title: control

city: Nanjing

first: Ling

last: Zhang

state: Jiangsu

address: 22 Hankou Road

institute: Nanjing University

data_processing:
Illumina Casava1.6 software used for basecalling.
The final clean reads were obtained by getting rid of short reads (< 10 nucleotides) and contaminant reads (including reads with 5’ primer contaminants or poly A and reads without 3’ primer).
Sequenced reads with no more than 2 mismatches were identified as one piRNA and formed the final piRNA expression profiles.
After masking the adaptor sequences, the clean reads were aligned to the reference Mus musculus (house mouse) genome. The sequences that correspond to known piRNAs were determined by perfect sequence matching to the NCBI database.
Genome_build: mm8
Supplementary_files_format_and_content: counts

source_name: GC-1 cells

growth_protocol: Approximately 5 × 105 cells were plated into each well of six-well culture plates and incubated for 24 h in DMEM supplemented with 10% FBS at 37 °C and 5% CO2.

extract_protocol:
Total RNA was extracted from GC-1 cells using TRIzol Reagent (Takara, Dalian, China) according to the manufacturer’s instructions. RNA libraries were prepared for sequencing using standard Illumina protocols
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Then the cells were incubated with 0 or 500 nM MC-LR for 24 hours in DMEM supplemented with 10% FBS .

tag: cell type

value: spermatogonia

value: 0 nM MC-LR


title: MC-LR

status: Public on Jul 09 2018

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: treatment

value: 500 nM MC-LR


title: 4N_B.Lab4.SynthB

city: Ann Arbor

first: Muneesh

last: Tewari

state: MI

address: 109 Zina Pitcher Pl

country: USA

institute: University of Michigan

data_processing:
All FASTQ files were processed through the exceRpt small RNA-seq pipeline using the Genboree Workbench tools (http://genboree.org/java-bin/workbench.jsp). Default parameters were used, except for changing "minimum read length" to 15, and uploading the FASTQ file with the synthetic pool sequences as a "Spike-in". For the subset of "4N" libraries, the "Random Barcodes Present in Samples" option was checked, and the corresponding default subsettings were used (barcode length = 4; barcode location -5p and -3p).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_fastq.clipped.trimmed.filtered.calibratormapped.counts.txt: Tab-delimited text files contain the name of the synthetic RNA in column 1, and mapped read counts in the second. The sequence ID contains the equimolar and ratiometric pool IDs, if present in both pools; an "NA", if not. The ratiometric pool ID contains the name of the sequence, relative concentration in pool A and relative concentration in pool B, delimited by "|".

molecule: other

organism: synthetic construct

source_name: Synthetic smallRNA; Ratiometric Pool B

extract_protocol:
The RNA sample was provided as a single aliquot containing all the synthetic RNAs. 10 femtomoles of the RNA pool was used as input for each library.
Library construction protocols varied by sample (See lib.method.simple and lib.method.detail sample characteristics). TruSeq, CleanTag, NEBNext and 4N_NEXTflex protocols use the commercial kits and were optimized for sequencing of small RNAs from low-input biosamples. 4N_A, _B, _C and _D are in-house protocols using 5' and 3' adapters with 4N randomized terminal nucleotides.

tag: lab

tag: pool

value: SynthB


title: 4N_B.Lab4.SynthEQ

data_processing:
All FASTQ files were processed through the exceRpt small RNA-seq pipeline using the Genboree Workbench tools (http://genboree.org/java-bin/workbench.jsp). Default parameters were used, except for changing "minimum read length" to 15, and uploading the FASTQ file with the synthetic pool sequences as a "Spike-in". For the subset of "4N" libraries, the "Random Barcodes Present in Samples" option was checked, and the corresponding default subsettings were used (barcode length = 4; barcode location -5p and -3p).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_fastq_readCounts_miRNAmature_sense.txt: Mature miRNA Read Counts: Tab-delimited text files contain counts for genomic alignments to known human miRNAs, including only reads mapping in the same orientation as the indicated miRNA. For each miRNA, counts are provided to indicate i) number of unique reads, ii) total reads and iii) total reads, adjusted for ambiguous mapping to other genomic loci. Libraries generated using 4N adapters have an additional column that includes the number of unique random barcodes, also adjusted for multi-mapping. Our study used the "multimapAdjustedReadCount" column for all our calculations.
Supplementary_files_format_and_content: *_fastq.clipped.trimmed.filtered.calibratormapped.counts.txt: Mapped Calibrator Counts: Tab-delimited text files contain the name of the synthetic RNA in column 1, and mapped read counts in the second. The sequence ID contains the equimolar and ratiometric pool IDs, if present in both pools; an "NA", if not. The ratiometric pool ID contains the name of the sequence, relative concentration in pool A and relative concentration in pool B, delimited by "|".

source_name: Synthetic smallRNA; Equimolar Pool

value: SynthEQ


title: input DNA

status: Public on Jul 07 2018

city: Shanghai

first: Li

last: Li

address: 1954 Huashan Road

department: State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center

institute: Shanghai Jiao Tong University

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were adaptor-trimmed and mapped with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: bed files with MACS called peaks.

molecule: genomic DNA

source_name: intestinal cells

extract_protocol:
Lysates were clarified from sonicated nuclei.
library construction protocol not provided.

tag: tissue

value: intestine

tag: genotype

tag: age

value: 6 week

tag: strain

tag: chip antibody


title: WT129_H3K9me3_ChIPSeq

status: Public on Jul 08 2018

city: Clayton

first: Hsiao Phin

middle: Joanna

last: Voon

state: Victoria

address: Monash University, Wellington Road

department: Biochemistry and Molecular Biology

country: Australia

institute: Monash University

data_processing:
ChIP-seq of H3K36me3 and H3K9me3 from WT and H3.3 G34R mutants were aligned to the mouse genome (mm9) with Bowtie (v1.0.0) with default settings except (m -5) to allow restricted multi-mapping to short repeats.
Data were imported into Seqmonk (v 0.32.1) with PCR duplicates excluded. Reads were counted across 200 bp genomic bins and samples were normalised for total reads (per million reads). WT and H3.3 G34R datasets were normalised against each other using the “match distribution quantitation” tool on Seqmonk.
Selected bins which overlapped UCSC annotated genes and only analysed sites which were enriched for H3K36me3/H3K9me3 (>95th percentile) in either WT or G34R cells. All windows within 100 bp were merged using MergeBed (-d 100 -o mean) function in BedTools (v 2.20.1). Merged regions >500 bp and regions with extreme read counts (top 0.01%), typically associated with poorly annotated genomic regions, were excluded from further analysis. A total of 31,593 WT/G34R H3K36me3 enriched sites and 32,502 WT/G34R H3K9me3 enriched sites were used for downstream analyses.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files were generated with Wig/BedGraph-to-bigWig (v1.1.0) in Galaxy with default parameters. Scores represent normalised read counts in 200 bp bins.
Supplementary_files_format_and_content: Tab delimited text files represent regions which were deemed to be enriched for either H3K36me3 or H3K9me3.

source_name: ES Cells

growth_protocol: Mouse ESCs were cultured in Dulbecco's modified Eagle's medium supplemented with 15% heat-inactivated foetal calf serum, 10e3 units/ml leukemia inhibitory factor and 0.1 mM β-mercaptoethanol.

extract_protocol:
5 million cells were fixed in growth media with 0.4% formaldehyde for 10 min and quenched with 125 mM glycine. Chromatin was released by sequential lysis with cells lysis buffer (10 mM Tris pH 8, 10 mM NaCl, 0.2% Igepal) and nuclear lysis buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS). Chromatin was sheared to ≈300 bp with 12 rounds of sonication (30 s on, 30 s off) on a Bioruptor (Diagenode) and incubated overnight at 4 ᵒC with either 5 μg H3K9me3 antibody (Abcam ab8898) or 10 μg H3K36me3 antibody (Abcam??). Samples were immunoprecipitated with Protein A Agarose beads (Sigma-Aldrich, 05015979001) and washed sequentially with low salt (20 mM Tris pH 8, 2 mM EDTA, 50 mM NaCl, 1% Triton X-100, 0.1% SDS), high salt (20 mM Tris pH 8, 2 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.01% SDS), and LiCl buffers (10 mM Tris pH 8, 1 mM EDTA, 0.25 M LiCl, 1% Igepal, 1% sodium deoxycholate). Chromatin was eluted with elution buffer (1% SDS, 100 mM NaHCO3), decrosslinked overnight at 65ᵒC, incubated with Proteinase K, phenol chloroform extracted and ethanol precipitated.
Sample concentrations were determined by Qubit (ThermoFisher Scientific) and 20 ng of DNA was used as starting material. ChIP libraries were prepared with Nugen Ovation Ultralow System V2 (Nugen protocol M01379v1, 2014) with 10 cycles of amplification. Libraries quality was assessed by Qubit, Bioanalyzer (Agilent) and qPCR, and a single equimolar pool was made based on size adjusted qPCR quantitation. Following denaturation, 12 pM of library pools were used for cBot hybridisation and cluster generation (Illumina Protocol 15006165 v02 Feb 2016), and samples were sequenced on an Illumina HiSeq 1500 rapid mode (50 bp SR sequencing, Illumina Protocol 15035788 Rev D, Apr 2014).

value: WT ES cells

tag: passages

value: H3K9me3 (Abcam, ab8898)


title: G34R_RNASeq

data_processing:
Stranded 50 bp single-end RNA-seq reads were aligned to mouse (mm9) with STAR (v.2.4.2a) using default parameters.
Primary alignments were imported into Seqmonk as single-ended RNA-seq. The RNA-Seq quantitation pipeline was used to estimate RPKM read counts with the following parameters: mRNA as transcript feature, strand-specific, merge transcript isoforms, apply transcript length correction and exclude probes with no counts. A total of 26127 mRNA probes were quantitated.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files were generated with Wig/BedGraph-to-bigWig (v1.1.0) in Galaxy with default parameters. Wig files of genomic read distribution were produced using a sliding 300bp window moving at 30 bp increments.
Supplementary_files_format_and_content: Tab delimited text files contain RPKM values of UCSC annotated genes.

extract_protocol:
RNA was extracted from 5 million cells with TRI Reagent (Sigma, 93289) according to manufacturer’s instructions.
Sample quality was assessed using a Bioanalyzer and quantified by Qubit. All samples were processed starting with 500 ng of total RNA according to the Illumina Stranded Total RNA protocol (15031048 Rev C, Sept 2012) except that 12 cycles of amplification was used to minimise amplification artefacts. Libraries were quantitated by Qubit and qPCR, and an equimolar pool were made based upon qPCR results. Following denaturation, 200 pM of the library pool was clustered in one lane of a HiSeq 3000 (Illumina Protocol 15006165 v02 Jan 2016) and 50 bp SR sequencing was carried out (Illumina Protocol 15066493 Rev A, February 2015).

value: Targeted H3.3 G34R ES cells


title: WT129_RNASeq


title: 4N_D.Lab1.SynthA

source_name: Synthetic smallRNA; Ratiometric Pool A

value: SynthA


title: G34R_H3K36me3_ChIPSeq

value: H3K36me3 antibody (Abcam)


title: WT129_H3K36me3_ChIPSeq


title: H3K36me3_ChIPSeq

value: H3K36me3 (Abcam, ab9050)


title: leaf rust on resistant wheat rep 1

city: Zürich

first: Coraline

middle: Rosalie

last: Praz

address: Zollikerstrasse 107

department: Institute of Plant and Microbial Biology

country: Switzerland

institute: University of Zürich

data_processing:
Alignement was performed using the STAR guideline (Dobin et al., 2013) with following parameters: --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.01
Read counts were determined using featureCounts 1.4.6 (Liao et al., 2014)
statistical analysis was performed with edgeR package from R software (Robinson et al., 2010; R Development Core Team, 2011)
Genome_build: Blumeria graminis f.sp. hordei (assembly EF1) (Spanu et al., 2010) and reference transcriptome of Puccinia triticina (assembly  ASM15152v1) (Xu et al., 2011)
Supplementary_files_format_and_content: text file with counts

organism: Puccinia triticina

source_name: pathogen growing on entire plant in the field

growth_protocol: pathogen was inoculated on 3 week old barley plants in the greenhouse. Field infection was performed by planting already artifically infected plants into spreader rows.

extract_protocol:
samples were direcly frozen into liquid nitrogen and RNA extraction was performed using the  miRNeasy kit (QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols, Illumina sequencing Hi-Seq 2000 with 125 bp single end reads.

tag: host

value: Lr34 resistant wheat plants

tag: fungal isolate

value: Mixture of 16 Swiss fungal isolates


title: leaf rust on resistant wheat rep 2


title: leaf rust on resistant wheat rep 3


title: leaf rust on susceptible wheat rep 3

value: susceptible wheat plants


title: SETD2_ChIPSeq

value: setd2 (Life, LS-C341561)


title: leaf rust on susceptible wheat rep 2


title: powdery mildew on susceptible barley at 5 dpi rep 2

organism: Blumeria hordei

source_name: pathogen growing on entire plant in the greenhouse

value: susceptible barley plants

value: fungal isolate K1


title: powdery mildew on susceptible barley at 5 dpi rep 3


title: powdery mildew on susceptible barley at 5 dpi rep 1


title: powdery mildew on susceptible barley at 48 hpi rep 2


title: powdery mildew on susceptible barley at 48 hpi rep 3


title: powdery mildew on resistant barley at 5 dpi rep 3

value: Lr34 resistant barley plants


title: powdery mildew on susceptible barley at 48 hpi rep 1


title: G34R_H3K9me3_ChIPSeq


title: powdery mildew on resistant barley at 5 dpi rep 2


title: powdery mildew on resistant barley at 48 hpi rep 2


title: powdery mildew on resistant barley at 48 hpi rep 3


title: powdery mildew on resistant barley at 5 dpi rep 1


title: leaf rust on susceptible wheat rep 1


title: p65-GOX-60-1

status: Public on Jul 06 2018

city: Galveston

first: Istvan

last: Boldogh

state: Texas

address: 301 UNIVERSITY BLVD.

department: Microbiology & Immunology

institute: UNIVERSITY OF TEXAS MEDICAL BRANCH

data_processing:
The raw sequence reads were aligned to the latest human genome (hg38) using bowtie2
The Homer program was used to make peak calls (for each sample alone, without control samples).
The tiled data file (TDF) were generated with IGV Tools (Broad Institute) to read coverage and visualize peaks across the samples.
Data were viewed using IGV or UCSC genome browser
Binding motifs (6-20 bp) were idenfified using Homer software and confirmed with MEME v4.3.0.
Position-dependent letter probability matrices were generated by MEME using WebLogo application.
Genome_build: hg38
Supplementary_files_format_and_content: tdf

organism: Homo sapiens

source_name: Human Embryonic Kidney 293 cells

growth_protocol: Cells were maintained in Eagle's Minimum Essential Medium, supplemented with 10% FBS and Pen/Strept in a humidified 5% CO2 incubator at 37 C degrees.

extract_protocol:
Formalin-fixed protein-DNA complexes were sonicated and isolated with antibody.
Libraries were prepared according to Illumina's instructions using DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: For ChIP, cells were plated in 10 cm Petri dishes, and exposed to 1 µU GOx when cells were at 70% confluency and harvested at 0, 15, 30 and 60 min thereafter.

tag: cell line

tag: cell line type

value: Hypotriploid human cell line

tag: expressing

value: FLAG-tagged OGG1

value: stimulated with GOx

tag: time

value: 60 minutes

value: anti-RelA/p65 (Santa Cruz Biotechnology, Catalog# SC-372, Lot# E0416)


title: Flag-OGG1-GOX-60-1

value: anti-FLAG (Sigma, Catalog# F1804-50, Lot# SLBQ6349V)


title: powdery mildew on resistant barley at 48 hpi rep 1


title: p65-GOX-15-1

value: 15 minutes


title: p65-GOX-30-1

value: 30 minutes


title: Flag-OGG1-Con-2

value: control


title: Flag-OGG1-GOX-15-1


title: SNA_NAC rep1

city: Columbus

first: Ilaria

last: Palmisano

state: Ohio

address: 460 West 12th Avenue

institute: Ohio State University

data_processing:
Sequence reads were aligned to the mm10 mouse reference genome sequence using tophat version 2.0.12 running Bowtie2-2.2.3.
Gene structure annotations corresponding to the Ensembl annotation of the mm10 genome sequence were used to build a transcriptome index and provided to tophat during the alignment step
The aligned reads were sorted using samtools-0.1.19, then read counts per gene were obtained from mapped reads using HTSeq-0.6.0
EdgeR version 3.8.6 (using limma-3.22.7) in R-3.1.1 was used to identify differentially expressed genes.
GC-content bias was controlled for using full quantile normalization in EDASeq-2.0.0 running in R-3.1.1.
EDASeq was also used to generate quality checking figures before and after this normalization.
Differential expression testing was performed on the normalized output from EDASeq using edgeR
Read-level quality checking was performed using fastqc-0.10.1 and the fastqc-aggregator (https://github.com/staciaw/fastqc_aggregator) and gene-level quality checking was performed using RSeQC-2.6.1 (Wang et al., 2012).
Further data filtering and processing was performed in Matlab R2014b and R-3.1.1 including creating visualizations with cummerbund-2.8.2.
Genome_build: mm10
Supplementary_files_format_and_content: RawCounts.txt: tab-delimited txt file of raw sequencing reads
Supplementary_files_format_and_content: ROSData.FPKMs_2013Anno.txt: tab-delimited txt file represents the normalized expression data as FPKM, produced by EdgeR

source_name: DRG

extract_protocol:
RNA was extracted using RNeasy kit (Qiagen), according to manufacturer’s guidelines. Residual DNA contamination was removed by treating the spin column with 40 units of RNase-free DNase I (Qiagen) for 15 min at room temperature prior to RNA elution. RNA concentrations and purity were verified for each sample following elution with Agilent 2100 Bioanalyzer (Agilent). RNA with RIN factor above 7.5 was used for library preparation.
Libraries were generated using the TruSeq stranded mRNA Sample Preparation Kit A (Illumina, San Diego CA) according to the recommended low-sample TruSeq RNA Sample Preparation Guide protocol. cDNA wasgenerated through reverse transcriptase PCR using Superscript II reverse transcriptase (Invitrogen). cDNA was bound for purification during the protocol with Agencourt AMPure XP beads (Beckman-Coulter). Following ligation of unique adapter sequences, the DNA was enriched by PCR with 15 cycles of amplification according to the TruSeq protocol. Ligation and library integrity was verified using a High Sensitivity DNA chip on the Agilent 2100 Bioanalyzer (Agilent) with clean elution profiles at the correct size peak of about 260 bp. The Illumina TruSeq kit “A” adapter sequences were ligated to each sample in each group to allow for sequencing multiplexing. Sample libraries ligated with unique adapter sequences were multiplexed six to a lane and were sequenced using Illumina HiSeq 2000 100-cycle, single end sequencing.

treatment_protocol: Mice (6-8 weeks old) underwent the following procedures: a) spinal cord dorsal column injury b) laminectomy c) sciatic nerve injury  in presence of saline d) sham in presence of saline, e) sciatic nerve injury in presence of 30 mM NAC (N-acetyl-cysteine), f) sham in presence of 13 mM H2O2.

value: sciatic dorsal root ganglia (DRG)

value: 6-8 weeks old

tag: index sequence

value: AGTCAA(C )

tag: lane


title: Sham_H202 rep2

value: AGTTCC(G)


title: SNA_NAC rep2

value: AGTCAA(C)


title: p65-Con-2

tag: treatment


title: SNA_Saline rep3

value: GCCAAT(A)


title: LAM rep2

value: CAGATC(A)


title: LAM rep3


title: LAM rep1

value: CTTGTA(A)


title: DCA rep2

value: CCGTCC (C)


title: SNA_NAC rep3

value: GTCCGC(A)


title: SNA_Saline rep1


title: SNA_Saline rep2

value: TGACCA(A)


title: Sham_Saline rep3

value: CGATGT(A)


title: Pt+LL_leaf_bio2

city: Wuhan

first: Juxun

last: Wu

state: Hubei

address: No.1 of Shizishan street, Hongshan District

institute: Huazhong Agricultral University

data_processing:
To get the clean reads, removing the dirty raw reads is needed before data analysis.    Filter steps:    Remove reads with adaptors;  Remove reads in which unknown bases are more than 10%;   Remove low quality reads (the percentage of the low quality bases of quality value ≤ 5 is more than 50% in a read) .
Clean reads were mapped to reference sequences using SOAPaligner/soap2. Mismatches no more than 2 bases were allowed in the alignment.
The gene expression level is calculated by using FPKM method (Fragments Per Kilobase of transcript per Million mapped reads).
Genome_build: Citrus sinensis Annotation Project (CAP) (http://citrus.hzau.edu.cn/).
Supplementary_files_format_and_content: [.txt] FPKM represent the expression of genes

organism: Citrus sinensis

source_name: leaf

growth_protocol: The grafted materials Cj+LL and Pt+LL (rootstock+scion) were planted in the same orchard in 2009, which was located in Changyang city, Hubei province, China.

extract_protocol:
Approximate 2 to 3 g of powdered material was subjected to each RNA extraction, including 10 mL buffer extraction, 5 mL chloroform-isoamylalcohol extraction (twice), 5 mL isopropanol precipitation, 5 mL 75% ethanol cleaning and RNA purification as described by Camacho-Villasana YM et al.
mRNA of eukaryotes is enriched by using the oligo(dT) magnetic beads. Adding the fragmentation buffer, the mRNA is interrupted to short fragments (about 200 bp), then the first strand cDNA is synthesized by random hexamer-primer using the mRNA fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I are added to sythsize the second strand. The double strand cDNA is purified with QiaQuick PCR extraction kit and washed with EB buffer for end repair and single nucleotide A (adenine) addition. Finally, sequencing adaptors are ligated to the fragments. The required fragments is purified by agrose gel electrophoresis and enriched by PCR amplification.

value: leaf

tag: development stage

value: 140 DAF

tag: cultivar

value: 'Lane Late' navel orange


title: Flag-OGG1-GOX-30-1

value: Hypotriploid human cell line

value: FLAG-tagged OGG1

value: stimulated with GOx

value: 30 minutes

value: anti-FLAG (Sigma, Catalog# F1804-50, Lot# SLBQ6349V)


title: Sham_H202 rep1

tag: tissue

value: sciatic dorsal root ganglia (DRG)

value: 6-8 weeks old

value: ATGTCA(G)


title: DCA rep3

value: GTGAAA(C)


title: Pt+LL_leaf_bio1


title: Sham_H202 rep3


title: Pt+LL_stem_bio2

source_name: stem

value: stem


title: Cj+LL_stem_bio2


title: Pt+LL_root_bio2

organism: Citrus trifoliata

source_name: root

value: root

value: Poncirus trifoliata


title: Pt+LL_stem_bio1


title: Cj+LL_leaf_bio2


title: DCA rep1


title: Cj+LL_leaf_bio1


title: Cj+LL_stem_bio1


title: Pt+LL_root_bio1


title: 5hmC-BC3N

status: Public on Jul 05 2018

city: Gosselies

first: Martin

last: Bizet

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

description: 5hmC level in adjacent normal breast tissue from patient BC3

data_processing:
The Bowtie2 software (version 2.2.5) was used to map reads on human genome (NCBI 37; UCSC hg19).
sam files were converted into bam and sorted using samtools (version 1.3.1)
Duplicates reads (i.e. mapping to the same location) were removed using Picardtool MarkDuplicates (version 1.64)
For visualisation, bam were converted into bedgraph using bamTobw tool (https://github.com/YangLab/bamTobw)
and then into wig using bedgraph_to_wig tool (https://gist.github.com/svigneau/8846527) with a step size of 40
Genome_build: NCBI 37; hg19
Supplementary_files_format_and_content: wig file containing hmC enrichment profile across hg19 genome

source_name: Breast tissue

extract_protocol:
Genomic DNA from frozen samples was extracted from twenty 10-µm sections using the Qiagen-DNeasy Blood &Tissue Kit according to the supplier's instructions (Qiagen, Hilden, Germany). This included a proteinase K digestion at 55C overnight. DNA was quantitated with the NanoDrop® ND-1000 UV-Vis Spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA).
Library preparation was done with the TruSeq ChIP Sample Prep Kit (Illumina)
hMeDIP-Seq

tag: tumor status

value: Adjacent normal

tag: patient id

tag: tet1 qpcr level

tag: ip

value: hydroxymethylcytosine (5hmC)


title: 5hmC-BC3T

description: 5hmC level in TET1-low primary breast tumour from patient BC3

value: Primary tumor

value: Low


title: 5hmC-BC1N

description: 5hmC level in adjacent normal breast tissue from patient BC1


title: 5hmC-BC1T

description: 5hmC level in TET1-low primary breast tumour from patient BC1


title: Cj+LL_root_bio1

description: Citrus junos Sieb.

organism: Citrus junos

value: 140 DAF

value: Ziyangxiangcheng


title: Cj+LL_root_bio2

description: Citrus junos Sieb.


title: WT_Input

city: Irvine

first: Jiejun

last: Shi

state: CA

address: 5270 California Ave

department: School of Medicine

institute: University of California Irvine

data_processing:
Basecalls performed by Illumina CASAVA 1.8.2
The raw reads (single-end, 50 bp) were aligned to human reference genome hg19 using bowtie (v1.1.0) allowing up to one mismatch.
Genome_build: hg19
Supplementary_files_format_and_content: Peak calling was performed using MACS (v1.4.2) with the cutoff of P ≤ 1 × 10-8. Clonal reads were automatically removed by MACS.

source_name: UMRC6, WT

growth_protocol: Cells were cultured in Dulbecco's Modified Eagle's Medium  with 10% foetal bovine serum (FBS), 2 mM glutamine and100 U penicillin / 0.1 mg/ml streptomycin. When the cells were approximately 80% confluent,  1:3 split was carried out to keep sub-culturing.

extract_protocol:
Chromatin immunoprecipitation was performed using the SimpleChIP® Enzymatic Chromatin IP Kit (Cell Signaling Technology, 9003) following the instructions of the manufacturer. 20 μg of chromatin was incubated overnight with 5 μl H2Aub antibody (Cell Signaling Technology, 8240). 100 ng fly chromatin and 0.5 μg H2Av antibody (ActiveMotif, 61686) was added in each tube as spike-in control. Purified ChIP-DNA was verified by agarose gel to make sure properly fragmented and sent to Sequencing and Microarray Facility at MD Anderson Cancer Center for ChIP-seq.
ChIP–seq samples were sequenced using the Illumina Solexa Hiseq 2000.

tag: antibody


title: WT_H2Aub_ChIP

value: Cell Signaling Technology, 8240


title: Nutlin-3a-rep2

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

data_processing:
Raw Data Quality Control using NGS QC Tool Kit
Alignment against mm10 reference genome using TopHat 2.0.11
Quantitation and DGE using Cufflink pipeline
Genome_build: mm10
Supplementary_files_format_and_content: FPKMs

growth_protocol: 3T3L1 cells were grown in DMEM supplemented with 10% FBS

extract_protocol:
Total RNA was harvested using TRIzol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 3T3L1 cells treated with Nutlin-3a (prepared in DMSO) at 25uM concentration for 24 hours was further considered for sample preparation. In parallel treatment with DMSO of equivalent amounts was taken as vehicle control.

value: 3T3L1 preadipocytes

tag: agent

value: Nutlin


title: WT Naïve

city: New York

first: Sankar

last: Ghosh

institute: Columbia University

data_processing:
RTA (Illumina) used for base calling.
bcl2fastq (version 1.8.4) used for converting BCL to fastq format, coupled with adaptor trimming.
Reads were mapped to a reference genome (Mouse: UCSC/mm9) using Tophat [1] (version 2.1.0) with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10)
The relative abundance (aka expression level) of genes and splice isoforms were estimated using cufflinks [2] (version 2.0.2) with default settings.
Genome_build: UCSC/mm9
Supplementary_files_format_and_content: abundance measurements

source_name: Peritoneal macrophages

growth_protocol: Cells were maintained in DMEM supplemented with 10% FBS and 1% pen/strep.

extract_protocol:
Total RNA was extracted using the Qiagen miRNeasy Micro kit.  Poly-A pull-down used to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required). Library prepared by using the Illumina TruSeq RNA prep kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were either untreated (Naïve), treated with 1000 ng/ml LPS for 4 hours (LPS), or treated with 10 ng/ml LPS for 15 hours, washed, allowed to rest for 2 hours, and re-stimulated with 1000 ng/ml LPS for 4 hours (Tolerized+LPS).

tag: strain background

tag: genotype/variation

value: wildtype

tag: cell type

value: Peritoneal macrophages

tag: treated with

value: none (untreated; naïve)


title: WT Tolerized+LPS

value: 10 ng/ml LPS for 15 hrs, wash/rest for 2hrs and 1000 ng/ml LPS for 4hr


title: KO LPS

value: 1000 ng/ml LPS for 4 hrs


title: C91A_H2Aub_ChIP

source_name: UMRC6, BAP1 C91A mutant

tag: cell line


title: KO Tolerized+LPS


title: KO Naïve


title: EV_H2Aub_ChIP

source_name: UMRC6, empty vector


title: Nutlin-3a-rep1


title: WT LPS


title: DMSO-rep1

source_name: DMSO

value: DMSO


title: C91A_Input


title: Pip2p_Glu-lim_rep1

city: Mölndal

first: David

last: Bergenholm

state: SWEDEN

address: Axgatan 139

country: Sweden

institute: Chalmers tekniska högskola

description: ChIP-exo: P27

data_processing:
ChIP-exo sequencing reads (R1 reads) were mapped to reference genome assembly with Bowtie2 using default settings to generate SAM files.
SAM files were treated with SAMtools option –q 20 to remove low-quality reads and then converted to sorted BAM files.
BAM files were trimmed 70 bp (or 145 bp for Pip2) from 3’ end using trimBam (http://genome.sph.umich.edu/wiki/BamUtil:_trimBam) to increase resolution.
GEM was used to identify peaks and compare biological duplicates. The noise level was calculated from averaged noise throughout each replicate.
Bedtools was used to identify the genome wide targets.
Genome_build: R64-2-1 of S. cerevisiae S288C
Supplementary_files_format_and_content: Excel .xlsx file containing summit position, motif, distance to closest gene (ATG) and signal-to-noise values of peaks for all cultivation conditions

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

growth_protocol: Cells were cultivated in four different limited media in chemostat: n-lim, glu-lim, et-lim and oxy.glu-lim

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

tag: strain

value: PIP2-TAP constructed from CEN.PK 113-5D by adding a C-terminal CBP-ProtA tag to PIP2p

tag: carbon source

value: 0.75% (w/v) glucose


title: Pip2p_Ox,Glu-lim_rep2

description: ChIP-exo: P26

value: 1% (w/v) glucose


title: EV_Input


title: DMSO-rep2


title: Pip2p_Glu-lim_rep2

description: ChIP-exo: P28


title: 2.7 Rod+

city: Barcelona

first: Manuel

last: Serrano

state: Barcelona

address: Parc Científic de Barcelona, C/ Baldiri Reixac 10

department: Molecular Medicine

country: Spain

institute: IRB

description:
Rodplus_2.7
processed data file:
BLEOMYCINminus_vs_BLEOMYCINplus.normalizedCounts.xls

data_processing:
RNA-seq processing:
RNA-seq data was analysed with the nextpresso pipeline (http://bioinfo.cnio.es/nextpresso/) as follows:
Read files were quality-checked with FastQC.
Reads were aligned to the mouse genome (GRCm38/mm10) with TopHat-2.0.10 (using Bowtie 1.0.0 and Samtools 0.1.19), allowing 2 mismatches and 5 multihits.
Transcripts quantification and differential expression calculated with DESeq2, using the Mus musculus GRCm38/mm10 transcript annotations from the UCSC Genome Browser
Genome_build: mm10
Supplementary_files_format_and_content: The tables generated with DESeq2 and contain transcripts abundance measured in normalized counts

source_name: Bleomycin_GalNP(rho)_CD45- CD31- Rho+

extract_protocol:
For RNA-seq Total RNA was extracted using the RNeasy kit (Qiagen)
~2 ng of total RNA samples (range 0.4-5 ng) were processed with the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech) following the manufacturer instructions.
Resulting cDNA was sheared on a S220 Focused-ultrasonicator (Covaris) and subsequently processed with the "NEBNext Ultra II DNA Library Prep Kit for Illumina" (NEB #E7645).
Briefly, oligo(dT)-primed reverse transcription was performed in presence of a template switching oligonucleotide, double stranded cDNA was produced by 14 cycles of PCR and submitted to acoustic shearing.
Fragments were processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to Illumina adapters. Adapter-ligated libraries were completed by limited-cycle PCR (8 cycles).

tag: age

value: 8- to 10-week

tag: inoculated with

value: bleomycin at 1.5 U/kg of b.w.

tag: injected with

value: rhodamine [GalNP(rho)] at 4 mg/ml

value: Lung

value: CD45- CD31- Rho+


title: 2.8 Rod+

description:
Rodplus_2.8
processed data file:
BLEOMYCINminus_vs_BLEOMYCINplus.normalizedCounts.xls

tag: tissue


title: Pip2p_Ox,Glu-lim_rep1

description: ChIP-exo: P25


title: Pip2p_Et-lim_rep1

description: ChIP-exo: P23

value: 0.5% (w/v) ethanol


title: Pip2p_Et-lim_rep2

description: ChIP-exo: P24


title: 2.6 Rod+

description:
Rodplus_2.6
processed data file:
CONTROLminus_vs_CONTROLplus.normalizedCounts.xls

source_name: Control_GalNP(rho)_CD45- CD31- Rho+

value: none (control)


title: 2.2 Rod+

description:
Rodplus_2.2
processed data file:
CONTROLminus_vs_CONTROLplus.normalizedCounts.xls


title: Pip2p_N-lim_rep2

description: ChIP-exo: P22

value: 6% (w/v) glucose


title: 1.5 Rod+

description:
Rodplus_1.5
processed data file:
CONTROLminus_vs_CONTROLplus.normalizedCounts.xls


title: 1.8 Rod+

description:
Rodplus_1.8
processed data file:
BLEOMYCINminus_vs_BLEOMYCINplus.normalizedCounts.xls


title: Pip2p_N-lim_rep1

description: ChIP-exo: P21


title: 1.3 Rod+

description:
Rodplus_1.3
processed data file:
CONTROLminus_vs_CONTROLplus.normalizedCounts.xls


title: 2.8 Rod-

description:
Rodminus_2.8
processed data file:
BLEOMYCINminus_vs_BLEOMYCINplus.normalizedCounts.xls

source_name: Bleomycin_GalNP(rho)_CD45- CD31- Rho-

value: CD45- CD31- Rho-


title: Oaf1p_Glu-lim_rep1

description: ChIP-exo: O17

data_processing:
ChIP-exo sequencing reads (R1 reads) were mapped to reference genome assembly with Bowtie2 using default settings to generate SAM files.
SAM files were treated with SAMtools option –q 20 to remove low-quality reads and then converted to sorted BAM files.
BAM files were trimmed 70 bp from 3’ end using trimBam (http://genome.sph.umich.edu/wiki/BamUtil:_trimBam) to increase resolution.
GEM was used to identify peaks and compare biological duplicates. The noise level was calculated from averaged noise throughout each replicate.
Bedtools was used to identify the genome wide targets.
Genome_build: R64-2-1 of S. cerevisiae S288C
Supplementary_files_format_and_content: Excel .xlsx file containing summit position, motif, distance to closest gene (ATG) and signal-to-noise values of peaks for all cultivation conditions

value: OAF1-TAP constructed from CEN.PK 113-5D by adding a C-terminal CBP-ProtA tag to Oaf1p


title: 2.2 Rod-

description:
Rodminus_2.2
processed data file:
CONTROLminus_vs_CONTROLplus.normalizedCounts.xls


title: Oaf1p_Ox,Glu-lim_rep2

description: ChIP-exo: O16


title: 1.8 Rod-

description:
Rodminus_1.8
processed data file:
BLEOMYCINminus_vs_BLEOMYCINplus.normalizedCounts.xls

source_name: Control_GalNP(rho)_CD45- CD31- Rho-


title: 1.3 Rod-

description:
Rodminus_1.3
processed data file:
CONTROLminus_vs_CONTROLplus.normalizedCounts.xls


title: 2.7 Rod-

description:
Rodminus_2.7
processed data file:
BLEOMYCINminus_vs_BLEOMYCINplus.normalizedCounts.xls


title: Oaf1p_Et-lim_rep2

description: ChIP-exo: O14


title: Oaf1p_N-lim_rep1

description: ChIP-exo: O11


title: Hap1p_Glu-lim_rep2

description: ChIP-exo: H18

value: HAP1-TAP constructed from CEN.PK 113-5D by adding a C-terminal CBP-ProtA tag to Hap1p


title: Adult rep 3

city: Minneapolis

first: Sunny

middle: Sun-Kin

last: Chan

state: MN

department: Pediatrics

institute: University of Minnesota

data_processing:
Basecalls with CASAVA version 1.8.2
Reads filtered and trimmed to eliminate low-quality reads and adapter sequences in Galaxy
Reads mapped to mm10 using Tophat 0.7 in Galaxy
Gene expression estimation (FPKM values) using Cufflinks 2.2.1.0 in Galaxy
Hierarchical clustering and ANOVA of FPKM values were performed using Partek Genomic Suite 6.6
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file containing FPKM expression estimates calculated by Cufflinks

source_name: Hindlimbs

extract_protocol:
Tissues were digested with collagnase II and disapase.  Mononuclear cells were FACS-sorted for  CD31- CD45- a7-Integrin+ VCAM+.  RNA was extracted using Qiagen RNeasy mini kit with on-column DNase I treatment.
Samples were then prepared for sequencing using the Clontech SMARTer Stranded Total RNA-seq Kit - Pico Input Mammaian Kit, according to the manufacturer's protocol

value: 8-week-old male

tag: cell types

value: a7-Integrin+ VCAM+ cells from total hindlimbs


title: Adult rep 2


title: Oaf1p_Glu-lim_rep2

description: ChIP-exo: O18


title: Oaf1p_N-lim_rep2

description: ChIP-exo: O12


title: Hap1p_Glu-lim_rep1

description: ChIP-exo: H17


title: Embryo rep 3

source_name: Embryos

value: E14.5 embryo

value: a7-Integrin+ VCAM+ cells from whole embryo


title: Hap1p_Ox,Glu-lim_rep2

description: ChIP-exo: H16


title: Hap1p_Ox,Glu-lim_rep1

description: ChIP-exo: H15


title: Embryo rep 2


title: Hap1p_Et-lim_rep2

description: ChIP-exo: H14


title: 2.6 Rod-

description:
Rodminus_2.6
processed data file:
CONTROLminus_vs_CONTROLplus.normalizedCounts.xls


title: Embryo rep 1


title: Oaf1p_Ox,Glu-lim_rep1

description: ChIP-exo: O15


title: Oaf1p_Et-lim_rep1

description: ChIP-exo: O13


title: Hap1p_N-lim_rep2

description: ChIP-exo: H12


title: 1.5 Rod-

description:
Rodminus_1.5
processed data file:
CONTROLminus_vs_CONTROLplus.normalizedCounts.xls


title: Transplant rep 1

source_name: Pluripotent stem cell derivatives

value: a7-Integrin+ VCAM+ cells from tibialis anterior muscle 1 month after transplanted with teratoma-derived a7-Integrin+ VCAM+ cells


title: Transplant rep 3


title: Hap1p_Et-lim_rep1

description: ChIP-exo: H13


title: Transplant rep 2


title: Hap1p_N-lim_rep1

description: ChIP-exo: H11


title: Teratoma rep 3

value: a7-Integrin+ VCAM+ cells from 3-week-old teratoma


title: Ino4p_Glu-lim_rep2

description: ChIP-exo: I48

value: INO4-TAP constructed from CEN.PK 113-5D by adding a C-terminal CBP-ProtA tag to Ino4p

value: 0.75% (w/v) glucose


title: Ino4p_Ox,Glu-lim_rep2

description: ChIP-exo: I46

value: 1% (w/v) glucose


title: Ino4p_Glu-lim_rep1

description: ChIP-exo: I47


title: Teratoma rep 1


title: Ino4p_Et-lim_rep1

description: ChIP-exo: I43


title: Adult rep 1


title: Ino4p_Ox,Glu-lim_rep1

description: ChIP-exo: I45


title: Ino4p_Et-lim_rep2

description: ChIP-exo: I44


title: Ino4p_N-lim_rep2

description: ChIP-exo: I42


title: Ino4p_N-lim_rep1

description: ChIP-exo: I41


title: Ino2p_Glu-lim_rep2

description: ChIP-exo: I28

value: INO2-TAP constructed from CEN.PK 113-5D by adding a C-terminal CBP-ProtA tag to Ino2p


title: 5hmC-BC6T

description: 5hmC level in TET1-high primary breast tumour from patient BC6

tag: tumor status

value: Primary tumor

tag: patient id

value: High

value: hydroxymethylcytosine (5hmC)


title: 5hmC-BC5N

description: 5hmC level in adjacent normal breast tissue from patient BC5

value: Adjacent normal

tag: tet1 qpcr level

tag: ip


title: Ino2p_Et-lim_rep2

description: ChIP-exo: I24

value: 0.5% (w/v) ethanol


title: 5hmC-BC5T

description: 5hmC level in TET1-high primary breast tumour from patient BC5


title: Sham_Saline rep1

source_name: DRG

value: sciatic dorsal root ganglia (DRG)

value: 6-8 weeks old

tag: index sequence

value: ACAGTG(A)

tag: lane


title: Ino2p_Et-lim_rep1

description: ChIP-exo: I23


title: Ino2p_Ox,Glu-lim_rep1

description: ChIP-exo: I25


title: Teratoma rep 2


title: Ino2p_N-lim_rep2

description: ChIP-exo: I22

value: 6% (w/v) glucose


title: Ino2p_N-lim_rep1

description: ChIP-exo: I21


title: IMS-M2 RNA-Seq

city: San Diego

first: Ian

middle: M

last: Silverman

state: California

address: 4545 Towne Centre Court

department: Computational Biology

institute: Ignyta Inc.

data_processing:
Raw FASTQ files were mapped to the human genome (hg19) with STAR (v2.5.1b_modified) aligner
Mapped reads were filtered and deduplicated using sambamba (v0.5.9)
Feature quantification was performed using featureCounts (v1.5.0-p1) against the RefSeq database (downloaded from the UCSC genome browser on 03/06/2016)
Exon-level FPKM values were determined using a custom python script.
De-novo fusion transcript identification was performed using STAR-Fusion (v0.7.0), FusionAnnotator, FusionInspector
Genome_build: hg19
Supplementary_files_format_and_content: counts files were generated using FeatureCounts and a custom python script for FPKM determination. Scores represent the raw counts and fpkm
Supplementary_files_format_and_content: abridged files were generated using STAR-FUSION, FusionInspector and FusionAnnotator. Scores represent the Junction Read Count and Spanning Fragment Count

source_name: AML Cells

growth_protocol: IMS-M2 and M0-91 AML cell lines were kindly provided by Brunangelo Falini (University of Perugia, Perugia, Italy) and by Mikko Taipale (University of Toronto, Toronto, Canada), respectively, and were maintained at 37°C/5%CO2 in RPMI/10% FBS medium as previously described (5,32).  Cell line authentication and pathogen testing was performed to confirm cell line identities and pathogen-free status (IDEXX BioResearch, Columbia, MO).  Kasumi-1 AML cells were obtained from American Type Culture Collection (Manassas, VA) and were maintained in accordance with provided specifications.

extract_protocol:
Total RNA was isolated using Qiagen AllPrep kit per manufacturer’s instructions.
RNA sequencing libraries were prepared using the KAPA Stranded RNA-Seq Kit with RiboErase (HMR) (KAPA Biosystems). Libraries were constructed following the manufactures protocol using 300ng of total RNA. RNA was fragmented to a size of 100-200 nucleotides and amplified for 11 cycles. Final libraries were quantified on a high sensitivity bioanalyzer chip and sequenced at 1.6 pM on a High Output Flowcell on the Illumina NextSeq 500.

tag: tumor type

value: Acute myeloid leukemia


title: M0-91 RNA-Seq


title: RNA mouse brain 12 month 150 mg/kg SAHA rep1

status: Public on Jul 04 2018

city: Beijing

first: Jing-Dong

middle: Jackie

last: Han

address: 5 Yiheyuan Rd, Haidian District

institute: Peking University

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were mapped by using STAR (v2.5.2a) with 2% max mismatch.
Cuffdiff (v2.2.1) 37 with default parameters was used to generate RPKM.
R (v3.1.0) was used to transform RPKM to log2 scale.
Genome_build: hg19, mm10
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each samples derived from cuffdiff (v2.2.1) with default parameters. Then all values were log2 transformed.

source_name: brain

growth_protocol: Cells were cultured in DMEM with 10% FBS and 1% Penicillin-Streptomycin-Glutamine. All cells were grown at 37oC with 5% CO2.

extract_protocol:
Tissues were lysed in TRIzol using a TissueRuptor,total RNA wasextracted according to TRIzol standard procedures. Cells were directly harvested with TRIzol standard procedures.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were treated three times a week with DMSO or SAHA which diluted to 5% in normal saline for 3 months by using intragastric administration. DMSO or SAHA were added to cultured cells 1 day after plating. Then cells were harvested with TRIzol after 12h.

value: brain

value: 12 month old

tag: treatment

value: 150 mg/kg SAHA


title: RNA mouse brain 12 month DMSO rep1

value: DMSO


title: RNA mouse brain 12 month DMSO rep2


title: RNA mouse brain 13 month 50 mg/kg SAHA rep11

molecule: polyA RNA

value: 13 month old

value: 50 mg/kg SAHA


title: RNA mouse brain 12 month 75 mg/kg SAHA

value: 75 mg/kg SAHA


title: RNA mouse brain 12 month 150 mg/kg SAHA rep2


title: RNA mouse brain 13 month 50 mg/kg SAHA rep9


title: Ino2p_Glu-lim_rep1

description: ChIP-exo: I27

value: INO2-TAP constructed from CEN.PK 113-5D by adding a C-terminal CBP-ProtA tag to Ino2p

value: 0.75% (w/v) glucose


title: Chat17_GFP-Nova_CLIP_1

first: Yuan

last: Yuan

state: NY

address: 1230 York Ave

department: Laboraotry of Molecular Neuro-Oncology

institute: The Rockefeller University

description:
5' barcode: NNNNG, 3' adaptor: GTGTCAGTCACTTCCAGCGG
GFP-Nova HITS-CLIP on pooled spinal cords from Chat:GFP-Nova #17, biological replicate 1

data_processing:
library strategy: CLIP-seq
filter fastq files by quailty scores, min:0-4:20; mean:5-29:20, output FASTA
collapse exact sequences
strip 5' degenerate linker NNNNG
remove 3' adaptor sequence (GTGTCAGTCACTTCCAGCGG)
align to mm9 using novoalign (unambigous mapping)
collapse of PCR duplicates
filter out reads immediately upstream of genomic GTGTC
Genome_build: mm13
Supplementary_files_format_and_content: bed files containing genomic coordinates of unique unambigously mapped reads; 9 column-BED, the 7th, 8th, and 9th columns are thickStart, thickEnd, and itemRgb.

extract_protocol:
HITS-CLIP was performed on freshly isolated spinal cords using anti-GFP antibodies. The monoclonal anti-GFP antibodies 19C8 and 19F7 from Memorial Sloan Kettering Antibody Facility were used.
partial RNAse digestion, 3' and 5' RNA linker ligation and two rounds of PCR amplificiation

tag: strain background

tag: genotype/variation

value: Chat:GFP-Nova #17 hemizygous

value: Pooled spinal cords


title: Ino2p_Ox,Glu-lim_rep2

description: ChIP-exo: I26

tag: strain

value: 1% (w/v) glucose


title: Chat6_GFP-Nova_CLIP_2

description:
5' barcode: CANNNNG, 3' adaptor: GTGTCAGTCACTTCCAGCGG
GFP-Nova HITS-CLIP on pooled spinal cords from Chat:GFP-Nova #6, biological replicate 2

data_processing:
library strategy: CLIP-seq
filter fastq files by quailty scores, min:0-6:20, mean:7-31:20, output FASTA
collapse exact sequences
strip 5' degenerate linker CANNNNG
remove 3' adaptor sequence (GTGTCAGTCACTTCCAGCGG)
align to mm9 using novoalign (unambigous mapping)
collapse of PCR duplicates
filter out reads immediately upstream of genomic GTGTC
Genome_build: mm10
Supplementary_files_format_and_content: bed files containing genomic coordinates of unique unambigously mapped reads; 9 column-BED, the 7th, 8th, and 9th columns are thickStart, thickEnd, and itemRgb.

source_name: Chat6_GFP-Nova_CLIP_pooled spinal cords

value: Chat:GFP-Nova #6 hemizygous


title: Chat6_GFP-Nova_CLIP_1

description:
5' barcode: NNNNG, 3' adaptor: GTGTCAGTCACTTCCAGCGG
GFP-Nova HITS-CLIP on pooled spinal cords from Chat:GFP-Nova #6, biological replicate 1

data_processing:
library strategy: CLIP-seq
filter fastq files by quailty scores, min:0-4:20; mean:5-29:20, output FASTA
collapse exact sequences
strip 5' degenerate linker NNNNG
remove 3' adaptor sequence (GTGTCAGTCACTTCCAGCGG)
align to mm9 using novoalign (unambigous mapping)
collapse of PCR duplicates
filter out reads immediately upstream of genomic GTGTC
Genome_build: mm9
Supplementary_files_format_and_content: bed files containing genomic coordinates of unique unambigously mapped reads; 9 column-BED, the 7th, 8th, and 9th columns are thickStart, thickEnd, and itemRgb.


title: Chat17_GFP-Nova_CLIP_2

description:
5' barcode: GANNNNG, 3' adaptor: GTGTCAGTCACTTCCAGCGG
GFP-Nova HITS-CLIP on pooled spinal cords from Chat:GFP-Nova #17, biological replicate 2

data_processing:
library strategy: CLIP-seq
filter fastq files by quailty scores, min:0-6:20, mean:7-31:20, output FASTA
collapse exact sequences
strip 5' degenerate linker GANNNNG
remove 3' adaptor sequence (GTGTCAGTCACTTCCAGCGG)
align to mm9 using novoalign (unambigous mapping)
collapse of PCR duplicates
filter out reads immediately upstream of genomic GTGTC
Genome_build: mm14
Supplementary_files_format_and_content: bed files containing genomic coordinates of unique unambigously mapped reads; 9 column-BED, the 7th, 8th, and 9th columns are thickStart, thickEnd, and itemRgb.


title: 5hmC-BC6N

description: 5hmC level in adjacent normal breast tissue from patient BC6

source_name: Breast tissue

value: Adjacent normal

value: hydroxymethylcytosine (5hmC)


title: RNA mouse brain 13 month 50 mg/kg SAHA rep8


title: RNA mouse brain 13 month 50 mg/kg SAHA rep3


title: RNA mouse brain 13 month 50 mg/kg SAHA rep4


title: RNA mouse brain 13 month 50 mg/kg SAHA rep1


title: RNA mouse brain 13 month DMSO rep5


title: RNA mouse brain 13 month 50 mg/kg SAHA rep6


title: RNA mouse brain 13 month DMSO rep6


title: RNA mouse brain 13 month 50 mg/kg SAHA rep10


title: 12wk_SOD1_WT_RNAseq_F

description:
Standard illumina TruSeq linkers
mRNA-seq on 12-week-old female SOD1 WT transgenic spinal cord

data_processing:
align using OLego default parameters (15 nt seed with 1 nt overlapping, ? 4 mismatches per read) (Wu et al., 2013).
Alternative splicing and gene expression analysis using Quantas
Genome_build: mm20
Supplementary_files_format_and_content: Normalized gene expression files; cassette exon alternative splicing files with number of reads mapped to exons and junctions, as well as calculated exon inclusion rates

source_name: 12wk_SOD1_WT_RNAseq_F_spinal cord

extract_protocol:
Poly-A selection RNA-seq on Trizol-extracted total RNA
Illumina TruSeq

tag: gender

value: female

value: Spinal cord


title: RNA mouse brain 13 month DMSO rep4

value: brain

tag: age


title: RNA mouse brain 13 month DMSO rep2


title: 12wk_SOD1_WT_RNAseq_M

description:
Standard illumina TruSeq linkers
mRNA-seq on 12-week-old male SOD1 WT transgenic spinal cord

data_processing:
align using OLego default parameters (15 nt seed with 1 nt overlapping, ? 4 mismatches per read) (Wu et al., 2013).
Alternative splicing and gene expression analysis using Quantas
Genome_build: mm19
Supplementary_files_format_and_content: Normalized gene expression files; cassette exon alternative splicing files with number of reads mapped to exons and junctions, as well as calculated exon inclusion rates

source_name: 12wk_SOD1_WT_RNAseq_M_spinal cord

value: male


title: RNA mouse brain 10 month rep3

value: 10 month old


title: RNA mouse brain 10 month rep6


title: RNA mouse brain 13 month DMSO rep1

value: DMSO


title: RNA human brain R group 95.8

source_name: prefrontal cortex

value: prefrontal cortex

value: Medium age 95.8 year old


title: RNA mouse brain 10 month rep1


title: RNA human brain R group 90.1

value: Medium age 90.1 year old


title: RNA mouse brain 10 month rep5


title: RNA mouse brain 10 month rep2


title: RNA mouse brain 18 month rep3

value: 18 month old


title: Sham_Saline rep2

data_processing:
Sequence reads were aligned to the mm10 mouse reference genome sequence using tophat version 2.0.12 running Bowtie2-2.2.3.
Gene structure annotations corresponding to the Ensembl annotation of the mm10 genome sequence were used to build a transcriptome index and provided to tophat during the alignment step
The aligned reads were sorted using samtools-0.1.19, then read counts per gene were obtained from mapped reads using HTSeq-0.6.0
EdgeR version 3.8.6 (using limma-3.22.7) in R-3.1.1 was used to identify differentially expressed genes.
GC-content bias was controlled for using full quantile normalization in EDASeq-2.0.0 running in R-3.1.1.
EDASeq was also used to generate quality checking figures before and after this normalization.
Differential expression testing was performed on the normalized output from EDASeq using edgeR
Read-level quality checking was performed using fastqc-0.10.1 and the fastqc-aggregator (https://github.com/staciaw/fastqc_aggregator) and gene-level quality checking was performed using RSeQC-2.6.1 (Wang et al., 2012).
Further data filtering and processing was performed in Matlab R2014b and R-3.1.1 including creating visualizations with cummerbund-2.8.2.
Genome_build: mm10
Supplementary_files_format_and_content: RawCounts.txt: tab-delimited txt file of raw sequencing reads
Supplementary_files_format_and_content: ROSData.FPKMs_2013Anno.txt: tab-delimited txt file represents the normalized expression data as FPKM, produced by EdgeR

value: sciatic dorsal root ganglia (DRG)

value: 6-8 weeks old

value: CGATGT(A)


title: RNA mouse brain 18 month rep1


title: RNA human brain R group 84

value: Medium age 84 year old


title: RNA mouse brain 13 month 50 mg/kg SAHA rep7

value: 13 month old

value: 50 mg/kg SAHA


title: RNA mouse brain 13 month 50 mg/kg SAHA rep5


title: RNA mouse brain 13 month 50 mg/kg SAHA rep2


title: RNA human brain R group 76.7

value: Medium age 76.7 year old


title: RNA mouse brain 13 month DMSO rep3


title: RNA mouse brain 3 month rep3

value: 3 month old


title: RNA mouse brain 3 month rep2


title: RNA mouse brain 3 month rep1


title: RNA human brain R group 40

value: Medium age 40 year old


title: ChIP input mouse brain 12 month 75 mg/kg SAHA rep2

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were mapped by using bowtie (v1.1.1) (reads shorter than 150 bp) or bowtie2 (v2.2.4) (reads length is 150 bp)
Heatmaps and profiles for ChIP-seq data were generated and normalized with danpos2 (v2.2.2), total reads were normalized to 1x107
Genome_build: hg19, mm10
Supplementary_files_format_and_content: wig files were generated by danpos2 (v2.2.2), total reads were normalized to 1x107

extract_protocol:
Tissues were homogenize and crosslinked, 10 m~1mg lysis buffer. Samples were sonicated for 40 min.
ChIP libraries were constructed using Illumina standard protocols.

treatment_protocol: Mice were treated three times a week with DMSO or SAHA which diluted to 5% in normal saline for 3 months by using intragastric administration.

value: brain

value: 12 month old

value: 75 mg/kg SAHA

tag: chip antibody


title: RNA mouse brain 10 month rep4

value: 10 month old


title: RNA human brain R group 37.5

value: prefrontal cortex

value: Medium age 37.5 year old


title: ChIP input mouse brain 12 month 75 mg/kg SAHA rep1


title: ChIP H3K27ac mouse brain 12 month 75 mg/kg SAHA rep2

value: H3K27ac (Abcam, Cat. # ab4729)


title: ChIP H3K27ac mouse brain 12 month 75 mg/kg SAHA rep1


title: RNA mouse brain 18 month rep2

value: 18 month old


title: ChIP input mouse brain 12 month DMSO rep2

value: DMSO


title: ChIP H3K27ac human brain N group 46

value: Medium age 46 year old


title: ChIP input mouse brain 13 month 50 mg/kg SAHA


title: ChIP H3K27ac human brain N group 64

value: Medium age 64 year old


title: ChIP H3K27ac mouse brain 13 month 50 mg/kg SAHA rep9


title: ChIP H3K27ac mouse brain 13 month 50 mg/kg SAHA rep8


title: ChIP H3K27ac mouse brain 12 month DMSO rep1


title: ChIP H3K27ac human brain N group 33

value: Medium age 33 year old


title: ChIP H3K27ac mouse brain 12 month DMSO rep2


title: ChIP H3K27ac mouse brain 13 month 50 mg/kg SAHA rep5

value: 13 month old


title: ChIP H3K27ac mouse brain 13 month 50 mg/kg SAHA rep7

value: 50 mg/kg SAHA


title: ChIP H3K27ac mouse brain 13 month 50 mg/kg SAHA rep6


title: ChIP H3K27ac mouse brain 13 month 50 mg/kg SAHA rep1


title: ChIP H3K27ac mouse brain 13 month 50 mg/kg SAHA rep4


title: ChIP H3K27ac mouse brain 13 month 50 mg/kg SAHA rep2


title: ChIP H3K27ac human brain R group 90.1

value: Medium age 90.1 year old


title: ChIP H3K27ac mouse brain 13 month DMSO rep3


title: RNA human brain R group 56.5

value: Medium age 56.5 year old


title: ChIP H3K27ac human brain R group 95.8

value: Medium age 95.8 year old


title: ChIP input mouse brain 12 month DMSO rep1

value: brain


title: ChIP H3K27ac human brain N group 25

value: Medium age 25 year old


title: ChIP H3K27ac mouse brain 13 month 50 mg/kg SAHA rep3


title: RNA human brain R group 27

value: Medium age 27 year old


title: ChIP H3K27ac human brain R group 87.3

value: Medium age 87.3 year old


title: ChIP H3K27ac mouse brain 13 month DMSO rep2


title: ChIP H3K27ac human brain R group 56.5

value: prefrontal cortex


title: ChIP input mouse brain 10 month

value: 10 month old


title: ChIP H3K27ac mouse brain 13 month DMSO rep1

value: H3K27ac (Abcam, Cat. # ab4729)


title: ChIP H3K27ac mouse brain 10 month rep3


title: ChIP H3K27ac human brain R group 40

value: Medium age 40 year old


title: ChIP H3K27ac mouse brain 10 month rep2


title: ChIP H3K27ac human brain R group 27


title: ChIP H3K27ac mouse brain 18 month rep2

value: 18 month old


title: ChIP input mouse brain 3 month

value: 3 month old


title: ChIP input mouse brain 18 month


title: ChIP input mouse brain 13 month DMSO

value: DMSO


title: ChIP H3K27ac mouse brain 3 month rep2


title: ChIP H3K27ac mouse brain 18 month rep3


title: Ctrl Th1 cells Rep 2

first: Xing

last: Chang

address: 320 Yueyang road

institute: Shanghai Institute for Biological Sciences

description:
CD4 T cells
rRNA depleted RNA
processed data files: RNAseq_pcbp1kd_vs_control_DESeq2.txt, RPM.txt

data_processing:
Adaptors were first trimmed from the sequence reads with CUTADAPT
RNA seq reads were aligned to mm9 with STAR
The number of aligned reads that overlap each gene in the annotations (mm9) was counted with HTseq-count, and normalized gene expression (RPM) was determined by Deseq 2.
Differential gene expression was analyzed with Deseq
Genome_build: mm9
Supplementary_files_format_and_content: [.txt] tab-delimited text files include RPM values for each Sample and differential gene expression.

source_name: Ctrl Th1 cells

growth_protocol: T cells were purified and activated with plate-bound anti-Hamster IgG (MP Biomedicals) and anti-CD3 (2C11, Bio X cell) +anti-CD28 (37N, Bio X cell) in the presence of anti-IL-4 (5 _g/ml; 11B11) and IL-12 (2 ng/ml; PeproTech)

extract_protocol:
Total RNA was isolated with RNeasy plus kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: In vitro IL12 differentiated Th1 cells

value: sh Scramble transduced


title: ChIP H3K27ac human brain R group 37.5

tag: tissue

value: Medium age 37.5 year old


title: ChIP H3K27ac mouse brain 3 month rep3


title: WSC_Nova_CLIP_1

description:
5' barcode: CGAAGGGAGGACGATGCGGNNNNG for WSC1_LN.fastq.gz and TCGAGGGAGGACGATGCGGNNNNG for WSC1_SN.fastq.gz, 3' adaptor: GTGTCAGTCACTTCCAGCGG
Nova HITS-CLIP on WT whole spinal cord, biological replicate 1

data_processing:
library strategy: CLIP-seq
filter fastq files by quailty scores, min:0-2:20, mean:3-48:20, output FASTA
collapse exact sequences
strip 5' degenerate linker CGAAGGGAGGACGATGCGGNNNNG
remove 3' adaptor sequence (GTGTCAGTCACTTCCAGCGG)
align to mm9 using novoalign (unambigous mapping)
collapse of PCR duplicates
filter out reads immediately upstream of genomic GTGTC
Genome_build: mm17
Supplementary_files_format_and_content: bed files containing genomic coordinates of unique unambigously mapped reads; 9 column-BED, the 7th, 8th, and 9th columns are thickStart, thickEnd, and itemRgb.

source_name: WSC_Nova_CLIP_spinal cord

extract_protocol:
HITS-CLIP was performed on freshly isolated spinal cord using anti-Nova anti-sera
partial RNAse digestion, 3' and 5' RNA linker ligation and two rounds of PCR amplificiation

value: wild type

value: Spinal cord


title: PCBP1 CLIP 1

description:
PCBP1 IP RNA
processed data file: PCBP1_CLIP_Peaks_2.bed

data_processing:
Adaptors were first trimmed from the sequence reads with CUTADAPT
seq reads were aligned to Hg19 with STAR
PCBP1 CLIP peaks were identified with CLIPper
Genome_build: Hg19
Supplementary_files_format_and_content: [.bed] files include PCBP1 CLIP peaks, relative enrichment over input and p values

source_name: PCBP1 CLIP

growth_protocol: Jurkat T cells were grown at 37 degree in RPMI with 10% FBS

extract_protocol:
protein-RNA complex was immunoprecipated with anti-PCBP1, and associated RNA was extracted.
3' RNA adaptor was first ligated to the RNA with T4 RNA ligase. Protein-RNA complex was then purified with SDS-PAGE, and RNA was extracted. Next purified RNA was reverse transcribed and 5' DNA adaptor was ligated to cDNA.

treatment_protocol: UV crosslinking to induce covalent bonds between RNA and proteins

tag: cell line

value: Jurkat T cell lymphoma cell line

value: UV crosslinking

tag: rip antibody


title: PCBP1 CLIP Input 1

description:
input RNA
processed data file: PCBP1_CLIP_Peaks_1.bed

source_name: PCBP1 CLIP Input

value: none (input)


title: ChIP H3K27ac mouse brain 18 month rep1

value: brain


title: PCBP1 KD Th1 cells Rep 2

source_name: PCBP1 KD Th1 cells

value: sh PCBP1 transduced


title: PCBP1 CLIP 2


title: ChIP H3K27ac mouse brain 3 month rep1


title: PCBP1 CLIP Input 2


title: Ctrl Th1 cells Rep 1


title: Chat17_GFP-Nova_CLIP_4

description:
5' barcode: GCTAGGGAGGACGATGCGGNNNNG, 3' adaptor: GTGTCAGTCACTTCCAGCGG
GFP-Nova HITS-CLIP on pooled spinal cords from Chat:GFP-Nova #17, biological replicate 4

data_processing:
library strategy: CLIP-seq
filter fastq files by quailty scores, min:0-2:20, mean:3-48:20, output FASTA
collapse exact sequences
strip 5' degenerate linker GCTAGGGAGGACGATGCGGNNNNG
remove 3' adaptor sequence (GTGTCAGTCACTTCCAGCGG)
align to mm9 using novoalign (unambigous mapping)
collapse of PCR duplicates
filter out reads immediately upstream of genomic GTGTC
Genome_build: mm16
Supplementary_files_format_and_content: bed files containing genomic coordinates of unique unambigously mapped reads; 9 column-BED, the 7th, 8th, and 9th columns are thickStart, thickEnd, and itemRgb.

value: Chat:GFP-Nova #17 hemizygous

value: Pooled spinal cords


title: WSC_Nova_CLIP_4

description:
5' barcode: GTGAGGGAGGACGATGCGGNNNNG for WSC4_LN.fastq.gz and CACAGGGAGGACGATGCGGNNNNG for WSC4_SN.fastq.gz, 3' adaptor: GTGTCAGTCACTTCCAGCGG
Nova HITS-CLIP on WT whole spinal cord, biological replicate 4

data_processing:
library strategy: CLIP-seq
filter fastq files by quailty scores, min:0-2:20, mean:3-48:20, output FASTA
collapse exact sequences
strip 5' degenerate linker GTGAGGGAGGACGATGCGGNNNNG
remove 3' adaptor sequence (GTGTCAGTCACTTCCAGCGG)
align to mm9 using novoalign (unambigous mapping)
collapse of PCR duplicates
filter out reads immediately upstream of genomic GTGTC
Genome_build: mm20
Supplementary_files_format_and_content: bed files containing genomic coordinates of unique unambigously mapped reads; 9 column-BED, the 7th, 8th, and 9th columns are thickStart, thickEnd, and itemRgb.


title: PCBP1 KD Th1 cells Rep 1


title: Chat17_GFP-Nova_CLIP_3

description:
5' barcode: AGCAGGGAGGACGATGCGGNNNNG, 3' adaptor: GTGTCAGTCACTTCCAGCGG
GFP-Nova HITS-CLIP on pooled spinal cords from Chat:GFP-Nova #17, biological replicate 3

data_processing:
library strategy: CLIP-seq
filter fastq files by quailty scores, min:0-2:20, mean:3-48:20, output FASTA
collapse exact sequences
strip 5' degenerate linker AGCAGGGAGGACGATGCGGNNNNG
remove 3' adaptor sequence (GTGTCAGTCACTTCCAGCGG)
align to mm9 using novoalign (unambigous mapping)
collapse of PCR duplicates
filter out reads immediately upstream of genomic GTGTC
Genome_build: mm15
Supplementary_files_format_and_content: bed files containing genomic coordinates of unique unambigously mapped reads; 9 column-BED, the 7th, 8th, and 9th columns are thickStart, thickEnd, and itemRgb.


title: Chat6_GFP-Nova_CLIP_4

description:
5' barcode: CACAGGGAGGACGATGCGGNNNNG, 3' adaptor: GTGTCAGTCACTTCCAGCGG
GFP-Nova HITS-CLIP on pooled spinal cords from Chat:GFP-Nova #6, biological replicate 4

data_processing:
library strategy: CLIP-seq
filter fastq files by quailty scores, min:0-2:20, mean:3-48:20, output FASTA
collapse exact sequences
strip 5' degenerate linker CACAGGGAGGACGATGCGGNNNNG
remove 3' adaptor sequence (GTGTCAGTCACTTCCAGCGG)
align to mm9 using novoalign (unambigous mapping)
collapse of PCR duplicates
filter out reads immediately upstream of genomic GTGTC
Genome_build: mm12
Supplementary_files_format_and_content: bed files containing genomic coordinates of unique unambigously mapped reads; 9 column-BED, the 7th, 8th, and 9th columns are thickStart, thickEnd, and itemRgb.

value: Chat:GFP-Nova #6 hemizygous


title: WSC_Nova_CLIP_2

description:
5' barcode: AAGAGGGAGGACGATGCGGNNNNG for WSC2_LN.fastq.gz and CTTAGGGAGGACGATGCGGNNNNG for  WSC2_SN.fastq.gz, 3' adaptor: GTGTCAGTCACTTCCAGCGG
Nova HITS-CLIP on WT whole spinal cord, biological replicate 2

data_processing:
library strategy: CLIP-seq
filter fastq files by quailty scores, min:0-2:20, mean:3-48:20, output FASTA
collapse exact sequences
strip 5' degenerate linker AAGAGGGAGGACGATGCGGNNNNG
remove 3' adaptor sequence (GTGTCAGTCACTTCCAGCGG)
align to mm9 using novoalign (unambigous mapping)
collapse of PCR duplicates
filter out reads immediately upstream of genomic GTGTC
Genome_build: mm18
Supplementary_files_format_and_content: bed files containing genomic coordinates of unique unambigously mapped reads; 9 column-BED, the 7th, 8th, and 9th columns are thickStart, thickEnd, and itemRgb.


title: ChIP H3K27ac mouse brain 10 month rep1

value: 10 month old

value: H3K27ac (Abcam, Cat. # ab4729)


title: Chat6_GFP-Nova_CLIP_3

description:
5' barcode: GTGAGGGAGGACGATGCGGNNNNG, 3' adaptor: GTGTCAGTCACTTCCAGCGG
GFP-Nova HITS-CLIP on pooled spinal cords from Chat:GFP-Nova #6, biological replicate 3

data_processing:
library strategy: CLIP-seq
filter fastq files by quailty scores, min:0-2:20, mean:3-48:20, output FASTA
collapse exact sequences
strip 5' degenerate linker GTGAGGGAGGACGATGCGGNNNNG
remove 3' adaptor sequence (GTGTCAGTCACTTCCAGCGG)
align to mm9 using novoalign (unambigous mapping)
collapse of PCR duplicates
filter out reads immediately upstream of genomic GTGTC
Genome_build: mm11
Supplementary_files_format_and_content: bed files containing genomic coordinates of unique unambigously mapped reads; 9 column-BED, the 7th, 8th, and 9th columns are thickStart, thickEnd, and itemRgb.


title: WSC_Nova_CLIP_3

description:
5' barcode: TAGAGGGAGGACGATGCGGNNNNG for WSC3_LN.fastq.gz and CTAAGGGAGGACGATGCGGNNNNG for WSC3_SN.fastq.gz, 3' adaptor: GTGTCAGTCACTTCCAGCGG
Nova HITS-CLIP on WT whole spinal cord, biological replicate 3

data_processing:
library strategy: CLIP-seq
filter fastq files by quailty scores, min:0-2:20, mean:3-48:20, output FASTA
collapse exact sequences
strip 5' degenerate linker TAGAGGGAGGACGATGCGGNNNNG
remove 3' adaptor sequence (GTGTCAGTCACTTCCAGCGG)
align to mm9 using novoalign (unambigous mapping)
collapse of PCR duplicates
filter out reads immediately upstream of genomic GTGTC
Genome_build: mm19
Supplementary_files_format_and_content: bed files containing genomic coordinates of unique unambigously mapped reads; 9 column-BED, the 7th, 8th, and 9th columns are thickStart, thickEnd, and itemRgb.


title: DMSO treated Th1 cells Rep 2

description:
CD4 T cells
processed data files: RNAseq_cpx_vs_dmso_DESeq2.txt, RPM.txt

source_name: DMSO treated Th1 cells

value: DMSO treated


title: WT_mRNA_replicate3

city: Muenster

first: Benedikt

middle: Sebastian

last: Nilges

address: Von-Esmarch-Straße 54

department: RNA Biology Group

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

description: Accessioned previously in GEO as: GSM2552201

data_processing:
for fooprints: linkers were removed from reads using the fastx_clipper and randomized sequences removed using the fastx_trimmer (FASTX Toolkit). Already performed for uploaded files.
Data was mapped to human rRNA with bowtie and unaligned reads used for subsequent steps.
Data was mapped to the hg38 transcriptome (UCSC knownCanonical) with bowtie (-m 1 -v1 -l 25 --best --strata) and reads counted using a custom script.
Genome_build: genome: hg38/GRCh38
Supplementary_files_format_and_content: Comma seperated table with raw counts for all WT and KO samples in this study. UCSC_IDs are are from hg38 known_canonical (Gencode v24, available from UCSC table browser).

growth_protocol: Wild type and EEF1AKMT4-deficient HAP-1 cells were cultured in IMDM GlutaMAX™, 10 % FBS and 100 U/ml penicillin-streptomycin.

extract_protocol:
For ribosome profiling, lysates were treated with 250 U RNase I (Ambion) for 10 min at 22 °C and shaking at 1400 rpm. The digestion was stopped by addition of 100 U SUPERase In RNase inhibitor (Ambion). Ribosomes were separated on a 10-50 % (w/v) sucrose density gradient in 50 mM Tris pH 7.5, 50 mM NH4Cl, 12 mM MgCl2, 0.5 mM DTT, 100 µg/ml CHX for 3 h at 35 000 rpm and 4 °C in a TH-641 rotor (Thermo Scientific). Gradients were fractionated at 0.75 ml/min with continuous monitoring of OD254 on a density gradient fractionator (Isco) coupled to a SYR-101 syringe pump (Brandel). SDS was added immediately to 1 % and 400 µl fractions were flash-frozen in liquid nitrogen and stored at -80 °C until further processing. Monosome fractions were pooled, RNA isolated and separated on 15 % polyacrylamide gels (8 M urea, 1 x TBE). Ribosome footprints were excised between 28 nucleotide (nt) and 32 nt RNA size markers.
Sequencing libraries from ribosome footprints were generated essentially as described by Ingolia and colleagues (Ingolia et al. Nat Prot 2012 , except for ligation to a preadenylated 3’-adapter (5’ rAppNNNNCTGTAGGCACCATCAAT/3ddC/ 3’) in a reaction containing 200 000 U T4 RNA ligase 2 (truncated, NEB), 25 % PEG 8000 and 10 U SUPERase In RNase inhibitor for 4 h at 22 °C. RNAseq libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina).

treatment_protocol: Cells were treated with 100 µg/ml cycloheximide (CHX) for 1 min, washed with ice cold PBS containing 100 µg/ml CHX and subsequently lysed in lysis buffer (10 mM Tris pH 7.5, 100 mM NaCl, 10 mM MgCl2, 1 % Triton X-100, 0.5 mM DTT, 100 µg/ml CHX).

tag: genotype

value: HAP-1 cells


title: METTL13_KO_mRNA_replicate3


title: CPX treated Th1 cells Rep 2

source_name: CPX treated Th1 cells

value: In vitro IL12 differentiated Th1 cells

value: Iron Chelator CPX treated


title: WT_RPF_replicate2

description: Accessioned previously in GEO as: GSM2552195

data_processing:
Library strategy: ribosome profiling
for fooprints: linkers were removed from reads using the fastx_clipper and randomized sequences removed using the fastx_trimmer (FASTX Toolkit). Already performed for uploaded files.
Data was mapped to human rRNA with bowtie and unaligned reads used for subsequent steps.
Data was mapped to the hg38 transcriptome (UCSC knownCanonical) with bowtie (-m 1 -v1 -l 25 --best --strata) and reads counted using a custom script.
Genome_build: genome: hg38/GRCh38
Supplementary_files_format_and_content: Comma seperated table with raw counts for all WT and KO samples in this study. UCSC_IDs are are from hg38 known_canonical (Gencode v24, available from UCSC table browser).


title: WT_RPF_replicate1

description: Accessioned previously in GEO as: GSM2552194


title: METTL13_KO_RPF_replicate2


title: METTL13_KO_mRNA_replicate1


title: WT_mRNA_replicate1

description: Accessioned previously in GEO as: GSM2552199


title: METTL13_KO_RPF_replicate3


title: DMSO treated Th1 cells Rep 1


title: wt_LPS_CD45hi_5426

status: Public on Jul 03 2018

city: Freiburg

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

institute: University Medical Center Freiburg

description:
5426_CNS_Phi
Processed data file: counts.txt
Processed data file: cpm.txt
Processed data file: Voom_Matrix.txt

data_processing:
Basecalling was performed using RTA 1.18.61.
bcl files were converted to fastq using bcl2fastq.
Fastq files were aligned to the mouse genome (Gencode M11) using the Star aligner (version STAR_2.5.2b).
Gene counts were generated using featureCounts from the Subread package (featureCounts v1.5.1).
Prior to differential gene expression analysis, low gene counts were removed with the lowest 32% of genecounts (sums of all samples) being removed.
Count normalization and differential gene expression analysis were performed using the limma/voom pipeline (limma version 3.30.8).
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text files with raw transcript counts ("counts.txt"), counts per million ("cpm.txt") and normalized counts ("Voom_matrix.txt").

source_name: FACS-sorted CD45hi cells, WT, LPS

growth_protocol: CD11b+ CD45hi cells were sorted in RNAprotect [from: RNeasy Plus Micro Kit (QIAGEN, Hilden, Germany)] cell reagent using FACS.

extract_protocol:
Cells were stored and shipped in RNAprotect buffer at 2-8 °C. After pelleting, the RNAprotect buffer was replaced by RLT Plus and the samples were homogenized by vortexing for 30 sec. Genomic DNA contamination was removed using gDNA Eliminator spin columns. Next, ethanol was added and the samples were applied to RNeasy MinElute spin columns followed by several wash steps. Finally, total RNA was eluted in 12 μl of nuclease-free water. Purity and integrity of the RNA were assessed on the Agilent 2100 Bioanalyzer with the RNA 6000 Pico LabChip reagent set (Agilent, Palo Alto, CA, USA).
The SMARTer Ultra Low Input RNA Kit for Sequencing v4 (Clontech Laboratories, Inc., Mountain View, CA, USA) was used to generate first strand cDNA from 1 ng total-RNA. Double-stranded cDNA was amplified by LD PCR (11 cycles) and purified via magnetic bead clean-up. Library preparation was carried out as described in the Illumina Nextera XT Sample Preparation Guide (Illumina, Inc., San Diego, CA, USA). 150 pg of input cDNA were tagmented (tagged and fragmented) by the Nextera XT transposome. The products were purified and amplified via a limited-cycle PCR program to generate multiplexed sequencing libraries. For the PCR step, 1:5 dilutions of index 1 (i7) and index 2 (i5) primers were used. The libraries were quantified using the KAPA SYBR FAST ABI Prism Library Quantification Kit (Kapa Biosystems, Inc., Woburn, MA, USA).

treatment_protocol: Gene Knockout in microglia-specific A20 knockout mice, i. p. treatment with LPS (3.5 mg/kg).

tag: strain/background

value: WT

value: LPS

value: Brain

value: CD11b+ CD45hi


title: WT_mRNA_replicate2

description: Accessioned previously in GEO as: GSM2552200

value: wild type


title: METTL13_KO_mRNA_replicate2


title: A20_LPS_CD45hi_5430

description:
5430_CNS_Phi
Processed data file: counts.txt
Processed data file: cpm.txt
Processed data file: Voom_Matrix.txt

source_name: FACS-sorted CD45hi cells, A20 KO, LPS

value: A20 knockout


title: wt_LPS_CD45hi_5425

description:
5425_CNS_Phi
Processed data file: counts.txt
Processed data file: cpm.txt
Processed data file: Voom_Matrix.txt


title: METTL13_KO_RPF_replicate1


title: A20_LPS_CD45hi_5424

description:
5424_CNS_Phi
Processed data file: counts.txt
Processed data file: cpm.txt
Processed data file: Voom_Matrix.txt


title: A20_LPS_CD45hi_5408

description:
5408_CNS_Phi
Processed data file: counts.txt
Processed data file: cpm.txt
Processed data file: Voom_Matrix.txt


title: control_rep1

city: Chicago

first: Megan

middle: E.

last: McNerney

state: Illinois

address: 900 East 57th Street, KCBD 5128

department: Pathology

institute: The University of Chicago

description: RNA-seq

data_processing:
RNA-seq reads were aligned to hg19 with Tophat using default parameters. Reads with quality scores >30 were counted using HTseq-tools and analyzed with EdgeR
Genome_build: Hg19
Supplementary_files_format_and_content: RNA-seq text file contains EdgeR results for Gene ID, log fold change, log counts per million, p value and q values for control versus knockdown.

source_name: CD34+ human HSPC

growth_protocol: HSPCs were grown in Stemline II media supplemented with 50 ng/mL each of IL-3, IL-6, thrombopoietin, SCF, and Fms-like tyrosine kinase 3 ligand

extract_protocol:
RNA was isolated using Trizol.
Barcoded RNA-seq libraries were generated using the standard Illumina TruSEQ v2 kit.

treatment_protocol: Cells were transduced with lentivirus containing the shRNAs.  RNA was collected three days after transduction by sorting for CD34+ GFP+ cells.

tag: shRNA

value: control shRNA


title: wt_LPS_CD45hi_5365

description:
5365_CNS_Phi
Processed data file: counts.txt
Processed data file: cpm.txt
Processed data file: Voom_Matrix.txt


title: A20_LPS_CD45hi_5318

description:
5318_CNS_Phi
Processed data file: counts.txt
Processed data file: cpm.txt
Processed data file: Voom_Matrix.txt


title: shCUX1-B_rep2

description: RNA-seq


title: shCUX1-A_rep1

description: RNA-seq


title: shCUX1-A_rep2

description: RNA-seq


title: shCUX1-B_rep1

description: RNA-seq


title: control_rep2

description: RNA-seq


title: wt_LPS_CD45hi_5276

description:
5276_CNS_Phi
Processed data file: counts.txt
Processed data file: cpm.txt
Processed data file: Voom_Matrix.txt


title: CPX treated Th1 cells Rep 1

city: Shanghai


title: A20_ctrl_CD45hi_5224

description:
5224_CNS_Phi
Processed data file: counts.txt
Processed data file: cpm.txt
Processed data file: Voom_Matrix.txt

source_name: FACS-sorted CD45hi cells, A20 KO, control

value: control


title: A20_ctrl_CD45hi_5223

description:
5223_CNS_Phi
Processed data file: counts.txt
Processed data file: cpm.txt
Processed data file: Voom_Matrix.txt


title: A20 knockout (KO) LPS stimulated [5317_MG]

description:
5317_MG
Processed data file: counts.txt
Processed data file: cpm.txt
Processed data file: Voom_Matrix.txt

data_processing:
Basecalling was performed using RTA 1.18.61.
bcl files were converted to fastq using CASAVA 1.8.2.
Fastq files were aligned to the mouse genome (Gencode M11) using the Star aligner (version STAR_2.5.2b).
Gene counts were generated using featureCounts from the Subread package (featureCounts v1.5.1).
Prior to differential gene expression analysis, low gene counts were removed with the lowest 32% of genecounts (sums of all samples) being removed.
Count normalization and differential gene expression analysis was performed using the limma/voom pipeline (limma version 3.28.21).
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text files with raw transcript counts ("counts.txt"), counts per million ("cpm.txt") and normalized counts ("Voom_matrix.txt").

source_name: FACS-sorted microglia, A20 KO, LPS

growth_protocol: CD11b+ CD45Int microglia were sorted in RNAprotect [from: RNeasy Plus Micro Kit (QIAGEN, Hilden, Germany)] cell reagent using FACS.

value: microglia


title: A20 knockout (KO) LPS stimulated [5430_MG]

description:
5430_MG
Processed data file: counts.txt
Processed data file: cpm.txt
Processed data file: Voom_Matrix.txt


title: Wild-type (WT) LPS stimulated [5426_MG]

description:
5426_MG
Processed data file: counts.txt
Processed data file: cpm.txt
Processed data file: Voom_Matrix.txt

source_name: FACS-sorted microglia, WT, LPS


title: wt_ctrl_CD45hi_4847

description:
4847_CNS_Phi
Processed data file: counts.txt
Processed data file: cpm.txt
Processed data file: Voom_Matrix.txt

source_name: FACS-sorted CD45hi cells, WT, control


title: A20 knockout (KO) LPS stimulated [5424_MG]

description:
5424_MG
Processed data file: counts.txt
Processed data file: cpm.txt
Processed data file: Voom_Matrix.txt


title: Wild-type (WT) LPS stimulated [5276_MG]

description:
5276_MG
Processed data file: counts.txt
Processed data file: cpm.txt
Processed data file: Voom_Matrix.txt


title: A20 knockout (KO) LPS stimulated [5318_MG]

description:
5318_MG
Processed data file: counts.txt
Processed data file: cpm.txt
Processed data file: Voom_Matrix.txt


title: A20_ctrl_CD45hi_5088

description:
5088_CNS_Phi
Processed data file: counts.txt
Processed data file: cpm.txt
Processed data file: Voom_Matrix.txt


title: wt_ctrl_CD45hi_5222

description:
5222_CNS_Phi
Processed data file: counts.txt
Processed data file: cpm.txt
Processed data file: Voom_Matrix.txt


title: wt_ctrl_CD45hi_4848

description:
4848_CNS_Phi
Processed data file: counts.txt
Processed data file: cpm.txt
Processed data file: Voom_Matrix.txt


title: wt_ctrl_CD45hi_5221

description:
5221_CNS_Phi
Processed data file: counts.txt
Processed data file: cpm.txt
Processed data file: Voom_Matrix.txt


title: A20_ctrl_CD45hi_5090

description:
5090_CNS_Phi
Processed data file: counts.txt
Processed data file: cpm.txt
Processed data file: Voom_Matrix.txt


title: wt_ctrl_CD45hi_5081

description:
5081_CNS_Phi
Processed data file: counts.txt
Processed data file: cpm.txt
Processed data file: Voom_Matrix.txt


title: A20_LPS_CD45hi_5317

description:
5317_CNS_Phi
Processed data file: counts.txt
Processed data file: cpm.txt
Processed data file: Voom_Matrix.txt


title: Wild-type (WT) LPS stimulated [5365_MG]

description:
5365_MG
Processed data file: counts.txt
Processed data file: cpm.txt
Processed data file: Voom_Matrix.txt


title: A20 knockout (KO) unstimulated [5088_MG]

description:
5088_MG
Processed data file: counts.txt
Processed data file: cpm.txt
Processed data file: Voom_Matrix.txt

source_name: FACS-sorted microglia, A20 KO, unstimulated


title: Wild-type (WT) unstimulated [5222_MG]

description:
5222_MG
Processed data file: counts.txt
Processed data file: cpm.txt
Processed data file: Voom_Matrix.txt

source_name: FACS-sorted microglia, WT, unstimulated


title: Wild-type (WT) unstimulated [5081_MG]

description:
5081_MG
Processed data file: counts.txt
Processed data file: cpm.txt
Processed data file: Voom_Matrix.txt


title: A20 knockout (KO) unstimulated [5090_MG]

description:
5090_MG
Processed data file: counts.txt
Processed data file: cpm.txt
Processed data file: Voom_Matrix.txt


title: A20 knockout (KO) unstimulated [5224_MG]

description:
5224_MG
Processed data file: counts.txt
Processed data file: cpm.txt
Processed data file: Voom_Matrix.txt


title: A20 knockout (KO) LPS stimulated [5408_MG]

description:
5408_MG
Processed data file: counts.txt
Processed data file: cpm.txt
Processed data file: Voom_Matrix.txt


title: Wild-type (WT) unstimulated [5221_MG]

description:
5221_MG
Processed data file: counts.txt
Processed data file: cpm.txt
Processed data file: Voom_Matrix.txt


title: Wild-type (WT) LPS stimulated [5425_MG]

description:
5425_MG
Processed data file: counts.txt
Processed data file: cpm.txt
Processed data file: Voom_Matrix.txt


title: Wild-type (WT) unstimulated [4848_MG]

description:
4848_MG
Processed data file: counts.txt
Processed data file: cpm.txt
Processed data file: Voom_Matrix.txt


title: Wild-type (WT) unstimulated [4847_MG]

description:
4847_MG
Processed data file: counts.txt
Processed data file: cpm.txt
Processed data file: Voom_Matrix.txt


title: A20 knockout (KO) unstimulated [5223_MG]

description:
5223_MG
Processed data file: counts.txt
Processed data file: cpm.txt
Processed data file: Voom_Matrix.txt


title: H4K20 ChIP-seq in KAP1 WT

city: Lausanne

first: Julien

last: Duc

state: VAUD

address: Station 19 CH-1015 Lausanne

department: School of Life Science

institute: EPFL

data_processing:
Illumina pipeline Casava 1.82
Reads were mapped to the mouse genome (mm9) using Bowtie2 (v2.2.1) in sensitive mode (bowtie2 -p 6 --sensitive-local -x $index -U $reads)
Peaks were called using MACS v1.4
Genome_build: mm9
Supplementary_files_format_and_content: MACS peaks

source_name: MEF

extract_protocol:
Cells were harvested, washed with PBS 1X, fixed in 2mL per 1x107 cells (10 min in 1% formaldehyde), quenched with 250mM Tris HCL pH 8  in 10mL (at 125 mM final), washed three times with PBS 1X, and pelleted. Each pellet containing 1x107 cells was lysed, resuspended in 1 mL of sonication buffer on ice (10 mM Tris at pH 8, 1 mM EDTA, 0.2% SDS, and protease inhibitors), transferred to TC 12x12 tubes (Covaris), and sonicated (Covaris settings: 20 min, 5% duty cycle, 140W, 200 cycles). Sonication was assessed by reverse cross-linking (65oC, RNAse A at 1µg/µL, overnight), followed by DNA extraction. Fragment size (between 200-400bp) was checked on a Bioanalyzer (Agilent 2100). Immunoprecipitations were performed with chromatin from 4x107, with Dynabeads (Protein G, ThermoFisher) in IP buffer (10 mM Tris at pH 8, 1 mM EDTA, 0.1% SDS, 150 mM NaCl, 10% Triton X-100, and protease inhibitors) overnight. Chromatin was reversed cross-linked (65oC, Proteinase K at 400ng/µL, overnight) and DNA was extracted.
Illuminal ChIP-seq protocol

tag: antibodies


title: H3K9 ChIP-seq in KAP1 KO

value: Anti-H3K9me3 (ab8898)

value: KAP1 KO


title: Total input Histones marks WT


title: Total input Histones marks KO


title: H4K20 ChIP-seq in KAP1 KO


title: Total input KAP1


title: KAP1 ChIP-seq

value: Anti-KAP1 (ab10843)


title: Posterior60-100_2

city: Delhi

first: Beena

last: Pillai

address: Mathura Road

institute: IGIB

data_processing:
The quality of RNA sequencing reads were checked using FastQC followed by adapter trimming by Trimmomatic (default parameters) .
The data was then de novo assembled using Trinity package (Grabherr et al., 2011). to align reads to the reference. To get a common reference, all the samples were assembled together in a single assembly using Trinity.
The assemblies were annotated using Trinotate pipeline (https://trinotate.github.io/).
Denovo RNA seq differential expression analysis was done using reference made by Trinity and Tuxedo pipeline.
Genome_build: To get a common reference, all the samples were assembled together in a single assembly using Trinity and annotated by Trinotate.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Eisenia fetida

source_name: Posterior segments after cut (collected on day of cutting)

growth_protocol: Eisenia fetida earthworms were procured from farmers engaged in vermicomposting and then maintained in a culture in the laboratory at around 22oC with moderate humidity.

extract_protocol:
The regenerated tissue and the tissue adjacent to it, termed control, were collected separately. RNA was isolated using the Trizol method. Briefly, the tissues were frozen in liquid nitrogen, homogenized using a mortar and pestle in the presence of 1ml Trizol reagent and transferred to a microfuge tube. Phase separation was done by adding 200uL chloroform and centrifugation at 10,000g. The aqueous phase was collected and equal volume of isopropanol was added to precipitate RNA. Pellet was collected by centrifugation at 10,000g, followed by repeated 70% ethanol washes. The RNA was then air dried and dissolved in nuclease-free water
Approximately, 1ug of RNA was taken per sample and RNA sequencing libraries were made using TruSeq v2 Library Prep Kit as per manufacturer's protocol. Briefly, the RNA was polyA selected using OligodT magnetic beads followed by shearing into 200-500bp fragments. This sheared RNA was then used to generate cDNA. The cDNA was end-repaired to blunt ends . These blunt ends were then A-tailed i.e. a "A" overhang was added so as to ligate the adapters in the next step. The adapter ligated cDNA was then amplified by PCR and purified by AMPure XP beads. This library was then quality checked and sequenced on Illumina HiSeq 2500. For small RNA sequencing, total RNA was isolated from bodywall and sequenced on the illumina platform. ~800ng of Total RNA was used as the starting material. Briefly, 3’ adaptors were ligated to the   specific 3’OH group of microRNAs followed by 5’ adaptor ligation. The ligated products were  reverse transcribed with Superscript III Reverse transcriptase by priming with Reverse   transcriptase primers. The cDNA was enriched and barcoded by PCR (15 cycles) and   cleaned using Polyacrylamide gel. The library was size selected in the range of 140 – 160 bp   followed by overnight gel elution and salt precipitation using Glycogen, 3M Sodium Acetate and absolute ethanol. The precipitate was re-suspended in Nuclease free water. The prepared library was quantified using Qubit Fluorometer, and validated for quality on High Sensitivity Bioanalyzer Chip (Agilent).

treatment_protocol: Earthworms were cut transversely at approximately two thirds of the body length (60 +/- 6 segments) and allowed to regenerate for 15, 20 or 30 days . At 15, 20 and 30 days post cut (dpc), the regenerated tissue (15R,20R and 30R) and the adjacent tissue (15C, 20C and 30C) were collected.  Samples from non-regenerating worms were collected from the 60th+3segments (control) on day0. One set of samples (sample 22-24) are segments 60-posterior end collected on day0.

tag: number of worms

value: pooled from 50 worms

tag: type of tissue

value: Original Posterior Tissue


title: Posterior60-100_3


title: 30dpc_R1

source_name: Regenerated tissue posterior to the cut, 30days after cutting

value: Regenerated Tissue 30 days post cut


title: 30dpc_R2


title: 20dpc_R3

source_name: Regenerated tissue posterior to the cut, 20days after cutting

value: Regenerated Tissue 20 days post cut


title: 30dpc_R3


title: 20dpc_R4


title: Posterior60-100_1


title: 20dpc_R2


title: 20dpc_R1


title: 15dpc_R3

source_name: Regenerated tissue posterior to the cut, 15days after cutting

value: Regenerated Tissue 15 days post cut


title: A20 knockout (KO) unstimulated [5089_MG]

description:
5089_MG
Processed data file: counts.txt
Processed data file: cpm.txt
Processed data file: Voom_Matrix.txt

tag: treatment


title: 30dpc_C3

source_name: Three segments anterior to the cut, 30days after cutting

value: Tissue adjacent to Regenerated tissue 30days post cut


title: 15dpc_R1


title: 15dpc_R2


title: 30dpc_C1


title: 30dpc_C2


title: 20dpc_C2

source_name: Three segments anterior to the cut, 20days after cutting

value: Tissue adjacent to Regenerated tissue 20days post cut


title: H3K9 ChIP-seq in KAP1 WT

value: WT


title: 20dpc_C3


title: 20dpc_C1


title: 15dpc_C3

source_name: Three segments anterior to the cut, 15days after cutting

value: Tissue adjacent to Regenerated tissue 15days post cut


title: 0dpc_2

source_name: Three segments around the 60th segment (from anterior)

value: Tissue collected immediately after cutting for regeneration experiment.


title: 15dpc_C2


title: 15dpc_C1


title: PJ030

status: Public on Jul 02 2018

first: Peter

last: Sims

address: 3960 Broadway, 2nd Floor, Room 203AC

data_processing:
Read 1 and read 2 fastq files were generated on basespace.
12-nt cell barcodes (CBs) and 8-nt unique molecular identifiers (UMIs) were extracted from read 1. Degenerate CBs containing either 'N's or more than four consecutive 'G's were discarded. Synthesis errors, which can result in truncated 11-nt cell barcodes, were corrected.
Read 2 were trimmed to remove poly(A) tails (> dA(7)) from the 3'-ends of each read. Any resulting fragment shorter than 24 nucleotides were discarded.
Trimmed reads were then aligned to GRCh38 (GENCODE v.24) using STAR v.2.5.0 with parameters "-- sjdbOverhang 65 --twopassMode Basic --outSAMtype BAM Unsorted". Only reads with unique, strand-specific alignments to exons were kept for further analysis.
All reads with the same CB, UMI, and gene mapping were collapsed to represent a single molecule. To correct for sequencing errors in UMIs, we further collapsed UMIs that were within Hamming distance 1 of another UMI with the same barcode and gene. To correct for sequencing errors in cell barcodes, we then collapsed CBs that were within Hamming distance one of another cell barcode, had at least 20 unique IMI-gene pairs, and had at least 75% overlap of their UMI-gene pairs. A digital gene expression matrix was then generated from these corrected barcode-UMI-gene triplets.
We estimated the number of cell barcodes corresponding beads associated with cells in our microwell system using the cumulative histogram of reads associated with each barcode
To avoid dead cells and library construction artifacts, we removed cell barcodes that failed to satisfy certain criteria.  We removed all cells where >10% of molecules aligned to genes expressed from the mitochondrial genome or where the ratio of molecules aligning to whole gene bodies (including introns) to molecules aligning exclusively to exons was >1.5. These measures remove cells with compromised plasma membranes, which results in retention of mitochondrial or nuclear transcripts. We also removed cells where the number of reads per molecule (indicative of amplification efficiency) or the number of molecules per gene deviated by more than 2.5 standard deviations from the mean for a given sample.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files that contain the gene expression level of each individual cell.

source_name: High grade glioma tissue

extract_protocol:
mRNA molecues were captured using bead-bound oligo dT(30).
Captured mRNA molecues were reverse transcriped to obtain cDNA which is then amplified by PCR reactions. The cDNA PCR reaction product was then purified with AMPure XP beads. The purified cDNA PCR product was used as the input for Nextera XT reactions to generate sequencing library.

value: Female

tag: location

value: left temporal

tag: diagnosis

value: Anaplastic Astrocytoma, WHO grade III

tag: idh1 status

value: wt

tag: egfr status

value: not amplified


title: PJ035

tag: age

tag: gender

value: Male

value: Glioblastoma, recurrent

value: amplified in initial resection


title: PJ032

value: amplified in recurrent tumor


title: PJ018

value: Glioblastoma, WHO grade IV


title: PJ025

value: right frontal

value: amplified


title: PJ017


title: PJ016