title: H3K36me3 Input (Nitrogen starvation 1 hr)


title: H3K36me3 ChIP-Seq (Nitrogen starvation 1 hr)

status: Public on Jul 28 2015

type: SRA

city: Walnut Creek

first: Chia-Lin

last: Wei

state: California

address: 2800 Mitchell Drive

department: Genomic Technologies

country: USA

institute: DOE Joint Genome Institute

description:
H3K36m3ND1hrIPR1
processed data file:
emissions_16.txt.gz
transitions_16.txt.gz
processed data file: Cre4A+Nitrogen_starvation_1hr_16states_genome_segmentation.bed.gz

library_source: genomic

data_processing:
Raw reads were mapped to C. reinhardtii genome (v5.3.1) by BWA v0.6.2 with default parameters
Enriched regions in the non-redundant mapped reads were identified by MACS2 v2.0.10 (effective genome size=107270392, FDR< 5%)
ChromHMM v1.0.6 (Ernst and Kellis, 2010) was used to perform unsupervised segmentation of the genome into 16 states initialized by information initialization strategy based on the combination of chromatin modifications from baseline (0 hr), nitrogen starvation (1hr) and sulfur starvation (1 hr).   * Ernst and Kellis. 2010. Discovery and characterization of chromatin states for systematic annotation of the human genome. Nature biotechnology 28, 817-825.
Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced.
Genome_build: Chlamydomonas reinhardtii genome (Phytozome v5.3.1); C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz
Supplementary_files_format_and_content: peaks list, tab-delimited text files include FPKM values for each sample and the gene/transcript annotations

molecule: genomic DNA

organism: Chlamydomonas reinhardtii

growth_protocol: C. reinhardtii wild type strain 4a+ was cultured using Tris-acetate-phosphate (TAP) medium.

extract_protocol:
ChIP-seq was performed as previously described (Chen et al., 2008). Briefly, cross-linked cells were lysed with Lysis Buffer (50 mM Tris-HCl pH8, 5 mM EDTA, 1% SDS) and chromatin was then sheared. 5-50 ug of chromatin was used in each immuno-precipitation.  Chromatin was first pre-cleared and then mixed with beads pre-bound with antibody. Beads were washed and eluted at 37ºC. The eluate was then de-crosslinked and DNA was purified by phenol/ chloroform extraction, followed by ethanol precipitation (Chen et al. 2008). Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133, 1106-1117.
5-10 ng of purified DNA was used in ChIP-seq library preparation using Truseq DNA Sample Preparation Kit (Illumina)

treatment_protocol: N-free (TAP-N) and SO42--free (TAP-S) media were prepared as described (Boyle et al., 2012; Kropat et al., 2011). For N- and S- starvation conditions, cells were grown to mid-log phase, washed twice with depleted media and re-suspended in TAP-N or TAP-S media to a density of 2x10^6 cells/ml (Boyle et al. 2012). Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas (The Journal of biological chemistry 287, 15811-15825; Kropat et al. 2011). A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii (The Plant journal for cell and molecular biology 66, 770-780).

tag: strain

tag: time

value: 1 hr

tag: chip antibody

value: H3K36me3 (Abcam ab9050)


title: RNA Pol2 ChIP-Seq (Nitrogen starvation 1 hr)

description:
RNAPol2ND1hrIPR1
processed data file:
emissions_16.txt.gz
transitions_16.txt.gz
processed data file: Cre4A+Nitrogen_starvation_1hr_16states_genome_segmentation.bed.gz

value: RNAPII (clone 8WG16, Covance MMS-126R)


title: PSR1 Input (Peptide A, Sulfur starvation 1 hr)

data_processing:
Raw reads were mapped as single-end read to C. reinhardtii genome (v5.3.1) by BWA v0.6.2 with default parameters
Enriched regions in the non-redundant mapped reads were identified by MACS2 v2.0.10 (effective genome size=107270392, FDR< 5%)
Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced.
Genome_build: Chlamydomonas reinhardtii genome (Phytozome v5.3.1); C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz
Supplementary_files_format_and_content: peaks list, tab-delimited text files include FPKM values for each sample and the gene/transcript annotations

value: 0 hr


title: H3K27me3 ChIP-Seq (Nitrogen starvation 1 hr)

description:
H3K27m3ND1hrIPR1
processed data file:
emissions_16.txt.gz
transitions_16.txt.gz
processed data file: Cre4A+Nitrogen_starvation_1hr_16states_genome_segmentation.bed.gz

value: H3K27me3 (Abcam ab6002)


title: H3K4me3 Input (0 hr before starvationr; baseline)

data_processing:
Raw reads were mapped to C. reinhardtii genome (v5.3.1) by BWA v0.6.2 with default parameters
Enriched regions in the non-redundant mapped reads were identified by MACS2 v2.0.10 (effective genome size=107270392, FDR< 5%)
Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced.
Genome_build: Chlamydomonas reinhardtii genome (Phytozome v5.3.1); C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz
Supplementary_files_format_and_content: peaks list, tab-delimited text files include FPKM values for each sample and the gene/transcript annotations


title: H3K27ac ChIP-Seq replicate 1 (Nitrogen starvation 1 hr)

description:
H3K27acND1hrIPR1
processed data file:
emissions_16.txt.gz
transitions_16.txt.gz
processed data file: Cre4A+Nitrogen_starvation_1hr_16states_genome_segmentation.bed.gz

source_name: H3K27ac ChIP-Seq (Nitrogen starvation 1 hr)

value: H3K27ac (Abcam ab4729)


title: H3K27ac ChIP-Seq replicate 2 (Nitrogen starvation 1 hr)

description:
H3K27acND1hrIPR2
processed data file:
emissions_16.txt.gz
transitions_16.txt.gz
processed data file: Cre4A+Nitrogen_starvation_1hr_16states_genome_segmentation.bed.gz


title: PSR1 ChIP-Seq (Peptide A, Nitrogen starvation 30 min)

value: polyclonal antibodies against PSR1 peptide sequences aa54-69 (peptide A:C-QQQGLALGGYGLTQQP)


title: H3K9me3 Input (Sulfur starvation 1 hr)

description:
H3K9m3SD1hrInputR1
Please note that the raw data associated with this sample was also used as 'H3K36me3 Input replicate 1 (Sulfur starvation 1 hr)'

source_name: H3K9me3 Input (Sulfur starvation 1 hr)


title: H3K27me3 Input (Nitrogen starvation 1 hr)


title: H3K9me3 Input (Nitrogen starvation 1 hr)

description:
H3K9m3ND1hrInputR1
Please note that the raw data associated with this sample was also used as 'H3K36me3 Input (0 hr before starvationr; baseline)'


title: H3K9me3 ChIP-Seq (Nitrogen starvation 1 hr)

description:
H3K9m3ND1hrIPR1
processed data file:
emissions_16.txt.gz
transitions_16.txt.gz
processed data file: Cre4A+Nitrogen_starvation_1hr_16states_genome_segmentation.bed.gz

value: H3K9me3 (Abcam ab8898)


title: RNA Pol2 ChIP-Seq (Sulfur starvation 1 hr)

description:
RNAPol2SD1hrIPR1
processed data file:
emissions_16.txt.gz
transitions_16.txt.gz
processed data file: Cre4A+Sulfur_starvation_1hr_16states_genome_segmentation.bed.gz


title: H3K36me3 ChIP-Seq replicate 2 (Sulfur starvation 1 hr)

description:
H3K36m3SD1hrIPR2
processed data file:
emissions_16.txt.gz
transitions_16.txt.gz
processed data file: Cre4A+Sulfur_starvation_1hr_16states_genome_segmentation.bed.gz

source_name: H3K36me3 ChIP-Seq (Sulfur starvation 1 hr)


title: H3K4me3 ChIP-Seq (0 hr before starvationr; baseline)

value: H3K4me2 (Abcam ab11946)


title: RNA Pol2 Input (0 hr before starvationr; baseline)


title: H3K27me3 Input (0 hr before starvationr; baseline)


title: H3K27ac Input replicate 1 (0 hr before starvationr; baseline)

source_name: H3K27ac Input (0 hr before starvationr; baseline)


title: H3K27me3 ChIP-Seq (0 hr before starvationr; baseline)

description:
H3K27m3ND0hrIPR1
processed data file:
emissions_16.txt.gz
transitions_16.txt.gz
Cre4A+Baseline_16states_genome_segmentation.bed.gz


title: H3K9me3 Input (0 hr before starvationr; baseline)


title: H3K27ac ChIP-Seq replicate 2 (0 hr before starvationr; baseline)

description:
H3K27acND0hrIPR2
processed data file:
emissions_16.txt.gz
transitions_16.txt.gz
Cre4A+Baseline_16states_genome_segmentation.bed.gz

source_name: H3K27ac ChIP-Seq (0 hr before starvationr; baseline)


title: H3K36me3 ChIP-Seq (0 hr before starvationr; baseline)

description:
H3K36m3ND0hrIPR1
processed data file:
emissions_16.txt.gz
transitions_16.txt.gz
Cre4A+Baseline_16states_genome_segmentation.bed.gz


title: H3K9me3 ChIP-Seq (0 hr before starvationr; baseline)

description:
H3K9m3ND0hrIPR1
processed data file:
emissions_16.txt.gz
transitions_16.txt.gz
Cre4A+Baseline_16states_genome_segmentation.bed.gz


title: H3K4me3 Input (Nitrogen starvation 48 hr)

value: 48 hr


title: H3K4me3 Input (Nitrogen starvation 24 hr)

value: 24 hr


title: H3K4me3 ChIP-Seq (Nitrogen starvation 48 hr)

value: H3K4me3 (Abcam ab8580)


title: H3K4me3 Input (Nitrogen starvation 6 hr)

value: 6 hr


title: H3K4me3 ChIP-Seq (Nitrogen starvation 8 hr)

value: 8 hr


title: H3K4me3 Input (Nitrogen starvation 2 hr)

value: 2 hr


title: H3K4me3 Input replicate 2 (Nitrogen starvation 1 hr)

description:
H3K4m3ND1hrInputR2
Please note that the raw data associated with this sample was also used as 'H3K27ac Input replicate 2 (Nitrogen starvation 1 hr)'

source_name: H3K4me3 Input (Nitrogen starvation 1 hr)


title: H3K4me3 ChIP-Seq (Nitrogen starvation 2 hr)


title: Rgcc_Skms_CpG_WT

city: Oakland

first: David

middle: B

last: West

address: 5700 Martin Luther King Jr way

institute: CHORI

data_processing:
Bowtie2  and Bismark were used for base calling and alignment
Sequenced reads were trimmed for adaptor sequence, reference chromosomes were converted to bisulfite treated and indexed using Bismark,  then reads were mapped to specific chromosomes of mm9 genome assembly using bismark and bowtie2 with default parameters
Methylation calling with Bismark methylation extractor using merge non-CpG option
Genome_build: MM9
Supplementary_files_format_and_content: text files contain counts of methylated and unmethylated C's at each CpG site
Supplementary_files_format_and_content: column headers: Seq-ID, start position, end position, methylation %, methylated calls, non-methylated calls

organism: Mus musculus

source_name: Muscle

extract_protocol:
Tissues were removed, flash frozen in LN2, and DNA was isolated using Tri-reagent.
Illumina TruSeq RNA Sample Prep Kit (Illumina RS-122-2001/2) was used to construct sequencing libraries from double stranded amplicons of Bisulfite treated DNA. Illumina protocol

treatment_protocol: Genomic DNA was treated with bisulfite using the MethylEasy Xceed kit (Human Genetic Signature, Australia) according to the manufacture’s protocol.

tag: strain background

tag: age

value: 7 weeks

tag: genotype/variation

value: Wild Type

tag: tissue

value: Muscle

tag: accession # for mapping


title: H3K4me3 ChIP-Seq (Nitrogen starvation 6 hr)


title: H3K4me3 Input replicate 1 (Nitrogen starvation 1 hr)

description:
H3K4m3ND1hrInputR1
Please note that the raw data associated with this sample was also used as 'H3K27ac Input  replicate 1'

value: 1 hr


title: H3K4me3 ChIP-Seq replicate 2 (Nitrogen starvation 1 hr)

description:
H3K4m3ND1hrIPR2
processed data file:
emissions_16.txt.gz
transitions_16.txt.gz
processed data file: Cre4A+Nitrogen_starvation_1hr_16states_genome_segmentation.bed.gz

source_name: H3K4me3 ChIP-Seq (Nitrogen starvation 1 hr)


title: Corpus_epithelium_rep1

status: Public on Jul 29 2015

city: Callaghan

first: Bettina

middle: P

last: Mihalas

state: NSW

address: Level 4 Life Science Building, University Drive

department: Life Sciences

country: Australia

institute: University of Newcastle

description:
8_GTGGCC
processed_data_file: Epithelial_counts.txt

library_source: transcriptomic

data_processing:
Basecalls were dones using CASAVA pipeline version 1.8.2.
Reads were screened and trimmed based on matches to Illumina smallRNA adaptors, PhiX, ChrM and rRNAs using flicker script with Illumina smallRNA kit with default settings
Cleaned reads were aligned using the bowtie ver 1.1.1 against human genome and miRNA database version 21
miRNA gene counts were summarised with custom shell scripts
Differential expression analysis was performed using the R-bioconductor libraies: limma and voom
Genome_build: miRNA database version 21
Supplementary_files_format_and_content: miRNA gene counts

molecule: total RNA

source_name: Epididymal epithelial cells

extract_protocol:
Total RNA was extracted from purified epididymal epithelial cells and total epididymis  (caput, corpus and cauda) using a Direct-zol™ RNA MiniPrep Kit (Zymo Research Corporation, Irvine, CA, USA) according to manufacturer’s instructions before being incubated with 1% DNase (Promega) to eliminate genomic DNA contamination.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Swiss

value: 8 weeks

tag: Sex

value: Male

tag: cell type

value: Epididymal epithelial cells

value: Epididymis

tag: tissue compartment

value: Corpus


title: H3K27ac ChIP-Seq replicate 1 (0 hr before starvationr; baseline)

description:
H3K27acND0hrIPR1
processed data file:
emissions_16.txt.gz
transitions_16.txt.gz
Cre4A+Baseline_16states_genome_segmentation.bed.gz

value: 0 hr

value: H3K27ac (Abcam ab4729)


title: Rgcc_Lng_CpG_WT

source_name: Lung

value: Lung


title: Rab32_Spl_CpG_WT

source_name: Spleen

value: Spleen


title: Rgcc_Hrt_CpG_WT

source_name: Heart

value: Heart


title: H3K4me3 ChIP-Seq (Nitrogen starvation 24 hr)

value: 24 hr

value: H3K4me3 (Abcam ab8580)


title: Ninj_Spl_CpG_WT

value: 7 weeks


title: RNA Pol2 ChIP-Seq (0 hr before starvationr; baseline)

description:
RNAPol2ND0hrIPR1
processed data file:
emissions_16.txt.gz
transitions_16.txt.gz
Cre4A+Baseline_16states_genome_segmentation.bed.gz

value: RNAPII (clone 8WG16, Covance MMS-126R)


title: H3K4me3 Input (Nitrogen starvation 8 hr)

value: 8 hr


title: Ninj_Lng_CpG_WT

value: Wild Type


title: H3K4me3 ChIP-Seq (Nitrogen starvation 30 min)

value: 30 min


title: Ninj1_Liv_CpG_WT

source_name: Liver

value: Liver


title: Rab32_Liv_CpG_WT


title: H3K4me3 ChIP-Seq replicate 1 (Nitrogen starvation 1 hr)

description:
H3K4m3ND1hrIPR1
processed data file:
emissions_16.txt.gz
transitions_16.txt.gz
processed data file: Cre4A+Nitrogen_starvation_1hr_16states_genome_segmentation.bed.gz

value: 1 hr


title: H3K4me3 Input (Nitrogen starvation 30 min)


title: H3K4me3 Input (Nitrogen starvation 10 min)

value: 10 min


title: Ninj_Brn_CpG_WT

source_name: Brain

value: Brain


title: Lyplal_Kid_CpG_WT

source_name: Kidney

value: Kidney


title: Dstn_Spl_CpG_WT


title: H3K4me3 Input replicate 2 (0 hr before starvationr; baseline)

description:
H3K4m3ND0hrInputR2
Please note that the raw data associated with this sample was also used as 'H3K27ac Input replicate 2 (0 hr before starvationr; baseline)'

source_name: H3K4me3 Input (0 hr before starvationr; baseline)

value: 0 hr


title: Dstn_Liv_CpG_WT


title: Dstn_Kid_CpG_WT


title: Ninj_Skms_CpG_WT

value: Muscle


title: Dstn_Lng_CpG_WT

value: Lung


title: Dstn_Hrt_CpG_WT


title: H3K4me3 ChIP-Seq replicate 2 (0 hr before starvationr; baseline)

description:
H3K4m3ND0hrIPR2
processed data file:
emissions_16.txt.gz
transitions_16.txt.gz
Cre4A+Baseline_16states_genome_segmentation.bed.gz

source_name: H3K4me3 ChIP-Seq (0 hr before starvationr; baseline)


title: Lyplal_Liv_CpG_WT


title: H3K4me3 ChIP-Seq replicate 1 (0 hr before starvationr; baseline)

description:
H3K4m3ND0hrIPR1
processed data file:
emissions_16.txt.gz
transitions_16.txt.gz
Cre4A+Baseline_16states_genome_segmentation.bed.gz


title: H3K4me3 Input replicate 1 (0 hr before starvationr; baseline)


title: Ninj_Kid_CpG_WT


title: Rgcc_Skms_CpG_KO

value: Rgcc -/-


title: Rgcc_Lng_CpG_KO


title: Rgcc_Hrt_CpG_KO

value: Heart


title: Rgcc_Hrt_LacZ_KO

value: LacZ reference


title: Rgcc_LacZ_Skms_KO


title: Rab32_Spl_LacZ_KO

value: Spleen


title: Dstn_Brn_CpG_WT

value: 7 weeks


title: Rab32_Spl_CpG_KO


title: Rab32_Liv_CpG_KO


title: Rgcc_Lng_LacZ_KO


title: Ninj1_Skms_Lacz_KO

value: Ninj1 -/-


title: Rab32_Liv_LacZ_KO


title: Ninj1_Brn_LacZ_KO


title: Ninj_Spl_CpG_KO

value: Ninj -/-


title: Ninj_Lng_CpG_KO


title: Ninj_Skms_CpG_KO


title: H3K4me3 ChIP-Seq (Nitrogen starvation 10 min)

value: H3K4me3 (Abcam ab8580)


title: Ninj_Liv_CpG_KO


title: Ninj_Kid_CpG_KO


title: Ninj1_SpL_LacZ_KO


title: Lyplal_Kid_LacZ_KO

value: Lyplal -/-


title: Ninj1_Kid_LacZ_KO


title: Lyplal_Liv_LacZ_KO

value: Liver


title: Dstn_Spl_LacZ_KO

value: Dstn -/-


title: Lyplal1_Kid_CpG_KO

value: Lyplal1 -/-


title: Lyplal1_Liv_CpG_KO


title: Dstn_Spl_CpG_KO


title: PolyA Transcripts replicate 2 (Sulfur starvation 48 hr)

description:
polyASD48hrR2
processed data file: master_gene_model.gtf.gz
processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz

data_processing:
Sequenced reads were trimmed for adaptor sequence and other artifacts. Trimmed reads with average quality ≥20, ≤3 Ns, and ≥32 bases were mapped to C. reinhardtii genome (Phytozome v5.3.1) using TopHat v2.0.8 with Bowtie v2.1.0. Sensitive and fusion mapping was enabled. Valid intron length was 20bp to 25 kbp and minimum distance between intra-chromosomal fusions was 1 Mbp. The library type “fr-firststrand” stated and read alignments with >3 mismatches were discarded.
Cufflinks v2.1.1 (modified to work on compact genomes) was used to reconstruct the transcripts guided with the Phytozome v5.3.1 reference transcriptome (See supplementary file: reference_gene_model.gtf.gz). Multi-mapped read correction was turned on and transcript composed of >50% multi-mapped reads or <25 reads were discarded. The remaining transcript assemblies from different time points were merged into a unified set of gene models, which was then compared to the annotated transcriptome. Potential noise was filtered from these predicted transcripts. Sequential steps of filtering criteria were applied as follows; 1). FPKM >0 for both replicates at least at one time point; 2) length of CDS>=50 amino acid; candidate coding regions were predicted based on transcript sequences using TransDecoder script v2013-02-25 from the Trinity package, 3) Remove “noise” transcripts of CuffDiff classes ‘E’, ‘O’ and ‘P’ and single exon transcripts of CuffDiff classes ‘.’, ‘C’ and ‘I’.
Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced.
Genome_build: Chlamydomonas reinhardtii genome (Phytozome v5.3.1); C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz
Supplementary_files_format_and_content: peaks list, tab-delimited text files include FPKM values for each sample and the gene/transcript annotations

molecule: polyA RNA

source_name: PolyA Transcripts (Sulfur starvation 48 hr)

extract_protocol:
Cells were first lysed and total RNA extracted using Trizol and cleaned up using RNeasy column (Qiagen). PolyA+ RNA was isolated from 5ug of total RNA.
RNA was fragmented using RNA Fragmentation Reagents (Ambion).  Strand-specific RNA-seq library (Parkhomchuk et al., 2009) was constructed using Kapa Library Amplification Kit (Kapa Biosystems) with 10 cycles PCR amplification (Parkhomchuk et al.(2009). Nucleic acids research 37, e123).

value: 48 hr


title: PolyA Transcripts replicate 2 (Sulfur starvation 24 hr)

description:
polyASD24hrR2
processed data file: master_gene_model.gtf.gz
processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz

source_name: PolyA Transcripts (Sulfur starvation 24 hr)

value: 24 hr


title: Dstn_Lng_CpG_KO


title: Ninj_Liv_LacZ_KO


title: Dstn_Liv_CpG_KO


title: PolyA Transcripts replicate 1 (Sulfur starvation 48 hr)

description:
polyASD48hrR1
processed data file: master_gene_model.gtf.gz
processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz


title: Dstn_KiD_LacZ_KO

value: Kidney


title: Ninj_Lng_LacZ_KO


title: PolyA Transcripts replicate 1 (Sulfur starvation 24 hr)

description:
polyASD24hrR1
processed data file: master_gene_model.gtf.gz
processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz


title: PolyA Transcripts replicate 2 (Sulfur starvation 8 hr)

description:
polyASD8hrR2
processed data file: master_gene_model.gtf.gz
processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz

source_name: PolyA Transcripts (Sulfur starvation 8 hr)

value: 8 hr


title: Dstn_Liv_LacZ_KO


title: Dstn_Hrt_CpG_KO


title: Dstn_Kid_CpG_KO


title: Ninj_Brn_CpG_KO

value: Brain


title: PolyA Transcripts replicate 2 (Sulfur starvation 6 hr)

description:
polyASD6hrR2
processed data file: master_gene_model.gtf.gz
processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz

source_name: PolyA Transcripts (Sulfur starvation 6 hr)

value: 6 hr


title: PolyA Transcripts replicate 1 (Sulfur starvation 8 hr)

description:
polyASD8hrR1
processed data file: master_gene_model.gtf.gz
processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz


title: Dstn_Brn_LacZ_KO


title: Dstn_Hrt_LacZ_KO

value: Heart


title: PolyA Transcripts replicate 1 (Sulfur starvation 1 hr)

description:
polyASD1hrR1
processed data file: master_gene_model.gtf.gz
processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz

source_name: PolyA Transcripts (Sulfur starvation 1 hr)

value: 1 hr


title: PolyA Transcripts replicate 1 (Sulfur starvation 6 hr)

description:
polyASD6hrR1
processed data file: master_gene_model.gtf.gz
processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz


title: M_Hnf6_ChIPSeq_G73_M3

city: Boston

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

description: Chromatin IP using Hnf6 antibody

data_processing:
Map each read to mm9 genome using Bowtie 0.12.7
Combine reads from different samples by sex (Female HNF6 samples 1-4, male HNF6 samples 5-8) also combine all controls (samples 9-12)
Filter the samplesto remove all reads having >5 exact duplicates that do not overlap with any other read ("straight peaks")
Perform peak discovery using MACS 2.0, default parameters (narrow peaks discovery)
MACS 2.0 peak discovery using reads from combined male and female samples with combined control
Filter: All peaks from male and female livers must satisfy MACS 2.0 -log10(qvalue) > 25
MA norm analysis (PMID:22424423) was used to normalize reads in peaks for merged set of female and male peaks (differential peak analysis)
Genome_build: mm9

source_name: liver tissue

growth_protocol: Male and female CD-1 mice (Charles River Laboratories), 7-8 weeks old, were euthanized and their livers extracted.

extract_protocol:
Liver tissue was homogenized. Nuclei then isolated, cross-linked with formaldehyde and sonicated.
Multiplexed samples were prepared for Illumina sequencing at the MIT BioMicroCenter using standard library preparation methods.

value: ICR (CD-1)

value: male

value: liver

value: 7-8 weeks old

tag: antibody manufacturer

value: Santa Cruz Biotechnology, Inc

tag: antibody catalog number


title: PolyA Transcripts replicate 2 (Sulfur starvation 2 hr)

description:
polyASD2hrR2
processed data file: master_gene_model.gtf.gz
processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz

source_name: PolyA Transcripts (Sulfur starvation 2 hr)

value: 2 hr


title: M_Hnf6_ChIPSeq_G73_M4

description: Chromatin IP using Hnf6 antibody


title: PolyA Transcripts replicate 1 (Sulfur starvation 2 hr)

description:
polyASD2hrR1
processed data file: master_gene_model.gtf.gz
processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz


title: M_Hnf6_ChIPSeq_G76_M13

description: Chromatin IP using Hnf6 antibody


title: PolyA Transcripts replicate 2 (Sulfur starvation 10 min)

description:
polyASD10minR2
processed data file: master_gene_model.gtf.gz
processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz

source_name: PolyA Transcripts (Sulfur starvation 10 min)

value: 10 min


title: PolyA Transcripts replicate 1 (Sulfur starvation 30 min)

description:
polyASD30minR1
processed data file: master_gene_model.gtf.gz
processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz

source_name: PolyA Transcripts (Sulfur starvation 30 min)

value: 30 min


title: M_Hnf6_ChIPSeq_G76_M12

description: Chromatin IP using Hnf6 antibody


title: PolyA Transcripts replicate 1 (Sulfur starvation 10 min)

description:
polyASD10minR1
processed data file: master_gene_model.gtf.gz
processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz


title: PolyA Transcripts replicate 2 (Sulfur starvation 1 hr)

description:
polyASD1hrR2
processed data file: master_gene_model.gtf.gz
processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz


title: PolyA Transcripts replicate 2 (Sulfur starvation 30 min)

description:
polyASD30minR2
processed data file: master_gene_model.gtf.gz
processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz


title: F_Hnf6_ChIPSeq_G76_M10

description: Chromatin IP using Hnf6 antibody

value: female


title: PolyA Transcripts replicate 2 (Sulfur starvation 0 hr; baseline)

description:
polyASD0hrR2
processed data file: master_gene_model.gtf.gz
processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz

source_name: PolyA Transcripts (Sulfur starvation 0 hr; baseline)

value: 0 hr


title: F_Hnf6_ChIPSeq_G76_M11

description: Chromatin IP using Hnf6 antibody


title: F_Hnf6_ChIPSeq_G73_M2

description: Chromatin IP using Hnf6 antibody


title: PolyA Transcripts replicate 1 (Sulfur starvation 0 hr; baseline)

description:
polyASD0hrR1
processed data file: master_gene_model.gtf.gz
processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz


title: GHMT2mA83-01

city: Aurora,

first: Kunhua

last: Song

state: CO

institute: University of Colorado

description: Fibroblasts expressing GHMT2m and treated with A83-01 for 6 days a

data_processing:
Illumina Real-Time Analysis (RTA) version 1.18.64.0 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using Partek Flow software (2014 Partek Inc.)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated by using  Partek Flow software  (2014 Partek Inc.)
Genome_build: mm9

source_name: fibroblasts

growth_protocol: MEFs were plated and cultured in growth medium (DMEM/Hi glucose (Hyclone),10% FBS (Gemini), 1.1% Penicillin-Streptomycin (Gibco) and 1.1% GlutaMAX supplement (Gibco)) at 370C with 5% CO2 at day 0. Fibroblasts were transduced with retroviruses at day 1 and day2. At day 3, viral media were be replaced with induction medium composed of DMEM/199 (4:1) (Gibco),  10% FBS (Gemini) , 5% horse serum(Gemini), antibiotics (Gibco), 1 × non-essential amino acids (Gibco), 1 × essential amino acids (Gibco), 1 × B-27(Gibco), 1 × insulin-selenium-transferin (Gibco), 1 × vitamin mixture (Gibco), and 1 × sodium pyruvate (Gibco).

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA Sample Prep Kit (Cat# RS-122-2101) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA Libraries were constructed using Illumina TruSEQ mRNA Sample Prep Kit (Cat# RS-122-2101). Total RNA is combined with RNA purficiation beads to bind PolyA RNA to oligodT magnetic beads.  mRNA is eluted and converted to double stranded DNA.  A Tailing, adapter ligation, and PCR amplification using 15 cycles is done to complete the library construction.  Libraries are quantitated via Qubit, analzyed on a Bioanalyzer Tape and diluted to appropriate concentration to run on HiSEQ 2500 High Throughput Flow Cell.

treatment_protocol: After retroviral infection, cells were treated with 0.5 uM A83-01 in induction medium if it was applied.

value: embryos


title: GHMT2m

description: Fibroblasts expressing GHMT2m for 6 days


title: F_Hnf6_ChIPSeq_G73_M1

description: Chromatin IP using Hnf6 antibody


title: PolyA Transcripts replicate 2 (Nitrogen starvation 48 hr)

description:
polyAND48hrR2
processed data file: master_gene_model.gtf.gz
processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz

source_name: PolyA Transcripts (Nitrogen starvation 48 hr)

extract_protocol:
Cells were first lysed and total RNA extracted using Trizol and cleaned up using RNeasy column (Qiagen). PolyA+ RNA was isolated from 10ug of total RNA.
RNA was fragmented using RNA Fragmentation Reagents (Ambion). Strand-specific RNA-seq library (Parkhomchuk et al., 2009) was constructed using Illumina DNA Sample Preparation Kit (Illumina) with 10 cycles PCR amplification (Parkhomchuk et al.(2009). Nucleic acids research 37, e123).

value: 48 hr


title: NMCM

description: cardiomyocytes isolated from P1 hearts

source_name: cardiomyocytes

value: hearts


title: Dstn_Brn_CpG_KO

source_name: Brain

value: 7 weeks

value: Dstn -/-

value: Brain


title: Dstn_Lng_LacZ_KO

source_name: Lung

value: Lung

value: LacZ reference


title: PolyA Transcripts replicate 1 (Nitrogen starvation 6 hr)

description:
polyAND6hrR1
processed data file: master_gene_model.gtf.gz
processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz

source_name: PolyA Transcripts (Nitrogen starvation 6 hr)

value: 6 hr


title: PolyA Transcripts replicate 2 (Nitrogen starvation 24 hr)

description:
polyAND24hrR2
processed data file: master_gene_model.gtf.gz
processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz

source_name: PolyA Transcripts (Nitrogen starvation 24 hr)

value: 24 hr


title: PolyA Transcripts replicate 1 (Nitrogen starvation 48 hr)

description:
polyAND48hrR1
processed data file: master_gene_model.gtf.gz
processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz


title: PolyA Transcripts replicate 2 (Nitrogen starvation 8 hr)

description:
polyAND8hrR2
processed data file: master_gene_model.gtf.gz
processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz

source_name: PolyA Transcripts (Nitrogen starvation 8 hr)

value: 8 hr


title: TMX-Bcl11bF/F Cre-ERT2

city: albany

first: dorina

last: avram

address: 47 new scotland ave

department: center for immunology and microbial disease

institute: albany medical college

data_processing:
Sequenced reads were cleaned according to a rigorous pre-processing workflow (Trimmomatic-0.32) before mapping them to the mouse genome (mm10) with SHRiMP2.2.3
Used cufflinks2.0.2 (cuffdiff2 - Running Cuffdiff) to perform differential expression analysis with an FDR cutoff of 0.05 (95% confidence interval).
Genome_build: mm10
Supplementary_files_format_and_content: differential expression

source_name: TMX-Bcl11bF/F Cre-ERT2

extract_protocol:
mLNs were removed at Day 9 following tamoxifen treatment by oral gavage. ILC2s (Lin-CD90+Klrg1+) were purified using a FACsAria II cell sorter.  RNA was harvested using Rneasy mini Kit (cat # 74104) from Qiagen.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mesenteric lymph nodes

value: Type 2 Innate lymphoid cell


title: GHMT

description: Fibroblasts expressing GHMT for 6 days


title: PolyA Transcripts replicate 1 (Nitrogen starvation 8 hr)

description:
polyAND8hrR1
processed data file: master_gene_model.gtf.gz
processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz


title: PolyA Transcripts replicate 2 (Nitrogen starvation 6 hr)

description:
polyAND6hrR2
processed data file: master_gene_model.gtf.gz
processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz


title: PolyA Transcripts replicate 2 (Nitrogen starvation 2 hr)

description:
polyAND2hrR2
processed data file: master_gene_model.gtf.gz
processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz

source_name: PolyA Transcripts (Nitrogen starvation 2 hr)

value: 2 hr


title: TMX-Wild type control

source_name: TMX-Wild type control

value: Wild type


title: PolyA Transcripts replicate 1 (Nitrogen starvation 2 hr)

description:
polyAND2hrR1
processed data file: master_gene_model.gtf.gz
processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz


title: PolyA Transcripts replicate 1 (Nitrogen starvation 24 hr)

description:
polyAND24hrR1
processed data file: master_gene_model.gtf.gz
processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz


title: PolyA Transcripts replicate 1 (Nitrogen starvation 1 hr)

description:
polyAND1hrR1
processed data file: master_gene_model.gtf.gz
processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz

source_name: PolyA Transcripts (Nitrogen starvation 1 hr)

value: 1 hr


title: PolyA Transcripts replicate 1 (Nitrogen starvation 30 min)

description:
polyAND30minR1
processed data file: master_gene_model.gtf.gz
processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz

source_name: PolyA Transcripts (Nitrogen starvation 30 min)

value: 30 min


title: PolyA Transcripts replicate 2 (Nitrogen starvation 1 hr)

description:
polyAND1hrR2
processed data file: master_gene_model.gtf.gz
processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz


title: PolyA Transcripts replicate 2 (Nitrogen starvation 10 min)

description:
polyAND10minR2
processed data file: master_gene_model.gtf.gz
processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz

source_name: PolyA Transcripts (Nitrogen starvation 10 min)

value: 10 min


title: MEFs

description: MEFs cultured for 2 days

value: embryos


title: PolyA Transcripts replicate 1 (Nitrogen starvation 0 hr; baseline)

description:
polyAND0hrR1
processed data file: master_gene_model.gtf.gz
processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz

source_name: PolyA Transcripts (Nitrogen starvation 0 hr; baseline)

value: 0 hr


title: PolyA Transcripts replicate 2 (Nitrogen starvation 30 min)

description:
polyAND30minR2
processed data file: master_gene_model.gtf.gz
processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz


title: PolyA Transcripts replicate 2 (Nitrogen starvation 0 hr; baseline)

description:
polyAND0hrR2
processed data file: master_gene_model.gtf.gz
processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz


title: PolyA Transcripts replicate 1 (Nitrogen starvation 10 min)

description:
polyAND10minR1
processed data file: master_gene_model.gtf.gz
processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz


title: TH1_Rep2

status: Public on Jul 27 2015

city: La Jolla

first: Shane

last: Crotty

state: CA

address: 9420 Athena Circle

institute: La Jolla Institute for Allergy and Immunology

data_processing:
The single-end reads were premapped and filtered for reads aligning to tRNA, rRNA, adapter sequences, and spike-in controls.
Mouse RNA-Seq data was mapped against mm9 reference genome using tophat (v1.4.1., --library-type fr-secondstrand -C) and the RefSeq gene annotation downloaded from the UCSC genome bioinformatics site.
The alignment results (sam files) were converted into bam files and sorted by using samtools.
DUST scores were calculated with PRINSEQ Lite (v 0.20.3) and low-complexity reads (DUST > 4) were removed from the BAM files.
Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -t exon -i gene_id).
Negative binomial tests were performed for pairwise comparisons of TH1 and TFH cells employing the Bioconductor package DESeq2 and allowing for a false discovery rate of 0.05.
Genome_build: mm9
Supplementary_files_format_and_content: text file with raw counts of sequencing reads per gene generated by HTSeq-count; text file with  P-values for differential expression genes were calcuated by DESeq2 package on the basis of normalized abandunce measurement.

source_name: Early Th1 cells

extract_protocol:
Early Tfh and Th1 cells were sorted from the spleens and total RNA was extracted using standard Qiagen RNeasy columns
RNA libraries were prepared for sequencing using standard Solid NGS protocols

tag: genotype

value: wild type

value: spleen

tag: cell phenotype

value: Blimp1-YFP+ IL2Ra+ Smarta cells


title: TFH_Rep1

source_name: Early Tfh cells

value: Blimp1-YFP- IL2Ra- Smarta cells


title: DlaeA-60h

city: Jinan

first: Yanan

last: Li

address: Shanda south road 27

country: China

institute: Shandong University

data_processing:
3' adaptor sequences were first removed from the sequencing reads to produce 21-nt long tags. Then low quality tags, one copy tags and tags which are not 21-nt long were removed to generate clean tags. Reference 21-nt tag databases were created from predicted P. decumbens transcripts plus downstream 300-nt sequences of two strains. All clean tags were mapped to corresponding reference tag databases and no mismatch was allowed. The copy number of unambiguous tags (tags mapped to one single gene) for each gene was normalized to TPM (number of transcripts per million clean tags) for differential expression analysis.
Genome_build: Whole Genome Shotgun project in GenBank under the accession number AGIH00000000
Supplementary_files_format_and_content: .txt files with the following columns: SEQUENCE (sequence of clean tags), COPYNUMBER (copynumber of clean tags), TPM (normalized COPYNUMBER; number of tags per million clean tags).

organism: Penicillium oxalicum

source_name: Fungal mycelia

growth_protocol: The conidia of Penicillium oxalicum were inoculated in modifeid Mendal's culture medium with 2% glucose as carbon resource for 24 h at 30 °C as the pre-culture, and then mycelia were transferred and grown in the modified Mendal’s agar medium with 1% microcrystalline cellulose and 1% wheat bran as carbon resource for 24h or 60h. Total RNA was extracted for DGE analysis.

extract_protocol:
Total RNA was extracted, and oligo (dT) beads were used to purify mRNA and guide double-stranded cDNA synthesis. The enzyme NlaIII was used to cut the cDNA at CATG sites. After Illumina adapter 1 was linked to the CATG site, MmeI was used to cut at 17-bp downstream of the CATG site. Then Illumina adapter 2 was linked at 3' end and the fragments were PCR amplified. Finally, the 85-bp strips were gel purified and digested for Solexa sequencing. Each tunnel generated millions of raw reads with sequencing length of 35bp.
3' adaptor sequences were first removed from the sequencing reads to produce 21-nt long tags. Then low quality tags, one copy tags and tags which are not 21-nt long were removed to generate clean tags. Reference 21-nt tag databases were created from predicted P. decumbens transcripts plus downstream 300-nt sequences of two strains. All clean tags were mapped to corresponding reference tag databases and no mismatch was allowed. The copy number of unambiguous tags (tags mapped to one single gene) for each gene was normalized to TPM (number of transcripts per million clean tags) for differential expression analysis.

value: laeA deletion strain

tag: medium

value: Modified Mendal's agar medium with 1% microcrystalline cellulose and 1% wheat bran as carbon source

tag: culture time

value: 60h after transferring washed mycelia to the new medium


title: 114-60h

tag: strain

value: 114-2 (wild type)


title: DlaeA-24h

value: 24h after transferring washed mycelia to the new medium


title: 114-24h


title: TFH_Rep2


title: H3K27ac Input (Sulfur starvation 1 hr)

source_name: H3K27ac Input (Sulfur starvation 1 hr)

tag: time


title: CTL-IP (IgG)

city: RTP

first: Trevor

last: Archer

address: 111 TW Alexander

institute: NIH

description: immortalized tumor cell line

data_processing:
Aligned with Bowtie version 0.12.8 with the following parameters: -m 1
Read counts obtained using htseq-count from the HTSeq framework version 0.6.0
Genome_build: hg19
Supplementary_files_format_and_content: read_counts: 1st column = gene symbol, 2nd column = read count

organism: Homo sapiens

source_name: MCF-7M cells

extract_protocol:
LIN28 interacting mRNAs were prepared from mRNA–protein complexes by standard phenol chloroform methods.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MCF-7M cells were seeded on 15 cm plates in MEM with 5% charcoal stripped serum. Next day, cells were rinsed with PBS and LIN28 protein- mRNA complexes prepared as decribed in the methods.

tag: parental cell line

tag: cell line

value: breast

tag: antibody

value: IgG


title: Satb1_siRNA_Control_3

city: New York

first: William

last: Shin

state: NY

address: 1130 St Nicholas Ave

department: Systems Biology

institute: Columbia University

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were mapped to the Mus musculus assembly 10 reference genome (mm10) using TopHat version 2.0.8
Reads mapping to known genes, based on Entrez gene identifiers, were then counted using the GenomicFeatures  R-system package (Bioconductor) version 1.10.2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes Raw Counts for each gene in each sample.

source_name: Dopaminergic Neurons from Midbrain

growth_protocol: 3 four-month-old Dat bacTRAP mice were used for the experiments.

extract_protocol:
Brains were removed and sectioned using an ice-cold Adult Mouse Brain Slicer with 1 mm coronal slice intervals (Zivic Instruments). From the tissue section containing the midbrain, the SNpc and VTA regions were dissected and separated under a Nikon SMZ645 light microscope using a 10x lens
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RNA-SEQ profiling of mouse dopaminergic neurons from the mouse mid-brain, with AAV1 injections using a Satb1 shRNA-EGFP construct or a scrambed shRNA-EGFP construct

tag: strain background

value: Dopaminergic Neurons


title: Satb1_siRNA_KnockDown_3


title: Satb1_siRNA_Control_2


title: Satb1_siRNA_KnockDown_2


title: Satb1_siRNA_Control_1


title: E168D2_P21_C

city: St. Louis

first: Philip

last: Ruzycki

state: MO

department: Ophthalmology and Visual Sciences

institute: Washington University in St. Louis

data_processing:
Reads mapped to NCBI37/mm9 using Tophat (Version 2.0.5) with automatic parameters
Reads assigned to UCSC annotated genes using Htseq (Version 0.6.1p1)
Expression of mutants was compared to age matched WT control using EdgeR (Version 3.6.8). Genes that passed the filter criteria of CPM >5 in all replicates in one comparison groups were included in the comparison
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: Data file includes HTSeq determined CPM values for each gene in all genotypes.  Also includes EdgeR calculated FC and FDR values for each gene.

source_name: Whole Retina

extract_protocol:
Four retinas (2Male, 2Female) were collected and pooled to represent each biological replicate. Retinas were processed for RNA using the PerfectPure RNA tissue kit (5Prime).  Quality was assessed using the Agilent Bioanalyzer, and samples with minimum 8.0 RIN score submitted for library preparation.
mRNA was extracted using the DynaI mRNA Direct Kit (Life Technologies), mRNA was then fragmented and reverse transcribed to double stranded cDNA using andom primers before the additon of Illumina adaptors.  rRNA was depleted using Ribo-Zero (Epicentre).

tag: age

tag: genotype/variation

tag: tissue

value: retina


title: LIN28-IP

description: immortalized tumor cell line


title: E168D2NEO_P21_B


title: E168D2NEO_P21_C


title: E168D2NEO_P21_A


title: TH1_Rep1


title: R90W_P21_C


title: E168D2_P21_A


title: E168D2_P21_B


title: R90W_P21_A


title: 6V_17d_RNASeq

city: Szeged

first: Attila

last: Szűcs

address: Somogyi utca 4

department: Faculty of Medical Research

country: Hungary

institute: University of Szeged

data_processing:
Basecalls performed using Abi 5500xl ICS (Instrument Controller version 2011.09)
Data were filtered using the following specifications: minimum number of nucleotides in reads = 50
RNA reads were aligned to Medicago truncatula genome MedtrA17_4.0 (GCA_000219495.2)  assembly using these parameters Similarity fraction = 0.9,Length fraction = 0.9, Mismatch cost = 2,Insertion cost = 3,Deletion cost = 3
Read counts were normalized and differential expression was called using Deseq
Genome_build: Medicago truncatula genome MedtrA17_4.0 assembly (GCA_000219495.2)
Supplementary_files_format_and_content: Tab delimited text file with columns:LocusTag, basemean, basemena of A17 expression, basemean of 6V expression, fold Change, log2 fold change, pVal and pAdj.

organism: Medicago truncatula

source_name: Whole Nodule

growth_protocol: Plants were growin in aeroponic cassions (www.noble.org/MedicagoHandbook).

extract_protocol:
Briefly, total RNA was DNaseI treated and rRNA-depleted using RiboMinus Plant Kit.
Libraries were processed according to the SOLID transcriptome sequencing protocol (Publication Part Number 4452437).  After the fragmentation of RNA, the 50-200nt fraction was cleaned and was the subject of adaptor hybridization and reverse transcription. The cDNA library was cleaned with Qiagen MinElute PCR purification Kit and size-selected on a 6% TBE-Urea denaturing polyacrylamide gel.  The 150-250nt cDNA fraction was amplified to generate sufficient template for SOLID sequencing. To determine the accurate concentration of each library, a SOLID Library TaqMan Quantitation Kit was used according to the manufacturer's instructions. After, each library was clonally amplified on SOLiD P1 DNA Beads by emulsion PCR (ePCR). ePCR beads were enriched for template-positive beads by hybridization with capture beads. Template-enriched beads were extended at the 3' end in the presence of terminal transferase and 3' bead linker. Approximately 60 million beads per sample with clonally amplified DNA were deposited onto one lane of the 5500 SOLID sequencing flowchip . The flowchip was then loaded onto a SOLID 5500xl Instrument and the 50-base sequences were obtained according to manufacturer's protocol.

treatment_protocol: Plants were treated Sinorhizobium meliloti WSM419 strain.

value: whole nodule


title: WT_P21_C

value: wildtype


title: E168D2D2_P10_C


title: WT_P21_B


title: E168D2D2_P10_B


title: E168D2D2_P10_A


title: E168D2NEO_P10_C


title: E168D2_P10_B


title: E168D2_P10_A


title: E168D2_P10_C


title: Satb1_siRNA_KnockDown_1

tag: cell type


title: E168D2NEO_P10_B


title: E168D2NEO_P10_A


title: R90W_P21_B


title: R90WW_P10_B


title: R90WW_P10_A


title: WT_P10_C


title: R90W_P10_A


title: WT_P21_A


title: R90W_P10_B


title: R90W_P10_C


title: MidbrainDANeurons_4

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were mapped to the Mus musculus assembly 10 reference genome (mm10) using TopHat version 2.0.8
FPKM values for all genes in each sample were calculated with Cufflinks version 2.1.1
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each gene in each sample.

extract_protocol:
Samples underwent DNase digestion using the RNase-Free DNase Set (Qiagen, #79254) and were subsequently purified with the RNeasy MinElute Cleanup Kit (Qiagen, #74204). Eluted RNA samples were analyzed on a 2100 Bioanalyzer (Agilent) using RNA Pico Chips (Agilent, #5067-1513) to confirm RNA integrity, followed by the measurement of RNA concentrations with the Quant-iT RiboGreen RNA Assay Kit (Life Technologies, #R11490). cDNAs were prepared with the Ovation RNA-Seq System V2 kit (NuGEN, #7102-32), using an input of 2.5 ng RNA. 500 ng cDNA from each sample were fragmented on a Covaris S2 Focused Ultrasonicator using the operating conditions recommended by the manufacturer for a target fragment size of 200 bp. Fragment size was confirmed on a 2100 Bioanalyzer using High Sensitivity DNA Chips (Agilent, #5067-4626).Libraries for RNA sequencing were prepared with the TruSeq RNA Sample Preparation v2 kit (Illumina, #RS-122-2002), starting the manufacturer’s low-throughput protocol with the end repair step. The concentration of the RNA-Seq libraries was determined on a 2100 Bioanalyzer using High Sensitivity DNA Chips. Subsequently, two libraries with different adapters were multiplexed for sequencing. After confirming the concentration of the multiplexed samples on a 2100 Bioanalyzer using High Sensitivity DNA Chips, samples were analyzed on an Illumina HiSeq 2000 sequencer using 100 bp single-end sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Dopaminergic Neurons from Midbrain


title: MidbrainDANeurons_2


title: WT_P10_A


title: WholeMidbrain_2

source_name: Whole Midbrain

value: Whole Midbrain


title: WholeMidbrain_3


title: MidbrainDANeurons_3


title: WholeMidbrain_4


title: MidbrainDANeurons_1


title: WholeMidbrain_5


title: A17_17d_RNASeq

value: A17 (wild-type)


title: VT_6

source_name: Dopaminergic Neurons from VTA

extract_protocol:
TRAP samples underwent DNase digestion using the RNase-Free DNase Set (Qiagen, #79254) and were subsequently purified with the RNeasy MinElute Cleanup Kit (Qiagen, #74204). Eluted RNA samples were analyzed on a 2100 Bioanalyzer (Agilent) using RNA Pico Chips (Agilent, #5067-1513) to confirm RNA integrity, followed by the measurement of RNA concentrations with the Quant-iT RiboGreen RNA Assay Kit (Life Technologies, #R11490). cDNAs were prepared with the Ovation RNA-Seq System V2 kit (NuGEN, #7102-32), using an input of 1 ng RNA. 500 ng cDNA from each sample were fragmented on a Covaris S2 Focused Ultrasonicator using the operating conditions recommended by the manufacturer for a target fragment size of 200 bp. Fragment size was confirmed on a 2100 Bioanalyzer using High Sensitivity DNA Chips (Agilent, #5067-4626).Libraries for RNA sequencing were prepared with the TruSeq RNA Sample Preparation v2 kit (Illumina, #RS-122-2002), starting the manufacturer’s low-throughput protocol with the end repair step. The concentration of the RNA-Seq libraries was determined on a 2100 Bioanalyzer using High Sensitivity DNA Chips. Subsequently, two libraries with different adapters were multiplexed for sequencing. After confirming the concentration of the multiplexed samples on a 2100 Bioanalyzer using High Sensitivity DNA Chips, samples were analyzed on an Illumina HiSeq 2000 sequencer using 100 bp single-end sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: region

value: ventral tegmental


title: VT_4


title: VT_5


title: VT_3


title: VT_1


title: SN_6

source_name: Dopaminergic Neurons from SNpc

value: substantia nigra pars compacta


title: VT_2


title: SN_4


title: SN_3


title: SN_5


title: WT_P10_B


title: WholeMidbrain_1


title: SN_1


title: hs87l5_2_PolII_KClplus_LSD1n_KO

first: Yuliang

last: Tan

address: Room 345, CMM West, 9500 Gilman Drive, Mail Code 0648

department: School of Medicine

institute: University of California, San Diego

description:
Pol II ChIP-seq
KCl 1 hr

data_processing:
All Raw fastq files are treated with prinseq-lite.pl to remove PCR amplification duplicates.
Then the remaining reads are trimmered 6 bp from the 5' end and keep 36bp for each reads for the mapping.
After that, all reads are mapped to the mm9 genome with bowtie
bedGraph files are generated with HOMER using makeUCSCfile, and ChIP peaks are determined with the following parameters: -style factor -center -size 200 -minDist 500 -fdr 0.001 -fragLength 150.
Genome_build: mm9

source_name: mouse primary cortical neuron

growth_protocol: Primary cortical neurons were cultured using Neural Basal with 2% B-27 supplement, 0.5uM Glutamate and antibotics

extract_protocol:
Sonicated nuclei were precleared with Protein G magnetic beads and antibody chromatin complexes were isolated, and eluted DNA was reverse cross-linked overnight and DNA was purified using Qiagen DNA purification columns using Manufacturer's recommended protocol.
Libraries were prepared using Illumina's recommended protocol

treatment_protocol: 55mM KCl bath (final concentration)

value: Anti- Pol II Santa Cruz Biotechnology (Cat. No. sc-899X)

tag: passages

value: LSD1n KO DIV10

value: mouse primary cortical neuron

tag: treatment

value: KCl

value: 1 hr


title: hs19l3_4_LSD1n_KO_KCl_6hr

description:
RNA-seq
KCl 6hr


title: hs19l3_2_LSD1n_HT_KCl_6hr

description:
RNA-seq
KCl 6hr

value: LSD1n HT DIV10


title: hs87l5_1_PolII_KClminus_LSD1n_KO

description:
Pol II ChIP-seq
KCl 0 hr

value: 0 hr


title: hs76l6_6_LSD1n_WT

description:
LSD1 ChIP-seq
KCl 0hr

value: Anti- LSD1 Abcam (Cat. No. ab17721)

value: LSD1n WT DIV10


title: hs60l3_3_LSD1_KClminus

description:
LSD1 ChIP-seq
KCl 0 hours

value: wild type DIV10

value: 0 hours


title: hs60l3_4_LSD1_KClplus

description:
LSD1 ChIP-seq
KCl 1 hours

value: 1 hours


title: hs87l5_4_PolII_KClplus_LSD1n_WT

description:
Pol II ChIP-seq
KCl 1 hr


title: hs87l5_3_PolII_KClminus_LSD1n_WT

description:
Pol II ChIP-seq
KCl 0 hr


title: hs76l5_7_LSD1n_KO

description: LSD1 ChIP-seq


title: Mut2_mRNA

city: Philadelphia

first: Long

last: Gao

state: PA

address: 4002 Colket Translational Research Building (CTRB) 3501 Civic Center Boulevard

institute: The Children’s Hospital of Philadelphia

data_processing:
Sequenced reads mapped to the combination reference of mouse genome (release mm9), ERCC transcripts and rDNA region through Tophat
Gene level read counts estimated by FeatureCounts for combination of Ensembl genes(release 66), ERCC transcripts and rRNA genes
Differentially expressed genes were called by edgeR
Genome_build: mm9 + ERCC + rDNA
Supplementary_files_format_and_content: text file, gene level read counts matrix

growth_protocol: Mice were treated according to the University of Pennsylvania’s Animal Resources Center and IACUC protocols.

extract_protocol:
24,000 Flt3- LSK cells were sorted into Trizol and RNA was purified (Qiagen). Spike-in RNA (ERCC RNA Spike-In Mix, Life Technologies) was added following the manufacturer’s instructions.
Two types of sequencing libraries were prepared; one from polyA-selected RNA to analyze mRNAs, and one from total RNA to compare rRNA levels. mRNA was isolated from total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490, NEB). PolyA-selected mRNA was fragmented to average size of 300 nt, reverse transcribed to generate double-stranded cDNA, and converted to a paired end library using NEBNext Ultra RNA Library Prep Kit for Illumina (E7530, NEB) according to manufacturer's instructions including the optional double size selection procedure using Agencourt AMPure XP beads. Prepared libraries were quantified with dsDNA HS Kit (Q32851) for Qubit and the size distribution was assessed using High Sensitivity DNA Kit (5067-462) for Bioanalyzer

tag: genotype

value: Runx1 deficient

value: Bone Marrow


title: WT2_mRNA

value: wild type


title: hs63l8_7_LSD1c_Flag_KClplus

description:
Flag-LSD1c ChIP-seq
KCl 1 hours

value: Anti- M2 Sigma (Cat. No. A2220)

value: R26/LSD1c DIV10


title: WT1_mRNA


title: hs60l3_5_LSD1n_Flag_KClminus

description:
Flag-LSD1n ChIP-seq
KCl 0 hours

value: R26/LSD1n DIV10


title: hs60l3_6_LSD1n_Flag_KClplus

description:
Flag-LSD1n ChIP-seq
KCl 1 hours


title: Mut1_mRNA


title: hs63l8_6_LSD1c_Flag_KClminus

description:
Flag-LSD1c ChIP-seq
KCl 0 hours


title: hs43l4_3_LSD1n_KO_KClminus

description:
GRO-seq
KCl 0 hours

value: LSD1n KO DIV10


title: SN_2

value: substantia nigra pars compacta


title: hs43l3_4_LSD1n_KO_KClplus

description:
GRO-seq
KCl 1 hours

value: mouse primary cortical neuron

value: KCl


title: Mut1_total_RNA


title: hs19l3_3_LSD1n_KO_KCl_0hr

description:
RNA-seq
KCl 0hr


title: hs19l3_1_LSD1n_HT_KCl_0hr

description:
RNA-seq
KCl 0hr

value: LSD1n HT DIV10


title: hs43l4_2_LSD1n_WT_KClminus

description:
GRO-seq
KCl 0 hours


title: Mut2_total_RNA


title: hs43l4_1_LSD1n_WT_KClplus

description:
GRO-seq
KCl 1 hours


title: hs82l1_6_LSD1n_KO_KCl_3_hr

description:
GRO-seq
KCl 3 hours

value: 3 hours


title: hs82l1_2_LSD1n_WT_KCl_3_hr

description:
GRO-seq
KCl 3 hours


title: hs82l1_4_LSD1n_KO_KCl_0_hr

description:
GRO-seq
KCl 0 hours


title: WT2_total_RNA


title: hs82l1_1_LSD1n_WT_KCl_1_hr

description:
GRO-seq
KCl 1 hours


title: hs82l1_3_LSD1n_WT_KCl_0_hr

description:
GRO-seq
KCl 0 hours


title: hs70l2_2_H4K20me1_LSD1n_KO_Kclplus

description:
H4K20me1 ChIP-seq
KCl 1 hours

value: Anti- H4K20me1 Abcam (Cat. No. ab9051)


title: hs70l2_1_H4K20me1_LSD1n_WT_Kclplus

description:
H4K20me1 ChIP-seq
KCl 1 hours

value: LSD1n WT DIV10


title: pMIG_TH1_Rep1

data_processing:
The single-end reads that passed Illumina filters were filtered for reads aligning to tRNA, rRNA, adapter sequences, and spike-in controls.
Mouse RNA-Seq data was mapped against mm9 reference genome using tophat (v1.4.1., --library-type fr-secondstrand -C) and the RefSeq gene annotation downloaded from the UCSC genome bioinformatics site.
The alignment results (sam files) were converted into bam files and sorted by using samtools.
DUST scores were calculated with PRINSEQ Lite (v 0.20.3) and low-complexity reads (DUST > 4) were removed from the BAM files.
Sequencing read coverage per gene was counted using HTSeq-count (-m union -s yes -t exon -i gene_id).
Negative binomial tests were performed for pairwise comparisons of pMIG_TH1 and LEF1_TH1 conditions employing the Bioconductor package DESeq2 and allowing for a false discovery rate of 0.05.
Genome_build: mm9
Supplementary_files_format_and_content: text file with raw counts of sequencing reads per gene generated by HTSeq-count; text file with P-values for differential expression genes were calcuated by DESeq2 package on the basis of normalized abandunce measurement.

source_name: GFP-RV+ Th1

extract_protocol:
Th1 cells were sorted from the spleens and total RNA was extracted using standard Qiagen RNeasy columns
RNA libraries were prepared for sequencing using stardard Illumina protocol

value: spleen

tag: cell phenotype

value: CXCR5- Smarta cells


title: hs64l8_5_H4K20me1_LSD1n_WT_KClplus

description:
H4K20me1 ChIP-seq
KCl 1 hours

value: 1 hours


title: LEF1_TH1_Rep2

source_name: Lef1-RV+ Th1


title: hs60l3_2_H4K20me1_LSD1n_KO_KClminus

description:
H4K20me1 ChIP-seq
KCl 0 hours

value: 0 hours


title: hs60l3_1_H4K20me1_LSD1n_WT_KClminus

description:
H4K20me1 ChIP-seq
KCl 0 hours


title: hs70l2_4_H3K4me2_LSD1n_WT_KClplus

description:
H3K4me2 ChIP-seq
KCl 1 hours

value: Anti- H3K4me2 Millipore (Cat. No. 07-030 )


title: hs70l2_3_H3K4me2_LSD1n_WT_KClminus

description:
H3K4me2 ChIP-seq
KCl 0 hours


title: hs52l7_4_H3K4me1_LSD1n_KO_KClplus

description:
H3K4me1 ChIP-seq
KCl 1 hours

value: Anti-H3K4me1 Abcam (Cat. No. ab8895)


title: LIN28 +A1 (LIN28A1) [rep 2]

description: Immortalized tumor cell line

data_processing:
Aligned with TopHat2 version 2.0.4 with the following parameters: -g 10
FPKM measurements obtained using CuffLinks version 2.0.2
Genome_build: hg19
Supplementary_files_format_and_content: FPKM: 1st column = RefSeq ID, 2nd column = fragments per kilobase of exon per million mapped reads (FPKM value)

extract_protocol:
Cells were collected by centrifugation and RNA prepared using total RNA Kit Norgen (Norgen Biotek Corp)). Eight total RNA samples were submitted NIH Intramural Sequencing Center (NISC) for Sequencing using established Illumina TruSeq RNA Sample Prep Kit protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 0.2 X 106 cells were cultured in 6 well plates in MEM without antibiotics. Next day, cells were rinsed twice with OPTIMEM media and transfected with 50-100 pM siRNA using lipofectamine according to manufacturer’s instructions (Invitrogen Life Technology, Grand Island, NY). Small (si) RNA targeting LIN28, hnRNP A1 and control siRNA were obtained from Dharmacon, Thermo Scientific.

value: breast

tag: sirna


title: hs52l7_3_H3K4me1_LSD1n_KO_KClminus

description:
H3K4me1 ChIP-seq
KCl 0 hours


title: hs52l7_2_H3K4me1_LSD1n_WT_KClplus

description:
H3K4me1 ChIP-seq
KCl 1 hours


title: hs52l5_4_H3K36me3_LSD1n_KO_KClplus

description:
H3K36me3 ChIP-seq
KCl 1 hours

value: Anti- H3K36me3 Millipore (Cat. No. 07-549 )


title: LIN28 +A1 (LIN28A1) [rep 1]

description: Immortalized tumor cell line


title: hs52l7_1_H3K4me1_LSD1n_WT_KClminus

description:
H3K4me1 ChIP-seq
KCl 0 hours


title: hnRNP A1 (A1) [rep 2]

description: Immortalized tumor cell line

value: hnRNP A1 (A1)


title: hs52l5_2_H3K36me3_LSD1n_WT_KClplus

description:
H3K36me3 ChIP-seq
KCl 1 hours


title: pMIG_TH1_Rep2

value: wild type


title: WT1_total_RNA

value: Bone Marrow


title: LEF1_TH1_Rep1


title: hs82l1_5_LSD1n_KO_KCl_1_hr

description:
GRO-seq
KCl 1 hours

value: LSD1n KO DIV10

value: mouse primary cortical neuron


title: hnRNP A1 (A1) [rep 1]

description: Immortalized tumor cell line


title: S1_4

description: Sample 20

source_name: Saline_dopaminergic neurons_4 days

extract_protocol:
TRAP samples underwent DNase digestion using the RNase-Free DNase Set (Qiagen, #79254) and were subsequently purified with the RNeasy MinElute Cleanup Kit (Qiagen, #74204). Eluted RNA samples were analyzed on a 2100 Bioanalyzer (Agilent) using RNA Pico Chips (Agilent, #5067-1513) to confirm RNA integrity, followed by the measurement of RNA concentrations with the Quant-iT RiboGreen RNA Assay Kit (Life Technologies, #R11490). cDNAs were prepared with the Ovation RNA-Seq System V2 kit (NuGEN, #7102-32), using an input of either 2.5 ng RNA (TRAP samples from SNpc and VTA DA neurons combined) or 1 ng RNA (TRAP samples from either SNpc DA neurons or VTA DA neurons). 500 ng cDNA from each sample were fragmented on a Covaris S2 Focused Ultrasonicator using the operating conditions recommended by the manufacturer for a target fragment size of 200 bp. Fragment size was confirmed on a 2100 Bioanalyzer using High Sensitivity DNA Chips (Agilent, #5067-4626).Libraries for RNA sequencing were prepared with the TruSeq RNA Sample Preparation v2 kit (Illumina, #RS-122-2002), starting the manufacturer’s low-throughput protocol with the end repair step. The concentration of the RNA-Seq libraries was determined on a 2100 Bioanalyzer using High Sensitivity DNA Chips. Subsequently, two libraries with different adapters were multiplexed for sequencing. After confirming the concentration of the multiplexed samples on a 2100 Bioanalyzer using High Sensitivity DNA Chips, samples were analyzed on an Illumina HiSeq 2000 sequencer using 100 bp single-end sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: treated with

value: daily intraperitoneal injection of saline for 5d

value: Dopaminergic Neurons from Midbrain

tag: time after last injection

value: 4 days


title: M4_4

description: Sample 16

source_name: MPTP_dopaminergic neurons_4 days

tag: strain

value: daily intraperitoneal injection of MPTP-HCl (30 mg/kg free base) for 5d


title: non Targeting Control (NT) [rep 2]

description: Immortalized tumor cell line

value: non Targeting Control (NT)

tag: parental cell line


title: S2_4

description: Sample 24


title: M3_4

description: Sample 12


title: LIN28 [rep 1]

description: Immortalized tumor cell line

tag: cell line


title: LIN28 [rep 2]

description: Immortalized tumor cell line


title: non Targeting Control (NT) [rep 1]

description: Immortalized tumor cell line


title: hs52l5_1_H3K36me3_LSD1n_WT_KClminus

description:
H3K36me3 ChIP-seq
KCl 0 hours

tag: antibody

value: LSD1n WT DIV10

value: KCl

tag: time


title: S3_4

description: Sample 28


title: M2_4

description: Sample 8


title: S4_4

description: Sample 32


title: light 4h translatome [mRNAseq]

status: Public on Jul 26 2015

city: Taipei

first: Chiung-Swey

middle: Joanne

last: Chang

address: 128 Sec. 2, Academia Rd, Nankang,

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

description:
Sample name: polysome_L4h
BioSample: SAMN02251446
processed data file: RPKM.txt
processed data file: polysome_AS_event.txt
processed data file: Light_AS.txt

data_processing:
Sequence reads were mapped to the TAIR10 (http://www.arabidopsis.org) genome sequences with the use of BLAT program (Kent 2002, PMID11932250) with 95% identity.
Genes with RPKM larger than 0.5 either in the D or L4h Seq-results, only reads with 100% identity of splice junctions counted, events supported by at least 5 RNA-seq reads, greater than 5% and a minimum predicted intron length of 20.
The RPKM calculation and splice junctions detection were based on the algorithms in RACKJ package (Mortazavi et al. 2008, PMID18516045).
Genome_build: TAIR10
Supplementary_files_format_and_content: The tab-delimited text files (linked as supplementary files on Series record) include RPKM values for each Sample.

organism: Arabidopsis thaliana

growth_protocol: Seeds were surface sterilized and plated on 1/2 MS plates and grown 4 days at 22 under the dark.

extract_protocol:
For D and L4h, Pine Tree Method as in PMID 18182030. For polysomal D and L4h, Phenol-chloroform extraction as in PMID 22252389.  mRNA was purified by Oligotex mRNA isolation kit (Qiagen, Valenica, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 4-day-old etiolated seedlings were illuminated with white light (100 umole m-2 s-1) at 22℃ for 4 h (L4 h).

tag: ecotype

tag: developmental stage

value: seedling

tag: age

tag: growth protocol

tag: mrna source

value: polysomal RNA


title: CCA1_ChIPSeq_LD1

city: Raleigh

first: Colleen

middle: J

last: Doherty

state: NC

address: 128 Polk Hall CB7622

department: Biochemistry

institute: North Carolina State University

description: IP of CCA1-GFP seeldings in diel conditions at ZT2 Rep 1

data_processing:
BaseCalls Using Illumina CASAVA 1.8
Adaptor removal using TagDust v1.12
Adaptor removal using Trimmomatic v0.33
Duplicate removal using PRINSEQ v 0.20.4
Data were aligned to genome using Bowtie 2.2.1 selecting the best mapped read using MAPQ
Tag Directories were made using HOMER v4.7, peaks were called using HOMER v4.7 and the parameters findPeaks LL1 -P .1  -LP .1 -poisson .1 -fragLength 100 -style factor -i Input
Peaks were annotated using HOMER v4.7 and assignment to nearest TSS or using GenomicRanges and assignment to all TSS within 1kb of peak
Genome_build: TAIR10
Supplementary_files_format_and_content: Peaks file- .peaks.txt tab-delimited Top peaks passing IDR threshold, peakID, Chromosome, start,stop, strand (N/A), Normalized Tag counts, Focus ratio, PeakScore, Control Tag counts, Fold change vs Control, p-value vs control, Fold  Change vs Local, p-value vs Local , Clonal Fold change
Supplementary_files_format_and_content: UCSCbedFiles- ucsc.bedGraph.gz Normalized read counts in UCSC friendly bed format
Supplementary_files_format_and_content: Annotated Peaks- .txt tab-delimited Top peaks annotated to nearest TSS in TAIR: peakID, Chromosome, start,stop, strand (N/A), Peak score, Focus ratio, Annotation, Distance to TSS, Nearest Promoter Udm Ebtrez ID, Nearest Unigene ID, Nearest Refseq, Gene Name, Gene Alias, Gene Description, Gene Type, CpG%, GC%

source_name: Arabidopsis thaliana seedlings, WS-2 ecotype

growth_protocol: Plants were grown on MS media plus agar on plates in 12h:12h light:dark cycles. 14d old whole seedlings were harvested.

extract_protocol: Plants were harvested, fixed via vacuum infiltration with 1% formaldehyde fir 20 minutes. The reaction was stopped with 0.125 M glycine. Nuclei were isolated, lysed, and sonicated. Chromatin was immunoprecipitated with anti-GFP or IgG (mock control & input).

tag: harvest time

tag: light regime

value: Diel 12h:12h Light:Dark

tag: plant tissue

value: whole seedlings

tag: plant stage

value: 14 day old seedlings


title: CCA1_ChIPSeq_ZT14

description: IP of CCA1-GFP seeldings in continuous light at ZT14 Rep1

value: Comstant Light after entrainment in 12h:12h Light:Dark


title: dark translatome [mRNAseq]

description:
Sample name: polysome_D
BioSample: SAMN02251445
processed data file: RPKM.txt
processed data file: polysome_AS_event.txt
processed data file: Light_AS.txt

source_name: dark-grown

treatment_protocol: 4-day-old etiolated seedlings

tag: genotype/variation

value: wild type

value: dark-grown


title: CCA1_ChIPSeq_LD2

description: IP of CCA1-GFP seeldings in diel conditions at ZT2 Rep 2


title: hs52l5_3_H3K36me3_LSD1n_KO_KClminus

description:
H3K36me3 ChIP-seq
KCl 0 hours

value: Anti- H3K36me3 Millipore (Cat. No. 07-549 )

tag: passages

value: LSD1n KO DIV10

tag: cell type

tag: treatment

value: 0 hours


title: CCA1_ChIPSeq_Input

description: Input DNA


title: CCA1_ChIPSeq_LL1

description: IP of CCA1-GFP seeldings in continuous light at ZT2 Rep1


title: M1_4

description: Sample 4

tag: strain

tag: treated with

tag: tissue

value: Dopaminergic Neurons from Midbrain

tag: time after last injection


title: CCA1_ChIPSeq_LL3

description: IP of CCA1-GFP seeldings in continuous light at ZT2 Rep3

tag: ecotype


title: CCA1_ChIPSeq_LL2

description: IP of CCA1-GFP seeldings in continuous light at ZT2 Rep2


title: dark [mRNAseq]

description:
Sample name: D
BioSample: SAMN02251443
processed data file: RPKM.txt
processed data file: All_AS_events.txt
processed data file: Light_AS.txt

tag: developmental stage

value: 4 days

value: total RNA


title: WT.Nrp1neg.TR#2

status: Public on Jul 25 2015

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
Raw sequencing reads were processed using custom scripts. Read 1 contains the transcript sequence, Read 2 the UMIs.
Raw reads were first trimmed using the FASTX-Tollkit v0.0.13 (fastx_trimmer –Q 33). Read 2 was trimmed in order to extract the UMI (1-4bp), and Read 1 was trimmed to 30bp eliminate a potential oligo-dT sequence.
Reads were filtered for quality (more than 80% of the sequence having a Sanger Phred+33 quality score > 33) using fastq_quality_filter -v -Q 33 -q 20 -p 80.
Mapping was performed with Tophat2 to the mm10 mouse transcriptome {10042} keeping the strand information with the following options: tophat -p 2 --library-type fr-firststrand --read- mismatches 5 --read-gap-length 5 --read-edit-dist 5 --no-coverage-search --segment- length 15 --transcriptome-index.
Duplicated mapping reads were filtered out using the UMIs as follows. First duplicated mapped reads were marked using picard-tools- 1.79/MarkDuplicates.jar.
The genomic position of the duplicated reads were extracted and for each of these positions, only reads having different UMIs were kept. Reads that mapped to multiple positions were filtered out using samtools 0.1.19 flag 256 {10010}. Finally, reads were assigned to genes using a modified version of htseq-count with the mm10 gene annotation from UCSC Transcript database. Samples were normalized with DESeq using the estimateSizeFactors function
Genome_build: mm10
Supplementary_files_format_and_content: .txt files reporting raw read counts and normalized read counts.

source_name: Colonic lamina propria

extract_protocol:
For low-input RNAseq, 1,000 Foxp3+Nrp1-CD4+TCRb+ cells were sorted into TRIZOL and RNA was extracted.
RNA was reverse-transcribed using ArrayScript (Ambion) using a specific primer containing T7 promoter, the 5’ TruSeq Illumina adapter, a  8-positions with random nucleotide assignment as a unique molecular identifier (UMI), and a oligodT sequence. Second-strand synthesis was performed using the mRNA Second strand synthesis module (NEBNext #E6111L). After cDNA size selection using AMPure XP beads (0.8x and 1x, BeckmanCoulter- A63987), the product was amplified via in vitro transcription (MEGAshortscript, Invitrogen) for 10 hours and then fragmented (Magnesium RNA Fragmentation Module, New England Biolabs). 3’ indexing adaptor was ligated (truncated T4 RNA ligase 2 -Enzymatics), reverse-transcribed (Superscript II, Invitrogen), and amplified by PCR for 15 cycles (HiFi hotstart PCR kit, Kapa). cDNA cleanup and size selection were performed on AMPure XP beads. Libraries were quantitated by BioAnalyzer using the Agilent High Sensitivity DNA Kit (Agilent 5067-4626) and qPCR using Kapa library quantification kits, and sequenced on a MiSeq (nano kit) and HiSeq 2500 (rapid mode).

tag: age

value: 11 Weeks Old

tag: Sex

value: Male

tag: exclusion markers

value: CD19, DAPI

tag: phenotype markers

value: TCR+ CD4+ YFP(Foxp3)+Nrp1-

tag: separation method

value: MoFlo Sorter

tag: source prep description

value: Epithelial layer was removed by EDTA and DTT treatment. Lamina propria was isolated by Collagenase II and Dispase digestion


title: WT.Nrp1neg.TR#3

value: 12 Weeks Old


title: WT.Nrp1neg.TR#1

value: 10 Weeks Old


title: KO.Nrp1neg.TR#3

value: 15 Weeks Old


title: KO.Nrp1neg.TR#2

value: 14 Weeks Old


title: KO.Nrp1neg.TR#1

value: 13 Weeks Old


title: PC-3 Control2

city: Goettingen

first: Andreas

last: Leha

address: Humboldtallee 32

department: Medical Statistics

country: Germany

institute: University Medical Center Goettingen

data_processing:
Illumina Casava 1.8.2 software used for basecalling. Quality check was done via fastqc (v. 0.10.0, Babraham Bioinformatics)
The Alignment was performed using bismark v0.7.4 (26 Apr 2012) to hg19.  Bases with less than 10X coverage ore more than 99% quantile were discarded.
Methylation levels were extracted and tested for differentiality using methylKit 0.5.3.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include coverage and frequencies of C/T for each relevant position.

source_name: PC-3 cells

extract_protocol: DNA was isolated using Quiagen Blood and Tissue Kit

tag: cell line

value: Prostatecarcinoma

value: PBS

tag: treatment period


title: PC-3 SAM1

value: S-adenosylmethionine 160 mikromolar


title: PC-3 Control1


title: PC-3 SAM2


title: PC-3 SAM3


title: T31 [RRBS-seq]

city: Smithville

first: C. Marcelo

last: Aldaz

address: POB 389

department: Molecular Carcinogenesis

institute: The University of TX M.D. Anderson Cancer Center

description: processed data column: 657069

data_processing:
We performed 36 nt single end read Illumina HiSeq2000 platform.
Illumina Casava1.7 software used for basecalling.
The bisulfite treated sequencing reads were mapped to the human reference genome (hg19) by  Bismark software.
Promoter regions were calculated based on RefSeq gene annotations, such that the region starts 2 kb upstream of the annotated transcription start site and extends to 500 downstream of the TSS. CpG islands were downloaded from UCSC genome annotation database assembled by NCBI (hg19).
To identify differentially methylated sites first we filtered samples based on read coverage ≥ 20. And the significant differentially methylated CpGi sites (DMC) were identified when the difference of methylation percentages between normal breast epithelia and DCIS were greater than 0.25 and q-value <0.01.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file include methylated reads number for each Sample

source_name: pure HG-DCIS

extract_protocol:
DNA was purified using the DNeasy Blood and Tissue Kit (Qiagen). Only DNA samples with 260/280 ratios greater than 2.0 were processed for library construction.
1ug of genomic DNA was digest with MspI, end-repaired, 3-prime adenylated, and methylated adapters were ligated to the fragments. Adapter-ligated fragments corresponding to an insert size of 40bp to 220bp were excised and eluted from agarose gels, bisulfite treated and amplified by PCR.
Reduced Representation Bisulfite Sequencing analysis (RRBS; Meissner et al., Nature 2008).

tag: age (yrs)

tag: race

value: Asian

value: breast ductal carcinoma in situ


title: T8 [RRBS-seq]

description: processed data column: 119203

value: Black


title: 4 h light treated [mRNAseq]

description:
Sample name: L4h
BioSample: SAMN02251444
processed data file: RPKM.txt
processed data file: All_AS_events.txt
processed data file: Light_AS.txt

tag: genotype/variation

value: wild type

value: seedling

value: 4 days

tag: growth protocol

tag: mrna source

value: total RNA


title: T9 [RRBS-seq]

description: processed data column: 154979R

value: White

tag: tissue


title: T5 [RRBS-seq]

description: processed data column: 90724


title: T24 [RRBS-seq]

description: processed data column: 723711


title: T4 [RRBS-seq]

description: processed data column: 411611


title: T6 [RRBS-seq]

description: processed data column: 92468


title: T3 [RRBS-seq]

description: processed data column: 402513


title: T25 [RRBS-seq]

description: processed data column: 750937

value: Hispanic


title: Gill_25C_3hrs_rep2

city: Davis

first: Bernie

last: May

state: CA - California

address: 1 Shields Avenue

department: Animal Science

institute: UC Davis

description: Replicate 2. 11 indivudal RNA samples from the individuals in this replicate were proportionally pooled and used to make the Illumina library

data_processing:
Illumina Casava1.8 software used for basecalling.
Barcodes were removed and data were quality filtered and trimmed using the default parameters in CLC GenomeWorkBench v.4.9.
All reads were used to assemble a de novo reference transcriptome in CLC GenomeWorkBench v.4.9.
Filtered reads were aligned to the de novo transcriptome and in read counts were generated. Baggerly's test with an FDR of 0.1 was performed comparing the 15C, 18C, 21C, and 25C groups to the 12C controls in CLC GenomeWorkBench v.4.9.
The de novo reference transcriptome was annotated using Blast2GO.
Genome_build: Salmon_reference_183kcontigs.fasta
Supplementary_files_format_and_content: CVS file that contains all Baggerly's statistics as well as basic analysis of each sample group including RPKM.

organism: Oncorhynchus tshawytscha

source_name: 3 hrs at 25C

growth_protocol: Fry were reared in circular flow-through tanks at 12 degrees C and were fed commercial salmon feed.

extract_protocol:
Total RNA was isolated using Trizol extraction. RNA was quality checked using 2100 Agilent Bioanalyzer and RNA 6000 Nano kit.
Libraries were constructed using the Illumina TruSeq RNA Sample Preparation Kit and associated protocol (TruSeq RNA Sample Preparation Guide, part #15008136, November 2010 release)

treatment_protocol: Treatments consisted of a three-hour water bath at 15°C, 18°C, 21°C or 25°C, followed by one hour of recovery at 12°C. The experimental  chambers were moved to water baths held at a constant temperature, facilitating very rapid change in the temperature experienced by the fish. Controls were handled identically to the other four treatment groups, but remained at 12°C. Following recovery, fish were euthanized with buffered tricaine methanesulfonate (500mg/L tricaine, and 420mg/L NaCO3) and gill tissue was immediately collected.

value: 5 months post hatch

tag: source

value: Merced River Hatchery, California

tag: run-type

value: Fall run

tag: treatment group

value: 3hr water bath at 25C followed by 1h recovery at 12C

value: Gill arch


title: Gill_25C_3hrs_rep1

description: Replicate 1. 11 indivudal RNA samples from the individuals in this replicate were proportionally pooled and used to make the Illumina library

tag: age


title: Gill_25C_3hrs_rep3

description: Replicate 3. 11 indivudal RNA samples from the individuals in this replicate were proportionally pooled and used to make the Illumina library


title: Gill_21C_3hrs_rep3

source_name: 3 hrs at 21C

value: 3hr water bath at 21C followed by 1h recovery at 12C


title: T22 [RRBS-seq]

description: processed data column: 70811


title: Gill_21C_3hrs_rep2


title: T20 [RRBS-seq]

description: processed data column: 125376


title: PC-3 Control3

tag: cell type

value: Prostatecarcinoma

tag: treatment

value: PBS


title: T23 [RRBS-seq]

description: processed data column: 726783


title: Gill_21C_3hrs_rep1


title: T2 [RRBS-seq]

description: processed data column: 401651


title: T17 [RRBS-seq]

description: processed data column: 642256


title: T18 [RRBS-seq]

description: processed data column: 648979


title: T7 [RRBS-seq]

description: processed data column: 108731

value: AMIndian/AlaskaNativ


title: Gill_18C_3hrs_rep2

source_name: 3 hrs at 18C

value: 3hr water bath at 18C followed by 1h recovery at 12C


title: Gill_18C_3hrs_rep3


title: Gill_15C_3hrs_rep3

source_name: 3 hrs at 15C

value: 3hr water bath at 15C followed by 1h recovery at 12C


title: Gill_18C_3hrs_rep1


title: Gill_15C_3hrs_rep2


title: T11 [RRBS-seq]

description: processed data column: 192373

value: breast ductal carcinoma in situ


title: T16 [RRBS-seq]

description: processed data column: 641358


title: T14 [RRBS-seq]

description: processed data column: 207178

value: Asian


title: T1 [RRBS-seq]

description: processed data column: 401044


title: T12 [RRBS-seq]

description: processed data column: 196782


title: Gill_15C_3hrs_rep1


title: Gill_12C_3hrs_rep3

source_name: 3 hrs at 12C

value: control (remained at 12C)


title: T10 [RRBS-seq]

description: processed data column: 159770


title: Gill_12C_3hrs_rep2


title: N6 [RRBS-seq]

description: processed data column: A6

source_name: normal breast epithelium

value: Black

value: normal breast epithelial organoid


title: Gill_12C_3hrs_rep1


title: N5 [RRBS-seq]

description: processed data column: A5


title: N1 [RRBS-seq]

description: processed data column: A1.2

value: White


title: N7 [RRBS-seq]

description: processed data column: A8


title: N4 [RRBS-seq]

description: processed data column: A4.2


title: T9

data_processing:
We performed 76 nt paired-end sequencing using an Illumina HiSeq2000 platform.
Illumina Casava1.7 software used for basecalling.
The short sequenced reads were mapped to the human reference genome (hg19) by the splice junction aligner TopHat V2.0.6.
The number of reads mapped to each gene based on the UCSC.hg19.KnownGene database were counted, reported and annotated using the GenomicFeatures, Rsamtools and org.Hs.eg.db packages.
To identify differentially expressed genes between normal breast epithelium and DCIS samples, we utilized the edgeR-test based on the normalized number of reads mapped to each gene.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include log2 count per million values for each Sample

extract_protocol:
RNA was isolated and purified using TRIzol reagent (Life Technologies) and RNeasy mini kit (Qiagen). RNA concentration and integrity were measured on a Agilent 2100 Bioanalyzer (Agilent Technologies). Only RNA samples with RNA integrity values (RIN) over 8.0 were considered for subsequent analysis.
mRNA from normal breast epithelial samples and  DCIS samples were processed for directional mRNA-seq library construction using the ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre) according to the manufacturer's protocol.


title: T19 [RRBS-seq]

description: processed data column: 1213079


title: T8


title: T6


title: T4


title: T13 [RRBS-seq]

description: processed data column: 203403


title: T3


title: T22


title: T23


title: T5


title: T25

value: Hispanic


title: T2


title: T20


title: T19


title: T21


title: T17


title: T16


title: T18


title: T15


title: T13


title: T14


title: T11


title: T12


title: T7


title: N7


title: T1


title: T10


title: N8


title: N5


title: N6


title: N4


title: N2


title: N1


title: N3


title: T24


title: N10


title: Hcn4-CreERT2;Isl1_ctrl_SAN

status: Public on Jul 24 2015

city: Milan

first: Paola

last: Cattaneo

address: Via Fantoli 16/15

department: Institute of Genetic and Biomedical Research

country: Italy

institute: National Research Council of Italy

data_processing:
RNA-seq libraries were sequenced using Illumina HiSeqTM 2000 with paired end sequencing at 90 bp read length (BGI, Shenzhen, China).
Adapter and poor quality read sequences were trimmed with Trim Galore using default settings for paired end reads.
Trimmed reads were then quality controlled with FastQC (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc). On average each read pair resulted in ~22 million uniquely mapped reads after mapping to the mm9 reference genome with TopHat2 and Bowtie2.
Transcript expression values were determined after transcript normalization (reads per kilobase per million reads–RPKM) with AltAnalyze. Transcripts were considered significantly expressed if RPKM ≥ 1 in either one of the two condition.
Genome_build: mm9
Supplementary_files_format_and_content: .txt tab-delimited file continaing annotation identifier and expression values for each Sample

source_name: Sinoatrial node (SAN) cells

growth_protocol: Tamoxifen was given at E10.5 and samples were harvested 36 hours post induction at E12-12.5. Tomato+ SANs of Isl1 mutant and control embryos were dissected under fluorescence microscopy. The samples for the same genotype were pooled, digested with collagenase II (1mg/ml)/trypsin (0.1%). The cell suspension was filtered through a 40um filter unit (Fisher) and endothelial cells were removed by incubation with CD31 microbeads (Miltenyl Biotec). SAN cells were resuspended in 0.5ml DMEM medium and kept on ice until sorting. Hcn4-CreERT2 expressing pacemaker cells (Tomato+) were FACS sorted (BD FACSAria).

extract_protocol:
RNA was prepared using the RNeasy Mini kit (Qiagen Cat. 74104) following the manufacturer’s instructions. Total RNA (10ng) was incubated with  Oligo (dT) magnetic beads to isolated mRNA.
RNA-seq libraries were prepared with the SMARTer cDNA library construction kit (Clontech Cat. 634901) according to manufacturers instructions and sequenced using Illumina HiSeqTM 2000 with paired end sequencing at 90 bp read length (BGI, Shenzhen, China).

tag: strain

value: ICR

tag: genotype

value: Hcn4-CreERT2; Isl1+/+; Rosa-tdTomato

tag: developmental stage

value: Induced at E10.5-harvested at E12.5


title: mEpiSC1000_Exp1

city: Beijing

first: Yusi

last: Fu

address: biopic,PKU

institute: PKU

data_processing:
Base-calling performed by RTA v1.9 and CASAVA v1.8.2
filter reads that have too many N, of too low quality or with the adaptor sequence
align reads with Bowtie 2 version 2.1.0, default setting
peak-calling with macs14 1.4.2 20120305 ,  --keep-dup all --bw 180
Genome_build: mm9
Supplementary_files_format_and_content: wig file is generated by MACS

source_name: 1000 mEpiSCs

extract_protocol:
use microfludic chip to do ChIP
The reagents for library preparation were provided by Illumina and were used according to the manufacturer’s protocol with appropriate modifications as described below. We purified DNA from the ChIP assay by AMPure XP beads and eluted the DNA by 20µl Resuspension Buffer. The DNA suspension was concentrated from 20µl to 5µl by evaporation. Then, 4µl End Repair Mix and 1µl Resuspension Buffer were added to the 5µl cleaned up DNA suspension before incubating at 30°C for 30 minutes and inactivating at 75°C for 15 minutes for end repairing. Adenylation  of  3’  ends  is  performed  by  adding  8.4µl  thawed  A-Tailing  Mix  and  1.6µl Resuspension Buffer, incubating at 37°C for 30 minutes. We ligated adapters by adding 1.7µl of DNA ligase Mix, 3.1µl Resuspension Buffer and 0.2µl Adapter Index. 30°C for 10 minutes is the duration for adapter ligation. We added 1µl DNA which contains 100 ng of 5kb sized plasmid DNA as carrier, and then purified DNA twice by AMPure XP Beads.

tag: development stage

value: cell strain

value: mESC

tag: chip antibody

tag: genetic background

value: mixed background of MF1, 129/sv, and C57BL/6J strains


title: mESC1000_Exp1

source_name: 1000 mESCs


title: mEpiblast_Exp1

source_name: 1000 E6.5 epiblasts

value: E6.5 embryo

value: epiblast


title: mESCbulk

source_name: 1 million mESCs


title: N9

tag: race


title: unfertilized eggs from Oikopleura dioica

status: Public on Jul 23 2015

city: Shanghai

first: Kaile

last: Zhang

address: No. 600 Yishan Road

department: Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

institute: Shanghai Jiao Tong University

data_processing:
In order to achieve a high quality transcriptome assembly, all raw reads were filtered in the following steps: (1) Adapter and contamination sequences were removed. (2) Low-quality bases whose quality is less than 25 from both 5’ and 3’ ends were trimmed. (3) Sequences whose length is less than 35 nt were discarded. (4) Sequences with Q20 or unknown (Ns) bases more than 10% were also discarded. (5) Unpaired reads after the above processes were removed.
Reads of egg and larval stages were merged, and de novo transcriptome assembly was carried out using Trinity.  We set the k-mer parameter as 25 and transcripts whose length no less than 100 bp were kept.
The amounts of mRNAs were calibrated by fragments per kilobase of exon per million fragments mapped (FPKM) method using RSEM and log2 transformed.
Supplementary_files_format_and_content: text files include FPKM values for each biological sample

organism: Oikopleura dioica

source_name: unfertilized eggs

growth_protocol: they were reared in 10 liter containers in artificial seawater (REI-SEA Marine, REI-SEA, Tokyo, Japan) with stirring by a puddle (15 rpm) at 20 °C and fed with the flagellates Isochrysis galbana and Rhinomonas reticulata, the diatom Chaetoceros calcitrans, and the cyanobacterium Synechococcus sp. O. dioica sexually matures and spawns at 5 days post-fertilization.

extract_protocol:
Total RNA was isolated by guanidium thiocyanate-phenol-chloroform extraction. The OD260/280 and OD260/230 were 2.09-2.31 and 1.88-1.92, respectively, ensuring purity of RNA samples. The amounts of total RNA sample were more than 20 ug. Integrity of total RNA was confirmed by agarose gel electrophoresis and Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA).
Strand specific RNA-Seq was performed by Beijing Genome Institute (BGI, Shenzhen, China) using a paired-end libraries. In brief, mRNA was purified with oligo dT and fragmented. First strand cDNA was synthesized using random hexamers, and strand-oriented library was generated. Libraries of oocyte and larvae were sequenced using Illumina HiSeqTM 2000. The insert size of library and read length was 200 bp and 90 bp, respectively.

treatment_protocol: To minimize inter-individual allelic variations in sequencing results, samples were prepared from cohorts of a single pair. A male and a female were transferred to 2 liter container to allow spawning, and the cohorts were reared over several generations. Unfertilized eggs were obtained from 46 female cohorts. Larval samples were collected from cohorts of 63 adult pairs. Matured females were placed in gelatin-coated 6-well culture plates to allow natural spawning. Oocytes were collected in a petri dish, and fertilized by adding drops of seawater containing sperm. Larvae reached to 8 hours post-fertilization (hpf) were anesthetized and collected in 1.5 ml tube. Eggs and larvae were frozen immediately in liquid nitrogen and stored at -80 °C until isolation of total RNA.

tag: Stage

value: egg


title: IgG_MyoG-1_ChIP-seq

city: Rehovot

first: kfir

middle: baruch

last: Umansky

state: Rehovot

address: POB 25

country: Israel

institute: Weizmann Institute

description: first IP experiement of mouse IgG (for MyoG)

data_processing:
For Samples 1-4 and 13-16, basecalls were performed using CASAVA version 1.8.2. For Samples 5-12,  basecalls were performed using CASAVA version 1.7.0.
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie with the following options: -a -m 1 --best --strata -v 1.
Peaks of enriched binding regions were detected by  merging  biological replicates of IP and NIS or IgG. Peaks were called using MACS1.4.
Genome_build: mm9
Supplementary_files_format_and_content: Bed files containing peaks detected by MACS1.4.

source_name: Primary myotubes (24hr post differentiation induction)

growth_protocol: We isolated SC from gastrocnemius muscles of 2-3 weeks old C57bl/6 WT mice. Cells were grown at 37°C, 5% CO2 on GHR MatrigelTM (BD Biosciences, USA) in proliferation medium (BIOAMF-2, Biological Industries, Israel), which was replaced daily. For MyoG ChIP-seq, PMs were differntiate for 24hr: cells were grown as above to 75-80% confluency and then induced to differentiate by serum starvation in differentiation media (DM): DMEM containing 4% horse serum (Gibco, UK) and 0.04U/mL human Insulin.  Each transcription factor experiment was performed in biological replicates.

extract_protocol:
Lysates were clarified from sonicated nuclei (sonicated to yield DNA fragments of ~300bp) and TF-DNA  complexes were isolated with  relevant antibody, washed and DNA was purified using Qiagen Minelute kit.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Cell were fixed with formaldehyde and nuclear lysate were made

value: muscle

value: primary

tag: days in culture

value: 4(3+ 1 in differentiation media)

value: mouse IgG (278-010, Ancell)


title: Hcn4-CreERT2;Isl1_ko_SAN

value: Hcn4-CreERT2; Isl1f/f; Rosa-tdTomato


title: IgG_MyoG-2_ChIP-seq

description: second IP experiement of mouse IgG  (for MyoG)


title: WT_ChIP2

city: Heidelberg

first: Jan

last: Lohmann

address: Im Neuenheimer Feld 230

department: Centre for Organismal Studies Heidelberg

institute: University Heidelberg

data_processing:
Base-callling was performed using Illumina pipeline CASAVA-1.7.0.
All reads were mapped to chromosomes 1-5 of the TAIR10 genome using bowtie2 (v2.0.5) (Langmead and Salzberg, 2012) with default settings of the --fast option.
Identification of binding sites was performed independently for each biological replicate using MACS (v1.4.2) (Zhang et al., 2008) with the following options: --nomodel --shiftsize 75  --keep-dup auto -g 1.2e8 -w -S
Genome_build: TAIR10
Supplementary_files_format_and_content: Tabular files generated by MACS containing peaks information, including chromosome name, start position of peak, end position of peak, length of peak region, peak summit position related to the start position of peak region, number of tags in peak region, -10*log10(pvalue) for the peak region, fold enrichment for this region against random Poisson distribution with local lambda, FDR in percentage.

source_name: whole seedlings

growth_protocol: Transgenic RGA::RGA-GFP and the control non-transgenic seeds were sown on MS plates and stratified for 4 days at 5°C. Seedlings were grown at 150 µmol m-2 s-1 for 10 days under long day conditions (16 h light, 8 h dark) before being transferred to a hormone liquid treatment.

extract_protocol:
Fixation of the plant material and ChIP was performed as described in Gendrel, et al. 2005, (Nature Methods, 2(3), 213–8). Nuclear extracts were split in two and incubated each with 20 µl of GFP-Trap_A (ChromoTek) for 4 h at 5°C for immunoprecipitation. MinElute Reaction Cleanup Kit columns (Qiagen) were used for purification of the DNA fragments.
Sequencing libraries were generated using pooled DNA from each 7 to 10 individual ChIP preparations of either RGA-GFP or WT material.   Libraries were prepared for Illumina Sequencing using the NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (E6240) with the NEBNext Multiplex Oligos for Illumina (E7335 and E7500). Libraries were quantified using the Qubit Fluorometer from Invitrogen, and their size determined using the DNA 1000 Assay on the BioAnalyzer. Sequencing was performed on the Illumina HiSeq 2000 Instrument 50 base SE (plus index read).

treatment_protocol: 10-day-old seedlings were transfered to a hormone liquid treatment with 10 µM paclobutrazol PAC (Duchefa) for 18 hours. For another 6 hours BA (Duchefa) was added to the treatment at a final concentration of 5 µM.

tag: transgene

value: GFP-Trap_A (ChromoTek)

tag: growth condition

value: long day (16 h light, 8 h dark)

value: 18 h 10 µM PAC, 6 h 5 µM BA

tag: ecotype


title: 8HPF larvae from Oikopleura dioica

source_name: 8HPF larvae

value: larvae


title: MyoG-2_ChIP-seq

description: second IP experiement of MyoG

tag: tissue

value: Mouse anti MyoG (sc-12732, Santa Cruz Biotechnology)


title: WT_ChIP3


title: RGA_ChIP3

value: Ler


title: WT_ChIP1


title: MyoG-1_ChIP-seq

description: first IP experiement of MyoG


title: RGA_ChIP2


title: RGA_ChIP1


title: MyoD-2_ChIP-seq

description: second IP experiement of MyoD

source_name: Primary proliferating myoblasts

value: Mouse anti MyoD (sc-32758, Santa Cruz Biotechnology)


title: mEpiSC1000_Exp2

value: cell strain

value: mESC


title: IgG_MyoD-1_ChIP-seq

description: first IP experiement of mouse IgG (for MyoD)


title: mEpiblast_Exp2

value: E6.5 embryo

value: mixed background of MF1, 129/sv, and C57BL/6J strains


title: mESC1000_Exp2


title: IgG_MyoD-2_ChIP-seq

description: second IP experiement of mouse IgG  (for MyoD)


title: mEpiSCbulk 2

source_name: 1 million mEpiSCs