

value: glycerol

value: Glc/Gly Generalist


title: Brain_8W-BS-rep1

value: male


title: Muscle_8W-BS-rep1

description:
bisulfite treated mRNA
8-week-old Mouse muscle
Mouse_m5C_sites_information.xls

value: muscle


title: Xyl1_xyl


title: Muscle_8W-BS-rep2


title: Gly1_gly


title: Heart_8W-BS-rep1

description:
bisulfite treated mRNA
8-week-old Mouse heart
Mouse_m5C_sites_information.xls

value: heart


title: Ac1_ac

value: acetate


title: WT_gly


title: Heart_8W-BS-rep2


title: Glc/Xyl Generalist_glc

source_name: whole cells, glucose

value: glucose


title: Gly2_gly


title: Small-Intestine_8W-BS-rep2

description:
bisulfite treated mRNA
8-week-old Mouse small intestine
Mouse_m5C_sites_information.xls

value: small intestine


title: Glc/Gly Generalist_glc


title: Small-Intestine_8W-BS-rep1


title: Glc3_glc


title: Glc/Ac Glc Specialist_glc

value: Glc/Ac Glc Specialist


title: Glc/Ac Ac Specialist_glc

value: Glc/Ac Ac Specialist


title: Glc1_glc


title: Glc2_glc


title: WT_glc

value: wild-type


title: WT_xyl


title: iMGL nTGFb-2

city: Irvine

first: Ricardo

middle: Noel

last: Ramirez

state: California

address: 2300 Biological Sciences III

department: Developmental and Cell Biology

institute: University of California Irvine

description: iMGL without TGFB

data_processing:
RNA-seq reads were mapped to the hg38 reference genome using STAR (Dobin et al., 2013) aligner.
Reads were mapped to Gencode version 24 gene annotations using RSEM (Li and Dewey, 2011).
FPKM files were generated per sample using RSEM with gene ENSEMBL ID's and common gene names
Genome_build: hg38
Supplementary_files_format_and_content: *FPKM.txt: Tab-delimited text files include FPKMs, ENSEMBL ID's and common gene names.

source_name: human iPS microglia

growth_protocol: Cultured in custom serum-free media and fully defined conditions stated in manuscript.

extract_protocol:
RNeasy Qiagen extraction for RNA
Cells were harvested and washed three times with DPBS (1X) and stored in RNAlater, RNA preservation solution. RNA was extracted from all cell types using using RNeasy Mini Kit (Qiagen) following manufacturer’s guidelines. RNA integrity (RIN) was measured for all samples using the Bioanalzyer Agilent 2100 series. All sequencing libraries analyzed were generated from RNA samples measuring a RIN score ≥ 9. The Illumina TruSeq mRNA stranded protocol was used to obtain poly-A mRNA from all samples. A total of 200 ng of isolated mRNA was used to construct RNA-seq libraries. Libraries were quantified and normalized using the Library Quantification Kit from Kapa Biosystems and sequenced as paired-end 100 bp reads on the Illumina HiSeq 2500 platform.

treatment_protocol: iPS-derived cells were differentiated as stated in manuscript. Primary samples were isolated according as stated in manuscript.

tag: stimulus/treatment

value: TGFB withdrawl

tag: time (hours)

tag: cell type

value: iMGL


title: ALYREF-RIP-rep2

description: ALYREF RIP-seq of normal HeLa cells rep2.

data_processing:
Reads were aligned to hg19 genome using TopHat v2.0.9.
The ALYREF binding regions (peaks) were identified by using the MACS2 (version 2.0.10) with p value < 10-5.
Genome_build: hg19.

source_name: Human HeLa cells

extract_protocol:
Flag-ALYREF overexpressed cells pellets were resuspended with 2 volume of lysis buffer (150 mM KCl, 10 mM HEPES pH 7.6, 2 mM EDTA, 0.5% NP-40, 0.5 mM DTT, 1:100 protease inhibitor cocktail, 400 U/ml RNase inhibitor), and incubated at 4 °C for 30 min with rotation. Then the lysate was centrifuged at 15,000 g for 20 min. The anti-Flag M2 magnetic beads (Sigma, 10 µl per mg lysate) was washed with a 600 ml NT2 buffer (200 mM NaCl, 50 mM HEPES pH 7.6, 2 mM EDTA, 0.05% NP-40, 0.5 mM DTT, 200 U/ml RNase inhibitor) four times and then resuspended in 800 ml ice-cold NT2 buffer. Cell lysate was mixed with M2 beads and incubated at 4 °C for 4 hr with rotation. The beads were washed two times with 1 ml ice-cold NT2 buffer. Then the beads were subject to Micrococal nuclease (NEB) digestion (1:1,000,000 dilution) for 8 min at 37°C. The beads were cooled on ice immediately for 5 min and washed two times with 1 ml ice-cold 1× PNK+EGTA buffer (50 mM Tris-HCl pH 7.5, 20 mM EDTA, 0.05% NP-40, 200 U/ml RNase inhibitor) and two times with 1 ml ice-cold 1× PK buffer (50 mM NaCl, 100 mM Tris-HCl pH 7.5, 10 mM EDTA, 0.2% SDS, 200 U/ml RNase inhibitor). Then the beads were digested with 200 μl pre-heated (20 min at 50°C) Proteinase K solution (4 mg/ml) for 40 min at 50°C with rotation at 2000 rpm/min. After centrifuge at top speed for 5 min, the supernatant was transferred to a new 1.5 ml tube and isolated the RNAs with equal volume Acid-Phenol: Chloroform, pH 4.5 (Ambion). The RNAs were subjected to RIP seq.
Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2500 in paired-read mode, creating reads with a length of 125 bp.

value: HeLa

tag: rip antibody

value: ALYREF (Sigma, Cat# A2220, lot# SLBN7698V)

value: carcinoma cervical


title: iMGL nTGFb-3

description: iMGL without TGFB


title: iMGL nTGFb-1

description: iMGL without TGFB


title: ALYREF-RIP-rep1

description: ALYREF RIP-seq of normal HeLa cells rep1.


title: ALYREF-RIP-BS-rep1

description: RNA-BisSeq for ALYREF RIP in normal HeLa cells rep1.

data_processing:
Raw Reads were stripped of adaptor sequence and removed low quality bases using Trimmomatic, clean reads were aligned to the hg19 genome assembly using bismark
The m5C sites were called by bismark.
Genome_build: hg19
Supplementary_files_format_and_content: m5C_sites_in_ALYREF-RIP.xls

extract_protocol:
Flag-ALYREF overexpressed cells pellets were resuspended with 2 volume of lysis buffer (150 mM KCl, 10 mM HEPES pH 7.6, 2 mM EDTA, 0.5% NP-40, 0.5 mM DTT, 1:100 protease inhibitor cocktail, 400 U/ml RNase inhibitor), and incubated at 4 °C for 30 min with rotation. Then the lysate was centrifuged at 15,000 g for 20 min. The anti-Flag M2 magnetic beads (Sigma, 10 µl per mg lysate) was washed with a 600 ml NT2 buffer (200 mM NaCl, 50 mM HEPES pH 7.6, 2 mM EDTA, 0.05% NP-40, 0.5 mM DTT, 200 U/ml RNase inhibitor) four times and then resuspended in 800 ml ice-cold NT2 buffer. Cell lysate was mixed with M2 beads and incubated at 4 °C for 4 hr with rotation. The beads were washed two times with 1 ml ice-cold NT2 buffer. Then the beads were subject to Micrococal nuclease (NEB) digestion (1:1,000,000 dilution) for 8 min at 37°C. The beads were cooled on ice immediately for 5 min and washed two times with 1 ml ice-cold 1× PNK+EGTA buffer (50 mM Tris-HCl pH 7.5, 20 mM EDTA, 0.05% NP-40, 200 U/ml RNase inhibitor) and two times with 1 ml ice-cold 1× PK buffer (50 mM NaCl, 100 mM Tris-HCl pH 7.5, 10 mM EDTA, 0.2% SDS, 200 U/ml RNase inhibitor). Then the beads were digested with 200 μl pre-heated (20 min at 50°C) Proteinase K solution (4 mg/ml) for 40 min at 50°C with rotation at 2000 rpm/min. After centrifuge at top speed for 5 min, the supernatant was transferred to a new 1.5 ml tube and isolated the RNAs with equal volume Acid-Phenol: Chloroform, pH 4.5 (Ambion). The RNAs were subjected to RNA-BisSeq.
Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2500 in paired-read mode, creating reads with a length of 125 bp.


title: HeLa-siNSUN2-BS-rep2

description:
bisulfite treated mRNA
NSUN2 deficient HeLa cells rep2
Human_m5C_sites_information.xls


title: HeLa-siNSUN2-BS-rep1

description:
bisulfite treated mRNA
NSUN2 deficient HeLa cells rep1
Human_m5C_sites_information.xls


title: ALYREF-RIP-BS-rep2

description: RNA-BisSeq for ALYREF RIP in normal HeLa cells rep2.


title: HeLa-siCTRL-BS-rep2

description:
bisulfite treated mRNA
normal  HeLa cells rep2
Human_m5C_sites_information.xls

value: siCTRL


title: A3

data_processing:
RNA-seq reads were mapped to the hg38 reference genome using STAR (Dobin et al., 2013) aligner.
Reads were mapped to GENCODE version 24 gene annotations using RSEM (Li and Dewey, 2011).
FPKM files were generated per sample using RSEM with gene ENSEMBL ID's and common gene names.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *FPKM.txt: Tab-delimited text files include FPKMs, ENSEMBL ID's and common gene names.

source_name: Fetal microglia

extract_protocol:
Cells were harvested and washed three times with DPBS (1X) and stored in RNAlater, RNA preservation solution. RNA was extracted from all cell types using RNeasy Mini Kit (Qiagen) following manufacturer's guidelines. RNA integrity (RIN) was measured for all samples using the Bioanalyzer Agilent 2100 series.
All sequencing libraries analyzed were generated from RNA samples measuring a RIN score ≥ 9. The Illumina TruSeq mRNA stranded protocol was used to obtain poly-A mRNA from all samples. A total of 200 ng of isolated mRNA was used to construct RNA-seq libraries. Libraries were quantified and normalized using the Library Quantification Kit from Kapa Biosystems and sequenced as paired-end 100 bp reads on the Illumina HiSeq 2500 platform.

treatment_protocol: iPS-derived cells were differentiated as stated in manuscript. Primary samples were isolated as stated in manuscript.

value: Fetal microglia


title: A18

source_name: Adult microglia

value: Adult microglia


title: A16


title: A7


title: A2


title: A15


title: IM-3

source_name: Monocytes


title: S22

source_name: Dendritic cells

value: Myeloid dendritic cells


title: S8


title: HC-1

source_name: iPS microglia

value: Rat hippocampal neurons


title: HC-3


title: S25


title: HC-2


title: IM-2


title: M-3


title: IM-4


title: HC-4


title: iPS7022

source_name: iPS

value: iPS


title: HC-6


title: M-2


title: iPS6160


title: iPS10203


title: IM-1


title: HeLa-siCTRL-BS-rep1

description: RNA m5C data of normal  HeLa cells rep1.

data_processing:
Raw Reads were stripped of adaptor sequence and removed low quality bases using Trimmomatic, clean reads were aligned to the hg19 genome assembly using bismark.
The m5C sites were called by bismark.
Genome_build: hg19.
Supplementary_files_format_and_content: Human_m5C_sites_information.xls.


title: M-5


title: M-4


title: M-1


title: HC-5


title: iHPC7028

source_name: iHPC

value: iHPC


title: iPS7028


title: HPCCDI


title: wt_I_Ly6Cint

city: REHOVOT

first: Steffen

last: Jung

address: Herzl

department: Immunology and Regenerative Biology

country: Israel

institute: The Weizmann Institute of Science

description:
processed data file:
Expression_data.txt

data_processing:
Illumina bcl2fastq software used for basecalling.
Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1. Barcode is of size 7
alignment: hisat 0.1.5  with deafult parameters
create tag directory using makeTagDirectory from HOMER tools (http://homer.salk.edu/homer/ngs/)
HOMER, quantifying RNA expression in genes: analyzeRepeats.pl rna mm9 -d <List of tag dir> -count exons -condenseGenes -strand + -norm 1e7
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

source_name: Freshly isolated blood monocyte

extract_protocol:
Enzymatic digestion and gradient seperation. Antibodies used throughout the research are: CD11b (clone M1/70),  CD115 (clone AFS98), Ly6C/G (clone RB6-8C5), Ly6C (clone AL21), Ly6G (clone H129.19), CD4 (clone H129.19), CD45 (clone 30F11),  CD3 (clone 145-2C11) , CD19 (clone 1D3/CD19), NK1.1 (clone PK136).
3' end mRNA libraries were prepared for sequencing using a method developed at Dr. Ido Amit's lab, Weizmann Institute of Science
3' RNA-seq for digital gene expression quantitation

treatment_protocol:
FACS sorted cells
Steady state untreated cells

value: blood

tag: cell type origin

value: Freshly isolated blood monocyte

tag: selection marker for facs sorting

value: CD11b+, CD115+, Ly6C/G+/-, TCRbeta -


title: wt_I_Ly6C_M


title: WT 8weeks plus TNF H3K4me3-Seq replicate 3

city: Vari

first: George

last: Kollias

address: 34 Fleming Street

department: Institute of Immunology/Department of Physiology, School of Medicine

country: Greece

institute: BSRC "Alexander Fleming"/National and Kapodistrian University of Athens

data_processing:
RNA-seq samples were analysed with the tophat-cufflinks pipeline (Trapnell C et al., Nat Protoc 2012, Kim D et al., Genome Biol 2013, Trapnell C et al.,  Bioinformatics 2009)
Reads were mapped to the mm9 genome with tophat2. Transcripts were assembled using cufflinks. Final transcriptome assembly was performed with cuffmerge and differential expression was identified with cuffdiff.
MethylCap- and H3K4me3-seq reads were mapped using the BWA tool (Li H et al., Bioinformatics 2009)
Differential Methylated and H3K4me3 marked regions were extracted with the use of diffReps (Shen L et al., PLoS One 2013)
The default normalisation procedure of diffReps and windows of 500 bases for MethylCap-seq and 1000 bases for H3K4me3-seq were used for the analyses.
Genome_build: mm9
Supplementary_files_format_and_content: Processed/H3K4me3-Seq/3weeks.annotated is the differential H3K4me3 analysis output of diffReps, annotated according to the position of the closest gene. It includes all the results of the Tg197/WT H3K4me3-Seq comparison(3 weeks).
Supplementary_files_format_and_content: Processed/H3K4me3-Seq/8weeks.annotated  is the differential H3K4me3 analysis output of diffReps, annotated according to the position of the closest gene. It includes all the results of the Tg197/WT H3K4me3-Seq comparison(8 weeks).
Supplementary_files_format_and_content: Processed/H3K4me3-Seq/11weeks.annotated is the differential H3K4me3 analysis output of diffReps, annotated according to the position of the closest gene. It includes all the results of the Tg197/WT H3K4me3-Seq comparison(11 weeks).
Supplementary_files_format_and_content: Processed/H3K4me3-Seq/8weekstnf.annotated  is the differential H3K4me3 analysis output of diffReps, annotated according to the position of the closest gene. It includes all the results of the WTplusTNF/WT H3K4me3-Seq comparison(8 weeks).

source_name: Synovial Fibroblasts

extract_protocol:
RNA was extracted from mouse SFs using the Absolutely RNA Miniprep Kit (Agilent Technologies) and from human SFs using the miRNeasy Mini kit (Qiagen). DNA was extracted from mouse SFs using the PureLink Genomic DNA Mini Kit (Invitrogen). In order to enrich for methylated DNA, the MethylMiner DNA Enrichment Kit from Invitrogen was used as per the manufacturer’s instructions. DNA was firstly fragmented by sonication to an average size of 250 bp. Then enrichment was performed with a double elution (high and low salt) in order to capture both sparsely- and densely-methylated DNA; fractions were combined in the end. To enrich for H3K4me3, DNA was processed using the iDeal ChIP-seq Kit (Diagenode) in combination with a ChIP-grade H3K4me3 antibody (Diagenode), as per the manufacturer’s instructions. Chromatin was firstly sheared by sonication using a Bioruptor (Diagenode) and then subjected to the H3K4me3 enrichment protocol with a minor modification: after performing an RNase I digestion for 30 min at 37oC, the de-crosslinked DNA was eluted using the QIAquick PCR Purification Kit (Qiagen). Enrichment (in comparison to a non-enriched input control) was confirmed by quantitative PCR.
All library preparations, next generation sequencing and quality control steps were performed by the McGill University and Genome Quebec Innovation Centre. More specifically, for RNA-seq, TruSeq RNA libraries were prepared and samples were run in an Illumina HiSeq2000 platform using a 100 bp paired-end setup. For MethylCap-seq, TruSeq genomic DNA libraries were prepared and samples were run in an Illumina HiSeq platform using a 100 bp paired-end setup. For ChIP-seq, TruSeq genomic DNA libraries were prepared and samples were run in an Illumina HiSeq platform using a 100 bp paired-end setup.

value: Synovial Fibroblasts

tag: passages

value: CBA x C57BL/6J

tag: genotype

value: wild type

tag: chip antibody

value: H3K4me3 (Diagenode)


title: WT 8weeks plus TNF H3K4me3-Seq replicate 1

description: Processed/H3K4me3-Seq/8weekstnf.annotated

tag: strain


title: Tg197 11weeks H3K4me3-Seq replicate 1


title: Tg197 8weeks H3K4me3-Seq replicate 3


title: WT 11weeks H3K4me3-Seq replicate 1


title: Tg197 11weeks H3K4me3-Seq replicate 2


title: WT 11weeks H3K4me3-Seq replicate 2


title: WT 8weeks H3K4me3-Seq replicate 3

description:
Processed/H3K4me3-Seq/8weeks.annotated
Processed/H3K4me3-Seq/8weekstnf.annotated


title: WT 8weeks H3K4me3-Seq replicate 2


title: WT 8weeks H3K4me3-Seq replicate 1


title: wt_II_Ly6Cint

tag: tissue


title: WT 11weeks H3K4me3-Seq replicate 3


title: Tg197 3weeks H3K4me3-Seq replicate 3


title: wt_II_Ly6C_P


title: WT 8weeks plus TNF H3K4me3-Seq replicate 2


title: Tg197 3weeks H3K4me3-Seq replicate 2


title: wt_II_Ly6C_M


title: Tg197 8weeks H3K4me3-Seq replicate 1


title: Tg197 3weeks H3K4me3-Seq replicate 1


title: WT 3weeks H3K4me3-Seq replicate 3


title: H3K4me3 Input

value: mixed


title: iHPC10318


title: Monocytes D

description:
processed data file:
Compare_monocytes.txt

source_name: Freshly isolated BM monocytes

value: Bone marrow

value: Freshly isolated BM monocytes


title: wt_I_Ly6C_P


title: Monocytes C


title: WT 3weeks H3K4me3-Seq replicate 2


title: WT 3weeks H3K4me3-Seq replicate 1


title: Monocytes A


title: WT_blood_Ly6C_P_II.M


title: WT 11weeks MethylCap-Seq replicate 2

data_processing:
RNA-seq samples were analysed with the tophat-cufflinks pipeline (Trapnell C et al., Nat Protoc 2012, Kim D et al., Genome Biol 2013, Trapnell C et al.,  Bioinformatics 2009)
Reads were mapped to the mm9 genome with tophat2. Transcripts were assembled using cufflinks. Final transcriptome assembly was performed with cuffmerge and differential expression was identified with cuffdiff.
MethylCap- and H3K4me3-seq reads were mapped using the BWA tool (Li H et al., Bioinformatics 2009)
Differential Methylated and H3K4me3 marked regions were extracted with the use of diffReps (Shen L et al., PLoS One 2013)
The default normalisation procedure of diffReps and windows of 500 bases for MethylCap-seq and 1000 bases for H3K4me3-seq were used for the analyses.
Genome_build: mm9
Supplementary_files_format_and_content: Processed/MethylCap-Seq/3weeks.annotated is the differential methylation analysis output of diffReps, annotated according to the position of the closest gene. It includes all the results of the Tg197/WT MethylCap-Seq comparison(3 weeks).
Supplementary_files_format_and_content: Processed/MethylCap-Seq/8weeks.annotated  is the differential methylation analysis output of diffReps, annotated according to the position of the closest gene. It includes all the results of the Tg197/WT MethylCap-Seq comparison(8 weeks).
Supplementary_files_format_and_content: Processed/MethylCap-Seq/11weeks.annotated is the differential methylation analysis output of diffReps, annotated according to the position of the closest gene. It includes all the results of the Tg197/WT MethylCap-Seq comparison(11 weeks).
Supplementary_files_format_and_content: Processed/MethylCap-Seq/8weekstnf.annotated  is the differential methylation analysis output of diffReps, annotated according to the position of the closest gene. It includes all the results of the WTplusTNF/WT MethylCap-Seq comparison(8 weeks).

tag: methylcap

value: Methylation (MethylMiner - Invitrogen)


title: Monocytes B


title: WT 11weeks MethylCap-Seq replicate 3

description: Processed/MethylCap-Seq/11weeks.annotated


title: Tg197 11weeks MethylCap-Seq replicate 1


title: Tg197 11weeks MethylCap-Seq replicate 2


title: WT 8weeks plus TNF MethylCap-Seq replicate 3

description: Processed/MethylCap-Seq/8weekstnf.annotated


title: WT_blood_Ly6C_M_II.M


title: Tg197 8weeks MethylCap-Seq replicate 3

description: Processed/MethylCap-Seq/8weeks.annotated


title: Tg197 11weeks MethylCap-Seq replicate 3


title: WT 8weeks plus TNF MethylCap-Seq replicate 1


title: Tg197 8weeks MethylCap-Seq replicate 2


title: MDP_II

source_name: Freshly isolated BM monocyte precursors

value: Freshly isolated BM monocyte precursors


title: Tg197 8weeks MethylCap-Seq replicate 1


title: Tg197 11weeks H3K4me3-Seq replicate 3


title: WT 8weeks MethylCap-Seq replicate 2

description:
Processed/MethylCap-Seq/8weeks.annotated
Processed/MethylCap-Seq/8weekstnf.annotated


title: WT_blood_Ly6C_M_I.M


title: WT 8weeks MethylCap-Seq replicate 3


title: MDP_I


title: Tg197 3weeks MethylCap-Seq replicate 3

description: Processed/MethylCap-Seq/3weeks.annotated


title: WT 8weeks MethylCap-Seq replicate 1


title: CMOPS_II


title: Tg197 3weeks MethylCap-Seq replicate 2


title: Tg197 8weeks H3K4me3-Seq replicate 2


title: CMOPS_I


title: Tg197 3weeks MethylCap-Seq replicate 1


title: WT 11weeks MethylCap-Seq replicate 1


title: WT 3weeks MethylCap-Seq replicate 3


title: WT 8weeks plus TNF MethylCap-Seq replicate 2


title: WT 3weeks MethylCap-Seq replicate 2


title: Tg197 11weeks RNA-Seq replicate 3

data_processing:
RNA-seq samples were analysed with the tophat-cufflinks pipeline (Trapnell C et al., Nat Protoc 2012, Kim D et al., Genome Biol 2013, Trapnell C et al.,  Bioinformatics 2009)
Reads were mapped to the mm9 genome with tophat2. Transcripts were assembled using cufflinks. Final transcriptome assembly was performed with cuffmerge and differential expression was identified with cuffdiff.
MethylCap- and H3K4me3-seq reads were mapped using the BWA tool (Li H et al., Bioinformatics 2009)
Differential Methylated and H3K4me3 marked regions were extracted with the use of diffReps (Shen L et al., PLoS One 2013)
The default normalisation procedure of diffReps and windows of 500 bases for MethylCap-seq and 1000 bases for H3K4me3-seq were used for the analyses.
Genome_build: mm9
Supplementary_files_format_and_content: Processed/RNA-Seq/3weeks.diff is the differential expression analysis output of cuffdiff. It includes all the results of the Tg197/WT RNA-Seq comparison(3 weeks).
Supplementary_files_format_and_content: Processed/RNA-Seq/8weeks.diff  is the differential expression analysis output of cuffdiff. It includes all the results of the Tg197/WT RNA-Seq comparison(8 weeks).
Supplementary_files_format_and_content: Processed/RNA-Seq/11weeks.diff is the differential expression analysis output of cuffdiff. It includes all the results of the Tg197/WT RNA-Seq comparison(11 weeks).
Supplementary_files_format_and_content: Processed/RNA-Seq/8weekstnf.diff  is the differential expression analysis output of cuffdiff. It includes all the results of the WTplusTNF/WT RNA-Seq comparison(8 weeks).


title: WT 3weeks MethylCap-Seq replicate 1

description:
Processed/RNA-Seq/3weeks.diff
Processed/MethylCap-Seq/3weeks.annotated


title: BM_Ly6C_int_I


title: BM_Ly6C_int_II


title: Tg197 11weeks RNA-Seq replicate 2


title: WT 11weeks RNA-Seq replicate 3


title: WT 11weeks RNA-Seq replicate 2


title: BM_Ly6C_P_I


title: Tg197 11weeks RNA-Seq replicate 1


title: WT 8weeks plus TNF RNA-Seq replicate 3

description:
Processed/RNA-Seq/8weekstnf.diff
Processed/H3K4me3-Seq/8weekstnf.annotated


title: WT 11weeks RNA-Seq replicate 1


title: WT 8weeks plus TNF RNA-Seq replicate 2


title: BM_Ly6C_P_II


title: spinal cord monocytes EAE day 9 A

source_name: Freshly isolated effector monocytes infiltrating the spinal cord

treatment_protocol:
FACS sorted cells
Cells isolated from MOG 35-55 immunized mice at day 9 after immunization

value: Spinal cord


title: spinal cord monocytes EAE day 9 B

value: Freshly isolated effector monocytes infiltrating the spinal cord


title: Tg197 8weeks RNA-Seq replicate 3


title: WT 8weeks plus TNF RNA-Seq replicate 1


title: Tg197 8weeks RNA-Seq replicate 2


title: Tg197 8weeks RNA-Seq replicate 1


title: ScreA_EMM_2

city: Hanover

first: Robert

last: Cramer

state: NH

address: 74 College St

department: Microbiology&Immunology

institute: Geisel School of Medicine at Dartmouth College

description:
RPKM.txt
CountTable.txt

data_processing:
Basecalls performed using RTA v2
Sequenced reads were mapped to the unmasked AF1163 genome using tophat v2.1.0 with parameters -p 8
Transcript abundances were estimated and annotated using cufflinks v2.1.0 and the Aspergillus_fumigatusa1163.CADRE.30.gtf annotation file with parameters -p 8 -G
A count table of raw counts of sequencing reads per transcript was generated using the summarizeOverlaps function in the GenomicRanges Biocounductor Package
RPKM normalized abundance values was calculated using DESeq2 following the DESeq2 provided vignette on Bioconductor
Genome_build: Aspergillus_fumigatusa1163.CADRE.30
Supplementary_files_format_and_content: A count table of raw counts of sequencing reads per transcript in a tab-delimited text file for all samples, and a matrix file of RPKM for normalized strains in a tab-delimited text file.

organism: Aspergillus fumigatus

source_name: Fungal mycelia

growth_protocol: Cultures of 1x10^6 conidia/mL were grown in 1% glucose minimal media for 16 hours at 37C with shaking at 250rpm, then mycelia were washed with steril H2O and transferred to fresh 1% glucose minimal media or 1% ethanol minimal media and incubated for 2 hours at 37C, 200rpm.

extract_protocol:
RNA was extracted from lyophilized mycelia using triazol reagent, then purified with Quiagen Rneasy columns. RNA was treated with DNAse to remove DNA contamination.
Library was prepared with Illumina’s TruSeq Directional polyA+ library prep kit following the manufacturer’s protocol, with TruSeqLT sequencing adapters/indices

value: creA::pyrG (CEA10 background)

tag: media

value: 1% Ethanol minimal media


title: Nup60-TAP_glucose_input

source_name: Cells

growth_protocol: Cells were grown overnight, shaking at 30C in YPD media (1% yeast extract, 2% peptone, 2% dextrose), or for "galactose" cultures, YP + 2% galactose. Fresh cultures were inoculated to OD600=0.1 in the same media and grown until OD600 ~ 0.8.

extract_protocol:
Crosslinked cell pellets were resuspended in 500 µl lysis buffer with 1x cOmplete Protease Inhibitor tablet (Roche, Basel, Switzerland), and then 700 µl of 500 µm acid-washed glass beads were added. The cells were vortexed for 12 minutes total, in cycles of 2 minutes shaking and 2 minutes resting on ice. The lysate was pelleted and resuspended in fresh lysis buffer, and then sonicated for 3x10 min runs on a Diagenode Bioruptor (Diagenode, Liège, Belgium), on high power with cycles of 30 seconds on and 30 seconds off, to an average of ~300 bp. The sonicate was cleared by centrifugation, and the resulting supernatant was split into an input aliquot (1/20 of IP volume) and two halves for the IP and mock-IP (BSA instead of antibody). For each sample, 5 ug of anti-TAP (Thermo Fisher Scientific, Waltham, MA; #CAB1001, Lot #RL240352) was used with 10 ul Dynabeads Protein A (Thermo). The antibody or BSA was incubated with pre-washed beads for 2 hours and then washed twice in fresh lysis buffer before being added to the lysate and then incubated overnight. After washing the beads four times in lysis buffer and eluting, the eluate was reverse crosslinked and then treated with RNase A and Proteinase K. DNA was purified using Zymo ChIP DNA Clean & Concentrator (Zymo Research, Irvine, CA) and eluted in 30 µl water.
ChIP-seq libraries were prepared using the Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences, Ann Arbor, MI), from equal volume pools of the biological replicates, either 1 ng total from input samples or 21 ul of total IP sample. Input and IP libraries were amplified for 6 and 7 cycles, respectively.

treatment_protocol: Cells were crosslinked by addition of 37% formaldehyde to 1% v/v and incubation at room temperature for 5 minutes, then quenched by addition of glycine to 150 mM and washed twice with Tris-buffered saline.

tag: growth conditions

value: exponential

tag: growth medium

value: YPD

tag: growth phase

tag: growth temperature


title: ScreA_EMM_1

description:
RPKM.txt
CountTable.txt


title: WT 8weeks RNA-Seq replicate 3

description:
Processed/RNA-Seq/8weeks.diff
Processed/RNA-Seq/8weekstnf.diff
Processed/H3K4me3-Seq/8weekstnf.annotated


title: WT 8weeks RNA-Seq replicate 2


title: WT_EMM_2

description:
RPKM.txt
CountTable.txt


title: Nup60-TAP_galactose_input

value: galactose

value: YP+galactose


title: Nup60-TAP_glucose_IP


title: Tg197 3weeks RNA-Seq replicate 3

value: Synovial Fibroblasts


title: WT 8weeks RNA-Seq replicate 1

value: CBA x C57BL/6J


title: SCreA_GMM_2

description:
RPKM.txt
CountTable.txt

value: 1% glucose minimal media


title: WT_EMM_1

description:
RPKM.txt
CountTable.txt


title: Nup60-TAP_galactose_IP


title: Tg197 3weeks RNA-Seq replicate 1


title: spinal cord monocytes EAE day 9 C


title: HeLa-siNSUN2-T-rep2

description: NSUN2 deficient HeLa cells rep2

data_processing:
Reads were aligned to the hg19 or mm10 genome assembly using TopHat v2.0.9
For each sample, reads counts of all genes were computed using HTSeq v0.5.3p9
Genome_build: hg19 or mm10
Supplementary_files_format_and_content: all-samples-reads-count.xls

tag: cell line

value: HeLa

tag: treatment

tag: age

value: carcinoma cervical


title: YMD3377_galactose_Sau3AI

description:
ScSu.32000.bed
Surep-rDNA.bed

data_processing:
Library strategy: HiC-Seq
Hi-C
Basecalls were converted to FASTQ using bcl2fastq 2.17
Sequencing reads were quality-trimmed (cutadapt -q 20) trimmed of adapter sequences and then trimmed up to the ligation junction (if present), excluding read pairs in which either read was shorter than 20 bp after trimming.
Reads were independently mapped using bowtie2 2.2.3 using the parameter set --very-sensitive. For interspecific hybrids, reads were mapped to a combined reference containing both species references, where if secondary mappings were present the best alignment must have a score ≥ 10 greater than the next best alignment. For intraspecific S. cerevisiae hybrids, reads were mapped separately to both strain references, keeping only read pairs mapping to both—perfectly to one reference and with ≥ 2 mutations including ≥ 1 substitution to the other. In both cases, only read pairs in which both reads mapped with MAPQ ≥ 30 were used.
PCR duplicates (with identical fragment start and end positions) were removed, as were read pairs mapping within 1 kb of each other or in the same restriction fragment, which represent either unligated or invalid ligation products.
The genome was then binned into 32 kb fragments (except the last fragment of each chromosome), and the number of read pairs mapping to each 32 kb genomic bin was counted based on the position of the restriction sites that were ligated together. Due to gaps in the reference genomes of S. uvarum, some repetitive sequences were only represented once and therefore artifactually mapped uniquely; therefore, reads mapping to annotated repetitive sequences were masked from further analysis. Similarly, gaps in the S. paradoxus reference led to mismapping of reads to the corresponding S. cerevisiae sequence; therefore, for S. cerevisiae x S. paradoxus libraries we masked regions in the S. cerevisiae genome where > 1 read from a S. paradoxus Hi-C library mapped, and vice versa. We took a similar approach to mask regions of the Y12 and DBVPG6044 references that were prone to mismapping, as estimated by haploid Y12 and DBVPG6044 Hi-C libraries. For knock-in experiments, the HAS1pr-TDA1pr region was masked to account for its altered genomic location. The resulting matrices were then normalized by excluding the diagonal (interactions within the same genomic bin), filtering out rows/columns with an average of less than 1 read per bin, and then multiplying each entry by the total number of read pairs divided by the column and row sums.
Genome_build: Saccharomyces cerevisiae R64.2.1 from SGD and Saccharomyces cerevisiae and Saccharomyces uvarum (bayanus var. uvarum) from saccharomycessensustricto.org, with minor modifications; Y12 and DBVPG6044 references generated by Pacbio sequencing
Supplementary_files_format_and_content: tab-delimited text files ending in "matrix.txt" include the raw read counts and normalized interaction frequencies for each pair of 32 kb genomic bins; those ending in "rowsums.txt" include the raw sums across each row of these matrices. BED files include either the genomic regions included in each matrix bin or those masked from the matrices.
ChIP-seq
Basecalls were converted to FASTQ using bcl2fastq 2.17
Sequencing reads were quality-trimmed (cutadapt -q 20), trimmed of adapter sequences, excluding read pairs in which either read was shorter than 28 bp after trimming.
Reads were mapped using bowtie2 2.2.3 using the parameter set --very-sensitive -X 2000
PCR duplicates (with identical fragment start and end positions) were removed.
Coverage across the genome was calculated using bedtools genomecov, using only read pairs with a minimum MAPQ score of 30.
Genome_build: sacCer3
Supplementary_files_format_and_content: bedgraph files of fragment coverage across the genome
RNA-seq
Basecalls were converted to FASTQ using bcl2fastq 2.17
Sequencing reads were quality-trimmed (cutadapt -q 20), trimmed of adapter sequences, excluding read pairs in which either read was shorter than 28 bp after trimming.
Reads were mapped using bowtie2 2.2.3 using the parameter set --very-sensitive -X 500
The number of read pairs with a minimum MAPQ score of 30 that overlap each gene uniquely were counted using HTSeq-count.
Genome_build: sacCer3
Supplementary_files_format_and_content: sacCer3_genes.gff are the gene annotations used; tab-delimited text files ending in "counts.txt" include the number of read pairs mapping to each gene.

organism: Saccharomyces cerevisiae x Saccharomyces uvarum

growth_protocol: Cells were grown overnight, shaking at 30C (room temperature for S. uvarum) in YPD media (1% yeast extract, 2% peptone, 2% dextrose), or for "raffinose" cultures, YP + 2% raffinose, or for "galactose" cultures, YP + 2% galactose. For non-saturated cultures, fresh cultures were inoculated to OD600=0.1 in the same media and grown until OD600 = 0.6-0.8.

extract_protocol:
Cells were lysed using glass beads and chromatin was extracted, digested using restriction enzyme Sau3AI or HindIII, gap-filled in using biotinylated dCTP, and ligated. Crosslinks were reversed and DNA was purified by phenol/chloroform extraction.
Libraries were prepared according to manufacturer's instructions using the KAPA Hyper Prep kit.

treatment_protocol: Cells were crosslinked by resuspension and incubation in 1% formaldehyde in PBS for 20 minutes at room temperature, and then quenched by addition of 1% solid glycine, incubation for 20 minutes, and a PBS wash. For nocodazole culture, media was supplemented with 15 ug/ml nocodazole and grown for an additional 2 hours prior to crosslinking.

tag: restriction enzyme


title: ScreA_GMM_1

description:
RPKM.txt
CountTable.txt


title: HeLa-siCTRL-T-rep2

description: normal  HeLa cells rep2

value: siCTRL


title: WT 3weeks RNA-Seq replicate 3

tag: cell type

value: wild type


title: HeLa-siNSUN2-T-rep1

description: NSUN2 deficient HeLa cells rep1


title: WT 3weeks RNA-Seq replicate 1


title: WT_GMM_1

description:
RPKM.txt
CountTable.txt


title: WT 3weeks RNA-Seq replicate 2


title: YMD3377_exponential_Sau3AI

description:
ScSu.32000.bed
Surep-rDNA.bed


title: YMD3377_saturated_Sau3AI

description:
ScSu.32000.bed
Surep-rDNA.bed

value: saturated


title: HeLa-siCTRL-T-rep1

description: normal  HeLa cells rep1


title: Tg197 3weeks RNA-Seq replicate 2


title: DP6_H2

status: Public on Apr 18 2017

first: Hanseul

last: Yang

address: 1230 York Avenue

institute: Rockefeller University

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse genome (mm10) using the Bowtie2 program (version 2.2.9).
The expression values of each gene were quantified as transcript per million (TPM) using RSEM (v1.2.30)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: Mouse back skin

extract_protocol:
Single bulge hair follicle stem cells, hair germ cells and basal hair bulb cells at indicated age were FACS-purified, collected into 96 well plates containing lysis buffer and stored in -80oC
Single cells were lyzed by incubating at 72oC for 3 min. Reverse transcription reaction and whole transcriptome amplification were perforemd according to Smart-seq2 protocol. The amplified cDNA libraries were purified by Ampure XP beads (Beckman Coulter), and tagmentation reaction was perforemd by Illumina Nextera XT DNA Library Prep Kit. The libraries were pooled and sequecned on Illumina Nextseq 500 with mid-output 75cycles paired-end mode.

tag: Sex

value: Male

tag: sorting markers

value: GFP, RFP, integrinα9, CD117


title: DP6_H3

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_H4

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_H9

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: WT_GMM_2

description:
RPKM.txt
CountTable.txt


title: DP6_H12

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_H11

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_H10

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_G8

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_G7

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_G6

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_H5

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_G3

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_G4

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_G1

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_G12

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_G2

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_H6

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_F3

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_F6

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_F9

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_F2

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_F1

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_F7

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_F4

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_F11

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_H1

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_E4

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_E8

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_F10

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_E6

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_E9

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_G5

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_E2

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_E11

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_G10

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_E12

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_E10

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_F8

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_D7

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_D8

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_D9

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_D6

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_D4

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_F12

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_D11

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_D2

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_D12

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_C8

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_D1

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_E7

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text


title: DP6_C9

description:
Ana6_DP_TPM.txt
mm10
tab-delimited text