title: Sample98 Wild type preGM

description: Wild type preGM


title: Sample103 Wild type preGM

status: Public on Apr 04 2016

type: SRA

city: Oxford

first: Claus

last: Nerlov

address: John Radcliffe Hospital, University of Oxford

department: MRC Molecular Haematology Unit

country: United Kingdom

institute: Weatheral Institute of Molecular Medicine

description: Wild type preGM

library_source: transcriptomic

data_processing:
Reads were aligned to the murine genome (mm9) using STAR with default parameters.
Non-uniquely mapped reads were discarded. Transcript expression values were quantified using Cufflinks as fragments per kilobase of transcript per million mapped reads (FPKM).
Genome_build: mm9

molecule: polyA RNA

organism: Mus musculus

source_name: Wild type mouse

extract_protocol:
From single sorted cells, cDNA was generated according to C1™ Single-Cell Auto Prep IFC for mRNA Sequencing (Fluidigm) using the Fluidigm C1 system and following manufacturer protocol.
Illumina sequenecing libraries were constructed in 96-well plates using the Illumina Nextera XT DNA Sample Preparation kit according to a protocol supplied by Fluidigm.

treatment_protocol: Cells isolated by FACS from mouse bone marrow

tag: tissue

value: Bone marrow

tag: strain

value: C57 BL6

tag: phenotype

value: 7AAD- Lin- Sca1- cKit+ CD41- FcRII/III- CD105- CD150-


title: M phase RNA-seq ribozero treated

city: Seoul

first: Jong-Eun

last: Park

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

description:
Total RNA
Count.txt
mRNA seq (ribozero)

data_processing:
For mRNA-seq and ribosome profiling analysis, FASTQ files were processed using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). The reads were first trimmed to retrieve 26 nt from the 5′ end (fastx_trimmer -l 26), filtered for quality (fastq_quality_filter -q 25 -p 80) and against artifact sequences (fastx_artifacts_filter) and collapsed (fastx_collapse). The processed sequences were first mapped to contaminant filter, which is composed of rDNA repeat units (GenBank accession BK000964.1 for NIH3T3 and U13369.1 for HeLa), PhiX genome (GenBank accession J02482.1), Illumina TruSeq primer sequences and all sequences for 5S and 5.8S rRNAs of respective species (retrieved from Rfam 11.0 of the Wellcome Trust Sanger Institute) using GSNAP with four maximum mismatches. Sequences with any match to the contaminants were removed from the subsequent analysis. The remaining sequences were aligned to hg19 genome using GSNAP allowing one mismatch. All multi-mapped reads were resolved to unique mapped reads using custom algorithm. For transcript annotations, reference annotations for human and mouse were compiled using NCBI RefSeq, RepeatMasker, gtRNAdb, Rfam and miRBase databases (the first three were downloaded from the UCSC Genome Browser on Apr 25, 2013; Rfam version 11; miRBase version 19). The alignments were annotated by intersecting with the compiled annotations using BEDTools (Quinlan and Hall, 2010). To quantify RNA or RPF abundance, annotations with more than 60 mapped reads were selected and normalized using Trimmed Mean of M values (TMM) method implemented in the edgeR Bioconductor package (Robinson et al., 2010). Translation efficiency was calculated by dividing TMM normalized RPF value to that of RNA.
TAIL-seq analysis was performed as previously described (Chang et al., 2014), with a slight modification for poly(A) tail length measurement to include short poly(A)-tailed RNAs. Briefly, genes with more than 50 poly(A)-containing reads were analysed for poly(A) tail length measurement. If poly(A) tail length measured using the previous TAIL-seq algorithm was ≥ 15 nt, the read out value was accepted as the final poly(A) tail length. For reads with poly(A) tail length < 15 nt, they were discarded if the length of untemplated sequence at the 3′ end was < 5 nt. For the remaining reads (poly(A) tail length < 15 nt and untemplated sequence ≥ 5 nt), G and C residues were removed from the untemplated sequence and the number of A residues in the resulting sequence was counted to assign poly(A) tail length.
Genome_build: hg19
Supplementary_files_format_and_content: Count.txt file contains read counts from RNA-seq and ribosome profiling libraries. TAIL_M.csv and TAIL_S.csv contains summary of TAIL-seq results

molecule: total RNA

organism: Homo sapiens

source_name: HeLa

growth_protocol: HeLa cells were maintained in RPMI (Welgene) supplemented with 10% fetal bovine serum (Welgene).

extract_protocol:
Total RNAs were extracted by TRIzol (Invitrogen)
For ribozero treated mRNA-seq, total RNA extracted by TRIzol (Life Technologies) was treated with DNaseI (Takara) and purified by RNeasy Minelute Cleanup kit (QIAGEN). RNAs were depleted of rRNAs using Ribo-Zero kit (Epicentre). 5 μg of RNAs were fragmented by incubating in the fragmentation buffer provided by NEBNext Magnesium RNA Fragmentation Module at 95 °C for 6.5 min. Fragmented RNAs were size-selected for 60-80 nt RNAs, dephosphorylated by Antarctic phosphatase (NEB) and 5′ phosphorylated by PNK reaction (Takara). RNAs were then subjected to the library preparation protocol used in ribosome profiling described above. The cDNA libraries were sequenced by Illumina HiSeq (1 × 51 bp single run).

treatment_protocol: For S phase-arrest, cells were arrested by 2 mM thymidine for 18 hr and then released into fresh medium for 9 hr, which was followed by second thymidine block for 17 hr. For M phase-arrest, cells were treated with 2 mM thymidine for 18 hr, released for 4 hr and then treated with 100 ng/mL nocodazole for 10 hr.

tag: cell type

value: human cervical cancer cell line


title: M phase RNA-seq oligo-dT enriched replicate 1

description:
Total RNA
Count.txt
mRNA seq (oligo-dT)

extract_protocol:
Total RNAs were extracted by TRIzol (Invitrogen)
For oligo-dT enriched mRNA-seq, total RNA extracted by TRIzol (Life Technologies) was treated with DNaseI (Takara) and purified by RNeasy Minelute Cleanup kit (QIAGEN). mRNAs were enriched by oligo dT capture. 5 μg of RNAs were fragmented by incubating in the fragmentation buffer provided by NEBNext Magnesium RNA Fragmentation Module at 95 °C for 6.5 min. Fragmented RNAs were size-selected for 60-80 nt RNAs, dephosphorylated by Antarctic phosphatase (NEB) and 5′ phosphorylated by PNK reaction (Takara). RNAs were then subjected to the library preparation protocol used in ribosome profiling described above. The cDNA libraries were sequenced by Illumina HiSeq (1 × 51 bp single run).


title: S phase RNA-seq ribozero treated

description:
Total RNA
Count.txt
mRNA seq (ribozero)


title: Sample100 Wild type preGM

description: Wild type preGM


title: Sample94 Wild type preGM

description: Wild type preGM


title: Sample97 Wild type preGM

description: Wild type preGM


title: Sample93 Wild type preGM

description: Wild type preGM


title: Sample92 Wild type preGM

description: Wild type preGM


title: LNCaP_Input

city: Adelaide

first: Joanna

last: Achinger-Kawecka

state: SA

address: AHMS Building, North Terrace

country: Australia

institute: South Australian Immunogenomics Cancer Institute

library_source: genomic

data_processing:
ChIP-seq reads were aligned to hg19 using bowtie v0.12.8 allowing up to 3 mismatches, discarding ambiguous and clonal reads.
Broad peaks were called with Peak Ranger version 1.16 with parameters ccat: format: bam, read extension length: 200, FDR cut off: 0.11, sliding window size: 500, window moving step: 50, min window reads: 4 and min window fold change: 5.
Genome_build: hg19
Supplementary_files_format_and_content: bed files were generated using Peak Ranger version 1.16

molecule: genomic DNA

source_name: prostate cancer cells LNCaP

growth_protocol: Cell lines were cultured according to manufacturer's instructions

extract_protocol:
Nuclei were purified after formaldehyde crosslinking, collected and resuspended in SDS Lysis buffer before sonication. Chromatin was sonicated to generate a majority of fragments between 200 and 600 bp. 10µg of each antibody was used per ChIP.
Libraries for ChIP-Seq were prepared following Illumina protocols. The resulting libraries were sequenced on the Illumina HiSeq 2000 platform configured for 50bp single-end reads.

value: prostate

tag: cell line

value: LNCaP

tag: chip-antibody


title: S phase RNA-seq oligo-dT enriched replicate 1

description:
Total RNA
Count.txt
mRNA seq (oligo-dT)


title: Sample91 Wild type preGM

description: Wild type preGM


title: Sample89 Wild type preGM

description: Wild type preGM


title: Sample90 Wild type preGM

description: Wild type preGM


title: Sample88 Wild type preGM

description: Wild type preGM


title: Sample102 Wild type preGM

description: Wild type preGM


title: Sample86 Wild type preGM

description: Wild type preGM


title: Sample87 Wild type preGM

description: Wild type preGM


title: Sample85 Wild type preGM

description: Wild type preGM


title: LNCaP_H3K27ac_ChIP-seq

value: H3K27Ac (#39297, Active Motif)


title: Sample84 Wild type preGM

description: Wild type preGM


title: LNCaP_H3K4me1_ChIPSeq

value: H3K4me1 (#39298, Active Motif)


title: Input.SIRT6KD_rep2

city: Houston

first: Yuanxin

last: Xi

state: TX

address: 1400 Pressler St

department: Bioinformatics and Computational Biology

country: USA

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Basecalls performed by Illumina CASAVA 1.8.2
ChIP-seq reads were aligned to the hg19 genome using Bowtie2 v2.1.0
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq wig files were generated using DANPOS 2; Scores represent the ChIP-seq tag numbers

source_name: U2Os cells

growth_protocol: U2OS cells were growth in MEM with 10% FBS, 2mM L-Glutamine and Pen/Strep

extract_protocol:
Cells were fixed with 1% formaldehyde for 8 min, quenched with 1.25 M glycine, washed in PBS. Cells were resuspended in cells lysis buffer (50 mM Tris pH 8.0, 10 mM EDTA, 1% SDS, 1x Roche Complete Protease inhibitor), kept in ice for 10 min, and sonicated using Bioruptor. Following sonication insoluble material was pelleted by centrifugation at 16000g for 10 minutes at 4°C. A small sample of soluble crosslinked chromatin was purified, checked for correct sonication size range. 25 ug of chromatin was diluted to 350ul with RIPA buffer (10 mM Tris pH 7.5, 140 mM NaCl, 1mM EDTA, 0.5 mM EGTA, 1% Triton, 0.1% SDS, 0.1% sodium deoxycholate, 1x Roche Complete Protease inhibitor). 10 μl of Protein A Dynabeads (Invitrogen) prebound with 2 μg of histone marks antibodies were added. Samples were incubated overnight at 4°C with rotation. Beads were precipitated on magnet stand and washed 3 times with 1 mL of RIPA buffer and once with TE. Crosslink was reversed with 250 μl of elution buffer (20 mM Tris pH 7.5, 5 mM EDTA, 50 mM NaCl, 1% SDS, 5 μg/mL proteinase K) at 65°C for 2 hours. DNA was purified with Qiagen PCR cleanup kit. Concentration of eluted chromatin was measured with Qubit dsDNA HS Assay Kit (Life Technology).
Sequencing libraries were prepared using the Illumina TruSeq DNA Sample Preparation Kit according to the manufacturer's protocol. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250-450 bp (insert plus adaptor) were band isolated from an agarose gel. DNA fragments were sequenced using paired-end sequencing technology on Illumina HiSeq 2000 platform.

treatment_protocol: For lentiviral packaging, 293T cells were co-transfected with pVPack-VSV-G, Δ8.2 and pSicoR containing shRNAs directed against SIRT6 or control constructs, and viral supernatant was collected after 48 h. For transduction, cells were incubated with virus-containing supernatant in the presence of 8 μg/ml polybrene. After 48 h, infected cells were selected for 72 h with puromycin (1.5 μg/ml). SIRT6 knockdown target sequence: S6KD 5’ -AAGAATGTGCCAAGTGTAAGA- 3′

tag: cell

value: U2Os cells

tag: treatment

value: SIRT6 Knock Down

tag: antibody

value: none, input


title: Sample80 Wild type preGM

description: Wild type preGM


title: Sample83 Wild type preGM

description: Wild type preGM


title: Sample81 Wild type preGM

description: Wild type preGM


title: Sample95 Wild type preGM

description: Wild type preGM


title: Sample79 Wild type preGM

description: Wild type preGM


title: Sample96 Wild type preGM

description: Wild type preGM


title: Input.Control_rep1

value: Control


title: Input.Control_rep2


title: S phase RNA-seq oligo-dT enriched replicate 2

description:
Total RNA
Count.txt
mRNA seq (oligo-dT)


title: Input.SIRT6KD_rep1


title: Sample78 Wild type preGM

description: Wild type preGM


title: Sample76 Wild type preGM

description: Wild type preGM


title: Sample77 Wild type preGM

description: Wild type preGM


title: ko32_RNA-Seq

city: New York

first: Yichi

last: Xu

state: NY

address: 1275 York Avenue

institute: MSKCC

data_processing:
Sequencing reads were mapped to mouse reference genome (mm9 essembly) by Tophat1.4 with default parameters.
HTSeq0.6 was applied to count the number of uniquely mapped reads that locate on the exons of genes. Only genes with at least one read in all samples were kept for downstream analysis.
DESeq3.1 was used to select differentially expressed genes between wild type and knockout.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include reads count of genes. The 1st column is gene symbol and the 2nd column is the number of reads mapped to exons of the gene.

source_name: mouse embryonic fibroblast cells

extract_protocol: Smc3-flox/flox MEF (mouse embryonic fibroblast) cells was originally derived from European conditional mouse mutagenesis program (White et al., 2013) (http://www.informatics.jax.org/allele/MGI:4434007). The Cre/GFP adenovirus and GFP adenovirus were purchased from Hanbio biotechnology Shanghai. MEF cells were cultured with 10% FBS in DMEM (Life technology). To avoid loss of viability in Smc3-deficient cells when they enter mitosis, we infected the cells at G0/1 stage of the cell cycle. The medium was changed two days after complete confluence. 10e9 pfu GFP and Cre/GFP adenovirus were used in 8-hr treatment for wild type and Smc3-/- MEF cells respectively. To allow cells to recover from viral infection, we changed the medium into serum-free DMEM and kept cells for 6 days at high confluence. MEF cells were then synchronized by dexamethasone (Sigma) with the final concentration of 100 nM for 1 hour. The cells were rinsed with PBS and cultured with serum-free DMEM. Wild type and Smc3 KO MEF cells were collected at 20, 24, 28, 32, 36, and 40 hr after synchronization. Total RNA in CT20 and CT32 samples were extracted using Trizol reagent and reverse-transcribed into cDNA by SuperScript II RT (Life Technologies). RNA-seq libraries were prepared by using Illumina TruSeq RNA Sample Prep Kit V2 and were subjected to deep sequencing with 100 bp read on HiSeq 2000 at CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai, China.

tag: circadian time

tag: genotype

value: Dexamethesone synchronization

value: MEF


title: H3K9me3.SIRT6KD

description: anti H3K9me3 abcam ab8899

value: anti H3K9me3 abcam ab8899


title: H3K9ac.SIRT6KD

description: anti H3K9Ac abcam ab10812

value: anti H3K9Ac abcam ab10812


title: H3K9me3.Control

description: anti H3K9me3 abcam ab8898

value: anti H3K9me3 abcam ab8898


title: wt32_RNA-Seq

value: wild type


title: n18_11_4C

data_processing:
Library strategy: 4C-seq
FASTQ reads of 4C-seq were demultiplexed using the bait primers (HindIII primer: CAGGCATGAGCAACGCAGA; DpnII primer: AGAAGAGGGTAAGCAGCAAAGGT), that is, removing the upstream of HindIII restriction site (AAGCTT) and the downstream of of DpnII restriction site (GATC).
The reads were aligned to mouse genome mm9 by Bowtie0.12 (-v 3 -m 1). Only reads uniquely mapped to the HindIII restriction sites on the cis-chromosome of the bait were kept and assigned the HindIII restricted fragments defined by two neighboring restriction sites.
Peak calling was performed as previously described (Tolhuis et al., 2011). Briefly, HindIII restricted fragments with more than one reads were smoothed by applying a running median with window size of 10 fragments. The background of read distribution along the chromosome was obtained by LOESS (local polynomial regression) on the smoothed and logarithm-transformed reads numbers. The HindIII restricted fragments bearing more reads than background were selected as candidate fragments. Continuous candidate fragments were merged into a single region. For each time point, we required interacting regions were called in at least two duplicates.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-separated plain file for reads count of HindIII restricted fragment on cis-chromosome (chr11). The 1st-3rd columns indicate the position of HindIII restricted fragment, which is defined by two neighboring HindIII restriction sites. The 4th column is the count of reads mapping to the fragment.

extract_protocol:
C57BL/6 male Mice of six weeks old were entrained to 12 hr light and 12 hr dark for one week and then switched to constant dark. Three mice were sacrificed in the dark at ZT6 and ZT18, respectively. Mice liver cells were quickly dispersed and filtered through the 40 mm cell strainer to make a single-cell suspension. Approximately 50-million cells were ﬁxed in 1% formaldehyde for 10 min at room temperature before being quenched with 0.125 M glycine. Cells were then lysed in cold lysis buffer (10 mM Tris HCl, 10 mM NaCl, 0.2% NP-40, 1×protease inhibitor) for 15 min on ice. After being washed twice, nuclei were re-suspended in Buffer 2.1 (New England Biolabs), including 0.1% SDS, and were incubated for 10 min at 65°C. 1% (final concentration) Triton X-100 was added to quench SDS and centrifuged to remove SDS and Triton. Nuclei were then digested overnight by 800U Hind III (NEB) at 37℃ with shaking. After inactivation by 1.6% (ﬁnal concentration) SDS at 65℃ for 20 min, samples were washed and re-suspended in ligation buffer, and ligated by 100U T4 DNA ligase (Thermo Fisher Scientific) at 16℃ for 4 h and then room temperature for 30 min. Ligated chromatin was digested by proteinase K before DNA purification. The purified DNA was further digested by Dpn II (NEB) and then circularized using T4 DNA ligase (Thermo Fisher Scientific).
After puriﬁcation, 200ng of DNA from each sample was used as template for the PCR amplification using the DyNAzyme EXT (Finnzymes). Primers specific to bait were applied to amplify the interactome of interest in a 25ul reaction volume under the following PCR conditions: 1 cycle at 94°C for 2 min; (94°C 30 sec; 60°C 30 min; 72°C 2 min) ×18 cycles; 1 cycle of 72°C 7 min. 1uL of PCR products was used as template for a second PCR reaction utilizing the primers with the addition of the Illumina adaptors in a 50ul volume under the same PCR conditions. The PCR-amplified library was purified and sequenced with a 100bp read length using the Illumina HiSeq2000.

value: liver

tag: age

value: six weeks

tag: gender

value: male


title: wt20_RNA-Seq


title: n18_10_4C


title: Sample82 Wild type preGM

description: Wild type preGM

value: Bone marrow

value: C57 BL6

value: 7AAD- Lin- Sca1- cKit+ CD41- FcRII/III- CD105- CD150-


title: vDG_F1_2 (RNAseq)

first: Shifra

middle: Liba

last: Klein

address: 1300 York Avenue

department: Pharmacology

institute: Weill Cornell

description: Replicate 2

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Alignment: DNA samples were aligned to the mm9 genome using Bismark software as part of an in-house pipeline (PMID 22737091).  RNA fragments were mapped to the mosue genome using TopHat version 2.0.2 (http://tophat.cbcb.umd.edu) with bowtie version 1.0.0 against mm9 and annotated with NCBIM37 coding transcripts
DNA methylation analysis was performed using MethylKit software (PMID 23034086). RNA samples were counted using Htseq-count -m -intersection-strict and analysis was performed using tagwise dispersion and default parameters in edgeR (PMCID: PMC2796818).
Genome_build: mm9
Supplementary_files_format_and_content: DNA files are in the wig format. RNA files are the raw counts per gene as processed by Htseq-count.

source_name: Ventral Dentate Gyrus

extract_protocol:
Following sacrifice animal brains were frozen, cryosectioned and microdissected. DNA was collected using Qiagen DNeasy Blood and tissue extraction kit (cat# 69582). RNA was harvested using Qiagen RNeasy mini kit (cat# 74106). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
DNA and RNA libraries were prepared for sequencing using standard Illumina protocols

value: Male

value: Swiss Webster

tag: maternal genotype

tag: grandmaternal genotype

tag: generation

value: vDG


title: vDG_F2_2 (RNAseq)

description: Replicate 2

value: WT


title: vDG_F2_1 (RNAseq)

description: Replicate 1


title: vDG_WT_1 (RNAseq)

description: Replicate 1


title: vDG_WT_2 (RNAseq)

description: Replicate 2


title: n18_9_4C


title: n6_7_4C


title: n6_6_4C


title: n6_8_4C


title: ko20_RNA-Seq


title: vDG_ETF2_2 (eRRBS)

description: Replicate 2


title: vDG_ETF2_1 (eRRBS)

description: Replicate 1


title: H3K18ac.SIRT6KD_rep1

description: anti H3K18Ac abcam ab1191

value: U2Os cells

value: SIRT6 Knock Down

value: anti H3K18Ac abcam ab1191


title: H3K56ac.SIRT6KD

description: anti H3K56Ac Epitomics 2134-1

value: anti H3K56Ac Epitomics 2134-1


title: H3K18ac.SIRT6KD_rep2

description: anti H3K18Ac abcam ab1191


title: H3K56ac.Control

description: anti H3K56Ac Epitomics 2134-1

value: Control


title: H3K18ac.Control_rep2

description: anti H3K18Ac abcam ab1191


title: H3K9ac.Control

description: anti H3K9Ac abcam ab10812

value: anti H3K9Ac abcam ab10812


title: vDG_WTETF2_2 (eRRBS)

description: Replicate 2


title: H3K18ac.Control_rep1

description: anti H3K18Ac abcam ab1191


title: vDG_F3_1 (eRRBS)

description: Replicate 1


title: vDG_WTETF2_1 (eRRBS)

description: Replicate 1


title: vDG_F3_2 (eRRBS)

description: Replicate 2


title: vDG_F2_2 (eRRBS)

description: Replicate 2


title: mES_3

city: Stanford

first: Zhipeng

last: Lu

state: CA

address: 269 Campus Drive

department: Department of Dermatology

institute: Stanford University

data_processing:
remove 5' and 3' adapters using trimmomatic-0.32.jar SE -threads 16 -phred33
removed PCR duplicates using splitFastqLibrary (in the icSHAPE pipeline)
mapped reads using STAR, version 2.4, with the following parameters: --outFilterMultimapNmax 100 --outSAMattributes All --alignIntronMin 1 --scoreGapNoncan -4 --scoreGapATAC -4 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --runThreadN 16
secondary mappings were removed using samtools
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: read count was calculated using bedtools v2.22.0

source_name: mouse J1 ES cells

growth_protocol: HeLa-S3 cells were cultured in DMEM+ 10% FBS + Pen/Strep at 37ºC with 5% CO2. Flp-In HEK293T-REx cells express doxycycline inducible 3XFLAG-DDX3X at a level comparable to endogenous DDX3X. The 293T cells were cultured with DMEM + 10% Tetracycline-free FBS (Clontech, Tet System Approved FBS, 631106) + Pen/Strep + 2mM Glutamax (Gibco). J1 mouse ES cells (male) were cultured on gelatin coated plates at 37ºC with mES media: 500ml Knockout DMEM (Gibco), 90ml FBS, 6ml non-essential amino acid (MEM NEAA, 100x, Gibco), 6ml glutamine or glutamax (200mM stock solution), 6ml Pen/Strep, 1ml BME and 60ul LIF (Millipore, ESG1106).

extract_protocol:
Cells were digested with S1 nuclease, proteinase K and RNA was extracted using TRIzol.
See previous publication for the protocol (PMID: 25799993)

treatment_protocol: HEK293T Cells were induced for 8 hours with 1 μg/ml Doxycycline before AMT crosslinking.


title: mES_2


title: mES_1


title: vDG_F1_1 (RNAseq)

description: Replicate 1


title: vDG_F1_2 (eRRBS)

description: Replicate 2


title: vDG_F1_1 (eRRBS)

description: Replicate 1


title: vDG_WT_2 (eRRBS)

description: Replicate 2


title: OPLL-2 mRNA

city: Shanghai

first: Chen

address: No, 800, Rd. Xiangyin

country: China

institute: The Second Military Medical University

description: Total RNA

data_processing:
[mRNA] Reads filtering under criteria removing reads with 20% of the base quality lower than 13
[mRNA] Mapsplice v2.1.8 mapping to reference genome
[mRNA] count counting
Genome_build: hg19_GRCh37
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: ligament cells

growth_protocol: Normal posterior longitudinal ligament were dissected during the surgery, all tissues were obtained with written informed consent signed by the donors voluntarily for research. Ligaments were further cut into pieces and cultured in DMEM supplemented with 20% fetal bovine serum, and cells of passage 3 were used for the experiments.

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
The complementary DNA (cDNA) libraries for single-end sequencing were prepared using Ion Total RNA-Seq Kit v2.0 (Life Technologies) according to the manufacturer’s instructions. The cDNA libraries were then processed for the Proton Sequencing process according to the commercially available protocols. Samples were diluted and mixed, the mixture was processed on a OneTouch 2 instrument (Life Technologies) and enriched on a OneTouch 2 ES station (Life Technologies) for preparing the template-positive Ion PI™ Ion Sphere™ Particles (Life Technologies) according to Ion PI™ Template OT2 200 Kit v2.0 (Life Technologies). After enrichment, the mixed template-positive Ion PI™ Ion Sphere™ Particles of samples was loaded on to 1 P1v2 Proton Chip (Life Technologies) and sequenced on Proton Sequencers according to Ion PI Sequencing 200 Kit v2.0 (Life Technologies) by NovelBio Corp. Laboratory, Shanghai.

value: Ossified Posterior longitudinal ligament

tag: passage

value: Passage 3


title: OPLL-1 miRNA

description: small RNA

data_processing:
[miRNA] We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) 30% base quality <13 b) read length < 17bp c) adaptor sequence.
[miRNA] Utilizing the BWA software, we mapped the clean data to miRBase 21.0 Homo Sapiens miRNA database and GRCH37.p13 genome.
[miRNA] count counting
Genome_build: miRBase 21.0
Supplementary_files_format_and_content: TXT file contain counts for each sample

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for miRNA purification. miRNA was purified by miRNeasy Mini Kit (Qiagen) and the purification result was validated by Gel electrophoresis.
The complementary DNA (cDNA) libraries for single-end sequencing were prepared using Ion Total RNA-Seq Kit v2.0 (Life Technologies) according to the manufacturer’s instructions. The cDNA library had been size selected by PAGE Gel electrophoresis for miRNA sequencing. The cDNA libraries were then processed for the Proton Sequencing process according to the commercially available protocols. Samples were diluted and mixed, the mixture was processed on a OneTouch 2 instrument (Life Technologies) and enriched on a OneTouch 2 ES station (Life Technologies) for preparing the template-positive Ion PI™ Ion Sphere™ Particles (Life Technologies) according to Ion PI™ Template OT2 200 Kit v2.0 (Life Technologies). After enrichment, the mixed template-positive Ion PI™ Ion Sphere™ Particles of samples was loaded on to 1 P1v2 Proton Chip (Life Technologies) and sequenced on Proton Sequencers according to Ion PI Sequencing 200 Kit v2.0 (Life Technologies) by NovelBio Corp. Laboratory, Shanghai.

tag: tissue


title: PLL-3 miRNA

description: small RNA

value: Posterior longitudinal ligament


title: PLL-1 miRNA

description: small RNA

value: male


title: OPLL-2 miRNA

description: small RNA


title: OPLL-3 mRNA

description: Total RNA


title: PLL-2 miRNA

description: small RNA


title: RNA-seq of human differentiated keratinocytes (DK) rep3

city: Segrate

first: Luca

last: Petiti

state: Milan

address: Via Fratelli Cervi, 93

country: Italy

institute: ITB-CNR

data_processing:
Sequence tags were mapped to reference genome Hg19 using TopHat v2.0.6 and transcript levels in triplicate samples were calculated as fragments per kb per 106 mapped reads (FPKM) using Cufflinks v2.0.2.
Genome_build: hg19
Supplementary_files_format_and_content: RPKM were obtained using Cufflinks

source_name: DK

growth_protocol: KP cells were obtained from foreskin biopsies of healthy neonatal donors and expanded by cultivation onto lethally irradiated 3T3-J2 cells in growth FAD medium, a DMEM and Ham’s F12 media mixture (2:1) containing FCS (10%), penicillin-streptomycin (1%), glutamine (2%), insulin(5ug/ml), adenine (24.3ug/ml), hydrocortisone (0.4ug/ml), cholera toxin (50ug/ml), triiodotyronine (2nM). DKs were cultivated in KGM serum-free medium (Invitrogen), penicillin-streptomycin (1%) and glutamine (2%).

extract_protocol:
Total RNA was isolated using Trizol (Invitrogen, Grand Island, NY) and treated sequentially with the RNeasy Mini Kit (Qiagen, Valencia, CA) and Turbo DNA Free (Ambion, Grand Island, NY).
RNA-seq libraries were prepared from 300 ng RNA using the TruSeq RNA Sample Preparation kit (Illumina) and 75-bp single-end sequences were obtained on a NextSeq 500 Instrument (Illumina)

tag: cell  type

value: Differentiated Keratinocytes


title: RNA-seq of human keratinocyte progenitors (KP) rep3

source_name: KP

value: Keratinocyte Progenitors


title: RNA-seq of human differentiated keratinocytes (DK) rep1


title: RNA-seq of human differentiated keratinocytes (DK) rep2


title: PLL-1 mRNA

description: Total RNA


title: HEK293T_3

source_name: human HEK293T cells


title: vDG_F2_1 (eRRBS)

description: Replicate 1

tag: strain


title: PLL-2 mRNA

description: Total RNA


title: HeLa_LowRNase

source_name: human HeLa cells

value: HeLa


title: HEK293T_1


title: RNA-seq of human keratinocyte progenitors (KP) rep1


title: vDG_WT_1 (eRRBS)

description: Replicate 1

value: Male


title: OPLL-3 miRNA

description: small RNA


title: PLL-3 mRNA

description: Total RNA


title: HeLa_HighRNase


title: OPLL-1 mRNA

description: Total RNA


title: NT4

status: Public on Apr 03 2016

city: Biberach

first: Fabian

last: Stiefel

address: Hubertus-Liebrecht-Strasse 35

country: Germany

institute: University of Applied Sciences Biberach

description: host cell

data_processing:
3' Adapter was cleaved. Read length shorter than 17 nt and longer than 26 nt were discarded with mirdeep2 package
Read were filtered genimoc tRNA database, Repbase, rRNA SILVA database with Vmatch
Reads were collapsed to remove redundant sequences. Read count for each sequences was saved in header with mirdeep2 package
Collapsed reads were mapped against chromosome sorted CH genome (Brinkrolf et al. 2013), allowing one substitution and collapsed into a single fasta file (all with miRdeep2 package)

organism: Cricetulus griseus

source_name: CHO cells

growth_protocol: CHO cells were grown in a 2L bioreactor as a batch culture.

extract_protocol:
RNA was extracted with Trizol reagent. RNA integrity was tested on an Agilent chip
Standard Illumina TrueSeq protocol for small RNA. 18 Barcoded samples were put on one lane
Sequencing of ready to load libraries was conducted by GATC, Germany on a Illumina HiSeq 2500 Analyser

treatment_protocol: In the control, temperature was maintained at 37°C for the whole cultivation period. For the temperature shift runs,  temperature was shifted to 30°C (from 37°C) in the middle of the exponential phase

tag: cell type

tag: phenotype

value: Non producer temperature shift

tag: passages

tag: sampling time


title: NT1

description: host cell


title: NT5

description: host cell


title: NT3

description: host cell


title: NT2

description: host cell


title: NC5c

description: host cell

value: Non producer control


title: NC3

description: host cell


title: NC5a

description: host cell


title: NC2

description: host cell


title: NC4

description: host cell


title: NC1

description: host cell


title: LT2

description: monoclonal antibody

value: Low producer temperature shift


title: LT5

description: monoclonal antibody


title: HEK293T_2

tag: cell line


title: NC5b

description: host cell


title: LT1

description: monoclonal antibody


title: LT4

description: monoclonal antibody


title: LC5c

description: monoclonal antibody

value: Low producer control


title: LC5a

description: monoclonal antibody


title: LC4

description: monoclonal antibody


title: LC5b

description: monoclonal antibody


title: LC3

description: monoclonal antibody


title: LC2

description: monoclonal antibody


title: HT2

description: monoclonal antibody

value: High producer temperature shift


title: LC1

description: monoclonal antibody


title: HT4

description: monoclonal antibody


title: HT3

description: monoclonal antibody


title: HT1

description: monoclonal antibody


title: HC5c

description: monoclonal antibody

value: High producer control


title: HC5b

description: monoclonal antibody


title: HC5a

description: monoclonal antibody


title: LT3

description: monoclonal antibody


title: HC4

description: monoclonal antibody


title: HC2

description: monoclonal antibody


title: HC1

description: monoclonal antibody


title: Symbiodinium_infected_48h_rep3

city: Brisbane

first: Amin

middle: Roushdy

last: Mohamed

state: Queensland

address: 306 Carmody Rd, University of Queensland

department: Agriculture and Food

institute: CSIRO

description: processed data: 48_Symbidinium_CladeB_3/48H_matrix.TMM.fpkm.matrix; 48_Symbidinium_CladeB_3/48H_matrix.counts.matrix

data_processing:
Reads were mapped using BOWTIE version 0.12.7
Transcripts abundance was estimated using RSEM version 1.1.17
Differential expression was performed using the r package edgeR comparining Symbiodinium-infected samples to control at 4, 12, and 48h timepoints
Genome_build: Adig_1.0; Acropora digitifera reference transcriptome assembly Shinzato et al 2011, PMID: 21785439; transcriptome assembly is available at: http://marinegenomics.oist.jp/coral/viewer?project_id=3
Supplementary_files_format_and_content: count matrix containing expression values (FPKM;Fragments Per Kilobase of transcript per Million) and raw count matrix

organism: Acropora digitifera

source_name: coral larvae_Symbiodinium_infected 48h

growth_protocol: Coral larvae were reared in 0.2 uM FSW under ambient conditions

extract_protocol:
RNA was extracted using TRIZOL
libraries were prepared using TruSeq sample preparation kit (Illumina)

treatment_protocol: Symbiodinium was inoculated and larvae were collected for RNA isolation 4, 12, 48 h post infection

value: larvae

tag: infection status

tag: time point


title: control_48h_rep2

description: processed data: 48_Negative_control_2/48H_matrix.TMM.fpkm.matrix; 48_Negative_control_2/48H_matrix.counts.matrix

source_name: coral larvae_control 48h

value: not infected


title: Symbiodinium_infected_48h_rep1

description: processed data: 48_Symbidinium_CladeB_1/48H_matrix.TMM.fpkm.matrix; 48_Symbidinium_CladeB_1/48H_matrix.counts.matrix


title: Symbiodinium_infected_48h_rep2

description: processed data: 48_Symbidinium_CladeB_2/48H_matrix.TMM.fpkm.matrix; 48_Symbidinium_CladeB_2/48H_matrix.counts.matrix


title: control_48h_rep3

description: processed data: 48_Negative_control_3/48H_matrix.TMM.fpkm.matrix; 48_Negative_control_3/48H_matrix.counts.matrix


title: Symbiodinium_infected_12h_rep3

description: processed data: 12_Symbiodinium_CladeB_3/12H_matrix.TMM.fpkm.matrix; 12_Symbiodinium_CladeB_3/12H_matrix.counts.matrix

source_name: coral larvae_Symbiodinium_infected 12h


title: Symbiodinium_infected_12h_rep2

description: processed data: 12_Symbiodinium_CladeB_2/12H_matrix.TMM.fpkm.matrix; 12_Symbiodinium_CladeB_2/12H_matrix.counts.matrix


title: control_12h_rep2

description: processed data: 12_Negative_control_2/12H_matrix.TMM.fpkm.matrix; 12_Negative_control_2/12H_matrix.counts.matrix

source_name: coral larvae_control 12h


title: Symbiodinium_infected_04h_rep3

description: processed data: Symbiodinium_CladeB_3/04H_matrix.TMM.fpkm.matrix; Symbiodinium_CladeB_3/04H_matrix.counts.matrix

source_name: coral larvae_Symbiodinium_infected 04h


title: HT5

description: monoclonal antibody


title: control_48h_rep1

description: processed data: 48_Negative_control_1/48H_matrix.TMM.fpkm.matrix; 48_Negative_control_1/48H_matrix.counts.matrix


title: Symbiodinium_infected_04h_rep1

description: processed data: Symbiodinium_CladeB_1/04H_matrix.TMM.fpkm.matrix; Symbiodinium_CladeB_1/04H_matrix.counts.matrix


title: control_04h_rep2

description: processed data: Negative_control_2/04H_matrix.TMM.fpkm.matrix; Negative_control_2/04H_matrix.counts.matrix

source_name: coral larvae_control 04h


title: RNA-seq of human keratinocyte progenitors (KP) rep2


title: control_04h_rep3

description: processed data: Negative_control_3/04H_matrix.TMM.fpkm.matrix; Negative_control_3/04H_matrix.counts.matrix


title: control_04h_rep1

description: processed data: Negative_control_1/04H_matrix.TMM.fpkm.matrix; Negative_control_1/04H_matrix.counts.matrix


title: HC3

description: monoclonal antibody


title: N2102363 estradiol rep3

city: Helsinki

first: Mikael

last: Brosché

address: Viikinkaari 1

department: Department of Biosciences

country: Finland

institute: University of Helsinki

data_processing:
RNA-seq data analysis was performed with the JAVA-based client-server system Chipster
Quality of sequences was checked with FastQC package
First 13 reads were trimmed PRINSEQ package, then mapped to wild type Col-0 whole genome using TopHat2 with following settings:Do not ignore novel junctions, hits allowed=2, allowing 2 nucleotide mismatches, minimum anchor length=8, Maximum number of mismatches allowed in the anchor=0, minimum intron length=20, Maximum intron length=2000
Generated BAM files were sorted and indexed with SAMtools package
Number of reads per gene was counted and calculated with HTSeq package (only unique alignments included)
Genome_build: Col-0 TAIR10.23
Supplementary_files_format_and_content: Tab-separated values files including AGI code, chromosome, start, end, length, strand and read count per gene

organism: Arabidopsis thaliana

source_name: whole rosette

growth_protocol: Before the treatment, plants were grown until the age of 3 weeks in the following conditions: Seeds were sown on 1:1 peat: vermiculite, stratified for three days, and then grown at 22° C/19° C for seven days. The geminated seedlings were transplanted into new 1:1 peat: vermiculite mixture. Plants were at 22°C/19°C, relative humidity of 70%/90% under a light cycle of 12 h/12 h.

extract_protocol:
Five rosettes per genotype per treatment were pooled and frozen into liquid nitrogen. Three biological replicates of RNA were isolated with RNA was isolated with a GeneJET Plant RNA Purification Mini Kit (Thermo Scientific). Quality and quantity of RNA was assessed using Agilent 2100 Bioanalyzer and NanoDrop.
Libraries were prepared from 100 ng of total RNA with Illumina TruSeq RNA Sample Prep Kit v2 according to the kit manual.

treatment_protocol: Plants were sprayed with 50 µM estradiol with 0.001% Silwet-L77. Controls for wild type were treated with water + Silwet, and the samples were harvested after 3 hours.

tag: genotype

value: WRKY75 overexpression

value: whole rosette

tag: developmental stage

value: 3 weeks old plants

tag: treatment

value: 50 µM estradiol with 0.001% Silwet-L77


title: N2102363 estradiol rep2


title: N2102362 estradiol rep4


title: N2102363 estradiol rep4


title: N2102363 estradiol rep1


title: N2102362 estradiol rep3


title: N2102362 estradiol rep2


title: Col-0 water rep2

value: wildtype


title: wrky75 ozone rep2

extract_protocol:
Five rosettes per genotype (Col-0, wrky25 wrky33, wrky75 ) from control and ozone treatment were pooled and frozen into liquid nitrogen. Three biological replicates of RNA were isolated with GeneJet Plant RNA purification Mini Kit (Thermo Scientific). Quality and quantity of RNA was assessed using Agilent 2100 Bioanalyzer and NanoDrop.
Libraries were prepared from 100 ng of total RNA with Illumina TruSeq RNA Sample Prep Kit v2 according to the kit manual.

treatment_protocol: Plants were exposed with 350 nL L-1 ozone for two hours.

value: 350 ppb ozone exposure for 2hr


title: Col-0 water rep3


title: N2102362 estradiol rep1


title: wrky75 ctrl rep1

value: control


title: wrky75 ctrl rep2


title: wrky25 wrky33 ozone rep1

value: wrky25 wrky33


title: wrky25 wrky33 ctrl rep2


title: control_12h_rep3

description: processed data: 12_Negative_control_3/12H_matrix.TMM.fpkm.matrix; 12_Negative_control_3/12H_matrix.counts.matrix


title: Col-0 estradiol rep3


title: Col-0 estradiol rep1


title: Col-0 water rep1


title: wrky75 ozone rep3


title: Symbiodinium_infected_04h_rep2

description: processed data: Symbiodinium_CladeB_2/04H_matrix.TMM.fpkm.matrix; Symbiodinium_CladeB_2/04H_matrix.counts.matrix


title: wrky75 ozone rep1


title: wrky25 wrky33 ozone rep3


title: wrky75 ctrl rep3


title: Col-0 estradiol rep2


title: wrky25 wrky33 ctrl rep1


title: Col-0 ozone rep2


title: Col-0 ozone rep4


title: Col-0 ozone rep3


title: Col-0 ctrl rep4


title: Col-0 ozone rep1


title: Col-0 ctrl rep2


title: Col-0 ctrl rep1


title: Col-0 ctrl rep3


title: wrky25 wrky33 ctrl rep3


title: Indian_fantail_hindlimb_H3K27_ChIP_Rep1

city: Orem

first: Eric

last: Domyan

state: UT

address: 800 W University Parkway

department: Department of Biology

institute: Utah Valley University

description:
indian.hindlimb_FE.bw
indian.hindlimb_peaks.bed
diff_indian.hindlimb_vs.homer.hindlimb_c3.0_cond1.bed
diff_indian.hindlimb_vs.homer.hindlimb_c3.0_cond2.bed

data_processing:
Basecalls were performed using Illumina Casava
Adapter contaminants were removed using SeqyClean
ChIP-seq reads were aligned to the pigeon reference genome assembly (GenBank Accession AKCR01000000) using bowtie2 v2.2.3 using the following parameters: -p 10 --end-to-end --no-unal
Aligned reads were filtered with samtools v0.1.19-44428cd using the following parameters: -q 10
Biological replicates were merged using samtools merge
peaks were called using MACS v1.4.2 with the following parameters: -g 1.3e9 -w -S --nomodel --shiftsize 75
differential binding events were called using MACS2 v2.0.10.20130915 using argument callpeak with the following paramters: -g 1.3e9 -B --SPMR --nomodel --shiftsize 75, followed by argument bdgcmp, followed by argument bdgdiff
Genome_build: Cliv_1.0
Supplementary_files_format_and_content: bigwig files were generated using MACS2 v2.0.10.20130915, scores indicate fold enrichment of the H3K27ac ChIP sample relative to input DNA control
Supplementary_files_format_and_content: NAME_peaks.bed files were generated using MACS v1.4.2, scores indicate -10*log10pvalue of each region
Supplementary_files_format_and_content: diff_NAME_cond1.bed files was generated using MACS2 v2.0.10.20130915, scores indicate log10 likelihood ratio of enriched binding in condition 1 relative to condition 2
Supplementary_files_format_and_content: diff_NAME_cond2.bed files was generated using MACS2 v2.0.10.20130915, scores indicate log10 likelihood ratio of enriched binding in condition 2 relative to condition 1

organism: Columba livia

source_name: Embryonic limb bud

extract_protocol:
Forelimb and hindlimb buds from HH25 racing homer and Indian fantail embryos were collected and placed in 1% formaldehyde for 20 minutes at room temperature, then washed 3x in ice-cold PBS and stored at -800C until chromatin extraction. ChIP was performed on 200 micrograms of chromatin isolated from embryonic pigeon limbs. Control libraries were prepared using 100ng of input chromatin. A total of 16 libraries were created (8 ChIP and 8 input controls for each breed and limb combination). A validated monoclonal antibody against H3K27ac was used to perform ChIP.
Sequencing libraries were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina with NEBNext Multiplex Oligos for Illumina (Index Primers Set 1). All libraries were size selected using SPRI magnetic beads to eliminate adaptor dimers. Single-end, 50-bp read sequencing was performed on Illumina HiSeq2000 platform at the University of Utah Genomics Core Facility.

tag: domestic breed

value: Indian fantail

value: Hamburger-hamilton stage 25

tag: limb type

value: hindlimb

tag: antibody

value: H3K27ac (Millipore, catalog #05-1334, lot #2318811)


title: Indian_fantail_hindlimb_input_DNA_Rep1


title: Homer_forelimb_H3K27ac_ChIP_Rep2

description:
homer.forelimb_FE.bw
homer.forelimb_peaks.bed

value: racing homer

value: forelimb


title: Indian_fantail_forelimb_input_DNA_Rep1

description:
indian.forelimb_FE.bw
indian.forelimb_peaks.bed


title: Homer_hindlimb_H3K27ac_ChIP_Rep1

description:
homer.hindlimb_FE.bw
homer.hindlimb_peaks.bed
diff_indian.hindlimb_vs.homer.hindlimb_c3.0_cond1.bed
diff_indian.hindlimb_vs.homer.hindlimb_c3.0_cond2.bed


title: Indian_fantail_forelimb_input_DNA_Rep2


title: Homer_hindlimb_input_DNA_Rep2


title: Indian_fantail_hindlimb_H3K27_ChIP_Rep2


title: Homer_hindlimb_input_DNA_Rep1


title: Indian_fantail_forelimb_H3K27_ChIP_Rep2


title: Homer_forelimb_input_DNA_Rep2


title: Homer_hindlimb_H3K27ac_DNA_Rep2


title: Indian_fantail_hindlimb_input_DNA_Rep2


title: scnRNAs co-IPed with Twi1p from wild-type cells @3 hpm

status: Public on Apr 02 2016

city: Montpellier

first: Kazufumi

last: Mochizuki

address: 141 rue de la Cardonille

country: France

institute: Institute of Human Genetics, CNRS

data_processing:
Following removal of the adapter sequences from the sequence reads, the reads from rRNAs, tRNA, snRNAs, the mitochondrial genome, and mixed phiX174 phage DNA were removed.
Supplementary_files_format_and_content: Normalized numbers (RPKM) of sequenced 26-32-nt RNAs that map uniquely to the assembled MIC chromosome sequences are shown as histograms with 50-kb bin

organism: Tetrahymena thermophila

source_name: Conjugating cells at 3 hpm

growth_protocol: Cells were grown in SPP medium (Gorovsky et al., 1975) containing 2% proteose peptone at 30 °C. For conjugation, growing cells (~5-7 x 105/ml) of two different mating types were washed, pre-starved (~12-24 hr) and mixed in 10 mM Tris (pH 7.5) at 30 °C.

extract_protocol: RNA libraries were prepared for sequencing according to Noto et al. (2014) Methods in Molecular Biology 1093,209-24

value: wild-type


title: RNAi CstF50, rRNA depleted RNA 1

city: Boulder

first: Alfonso

last: Garrido-Lecca

address: 347 UCB

institute: CU Boulder

description:
cpf1_RNAi-1
rRNA depleted RNA
Deseq_totalRNA.txt

data_processing:
We used Galaxy for processing and mapping all reads
Bases from reads were trimmed from either end that had a quality score less than 31 (scale 0-40), then the entire read length was filtered by a quality score no less than 20 and allowed 0 bases outside this range. Adapters and barcodes were cleaved from the ends of each read, and mapped to the C. elegans genome (ce10) using Bowtie (default settings).
Adapters and barcodes were cleaved from the ends of each read, and mapped to the C. elegans genome (ce10) using Bowtie (default settings).
Genome_build: ce10
Supplementary_files_format_and_content: Text files with normalized values and fold change enrichement were generated using Cuffdiffs (mRNA) and Deseq (total RNA)

organism: Caenorhabditis elegans

source_name: Young adults

growth_protocol: Worms were synchronized and grown in liquid culture

extract_protocol:
RNA was extracted from well washed worms using Trizol reagent.
V2 script epicentre

tag: age

value: Young adults

value: RNAi CstF50


title: RNAi CstF50, polyA selected 2

description:
SK412_16
polyA selected
cuffdiffs_mRNA.txt


title: Wt, rRNA depleted RNA 2

description:
N2_totalRNA_file3
rRNA depleted RNA
Deseq_totalRNA.txt

value: Wt


title: Wt, rRNA depleted RNA 1

description:
N2_totalRNA_file1
rRNA depleted RNA
Deseq_totalRNA.txt


title: Homer_forelimb_H3K27ac_ChIP_Rep1


title: RNAi CstF50, polyA selected 1

description:
SK412_15
polyA selected
cuffdiffs_mRNA.txt


title: WT Input DNA

description: InputDNA

data_processing:
We used Galaxy for processing and mapping all reads
Bases from reads were trimmed from either end that had a quality score less than 31 (scale 0-40), then the entire read length was filtered by a quality score no less than 20 and allowed 0 bases outside this range. Adapters and barcodes were cleaved from the ends of each read, and mapped to the C. elegans genome (ce10) using Bowtie (default settings).
Bam files containing aligned reads were used as input files for MACS, which outputs a wiggle file at 1 bp resolution (used for python script).
Wiggle files created by MACS were normalized using the java-genomics-toolkit package against a DNA input control
Genome_build: ce10
Supplementary_files_format_and_content: Wig files were generated with MACS using a p-value cutoff of 1e-5, the candidate peaks are selected and reported as fold enrichment over the local background level.

extract_protocol:
Lysates were clarified from sonicated worms and immunoprecipitated DNA complexes were isolated with antibody.
Illumina

tag: chip antibody


title: WT H3K9me3

value: Abcam (ab8898)


title: Indian_fantail_forelimb_H3K27_ChIP_Rep1


title: Wt, polyA selected 2

description:
SK412_14
polyA selected
cuffdiffs_mRNA.txt


title: RNAPII Ser2p in RNAi rep1 ChIP-seq

value: Ser2p Bethyl (A300-654A)


title: RNAPII Ser2p in RNAi ChIP-seq


title: Homer_forelimb_input_DNA_Rep1


title: RNAi CstF50, rRNA depleted RNA 2

description:
cpf1_RNAi-2
rRNA depleted RNA
Deseq_totalRNA.txt


title: 15-day-old jba-1D/+ er-20

city: Elche

first: Héctor

last: Candela

address: Edificio Vinalopó, Avenida de la Universidad s/n

department: Instituto de Bioingeniería

country: Spain

institute: Universidad Miguel Hernández de Elche

data_processing:
The reads (51 nt long) were quality filtered and trimmed using Trimmomatic version 0.32 with the following options: -threads 8 -phred33 ILLUMINACLIP:adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36.
The resulting reads were then aligned to the TAIR10 version of the Arabidopsis thaliana genome sequence (https://www.arabidopsis.org/) using TopHat version 2.0.12 (2) and Bowtie 2 version 2.1.0 with the following options: -p 8 (number of threads) -G TAIR10_nucleus.gff, where TAIR10_nucleus.gff is a file containing the annotation for the nuclear genes in the Arabidopsis genome in general feature format (GFF), and default values for all other parameters.
The resulting read alignments were used for transcript quantification with Cuffdiff version 2.2.1 with the following options: -p 8 (number of threads) -M filter_nucleus.gff, where filter_nucleus.gff is a file containing the annotation for rRNA, tRNA, snRNA and snoRNA genes in the Arabidopsis nuclear genome, which were masked for quantification purposes.
The gene expression level (RPKM) values were tabulated and subjected to k-means clustering using Gene Cluster 3.0 software, selecting a k value (number of clusters) of 1000, using "correlation (centered)" as the similarity metric, and converging for 1000 runs. Genes that were not expressed (i.e. with RPKM values equal to 0) across all samples were removed from the dataset before the k-means analysis.
Genome_build: TAIR10
Supplementary_files_format_and_content: The file genes.fpkm_tracking produced by Cuffdiff is included. This is a tab-delimited text file containing RPKM values and their confidence intervals for the ten samples. Numbering in the column headings matches the sample numbers (i.e. q1 corresponds to Sample 1, and so on).
Supplementary_files_format_and_content: The file fpkm_values_1000runsclusters_annotated_headings.txt is a tab-delimited text file containing the results of the k-means clustering analysis. The first raw contains the headings for the different columns. Column 1 is the gene identifier, columns 2 to 11 are the RPKM values for each of the 10 samples, column 12 indicates the cluster to which the gene has been assigned (in the k-means clustering analysis), and column 13 includes a short description of the gene's annotation. "NA" is used in column 12 to indicate genes nt included in the k-means analysis.

source_name: SAM-enriched tissue

growth_protocol: Plants were grown under long days (16 hours light/8 hours dark) and temperatures of 18-22°C on Murashige and Skoog (MS) plates.

extract_protocol:
Total RNA was isolated using Qiagen RNeasy Mini-kit.
Ten libraries were prepared using the TruSeq-RNA kit. Single-end sequencing was performed by multiplexing the libraries in an Illumina HiSeq2500 system at the Technion Genome Center (Israel).

treatment_protocol: Shoot apical meristems (SAM) from 8- and 15-day-old seedlings (including Col-0, clv3-2, jba‑1D/+, jba-1D/+ er-20, and jba-1D/+ er-20 clv3-2) were collected and were immediately frozen in liquid nitrogen (each sample comprised 40 to 45 meristems) .

value: 15 day old-seedling


title: Total RNAPII  in RNAi rep1 ChIP-seq

value: 8wg16 Millipore (05-952)


title: RNAPII Ser2p WT rep1 ChIP-seq


title: CstF64 in RNAi rep1 ChIP-seq

value: Blumenthal lab


title: Total RNAPII WT rep1 ChIP-seq

description: bentleyCTD

value: Bentley lab


title: Total RNAPII WT rep2 ChIP-seq


title: CstF64 in RNAi ChIP-seq


title: 15-day-old jba-1D/+ er-20 clv3-2


title: CstF64 in RNAi rep2 ChIP-seq


title: 15-day-old Col-0

value: Col-0 wild type


title: Total RNAPII WT ChIP-seq


title: Wt, polyA selected 1

description:
SK412_13
polyA selected
cuffdiffs_mRNA.txt


title: CstF50 WT rep1 ChIP-seq


title: RNAPII Ser2p WT ChIP-seq


title: 15-day-old jba-1D/+


title: 8-day-old jba-1D/+ er-20

value: 8 day old seedling


title: 8-day-old jba-1D/+


title: Total RNAPII  in RNAi ChIP-seq


title: CstF64 WT rep1 ChIP-seq


title: CstF64 WT ChIP-seq


title: 8-day-old clv3-2


title: CstF50 WT ChIP-seq


title: 8-day-old Col-0


title: 15-day-old clv3-2


title: PalVV1

status: Public on Apr 01 2016

city: Tulln

first: Harald

last: Berger

state: NOE

address: Konrad-Lorenzstraße 43

department: DAGZ

country: Austria

institute: Universität f. Bodenkultur Wien

data_processing:
Novoalign (Novocraft)was used for mapping the sequencing raw files onto the respective genomes and the python script HTSeq (Anders et al., 2014) was used to obtain coverage counts per exons.
Normalization and statistics of the coverage counts per transcript were done using R/Bioconductor packages limma(Smyth 2004), EdgeR and voom(Law et al. 2014) to identify differentially regulated genes using mean-variance weighting (voom) and TMM normalisation (Gentleman et al., 2004). A significance cut-off of p < 0.01 (adjusted for multiple testing by the false discovery rate method) was applied for analysis.
Genome_build: Phaeoacremonium aleophilum UCR-PA7
Genome_build: Phaeomoniella chlamydospora RR-HG1
Supplementary_files_format_and_content: Matrix of FPKM values and files with raw counts

organism: Phaeoacremonium minimum

source_name: Co-culture

growth_protocol: The two organisms (Vitis callus culture and P.ch respectively P.al) were transferred to new flasks. The co-cultures were incubated for 72 hours (80 rpm, 22 °C) on a rocking platform shaker. Samples were the fungi-callus-culture mixtures and the fungi without callus culture in B5VIT medium. The preparation of the samples without callus culture was the same as in the co-cultures, but the pelleted mycelia were dissolved in 50 mL B5VIT medium.

extract_protocol:
RNA was extracted using Qiagen RNeasy Plant Mini Kit and RNase-Free DNase Set for complete removal of genomic DNA. RNA was reverse transcribed using Biorad iScript™ cDNA Synthesis Kit and specific transcripts were verified using qPCR (iQ™ SYBR® Green Supermix, Biorad ).
Total RNA samples were further processed by VetCORE, VetMed University Vienna for high throughput sequencing. RNA fragmentation and Reverse Transcription were realized according to TruSeq RNA prep Kit v2 manual (Illumina, San Diego, US) and 50bp single end sequencing was performed using HiSeq V4 Illumina sequencer.

tag: v. vinifera co-culture

value: yes


title: PalVV2


title: CENH3-ChIPseq-CS

city: Wuhan

first: Handong

last: Su

state: Hubei

address: No.1,Shizishan Street · Hongshan District

institute: Huazhong Agricultural University

data_processing:
Basecalls performed using Illumina CASAVA.
ChIP-seq reads were mapped to wheat CS genome and DD genome, respectively with BWA version 0.6.1 with the following configurations.
All mappable reads were assigned a locus at random from the possible options, and duplicated reads were removed.
Reads per million (RPM) values of every scaffold in the genome were calculated to show normalized enrichment.
We selected the scaffolds that had read enrichment both in 4DS and in the control with RPM ratio between two samples ≥20, or scaffolds that had read enrichment only in 4DS with read counts ≥20.
Genome_build: Triticum_aestivum.IWGSP1.22 (CS-genome) and Aegilops_tauschii.GCA_000347335.1.22 (DD-genome)
Supplementary_files_format_and_content: bedGraph files were generated using bedtools.

organism: Triticum aestivum

source_name: wheat

growth_protocol: Suitable materials were planted in the greenhouse or in the field for ChIP experiments.

extract_protocol:
Extracted nuclei were digested with micrococcal nuclease (Sigma-Al drich) for ChIP experiments using the wheat CENH3 antibody.   The wheat CENH3 antibody is a rabbit polyclonal antiserum made in our laboratory.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).180-400 bp fragments (contained the joint) were selected by gel extraction.

tag: tissue

value: young leaves

tag: genotype/variation

value: control (CS)


title: Pch1

organism: Phaeomoniella chlamydospora

source_name: pure culture

value: no


title: Pal2


title: Pch2


title: Pal1


title: 8-day-old jba-1D/+ er-20 clv3-2


title: PchVV2


title: WT_S1

data_processing:
RNA-seq reads were mapped on the reference genome using tophat2 (v2.0.8). The interval for allowed intron lengths were set to min 20 nt and max 1 kb
We used cufflinks to determine the abundance of transcripts in FPKM (Fragments Per Kilobase of exon per Million fragments mapped) and calculated differentially expressed genes using cuffdiff (Trapnell et al., 2012, Trapnell et al., 2010). The gene models were included as raw junctions. Transcripts with a FPKM count of zero in one condition were set to the minimum global FPKM count of both conditions.
Genome_build: Fusarium graminearum PH-1 p3_p13839_Fus_grami_v32

organism: Fusarium graminearum PH-1

source_name: wildtype saprophytic growth

growth_protocol: The highly susceptible cultivar Remus (pedigree: Sappo/Mex//Famos) (Buerstmayr et al., 2002) was used in this study. On average 20 spikelets per wheat head were inoculated by pipetting 20 000 macroconidia (10 µL of a 2* 106 spores/ mL suspension) on the reproductive part between the lemma and palea of the two basal florets during anthesis (resulting in 800 spores per wheat head). Mock ears were inoculated the same way, but using water instead of spore suspension. Three ears were inoculated on the living plant representing pathogenic growth of the fungus and 3 ears, which were cut off the plant and shock-frozen in liquid N prior to spore application, were inoculated as “non- response” control from the wheat side or, in other words, representing saprophytic growth of the fungus. After inoculation the wheat heads on the living plants were covered with moistened plastic bags for the first 24 hours to provide high humidity. The inoculated dead wheat heads were placed in glass petri dishes (Ø 140 mm; h 20 mm). Incubation conditions were set at 20°C, 50% relative humidity during daytime and 18°C, 50% humidity during night with a 16 h photoperiod. Harvesting was performed 3 dai and 5 dai by freezing the plant material in liquid nitrogen. Only palea and lemma of the inoculated florets were sampled including the respective part of the rachis. Additionally completely untreated wheat heads were sampled

extract_protocol:
RNA isolation was performed using RNeasy Plant Mini Kit (Qiagen, 74904) following the instructions of the manufacturer with one modification and one extension: Instead of eluting RNA once in 30 µL RNase- free water, elution was performed in 2x 20 µL RNase- free water with a 3 minute standing period at room temperature after each water application to the column. Additionally on-column DNase digestion was done during the extraction protocol by using RNase-Free DNase Set (Qiagen, 79254). RNA quantity was first checked on the NanoDrop 2000c Spectrophotometer (Thermo Scientific). Afterwards RNA quantity and integrity was validated by using the Agilent RNA 6000 Nano Kit on an Agilent 2100 Bioanalyzer machine following the instructions of the provider. The cDNA Synthesis was done with the RevertAid H Minus First Strand cDNA Synthesis Kit (Thermo Scientific, # K1632) using random hexamer primer and following the manufacturer´s protocol.
Illumina sequencing libraries were made from RNA samples according to TruSeq RNA Sample prep kit v2 (Illumina) following the manufacturers protocol with 1µg total RNA input. 50 bp single end sequencing was performed using a HiSeq Illumina sequencer. Obtained sequences were de-multiplexed, quality controlled and mapped on the Aspergillus nidulans genome assembly (A_nidulans_FGSC_A4_version_s10-m03-r07).

tag: medium

value: Wheat

tag: host status

value: dead


title: WT_S2


title: EV3

city: Paris

first: Olivier

last: Espeli

address: 11 place Marcelin Berthelot

department: CIRB

institute: College de France

data_processing:
Basecalls performed using  CASAVA-1.8.2 (demultiplexing), Fastqc 0.10.1 (read quality),
RNA-seq reads were aligned to the NC_000913  genome assembly using Rockhopper
Supplementary_files_format_and_content: mRNA profiling and RKPM were performed with Rockhopper

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

source_name: MG1655 OD0,2 with MMC 40 min

growth_protocol: E. coli K12 MG1655 where grown in minimal medium A supplemented with casaminoacids 0,2% and glucose 0,25% until OD 0.2, treated or not with MMC (10µg/ml) for 20 or 40 min. Total RNA where immediatly extracted.

extract_protocol:
Genejet RNA purification kit (Thermo)
Libraries were prepared according to Illumina's instructions accompanying the TruSeq SBS Kit Transcriptome . Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: od

tag: strain


title: PchVV1


title: WT_P3

source_name: wildtype pathogenic growth

value: alive


title: WT_P1


title: WT_A2

source_name: wildtype axenic growth

value: Minimal medium


title: WT_S3


title: EV4

source_name: MG1655 recN OD0,2

value: MG1655 recN


title: WT_A1


title: EV1


title: EV5

source_name: MG1655 recN OD0,2 with MMC 20 min


title: Mouse kidney hMeDIP

first: Hao

last: Wang

address: 180 Fenglin Road

institute: Fudan University

data_processing:
base_calling: CASAVA package (Illumina v1.6)
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie-1.0.0
peaks were called using macs14 with the following setting:--pvalue=1e-5
normalized abundance on gene features is generated using home-made softwares
Genome_build: mm9
Supplementary_files_format_and_content: *peaks.bed: peaks bed files generated by Macs14, monoExt*.bed:mapped reads files in bed format, monoExt*.bg:ChIP-seq density files in bedgraph format.

source_name: Kidney tissue

extract_protocol:
Mouse kidneys were removed, flash frozen in liquid nitrogen and the genomic DNAs were extracted using Qiagen Genomic DNA Preparation Kit. hMeDIP was performed using the protocol described previously (Tan L et al., Nucleic Acids Research, 2013, Vol. 41, No.7 e84)
ChIP DNA libraries were prepared for sequencing using standard Illumina protocols.

value: 6-week old

tag: gender

value: male

tag: organ

value: kidney

value: 5hmC Active Motif


title: Veh_RNAP2_1hr_1D

city: Aurora

first: Tzu Lip

last: Phang

state: CO

address: 12700 East 19th Avenue

department: Medicine

institute: University of Colorado, Denver

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 2 with the default setting.
Mapped reads were compressed, sorted and indexed using Samtools
Peaks were called using MACS version 2 with the default setting
Genome_build: hg19
Supplementary_files_format_and_content: bed files were generated using MACS version 2

source_name: Cultured Beas-2B airway epithelial cells

growth_protocol: Beas-2B cells were obtained from ATCC and maintained in DMEM + 10% FBS.

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed as described previously described (PMID: 23508109), with the following modifications: cross-linking was performed by adding methanol-free 16% formaldehyde directly to the culture media to a final concentration of 1% and incubating for 5 minutes at room temperature with gentle rocking; samples were subsequently sonicated with a Diagenode Bioruptor at high power in 30-second bursts separated by 30-second incubations in ice water for a total of 34 cycles. GR antibody was a gift of Miles Pufall; RNAP2 antibody was from BioLegend (920101) and the p65 antibody was from Santa Cruz (sc-372x).
A minimum of 1 ng DNA from ChIP samples were used to prepare libraries using the Nugen Ovation Ultralow System V2 1-16 Part No. 0344 according to the manufacturer’s instructions. Samples were run on an Illumina HiSeq using 1X50 bp end reads

treatment_protocol: Beas-2B cells were plated in 10 cm dishes such that they would achieve confluence within 24-48 hrs. Once confluent, cells were treated with vehicle (ethanol), dexamethasone (100 nm final concentration), TNF (Life Technologies, final concentration 20 ng/ml) or both TNF+dex for 1 hour. Cells were subsequently crosslinked by adding formaldehyde directly to the dish and ChIP was performed (see extract protocol below)

value: vehicle


title: EV2

source_name: MG1655 OD0,2 with MMC 20 min


title: WT_P2


title: Mouse kidney input


title: CENH3-ChIPseq-4DS


title: Veh_RNAP2_1hr_1C


title: Veh_NFkB_1hr_3D


title: EV6

source_name: MG1655 recN OD0,2 with MMC 40 min


title: Veh_NFkB_1hr_3A


title: Veh_GR_1hr_2B

value: GR


title: Veh_GR_1hr_2D


title: Tnf_NFkB_1hr_5D

value: TNF


title: TnfDex_RNAP2_1hr_8B

value: dexamethasone + TNF


title: TnfDex_NFkB_1hr_10D


title: TnfDex_RNAP2_1hr_8C


title: TnfDex_GR_1hr_9D


title: TnfDex_GR_1hr_9C


title: Dex_RNAP2_1hr_6A

value: dexamethasone


title: Dex_RNAP2_1hr_6D


title: Dex_GR_1hr_7A


title: Background_3A_Input


title: TnfDex_NFkB_1hr_10A


title: Background_2A_Input


title: shLIN28b-1

city: Boston

first: Kenneth

middle: N

last: Ross

state: MA

address: 450 Brookline Ave., Rm M640

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description: Human Panc3.27 PDAC shLIN28B knockdown 1

data_processing:
Reads were trimmed, aligned, and expression profiles created using miRExpress (Wang et al., 2009) version 2.1.4 with default parameters. The miRExpress software takes unaligned fastq files as input and uses the four procedures:  “Raw_data_parse -> Trim_adaptor -> alignmentSIMD -> analysis" to produce miRNA expression profiles. The Trim_adaptor step uses a 3' adapter sequence input file Adapter.txt that contains the Illumina adapter sequence used which in this case was: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT. The alignmentSIMD step uses a miRNA precursor file hsa_precursor.txt which was used as supplied with the miRExpress package version 2.1.4 and the analysis step uses a file hsa_miRNA.txt with mature miRNA information for precursor sequences which was used as supplied with the miRExpress package version 2.1.4.
Differential expression analysis comparing the control to shLIN28B samples was performed using edgeR (Robinson et al., 2010) version 3.12 with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: txt files are sample specific expression data output from edgeR differential analysis with CPM data. The file SK_Panc0327_PLKO_vs_shLIN28B_miRNA_CPM_160316.txt is available on the series record and contains CPM data for all samples and averages.

source_name: Human Panc3.27 PDAC

growth_protocol: Human pancreatic cancer cell line Panc03.27 was obtained from American Type Culture Collection (ATCC; Rockville, MD), and grown in its required growth medium per ATCC description.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were made with the NEBNext Multiplex Small RNA Library Prep and 15 cycles of amplification (https://www.neb.com/products/e7300-nebnext-multiplex-small-rna-library-prep-set-for-illumina-set-1). Sequencing was PE50 (paired-end 50-cycles) on HiSeq 2000. The samples were run in 2 pools of 6 in 2 lanes. Approximately 35 million read pairs per sample were obtained.

treatment_protocol: Human pLKO.1-shLIN28B vector (TRCN0000122599) (target sequence: 5′-GCCTTGAGTCAATACGGGTAA-3′) was obtained from the MGH RNAi Consortium Library. Viral particles containing the plasmids were synthesized using either lentiviral (pCMV-dR8.91) packaging plasmids with pCMV-VSV-G (Addgene). Cells were infected by incubating with virus and 10 μg/ml polybrene. Twenty-four hours later, cells were selected in 2.5 μg/ml puromycin for at least two days and the pooled populations were used for small RNA-Seq.

tag: cell line

tag: cell type

value: PDAC

tag: lentiviral plasmids


title: Control-3

description: Human Panc3.27 PDAC PLKO Control 3

value: PLKO


title: shLIN28b-2

description: Human Panc3.27 PDAC shLIN28B knockdown 2


title: Control-1

description: Human Panc3.27 PDAC PLKO Control 1


title: shLIN28b-3

description: Human Panc3.27 PDAC shLIN28B knockdown 3


title: Control-2

description: Human Panc3.27 PDAC PLKO Control 2


title: 36-NPS3

city: Ramat-Gan

first: Tomer

last: Kalisky

address: Faculty of Engineering

department: Bioengineering

country: Israel

institute: Bar-Ilan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads were aligned by TopHat2 to the human hg19 genome. The reference genome and annotation files were obtained from the Illumina iGenomes collection (http://support.illumina.com/sequencing/sequencing_software/igenome.html)
Aligned reads were counted by HTSeq.
Data normalization and differential gene expression was done by DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: NPS_original_count.csv: Raw counts of sequencing reads
Supplementary_files_format_and_content: NPS_normal_count.csv: Normalized abundance measurements

source_name: Human fetal kidney NCAM-CD133+

extract_protocol:
Human fetal kidneys were collected from elective abortions. Fetal gestational age ranged from 15 to 19 weeks. All studies were approved by the local ethical committee and informed consent was given by the legal guardians of the patients involved according to the declaration of Helsinki. Each tissue was processed for immunohistochemical (IHC) staining and formation of single cell suspension. Single cells suspensions were suspended in Iscove’s Modified Dulbecco’s Medium (IMDM) medium supplemented with 10% Fetal Bovine Serum (FBS) and growth factors: 50 ng/ml of basic Fibroblast Growth Factor (bFGF), 50 ng/ml of Epidermal Growth Factor (EGF) and 5 ng/ml of Stem Cell Factor (SCF) (R&D Systems) and plated in flasks. Cells were incubated used for FACS sorting of cell subpopulations. Bulk total RNA was prepared from ~1.5*10^5 cells using the Direct-zol RNA MiniPrep kit (Zymo Research) and stored in -80C. RNA was quantified on an Agilent BioAnalyzer (Agilent Technologies) and aliquots of 270-500ng were made into cDNA libraries using the TruSeq mRNA-Seq library kit (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols. TruSeq RNA-Seq.

tag: cell population

value: 15 to 19 weeks of gestation


title: 35-NPS2

source_name: Human fetal kidney NCAM+CD133+


title: 34-NPS1

source_name: Human fetal kidney NCAM+CD133-


title: Tnf_RNAP2_1hr_4D

tag: treatment


title: Dex_GR_1hr_7C

tag: antibody


title: VCaP_Et_OCT1

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

country: Japan

institute: Tokyo Metropolitan Institute of Gerontology

data_processing:
Basecalls performed using CASAVA-1.8.2
ChIP-seq reads were aligned to the hg18 genome assembly using Bowtie version 0.12.8 with parameters -a --best --strata -m 1 -v 2.
Generate alignments in the SAM format given single-end reads. Convert SAM to BAM files using samtools view command. samtools version is 0.1.16.
Signal scores were calculated using Model-based analysis of ChIP-seq (MACS; P-value < 10xE-4 or -5)
Genome_build: hg18
Supplementary_files_format_and_content: *peaks.bed files can be visualized by Integrative genomic viewer ver 2.2 (IGV ver 2.2)

source_name: prostate cancer cells

growth_protocol: LNCaP and VCaP cells were cultured in DMEM or RPMI 1640 containing 10% FBS. Before hormone treatment, cells were incubated in Phenol red-free DMEM or RPMI 1640 containing 2.5% charcoal/dextran treated FBS for three days.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
The Chromatin immunoprecipitated DNA fragments (approx.10 ng in 30 µl water) are end repaired by using T4 DNA polymerase, Klenow DNA polymerase and T4 polynucleotide kinase in the presence of dNTPs. And an ‘A’ base is added to the 3’end of the blunt phosphorylated DNA fragments, using the polymerase activity of Klenow fragment. Then, adaptors (Adaptor oligo mix, Illumina) are ligated to the ends of the DNA fragments. The resulting DNA fragments are purified by MinElute column (QIAGEN).  300 ~ 500 bp DNA fragments are purified by using E-Gel SizeSelect agarose Gels (Invitrogen) according to manufacturer’s instruction.Size selected adaptor-modified DNA fragments are amplified by 18 cycles of PCR using Phusion polymerase and PCR primer 1.1 and 2.1 (Illumina). The resulting PCR products are purified by MinElute column (QIAGEN).

treatment_protocol: LNCaP and VCaP cells were treated with vehicle or DHT 10 nM for 24 h.

value: AR-positive prostate cancer cell line VCaP

tag: treatment (pre-hormone)

tag: hormone treatment

value: vehicle control

value: Oct1 (Abcam, catalog# ab8895, lot# GR114621-3)


title: VCaP_DHT_OCT1

value: DHT 10 nM

tag: chip antibody


title: LNCaP_DHT_OCT1

value: AR-positive prostate cancer cell line LNCaP


title: VCaP_DHT_FOXA1

value: FOXA1 (Abcam, catalog# ab94580)


title: VCaP_siFOXA1_OCT1


title: LNCaP_Et_OCT1


title: VCaP_Et_FOXA1


title: VCaP_input 2

value: none (input)


title: VCaP siOCT1DHT AR

value: AR (Santa Cruz, catalog# H-280, lot# K2912)


title: LNCaP_siFOXA1_OCT1


title: Tnf_RNAP2_1hr_4C


title: HCT116-siRNA-B-1

city: Aarhus

first: Morten

middle: Muhlig

last: Nielsen

address: Palle Juul-Jensens Bouleward 99

department: Department of Molecular Medicine

country: Denmark

institute: Aarhus University

description: SNHG5 siRNA B

data_processing:
Bam files created using TopHat v2.
Expression counts estimated wit HTSeq V2
GENCODE v15 was used as gene model.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: tab delimited flat file, genes=rows, samples=cols, gene ID = GENCODE v15

source_name: cell line

growth_protocol: cell lines were maintained in McCoy’s medium (Invitrogen) supplemented with 10% fetal bovine serum (Hyclone) and penicillin/streptomycin (Invitrogen).

extract_protocol:
total RNA was isolated using Trizol reagent (Invitrogen).
Single end, 50 bases, oligodT purified. Library preparation and sequencing on the Illumina Hiseq2000 by BGI Genomics (Hong Kong).

treatment_protocol: siRNA oligonucleotides were transfected at a final concentration of 25 nM by reverse transfection using RNAiMAX (Invitrogen), according to the manufacturer’s instructions.

tag: tissue

value: colon

tag: cell ine


title: HCT116-siRNA-A-3

description: SNHG5 siRNA A


title: VCaP control DHT AR

value: siControl


title: HCT116-siRNA-B-3

description: SNHG5 siRNA B


title: HCT116-siRNA-B-2

description: SNHG5 siRNA B


title: Day 5 CD40L+IL4+IL5 stimulated cells, Syndecan1+ (40/4/5 PB) rep2

city: Clayton

first: Wei

last: Shi

state: Victoria

address: Wellington Rd

institute: Monash University

data_processing:
Reads were aligned to the GRCm37/mm9 build of the Mus musculus genome using the Subread aligner. Ten ‘subreads’ were extracted from each read and at least three consensus ‘subreads’ were required for a ‘hit’ to be reported. Hamming distance was used to break the tie when more than one best location was found for a read. Only uniquely mapped reads were retained.
Genewise counts were obtained using featureCounts. Reads overlapping exons in annotation build 38.1 of NCBI RefSeq database were included. Genes were filtered from downstream analysis if they failed to achieve a CPM (counts per million mapped reads) value of 1 or greater in at least one library. Immunoglobulin genes were also excluded from the genome-wide expression analysis, due to the large difference between B cells and plasma cells in the percentage of reads mapped to immunoglobulin genes. Expression analysis for immunoglobulin genes was performed separately.
Counts were converted to log2 counts per million, quantile normalized and precision weighted with the voom function of the limma package. A linear model was fitted to each gene, and empirical Bayes moderated t-statistics were used to assess differences in expression. Empirical Bayes moderated-t p-values were computed relative to a fold-change cut-off of 1.5-fold by using treat. P-values were adjusted to control the global false-discovery rate across all comparisons with the ‘global’ option of the limma package. Genes were called differentially expressed if they achieved a false discovery rate of 0.05 or less and also had at least 8 FPKMs (fragments per kilo exonic bases per million mapped reads) in one or both of the two cell types being compared.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include normalized log2-FPKM values for each sample

source_name: Spleen

extract_protocol:
RNA was isolated from cells using Qiagen RNeasy Micro or Mini Kits (based on cell number), according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Spleen

tag: stimulus

tag: time

value: 120 hours

value: CD40L/IL4/IL5 plasmablasts

tag: markers

tag: culture

value: In vitro


title: HCT116-CTRL-2

description: control


title: HCT116-siRNA-A-2

description: SNHG5 siRNA A


title: HCT116-CTRL-3

description: control


title: VCaP input


title: KLF5flox/flox; Vil-CreERT2 Sample 3

city: Houston

first: Noah

middle: F

last: Shroyer

state: Texas

address: 1 Baylor Plaza

department: Medicine - Gastroenterology

institute: Baylor College of Medicine

data_processing:
Pooled concentration from the qPCR assay, the library was loaded onto a rapid run flow cell at a concentration of 12pM for on-board cluster generation and sequencing on the HiSeq 2500, at a read length of 100bp, paired-end.
TopHat was used to align the reads to the mouse genome.  Samples were mapped as follows: wildtype sample 1 contained 45589099 paired-end reads (95.2% mapped), wildtype sample 2 contained 50147474 paired-end reads (95.0% mapped), wildtype sample 3 contained 45676445 paired-end reads (94.7% mapped), knockout sample 1 contained 52022786 paired-end reads (93.6% mapped), knockout sample 4 contained 50327272 paired-end reads (94.5% mapped), and knockout sample 3 contained 4176659 paired-end reads (94.9% mapped).
The relative abundance of transcripts was found using Cufflinks to determine FPKM.  Differential expression was then found using Cuffdiff.
Genome_build: mm9
Supplementary_files_format_and_content: .diff file contains differential gene expression for each gene between the two genotypes, the .fpkm_tracking files contain FPKM information for each sample

source_name: Isolated Jejunal Crypts

extract_protocol:
Jejunal tissue was extracted and flushed of excrement then cut into pieces.  Tissue was then subjected to a 30 minute incubation in 2mM EDTA in PBS at 4C.  Tissue was then transferred to 5mL shaking buffer (43.3mM sucrose, 54.9mM sorbitol in PBS).  Tissue was shaken for 1 - 2 minutes until crypts were visible under the microscope.  After crypts were isolated, the buffer with chelated tissue was poured through a 70uM filter to remove villi.  RNA was then prepped using the Qiagen RNeasy kit.
A double-stranded DNA library was created using 250ng of total RNA, quantitated by picogreen, preparing the fragments for hybridization onto a flowcell. cDNA was created using the fragmented 3’ poly (A) selected portion of total RNA and random primers. Libraries were created from the cDNA first blunt ending the fragments, attaching an adenosine to the 3’ end, and ligating unique adapters to the ends. The ligated products were then amplified using 15 cycles of PCR. The resulting libraries were quantitated using NanoDrop and fragment size assessed with the Agilent 2100 Bioanalyzer. A qPCR assay was performed determine the concentration of adapter ligated fragments using the Applied Biosystems ViiA 7 instrument and a KAPA Library Quant Kit.

treatment_protocol: 6 week old mice were treated to 3 daily IP injects of tamoxifen (80mg/kg) then sacrificed the next day

value: Jejunal Crypt

tag: age

value: 6 weeks

tag: genotype

value: KLF5flox/flox; Vil-CreERT2


title: HCT116-siRNA-A-1

description: SNHG5 siRNA A


title: KLF5flox/flox; Vil-CreERT2 Sample 1


title: Day 5 CD40L+IL4+IL5 stimulated cells, Syndecan1+ (40/4/5 PB) rep1

tag: strain


title: LNCaP_input2

tag: cell line


title: KLF5+/+; Vil-CreERT2 Sample 3

value: KLF5+/+; Vil-CreERT2


title: KLF5+/+; Vil-CreERT2 Sample 2


title: KLF5flox/flox; Vil-CreERT2 Sample 2


title: KLF5+/+; Vil-CreERT2 Sample 1


title: mOPC NT (2)

city: New York

first: Gareth

last: John

state: New York

address: 1 Gustave Levy Place

department: Neurology

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Basecalls performed using CASAVA version 1.8
RNA-seq reads were aligned to the mm9 genome assembly using TopHat2 with default settings
Gene abundance and differential expression were processed using the Tuxedo Suite Ver.2.1.1  with default settings
Genome_build: mm9
Supplementary_files_format_and_content: Significant cuffdiff output

source_name: Oligodendrocyte progenitor cells

growth_protocol: Oligodendrocyte progenitor cells (OLP) were plated onto poly-D-lysine coated confocal dishes (Mat-Tek, Ashland, MA) in Sato media with the proliferative factors PDGF-AA (10 ng/ml) and bFGF (20 ng/ml). OLP were cultured in a humidified incubator at 5% CO2 and 37oC, with a half change of media every day.

extract_protocol:
Cell lysate was harvested and RNA was extracted using Qiagen RNeasy Mini kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: OLP were nucleofected using siRNA targeted vs. Klf6 or NT control (GE Healthcare Dharmacon, Lafayette, CO) and were either untreated or treated with 40ng/ml T3 for 18h.

tag: cell type

value: Oligodendrocyte progenitor cells


title: mOPC NT (1)


title: iOL siKlf6 (1)

source_name: Immature oligodendrocytes

value: Immature oligodendrocytes


title: HCT116-CTRL-1

description: control


title: iOL NT (2)


title: mOPC siKlf6 (2)


title: iOL NT (1)


title: mOPC siKlf6 (1)


title: iOL siKlf6 (2)


title: H3K56ac ChIP-Seq Sirt6 KO PDAC

description: H3K56ac ChIP-Seq in Sirt6 KO murine PDAC cell line SK03

data_processing:
ChIP libraries were indexed, pooled, and sequenced on Illumina HiSeq-2500 sequencers at the Broad Institute sequencing center.
ChIP-seq reads were aligned to the mouse mm9 genome assembly using bwa version 0.5.9 with parameters '-q 5 -l 32 -k 2 -t 4 -o 1 -f' for the aln command and '-t 4 -T -P -f' for the sampe command.
ChIP-seq duplicate reads were marked with Picard Tools MarkDuplicates version number 1.764.
Peak calling with MACS2 version 2.0.10 and parameters '-g mm -f BAM -B -q 0.01'
Ran the IGVtools version 2.3.18 utility 'count' on aligned bam files to compute the average alignment over 25 base windows across the genome and generate binary tiled data .tdf files.
Genome_build: mm9
Supplementary_files_format_and_content: text files are ChIP-Seq peak summary files from MACS2 in a tab delimited text file format.
Supplementary_files_format_and_content: tdf files are binary tiled data files of aligned ChIP-Seq data from the IGVtools count utility that conatin average alignment counts across the genome and can viewed in the IGV genome browser.

source_name: Murine PDAC

growth_protocol: Murine PDAC cells that are Sirt6 wild type (WT), Sirt6 knock-out (KO), and Sirt6 KO cells engineered to express Sirt6 WT (Sirt6 KO + WT Restored) were maintained on a mixed 129SV/C57BL/6 background. Sirt6-flox/flox conditional strain (Sebastian et al., 2012) were crossed with the p48-Cre strain (Kawaguchi et al., 2002), the conditional p53-flox strain (Marino et al., 2000) and the LSL-Kras-G12D strain (Jackson et al., 2001) which consists of a mutant Kras-G12D allele knocked into the endogenous Kras locus, preceded by an LSL cassette. To establish mouse pancreatic cancer cell lines, freshly isolated tumor specimens from Sirt6 flox/flox; Kras-G12D; p53-flox/+; p48-Cre (SIRT6 KO) and Sirt6+/+;Kras-G12D; p53-flox/+; p48-Cre (SIRT6 WT) mice were minced with sterile razor blades, digested with trypsin for 30 minutes at 37°C, and then 20 resuspended in RPMI 1640 and supplemented with 10% fetal bovine serum and 1% penicillin (100 U/ml)/streptomycin (100 Ug/ml) (Invitrogen Gibco) and seeded on plates coated with rat tail collagen (BD Biosciences). Cells were passaged by trypsinization. All studies were done on cells cultivated for less than ten passages.

extract_protocol:
Chromatin immunoprecipitation (ChIP) steps were performed using a modified version of our previous protocols (e.g., Ram & Goren et. al. (2011) Combinatorial Patterning of Chromatin Regulators Uncovered by Genome-wide Location Analysis in Human Cells. Cell. 147 (7). and Garber & Yosef et. al. (2012) A High-Throughput Chromatin Immunoprecipitation Approach Reveals Principles of Dynamic Gene Regulation in Mammals. Molecular Cell 47 (5).) adapted to the Bravo liquid handling platform (Agilent). Cells were crosslinked using formaldehyde (1%, 37C for 10 min), and then quenched with glycine (5min at 37C). The fixed cells were lysed in Lysis buffer (1% SDS, 10mM EDTA and 50mM Tris-HCl pH 8.1, containing protease inhibitors (Roche, 04693159001). Chromatin was sheared using Covaris E-220 at 4oC to a size range between 200 and 800 bp. 1 to 5µg of antibody were incubated 2 hours with a mix of Protein-A and Protein-G Dynabeads (Invitrogen, 100-02D and100-07D, respectively) in blocking buffer (PBS supplemented with 0.5% TWEEN and 0.5% BSA). Beads were washed added to the chromatin lysate, and incubated overnight. Next, samples were washed 6 times with RIPA buffer, twice with RIPA buffer containing 500mM NaCl, twice with LiCl buffer (10mM TE, 250mM LiCl, 0.5% NP-40, 0.5% DOC), twice with TE (10Mm Tris-HCl pH 8.0, 1mM EDTA), and then eluted in ChIP-Elution Buffer (0.5% SDS, 300 mM NaCl, 5 mM EDTA, 10 mM Tris Hcl pH 8.0) at 65C, 4 hours, and then treated with RNaseA (Roche, 11119915001) for 30 min and Proteinase K (NEB, P8102S) for 2 hours.
Illumina Library construction reactions were performed as we described previously (Garber & Yosef et. al. 2012). SPRI (Solid-phase reversible immobilization; AMPure XP beads (Agencourt)) cleanup steps were done using the Bravo liquid handling platform (Agilent) and a modified version of (Fisher et al., 2011). After the final ChIP step, 120µl SPRI was added to the reverse-crosslinked samples, pipette-mixed 15 times and incubated for 2 minutes. Supernatant was separated from the beads using a 96-well magnet for 4 minutes. Beads were washed on the magnet with 70% ethanol and then air dried for 4 minutes. DNA was eluted in 40µl EB buffer (10 mM Tris-HCl pH 8.0) by pipette mixing (25 times). The remainder of the library construction process (DNA end-repair, A-base addition, adaptor ligation and enrichment) the SPRI cleanup involves addition of PEG buffer (20% PEG and 2.5 M NaCl) to the reaction products. Next, plates were transferred to a magnet plate, incubated for 4 minutes and supernatant removed. Beads are washed on the magnet with 150µl 70% ethanol and air dried for 4 minutes. The DNA is eluted with 40µl of EB buffer (mixing 25 times). Reagent kits are prepared in advance for all enzymatic steps (New England Biolabs). The DNA end-repair was performed by adding 27µl of a master mix (17µl master mix (5µl T4 buffer, 5µl BSA-1mg/ml, 5µl ATP-10mM -2µl dNTPs 10 mM)) plus 5µl T4 PNK enzyme, 5µl T4 polymerase (3 units) to each well. Samples were incubated in a thermal cycler at 12C for 15 min, 25 oC for 15 min, and finally cooled to 4 oC. The SPRI bead clean up method was used to purify the product (147µl of 20% PEG, 2.5 M NaCl was added to each sample and eluted in 40µl EB). The A-base addition was performed by adding 20µl master mix (17µl A-base add mix, 3µl Klenow to each well and incubated at 37oC for 30 min in a thermal cycler. Product was purified using 132µl PEG buffer and eluted in 19µl EB. Adaptor ligation: was performed by adding 34µl of a master mix (29µl 2x DNA ligase buffer, 5µl DNA ligase) and 5µl indexed oligo adaptors (0.75 uM ) followed by 15min incubation in 25C in a thermal cycler. Next, ligated products were purified using SPRI bead clean up with size selection (15.5µl of PEG buffer) and eluted in 40µl EB.  The final step of PCR enrichment was was performed by adding 10µl of a master mix (2µl Forward/Reverse Index Primer, 0.5µl dNTP mix, 5µl 10x PfuUltra Buffer, 1µl PfuUltra-II Fusion, 1.5µl Nuclease free water) to each well. Using a thermal cycler, programed to 95C for 2 min, followed by 16 cycles of (95C for 30 sec, 55C for 30 sec, 72C for 60 sec), and a final incubation at 72C for 10 min. The last SPRI clean up was coupled to size selection (35µl SPRI beads were added to each sample and eluted in 40µl).

treatment_protocol: ChIP-Seq experiments used untreated murine PDAC cells that are Sirt6 wild type (WT), Sirt6 knock-out (KO), and Sirt6 KO cells engineered to express Sirt6 WT (Sirt6 KO + Sirt6 KO).

value: PDAC

tag: sirt6 status

value: KO

value: H3K56ac (abcam, ab76307)

value: mixed 129SV/C57BL/6 background


title: T3_B_Input

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie2 with default settings
Reads were filtered for quality using FASTAX
Peaks were called using MACS1.4 using a p-value cutoff of 10E-4
Peaks were annotated with ChIPpeakAnno 50kb downstream and 5kb upstream
Genome_build: mm9
Supplementary_files_format_and_content: MACS1.4 output with annotated peaks within window

extract_protocol:
Lysates were clarified from sonicated nuclei and Klf6-DNA complexes were isolated with a Rabbit polyclonal anti-Klf6 anitbody (Santa Cruz).
Illumina Truseq

treatment_protocol: OLP were either untreated or treated with 40ng/ml T3 for 18h.


title: WCE Sirt6 WT PDAC

description: WCE from Sirt6 WT murine PDAC cell line RP07

value: WT


title: OPC_A_Klf6

value: Klf6 (Santa Cruz, SC-7158X, Lot:F1212)


title: OPC_A_Input


title: OPC_B_Input


title: T3_A_Input


title: T3_A_Klf6


title: H3K56ac ChIP-Seq Sirt6 KO +WT Restore PDAC

description: H3K56ac ChIP-Seq in Sirt6 KO with WT Sirt6 restored in murine PDAC cell line SK03

value: KO + WT Restored


title: Vehicle (Nseqveh127)

city: Chapel Hill

first: Mark

last: Zylka

state: NC

address: 5109D Neuroscience Research Building

institute: University of North Carolina - Chapel Hill

description: processed data file: Pyraclostrobin_4reps_withVehicle_rawCounts_matrix.txt

data_processing:
RNA-seq reads were filtered using TagDust
Reads were aligned to the reference mouse genome (mm9) with TopHat using default parameters
Reads aligning to rRNA genes were removed
Transcript abundance was estimated by computing RPKM using RefSeq gene models aggregated by gene symbol
Genome_build: mm9
Supplementary_files_format_and_content: RPKM for all RefSeq genes and all samples were filtered such that a given gene had >90% of samples with RPKM >0 and gene length exceeded 500 bp.  RPKMs were then log10 transformed, quantile-normalized, median-centered, and subtle batch effects were removed using a mixed model ANOVA

source_name: Cortical neurons

growth_protocol: Primary mouse cortical neuron cultures were prepared as previously described from embryonic day 15 (E15) pregnant C57BL/6J (Cat. #000664, Jackson) dams crossed to CAST/EiJ (Cat. #000928, Jackson) males{King, 2013 #1414}.  Hybrid cultures are thought to better model genetic variation associated with human populations{French, 2015 #1509}.  Dissociated cells were placed in multiwell plates coated with poly-D-lysine (0.1 mg ml−1) in Neurobasal medium (Life Technologies) containing 5% FBS (Gibco), B27 (17504-044, Invitrogen), Antibiotic-Antimycotic (15240-062, Invitrogen), and GlutaMAX (35050-061, Invitrogen).  At days in vitro (DIV) 3 a half medium change was performed with feeding medium identical to the plating medium except that we omitted FBS and included 4.84 μg ml−1 uridine 5'-triphosphate (U6625, Sigma-Aldrich) and 2.46 μg ml−1 5-fluoro-2′-deoxyuridine (F0503, Sigma-Aldrich) to inhibit mitosis in dividing cells.

extract_protocol:
RNA was isolated with RNeasy plus mini kit (Cat. #74134, Qiagen).  RNA yield and quality was determined with a Nanodrop 1000 Spectrophotometer (Thermo Scientific).  Samples were further assessed for quality using either an Agilent Bioanalyzer 2100 or TapeStation 2200 to obtain a RNA integrity number (RIN).  RIN values exceeding 7 were used for sequencing.
RNA samples were used to generate and barcode cDNA libraries using the TruSeq RNA Library Preparation Kit at the UNC High Throughput Sequencing Facility.

treatment_protocol: Cultures were treated with the non-cytotoxic dose of each chemical on DIV 7 for 24 hours in 12-well plates at a density of 5 x 105 cells per well.

value: cortical neurons

tag: developmental stage

value: embryonic day E15

value: CAST x C57BL6


title: Pyraclostrobin 0.1uM Rep4


title: Vehicle (Nseqveh126)


title: Pyraclostrobin 0.1uM Rep3


title: Vehicle (Nseqveh125)


title: Pyraclostrobin 0.1uM Rep2


title: Vehicle + Fenamidone 10uM Rep3

description: processed data file: SULF10-FENAM-VS-VEH-FENAM_rawCounts_matrix.txt


title: T3_B_Klf6


title: H3K56ac ChIP-Seq Sirt6 WT PDAC

description: H3K56ac ChIP-Seq in Sirt6 WT murine PDAC cell line RP07


title: Vehicle + Fenamidone 10uM Rep2


title: Sulforaphane 10uM + Fenamidone 10uM Rep1


title: OPC_B_Klf6


title: Vehicle + Fenamidone 10uM Rep1


title: Sulforaphane 10uM + Fenamidone 10uM Rep2


title: Vehicle (Nseqveh90)

source_name: cultured cortical neurons

treatment_protocol: Cultures were treated with the non-cytotoxic dose of each chemical on DIV 7 for 24 hours in 12-well plates at a density of 5 x 10^5 cells per well.


title: Vehicle (Nseqveh89)


title: Vehicle (Nseqveh86)


title: Vehicle (Nseqveh88)


title: Input DNA

first: Tatsuya

last: Kobayashi

address: 50 Blossom Street, Thier 1101

department: Endocrine Unit

institute: Massachusetts General Hospital

data_processing:
Basecall was completed with CASAVA 1.8.4
bowtie2 as mapper to align the paired-end reads to mm10
peaks were called with MACS2 callpeak function
peaks from MACS2 were annotated with ChIPPeakAnno
Genome_build: mouse mm10
Supplementary_files_format_and_content: Peak files, Peak annotation in CSV

source_name: Mouse primary chodrnocytes

growth_protocol: Mouse primary chodnrocytes were isolated from new born CD1 mouse.  Rib cartilage was dissected, treated with collagenease 2 to release chondroyctes from the matrix.  Chondrocytes were strained to remove extracellular matrices, culutred overnight in a 10% bovine fetal serum-containting DMEM medium.

extract_protocol: Cell preparation was performed according to the SimpleCHIP enzymatic chromatin IP kit (# 9003 Cell Signaling Technology).  ChIP was performed using the H3K27me3 antibody (# 9733n Cell Signaling Technology)  ChIP'ed DNA and Input DNA were sequenced by Otogenetics (Necros, GA)

treatment_protocol: N/A;  wild type chondrocytes

tag: tisse

value: rib cartilage

value: chondrocytes


title: ChIP'ed DNA

value: input


title: Vehicle (Nseqveh87)