title: Grow 5

status: Public on Nov 27 2018

city: San Antonio

first: Yidong

last: Chen

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

data_processing:
The raw sequencing data were trimmed and filtered using the vendor-supplied post-sequence procedures, and afterward were also filtered using a customized Perl script  that removed low-scoring sections of each read.
The  filtered reads were truncated based on similarity to library adaptor sequences using customized Perl scripts, followed by merging of overlapping paired-end reads using FLASH.
Filtered sequences were aligned using Salmon (version 0.3.1). Transcripts without a minimum of two reads in at least two samples were excluded using edgeR (version 3.14.0)  and matrixStats packages (version 0.50.2).
Genome_build: The mouse reference transcriptome (NCBI37/mm9)
Supplementary_files_format_and_content: A csv file. Each column corresponds to a sample and each row reports the estimates for the  number of reads mapped to a transcript.

source_name: Liver

growth_protocol: Mice were maintained in specific-pathogen-free conditions, including free of H. hepaticus.  Fed standard lab chow ad libitum, housed in microisolator topped cages, 14:10 light:dark cycles.

extract_protocol:
Tumors were snap frozen at collection and stored at -80oC.  RNA isolated Qiagen Rneasy Mini Prep Kit.
Illumina TruSeq RNA Library Prep Kit v2 was used to construct the library and was conducted by Beckman Coulter.

treatment_protocol: Normal liver mice were given i.p. injections of phosphate citrate buffer (pH 6.4) 5 consecutive days every 28 days for 6 cycles, or temozolomide (TMZ; 31 mg/kg body weight), or suberoylanilide hydroxamic acid (SAHA; 100mg/kg body weight),  or SAHA + TMZ (85 mg/kg body weight + 22mg/kg body weight), 5 consecutive days every 28 days for 6 cycles.

value: male

value: Liver tumor

tag: age

tag: tumor or normal

value: Tumor/Grow

tag: treatment

value: DMSO


title: Regress 3

type: SRA

state: Texas

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: Sex

tag: tissue

value: Tumor/Regress

value: TMZ


title: Grow 3

value: SAHA + TMZ


title: Regress 4


title: Regress 1


title: Grow 2


title: Regress 2

value: phosphate citrate buffer


title: Grow 1


title: Normal Liver 4

value: Liver

value: normal


title: Input_MEF

status: Public on Nov 28 2018

city: Naples

first: Stefano

last: Amente

address: via pansini, 5

department: Department of  Molecular Medicine and Medical Biotechnologies

country: Italy

institute: University of Naples "FEDERICO II"

description: Normal growing MEF cells

library_source: genomic

data_processing:
Alignments were performed with BWA  to hg18 or mm9 using default parameters.
The 8-oxodG peaks were identified from uniquely mapped reads without duplicates using MACS and the p-value cutoff used for peak detection was 1e-5. The gH2AX peaks were identified from uniquely mapped reads without duplicates using SICER and FDR 0.01 was used as cutoff.
Genome_build: hg18 and mm9
Supplementary_files_format_and_content: SAMtools and BEDtools were used for filtering steps and file formats conversion.

molecule: genomic DNA

source_name: mouse embryonic fibroblast

growth_protocol: MCF10A cells were cultured in 1:1 mixture DMEM-F12 supplemented with 5% horse serum, 10 µg/ml insulin, 0,5 µg/ml hydrocortisone, 100 ng/ml cholera enterotoxin, and 20 ng/ml epidermal growth factor, and incubated at 37°C in humidified atmosphere with 5% CO2. Mouse embryonic fibroblasts MEF (3T9-MycER) were grown in DMEM medium supplemented with 10% serum, penicillin/streptomycin and 2 mM L-Gln.

extract_protocol:
Genomic DNA from MCF10A cells or from growing MEFs was extracted by using Dneasy Blood&Tissue kit. Genomic DNA were sonicated and immunoprecipitated with antibodies anti 8-oxodG O/N. Eluted DNA was processed for library preparation. For ChIp_Seq anti gH2AX, lysates were clarified from sonicasted nuclei and histone-DNA complexes were isolated with specific antibody.
Libraries were prepared according to Illumina's instructions

tag: cell line

value: MEF

tag: cell type

value: mouse embryonic fibroblast

tag: chip antibody


title: Normal Liver 2


title: Grow 6

value: SAHA


title: Normal Liver 1


title: Normal Liver 3


title: Grow 4


title: BCORL1_Q1076H A375 cells #3

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

institute: Ospedale San Raffaele

data_processing:
Image processing and basecall was performed using the Illumina Real Time Analysis Software.
Fastq files were aligned to the human genome (GRCh38/hg39) by using STAR (Dobin et al., 2013), a splice junction mapper for RNA-Seq data, together with the corresponding splice junctions Ensembl GTF annotation.
Differential gene expression and statistical analysis were performed with DESeq2 (Love et al., 2014) and SPSS (IBM), respectively.
Functional enrichment was performed with DAVID (Huang et al., 2009). Gene expression heatmap and unsupervised hierarchical clustering were performed with GENE-E (Broad Institute).
Genome_build: hg38
Supplementary_files_format_and_content: tab files with default STAR output. column 1: gene ID; column 2: counts for unstranded RNA-seq; column 3: counts for the 1st read strand aligned with RNA (htseq-count option -s yes); column 4: counts for the 2nd read strand aligned with RNA (htseq-count option -s reverse)

organism: Homo sapiens

source_name: A375 cell line

growth_protocol: ATCC-formulated Dulbecco's Modified Eagle's Medium, with fetal bovine serum to a final concentration of 10%.

extract_protocol:
RNA libraries were generated starting from 1 microgram of total RNA extracted from 5*106 cells using TRIzol (Invitrogen, Life technologies). RNA quality was assessed by using a Tape Station instrument (Agilent).
RNA was processed according to the TruSeq Stranded mRNA Library Prep Kit protocol. The libraries were sequenced on an Illumina HiSeq 3000 with 76bp paired-end reads using Illumina TruSeq technology.

tag: genotype/variation

value: overexpression of BCORL1_Q1076H


title: BCORL1_Q1076H A375 cells #4


title: BCORL1_Q1076H A375 cells #2


title: BCORL1_wt A375 cells #3

value: overexpression of BCORL1_wt


title: BCORL1_wt A375 cells #4


title: BCORL1_wt A375 cells #2


title: 19: HiC_S1

city: La Jolla

first: Ramya

last: Raviram

state: CA

address: 9500 Gilman Drive

institute: University of California San Diego

data_processing:
Data was processed using Hicup
Genome_build: hg19
Supplementary_files_format_and_content: .hic file (Juicebox)

source_name: HeLa

growth_protocol: HeLa F2 cells were generous gifts from Cedric Feschotte and Edward Chuong.

extract_protocol:
Following treatment cells were fixed with Formaldehyde for Hi-C.
Nuclei were obtained after lysis on ice for 30 minutes with 10 mM Tris-HCl pH8, 10 mM NaCl, 0.2% Igepal CA-630 and 1 Roche Complete EDTA-free tablet. After 10 minutes treatment with 0.1% SDS at 37°C, nuclei were incubated with Triton 10% for 10 minutes also at 37°C. Nuclei were then suspended in 1X DpnII buffer (NEB) and chromatin digested overnight with 400U of DpnII (NEB) at 37°C. Following an additional 4-hour incubation with extra 400U of DpnII, digestion was stopped by 65°C incubation for 30 minutes. DNA ends were then filled in with dATP-Biotin using polymerase klenow for 60 minutes at 37°C. Ligation was performed in-situ overnight (with nuclei intact) using 2000U of T4 DNA ligase from NEB (M0202) at 16°C. Decrosslinking was performed overnight with Proteinase K at 65°C. 40 mg of unligated biotin ends were removed by incubation with T4 DNA polymerase for 4 hours at 20°C. DNA fragments were then sonicated using an LE Covaris 220 instrument using 450 PIP, 30% duty factor, 200 cycles per burst for 60 seconds. Following sonication, DNA fragments were end-repaired using T4 DNA polymerase, T4 PNK and Klenow polymerase (all from NEB). DNA fragments were then bound to Streptavidin C1 beads and washed following manufacturer’s instructions and using 150 ml per 2.5 mg of sonicated DNA. A-tailing and adaptor ligation was then performed with DNA fragments bound to beads. A-tailing was done using Klenow polymerase without 3’ exonuclease activity. For ligation, adaptors from the NEBNext DNA library prep reagent set (E6040) were used and ligated overnight. Following ligation, enzyme USER treatment was used to open the stem loop. Hi-C library amplification was then amplified using 7 PCR cycles, with Phusion polymerase and PCR primers from NEBNext Multiplex Oligos for Illumina (E7335) and resulted in approximately 1 mg of Hi-C material.

treatment_protocol: Cells were treated for 24 hours with 1000 U/ml of recombinant human IFNg (cat# 11500-2, PBL assay science).

value: HeLa F2 cells


title: Parental A375 cells #4

value: parental


title: Parental A375 cells #3


title: Parental A375 cells #2


title: bou T-DNA insertion line, end of night [2_BOU_EON_1]

city: Düsseldorf

first: Andreas

middle: PM

last: Weber

address: Universitätsstr. 1

department: Institute for Plant Biochemistry

country: Germany

institute: Heinrich-Heine-University

data_processing:
Illumina Casava-1.9software used for basecalling.
The software kallisto (v 0.43.0) was used for quantification with the Arabidopsis thaliana genome as a reference (TAIR10 cDNA). The resulting normalized counts (transcripts per million, tpm) were used for downstream analyses.
Kallisto was run with 30 bootstrapping replications. The resulting .h5 files were fed forward into differential gene expression analysis using sleuth (v 0.28.1).
Means and standard deviation of tpm of biological triplicates group were calculated.
Supplementary_files_format_and_content: Tab-separated table (.tsv) file including Arabidopsis Gene Identifier (AGI) and TAIR10 description, raw estimated counts (kallisto), tpm (kallisto) for each sample and mean and standard deviation of tpm for biological triplicates, sleuth results of differential gene expression comparing each of the mutant lines against the wildtype at the respective time of sampling

organism: Arabidopsis thaliana

source_name: bou T-DNA insertion line, end of night

extract_protocol:
Mature leaves were harvested and immediately frozen in liquid nitrogen. RNA was isolated from ground tissue using the Qiagen RNeasy plant mini kit. Residues of DNA were removed with DNase (New England Biolabs). RNA integrity, sequencing library and fragment size were analyzed on a 2100 Bioanalyzer (Agilent). Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina), and quantified with a Qubit 2.0 (Invitrogen).
Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina). Samples were multiplexed with 12 libraries per lane and sequenced in paired-end mode (150 bp read length) on an Illumina HiSeq 3000 platform.

value: Leaf

tag: genotype

value: bou T-DNA insertion line

tag: time of sampling

value: end of night


title: bou T-DNA insertion line, end of night [2_BOU_EON_3]


title: Wildtype, end of night [1_WT_EON_3]

source_name: Wildtype, end of night

value: Wildtype


title: Wildtype, end of night [1_WT_EON_2]


title: bou T-DNA insertion line, end of night [2_BOU_EON_2]


title: Wildtype, end of night [1_WT_EON_1]


title: bou T-DNA insertion line, beginning of day [2_BOU_BOD_3]

source_name: bou T-DNA insertion line, end of day

value: end of day


title: adult 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: adult rep2

data_processing:
5’ and 3’ low-quality ends of raw reads were trimmed using Fastx-tools. Adaptor sequences were also trimmed using Fastx-tools. Reads with over 5 Ns or the length of which is shorter than 80bp were removed. The remained pair-end reads were kept as clean reads, which were used for de novo assembly.
Trinity (v2.0.6) software were used to assemble the clean reads with default parameters. After assembly, the contigs longer than 200 bases were used for subsequent analysis.
Supplementary_files_format_and_content: fpkm

organism: Nesidiocoris tenuis

source_name: adult rep2

extract_protocol:
RNA was isolated from adults using the TRIzol (Invitrogen) reagent by following the company manual. Poly(A) mRNA was isolated from 20 µl total RNA using Oligo (dT) magnetic beads and then was broken into short fragments (about 200bp) in the presence of fragmentation buffer at 94 °C for 5 min.
The short fragments (about 200 bp) were used as templates for first-strand cDNA synthesis using random hexamer-primers. Subsequently, second-strand cDNAs were synthesized using buffer, dNTPs, RNaseH, and DNA polymerase I. After purification of short fragments, samples were then washed with EB buffer for end reparation and single nucleotide adenine addition. Finally, the short fragments were connected to sequencing adapters. Suitable fragments (about 200bp), as judged by agarose gel electrophoresis, were enriched with PCR amplification to prepare the sequencing library.

value: adult

value: whole body


title: bou T-DNA insertion line, beginning of day [2_BOU_BOD_1]


title: adult rep1

description: adult rep1

source_name: adult rep1


title: Wildtype, beginning of day [1_WT_BOD_1]

source_name: Wildtype, end of day


title: bou T-DNA insertion line, beginning of day [2_BOU_BOD_2]


title: adult rep3

description: adult rep3

source_name: adult rep3


title: Wildtype, beginning of day [1_WT_BOD_3]


title: CB_20M

status: Public on Nov 26 2018

city: wuhan

first: dong

last: chen

state: Hubei

address: GaoXin 2nd Road

institute: ablife

description: Rnase R treated circular RNA

data_processing:
After reads were obtained from sequencing. Cutadapt (Martin, 2011) was used to trim adaptors (with 10% error rate) and low quality bases (less than 16). Reads that were less than 16nt in both ends were discarded.
Before prediction, we used bwa mem (Li and Durbin, 2010) method to align reads to the Rhesus Macaque (Rhesus Macaque Genome et al., 2007) reference genome in local mode (with parameters: -k 19 -T 19).
After alignment, CIRI software (Hoffmann et al., 2014) was used to predict circRNAs in macaque brain samples. Candidate circRNAs with no less than two head-to-tail junction reads were preserved.
After obtaining the circRNAs, TPM was calculated for each circRNA candidate. CircRNAs are constituted by two parts by CIRI: head-to-tail junction part and non-junction part. We set head-to-tail junctions reads as S, non-junction reads as N, and total circRNAs reads in each sample as T. The TPM value was calculated by the following formula:  TPM = (S*2 + N)*1000000/T
Genome_build: MMUL 1.0
Supplementary_files_format_and_content: tab-delimited text file includes circRNA TPM values for each Sample

organism: Macaca mulatta

source_name: Cerebellar cortex

growth_protocol: [animal protocol] Eight socially-housed healthy rhesus macaques used in this study were selected at random and were equally divided into two groups according to age (10 and 20 years respectively). Each group included 4 monkeys, with 2 males and 2 females. These two groups were euthanized by injected with excessive pentobarbital sodium (80 mg/kg, i.v.) and the monkeys’ carotid artery was cut to allow the blood drain. And then the whole brain was taken out and the corresponding brain tissue (4mm×2mm×2mm) was sampled with sterilized ophthalmic scissors and tweezers. According to a widely used macaque brain atlas and brainmaps (http://www. Brainmaps.org),the prefrontal cortex was sampled at the main sulci, the posterior cingulate cortex was sampled at the Brodmann’s area 23, the temporal cortex was sampled at the superior temporal gyrus, the parietal cortex was sampled at the middle sylvian fissure, the occipital cortex was sampled at the V1, and the cerebellar cortex was sampled at the cauda cerebelli. The hippocampus (including CA1 and dentate gyrus) was also sampled. All the collected samples were washed with RNA later solution (AM7021, Ambion, USA) and put in freezing tubes to store at liquid nitrogen temperature. All these operations above were completed inside one hour after the monkeys died. All animal procedures were in strict accordance with the guidelines for the National Care and Use of Animals approved by the National Animal Research Authority (P.R. China) and the Institutional Animal Care and Use Committee (IACUC) of the Kunming Institute of Zoology of Chinese Academy of Sciences.

extract_protocol:
For each sample, 10μg of total RNA was used for cirRNA-seq library preparation.Total RNA was treated with RQ1 DNase (Progema) to remove genomic DNA. A large proportion of mRNA was captured by oligo dT(25), and remaining RNA was purified with Ampure XP Beads. Ribosomal RNA was depleted away by RiboMinus Kit. Linear RNA (including residual rRNA, residual mRNA, and so on) was digested by RNase R.
CircRNA was iron fragmented at 95℃ followed by end repair and 5’ adaptor ligation. Then reverse transcription was performed with RT primer harboring 3’ adaptor sequence and randomized hexamer. The cDNAs were purified and amplified, then PCR products corresponding to 300~500bp were selectively captured and quantified. Libraries were stored at -70 C until used for sequencing.  For high-throughput sequencing, the libraries were prepared following the manufacture’s instructions and applied to Illumina NextSeq500 system with 150x2 paired-end type by ABlife. Inc (Wuhan, China).

value: 20 years

value: brain

tag: tissue region

value: Cerebellar cortex

value: Male


title: DG_10F

description: Rnase R treated circular RNA

source_name: Dentate Gyms

treatment_protocol: All the collected samples were washed with RNA later solution (AM7021, Ambion, USA) and put in freezing tubes to store at liquid nitrogen temperature. All these operations above were completed inside one hour after the monkeys died. All animal procedures were in strict accordance with the guidelines for the National Care and Use of Animals approved by the National Animal Research Authority (P.R. China) and the Institutional Animal Care and Use Committee (IACUC) of the Kunming Institute of Zoology of Chinese Academy of Sciences.

value: 10 years

value: Dentate Gyms

value: Female


title: DG_10M

description: Rnase R treated circular RNA


title: DG_20F

description: Rnase R treated circular RNA


title: CB_10F

description: Rnase R treated circular RNA


title: CB_10M

description: Rnase R treated circular RNA


title: CB_20F

description: Rnase R treated circular RNA


title: DG_20M

description: Rnase R treated circular RNA


title: CA1_20M

description: Rnase R treated circular RNA

source_name: Cornu Ammonis 1

value: Cornu Ammonis 1


title: CA1_10M

description: Rnase R treated circular RNA


title: CA1_20F

description: Rnase R treated circular RNA


title: OC_20M

description: Rnase R treated circular RNA

source_name: Occipital Cortex

value: Occipital Cortex


title: CA1_10F

description: Rnase R treated circular RNA


title: OC_10M

description: Rnase R treated circular RNA


title: OC_20F

description: Rnase R treated circular RNA


title: OC_10F

description: Rnase R treated circular RNA


title: PC_20M

description: Rnase R treated circular RNA

source_name: Parietal Cortex

value: Parietal Cortex


title: PC_10M

description: Rnase R treated circular RNA


title: Wildtype, beginning of day [1_WT_BOD_2]

value: Leaf


title: PC_10F

description: Rnase R treated circular RNA


title: PC_20F

description: Rnase R treated circular RNA


title: TC_20F

description: Rnase R treated circular RNA

source_name: Temporal Cortex

value: Temporal Cortex


title: TC_10M

description: Rnase R treated circular RNA


title: PCC_20M

description: Rnase R treated circular RNA

source_name: Posterior Cingulate Cortex

value: Posterior Cingulate Cortex


title: TC_10F

description: Rnase R treated circular RNA


title: PCC_20F

description: Rnase R treated circular RNA


title: PCC_10F

description: Rnase R treated circular RNA


title: PFC_20F

description: Rnase R treated circular RNA

source_name: Prefrontal cortex

value: Prefrontal cortex


title: PFC_10M

description: Rnase R treated circular RNA


title: PCC_10M

description: Rnase R treated circular RNA


title: SMMN_4

city: Bochum

first: Minou

last: Nowrousian

address: Universitaetsstr. 150

department: Molecular and Cellular Botany

institute: Ruhr-University Bochum

data_processing:
Reads were trimmed for low quality bases, and reads with undefined bases ("N") were removed as described in Teichert et al. 2012, BMC Genomics 13: 511
Reads were mapped to the Sordaria macrospora genome using Bowtie2 (v 2.2.6) (Langmead B and Salzberg S, 2012, Nature Methods 9:357-359) and converted to bed files with bedtools (Quinlan AR, 2014, Curr Protoc Bioinformatics 47:11.12.1-34) and samtools (Li et al., 2009, Bioinformatics 25:2078-2079)
Analysis of nucleosome distribution was done with iNPS based on bed files (Chen et al., 2014, Nat Commun 5:4909). Downstream analyses were performed with custom-written Perl scripts.
Genome_build: Sordaria macrospora genome version 02, accession numbers CABT02000001-CABT02001583
Supplementary_files_format_and_content: tab-delimited text files (wiggle format) for genome-wide nucleosome distribution for each sample (nucleosome density distribution as calculated by iNPS)

organism: Sordaria macrospora

source_name: asf1 replicate 2

growth_protocol: For micrococcal nuclease (MNase) digestion, samples were grown in BMM medium for 3d at 25 °C in surface cultures to induce sexual development.

extract_protocol:
After MNase digestion, DNA was purified by phenol/chloroform extraction and RNase-treated.
DNA libraries from MNase-treated samples were used for library construction for sequencing in a HiSeq using standard Illumina protocols.

treatment_protocol: Mycelia were harvested, ground in liquid nitrogen, and digested with MNase (3 Units per gramm mycelium, 10 min at 37 °C).

value: total sexual mycelium


title: SMMN_2

source_name: wild type replicate 2

value: wild type


title: SMMN_1

source_name: wild type replicate 1


title: SM26: pro44 protoperithecia replicate 1

description: pro44 protoperithecia replicate 1

data_processing:
reads were trimmed for low quality bases, and reads with undefined bases ("N") were removed as described in Teichert et al. 2012, BMC Genomics 13: 511
read counts and expression ratios for annotated gene models were determined with DESeq (Anders S, Huber W 2010, Genome Biol 11: R106) and LOX 1.8 (Zhang et al. 2010, Bioinf 26: 1918-1919) as described in Teichert et al. 2012, BMC Genomics 13:511.
read counts from protoperithecia from wild type and developmental mutants pro1 and nox1 from two previous studies (Teichert et al. 2012, BMC Genomics 13:511, GEO accession number GSE33668; Dirschnabel et al. 2014, Genetics 196:729-744, GEO accession number GSE49363) were also included in the analysis.
a consensus for differential expression was determined from the three analyses (DESeq, LOX) as described in  Teichert et al. 2012, BMC Genomics 13:511.
Genome_build: Sordaria macrospora genome version 02, accession numbers CABT02000001-CABT02001583
Supplementary_files_format_and_content: tab-delimited text file includes raw read counts and expression ratios (from LOX and DESeq) for all annotated genes.

growth_protocol: For microdissection, samples were grown on microdissection slides with 150-200 µl BMM medium (+0.8 % agar) for 4-5d at 25 °C.

extract_protocol:
Total RNA from microdissected samples was extracted and linearly amplified as described in Teichert et al. 2012, BMC Genomics 13: 511
RNA libraries from microdissected RNA as well as total mycelial RNA were prepared for sequencing in a HighSeq2500 using standard Illumina protocols

treatment_protocol: For microdissection, samples were fixated in ethanol at 4°C, and protoapothecia were harvested by laser microdissection as described in Teichert et al. 2012, BMC Genomics 13: 511

value: protoperithecia


title: SM23: pro44 replicate 2

description: pro44 replicate 2

source_name: total sexual mycelium


title: PFC_10F

description: Rnase R treated circular RNA


title: SMMN_3

source_name: asf1 replicate 1


title: SM21: asf1 replicate 2

description: asf1 replicate 2


title: SM18: wild type replicate 1

description: wild type replicate 1


title: SM19: wild type replicate 2

description: wild type replicate 2


title: SM22: pro44 replicate 1

description: pro44 replicate 1


title: ESC_2i_Aza_EedKO_RNA-Seq

status: Public on Nov 24 2018

city: Nijmegen

first: Hendrik

last: Marks

address: Geert Grooteplein 26/28

department: Molecular Biology

country: Netherlands

institute: Radboud University Nijmegen, RIMLS

data_processing:
For RNA-Seq and ChIP-Seq, Initial data processing and base calling was performed using the Illumina Analysis Pipeline. Initial data processing and base calling of Bisulfite-seq/WGBS was performed as in (Farlik et al., 2015).
For RNA-Seq, strand specific RNA-seq reads were aligned to the mm9 reference genome and counted using STAR v2.5.2b with parameters --quantMode GeneCounts --outSAMmapqUnique 255 --outSAMmultNmax 1 --outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 16
For ChIP-Seq, reads were mapped to a merged mm9 and dm3 genome using bowtie2 2.0.2 with parameters --very-sensitive --end-to-end. Duplicate and unmapped reads were removed. The data mapped to dm3 and mm9 genomes were split into separate files.
For RNA-Seq, only uniquely mapping tags (mapq=255) were kept. Bigwigs were generated using bam2bw (https://bitbucket.org/simonvh/bam2bw.git) v1.25 with parameters –e 150 –c –p.
For ChIP-Seq, Only uniquely mapping tags (mapq >=30) were kept for quantification. Bigwigs were generated using bam2bw (https://bitbucket.org/simonvh/bam2bw.git) v1.25 with parameter –e 180 and custom scaling factor -s set to account for the relative abundance of the dm3 spike-in chromatin.
Data processing and data analysis of Bisulfite-seq/WGBS data was performed as in Habibi et al. (2013)
Genome_build: mm9 + dm3
Supplementary_files_format_and_content: bigWig files are directly compatible with the UCSC genome browser.

source_name: Embryonic Stem Cells (ESCs)

growth_protocol: E14 ESCs (129/Ola background) were maintained in Dulbecco’s Modified Eagle Medium (DMEM) containing 15% fetal bovine serum, 5µM beta mercaptoethanol (BME) (Sigma) and Leukemia inhibitory factor (LIF; 1000U/ml) (Millipore), referred to as serum ESCs, or in serum-free N2B27 (or Ndiff) supplemented with PD0325901 (1 µM), CH99021 (3 µM) and LIF (1000U/ml), referred to as 2i ESCs. Serum+2i cells were grown in Serum medium supplemented with PD0325901 (1 µM) and CH99021 (3 µM). The Eed-/- and Suz12-/- ESCs originate from the lab of Anton Wutz (Schoeftner et al., 2006 and Wutz & Jaenisch, 2000) and Kristian Helin (Pasini et al., 2007), respectively

extract_protocol:
For RNA-Seq, total RNA was isolated using a RNeasy mini kit (Invitrogen) according to manufacturer’s instructions with on-column DNAseI treatment. Ribosomal RNA was depleted using Ribo-Zero Gold rRNGA Removal Kit (Illumina) according to manufacturer protocol starting from 5µg RNA. The resulting 180uL of rRNA depleted RNA was purified by mixing 18uL 3 M Sodium Acetate and 2 uL of 20 mg/mL glycogen, then adding 3x volumes of ice-cold 100% ethanol and incubation at -20°C for 1 hour. Samples were centrifuged at 10.000g for 30 minutes. After removal of supernatant, RNA pellet was washed in 500uL ice-cold 70% ethanol and centrifuged at 10.000g. Supernatant was removed and RNA was eluted in 40uL nuclease free H2O. rRNA depleted RNA was fragmented to ~200bp size using 10uL of a 5x 200mM Tris-acetate, 500 mM Potassium Acetate, 150 mM Magnesium Acetate, pH 8.2 solution at 95°C for 200 seconds, then incubated on ice for 10 minutes before repeating the ethanol purification procedure. First strand cDNA synthesis was performed using SuperScript III RT enzyme (Life Technologies), purified using Qiaquick MinElute Column (Qiagen). For ChIP-Seq, chromatin extracts were prepared by on-plate cell crosslinking in 1% PFA for 8 minutes. Crosslinking was quenched using 125 mM freshly dissolved Glycine final concentration. Fixed cells were washed in PBS twice, then collected by scraping. Pellets were lysed and sonicated in 50 mM Tris pH 8.0, 1% SDS and fresh protease inhibitor cocktail (Roche) at a density of 15 million cells per mL. The cells were sonicated in a Diagenode Bioruptor Pico for 8-10 30-second cycles. Proper sonication was verified using agarose gel size checks after decrosslinking and the eluted DNA was quantified using Qubit HS. 25ug DNA equivalent mouse chromatin was ChIPped using 4ug H3K27me3 (Millipore 04-779) or 2ug H3K36me3 (Diagenode pAb-192-050) antibody. Spike-in normalization was performed by adding 50ng Drosophila Melanogaster material (Active Motif 53083) and 2ug Drosophila-specific H2Av antibody (Active Motif 61686) to the mouse chromatin. ChIPs were diluted 9-fold using IP buffer (1% Triton X100, 1.2mM EDTA, 16.7mM Tris pH8.0, 167mM NaCl) and incubated overnight at 4°C while rotating. Subsequently, a mixture of 10uL Protein A and 10uL protein G (thermo) was blocked twice in IP buffer with 0.15% SDS and added to the ChIP. ChIPs with beads were left to incubate for 1 hour and precipitated using a magnetic rack. Chromatin was washed once (2mM EDTA, 20mM Tris pH8.0, 1% Triton, 0.1% SDS, 150mM NaCl), twice (2mM EDTA, 20mM Tris pH8.0, 1% Triton, 0.1% SDS, 500mM NaCl) and twice (1mM EDTA, 10 mM Tris pH8,0). Specific ChIPped DNA was eluted using 200mM NaCl, 1%SDS, 20mM Tris pH8.0 by shaking at 65°C for one hour, addition of and 1:100 10mg/mL Proteinase K and shaking at 55°C for one hour, then shaking at 65°C for at least four hours. The DNA was purified using Qiagen Minelute according to manufacturer instructions. For Bisulfite-seq, genomic DNA was extracted using the Wizard genomic DNA isolation kit (Promega). 200ng of purified genomic DNA was digested with Proteinase K before proceeding with sample processing for WGBS.
For RNA-Seq, second strand synthesis was performed using incorporation of dUNTP’s. Libraries were generated using Kapa Hyper Prep kit (KAPA Biosystems) according to manufacturer’s protocol with modification of dUNTP cleavage before amplification. Libraries were size selected using Agencourt Ampure XP beads (Beckman Coulter). For ChIP-Seq, libraries were generated using Kapa Hyper Prep on 5ng DNA according to manufacturer instructions and size selected using Ampure XP beads. DNA was quantified using Qubit HS and DNA fragment sizes checked using Agilent Bioanalyzer HS. For WGBS, sample prep, paired-end sequencing and further analysis of Bisulfite-seq/WGBS was performed as in (Farlik et al., 2015).

treatment_protocol: ESCs were adapted to defined media containing 2i between 14 and 28 days; Treatment with 5-azacytidine (Sigma) was performed for 6 days at a final concentration of 1 µM. 5-azacytidine was refreshed every day.

value: Eed-/-

value: ESCs

tag: strain background

value: Adapted to defined media containing 2i >14 days, 5-azacytidine administered for 6 days


title: TC_20M

description: Rnase R treated circular RNA

value: 20 years

value: brain

value: Male


title: ESC_2i_Aza_RNA-Seq


title: ESC_2i_EedKO_RNA-Seq

value: Adapted to defined media containing 2i >14 days


title: SM20: asf1 replicate 1

description: asf1 replicate 1


title: PFC_20M

description: Rnase R treated circular RNA


title: ESC_2i_RNA-Seq


title: Col-ABA repeat

city: Shijiazhuang

first: Wenqiang

last: Tang

state: Hebei Province

address: East 20 NanErHuang Road

department: College of Life Sciences

institute: Hebei Normal University

description: processed data file: Col+ABA vs Col-ABA original data.xls; bin2-1_vs_Col-ABA_original_data.xls

data_processing:
The sequence reads were mapped to the Arabidopsis genome (TAIR 10) using Tophat software
Differential gene expression was analyzed using Cufflink software
Genome_build: TAIR 10
Supplementary_files_format_and_content: excel files include averaged FPKM value for each sample. Differential expression analysis was performed using the program cufflinks

source_name: Arabidopsis thaliana_root_Col-ABA

growth_protocol: Arabidopsis Col, bin2-1 and bzr1-D/bin2-1 were grown vertically on 1/2 MS in growth chamber (Percival) at 22 degree under long-day (16h of light/8 h of dark) for 7 days

extract_protocol:
Total RNA was extracted using a RNeasy Plant Mini Kit (Qiagen)
The mRNA sequencing libraries were constructed with barcodes using the TruSeq RNA Sample Preparation Kit (Illumina),Six barcoded libraries were pooled together and sequenced by Illumina HiSeq2000

treatment_protocol: treated with or without 100 μM ABA for 3 h

tag: genetic background

value: Columbia

value: wildtype

value: root


title: bzr1-D/bin2-1

description: processed data file: bzr1-D/bin2-1 vs bin2-1 original data.xls

source_name: Arabidopsis thaliana_root_bzr1-D/bin2-1


title: bin2-1

description: processed data file: bzr1-D/bin2-1 vs bin2-1 original data.xls; bin2-1_vs_Col-ABA_original_data.xls

source_name: Arabidopsis thaliana_root_bin2-1


title: Col+ABA repeat

description: processed data file: Col+ABA vs Col-ABA original data.xls

source_name: Arabidopsis thaliana_root_Col+ABA


title: bin2-1 repeat


title: Col-ABA


title: bzr1-D/bin2-1 repeat


title: SM27: pro44 protoperithecia replicate 2

description: pro44 protoperithecia replicate 2


title: Col+ABA


title: M3 rep1

status: Public on Nov 23 2018

city: bethesda

first: Stefan

last: Ambs

state: md

address: 37 convent cir

institute: NIH

description:
M3
Lal_3
Poly A+ RNA
M3 (MCF10Ca1h) was derived from occasional carcinomas arising from xenografts of M2 cells.
M3 gives predominantly well-differentiated low-grade carcinomas on xenografting.
processed data file: RawCount.txt

data_processing:
The samples have 163 to 256 million pass filter reads with a base call quality of above 94% of bases with Q30 and above. Reads of the samples were trimmed for adapters and low-quality bases using Trimmomatic software before alignment with the reference genome (Human - hg19) and the annotated transcripts using STAR. The average mapping rate of all samples is 96%. Unique alignment is above 87%. There are 3.74 to 4.07% unmapped reads. The mapping statistics are calculated using Picard software. The samples have 0.59% ribosomal bases. Percent coding bases are between 67-72%. Percent UTR bases are 23-26%, and mRNA bases are between 94-96% for all the samples. Library complexity is measured in terms of unique fragments in the mapped reads using Picard’s MarkDuplicate utility. The samples have 31-52% non-duplicate reads. In addition, the gene expression quantification analysis was performed for all samples using STAR/RSEM tools.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: RawCount.txt: Tab-delimited text file includes raw counts.

source_name: mammary epithelial cells

growth_protocol: Acinar culture of M1-M4 cells was performed similar to three-dimensional culture of MCF10A cells. Briefly, growth-factor reduced Matrigel was used to coat multi-well plates. A single-cell suspension of each of the cell lines M1-M4 was prepared. M1-M2 cells were suspended in an assay medium containing growth medium (DMEM/F12 containing 2% Horse serum, 1 mg/ml hydrocortisone, 1 mg/ml cholera toxin, 10 mg/ml insulin, 10 ng/ml EGF, and 1% penicillin/streptomycin as well as 2.5% Matrigel dissolved in the medium). M3-M4 cells are prepared in the same way but omitting the EGF in the medium. The cells were seeded at a concentration of 8000 cells/mL. Media was changed every fourth day. Cells were cultured for 8 days prior to harvesting.

extract_protocol:
Trizol reagent (Invitrogen) was used to extract total RNA according to manufacturer’s protocol. The concentration was measured using Nanodrop instrument (ThermoFisher SCIENTIFIC). RNA was treated with RNase-free DNase I (Sigma, USA).
8 mRNA-seq samples were pooled and sequenced on HiSeq using Illumina TruSeq mRNA Prep Kit RS-122-2101 and paired-end sequencing.

value: M2-derived cells


title: M3 rep2

description:
M3
Lal_7
Poly A+ RNA
M3 (MCF10Ca1h) was derived from occasional carcinomas arising from xenografts of M2 cells.
M3 gives predominantly well-differentiated low-grade carcinomas on xenografting.
processed data file: RawCount.txt


title: M2 rep1

description:
M2
Lal_5
Poly A+ RNA
Transfection of MCF10A with activated T24-HRAS and selection by xenografting generated the M2 (MCF10AT1k.cl2) cell line.
M2 is highly proliferative and gives rise to premalignant lesions with the potential for neoplastic progression.
processed data file: RawCount.txt

value: M1-derived cells


title: M4 rep1

description:
M4
Lal_4
Poly A+ RNA
M4 (MCF10CA1a.cl1) was derived from occasional carcinomas arising from xenografts of M2 cells.
M4 gives rise to relatively undifferentiated carcinomas and colonizes to the lung upon injection of these cells into the tail vein.
processed data file: RawCount.txt


title: M1 rep1

description:
M1
Lal_1
Poly A+ RNA
processed data file: RawCount.txt

source_name: human mammary epithelial cell line (MCF10A)

value: mammary epithelial cells


title: M1 rep2

description:
M1
Lal_2
Poly A+ RNA
processed data file: RawCount.txt


title: M2 rep2

description:
M2
Lal_6
Poly A+ RNA
Transfection of MCF10A with activated T24-HRAS and selection by xenografting generated the M2 (MCF10AT1k.cl2) cell line.
M2 is highly proliferative and gives rise to premalignant lesions with the potential for neoplastic progression.
processed data file: RawCount.txt


title: NEURON_RNAseq_3

city: Heidelberg

first: Avni

last: Baser

address: Im Neuenheimer Feld 581

department: Molecular Neurobiology

institute: DKFZ

description:
mRNA with poly A tail
rawCounts.txt
expectedCounts.txt
TPM values.txt
Barcode: AAGAGGCA-ACTGCATA
11_Dxc4wpi_8047total

data_processing:
raw counts were extracted by start star RNAseq aligner version 020201 using the ENSEMBL reference genome sequence ENSEMBL_GRCm38_80  and the ENSEMBL gene annotation GRCm38.80
TPM values and expected counts were extracted by RSEM (rsem-1.2.21) with bowtie2-2.2.6 using the ENSEMBL reference genome sequence ENSEMBL_GRCm38_80 and the ENSEMBL gene annotation GRCm38.80
Genome_build: ENSEMBL reference genome sequence ENSEMBL_GRCm38_80 and ENSEMBL gene annotation GRCm38.80
Supplementary_files_format_and_content: TPMvalues.txt, rawCounts.txt, expectedCounts.txt

molecule: polyA RNA

source_name: adult mouse brain

growth_protocol: Male transgenic mice of DiCRY (Dcx-CreER-Rpl22.HA-eYFP) and TiCRY (Tlx-CreER-Rpl22.HA-eYFP) lines were used between 8 and 12 weeks of age for all sequencing experiments. These mice were generated by mating of RiboTag mice (B6N.129-Rpl22tm1.1Psam/J, purchased from The Jackson Laboratory) with Tlx-CreER-eYFP mice or Dcx-CreER-eYFP mice, respectively. All mice were backcrossed to a C57BL/6 background. All mice were bred inhouse at the DKFZ Center for Preclinical Research. Animals were housed under standard conditions and fed ad libitum. All procedures were in accordance with the DKFZ guidelines and approved by the Regierungspräsidium Karlsruhe.

extract_protocol:
Animals were sacrificed by cervical dislocation and brains were immediately placed on ice. The lateral SVZ was microdissected as a wholemount as previously described (Mirzadeh et al., 2010), further the olfactory bulb were dissected. Tissue of a 1-2 mice was used per replicate (SVZ or OB) for sequencing experiments. Tissue was digested with trypsin and DNase according to the Neural Tissue Dissociation kit in a Gentle MACS Dissociator (Miltenyi). Endogenous eYFP fluorescence was used to identify cells of interest. 200-500 cells of interest were sorted using FACS. During cell sorting, Sytox blue (Thermo Fisher Scientific) was used to exclude dead cells. For transcriptome analysis cells were sorted directly into Picopure lysis buffer (Thermo Fisher Scientific).
Sequencing libraries were prepared using Smart-seq2 technology as previously described (Picelli et al., 2014). Reverse transcription was performed using an oligo(dT) primer and a locked nucleic acid (LNA)-containing template-switching oligonucleotide (Exiqon). Full-length cDNAs were amplified by 15-18 cycles of PCR using KAPA HiFi DNA polymerase (KAPA biosystems). cDNAs were then converted into libraries for Illumina sequencing according to the Nextera XT Sample Preparation (Illumina) protocol. Samples were sequenced in an Illumina HiSeq 2000.

treatment_protocol: Recombination was induced by oral gavage of tamoxifen (TAM, Sigma-Aldrich) at a concentration of 200mg/kg body weight (volume ~100µL; solved in 90% sunflower oil/10% EtOH). TAM was administered twice per day for a total of 2-3 injections.

tag: background strain

value: Neuron

value: OB

tag: sample type

value: Total mRNA


title: LNB_NEURON_RIBOctr_3

description:
mRNA with poly A tail
Background control without HA
rawCounts.txt
expectedCounts.txt
TPM values.txt
Barcode: GCTACGCT-GTAAGGAG
06_Dxc4wpi_6837-Ribo

data_processing:
Library strategy: Ribo-seq
raw counts were extracted by start star RNAseq aligner version 020201 using the ENSEMBL reference genome sequence ENSEMBL_GRCm38_80  and the ENSEMBL gene annotation GRCm38.80
TPM values and expected counts were extracted by RSEM (rsem-1.2.21) with bowtie2-2.2.6 using the ENSEMBL reference genome sequence ENSEMBL_GRCm38_80 and the ENSEMBL gene annotation GRCm38.80
Genome_build: ENSEMBL reference genome sequence ENSEMBL_GRCm38_80 and ENSEMBL gene annotation GRCm38.80
Supplementary_files_format_and_content: TPMvalues.txt, rawCounts.txt, expectedCounts.txt

extract_protocol:
Tissue of interest was dissected and placed in tubes containing 1.4mm ceramic beads (PEQLAB). Homogenization buffer (50mM Tris HCl, 100mM KCl, 12mM Mg2Cl, 1% NP-40, 1mM DTT, 1x Roche complete protease inhibitor,  200U/mL RNAsin from Promega, 100µg/mL CHX, 1mg/mL Heparin) was added to a weight per volume ratio of 3% and tissue was homogenized using Minilys Personal Homogenizer (Bertin Instruments). Samples were centrifuged and supernatant was used for immunoprecipitation. Anti-HA antibody (Covance, 1:100) was added for four hours (indirect conjugation) following addition of Protein G magnetic beads (100µL, prewashed with homogenization buffer, Thermo Fisher Scientific) and overnight incubation (all steps at 4°C). Supernatant was discarded and beads were washed three times for ten minutes in high salt buffer (50mM Tris HCl, 300mM KCl, 12mM Mg2Cl, 1% NP-40, 1mM DTT, 100µg/mL CHX). Finally, beads were resuspended in Picopure lysis buffer (supplemented with β-mercaptoethanol, 10µL/1mL, Sigma) and RNA was isolated by Picopure RNA isolation kit (Thermo Fisher Scientific) following the manufacturer’s protocol.
Sequencing libraries were prepared using Smart-seq2 technology as previously described (Picelli et al., 2014). Reverse transcription was performed using an oligo(dT) primer and a locked nucleic acid (LNA)-containing template-switching oligonucleotide (Exiqon). Full-length cDNAs were amplified by 15-18 cycles of PCR using KAPA HiFi DNA polymerase (KAPA biosystems). cDNAs were then converted into libraries for Illumina sequencing according to the Nextera XT Sample Preparation (Illumina) protocol. Samples were sequenced in an Illumina HiSeq 2000.

value: Mix

value: Ribominus controls


title: NEURON_RNAseq_1

description:
mRNA with poly A tail
rawCounts.txt
expectedCounts.txt
TPM values.txt
Barcode: GCTACGCT-ACTGCATA
09_Dxc4wpi_7490total


title: NEURON_RNAseq_2

description:
mRNA with poly A tail
rawCounts.txt
expectedCounts.txt
TPM values.txt
Barcode: CGAGGCTG-ACTGCATA
10_Dxc4wpi_7652total


title: NEURON_RIBOseq_2

description:
mRNA with poly A tail
rawCounts.txt
expectedCounts.txt
TPM values.txt
Barcode: CTCTCTAC-ACTGCATA
07_Dxc4wpi_7154_plus_Ribo


title: LNB_NEURON_RIBOctr_2

description:
mRNA with poly A tail
Background control without HA
rawCounts.txt
expectedCounts.txt
TPM values.txt
Barcode: TAGGCATG-TATCCTCT
3_OB_DICRY3dpi_5518-


title: LNB_NEURON_RIBOctr_1

description:
mRNA with poly A tail
Background control without HA
rawCounts.txt
expectedCounts.txt
TPM values.txt
Barcode: GGACTCCT-TATCCTCT
2_OB_DICRY3dpi_5517-


title: LNB_RIBOseq_1

description:
mRNA with poly A tail
rawCounts.txt
expectedCounts.txt
TPM values.txt
Barcode: TAAGGCGA-TATCCTCT
1_OB_DICRY3dpi_5516_plus_

value: LNB

value: Ribosome-bound mRNA


title: LNB_RIBOseq_2

description:
mRNA with poly A tail
rawCounts.txt
expectedCounts.txt
TPM values.txt
Barcode: CGTACTAG-TATCCTCT
4_OB_DICRY3dpi_5519_plus_


title: LNB_RIBOseq_3

description:
mRNA with poly A tail
rawCounts.txt
expectedCounts.txt
TPM values.txt
Barcode: AGGCAGAA-TATCCTCT
5_OB_DICRY3dpi_5524_plus_


title: M4 rep2

description:
M4
Lal_8
Poly A+ RNA
M4 (MCF10CA1a.cl1) was derived from occasional carcinomas arising from xenografts of M2 cells.
M4 gives rise to relatively undifferentiated carcinomas and colonizes to the lung upon injection of these cells into the tail vein.
processed data file: RawCount.txt


title: LNB_RNAseq_3

description:
mRNA with poly A tail
rawCounts.txt
expectedCounts.txt
TPM values.txt
Barcode: AAGAGGCA-GTAAGGAG
11_DicryO6365YFP


title: LNB_RNAseq_2

description:
mRNA with poly A tail
rawCounts.txt
expectedCounts.txt
TPM values.txt
Barcode: TAGGCATG-ACTGCATA
18_DicryO8355_8492YF


title: ENB_RNAseq_3

description:
mRNA with poly A tail
rawCounts.txt
expectedCounts.txt
TPM values.txt
Barcode: TCCTGAGC-ACTGCATA
16_DicryS8355_8492YF

value: ENB

value: SVZ


title: NSC_ENB_RIBOctr_3

description:
mRNA with poly A tail
Background control without HA
rawCounts.txt
expectedCounts.txt
TPM values.txt
Barcode: CGTACTAG-GTAAGGAG
AB1_Cre-6654


title: NEURON_RIBOseq_1

description:
mRNA with poly A tail
rawCounts.txt
expectedCounts.txt
TPM values.txt
Barcode: CAGAGAGG-GTAAGGAG
05_Dxc4wpi_7155_plus_Ribo


title: ENB_RIBOseq_1

description:
mRNA with poly A tail
rawCounts.txt
expectedCounts.txt
TPM values.txt
Barcode: TCCTGAGC-TATCCTCT
6_SVZ_DICRY3dp_5516_plus_


title: NSC_ENB_RIBOctr_2

description:
mRNA with poly A tail
Background control without HA
rawCounts.txt
expectedCounts.txt
TPM values.txt
Barcode: CGAGGCTG-ACTGCATA
AV8_Cre-6846


title: NSC_ENB_RIBOctr_1

description:
mRNA with poly A tail
Background control without HA
rawCounts.txt
expectedCounts.txt
TPM values.txt
Barcode: GGACTCCT-AGAGTAGA
11_SVZ_TICRY4d_4633-


title: NSC_RNAseq_2

description:
mRNA with poly A tail
rawCounts.txt
expectedCounts.txt
TPM values.txt
Barcode: CGTACTAG-ACTGCATA
14_Ticry8165_8166YFP

value: NSC


title: ENB_RIBOseq_2

description:
mRNA with poly A tail
rawCounts.txt
expectedCounts.txt
TPM values.txt
Barcode: TAAGGCGA-AGAGTAGA
9_SVZ_DICRY3dp_5519_plus_


title: NSC_RNAseq_1

description:
mRNA with poly A tail
rawCounts.txt
expectedCounts.txt
TPM values.txt
Barcode: TAAGGCGA-GTAAGGAG
01_Ticry5547YFP


title: NSC_RNAseq_3

description:
mRNA with poly A tail
rawCounts.txt
expectedCounts.txt
TPM values.txt
Barcode: CGTACTAG-GTAAGGAG
02_Ticry6261YFP


title: NSC_RIBOseq_2

description:
mRNA with poly A tail
rawCounts.txt
expectedCounts.txt
TPM values.txt
Barcode: TCCTGAGC-AGAGTAGA
12_SVZ_TICRY4d_4943_plus_


title: NSC_RIBOseq_1

description:
mRNA with poly A tail
rawCounts.txt
expectedCounts.txt
TPM values.txt
Barcode: CGTACTAG-AGAGTAGA
10_SVZ_TICRY4d_4632_plus_


title: LNB_RNAseq_1

description:
mRNA with poly A tail
rawCounts.txt
expectedCounts.txt
TPM values.txt
Barcode: CGAGGCTG-GTAAGGAG
10_DicryO6364YFP


title: ENB_RNAseq_1

description:
mRNA with poly A tail
rawCounts.txt
expectedCounts.txt
TPM values.txt
Barcode: AGGCAGAA-ACTGCATA
15_DicryS8356_8495YF


title: ENB_RNAseq_2

description:
mRNA with poly A tail
rawCounts.txt
expectedCounts.txt
TPM values.txt
Barcode: CAGAGAGG-GTAAGGAG
08_DicryS6365YFP


title: MCF7 pLKO + E2

status: Public on Nov 22 2018

city: Indianapolis

first: Harikrishna

last: Nakshatri

state: IN

address: C218C, 980 West Walnut St

institute: Indiana University School of Medicine

description: Sample name: Sample 2

data_processing:
Basecalls performed using SOLiD5500xl
Sequence reads were aligned with BFAST (v.0.7.0a) to reference genome hg19 and junction library. Details refers to Breese and Liu, Bioinformatics, 2013, PMID: 23314324
Aligned reads were fitered with NGSUtils (Breese and Liu, Bioinformatics 2013), reads with mapping quality <=8 were excluded.
Gene based expression were quantified with NGSUtils.
Differential expression analysis was performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited file on sample record includes raw counts. edgeR output is available on the series record. sheet "Note" specified the group information for the 16 samples

source_name: MCF7 pLKO + E2

growth_protocol: Cells were maintained routienly in MEM plus 10% fetal calf serum. Four days prior to treatment, cells were plated with phenol-red free media with 5% charcoal-dextran treated fetal calf serum.

extract_protocol: RNA was extracted using RNAeasy kit from Qiagen

treatment_protocol: Cells were of ~70% confluency at the time of treatment. Cells were treated with vehicle (ethanol) or 0.1 nM estradiol (E2) for 3 hours

tag: knockdown

value: vector control

value: estradiol


title: MCF7 pLKO + E2 (2)

description: Sample name: Sample 4

source_name: MCF7 pLKO + E2 (2)


title: MCF7 UNC5AshRNA clone 5 + E2

description: Sample name: Sample 6

source_name: MCF7 UNC5AshRNA clone 5 + E2


title: T47D UNC5AshRNA clone 5 (2)

description: Sample name: Sample 15

source_name: T47D UNC5AshRNA clone 5 (2)

value: vehicle


title: MCF7 UNC5AshRNA clone 5 (2)

description: Sample name: Sample 7

source_name: MCF7 UNC5AshRNA clone 5 (2)


title: T47D pLKO

description: Sample name: Sample 9

source_name: T47D pLKO


title: T47D pLKO (2)

description: Sample name: Sample 11

source_name: T47D pLKO (2)


title: T47D pLKO + E2

description: Sample name: Sample 10

source_name: T47D pLKO + E2


title: T47D UNC5AshRNA clone 5 + E2

description: Sample name: Sample 14

source_name: T47D UNC5AshRNA clone 5 + E2


title: MCF7 pLKO (2)

description: Sample name: Sample 3

source_name: MCF7 pLKO (2)


title: T47D UNC5AshRNA clone 5

description: Sample name: Sample 13

source_name: T47D UNC5AshRNA clone 5


title: T47D pLKO + E2 (2)

description: Sample name: Sample 12

source_name: T47D pLKO + E2 (2)


title: WT_FG_rep3

city: Rehovot

first: Mike

last: Fainzilber

address: 234 Herzl Street

department: Department of Biomolecular Sciences

country: Israel

institute: Weizmann Institute of Science

description:
FG7142-treated mouse
Sample_525_WT_FG_count

data_processing:
Fastq files for each sample were generated by the usage of Illumina CASAVA-1.8.2 software (basecalling)
Reads were aligned to the mouse genome build mm10 using, Tophat (v2.0.10).
Counting reads on Refseq release mm10  genes, was done with HTSeq-count (version 0.6.1p1)
Differential analysis was carried out using DESeq (1.18.0)
Genome_build: mm10
Supplementary_files_format_and_content: Excel file includes the raw counts, genereted by HTSeq-count
Supplementary_files_format_and_content: Excel file includes the normalized counts (DESeq Normalization)

extract_protocol:
Total RNA was extracted from hippocampi dissected from either importin α5 or wild type animals treated with vehicle or FG7142 injection 30 minutes prior to dissection using the RNAqueous-Micro Kit (Ambion) according to manufacturer’s instructions. Replicates of high RNA integrity (RIN≥7) were processed for RNA-Seq at the Crown Institute for Genomics (G-INCPM, Weizmann Institute of Science).
TruSeq RNA sample preparation Kit v2 protocol (Illumina)

treatment_protocol: FG7142 (Sigma-Aldrich, #E006-100MG) was administered as described previously (Evans, A.K. and Lowry, C.A. - CNS Drug Rev. 13, 475–501, 2007) by intraperitoneal injection, at a final concentration of 5 mg/kg of body weight, 30 min before behavioral testing or harvesting the tissue.

value: wild-type

tag: treated with

value: Hippocampus


title: MCF7 UNC5AshRNA clone 5

description: Sample name: Sample 5

source_name: MCF7 UNC5AshRNA clone 5

tag: treatment


title: MCF7 UNC5AshRNA clone 5 + E2 (2)

description: Sample name: Sample 8

source_name: MCF7 UNC5AshRNA clone 5 + E2 (2)


title: T47D UNC5AshRNA clone 5 + E2 (2)

description: Sample name: Sample 16

source_name: T47D UNC5AshRNA clone 5 + E2 (2)


title: KO_FG_rep1

description:
FG7142-treated mouse
Sample_466_KO_FG_count

tag: strain

value: Importin alpha5-/-


title: KO_FG_rep2

description:
FG7142-treated mouse
Sample_669_KO_FG_count


title: MCF7 pLKO

description: Sample name: Sample 1

source_name: MCF7 pLKO


title: PlantL2_T1_HMW

city: Glen Osmond

first: Mark

middle: Raymond

last: Thomas

state: SA

address: PO Box 350

department: Plant Industry

country: Australia

institute: CSIRO

data_processing: Sequence reads were mapped to the grape genome using Bowtie (0.12.7 ) and Tophat (1.2.0) and provided as .bam files. Genome build: NCBI Vitis vinifera (wine grape) IGGP build 1 (based on 8x_WGS). Bioconductor R packages were used to calculate expression counts as RPKM (Reads per kilobase of exon model per million mapped reads) and the gene count files (.tab) lists NCBI Gene ID in the first column and associated RPKM in the second column.

organism: Vitis vinifera

source_name: tendril structures at position 1 from the apex

growth_protocol: Picovine genotypes 06C008V0003 and 04C021V0046 and control Pinot Meunier L2 plants were grown under controlled conditions of 16 h days at 25 oC  and 8 h 20 oC nights.

extract_protocol: Libraries were prepared using the Illumina mRNA Sequencing protocol and single-end sequenced.

treatment_protocol: Inflorescence structures at node postions 1, 2 and 3 from the apex were collected from two picovine genotypes 06C008V0003 and 04C021V0046. Leaves opposite the inflorescence structures were also collected. Tendril structures and leaves at node positions 1,2 and 3 from the apex of the control Pinot Meunier L2 plant were also sampled.

tag: cultivar

value: Pinot Meunier L2

value: tendril

tag: development stage

value: inmature, stage 1


title: Plant06C008V0003_F3_HMW.r2

source_name: inflorescent structures at position 3 from the apex

tag: tissue

value: inflorescence

value: inmature, stage 3


title: Plant06C021V0046_LeafMix_HMW

source_name: pooled leaf ample from leaves opposite influrensence structures

value: leaf

value: inmature, stages 1, 2, 3


title: Plant06C021V0046_F3_HMW.r1


title: PlantL2_T2_HMW

source_name: tendril structures at position 2 from the apex

value: inmature, stage 2


title: WT_FG_rep1

description:
FG7142-treated mouse
Sample_400_WT_FG_count


title: KO_Veh_rep3

description:
vehicle-treated mouse
Sample_510_KO_Veh_count


title: Plant06C008V0003_F2_HMW.r2

source_name: inflorescent structures at position 2 from the apex


title: PlantL2_T3_HMW

source_name: tendril structures at position 3 from the apex


title: PlantL2_LeafMix_HMW


title: PlantL2_T2_LMW

data_processing: Raw reads were trimmed by in-house scripts and processed data files contain read lengths of 10-35nt. Further analyses involved mapping to the grapevine genome the small RNA sequences with lengths of 21nt and 24nt using CASHX_2.3 and computational analyses to discover small RNAs that were only expressed in floral tissue.

extract_protocol: Oligoribonucleotide standards; Std 2 (UAUAUGCAAGUCCGGCCAUAC), Std 3 (UAGCUAACGCAUAUCCGCAUC) and Std 6 (UGAAGCUGACAUCGGUCAUCC) were added to the RNA sample prior to library construction as spike-in controls. Libraries were prepared using the Illumina v1.5 protocol for Small RNA Sequencing and single-end sequenced.


title: Plant06C008V0003_F1_HMW.r2

source_name: inflorescent structures at position 1 from the apex


title: Plant06C021V0046_F2_HMW.r1


title: PlantL2_T3_LMW


title: Plant06C021V0046_F1_HMW.r1


title: Plant06C021V0046_F3_LMW.r1


title: Plant06C021V0046_F1_LMW.r1


title: Plant06C021V0046_F2_LMW.r1


title: Plant06C008V0003_F3_LMW.r2


title: KO_Veh_rep1

description:
vehicle-treated mouse
Sample_496_KO_Veh_count


title: PlantL2_T1_LMW


title: WT_FG_rep2

description:
FG7142-treated mouse
Sample_499_WT_FG_count


title: KO_Veh_rep2

description:
vehicle-treated mouse
Sample_502_KO_Veh_count


title: WT_Veh_rep2

description:
vehicle-treated mouse
Sample_483_WT_Veh_count


title: Plant06C008V0003_F1_LMW.r2


title: WT_Veh_rep1

description:
vehicle-treated mouse
Sample_482_WT_Veh_count


title: PlantL2_LeafMix_LMW

source_name: pooled leaf sample from leaves opposite influrensence structures


title: Plant06C008V0003_F2_LMW.r2


title: Plant06C021V0046_LeafMix_LMW


title: RNAseq-SETD2-rep2

city: Riverside

first: LIN

last: LI

state: California

address: 501 Big Springs Road, University of California at Riverside

department: Department of chemistry

institute: UC, riverside

data_processing:
The sequencing reads of ChIP-seq were aligned to human hg19 reference genome using the Bowtie 1.1.2. Peak calling were generated using the Model-based Analysis of ChIP-Seq (MACS)
For RNA-seq analysis, the sequencing results were first aligned to human hg19 reference genome using the TopHat Gapped-read mapper for RNA-seq data. The differentially expressed transcripts or genes were subsequently generated using the Cuffdiff tools following the developers’ instructions
Genome_build: hg19
Supplementary_files_format_and_content: For ChIP-seq, wig files were generated using MACS, and converted to Bigwig files.For RNA-seq,tab-delimited text files were generated using Cuffdiff. Gene and transcript differential expressing testing, and gene FPKM tracking files were included.

source_name: HEK293T SETD2 KO cells

growth_protocol: Cells were cultured at 37 oC in a humidified incubator with 5% CO2.

extract_protocol:
RNA was extracted with Omega Total RNA Kit I (Omega).NEBNext rRNA Depletion Kit was used to remove the rRNA.
Libraries were conducted following the instructions for NEBNext® Ultra™ II RNA Library Prep Kit for Illumina.

tag: cell type

value: Human embryonic kidney cells

value: SETD2 Knockout

tag: cell line


title: Chipseq_SETD2_H3K36me3_rep2

extract_protocol:
Lysates were clarified from micrococcal nuclease digested chromatin and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to TruSeq ChIP Sample Preparation Kit (Illumina) following the manufacturer’s instructions.

tag: chip antibody

value: anti-H3K36me3 (Abcam, ab9050)


title: RNAseq-SETD2-rep1

tag: genotype


title: RNAseq-SETD2-rep3


title: Chipseq_SETD2_H4K16ac_rep1

value: anti-H4K16ac (Millipore, 07-329)


title: WT_Veh_rep3

description:
vehicle-treated mouse
Sample_495_WT_Veh_count

tag: genotype/variation


title: RNAseq-293T-rep3

source_name: HEK293T cells

value: wildtype


title: Chipseq_SETD2_H3K36me3_rep1


title: RNAseq-293T-rep2


title: RNAseq-293T-rep1


title: Chipseq_SETD2_H4K16ac_rep2


title: HSPposLMW-06.t1.r2

description: temperature treatment 38 °C

data_processing: Raw reads were trimmed by in-house scripts and processed data files contain read lengths of 10-35nt. Further analyses involved mapping to the grapevine genome the small RNA sequences with lengths of 21nt and 24nt using CASHX_2.3 and computational analyses to discover small RNAs present in either pre- or post- véraison berries before and after heatshock.

source_name: grape berries

growth_protocol: Fruiting L1 Pinot Meunier microvines were maintained in 20 cm diameter pots in a controlled environment growth room. The growth room was set at 16 °C with a photoperiod of 16 hours from 5:20 AM to 9:20 PM. The humidity was maintained at 46 % and the light intensity was 381 µmol.m-2s-1 at pot height.

treatment_protocol: Both pre-véraison (5-6 wpf (weeks post-anthesis)) and post-véraison berries (12-14 wpf) were sampled at 9 AM (T0) and 10 AM (T1). After sampling berries at 16 °C (T0) the temperature of the growth room was immediately raised to 38 °C and the berries sampled 1 hour later (T1).

value: L1 microvine

value: deseeded berries

value: post-veraison


title: Chipseq_293T_H4K16ac_rep2


title: HSPposLMW-06.t1.r1

description: temperature treatment 38 °C


title: MLL/AF9 #2 rep2

city: Fukuoka

first: Takuji

last: Yamauchi

address: 3-1-1, Maidashi, Higashi-ku

country: Japan

institute: Kyushu University

data_processing:
Mouse reference mm10 using STAR aligner
We assessed individual junction counts for each cohort by summing these counts over all samples in that cohort. Estimation of intron retention counts were performed by defining a 6 nt window over each exon-exon junction (3 nt in exon and 3 nt in intron), and all reads which completely overlapped this window were considered intronic (Darman et al., 2015) Individual junction usage in each cohort was then converted to a percent spliced in (PSI) measurement by dividing the count of that junction by the total count of all junctions sharing a splice site with it in that cohort. We assessed differential junction PSI between cohorts using a binomial z-test, and p-values were corrected using FDR. A q-value < 0.05 was considered significant.
Genome_build: mm10

source_name: MLL/AF9 #2

extract_protocol:
RNA was extracted using an RNeasy Mini Kit (Qiagen).
Libraries were generated using the Ovation Mouse RNA-Seq System following the manufacturer’s specifications (NuGEN)

treatment_protocol: RNA samples were prepared 0h, 6h and 10h after RG3039 treatment of cells

tag: disease state

value: AML

value: MLL/AF9 #2

value: hematopoietic cells


title: MLL/AF9 #2 rep3


title: MLL/AF9 #2 rep1


title: HSPposLMW-06.t0.r2

description: temperature treatment 16 °C


title: MLL/AF9 #1 rep3

source_name: MLL/AF9 #1

value: MLL/AF9 #1


title: MLL/AF9 #1 rep2


title: Chipseq_293T_H3K36me3_rep1


title: HSPpreLMW-06.t1.r1

description: temperature treatment 38 °C

value: pre-veraison


title: HSPpreLMW-06.t1.r2

description: temperature treatment 38 °C


title: CALM/AF10 #2 rep1

source_name: CALM/AF10 #2

value: CALM/AF10 #2


title: CALM/AF10 #2 rep3


title: CALM/AF10 #2 rep2


title: HSPpreLMW-06.t0.r1

description: temperature treatment 16 °C


title: CALM/AF10 #1 rep3

source_name: CALM/AF10 #1

value: CALM/AF10 #1


title: CALM/AF10 #1 rep2


title: Chipseq_293T_H4K16ac_rep1


title: Vector biological replication 3

city: Kunming

first: Yong-Gang

last: Yao

state: Yunnan

address: 32 Jiaochang Donglu

department: Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province

institute: Kunming Institute of Zoology

description:
U251-APP cells transfected with empty vector
M14-3

data_processing:
The processed final library was sequenced on an IlluminaHiseq 4000 platform, and 150 bp paired-ends reads were generated.
Raw RNA-seq reads were trimmed to remove sequencing adapters and low quality reads by Trimmomatic 0.33.
The clean reads were then aligned to the reference genome (GRCh38.p7) sequence using Tophat.
HTSeq-count (0.6.1p1) was used to count aligned reads that mapped to the annotated human genes (GRCh38.p7).
Gene-level differential expression analyses were performed using DESeq2.
Genome_build: GRCh38.p7
Supplementary_files_format_and_content: Processed datafiles were provided in TXT format, which contains rlog transformed gene expression levels by DESeq2.

source_name: U251 cell with a stably expression of mutant APP (K670N/M671L)

growth_protocol: U251 cells with stable expression of mutant APP (K670N/M671L) were cultured in Roswell RPMI-1640 medium (HyClone, C11875500BT) supplemented with 10% fetal bovine serum at 37 °C in a humidified atmosphere incubator with 5% CO2.

extract_protocol:
Cells were harvested at 72 h after transfection. Total RNA was extracted by using the RNAeasy kit (TianGen, co.td.) according to the manufacturer’s instructions.
1.5 μg total RNA per sample was used to prepare library for RNA-seq. Sequencing libraries were generated using the NEBNextUltraTM RNA Library Prep kit for Illumina (NEB, USA) following the manufacturer’s recommendation and index codes were added to attribute sequence to each sample.

treatment_protocol: Transfection of plasmid was performed using an electroporator (CUY21EDIT, Nepa gene, Japan) and electroporation cuvettes (EC-002S, Nepa gene, Japan) following manufactures’ instructions. U251-APP cells were harvested by trypsinization and washed three times with Opti-MEM medium. After cell counting, 1×10E6 cells were resuspended in 100 μL Opti-MEM medium with 10 μg plasmid DNA. After dispensing 100 μL mixture into a cuvette, electroporation was carried out. After electroporation, cells were seeded in pre-warmed growth medium in 6-well plates. Supernatant in each well was replaced with equal volume of new growth medium after 24 h, and 1 μg/mL doxycycline (Sigma; D9891) was added to induce APP expression.


title: C7 wild-type biological replication 2

description:
U251-APP cells transfected with wild-type C7
C7-WT-2


title: C7 mutant biological replication 1

description:
U251-APP cells transfected with mutant C7
C7-MT-1


title: C7 mutant biological replication 2

description:
U251-APP cells transfected with mutant C7
C7-MT-2


title: C7 wild-type biological replication 3

description:
U251-APP cells transfected with wild-type C7
C7-WT-3


title: C7 wild-type biological replication 1

description:
U251-APP cells transfected with wild-type C7
C7-WT-1


title: CALM/AF10 #1 rep1


title: Chipseq_293T_H3K36me3_rep2


title: HSPposLMW-06.t0.r1

description: temperature treatment 16 °C


title: HSPposHMW-06.t0.r2

description: temperature treatment 16 °C

data_processing: Sequence reads were mapped to the grape genome using Bowtie (0.12.7 ) and Tophat (1.2.0) and provided as .bam files. Bioconductor R packages were used to calculate expression counts as RPKM (Reads per kilobase of exon model per million mapped reads) and the gene count files (.tab) lists NCBI Gene ID in the first column and associated RPKM in the second column.


title: Vector biological replication 2

description:
U251-APP cells transfected with empty vector
M14-2


title: GMP 10hr rep2

description: Processed data in Series supplementary file Rna-seq DCPS.xlsx

source_name: normal bone marrow GMP

value: normal

value: normal bone marrow GMP

tag: time


title: HSPpreLMW-06.t0.r2

description: temperature treatment 16 °C


title: HSPposHMW-06.t1.r2

description: temperature treatment 38 °C


title: GMP 10hr rep3


title: HSPpreHMW-06.t1.r2

description: temperature treatment 38 °C


title: Vector biological replication 1

description:
U251-APP cells transfected with empty vector
M14-1


title: HSPpreHMW-06.t1.r1

description: temperature treatment 38 °C


title: GMP 6hr rep3


title: GMP 6hr rep1


title: GMP 10hr rep1


title: MLL/AF9 #1 rep1


title: GMP 6hr rep2


title: GMP 0hr rep3

value: 0hr (before)


title: GMP 0hr rep2


title: AML 10hr rep1


title: AML 10hr rep2


title: HSPpreHMW-06.t0.r1

description: temperature treatment 16 °C


title: HSPposHMW-06.t1.r1

description: temperature treatment 38 °C


title: HSPposHMW-06.t0.r1

description: temperature treatment 16 °C


title: AML 6hr rep2


title: AML 10hr rep3


title: AML 0hr rep3


title: C7 mutant biological replication 3

description:
U251-APP cells transfected with mutant C7
C7-MT-3


title: AML 6hr rep3


title: AML 0hr rep2


title: AML 0hr rep1


title: HSPpreHMW-06.t0.r2

description: temperature treatment 16 °C


title: control_CD44minus_replicate 2

city: Atlanta

first: Adam

middle: D

last: Gracz

state: GA

address: 615 Michael St. NE

department: Medicine

institute: Emory University

data_processing:
Initial processing and base calling was done using the Illumina pipeline - bcl2fastq (v2.17.4)
Low quality reads were removed using Trimmomatic (v0.36)
Reads were aligned to mm10 using STAR (v2.2.5b)
Reads were counted at mm10 genes using htseq-count (v0.6.1p1)
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text files contains read counts per gene for each sample and replicate

source_name: intestinal epithelial cells

extract_protocol:
50,000 cells per sample were sorted into media then pelleted and lysed in Lysis Buffer (Ambion). Total RNA was recovered with RNAqueous Micro Kit (Ambion), following manufacturer instructions. Bioanalyzer (Agilent) and Qubit (Life Tech) were used to determine RNA quality and concentration.
SMARTer Stranded Total RNA-seq: Pico Input (Clontech)

value: CD44- villus cells

tag: alleles

tag: Sex

value: male

tag: age

value: 6 wks


title: Sox4cKO_CD44minus_replicate 1


title: control_CD44minus_replicate 1


title: Sox4cKO_CD44plus_replicate 2

value: CD44+ crypt cells


title: control_CD44plus_replicate 1


title: Sox4cKO_CD44minus_replicate 2


title: control_CD44plus_replicate 2


title: Sox4cKO_CD44plus_replicate 1


title: GW15 (2) AGO_CLIP_mRNA

status: Public on Nov 21 2018

city: Santa Barbara

first: Kenneth

middle: S.

last: Kosik

address: UC Santa Barbara

department: NRI

institute: UCSB

data_processing:
Adapter sequences at both ends of reads were removed by using Cutadapt: cutadapt -e 0.10
Barcodes were identified and reads were separated into each sample, here is the six barcodes used:
5'-OH AGGGAGGACGAUGCGGAUGCG 3'- OH
5'-OH AGGGAGGACGAUGCGGUCAGG 3'- OH
5'-OH AGGGAGGACGAUGCGGUACCG 3'- OH
5'-OH AGGGAGGACGAUGCGGAGGUG 3'- OH
5'-OH AGGGAGGACGAUGCGGCGAAG 3'- OH
5'-OH AGGGAGGACGAUGCGGAAGCG 3'- OH
barcodes were removed
novoalign was used to align the read with genome
AGO binding sites were called as discribed in paper by using Piranha -p 1 -a 0.95 -u 0 -s
Genome_build: hg19
Supplementary_files_format_and_content: bed format for each ago binding sites

source_name: Brain

extract_protocol:
The experiments were performed as described earlier (M. J. Moore et al., Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis. Nature protocols 9, 263 (Feb, 2014)) except few modifications. Monoclonal anti-Ago2 antibody (Sigma, 11A9 clone, SAB4200085) was used to perform immunoprecipitation of protein on protein G dynabeads (Invitrogen, 100-03D). For the negative control, goat anti-rat IgG antibody (Sigma, A9037) was used.
For library preparation, all steps were performed as described before (M. J. Moore et al., Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis. Nature protocols 9, 263 (Feb, 2014)), except that the primers with adapter sequences were modified according to the Ion Torrent sequencing platform.

tag: developmental stage

value: Gestation Week 15

value: Primary Visual Cortex (V1)

tag: barcode


title: GW19 (5) AGO_CLIP_mRNA

value: Gestation Week 19


title: GW20.5 (3) AGO_CLIP_mRNA

value: Gestation Week 20.5

value: Prefrontal Cortex (PFC)


title: GW19.5 (2) AGO_CLIP_mRNA

value: Gestation Week 19.5


title: GW19.5 (1) AGO_CLIP_mRNA

value: Primary Motor Cortex (M1)


title: GW15 (2) AGO_CLIP_miRNA

data_processing:
Adapter sequences at both ends of reads were removed by using Cutadapt: cutadapt -e 0.10
Barcodes were identified and reads were separated into each sample, here is the six barcodes used:
5'-OH AGGGAGGACGAUGCGGAUGCG 3'- OH
5'-OH AGGGAGGACGAUGCGGUCAGG 3'- OH
5'-OH AGGGAGGACGAUGCGGUACCG 3'- OH
5'-OH AGGGAGGACGAUGCGGAGGUG 3'- OH
5'-OH AGGGAGGACGAUGCGGCGAAG 3'- OH
5'-OH AGGGAGGACGAUGCGGAAGCG 3'- OH
barcodes were removed
mirdeep2 was used to profile miRNAs
Genome_build: hg19
Supplementary_files_format_and_content: tab and miRNA profiling for each sample

value: No Identity


title: AML 6hr rep1

value: AML

value: hematopoietic cells


title: GW15 (4) AGO_CLIP_miRNA


title: GW19 (4) AGO_CLIP_miRNA


title: GW15 (3) AGO_CLIP_miRNA


title: GW16.5 (1) AGO_CLIP_miRNA

value: Gestation Week 16.5


title: GW20.5 (3) AGO_CLIP_miRNA


title: GW19.5 (2) AGO_CLIP_miRNA


title: GW19.5 (1) AGO_CLIP_miRNA


title: GW15 (4) AGO_CLIP_mRNA


title: GW16.5 (3) AGO_CLIP_mRNA


title: si-PADI2 T0 ChrRNA-seq replicate1

city: Barcelona

first: François

last: Le Dily

address: Dr. Aiguader, 88

country: Spain

institute: CRG-Centre for Genomic Regulation

description:
ps_003_01_01_chrrnaseq
si-PADI2 T0 without progesterone treatment

data_processing:
Both RNA-seq and ChrRNA-seq samples were processed as described below
Trimmomatic was used to trim sequencing adapters and low-quality ends
STAR was used to align reads to the genome reference sequence
featureCounts was used to generate gene quantifications
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files in the format specific of featureCounts with gene quantifications for each sample

source_name: T47D_si-PADI2 T0

growth_protocol: T47D carrying a single copy of luciferase reporter gene driven by MMTV promoter (T47D-MTVL), were grown in RPMI-1640 medium without phenol red supplemented with 10% dextran coated charcoal treated FBS (DCC/FBS), 2mM L-glutamine, 100U/ml penicillin-streptomycin at 37C with 5% CO2.

extract_protocol:
Total RNA from T47D-MTVL cells either transfected with sicontrol versus siPadi2 or expressing wild type (WTr) versus R1810Ar mutant form RNAP2 was extracted with RNeasy columnsfrom Qiagen followed by DNase  treaments.          For chromatin RNA, cells were lysed for 5 minutes in 4ml of ice-cold HLB+N [10mM Tris-HCl pH 7.5, 10mM NaCl, 2.5mM MgCl2 and 0.5% (vol/vol) NP-40], followed by addition of 1ml of ice cold HB+NS buffer [10 mM Tris-HCl pH 7.5, 10mM NaCl, 2.5mM MgCl2, 0.5% vol/vol, NP-40 and 10% wt/vol sucrose].Cell nuclei were collected by centrifugation at 1,400rpm for 5 minutes at 4°C, resuspended in 125µl of NUN1 buffer [20mM Tris-HCl pH 7.9, 75mM NaCl, 0.5mM EDTA and 50% vol/vol glycerol].After addition of 1.2 ml of ice cold NUN2 buffer [20mM HEPES-KOH pH 7.6, 300mM NaCl, 0.2mM EDTA, 7.5mM MgCl2, 1% vol/vol NP-40 and 1M urea], samples were incubated on ice for 15 minute, mixing by vortexing every 3 minutes. The chromatin pellet was resuspended in HSB buffer [10mM Tris pH 7.5, 500mM NaCl and 10mM MgCl2] and treated with TURBO™ DNase at 37˚C for 15 minutes, followed by Proteinase K for 10 minutes at 37˚C and chromatin-RNA was purified by Trizol.
Libraries were prepared using standadr Illumina instruction of TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero for Chromatin RNA seq and TruSeq Stranded mRNA Library Prep  kit for poly A RNA-sequencing.

treatment_protocol: Using standard protocol of Lipofectamine 3000 transfection, T47D-MTVL cells transfected either with sictrl or siPadi2 before harvesting for total RNA or chromatin RNA. For WTr versus R1810Ar mutant RNAP2, T47D–MMTVL cells were transfected with -amanitin resistant HA-tagged either wild type (WTr) or R1810Ar mutant RNAP2 for 24 hours followed by -amanitin treatment (6µg/ml) for 12hours before extracting total total RNA  .

value: si-PADI2 T0

tag: r5020 treatment

value: Untreated

tag: molecule subtype

value: chromatin-associated RNA


title: GW15 (1) AGO_CLIP_mRNA


title: si-PADI2 T0 ChrRNA-seq replicate2

description:
ps_003_02_01_chrrnaseq
si-PADI2 T0 without progesterone treatment


title: GW19.5 (4) AGO_CLIP_mRNA


title: si-control T0 ChrRNA-seq replicate5

description:
ps_001_02_05_chrrnaseq
si-control T0 without progesterone treatment

source_name: T47D_si-control T0

value: si-control T0


title: si-control T0 ChrRNA-seq replicate1

description:
ps_001_01_01_chrrnaseq
si-control T0 without progesterone treatment


title: T47D - R1810 mutant RNAP2 replicate 2

description:
ps_034_02_01_rnaseq
Poly A RNA Seq T47D cells expressing Amanitin resistant R1810 mutant RNAP2

source_name: T47D_R1810 mutant RNAP2

value: R1810 mutant RNAP2

value: messenger RNA


title: si-PADI2 RNA-seq rep1

source_name: T47D_si-PADI2 RNA-seq


title: T47D - R1810 mutant RNAP2 replicate1

description:
ps_034_01_01_rnaseq
Poly A RNA Seq T47D cells expressing Amanitin resistant R1810A mutant RNAP2


title: si-PADI2 RNA-seq rep2


title: T47D - WT RNAP2 replicate1

description:
ps_033_01_01_rnaseq
Poly A RNA Seq T47D cells expressing Amanitin resistant WT RNAP2

source_name: T47D_WT RNAP2

value: WT RNAP2


title: si-control RNA-seq rep2

source_name: T47D_si-control RNA-seq

value: si-control


title: T47D - WT RNAP2 replicate 2

description:
ps_033_02_01_rnaseq
Poly A RNA Seq T47D cells expressing Amanitin resistant WT RNAP2


title: si-control RNA-seq rep1


title: T47D R1810a Mutant RNAP2

description:
ps_032_01_01_chipseq
T47D cell expressing HA tagged R1810a Mutant form RNAP2

data_processing:
Trimmomatic was used to trim sequencing adapters and low-quality ends
BWA was used to align reads to the genome reference sequence
MACS2 was used to identify binding sites
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files with the normalised read counts profiles

source_name: T47D R1810a Mutant RNAP2

extract_protocol:
For RNAP2, 150 μg   chromatin was incubated with 20μg of antibody  anti-HA (ab9110) followed by 42μl of Protein A-Agarose Beads (Diagnose) .
T47D-MTVL cells, without treatment or transfected with -amanitin resistant HA-tagged wild type (WTr) versus R1810Ar mutant RNAP2 were cross-linked for 10 minutes with 1% formaldehyde. Lysate were sonicated to a DNA fragment size range of 200-300bp using a Biorupter sonicator (Diagenode). PADI2 was immunoprecipitated with 6μg of PADI2 antibody (z-22):sc-133877 lot number E1214 and H0715 by 50 μg and for RNAP2, 150 μg   chromatin was incubated with 20μg of anti-HA (ab9110) antibody followed by 42μl of Protein A-Agarose Beads (Diagenode).
Libraries were prepared using standadr Illumina instruction of  NEBNext® ChIP-Seq Library Prep Reagent.

treatment_protocol: Using standard protocol of Lipofectamine 3000 transfection,  T47D–MMTVL cells were transfected with -amanitin resistant HA-tagged either wild type (WTr) or R1810Ar mutant RNAP2 for 24 hours followed by -amanitin treatment (6µg/ml) for 12hours before chromatin prepration. There was no treatmnet for PADI2 ChIP sequencing.

value: anti-HA

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #

tag: chip antibody lot/batch #


title: T47D WT RNAP2

description:
ps_031_01_01_chipseq
T47D cell expressing HA tagged Wild type RNAP2

source_name: T47D WT RNAP2


title: T47D PADI2 T0 replicate2

description:
PADI2.T0-2
PADI2 ChIP-seq without treatment in T47D cells

source_name: T47D PADI2 T0

extract_protocol:
PADI2 was immunoprecipitated with 6μg of PADI2 antibody (z-22):sc-133877 lot number E1214 and H0715 by 50 μg of chromatin and 42μl of Protein A-Agarose Beads (Diagenode).
T47D-MTVL cells, without treatment or transfected with -amanitin resistant HA-tagged wild type (WTr) versus R1810Ar mutant RNAP2 were cross-linked for 10 minutes with 1% formaldehyde. Lysate were sonicated to a DNA fragment size range of 200-300bp using a Biorupter sonicator (Diagenode). PADI2 was immunoprecipitated with 6μg of PADI2 antibody (z-22):sc-133877 lot number E1214 and H0715 by 50 μg and for RNAP2, 150 μg   chromatin was incubated with 20μg of anti-HA (ab9110) antibody followed by 42μl of Protein A-Agarose Beads (Diagenode).
Libraries were prepared using standadr Illumina instruction of  NEBNext® ChIP-Seq Library Prep Reagent.

value: PADI2 antibody (z-22)

value: Santa Cruz


title: liver of saline treated mouse, biological rep5

city: Napoli

first: Annamaria

last: Carissimo

address: via Castellino

institute: Tigem

description: Gene expression data from liver  of saline treated mouse

data_processing:
Reads were aligned and assigned to Gencode Mouse release M4 transcripts and genes by using RSEM version 1.2.19 with standard parameters (Li & Dewey, 2011).
Genome_build: Genecode Mouse  release M4
Supplementary_files_format_and_content: tab-delimited text files include raw counts and  RPKM values for each Sample

source_name: liver tissue

growth_protocol: Wildtype, male, 6 weeks old C57BL/6N mice were maintained on 12h dark/light cycles with ad libitum access to standard rodent chow and water.

extract_protocol:
Extraction of total RNA was performed according to the manufacturer's instructions (Qiagen).
Total RNA (500 ng) from each sample was prepared using TruSeq RNA sample prep reagents (Illumina, San Diego, CA, USA) according to manufacturer's instructions. The amplified fragmented cDNA of ∼200 bp in size were sequenced in paired-end mode using the HiSeq 1000 (Illumina) with a read length of 2×100 bp

treatment_protocol: Male C57BL/6N mice (22–25 g) were injected intraperitoneally (i.p.) with CD95-activating antibody in a dose of 0.5 μg/g body weight. Saline mice received an injection with a volume of saline equivalent to the volume used in the CD95-Ab injections and the animals were sacrificed after 6 hours.

tag: tissue

value: Liver

tag: strain

value: male


title: liver of CD95 activating antibody treated mouse, biological rep4

description: Gene expression data from liver  of CD95 activating antibody treated mouse


title: liver of CD95 activating antibody treated mouse, biological rep5


title: liver of saline treated mouse, biological rep3


title: liver of CD95 activating antibody treated mouse, biological rep2


title: liver of CD95 activating antibody treated mouse, biological rep1


title: liver of saline treated mouse, biological rep2


title: liver of CD95 activating antibody treated mouse, biological rep3


title: T47D PADI2 T0 replicate1

description:
PADI2.T0-1
PADI2 ChIP-seq without treatment in T47D cells

tag: cell line

tag: chip antibody


title: GMP 0hr rep1

description: Processed data in Series supplementary file Rna-seq DCPS.xlsx

value: normal

value: normal bone marrow GMP

tag: cell type

value: 0hr (before)


title: liver of saline treated mouse, biological rep1


title: RNAseq.Ctrl.2

first: Ying

last: Cheng

address: 615 Michael Street

department: Human Genetics

description: RNAseq.txt

data_processing:
FASTQ sequence files from biological replicates were concatenated and aligned to the M. musculus reference genome (NCBI37v1/mm9) using Bowtie 1.1.0, keeping only unique non-duplicate genomic matches with no more than 2 mismatches within the first 25 bp. Unique, non-duplicate reads from input genomic DNA and each 5-hmC–enriched sequence set were counted in 100-, 1,000- and 10,000-bp bins genome wide and normalized to the total number of non-duplicate reads in millions. Input normalized values were subtracted from 5-hmC–enriched values per bin to generate normalized 5-hmC signals. Bins from each sample were clustered using uncentered correlation with pairwise complete linkage (Cluster3.0) to broadly asses patterns of 5-hmC–regulated loci. Overall, clustering of different sized bins generated similar clustering profiles. All data presented are those binned at 10,000 bp.
To identify Dynamically Hydroxymethylated Loci (DhML) between samples in mouse brain, we employed a Poisson-based peak identification algorithm (MACS) using unique non-duplicate reads. DhML form each replicate were merged by BEDTools. RNA-seq reads were aligned to mm9 using tophat v2.0.13 and differential RPKM expression values were extracted using cuffdiff v2.2.1
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited file; including gene name, sample name, RPKM value, log2 folder change value

source_name: Mice prefrontal cortex

growth_protocol: All the mice were housed in the animal facilities of Emory University, Atlanta, U.S.A.Institutional Animal Care and Use Committee.

extract_protocol:
Mouse prefrontal cortex were dissected from the brain. Genomic DNAs were isolated by different brain tissues in 600 μl digestion buffer (100 mM Tris-HCl, pH 8.5, 5 mM EDTA, 0.2% SDS, 200 mM NaCl), Proteinase K (Thermo) treatment at 55°C for overnight. The second day, 600 μl of Phenol:Chloroform:Isoamyl Alcohol (25:24:1 Saturated with 10 mM Tris, pH 8.0, 1 mM EDTA) (P-3803, Sigma) was added to samples, mixed completely, and centrifuged for 10 min at 12,000 rpm. The aqueous layer solution was transferred into a new Eppendorf tube and precipitated with 600 μl isopropanol. The pellet was washed with 75% ethanol, air-dried, and eluted with Nuclease-Free Water (Ambion).  RNA was then reverse transcribed using a SuperScript® III First-Strand Synthesis System (Invitrogen).
DNA libraries were generated following the Illumina protocol for “Preparing Samples for ChIP Sequencing of DNA” (Part# 111257047 Rev. A) using 25–50 ng of input genomic DNA or 5hmC-captured DNA to initiate the protocol. RNA-seq libraries were generated from duplicated samples per condition using the Illumina TruSeq RNA Sample Preparation Kit v2 following manufacturer’s protocol.

tag: stress

value: no


title: RNAseq.Stressed.3

description: RNAseq.txt

value: yes


title: RNAseq.Ctrl.1

description: RNAseq.txt


title: RNAseq.Stressed.2

description: RNAseq.txt


title: Hif1a-ChIP.WT.Stressed-2

description:
SI-HBR-Gain.txt
SI-HBR-Conserved.txt
SI-HBR-Loss.txt

tag: genotype/variation

value: wild type

tag: antibodies


title: Hif1a-ChIP.WT.Ctrl-2


title: 5hmC.Tet2WT.Ctrl-2

description:
WT-SI-DhML-Gain.txt
WT-SI-DhML-Loss.txt
PA-SI-DhML-Gain.txt
PA-SI-DhML-Loss.txt


title: Hif1a-ChIP.WT.Stressed-1


title: 5hmC.Tet2KO.Ctrl-1


title: 5hmC.Tet2WT.Ctrl-1


title: 5hmC.Tet2KO.Ctrl-2


title: RNAseq.Stressed.1

description: RNAseq.txt


title: 5hmC.Tet2KO.Stressed-2


title: liver of saline treated mouse, biological rep4

tag: Sex


title: 5hmC.Tet2KO.Stressed-1


title: 5hmC.Tet1KO.Stressed-2


title: 5hmC.Tet1KO.Stressed-1


title: 5hmC.WT.Ctrl-2


title: 5hmC.WT.Stressed-1


title: 5hmC.WT.Ctrl-1


title: 5hmC.WT.Stressed-2


title: RNAseq.Ctrl.3

description: RNAseq.txt


title: Hif1a-ChIP.WT.Ctrl-1


title: Anterior, 3 dpb, replicate 1

city: Pittsburgh

first: Gregory

last: Cary

state: PA

address: 4400 Fifth Ave

department: Biological Sciences

institute: Carnegie Mellon University

description: Barcode: ACTGAT

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Pmin_1.0 draft genome assembly using tophat v2.0.12 with parameters: --no-coverage-search --library-type fr-unstranded --b2-very-sensitive --transcriptome-index <bwtidx> -G <pm.genes.gff3>. Alignments were filtered to include only uniquely mapped reads using samtools 0.1.19-44428cd. Transcripts were assembled using cufflinks v2.2.1 with parameters: -u -b <pmin.scaff.fa> -g <pm.genes.gff3> and all cufflinks assemblies were merged using cuffmerge.
Transcript abundance was calculated against the merged transcriptome assemblies using HTSeq-count v0.6.1p1 using the parameters: --format=bam --minaqual=2 --stranded=no -i gene_id. Genes with at least 3 tag counts per 1x10^6 reads in at least two separate samples were retained for further analysis. Normalization, dispersion estimation and differential expression testing were all done using functions contained in the edgeR_3.10.5 Bioconductor package. The segment, time point, and sample batch (rep#) were included in the design model matrix (~0+seg:dayt+batch:rep). For each time point, the abundance of each gene in regenerating anterior or posterior segments was compared to the abundance in age-matched, sibling, non-bisected control larvae and significance was assessed using the quasi-liklihood F test (glmQLFit).
Genome_build: Pmin_1.0
Supplementary_files_format_and_content: Tab-delimited text files include sequence tag counts for each sample to the assembled genes as well as the output of the edgeR differential expression analysis for expressed genes, specifically the log2-transformed fold-change in gene expression at each timepoint in regeneration compared with control segments.

organism: Patiria miniata

source_name: Ant, 3d

growth_protocol: Regenerating and control larvae were cultured in artificial seawater at 16 °C and fed Rhodomonas les ad libitum every 2 days along with fresh artificial seawater beginning at 4 days post fertilization (dpf).

extract_protocol:
RNA was extracted using the GenElute Mammalian Total RNA Kit (Sigma-Aldrich).
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq)

treatment_protocol: Patiria miniata larvae (7 days post fertilization) were manually bisected stereotypically through the foregut, midway along the transverse anterior-posterior axis with a #11 sterile scalpel. Resulting anterior and posterior segments, as well as sibling control (non-bisected) larvae, were then transferred to separate 35 mm polystyrene dishes at a density of no more than 50 larval segments per ml of artificial seawater. Pools of of approximately 300 sibling regenerating posterior segments, anterior segments, and non-bisected sibling control larvae were collected at three points following bisection: one early (approximately 3 hours post bisection, hereafter 0 dpb), one intermediate timepoint (3 dpb), and one timepoint at the initiation of blastemal proliferation (6 dpb). Two biological replicate samples were prepared for each timepoint.

tag: segment

value: regenerating anterior segments

tag: time point

value: 3 dpb

tag: replicate


title: Anterior, 6 dpb, replicate 1

description: Barcode: GATCAG

source_name: Ant, 6d

value: 6 dpb


title: Posterior, 6 dpb, replicate 1

description: Barcode: TAGCTT

source_name: Post, 6d

value: regenerating posterior segments


title: Posterior, 0 dpb, replicate 1

description: Barcode: CGTACG

source_name: Post, 0d

value: 0 dpb


title: Posterior, 3 dpb, replicate 2

source_name: Post, 3d


title: Anterior, 0 dpb, replicate 1

description: Barcode: GTGAAA

source_name: Ant, 0d


title: Posterior, 0 dpb, replicate 2


title: Control, 6 dpb, replicate 2

source_name: Cont, 6d

value: Control (uncut larvae)


title: Anterior, 0 dpb, replicate 2


title: Posterior, 6 dpb, replicate 2


title: Anterior, 6 dpb, replicate 2


title: Control, 3 dpb, replicate 1

description: Barcode: GAGTGG

source_name: Cont, 3d


title: Control, 3 dpb, replicate 2


title: Control, 0 dpb, replicate 1

description: Barcode: GTCCGC

source_name: Cont, 0d


title: Control, 6 dpb, replicate 1

description: Barcode: ACTTGA


title: Control, 0 dpb, replicate 2


title: T47D_6h_population

status: Public on Nov 20 2018

city: Macau

first: Edwin

last: Cheung

address: Avenida da Universidade,Taipa

department: faculty of health sciences

institute: University of Macau

data_processing:
Reads were mapped as paired-end sequencing reads with the Tophat package (v.2.0.6) against the UCSC hg19 human gene annotation reference using default parameters
The FPKM (Fragments Per Kilobase of exon model per Million mapped fragments) expression values were calculated from the BAM file generated by Tophat using the Cufflink package (v.2.0.2).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

growth_protocol: MCF-7 and T47D ERα-positive human breast cancer cell lines were obtained from ATCC and maintained in DMEM and RPMI 1640 media (Gibco), respectively. Both media were supplemented with 5 % fetal bovine serum (FBS) (Gibco) and grown in a 37°C incubator with 5% CO2.

extract_protocol: Single cell and bulk population samples were barcoded and pooled together for library preparation using the Nextera XT Sample Prep Kit (Illumina). The pooled libraries were quantified through quantitative PCR using the KAPA Library Quantification Kit (KAPA Biosystems)

treatment_protocol: Three days prior to E2 stimulation, MCF-7 and T47D cells were transferred into phenol-red free DMEM/F12 and RPMI media (Gibco), respectively. Both media were supplemented with 5 % charcoal/dextran-stripped FBS (Hyclone). Cells were then stained with CellTracker Green CMFDA or Orange CMTMR (Molecular Probes) 24 h before drug treatment. Stained cells were treated with either ethanol (vehicle) or E2 at 4 time points (0 and 3 h: Green, 6 and 12 h: Orange), before being dissociated and triturated into single-cell suspensions for single-cell and bulk population analyses.

tag: time

value: ER-positive breast cancer cell line


title: T47D_6h_2G6


title: T47D_6h_2H8


title: T47D_6h_2H1


title: Posterior, 3 dpb, replicate 1

description: Barcode: ATTCCT


title: T47D_6h_2F3


title: T47D_6h_2F1


title: T47D_6h_2F9


title: T47D_6h_2F2


title: T47D_6h_2G2


title: T47D_6h_2G10


title: T47D_6h_2E5


title: T47D_6h_2E10


title: T47D_6h_2D7


title: T47D_6h_2E2


title: T47D_6h_2A10


title: T47D_6h_2A1


title: T47D_6h_2C6


title: T47D_6h_2C4


title: T47D_6h_2C12


title: T47D_6h_2B4


title: T47D_6h_2D4


title: T47D_3h_population


title: T47D_3h_2H6


title: T47D_6h_2E11


title: T47D_3h_2H3


title: T47D_3h_2G1


title: T47D_6h_2A4


title: T47D_6h_2A5


title: T47D_3h_2E9


title: T47D_3h_2F11


title: T47D_3h_2E12


title: T47D_3h_2E1


title: T47D_3h_2D9


title: T47D_3h_2D10


title: T47D_3h_2B9


title: T47D_3h_2C3


title: T47D_6h_2B3


title: T47D_3h_2C1


title: T47D_3h_2B8


title: T47D_3h_2B7


title: T47D_3h_2D6


title: T47D_3h_2B2


title: T47D_12h_population


title: T47D_3h_2A2


title: Anterior, 3 dpb, replicate 2


title: T47D_3h_2B6


title: T47D_12h_G8


title: T47D_3h_2B11


title: T47D_3h_2A7


title: T47D_12h_F12


title: T47D_12h_F2


title: T47D_12h_H4


title: T47D_12h_H7


title: T47D_12h_E7


title: T47D_12h_D2


title: T47D_12h_G5


title: T47D_12h_F9


title: T47D_12h_C8


title: T47D_12h_D1


title: T47D_12h_G10


title: T47D_12h_C1


title: T47D_12h_B7


title: T47D_12h_C11


title: T47D_12h_H12


title: T47D_12h_B12


title: T47D_12h_A9


title: T47D_12h_A12


title: T47D_12h_A3


title: T47D_0h_H5


title: T47D_0h_F8


title: T47D_0h_G9


title: T47D_0h_H2


title: T47D_0h_G3


title: T47D_0h_G12


title: T47D_0h_E11


title: T47D_0h_H6


title: T47D_0h_F1


title: T47D_0h_F7


title: T47D_0h_E12


title: T47D_0h_E9


title: T47D_0h_E1


title: T47D_0h_F11


title: T47D_12h_C5


title: T47D_0h_D12


title: T47D_12h_C12


title: T47D_0h_D11


title: T47D_12h_B5


title: T47D_0h_C2


title: T47D_0h_C6


title: T47D_0h_B4


title: T47D_0h_B2


title: T47D_0h_population


title: T47D_12h_D8


title: T47D_0h_H11


title: T47D_0h_B11


title: T47D_0h_A10


title: RHM303_6h


title: T47D_0h_A5


title: RHM301_6h


title: RHM300_6h


title: RHM294_6h


title: RHM270_6h


title: RHM245_6h


title: RHM244_6h


title: RHM253_6h


title: RHM239_6h


title: RHM246_6h


title: RHM229_6h


title: RHM237_6h


title: RHM222_6h


title: RHM221_6h


title: RHM310_3h


title: RHM309_3h


title: RHM285_3h


title: RHM293_3h


title: RHM287_3h


title: RHM284_3h


title: RHM279_3h


title: RHM276_3h


title: RHM268_3h


title: RHM286_6h


title: RHM278_3h


title: RHM271_6h


title: RHM263_6h


title: RHM255_3h


title: RHM292_3h


title: RHM261_3h


title: RHM247_3h


title: RHM236_3h


title: RHM269_3h


title: RHM295_3h


title: RHM306_12h


title: RHM254_3h


title: RHM305_12h


title: RHM291_12h


title: RHM231_3h


title: RHM297_12h


title: RHM273_12h


title: RHM283_12h


title: RHM277_3h


title: RHM267_12h


title: RHM266_12h


title: RHM264_12h


title: RHM265_12h


title: RHM258_12h


title: RHM250_12h


title: RHM249_12h


title: RHM257_12h


title: RHM241_12h


title: RHM234_12h


title: RHM243_12h


title: RHM223_3h


title: RHM227_12h


title: RHM225_12h


title: RHM224_12h


title: RHM307_0h


title: RHM304_0h


title: RHM299_0h


title: RHM219_12h


title: RHM298_0h


title: RHM296_0h


title: RHM259_0h


title: RHM280_0h


title: RHM256_0h


title: RHM251_0h


title: RHM290_0h


title: RHM282_0h


title: RHM248_0h


title: RHM242_0h


title: RHM232_0h


title: RHM240_0h


title: RHM233_0h


title: RHM226_0h


title: RHM218_0h


title: RHM220_0h


title: RHM216_0h


title: RHV143_6M_100k


title: RHM349_6M_10k


title: RHM289_0h


title: RHM341_3M_10k


title: RHV142_0M_10k


title: RHV127_0M_100k


title: MKN45 cell line ADAR knock-down small RNA seq

city: Daejeon

first: Jaeeun

last: Jung

address: 125 Gwahak-ro, Youseong-gu

country: South Korea

institute: KRIBB

data_processing:
Basecalls performed using bcl2fastq Conversion Software version 2.19.
Sequenced reads were trimmed for adaptor sequence using cutadapt v1.13, and trimmed low-quality sequence using sickle-maser v1.33, then mapped to hg19 whole genome using STAR v2.5 with parameters -outFilterMultimapNmax 1 -outFilterMismatchNoverReadLmax 0.05.
Variants were called using samtools v1.5.
False positive variants were eliminated using criteria: 1)less than 3 reads including mismatch, 2) less than 10% allele frequency, 3) less than 10 mapping depth, 4) annotated SNPs (using dbSNP build 138 except “cDNA” molecular types, 1000 Genomes Project and the University of Washington Exome Sequencing Project), 5) those in simple repeat region or segmental duplication (RepeatMasker, genomicSuperDups from UCSC genomic browser, respectively), 6) those within splice junction or homopolymeric region of ≥ 5 base pairs, 7) more than 99% strand biased reads, and end position biased mismatches (10% of 5’-end or 20% of 3’-end).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include RNA-editing information for each sample.

source_name: MKN-45 gastric epithelial cancer cell line

growth_protocol: AGS and MKN-45 were grown in RPMI medium with 10% fetal bovine serum. All cells were maintained at 37 °C and 5% CO2.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Gastric epithelial cancer cell line


title: RHM274_12h


title: MKN45 cell line small RNA seq


title: RHM260_6h


title: MKN45 cell line RNA seq