title: CD4SP_OTII_dKO2

first: Margaret

middle: C

last: Cam

institute: NIH

data_processing:
Illumina CASAVA_v1.7 was used for demultiplex and converting binary basecalls and qualities to qseq.txt format, and CASAVA_v1.8.2 was used for demultiplex and converting binary basecalls and qualities to fastq format.
The fastq files (36 bp, single end) were aligned against the genome reference mm9 and promoter reads (+/- 2Kb from the transcription start site) detected for each gene using the Rsubread package in R (1).
Promoter counts were normalized by loess using csaw package (2), and broad peaks were detected using SICER (3)
Promoter reads overlapping with SICER peaks in two biological replicates per group (KO and WT) were further analyzed for differential binding using the glmQLFit function in EdgeR (4,5).
Offsets were used to generate normalized bedgraph files for visualization in IGV.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph

source_name: Thymus

extract_protocol:
Sorted CD69lo wt DP thymocytes and mature (TCRhi or Vα2hi CD24lo) CD4 SP thymocytes from Wt, Jmjd3KO, UtxKO and dKO mice were digested with MNase, followed by sonication to generate mononucleosomes. Sonicated supernatants were pre-cleared with protein G beads and then immunoprecipitated with anti-H3K27Me3.
The libraries were prepared according to standard Illumina's protocol. The ChIP DNA is blunt-ended and phosphorylated. A single 'A' nucleotide is added to the 3' ends of the fragments in preparation for ligation to an adapter that has a single-base 'T' overhang. The ligation products are purified and size-selected. The size-selected DNA is purified and PCR-amplified to enrich for fragments that have adapters on both ends. The final purified product is then quantitated by qPCR before cluster generation and sequencing.  Clusters were generated on an Illumina flow cell and libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: Mature CD4 SP Thymocytes

value: OTII Kdm6bf/f, Kdm6af/f Cd4-Cre+

tag: chip antibody

value: H3K27me3 (Millipore, 17-622)


title: ROe14 CD4

status: Public on Sep 02 2015

type: SRA

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

country: USA

institute: Yerkes National Primate Research Center

library_source: transcriptomic

data_processing:
Illumina Casava1.8.2 software used for basecalling and demultiplexing.
Reads were mapped to Macaca_mulatta UNMC_v7.6 genome assembly with the STAR (v2.3.0e) aligner args: --outFileterMultimapNmax 1 --outFilterType BySJout --outSJfilterReads Unique --sjdbGTFfile UNMC_rhesus_annotation_v7.6 --outFilterIntronMotifs RemoveNoncanonicalUnannotated
Per sample annotated transcript models were quantitated with Cufflinks (v2.1.1) args: -G UNMC_rhesus_annotation_v7.6.gtf
Sample transcript models were merged with Cuffmerge (v2.1.1)
FPKM (Fragments per kilobase of exon per million reads mapped) abundance estimates and differential expression was caluclated with Cuffdiff (v2.1.1)
Genome_build: UNMC_v7.6 is a presubmission version of the MacaM GCA_000772875.1 assembly. (MaSuRCA_Rhesus_Genome_v7_20130927.fasta, UNMC_rhesus_annotation_v7.6.gtf)
Supplementary_files_format_and_content: tab delimited text file containing FPKM for each sample (in columns) and each annotated transcript (in rows).

molecule: total RNA

organism: Macaca mulatta

source_name: Splenocyte

extract_protocol:
Total RNA was prepared using the QIAGEN RNEasy Micro Kit.
Libraries were generated using the CLONTECH SMARTer HV kit, barcoding and sequencing primers were added using NexteraXT DNA kit.  Libraries were validated by microelectrophoresis, quantified, pooled and clustered on Illumina TruSeq v3 flowcell.  Clustered flowcell was sequenced on an Illumina HiSeq 1000 in 100-base single-read reactions.

tag: infection status

value: SIV negative

tag: time point

value: uninfected

tag: cell population

value: BULK CD4


title: ROe14 TREG

value: TREG


title: CD4SP_OTII_Wt2

city: Bethesda

state: MD

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: cell type

tag: genotype

value: OTII Kdm6bf/f, Kdm6af/f Cd4-Cre-


title: ROe14 TFR

value: TFR


title: RHH5 TFR


title: CD4SP_OTII_Wt1


title: CD4SP_Jmjd3KO

value: Kdm6bf/f Cd4-Cre+


title: RHH5 CD4


title: DP_Wt

value: DP Thymocytes

value: Kdm6af/f Cd4-Cre-


title: CD4SP_Wt

value: Kdm6bf/f Cd4-Cre-


title: CD4SP_dKO

value: Kdm6bf/f, Kdm6af/f Cd4-Cre+


title: CD4SP_OTII_dKO1


title: ROe14 TFH

value: TFH


title: RHH5 TREG


title: RHH5 TFH


title: RLM7 TREG


title: RQQ8 TFR


title: E11.5 heart, Nkx2-5 ChIP (S4)

city: London

first: Laurent

last: Dupays

address: The Ridgeway, Mill Hill

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie.
peaks were called using MACS1.4, p-value=1x10-14
Genome_build: mm9
Supplementary_files_format_and_content: .bed files containing MACS peaks

source_name: E11.5 heart, Nkx2-5 ChIP

extract_protocol:
Fixed embryonic hearts were homogenised using an Ultra-Turrax, sonicated and Nkx2-5-DNA complexes were isolated using NKX-2.5 (N-19) sc-8697 antibody from Santa Cruz.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

tag: strain

value: Parkes

tag: developmental stage

tag: tissue

value: heart


title: RLM7 CD4


title: RQQ8 TFH


title: RQQ8 CD4


title: E11.5 heart, Nkx2-5 ChIP (S1)


title: MCF-7 Hi-C

city: Durham

first: Rasim

last: Barutcu

state: NC

address: 6 Davis Drive

institute: ScitoVation

data_processing:
Library strategy:
The Hi-C data were mapped with Bowtie and  binned at 6.5Mb, 1Mb, 250kb, 100kb and 40kb non-overlapping genomic intervals.  Iterative mapping and correction of Hi-C data were performed as previously described (Imakaev et al. 2012).  Biological replicates showed high reproducibility (Pearson's correlation coefficient > 0.9 for 1Mb resolution data).  Similarly, the first eigenvector comparison of the replicates showed high reproducibility.  For the downstream analyses, sequences obtained from both biological replicates were pooled and ICE-corrected to serve as a combined dataset.
Compartment analysis: First, the z-scores of the interaction matrices at 250kb resolution were generated as described previously (Lieberman, 2009).  Then, Pearson Correlation on the Z-score matrices was calculated.  By performing principal component analysis (Lieberman-Aiden et al. 2009; Zhang et al. 2012), the first eigenvector typically represents the compartment profile(Lieberman-Aiden et al. 2009), where the positive and negative 1st eigenvalues represent different compartments.   Gene density for each compartment was calculated to call the “A” and “B” compartmentalization.
TAD Calling: TAD calling was performed as calculating the “insulation” score of each bin using the 40kb resolution combined Hi-C data (as previously described.  The mean of the interactions across each bin were calculated.  By sliding a 1Mb x 1Mb (25bins x 25bins) square along the diagonal of the interaction matrix for every chromosome, we obtained the “insulation score” of the interaction matrix.  Valleys in the insulation score indicated the depletion of Hi-C interactions occurring across a bin.  These 40kb valleys represent the TAD boundaries.  Based on the variation of boundaries between replicates, we chose to add a total of 160kb (80kb to each side) to the boundary to account for replicate variation.  The final boundaries span a 200kb region. All boundaries with a boundary strength < 0.15 were excluded as they were considered weak and non-reproducible.  The insulation plots for the biological replicates showed high reproducibility (Pearson correlation coefficient = 0.80 for MCF-7 and 0.90 for MCF-10A replicates), suggesting the robustness of the method.  Similarly, the overlap of detected boundaries also showed high reproducibility between the biological replicates (~85% TAD boundary overlap for MCF-7 and ~91% for MCF-10A).  Therefore, we used the combined Hi-C replicates for the TAD analyses.
Z-Score Calculation: We modeled the overall Hi-C decay with distance using a modified LOWESS method (alpha = 1%, IQR filter), as described previously (Sanyal et al. 2012).  LOWESS calculates the weighted-average and weighted-standard deviation for every genomic distance and therefore normalizes for genomic distance signal bias.
Genome_build: hg19
Supplementary_files_format_and_content: Hi-C: tar ball archive of all normalized/corrected Hi-C data matrices binned at 40kb/250kb/1Mb, TAD boundaries at 40kb and genomic compartments at 250kb resolution
Supplementary_files_format_and_content: RNA-Seq: raw gene counts after RSEM analysis and the output file for the DeSeq2 analysis

organism: Homo sapiens

source_name: Breast cancer cell line

growth_protocol: MCF-10A cells were obtained from the Barbara Ann Karmanos Cancer Institute (Detroit, MI). The cells were maintained in monolayer in Dulbecco's modified Eagle's medium-F12 (DMEM/F12) (Invitrogen, 21041025) supplemented with 5% horse serum (Invitrogen, 16050122), 1% penicillin/streptomycin (Invitrogen, 15140122), 0.5 μg/ml hydrocortisone (Sigma, H-0888), 100 ng/ml cholera toxin (Sigma, C-8052), 10 μg/ml insulin (Sigma, I-1882), and 20 ng/ml recombinant human EGF (Peprotech, 100-15) as previously described (Debnath et al. 2003).  MCF-7 cells were obtained from ATCC and were cultured in DMEM supplemented with 10% FBS and pen-strep.

extract_protocol: The Hi-C libraries were prepared as previously described (PMID:22652625).

tag: cell line


title: E11.5 heart, Input

description: Input

source_name: E11.5 heart, Input


title: RQQ8 TREG


title: Adrenal Cooked 3

city: Palmyra

first: Joseph

last: Dever

state: WI

address: 1200 W Royal Lee Dr.

institute: Standard Process

data_processing:
Base calls performed using Off-Line Basecaller software (OLB V1.8.0)
3’ adapter sequences were trimmed from clean reads (reads that passed Solexa CHASTITY quality filter) and the reads shorter than 15nt were discarded
3’-adapter-trimmed-reads (>= 15nt) were aligned to the latest known cow and human reference miRNA precursor set (Sanger miRBase 20) using Novoalign (v2.07.11)
Reads (counts < 2) were discarded when calculating the miRNA expression.
In order to characterize the isomiR variability, any sequence that matched the miRNA precursors in the mature miRNA region ±4nt (no more than one mismatch) were accepted as mature miRNA isomiRs, which were grouped according to the 5-prime (5p) or 3-prime (3p) arm of the precursor hairpin
Genome_build: miRBase 20
Supplementary_files_format_and_content: raw and normalized (tpm) read counts for cow and human miRNAs.

organism: Bos taurus

source_name: Adrenal

extract_protocol:
Total RNA was extracted from each raw (100 mg), cooked (100 mg), and dried tissue (25 mg) using the mirVana™ miRNA Isolation Kit (Life Technologies, Carlsbad, CA) based on the manufacturer’s instructions.
Libraries were preparred via 1) 3'-adapter ligation with T4 RNA ligase 2 (truncated); 2) 5'-adapter ligation with T4 RNA ligase; 3) cDNA synthesis with RT primer; 4) PCR amplification; 5) extraction and purification of ~135-155 bp PCR amplified fragments (correspond to ~15-35 nt small RNAs) from the PAGE gel. The completed library was captured on an Illumina flow cell, amplified in situ, and finally sequenced for 36 cycles on Illumina HiSeq® 2000 according to manufacturer's instructions

value: Adrenal


title: Adrenal Raw 3


title: Adrenal Raw 1


title: Adrenal Extract 2


title: Adrenal Extract 1


title: CD4SP_UtxKO

value: Mature CD4 SP Thymocytes

value: Kdm6af/f Cd4-Cre+


title: Adrenal Cooked 2


title: Adrenal Extract 3


title: Adrenal Raw 2


title: Heart Extract 3

source_name: Heart

value: Heart


title: Heart Cooked 2


title: Heart Cooked 1


title: Heart Raw 2


title: Heart Raw 1


title: Heart Extract 2


title: Sirloin Cooked 3

source_name: Top Sirloin

value: muscle


title: Sirloin Cooked 2


title: Heart Extract 1


title: MCF-10A Hi-C

data_processing:
Library strategy: HiC-Seq
The Hi-C data were mapped with Bowtie and  binned at 6.5Mb, 1Mb, 250kb, 100kb and 40kb non-overlapping genomic intervals.  Iterative mapping and correction of Hi-C data were performed as previously described (Imakaev et al. 2012).  Biological replicates showed high reproducibility (Pearson's correlation coefficient > 0.9 for 1Mb resolution data).  Similarly, the first eigenvector comparison of the replicates showed high reproducibility.  For the downstream analyses, sequences obtained from both biological replicates were pooled and ICE-corrected to serve as a combined dataset.
Compartment analysis: First, the z-scores of the interaction matrices at 250kb resolution were generated as described previously (Lieberman, 2009).  Then, Pearson Correlation on the Z-score matrices was calculated.  By performing principal component analysis (Lieberman-Aiden et al. 2009; Zhang et al. 2012), the first eigenvector typically represents the compartment profile(Lieberman-Aiden et al. 2009), where the positive and negative 1st eigenvalues represent different compartments.   Gene density for each compartment was calculated to call the “A” and “B” compartmentalization.
TAD Calling: TAD calling was performed as calculating the “insulation” score of each bin using the 40kb resolution combined Hi-C data (as previously described.  The mean of the interactions across each bin were calculated.  By sliding a 1Mb x 1Mb (25bins x 25bins) square along the diagonal of the interaction matrix for every chromosome, we obtained the “insulation score” of the interaction matrix.  Valleys in the insulation score indicated the depletion of Hi-C interactions occurring across a bin.  These 40kb valleys represent the TAD boundaries.  Based on the variation of boundaries between replicates, we chose to add a total of 160kb (80kb to each side) to the boundary to account for replicate variation.  The final boundaries span a 200kb region. All boundaries with a boundary strength < 0.15 were excluded as they were considered weak and non-reproducible.  The insulation plots for the biological replicates showed high reproducibility (Pearson correlation coefficient = 0.80 for MCF-7 and 0.90 for MCF-10A replicates), suggesting the robustness of the method.  Similarly, the overlap of detected boundaries also showed high reproducibility between the biological replicates (~85% TAD boundary overlap for MCF-7 and ~91% for MCF-10A).  Therefore, we used the combined Hi-C replicates for the TAD analyses.
Z-Score Calculation: We modeled the overall Hi-C decay with distance using a modified LOWESS method (alpha = 1%, IQR filter), as described previously (Sanyal et al. 2012).  LOWESS calculates the weighted-average and weighted-standard deviation for every genomic distance and therefore normalizes for genomic distance signal bias.
Genome_build: hg19
Supplementary_files_format_and_content: Hi-C: tar ball archive of all normalized/corrected Hi-C data matrices binned at 40kb/250kb/1Mb, TAD boundaries at 40kb and genomic compartments at 250kb resolution

source_name: Mammary epithelial cell line


title: Sirloin Raw 3


title: Sirloin Cooked 1


title: Sirloin Raw 2


title: GO2

city: Cambridge

first: Gavin

last: Kelsey

address: Babraham Research Campus

institute: The Babraham Institute

data_processing:
Raw reads were trimmed to remove both poor quality calls and adapters using TrimGalore v0.2.8 and mapped to the mouse genome (GRCm38 assembly) using TopHat v2.0.9 (option –g 1).
Genome_build: GRCm38
Supplementary_files_format_and_content: Read counts (RPKM-like) RNA-Seq data file is comma delimited and contain the following columns: (1) Gene ID (Ensembl),(2) Chrromosome,(3) Start,(4) End,(5) Strand,(6-9) Sample Read Counts. The values were corrected for the length

source_name: Growing oocytes

extract_protocol:
Oocytes were collected from 5-20-days old C57BL/6Babr mice and RNA was extracted using TRIsure reagent (Bioline) followed by RNA Clean & Concentrator (Zymo Research) with on-column DNAse treatment (RNase-free DNase I, Life Technologies).  Ribosomal RNA was depleted from total RNA using Ribo-Zero Magnetic Kit (Human/Mouse/Rat – Low Input, Epicentre
Libraries from samples GO1 and GO2 were prepared using ScriptSeq v2 RNA-seq Library Preparation Kit (Epicentre). To generate sequencing libraries from samples NGO and FGO oocytes reverse transcription was performed using SuperScript III (Life Technologies), followed by second DNA strand synthesis using dUTPs instead of dTTPs and DNA polymerase I (NEB); libraries were constructed using the NEBNext DNA Library Prep Master Mix Set for Illumina (NEB), including dUTPs excision step by USER Enzyme (NEB) before PCR.

tag: background strain

value: Oocytes

value: Wild-type


title: Adrenal Cooked 1


title: RLI8 CD4

value: SIV positive

value: 24 weeks post infection

value: BULK CD4


title: 8pDOX_chip_h3k27me3

city: Vancouver

first: Carolyn

last: Brown

state: BC

address: 2350 Health Sciences Mall

department: Medical Genetics

country: Canada

institute: University of British Columbia

description: Single-end 36bp reads

data_processing:
Fastq reads from RNA-seq were mapped to hg18 using Tophat with UCSC hg18 gene annotations, outputting only uniquely mapped reads.
FPKM values were obtained through Cufflinks.
Fastq reads from ChIP-seq were mapped to hg18 using Bowtie, keeping only uniquely mapped reads. PCR-duplicates were excluded.
ChIP-seq bam files were analyzed using SeqMonk to obtain normalized levels of H3K27ac and H3K27me3. Read Count Quantitation was done using All Reads and correcting for total count per million reads. Sites pertaining to the higest and lowest 5% in the input samples were excluded in the analysis.
Genome_build: hg18
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each gene in each RNA-seq samples; and RPM values for H3K27ac and H3K27me3 levels in 1Mb windows for each ChIP-seq samples.

source_name: fibroscarcoma cell line HT1080

extract_protocol:
ChIP was done as previous (Hawkins et al.,Cell stem cell 2010, 6(5):479-491) , using 20ug of chromatin and 3ug of antibody was used per IP
ChIP library was prepared according to Illumina protocol with modifications according to Hawkins et al.,Cell stem cell 2010, 6(5):479-491.

tag: dox treatment

value: 5day DOX

tag: antibody

value: H3K27me3 (Active Motif 61017)

tag: integration


title: GO1


title: 8pND_chip_h3k27me3

description: Single-end 36bp reads

value: No DOX


title: Heart Cooked 3


title: 8pDOX_chip_h3k27ac

description: Single-end 36bp reads

value: H3K27ac (Active Motif 39133)


title: 8pDOX_chip_input

description: Single-end 36bp reads


title: NGO

source_name: Non-growing oocytes


title: Heart Raw 3


title: 8pND_chip_h3k27ac

description: Single-end 36bp reads


title: 8pDOX2_XIST_rna

description:
Paired-end 50bp reads
FPKM_genes_all.txt

extract_protocol:
Total RNA was extracted using Trizol.
PolyA-selected RNA library was constructed with Illumina TruSeq RNA Sample Prep Kit. Strand-specificity was achieved through modifications of the manufacturer's protocol, as previously done in Xie eti al., Cell, 153(5):1134-1148.


title: Pomc fast rep4

city: Ashburn

first: Ken

last: Sugino

state: VA

address: 19700 Helix Dr

institute: Janelia Research Campus

data_processing:
Illumina Casava and BCL2FASTQ1.8.3 were used for basecalling
Sequenced reads were trimmed for NuGEN and Illumina adaptor sequences using cutadapt v1.7.1 with parameters --overlap=7 --minimum-length=30. Ribosomal RNA, mitochondrial and phiX sequences were filtered using bowtie2 v2.1.0 with default parameters. Remaining reads were then mapped to mm10 genome using STAR v2.4.0i with parameters  --chimSegmentMin 15 --outFilterMismatchNmax 3.
Uniquely mapped reads were assigned to genes using HTSeq v0.6.1p1 with parameter -s no -m intersection-nonempty and using EncodeGencodeVM4Basic annotation. FPKM for a gene was calculated by dividing assigned count by the sum of lengths of all exons belonging to the gene.
Genome_build: mm10
Supplementary_files_format_and_content: tab deliminated files include TPM values and raw counts for each sample

source_name: Hypothalamus, arcuate nucleus

extract_protocol:
Hypothalamus arcuate nucleus was sliced, digested with pronase for 1 hour at RT, triturated and GFP labeled cells were sorted manually. RNA was extracted using PicoPure kit (life technologies, KIT0204).
Extracted RNA was amplified using Ovation RNA-Seq System V2 (NuGEN, #7102). 1~1.5 ug of the amplified material was used for library construction using Encore NGS Multiplex System (NuGEN, #0314).

treatment_protocol: For both fast and fed conditions, each animal was separated into a fresh cage 24 hours before experiment. For fast condition, only water was provided. For fed condition, food was provided ad libitum.

value: Pomc-GFP

value: Hypothalamus arcuate nucleus

tag: neuron type

value: POMC

tag: condition

value: 24hr fasted

tag: age

value: postnatal day 54

tag: Sex

value: M

tag: weight_before (g; right before 24hr fasting)

tag: weight (g; right before sacrifice)

tag: num_cells (number of sorted cells in the sample)

tag: ercc5 (10^-5 dilution of ercc in ul)


title: 8pND_chip_input

description: Single-end 36bp reads


title: 8pND_XIST_rna


title: Sirloin Raw 1


title: 1pDOX_vector_rna


title: FGO

source_name: GV oocytes

tag: genotype


title: Pomc fed rep4

tag: strain

value: control

value: postnatal day 56


title: Pomc fast rep1

value: postnatal day 55


title: Pomc fast rep3


title: Pomc fast rep2


title: Pomc fed rep5


title: 8pDOX1_XIST_rna


title: Pomc fed rep2

value: postnatal day 51


title: Pomc fed rep1


title: Agrp fast rep6

value: NPY-hrGFP

value: AGRP


title: Pomc fed rep3


title: 1pDOX4_XIST_rna


title: Agrp fast rep2

value: postnatal day 47


title: Agrp fast rep5


title: Agrp fed rep4

value: postnatal day 46


title: Pineal-Day Tissue for pineal/mixed comparison

city: Rockville

first: Stephen

middle: William

last: Hartley

address: 5625 Fishers Lane

department: Cancer Genetics and Comparative Genomics Branch

institute: NHGRI, NIH

data_processing:
Initial processing (base calling, etc) by RTA version 1.17.21.3 and CASAVA 1.8.2
Alignment via RNA-STAR v2.3.1y, using the Ensembl RGSC3.4.69 transcript annotation
Quality control checks and gene counts via QoRTs, v0.0.23, using the Ensembl RGSC3.4.69 transcript annotation, "union" rule
Differential Expression analysis via DESeq2, R version 3.0.2, DESeq2 version 1.2.10
Genome_build: rn4
Supplementary_files_format_and_content: Tab delimited read-pair counts for each sample, generated via QoRTs. These use the "union" rule, and the methods are identical to those implemented by HTSeq.
Supplementary_files_format_and_content: tab delimited RPKM counts for each sample, calculated from the read counts. NOTE: these values are actual read pair counts per million, per kilobase, not estimates of RPKM generated using a more-advanced normalization method. For most purposes, raw counts and/or geometric or TMM normalization should be used for comparisons between samples.

organism: Rattus norvegicus

source_name: pineal gland

extract_protocol:
Total RNA was extracted with TRIzol reagent (Invitrogen, Carlsbad, CA), followed by clean-up using an RNeasy Micro Kit with on-column DNase treatment as per the manufacture’s protocol (Qiagen, Valencia, CA). The amount and quality of RNA were determined using a NanoDrop spectrophotometer (NanoDrop, Wilmington, DE) and an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Each pool yielded 2.1 to 3.7 micrograms of total RNA (RIN values > 9).
Stranded RNA-seq libraries were constructed from 0.7-1 µg total RNA using the TruSeq Stranded Total RNA Sample Prep Kits (Illumina cat. no. RS-122-2301) according to manufacturer’s instructions.

treatment_protocol: Other than the 3 samples for the pineal/mixed-tissue comparison, all conditions had 3 biological replicates. For the in-vivo data, there were 8 biological conditions: two time points (Day and Night) for each of four  surgical groups: Control (Ctrl) Sham-surgery (Sham), Decentralized (DCN), and Ganglionectomized (SCGX). For the in-vitro data there were 3 biological conditions: Untreated control (CN), DBcAMP-treated (DB), and Norepinephrine-treated (NE). Additionally, 3 samples were used to compare pineal tissue to mixed tissue: Pineal-Day (SD1), Pineal-Night (SN2), and Mixed-Tissue (SS3).

value: Sprague-Dawley

tag: experiment type

value: in-vivo

value: pineal gland

tag: time-point

value: Day

tag: surgical condition

tag: treatment condition


title: Mixed Tissue for pineal/mixed comparison

source_name: mixed-tissue

tag: tissue

value: mixed-tissue


title: Pomc fast rep5

value: Pomc-GFP

value: Hypothalamus arcuate nucleus

tag: background strain

value: POMC


title: Agrp fed rep3

value: M


title: Agrp fed rep2

value: control


title: Agrp fed rep1


title: Pineal-Night Tissue for pineal/mixed comparison

value: Night


title: Agrp fast rep4

value: 24hr fasted

value: postnatal day 55


title: Agrp fed rep5

value: NPY-hrGFP


title: pB1.3G input DNA

first: Xin

last: Ye

state: MA

address: 9 Cambridge Center

department: Whitehead Institute

institute: Whitehead Institute

description:
TGACCA
pB1.3G

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Aligned sequences were processed with MACS 1.4.2 with parameters -w -S --space=50 --keep-dup=auto -p 1e-9. Counts were normalized to reads per million.
Genome_build: mm10
Supplementary_files_format_and_content: bed files of the peaks

source_name: PyMT_high Snail expression

growth_protocol: Cells were grown in DMEM/F12 + 5% adult bovine serum + Non-essential amino acide + Pen/Strep

extract_protocol:
the cells were cross-linked with 1% formaldehyde for 10 min at room temperature, and formaldehyde was then inactivated by the addition of 125mM glycine. Cells were lysed, and genomic DNA sonicated to generate DNA fragments that are about 200-500bp
Illumina True-Seq Lirary Prep Kit

tag: cell line

value: MMTV-PyMT breast cancer cell line

tag: genotype/variation

value: Mesenchymal cell with high Snail expression


title: 12qDOX2A_XIST_rna

tag: dox treatment

value: 5day DOX

tag: antibody

tag: integration


title: Agrp fast rep1

tag: neuron type

value: AGRP

tag: condition

tag: age

value: postnatal day 47

tag: Sex

tag: weight_before (g; right before 24hr fasting)


title: Depleted BUD31, replicate 1

status: Public on Sep 03 2015

city: Houston

first: Chad

middle: A.

last: Shaw

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: BCM

description:
Sample name: 6-LowBUD31
rRNA-depleted RNA

data_processing:
RNA-seq NGS reads were mapped using STAR RNASeq aligner (version 2.3.1). In order to improve mapping accuracy, splice junctions’ database file (gencode.v.14.annotation.gtf.sjdb) was supplied at the genome index generation step with command line option –sjdbOverhang 74 together with hg19_Gencode14.overhang75/hg19_chrOnly.fa and default parameters. Duplicate reads were marked with the MarkDuplicates function of the Picard-tools software package (version 1.107) using default settings.
Duplicates were marked for each sample, using picard-tools-1.107.
Intron-exon junctions were obtained using the University of California Santa Cruz Genome Browser “knownGene” table (downloaded 06/04/2014). Constitutive junctions were defined as junctions that 1) appeared in each transcript annotated to a given gene symbol and 2) did not overlap with any transcript annotated to a different gene symbol and 3) failed to mark the start or stop of a transcript
We used R together with the Rsamtools package to calculate intron retention (IR). Briefly, for each intron-exon junction, we extracted all non-duplicate reads overlapping this junction. Next, we assigned these reads into two categories: 1) “intronic” if the read mapped to at least the first base of the intron, 2) “exonic” if none of the bases of the read mapped to the first base of the intron. We counted the total number of reads assigned into each category for each junction. IR was calculated as described in the paper.
Genome_build: hg19
Supplementary_files_format_and_content: [IntronRetentionScores.txt] Tab-delimited text file containing intron retention scores, where rows correspond to junctions and column correspond to samples.

source_name: MYC-ER HMECs with dox-inducible shBUD31

growth_protocol: Immortalized mammary epithelial cells are grown in 6cm plastic plates in MEGM medium (Lonza).

extract_protocol:
Total RNA was isolated using the Rneasy kit (Qiagen).
RNA samples were rRNA depleted, and RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MYC-ER HMECs with dox-inducible shBUD31 (pINDUCER-shBUD31-3'UTR) were cultured for 72 hours -/+ 16 ng/ml doxycycline and 48 hours -/+ 300 nM tamoxifen in triplicates.

tag: cell type

value: Immortalized mammary epithelial cell

tag: passages

value: Depleted BUD31


title: inVivo, SCGX, DAY, Sample 1

tag: strain

value: Sprague-Dawley

tag: experiment type

value: in-vivo

value: pineal gland

tag: time-point

value: Day

value: SCGX


title: Agrp fast rep3

tag: tissue

value: Hypothalamus arcuate nucleus

value: M

tag: weight (g; right before sacrifice)

tag: num_cells (number of sorted cells in the sample)

tag: ercc5 (10^-5 dilution of ercc in ul)


title: inVivo, SCGX, DAY, Sample 2

tag: surgical condition

tag: treatment condition


title: inVivo, SCGX, NIGHT, Sample 1

value: Night


title: pB1.1G input DNA

description:
CGATGT
pB1.1G

source_name: PyMT_high Slug expression

tag: cell line

tag: genotype/variation

value: epithelial cell with high Slug expression


title: inVivo, SCGX, NIGHT, Sample 2


title: inVivo, DCN, NIGHT, Sample 2

value: DCN


title: inVivo, SHAM, DAY, Sample 2

value: SHAM


title: inVivo, SHAM, NIGHT, Sample 2


title: inVivo, SHAM, NIGHT, Sample 1


title: inVivo, SHAM, DAY, Sample 3


title: inVivo, DCN, NIGHT, Sample 1


title: inVivo, DCN, NIGHT, Sample 3


title: inVivo, DCN, DAY, Sample 2


title: inVivo, DCN, DAY, Sample 3


title: inVivo, SCGX, NIGHT, Sample 3


title: inVivo, CTRL, NIGHT, Sample 3

value: CONTROL


title: inVivo, SHAM, NIGHT, Sample 3


title: inVivo, DCN, DAY, Sample 1


title: inVivo, CTRL, NIGHT, Sample 1


title: inVivo, CTRL, DAY, Sample 3


title: inVivo, SCGX, DAY, Sample 3


title: inVivo, SHAM, DAY, Sample 1


title: In Vitro, NE-treated, Sample 3

value: in-vitro

value: NE treated


title: In Vitro, DBcAMP-treated, Sample 2

value: DBcAMP treated


title: In Vitro, Untreated, Sample 3

value: Untreated Control


title: In Vitro, DBcAMP-treated, Sample 1


title: In Vitro, Untreated, Sample 2


title: inVivo, CTRL, DAY, Sample 1


title: In Vitro, NE-treated, Sample 1


title: In Vitro, NE-treated, Sample 2


title: inVivo, CTRL, DAY, Sample 2


title: In Vitro, DBcAMP-treated, Sample 3


title: In Vitro, Untreated, Sample 1


title: male miRNA

city: Hangzhou

first: Li

last: Qin

state: Zhejiang

address: No. 866, Yuhangtang Road

department: Horticulture

country: China

institute: Zhejiang University

data_processing:
A proprietary pipeline script, ACGT101-miR v4.2 (LC Sciences), was used for sequencing data analysis (Li et al. 2010; Wei et al. 2011). A Public software package, CleaveLand3.0 was used for analyzing degradome sequencing data.
Genome_build: EST
Supplementary_files_format_and_content: xls, miRNAs with its expression level in male and female individuals, miRNAs with its predicted targets

organism: Asparagus officinalis

source_name: asparagus plant

extract_protocol:
Total RNAs of each organ were extracted according to LC science TKR-1001. The quantity and quality of total RNAs were assayed with the NanoDrop ND-1000 spectrophotometer (Nano Drop). Equal amounts of total RNA from each organ were pooled to obtain the RNA of male and female plants. The sRNA fractions between 10-55 nt were isolated from the total RNA pool with a Novex 15% TBE-Urea gel (Invitrogen, USA).
Small RNA libraries were constructed using the IlluminaTruseq Small RNA Preparation kit according to the manufacturer’s protocol. The total RNA from different organs of male and female asparagus plants was equally mixed and used to construct the degradome library following the method described in Ma et al (2010)

value: three-year-old

value: leaves, roots, stems and flowers

tag: condition

value: green house

tag: gender

value: male


title: MCF7_RNA-Seq_R1

city: Burlington

first: Jonathan

middle: AR

last: Gordon

state: VT

address: 89 Beaumont Ave Given E209

department: Biochemistry

institute: University of Vermont

description:
MCF7 SAMPLE 1
Processed data file: MCF7_MCF10A_RSEM_expectedcounts.txt
Processed data file: DeSeq2_MCF7_vs_MCF10A_foldchange.txt

data_processing:
Remove adapter reads (Cutadapt v1.6).
Trim low-quality base calls from both ends. Min score >= 15, window of 10 step size of 1. (FASTQ Quality Trimmer 1.0.0).
The reads were aligned to a transcriptome and quantified using RSEM v1.2.7, genes with very low expression (<10 expected counts) were removed from the analysis.
Differential gene expression was calculated by using the Deseq2 version 1.4.5 package in R 3.1.0 using the mean value of gene-wise dispersion estimates.
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: MCF7_MCF10A_RSEM_expectedcounts.txt: Tab-delimited table showing the expected counts from the RSEM quantification.
Supplementary_files_format_and_content: DeSeq2_MCF7_vs_MCF10A_foldchange.txt: Tab-delimited table showing the log2FC for all genes from DeSeq2 v1.4.5 analysis.

source_name: MCF7 mammary gland/breast epithelial cells

growth_protocol: MCF10a cells were grown in DMEM: F12 (Hyclone-SH30271), 5% (v/v) horse serum (Gibco #16050 lot #1075876) + 10ug/ml human insulin (Sigma I-1882) + 20ng/ml recombinant hEGF (Peprotech AF-100-15) + 100ng/ml Cholera toxin (Sigma C-8052) + 0.5 ug/ml Hydrocortisone (Sigma H-0888) Pen/Strep (Life Technologies) and Glutamine (Life Technologies). MCF-7 cells were grown in DMEM (Corning Mediatech 10-017). 10% Fetal Bovin Serum (Atlanta-S11550 lot#H1030) Pen/Strep (Life Technologies) and Glutamine (Life Technologies).

extract_protocol:
Total RNA was isolated from Trizol using Direct-zol RNA mini-prep kit (Zymo Research #R2050) with DNaseI digestion.
RNA libraries were prepared for sequencing with the TruSeq Stranded Total RNA with Ribo-Zero Gold kit using standard Illumina protocols with the exception that library amplification was performed using KAPA HiFi™ Real-Time PCR Library Amplification Kit (Kapa Biosystems #KK2701). Illumina Barcodes used: MCF10A_sample1_AR002; MCF10A_sample2_AR004; MCF10A_sample3_AR001; MCF7_Sample1_AR002; MCF7_Sample2_AR004; MCF7_Sample2_AR005

treatment_protocol: Cells were seeded at 1.5x10^6 cells per 100 mm dish and grown to 80% confluence. Cells were washed twice with phosphate-buffered saline (PBS) and stored in TRIzol at -80C.

tag: atcc id

value: ATCC HTB-22

tag: tissue derivation

value: breast

value: metastatic site derived

tag: neoplasia type

value: adenocarcinoma


title: pBl.1G Slug ChIP

description:
ATCACG
pBl.1G

value: MMTV-PyMT breast cancer cell line

tag: chip antibody

value: Slug (C19G7) Rabbit mAb

tag: chip antibody vendor

value: Cell Signalling Technology

tag: chip antibody cat. #


title: MCF7_RNA-Seq_R2

description:
MCF7 SAMPLE 2
Processed data file: MCF7_MCF10A_RSEM_expectedcounts.txt
Processed data file: DeSeq2_MCF7_vs_MCF10A_foldchange.txt

tag: cell type


title: degradome

data_processing:
Library strategy: degradome-seq
A proprietary pipeline script, ACGT101-miR v4.2 (LC Sciences), was used for sequencing data analysis (Li et al. 2010; Wei et al. 2011). A Public software package, CleaveLand3.0 was used for analyzing degradome sequencing data.
Genome_build: EST
Supplementary_files_format_and_content: xls, miRNAs with its expression level in male and female individuals, miRNAs with its predicted targets

tag: age

tag: tissue

value: pooled male and female


title: female miRNA

value: female


title: MCF7_RNA-Seq_R3

description:
MCF7 SAMPLE 3
Processed data file: MCF7_MCF10A_RSEM_expectedcounts.txt
Processed data file: DeSeq2_MCF7_vs_MCF10A_foldchange.txt


title: pBl.3G Snail ChIP

description:
TTAGGC
pBl.3G

value: Mesenchymal cell with high Snail expression

value: Anti-SNAIL + SLUG antibody

value: abcam


title: MCF10A_RNA-Seq_R3

description:
MCF10A SAMPLE 3
Processed data file: MCF7_MCF10A_RSEM_expectedcounts.txt
Processed data file: DeSeq2_MCF7_vs_MCF10A_foldchange.txt

source_name: MCF10A mammary gland/breast epithelial cells

value: ATCC CRL-10317

value: luminal ductal cells

value: fibrocystic disease


title: inVivo, CTRL, NIGHT, Sample 2

tag: strain

value: Sprague-Dawley

tag: experiment type

value: in-vivo

value: pineal gland

tag: time-point

value: Night

value: CONTROL


title: Spruce_stem

city: Guangzhou

first: Rui

last: Xia

state: Guangdong

address: 483 Wushan Rd, Tianhe

institute: South China Agricultural University

description: small RNAs

data_processing:
Fastx toolkit was used for data pre-processing. Original .fastq files were converted to .fasta files using fastq_to_fasta command (fastq_to_fasta -v -r -i INPUT_FILE.fastq -o OUTPUT_FILE.fasta -Q 33);
Adaptor was trimmed using the fastx_clipper (fastx_clipper -a "TGGAATTCTCGGGTGCCAAGG" -c -v -i INPUT_FILE.fasta -o OUTPUT_FILE -l 15);
Trimmed read file was collapsed into tag_count file using fastx_collapser (fastx_collapser -i INPUT_FILE -o OUTPUT_FILE);
Collapsed reads were mapped to reference genome by Patman.
Genome_build: Pabies 1.0 (http://congenie.org/)
Supplementary_files_format_and_content: trimmed and collapsed read file in a tag_count formate. Only 18-21 nt long sRNAs were collected. In the .txt file, each row has two columns. The first column is a small RNA sequence, and the second column the read count of the sequence.

organism: Picea abies

source_name: Stem, from one-year old branches

growth_protocol: A Norway spruce tree in the University of Delaware Botanic  Gardens (Newark, Delaware, USA)

extract_protocol:
Total RNA was extracted from the four samples using the Purelink Plant RNA Reagent from Life Technologies (New York, USA) according to the manufacturer’s protocol.
PARE libraries were constructed as previously described in Zhai et al. (2014, Methods, 67:84-90) and sequenced on the Illumina HiSeq 2500 in the DNA Sequencing & Genotyping Center in the Delaware Biotechnology Institute (Newark, Delaware, USA).

tag: tissue type

value: stem


title: Spruce_needle

description: small RNAs

source_name: Needle, from one-year old branches

value: needle


title: MCF10A_RNA-Seq_R1

description:
MCF10A SAMPLE 1
Processed data file: MCF7_MCF10A_RSEM_expectedcounts.txt
Processed data file: DeSeq2_MCF7_vs_MCF10A_foldchange.txt

tag: cell line

value: breast


title: Spruce_mixed_tissue

description: small RNAs

source_name: Pooled samples, from one-year old branches

value: pooled


title: dt40 homozygous exon 8 deletion_rep1

status: Public on Sep 01 2015

city: Toronto

first: Serge

last: Gueroussov

state: Ontario

address: 160 College Street, Room 1030

department: Molecular Genetics

institute: University of Toronto

data_processing:
Splicing analysis: Detailed description of the analysis pipeline can be found in [Irimia et al. Cell 159, 1511-1523 (2014)]. A summary of the main steps is provided here. An RNA-Seq dataset is first aliged to the genome using Bowtie. Reads that map to the genome are discarded from further analysis since exon-exon junctions (EEJs) are absent from genomic sequence. Reads that failed to align to the genome are aligned to a custom library of EEJs using Bowtie. To quantify splicing, the combination of EEJs that define each splicing event was created. For the case of single exon skipping events, we generated EEJs for C1A, AC2 and C1C2 (A represents the alternative exon and C1 and C2 represent the neighboring constitutive exons), requiring a minimum of eight positions from each exon. For multi-exon events we generated all possible forward combinations from C1 to C2 exons. If multiple alternative 5’ and/or 3’ splice sites were associated with any alternative, C1 or C2 exons, they were also included in the combinations. Read counts for each EEJ were then used to calculate the Percent Spliced In (PSI) of each event. A  simplified format of the formula is: PSI = 100% * (reads supporting inclusion / total reads).
Genome_build: Homo sapiens, hg19; Gallus gallus, galGal3
Supplementary_files_format_and_content: 293_all_splicing_events.tab: tab delimited text file summarizing the splicing analysis of 293 data, where each row corresponds to a unique splicing event. The table has the following columns: GENE - gene ID, EVENT - unique event ID containing the ENSEMBL gene ID, COORD - genomic coordinates of the alternative exon, LENGTH - nucleotide length of the alternative exon, FullCO - genomic coordinates of alternative exon as well as the coordinates of the last and first basepairs of the upstream and downstream exons, respectively, COMPLEX - refers to type of splicing event (S/C1/C2/C3: alternative cassette exon > 15 nucleotides, ME: mutually exclusive exons, Alt3: alternative 3´ splice site, Alt5: alternative 5´ splice site, MIC: alternative micro cassette exon ≤ 15 nucleotides), siCon+siCon2 - PSI in cells treated with control siRNA (2 replicates), KD+KD2 - PSI in cells treated with PTBP1 + PTBP2 siRNA (2 replicates), Resc_L+Resc_L2  - PSI in cells treated with PTBP1 + PTBP2 siRNA with overexpression of full-length PTBP1 (2 replicates), Resc_S+Resc_S2 - PSI in cells treated with PTBP1 + PTBP2 siRNA with overexpression of exon-skipped PTBP1 (2 replicates), siCon.Q+siCon2.Q+KD.Q+KD2.Q+Resc_L.Q+Resc_L2.Q+Resc_S.Q+Resc_S2.Q - quality scores for the corresponding PSI values, see  [Irimia et al. Cell 159, 1511-1523 (2014)] for details. // dt40_all_splicing_events.tab: tab delimited text file summarizing the splicing analysis of dt40 data, where each row corresponds to a unique splicing event. First 6 columns are the same as in 293_all_splicing_events.tab, WT1 + WT2 - PSI in wildtype cells (2 replicateS), HET34 + HET48 - PSI in cells with PTBP1 exon 8 delted from one allele (2 indepndent clones), HOM3 + HOM7 - PSI in cells with PTBP1 exon 8 deleted from both alleles (2 independent clones), WT1.Q+WT2.Q+HET34.Q+HET48.Q+HOM3.Q+HOM7.Q - quality scores for the corresponding PSI values, see  [Irimia et al. Cell 159, 1511-1523 (2014)] for details.

molecule: polyA RNA

organism: Gallus gallus

source_name: DT40-Cre1 pre-B-cell line

growth_protocol: Suspension growth in RPMI 1640 with penicillin and streptomycin, 50 μM β-mercaptoethanol, 3% chicken serum (Gibco), 7% bovine calf serum (Gibco), and 4 mM L-Glut

extract_protocol:
Total RNA was extracted from cultured cells using TRI reagent (Sigma).
Standard illumina protocol with DNAse treatment and polyA selection.

treatment_protocol: no treatment

tag: genotype

value: homozygous PTBP1 exon 8 deletion


title: dt40 heterozygous exon 8 deletion_rep2

value: heterozygous PTBP1 exon 8 deletion


title: dt40 homozygous exon 8 deletion_rep2


title: Spruce_bud

description: small RNAs

source_name: Bud, from one-year old branches

value: bud


title: dt40 wildtype_rep2

value: wildtype


title: MCF10A_RNA-Seq_R2

description:
MCF10A SAMPLE 2
Processed data file: MCF7_MCF10A_RSEM_expectedcounts.txt
Processed data file: DeSeq2_MCF7_vs_MCF10A_foldchange.txt


title: dt40 heterozygous exon 8 deletion_rep1


title: dt40 wildtype_rep1


title: Nt-ERβ_noE2_2

city: Baronissi

first: Antonio

last: Rinaldi

state: SA

address: Via Salvatore Allende, 1

department: Faculty of Medicine and Surgery

country: Italy

institute: University of Salerno

data_processing:
Basecalls was performed using CASAVA version 1.8
Sequenced reads were mapped to hg19 whole genome using Tophat v.2.0.10
Fragments Per Kilobase of exon per Million reads mapped (FPKM) were calculated using Cuffdiff v2.1.1
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Breast cancer cells

extract_protocol:
Total RNA was extracted from cell lines using the standard RNA Extraction method with TRI Reagent (Sigma) method
Indexed libraries were prepared from 1 µg/ea. of purified RNA with TruSeq Stranded total RNA Sample Prep Kit (Illumina) according to the manufacturer’s instructions

tag: cell cultures

value: (+EtOH -E2)

tag: treatment

value: hormone-starved


title: MCF-7_E2_3

value: estradiol stimulation


title: MCF-7_E2_1


title: MCF-7_noE2_3


title: MCF-7_E2_2


title: Nt-ERβ_noE2_3


title: MCF-7_noE2_1


title: Nt-ERβ_E2_1


title: Nt-ERβ_E2_3


title: Nt-ERβ_E2_2


title: Nt-ERβ_noE2_1


title: Ct-ERβ_noE2_1


title: Ct-ERβ_noE2_2


title: Ct-ERβ_E2_1


title: Ct-ERβ_E2_3


title: Ct-ERβ_E2_2


title: smn_rep2_RNA-seq

city: cambridge

first: David

middle: G

last: Hendrickson

address: 7 divinity ave

institute: Harvard University

data_processing:
Basecalls performed using CASAVA version 1.4
We aligned sequencing reads to human genome assembly hg19 and UCSC coding genes as a reference annotation (Harrow et al. 2012) using TopHat (Trapnell, Pachter, and Salzberg 2009)
We made significance calls smn mutant vs control  using  Cuffdiff 2 with the -u option
Genome_build: hg19
Supplementary_files_format_and_content: the tab-delimited text filescontains CuffDiff 2 generated p and q values with significance calls and FPKM estimates for each gene per condition

growth_protocol: human iPSC lines BJ-riPS (Warren et al., 2010) and 18a (Boulting et al., 2011), a Type I SMA patient-specific iPSC line (1-38G) were routinely cultured on Matrigel-coated dishes in MTeSR media (Stem Cell Technologies). MNs were differentiated as previously described (Amoroso et al., 2013)

extract_protocol:
Day 28 MN cultures were dissociated into single cells using Accutase, and fixed in 4% paraformaldehyde (PFA). Monoclonal HB9 (MNR2) antibody (Developmental Studies Hybridoma Bank 81.5C10) was diluted 1:100 in blocking buffer (1% BSA) and 0.2% saponin (Sigma) in RNase-free PBS supplemented with 50 U/ml Superase.In (Ambion), and incubated with the cell suspension for 3 hours at room temperature. AlexaFluor-488 conjugated secondary antibody was diluted 1:1000 in blocking buffer, and incubated with the cell suspension for 45 minutes at room temperature. The cells were then washed with DPBS several times before FACS on BD FACS Aria. Sorted cells were treated with RNase-free Proteinase K for an hour at 50 °C, before addition of Trizol LS (Invitrogen) for RNA extraction. DNase treatment using Turbo DNA-free (Ambion) was performed to remove contaminating genomic.
Illumina mRNA-seq libraries were prepared using the TruSeq RNA kit, using 200 ng of total RNA. RNA was differentially fragmented, DSN-Lite was used to remove rRNA-derived cDNA following reverse transcription (Adiconis et al., 2013).
total DSN-lite RNA-seq, paired end seq

treatment_protocol: To generate MNs, iPSCs were passaged using dispase (1 mg/ml), triturated into small clumps, and cultured in an embryoid body (EB) suspension in neural induction media consisting of 1 µM Dorsomorphin, 10 µM SB431542 (Chambers et al., 2009), and 5 µM ROCK inhibitor Y-27632 in N2B27 media (Ying et al., 2003) for 7 days. After which, the neuralized EBs were directed towards motor neuron differentiation in N2B27 media supplemented with 1 µM retinoic acid (Sigma), 1 µM Purmorphamine (Stemgent) and 1 µM Sonic Hedgehog Agonist (Calbiochem).  From day 14 to 21, the media was supplemented with 10 ng/ml BDNF and 10 ng/ml GDNF and to support neuronal differentiation. AraC treatment was pursued from day 18 to 23 to eliminate progenitor cells from the culture. The cells were then cultured in MN media consisting BDNF, GDNF and ascorbic acid until day 31.

tag: derived cell typed

value: motor neurons


title: control_rep2_RNA-seq

source_name: human iPSC line BJ-riPS

value: BJ-riPS


title: smn_rep1_RNA-seq

source_name: Type I SMA patient-specific iPSC line (1-38G)


title: control_rep1_RNA-seq


title: MCF-7_noE2_2


title: dcl1-2 dcl4-2 (rep2)

city: Cold Spring Harbor

first: Marja

last: Timmermans

state: NY

address: 1 Bungtown Rd

department: Plant Biology

institute: Cold Spring Harbor Laboratory

description: small RNA

data_processing:
The RNA adapter AGATCGGAAGAGCACACGTCT was removed from the 3' end, keeping trimmed reads greater than 15 nt
trimmed reads 18- to 26-nt in length were aligned to the maize B73 RefGen_v2 genome (release 5a.57) using Bowtie v1.0.0 (Langmead et al. 2009), allowing no mismatches and up to 20 potential alignments per read
Reads matching known structural RNAs (rRNAs, tRNAs, sn-RNAs and sno-RNAs) from Rfam 10.0 (Griffiths-Jones et al. 2005) were removed from further analysis
Read counts were normalized by millions of mapped reads in each library (reads per million) for comparisons across samples.
Genome_build: B73 RefGen_v2 genome (release 5a)
Supplementary_files_format_and_content: tab-delimited txt files with normalized (rpm) small RNA abundance (21-24nt) for ta-siRNA, tasiR-ARF and siRNA derived from arf3 loci

organism: Zea mays

source_name: imbibed kernels

growth_protocol: mature kernels were imbibed for 24 hrs in water, then embryos were dissected and flash frozen in liquid nitrogen

extract_protocol:
Total RNA was extracted from embryos of 24 hr imbibed kernels using TRIzol reagent (Invitrogen). Small RNA libraries were prepared from 1 μg of total RNA using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 24 hr imbibed seed

value: embryo

tag: background


title: dcl1-2 dcl4-3 (rep2)

description: small RNA


title: dcl1-2 dcl4-3 (rep1)

description: small RNA


title: dcl4-2 (rep2)

description: small RNA


title: dcl1-2 dcl4-2 (rep1)

description: small RNA


title: dcl4-3 (rep2)

description: small RNA


title: Ct-ERβ_noE2_3


title: dcl4-3 (rep1)

description: small RNA


title: dcl1-2 (rep2)

description: small RNA


title: BicR DHT + Bicaltamide 24h

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

country: Japan

institute: Tokyo Metropolitan Institute of Gerontology

description: processed data file: CAGE_LNCaP_BicR.txt

data_processing:
Filter out artificial sequences from SMS file using heliscope filterSMS command. heliscope version is 1.0.389.154.
Convert SMS to FASTA format using heliscope sms2txt command. heliscope version is 1.0.389.154.
Remove sequences that match to rRNA references up to [error] errors. rRNAdust version is 1.00.
Mapped to hg19. Gene expression was measured with the number of reads aligned within a 500 bp distance from the RefSeq transcript 5′ ends, where their genomic coordinates were downloaded from the UCSC Genome Browser database.
The read counts were normalized to tags per million (tpm) based on the total number of aligned reads in the human genome reference. All CAGE tags with one or more overlapping base pair were grouped on the same strand into a single tag cluster (TC).
Genome_build: hg19
Supplementary_files_format_and_content: Excel data file  including tpm of each TC for each sample

source_name: prostate cancer cells

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

extract_protocol:
Total RNA was extracted using ISOGEN reagent.
First strand cDNA was produced using Superscript III (Invitrogen).  We chose AMPure RNAClean XP (Beckman Coulter) for the purification of RNA/DNA hybrids. After biotynation, the cap-trapping process, quality control was performed by measuring concentration (Oligreen). Poly-A tailing/blocking is carried out prior to HeliScope sequencing according to the instructions found in the HeliScope(TM) Low-Volume Sample Loading Protocol (LB-017 Rev. 01). .

treatment_protocol: Cells were treated with vehicle or R1881 10 nM for 24 h.

value: BicR

value: prostate cancer

value: DHT 10 nM + Bicalutamide 1μM 24h


title: BicR DHT  6h

value: DHT 10 nM treatment 6h


title: dcl1-2 (rep1)

description: small RNA


title: wt (rep2)

description: small RNA


title: wt (rep1)

description: small RNA


title: BicR Bicaltamide 24h

value: Bicalutamide 1μM 24h


title: BicR DHT 24h

value: DHT 10 nM treatment 24h


title: LNCaP DHT + Bicaltamide 24h

value: LNCaP


title: BicR Ethanol 24h

value: Ethanol treatment 24h


title: LNCaP DHT 24h


title: BicR DHT + Bicaltamide 6h

value: DHT 10 nM + Bicalutamide 1μM 6h


title: BicR Bicaltamide 6h

value: Bicalutamide 1μM 6h


title: dcl4-2 (rep1)

description: small RNA


title: BicR Ethanol 6h

value: Ethanol treatment 6h


title: LNCaP Bicaltamide 6h


title: LNCaP Bicaltamide 24h


title: LNCaP DHT 6h


title: LNCaP DHT + Bicaltamide 6h


title: LNCaP Ethanol 24h


title: LNCaP 72h rep2

description: processed data file: LNCaP_R1881.txt


title: LNCaP 0h

value: before treatment


title: LNCaP 48h rep2

description: processed data file: LNCaP_R1881.txt


title: LNCaP Ethanol  6h


title: LNCaP 18h rep2

description: processed data file: LNCaP_R1881.txt


title: LNCaP 12h rep2

description: processed data file: LNCaP_R1881.txt


title: LNCaP 0h rep2

description: processed data file: LNCaP_R1881.txt


title: LNCaP 3h rep2

description: processed data file: LNCaP_R1881.txt


title: LNCaP 6h rep2

description: processed data file: LNCaP_R1881.txt


title: LNCaP 72h rep1

description: processed data file: LNCaP_R1881.txt


title: LNCaP 48h rep1

description: processed data file: LNCaP_R1881.txt


title: LNCaP 3h rep1

description: processed data file: LNCaP_R1881.txt


title: LNCaP 0h rep1

description: processed data file: LNCaP_R1881.txt


title: LNCaP 12h rep1

description: processed data file: LNCaP_R1881.txt


title: BicR 0h


title: LNCaP 18h rep1

description: processed data file: LNCaP_R1881.txt


title: DstuA

city: jinan

first: Zhang

last: Xiujun

state: shandong province

address: south road of shanda

institute: shandong university

data_processing:
Base-calling using Illumina Casava 1.8.
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence.
Reads were mapped to Penicillium oxalicum 114-2 coding sequences using SOAPaligner/SOAP2 v2.21 with parameters -m 0 -x 10000 -s 28 -l 32 -v 3 -p 3
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Genome_build: Penicillium oxalicum 114-2 sequences (NCBI accession: PRJNA60877)
Supplementary_files_format_and_content: all.gene.rpkm.txt with unique reads numbers, coverage and RPKM values for each genes. Samples were named according to the names of raw files.

organism: Penicillium oxalicum

source_name: mutant_fungal mycelia

growth_protocol: The conidia of Penicillium oxalicum were inoculated in modifeid Czapek culture medium with 2% glucose as carbon resource for 20 h at 30 °C as the pre-culture, and then mycelia were transferred and grown in the new medium for 48 h.

extract_protocol:
Total RNA was prepared from the mycelia by grinding under liquid nitrogen with a mortar and pestle, followed by extraction using the RNAisoTM reagent (TaKaRa, Japan) according to manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mycelia were filtered by filter paper.

tag: genotype/variation

value: stuA deletion

value: Fungal mycelia


title: DflbD

value: flbD deletion


title: DflbC

value: flbC deletion


title: Dswi6

value: swi6 deletion


title: DabaA

value: abaA deletion


title: DflbB

value: flbB deletion


title: DflbA

value: flbA deletion


title: M12

source_name: WT_fungal mycelia

value: M12 (wild type)


title: MB202_7

city: Columbus

first: Amy

last: Hite

state: OH - Ohio

address: 1800 Cannon Drive 250 Lincoln Tower

department: Biomedical Informatics

institute: The Ohio State University

data_processing:
Raw reads aligned using lifescope to hg19 reference genome containing IUPAC ambiguity codes for SNPs listed in dbSNP 135.
Whole gene and isoform expression generated by cufflinks version 2.1.1 using multiread correction and without effective length correction.  Whole gene expression estimated by summation of isoform expression of measurments with status "OK".
SNP calling was performed through samtools mpileup specifically for known heterozygous SNP locations confirmed by SNP chip genotyping generating allele counts.  These allele counts are used to make allelic expression ratio calculations.
Genome_build: hg19 with IUPAC codes for dbSNP 135

source_name: posterior putamen

extract_protocol:
Frozen brain tissue was homogenized in Trizol (Invitrogen/Life Technologies, Carlsbad, CA), and then phase separated with chloroform. The RNA containing aqueous layer was diluted in binding buffer and applied to Qiagen (Venlo, Limburg, Netherlands) or Denville (South Plainfield, NJ) RNA isolation columns. The bound RNA was DNAse treated and eluted according to kit procedures. Fifty nanograms of total RNA was converted to cDNA and isothermally amplified using the NuGen Ovation RNA-Seq kit procedures (NuGen, San Carlos, CA).
The NuGen brain cDNA was sheared to approximately 150 bp fragments using the Covaris S (Woburn, MA). After shearing, fragments were recovered by centrifuging over an YM-30 spin filter (Amicon, Merck Millipore, Billerica, MA). Fragments greater than 100 bp were retained and eluted from the membrane, with ~ 90% recovery. Bar-coded paired-end SOLiD sequencing libraries were prepared using either SOLiD (Applied Biosystems/Life Technologies, Carlsbad, CA) or NEB (New England Biolab, Ipswich, MA) DNA library preparation kits. The cDNA was end repaired, and then barcoded SOLiD DNA sequencing adaptors were ligated to 1 microgram of input cDNA according to kit instructions. Ligated library product was size selected using a Pippin gel electrophoresis system (Sage Biosciences, Beverly, MA). The prepared library was enriched for correctly adapted product using 5-8 cycles of PCR.

tag: individual

tag: smoker

value: nonsmoker

tag: Sex

value: male


title: MB202_9

source_name: raphae nuclei


title: MB202_8

source_name: cerebellum


title: MB202_3


title: MB202_6

source_name: hippocampus


title: MB202_5

source_name: amygdala


title: MB202_2


title: MB202_4

source_name: insula


title: LNCaP 6h rep1

description: processed data file: LNCaP_R1881.txt

value: LNCaP

tag: cell type

value: prostate cancer


title: MB197_9


title: MB202_1


title: MB197_8


title: MB160_8

value: smoker


title: MB197_1


title: MB197_7


title: MB197_4


title: MB160_7


title: MB197_5


title: MB160_6


title: MB197_3


title: MB160_3


title: MB160_1


title: MB197_2


title: MB160_5


title: DwetA

value: wetA deletion


title: MB148_7


title: MB148_9


title: MB148_8


title: MB148_4


title: MB148_5


title: MB197_6


title: DflbE

value: flbE deletion


title: MB148_6


title: MB148_2


title: MB148_1


title: MB147_9


title: MB160_2


title: MB160_4


title: MB147_6


title: MB147_7


title: MB147_3


title: MB147_5


title: MB147_8


title: MB147_2


title: MB147_1


title: MB100_8


title: MB100_9


title: MB100_7


title: MB100_4


title: MB100_3


title: MB100_2


title: MB059_9


title: MB059_8


title: MB059_7


title: MB059_1


title: MB059_3


title: MB059_2


title: MB059_5


title: MB059_6


title: MB059_4


title: MB100_5


title: MB148_10


title: MB151_10


title: MB148_3


title: MB100_6


title: MB202_10


title: MB147_10


title: MB197_10


title: MB052_10


title: MB160_10


title: LNCaP ChIPed by TET2

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

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

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. For 5-mC and 5-hmC immunoprecipitation, we used methycollector and hydroxymethylcollector (Active motif) to obtain double stranded DNA modified with 5-mC and 5-hmC.
The Chromatin immunoprecipitated DNA fragments (approx.10 ng in 30 µl water) are end repaired by using T4 DNA polymerase, Klenow DNA polymerase and T4 polynucleotide kinase in the presence of dNTPs. And an ‘A’ base is added to the 3’end of the blunt phosphorylated DNA fragments, using the polymerase activity of Klenow fragment. Then, adaptors (Adaptor oligo mix, Illumina) are ligated to the ends of the DNA fragments. The resulting DNA fragments are purified by MinElute column (QIAGEN).  300 ~ 500 bp DNA fragments are purified by using E-Gel SizeSelect agarose Gels (Invitrogen) according to manufacturer’s instruction.Size selected adaptor-modified DNA fragments are amplified by 18 cycles of PCR using Phusion polymerase and PCR primer 1.1 and 2.1 (Illumina). The resulting PCR products are purified by MinElute column (QIAGEN).

treatment_protocol: LNCaP and BicR cells were treated with vehicle or DHT 10 nM for 24 h or 1h.

value: no treatment

tag: chip antibody

value: TET2 (abcam ab94580)


title: LNCaP input

value: input


title: MB011_10


title: BicR Et input

value: BicR

value: ethanol


title: BicR Et ChIPed by AR

value: AR (santacruz H-280)


title: BicR DHT ChIPed by AcH3

value: DHT 10 nM

value: AcH3(Millipore #06-599)


title: MB147_4


title: MB100_1


title: BicR DHT input_2


title: BicR Bicaltamide ChIPed by AR

value: Bicalutamide 1 μM


title: BicR Bicaltamide input


title: Donor 3 - H3K27ac

city: Luxembourg

first: Lasse

last: Sinkkonen

address: 162a, Avenue de la Faiencerie

department: Life Sciences Research Unit

country: Luxembourg

institute: University of Luxembourg

description: ChIP-Seq analysis of H3K27ac

data_processing:
After sequencing the quality of the raw reads was controlled by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The reads that had a low quality base pair calling or that were detected as read artefacts were removed (requiring minimum quality score of phred 10 across the read length). Read stacks were collapsed using the FASTX software (http://hannonlab.cshl.edu/fastx_toolkit/index.html).
Reads were aligned with Bowtie v0.1.25 with one mismatch and maximum three locations in the genome allowed (from which the highest quality match was reported).
QuEST v.2.4 was used in order to identify enriched regions. The ChIP enrichment was set to 15 and the ChIP to background enrichment to 3.
Genome_build: hg19

source_name: Human macrophages differentiated from primary CD14+ monocytes

growth_protocol: Primary human monocytes were extracted from the blood samples of three anonymous healthy male donors, donated by the blood transfer centre of the Luxembourgish Red Cross and were used in agreement with the convention between the Luxembourgish Red Cross and the University of Luxembourg from 16.05 2011. Extraction from blood was done by using anti-CD14-antibodies conjugated with superparamagnetic particles {CD14 MicroBeads (Miltenyi Biotec)}, a magnet {MACS separator (Miltenyi Biotec)} and LS Columns (Miltenyi Biotec). After the successful isolation of the CD14+ monocytes, the cells were counted and seeded in a density of 2 million cells/ml on a 10 cm2 plates (about 20 million cells) (Thermo scientific) in order to perform ChIP experiments.For culturing and differentiation of monocytes to macrophages RPMI 1640 medium (VWR) was supplemented with 10% human serum {off the clot, type AB (A&E Scientific, PAA, Pasching, Austria, lot number: C02108-1021)}, 0.1 mg/ml streptomycin (Invitrogen, Life Technologies), 100 U/ml penicillin (Invitrogen, Life Technologies) and 0.1 mM L-glutamine (Invitrogen, Life Technologies). The cells were kept at 37°C under a 5% CO2 atmosphere. The medium was changed, during the differentiation process of monocytes to macrophages, 4 and 7 days after seeding.

extract_protocol:
In order to perform ChIP experiments the chromatin of day 11 cells was cross-linked for 8 min with 1% formaldehyde in PBS. Then the formaldehyde was quenched for 5 min with 125 mM of glycine. Nuclei were isolated and the chromatin was sheared with 30 cycles at high intensity (30 sec off and 30 sec on) using a sonicator (BioruptorTM Next Gene, Diagenode). For each immunoprecipitation 5 μg of sheared chromatin was used. Pre-cleared chromatin was incubated overnight with 5 μg of an antibody against the active enhancer mark H3K27ac (Abcam; ab4729). Following day the antibodies were captured with 25 μl of protein A magnetic beads (Millipore)s for 2 hours on a rotating wheel at 4°C. The DNA was purified with a QIAquick PCR clean-up kit.
ChIP sequencing was performed at the GeneCore facility of EMBL Heidelberg (http://www.genecore.embl.de/) according to the Illumina protocol.

value: Primary human macrophages

tag: differentiation stage

value: Day 11


title: Donor 2 - Input

description: Input DNA


title: BicR DHT ChIPed by K4me3

value: K4me3 (Millipore #17-614)


title: MB100_10

value: male


title: Donor 2 - H3K27ac

description: ChIP-Seq analysis of H3K27ac


title: BicR DHT ChIPed by AR

value: prostate cancer


title: BicR DHT input_1


title: Donor 1 - H3K27ac

description: ChIP-Seq analysis of H3K27ac


title: BicR 0h_miRNA

data_processing:
Remove sequences that have low quality base N. Filter out artificial sequences using tagdust with default parameter. tagdust version is 1.13.
Remove sequences that match to rRNA references up to [error] errors. rRNAdust version is 1.00.
RNAs were aligned to the human genome and were used to search for miRNA sequences in the miRBase 9.1 database. We selected sequences with a single match.
Genome_build: hg19
Supplementary_files_format_and_content: text file of tag number matched to miRNAs

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

extract_protocol:
Total RNA was extracted using ISOGEN reagent.
RNA libraries were prepared for sequencing using Manufacture's protocol for Small RNA Sample Prep Kit v1.5 (illumina).

treatment_protocol: Cells were treated with vehicle or DHT 10 nM for 24 h.

value: before treatment


title: Donor 3 - Input

description: Input DNA


title: BicR DHT 24h_miRNA

value: DHT 10 nM 24 h


title: BicR DHT 6h_miRNA

value: DHT 10 nM  6 h


title: LNCaP Bicalutamide input

value: LNCaP


title: Donor 1 - Input

description: Input DNA


title: LNCaP 0h_miRNA


title: 1154337-RRBS-GM

city: Daejeon

first: Hee-jin

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

country: South Korea

institute: KRIBB

description: gastric normal mucosa cells

data_processing:
Base calling was performed throughout methylation specific mapping tool, BRAT software for short bisulfite treated reads because unmethylated cytosine within sequenced read from RRBS technique is converted into thymine.
RRBS of same normal tissue was carried out twice due to a small amount.
Regions of promoter known as primary candidate of epigenetic regulation were selected for consequential analysis focusing differentially methylated promoters (DMPs).
Methylated and unmethylated CpGs were counted and enrichment test (Fisher's exact test) was used about methylated frequency during gastric carcinogenesis with 2 by 3 contigency table.
DMPs having 3 or more significant CpG sites were selected as prospective candidates.
Genome_build: hg18
Supplementary_files_format_and_content: bed files include methylated and unmethylated read count of individual CpG sites. RRBS method provides single base pair resolution data of methylation signal in C of CpG site.

source_name: gastric normal mucosa cells

extract_protocol:
Standard DNA extraction protocol using QIAamp DNA Micro Kit
RRBS libraries were prepared according to Meissner's protocol.

value: gastric normal mucosa cells


title: 1154337-RRBS-GC

description: gastric cancer cells

source_name: gastric cancer cells

value: gastric cancer cells


title: LNCaP Bicaltamide ChIPed by AR


title: LNCaP DHT 6h_miRNA


title: 1154337-MBD-GC

description: gastric cancer cells

data_processing:
Base-calling was performed throughout the routine process of Illumina pipeline module, bclConverter v1.7 with 76 cycles of single-read.
The sequences were aligned to the human genome assembly (hg18) using the ELAND version 2 with default parameters.
In order to evaluate the methylation peak signature, aligned coordinated were extended up to 200 bp from start position.
Read count value was converted into methylation enrichment score (MES) to remove the bias among the amount of reads from different samples.
For identification of differentially methylated regions (DMRs), sliding window approach was applied to find methylation signal difference having more than 2-fold change between samples withing 1 kb range per 200 bp bin shift.
Genome_build: hg18
Supplementary_files_format_and_content: bed files include MES values

extract_protocol:
Standard DNA extraction protocol using QIAamp DNA Micro Kit
MBD libraries were prepared using Illumina ChIP Seq Sample Prep Kit according to Illumina's instructions.


title: 1154337-MBD-IM

description: gastric intestinal metaplasia cells

source_name: gastric intestinal metaplasia cells

value: gastric intestinal metaplasia cells


title: 1154337-MBD-GM

description: gastric normal mucosa cells


title: 1154337-RRBS-IM

description: gastric intestinal metaplasia cells


title: BicR DHT ChIPed by K4me1

value: BicR

value: K4me1 (Abcam ab8895)


title: 5mC_Human_Cerebellum

city: Copenhagen

first: Sheroy

last: Minocherhomji

state: Copenhagen N

address: Blegdamsvej 3B, Building 18.1

department: Nordea Centre for Healthy Aging, Faculty Of Health Sciences Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

description: IP against hypermethylated gDNA using his-MBD2b antibody

data_processing:
5mC_Human_Cerebellum.bedgraph; genome build: hg18
Alignment: Sequence reads were obtained and mapped to the human (March, 2006) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches with the first 28-32 bases were retained and aligned
Peaks: Peak detection was performed with Cisgenome software http://www.biostat.jhsph.edu/~hji/cisgenome/index.htm

growth_protocol: For methylation experiments genomic DNA from human cerebellum and peripheral blood lyphocytes obtained was used.

extract_protocol: Library generation of isolated/eluted methylated, hydroxymethylated or hypomethylated gDNA (from various human tissues) for Solexa sequencing namely MBD-Seq, hMeDIP-Seq and MRE-Seq respectively was performed using an Illumina recommended method and sequenced on a Genome Analyzer II (Illumina). Following high throughput sequencing, reads were aligned back to the hg18 (NCBI build 36) assembly using Bowtie. Two mismatches within the seed sequence (28-32 bases) of each unique read aligned were used as cut-offs to match back to the hg18 human genome assembly. Regions enriched for each modification were analyzed using Cisgenome software and a false discovery rate (FDR) of <0.01. Converted WIG files were visualized using the UCSC genome browser. All experiments were analyzed using Cisgenome. hMeDIP-Seq data were analyzed using Cisgenome and parameters for two sample analyses using IgG as a negative control. Genome-wide comparisons of MBD-Seq data was performed using the R statistical software. Average insert size of the paired-end libraries was between 150-300bp.

tag: tissue

value: Cerebellum

tag: antibody

value: his-MBD2b (Active Motif, USA, 5502 (Methyl Collector Kit))


title: Human_Cerebellum_RNA_Seq

description: Single read high-throughput sequencing of total RNA isolated from human cerebellum tissue

data_processing:
Alignment: Following high throughput sequencing, single reads were aligned back to the hg18 (NCBI build 36) assembly using Bowtie. Two mismatches within the seed sequence (28-32 bases) of each unique aligned read were used as cut-offs to match back to the hg18 human genome assembly. The average insert size (fragment length not including adapters) of the libraries was 200bp-400bp.
Genome Build:
Human_Cerebellum_RNA_Seq.bed: hg18

source_name: Human Cerebellum total RNA

growth_protocol: Human cerebellum total RNA was purchased (Capital Biosciences USA) and used for preparation of RNA-Seq libraries a standard Illumina recommended protocol using single read primers.

extract_protocol: Library generation of total RNA isolated from human cerebellum (termed RNA-Seq) for Illumina/Solexa sequencing was performed using an Illumina recommended method, single-read sequencing primers and sequenced (76bp run) on a Genome Analyzer II (Illumina).


title: IgG_Human_Peripheral_Blood_Lymphocytes

description: IP against IgG using a polyclonal IgG antibody

data_processing:
IgG_Peripheral_Blood_Lymphocytes.bedgraph; genome build: hg18
Alignment: Sequence reads were obtained and mapped to the human (March, 2006) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches with the first 28-32 bases were retained and aligned
Peaks: Peak detection was performed with Cisgenome software http://www.biostat.jhsph.edu/~hji/cisgenome/index.htm

value: Peripheral blood B-lymphocytes from whole Blood

value: IgG (Diagenode, kch-819-015)

tag: restriction enzyme

value: HpaII (New England Biolabs, USA, R0171L)


title: 5hmC_Human_Cerebellum

description: IP against hydroxymethylated gDNA using 5hmC mouse monoclonal antibody

data_processing:
5hmC_Human_Cerebellum.bedgraph; genome build: hg18
Alignment: Sequence reads were obtained and mapped to the human (March, 2006) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches with the first 28-32 bases were retained and aligned
Peaks: Peak detection was performed with Cisgenome software http://www.biostat.jhsph.edu/~hji/cisgenome/index.htm

value: 5hmC (Diagenode, AF-110-0016)


title: IgG_Human_Cerebellum

data_processing:
IgG_Human_Cerebellum.bedgraph; genome build: hg18
Alignment: Sequence reads were obtained and mapped to the human (March, 2006) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches with the first 28-32 bases were retained and aligned
Peaks: Peak detection was performed with Cisgenome software http://www.biostat.jhsph.edu/~hji/cisgenome/index.htm

source_name: IP against IgG using a polyclonal IgG antibody


title: LNCaP DHT 24h_miRNA


title: No Dox-WIs_rep2

city: Nashville

first: Alvin

last: Powers

state: Tennessee

address: 2213 Garland Avenue

department: Medicine

institute: Vanderbilt University Medical Center

data_processing:
Raw reads were mapped to reference mouse genome mm9 using TopHat v2.0 (Trapnell et al., 2009). Aligned reads were imported onto the Avadis NGS data analysis platform (Strand NGS, San Fransisco, CA, USA). Briefly imported mapped reads were first filtered on their quality metrics, and then duplicate reads were removed. Normalized gene expression was quantified using the TMM (Trimmed Mean of M-values) method (Dillies et al., 2012; Robinson and Oshlack, 2010). The transcriptional profile from each sample group (whole islets at No Dox, 1wk Dox, 2wk WD and sorted islet-derived MΦs and ECs at 1wk Dox) was compared by principle component analysis (PCA) and hierarchal clustering analysis to determine the layout and spread of the samples. Differential expression between conditions was calculated on the basis of fold change (cutoff ≥2.0) and the p-value was estimated by z-score calculations (cutoff 0.05) as determined by the Benjamini Hochberg false discovery rate (FDR) method (Benjamini and Hochberg, 1995). Differentially expressed genes underwent gene set enrichment analysis (GSEA), gene ontology (GO) analysis, and pathway analysis using DAVID, and Ingenuity Pathway Analysis.
Genome_build: mm9
Supplementary_files_format_and_content: txt file contains normalized expressions for each sample

source_name: whole pancreatic islets

extract_protocol:
Isolated whole islets (100-300) or sorted islet-derived cells (8,000-400,000) were added to 200-400 μL lysis/binding solution in the RNAqueous small scale or micro scale phenol-free total RNA isolation kits (Ambion, Austin, TX). Trace contaminating DNA was removed with TURBO DNA-free kit (Ambion, Austin, TX). RNA quantification and quality analysis was performed using a Qubit Fluorometer and an Agilent 2100 Bioanalyzer.
RNA samples that had RNA integrity number (RIN) ≥7.0. RNA was amplified using the NuGEN Technologies Ovation RNA amplification kit (Part # 7102-08) using manufacturer's instructions. Approximately, 2.5 µg amplified DNA from each sample was sheared on a Covaris S200 focused- ultrasonicator (Woburn, MA, USA) with a target yield of an average 200bp fragment size. The fragmented DNA was taken into standard library preparation protocol using NEBNext® DNA Library Prep Master Mix Set for Illumina® (New England BioLabs Inc., Ipswich, MA, USA) with slight modifications. Briefly, end-repair was done followed by polyA addition and custom adapter ligation. Post-ligated materials were individually barcoded with unique in-house genomics service lab (GSL) primers and amplified through 8 cycles of PCR using KAPA HiFi HotStart Ready Mix (Kapa  Biosystems,  Inc.,  Woburn,  MA,  USA).  The quality of the libraries were assessed by Qubit® 2.0 Fluorometer , and the concentration of the libraries was estimated by utilizing a DNA 1000 chip on an Agilent 2100 Bioanalyzer, respectively. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols.

tag: strain

value: RIP-rtTA; TetO-VEGF-A

value: No Dox

value: whole pancreatic islets


title: 1wk Dox-ECs_rep3

source_name: CD31+ islet-derived endothelial cells

value: 1 week Dox

value: CD31+ islet-derived endothelial cells


title: No Dox-WIs_rep3


title: 1wk Dox-ECs_rep2


title: 1wk Dox-WIs_rep3


title: 1wk Dox-Mphs_rep3

source_name: CD11b+ islet-derived macrophages

value: CD11b+ islet-derived macrophages


title: 1wk Dox-ECs_rep1


title: 1wk Dox-Mphs_rep2


title: 1wk Dox-WIs_rep2


title: 1wk Dox-Mphs_rep1


title: 1wk Dox-WIs_rep1


title: OldBeta_H3K27me3_Input

city: Jerusalem

first: Dana

last: Avrahami Tzfati

address: Ein-Kerem

department: Developmental Biology and cancer research

country: Israel

institute: Hadassah Hebrew University School of medicine

description: RapidRun

data_processing:
Illumina Casava-1.8.2 software was used for basecalling.
RNA-Seq: Low quality reads as well as ribosomal and other repeat sequences were filtered out before alignment. RUM software was used for aligning reads to mouse genome mm9 and Refseq transcriptome and for transcript quantitation. Differential expression analysis was carried out using a custom script implementing EdgeR software.
ChIP-Seq: Reads were aligned to mm9 genome using bowtie version 0.12.7 with parameters -v 3 -k 1 -m 1 --best --strata. Redundant reads were discarded before creating bedgraph profiles.
Peak calling was done using HOMER for H3K4me1 and H3K27Ac marks at FDR=0.01 with respect to corresponding Input. Peak calling using STAR was done for H3K27me3 marks at FDR=0.01.
BIS-Seq: DNA sequencing data was aligned to mouse genome (mm9) with the BS Seeker program. Data was reported as the fraction of reads that were methylated, calculated as the ratio of cytosine bases (indicating methylated CpGs) to total reads for each CpG coordinate.  Unmethylated cytosines are ultimately converted to thymine bases during the bisulfite conversion process.
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited file of transcript raw read counts.
Supplementary_files_format_and_content: Tab delimited file of transcript FPKM counts.
Supplementary_files_format_and_content: Peak files are tab-delimited listing genomic coordinates and their respective scores and p-values. Scores represent fold-change with respect to Input.
Supplementary_files_format_and_content: Tab-delimited files of loci, fraction of methylated cytosines and total read count.
Supplementary_files_format_and_content: RawReadCounts.txt: Raw transcript counts
Supplementary_files_format_and_content: TrancriptFPKMCounts.txt: Transcript FPKM counts
Supplementary_files_format_and_content: Old_H3K4me1.peaks.txt: peak
Supplementary_files_format_and_content: Old_H3K27me3.peaks.txt: peak
Supplementary_files_format_and_content: Young_H3K4me1.peaks.txt: peak
Supplementary_files_format_and_content: Young_H3K27me3.peaks.txt: peak
Supplementary_files_format_and_content: Young_H3K27Ac.peaks.txt: peak
Supplementary_files_format_and_content: OldBeta_bs_seeker-CG.tab: Percent methylated cytosines
Supplementary_files_format_and_content: YoungBeta_bs_seeker-CG.tab: Percent methylated cytosines

source_name: Pancreatic Beta Cells

extract_protocol:
RNA-Seq: Flow cytometry sorting was performed on live β cells from isolated pancreatic islets of young and old MIP-GFP mice. Total RNA were isolated using the RNeasy kit (Qiagen). ChIP-Seq: ChIP was performed on sonicated chromatin obtained from sorted old and young mouse β cells using antibody against H3K27ac (39685, Active Motif), H3K4me1 (ab8895, Abcam) and H3K27me3 (07-449, upstate). Input and bound DNA fractions were purified using PCR purification kit (Qiagen) for library preparation. BIS-Seq: Genomic DNA was extracted from FACS sorted old and young beta cells using FFPE AllPrep kit (Ambion), sonicated and bisulfite converted by Qiagen Epitect Bisulfite Kit and used for preparation of libraries.
RNA-Seq:Libraries were constructed from 200ng of total RNA using the standard TruSeq RNA sample prep kit (Illumina) using manufacturer's protocols. ChIP-Seq: Libraries were prepared using NEBNext ChIP-seq library prep reagent kit according to Illumina's instructions. BIS-Seq: Libraries were prepared following manufacturer's instructions using NEBNext ChIP-seq library prep reagent kit with methylated adapters (NEB).

tag: age

value: 16-18 months


title: No Dox-WIs_rep1


title: NeuroD2 ChIP-SEQ from embryonic cortex 2

city: Helsinki

first: Gulayse

last: Ince Dunn

state: Finland

address: Haartmaninkatu 8

department: Stem Cells and Metabolism Program

country: Finland

institute: University of Helsinki

data_processing:
Fastq Groomer (Galaxy tool version 1.0.4)
Map with Bowtie for Illumina (Galaxy tool version 1.1.2)
Remove duplicates (Galaxy tool version 1.0.0)
BAM-to-SAM (Galaxy tool version 1.0.3)
Filter SAM (Galaxy tool version 1.0.0)
MACS (Galaxy tool version 1.0.1), tag size 50, band width 200, p-value cutoff for peak detection: 10E-05
MACS (Galaxy tool version 1.0.1), MFOLD ratio:20, extend tag: -1, resolution for saving wiggle files: 10, 3 levels of regions around the peak region to calculate the maximum lambda as local lambda: 1000,5000,10000
Genome_build: mm10
Supplementary_files_format_and_content: wig and bed files

source_name: mouse embryonic cortex

growth_protocol: mouse were kept under standard conditions in their homecages.

extract_protocol:
Tissue was cross-linked by 10 min of 1% formaldehyde treatment. After IP, stringent washes, and proteinase K treatment, DNA was extracted by standard phenol-chloroform extraction and ethanol precipitation.
Library was prepared for the single end read Illumina HiSeq 2500 platform by Genewiz, Inc.

treatment_protocol: Times pregnancy was checked in female mice by checkig for vaginal plugs.

value: BALB/c

tag: developmental stage

value: E14.5 embryo

value: cerebral cortex

value: NeuroD2 antibody, vendor:Abcam, cat#:ab104430, lot#:GR94291-1


title: GFP ChIP-SEQ from embryonic cortex 1

description:
GFP
This dataset was used as the control file during MACS peak identification, therefore a processed version of it does not exist

value: GFP antibody, vendor:Santa Cruz, cat#:sc-8334, lot#:H0612


title: AH_dsxNullM_1

city: Tallahassee

first: Michelle

middle: N

last: Arbeitman

state: Florida

address: 1115 W. Call Street

department: Medicine Biomedical Sciences

institute: Florida State University

data_processing:
Basecalls performed using CASAVA version 1.3
Barcode, primer, and adapter sequences were trimmed using custom perl scripts..
Reads were aligned to the D. melanogaster genome FB5.30 (FlyBase v5.30) using Bowtie (v0.12.8; --tryhard, --best, --strata, -m1).
Unaligned reads were 3’ end quality trimmed and homopolymers (5+) were removed. Quality trimmed reads were mapped again using bowtie.
Unaligned reads were aligned to junctions estimated by Tophat.
Any remaining unaligned reads were mapped to FB5.30 genome using LAST (v193; -l 20, -Q3).
Using FlyBase annotions, overlapping exons regardless of strand were combined into the maximum exonic region.
Expression was then quantified for each exonic region using Reads Per Kilobase Per Million Mapped Reads (RPKM).
Genome_build: Flybase 5.30
Supplementary_files_format_and_content: Are in the CSV format. With the following columns: exonic region id, sample id, number of mapped reads, number of reads in the exonic region, coverage in exonic region (number of reads in exonic region / read length), exonic region length, average per nucleotide coverage, RPKM.

organism: Drosophila melanogaster

source_name: Adult Head Tissue

growth_protocol: Flies were raised on standard cornmeal food medium at 25˚C on a 12 hour light and 12 hour dark cycle.

extract_protocol:
Total RNA was extracted using TRIzol® Reagent (Invitrogen), and RNA was precipitated by addition of 250 µL 100% isopropanol and 250 µL 1.2 M NaCitrate, 0.8 M NaCl in DEPC-treated water. The Zymo Research RNA Clean & Concentrator™-25 In-Column DNase Digestion protocol and 10 units Ambion® TURBO™ DNase was used on ~25 µg total RNA. Poly(A)+ transcripts were subsequently isolated from total RNA using Ambion® MicroPoly(A)Purist™ Kit.
One hundred ng mRNA was chemically fragmented to a range of approximately 200-500 base pairs using the Ambion® RNA Fragmentation Reagent, and the reaction was cleaned using Zymo Research RNA Clean & Concentrator™-5. First strand cDNA was synthesized using SuperScript® II Reverse Transcriptase (Invitrogen™) and a combination of 3 µg random hexamers and 0.15 µg oligo(dT)20 primers. The second strand of the cDNA was synthesized using DNA polymerase I (Invitrogen™), RNase H (New England Biolabs® Inc.), dNTPs and second strand buffer (Invitrogen™). This reaction and all subsequent reactions were cleaned using Zymo Research DNA Clean & Concentrator™-5 kit. Double stranded cDNA templates were blunt ended using End-It™ Repair Kit (Epicentre®). A-overhangs were added to both ends with Klenow fragment (3'→5' exo-minus) (New England Biolabs® Inc.) and Illumina sequencing adapters were then ligated to both ends of the cDNA templates using Fast-Link™ DNA Ligation Kit (Epicentre®). cDNA templates were  amplified by performing PCR for 18 cycles, which extended the adapter and incorporated a different six base pair index into each sample. The product was then isolated by gel purification of 250-550 base pair fragments.

value: unknown

tag: genotype

value: w;dsxm+r15/dsxd+r3 (XY)

value: Male

value: adult

value: head


title: AH_dsxNullF_3

value: w/+; dsxm+r15/dsxd+r3 (XX)

value: Female


title: 5hmC_Human_Peripheral_Blood_Lymphocytes

data_processing:
5hmC_Human_Peripheral_Blood_Lymphocytes.bedgraph; genome build: hg18
Alignment: Sequence reads were obtained and mapped to the human (March, 2006) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches with the first 28-32 bases were retained and aligned
Peaks: Peak detection was performed with Cisgenome software http://www.biostat.jhsph.edu/~hji/cisgenome/index.htm

source_name: IP against hydroxymethylated gDNA using 5hmC mouse monoclonal antibody

value: Peripheral blood B-lymphocytes from whole Blood

value: 5hmC (Diagenode, AF-110-0016)


title: AH_dsxNullM_2


title: AH_dsxNullM_3


title: AH_dsxNullF_1


title: NeuroD2 ChIP-SEQ from embryonic cortex 3

value: NeuroD2 antibody, Abcam, cat#:ab109406, lot#:YK010204CS


title: AH_dsxD_3

value: w/+;DsxD/dsxm+r15 (XX)


title: AH_dsxD_2


title: AH_dsxD_1


title: AH_dsxNullF_2


title: RNA-seq lsm1(tm3585)

city: Hospitalet de Llobregat

first: Julián

last: Cerón

state: Barcelona

address: Gran via 199, Hospital Duran i Reynals, planta 3

department: Cancer and Human Molecular Genetics

country: Spain

institute: IDIBELL

description: RNA-seq lsm1 tm3585_ACTTGA.fastq

data_processing:
Each sample produced about 10 million reads that were processed using TopHat (Trapnell et al. 2009) to be mapped against the C. elegans genome (WS225). BAM files were analyzed with the SeqSolve NGS software (Integromics, S.L., Spain) using a False Discovery Rate of 0.05, and filtering reads displaying multiple mapping sites. SeqSolve uses Cufflinks (Trapnell et al. 2010) and Cuffdiff (Trapnell et al. 2013) programs to perform differential gene expression analyses between samples (p value <0.005). Expression values were normalized in FPKM (fragments per kilobase of exon per million fragments mapped).
Genome_build: WS225
Supplementary_files_format_and_content: Excel file. Fold change lsm-1(-) vs wild type

organism: Caenorhabditis elegans

source_name: L3 stage, lsm-1(tm3585) mutant

growth_protocol: Synchronized L1 animals were grown at 25C for 26 hours

extract_protocol:
RNA purified using the mirVana miRNA isolation kit, followed by ribosomal RNA depletion using the RiboMinus Eukaryote Kit
Libraries were prepared according to Illumina's instructions (Illumina TruSeq RNA Sample Preparation Kit)

treatment_protocol: Animals were washed and frozen in Trizol

value: lsm-1(tm3585) mutant


title: RNA-seq N2

description: RNA-seq N2 back3_GATCAG.fastq

source_name: L3 stage, N2 wild-type

value: N2 wild-type


title: GFP ChIP-SEQ from embryonic cortex 2

value: BALB/c

value: E14.5 embryo

value: GFP antibody, vendor:Pierce, cat#:4B10B2m lot#:MA5-15349


title: chimp ts 2

city: Berlin

first: Jorge

last: Ruiz-Orera

state: Berlin

address: Robert-Rössle-Straße 10

country: Germany

institute: Max Delbruck Center for Molecular Medicine

description:
dUTP stranded protocol, paired-end reads
Strand-specific and paired-end RNA-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor and low-quality sequences using Condetri with the following settings (-hq=30 –lq=10). Adapters were trimmed from filtered reads if at least 5 nucleotides of the adaptor sequence matched the end of each read. In all experiments, reads below 50 nucleotides or with only one member of the pair were not considered.
We aligned the reads to the correspondent reference species genome with Tophat (v. 2.0.8) with parameters –N 3, -a 5 and –m 1, and including the correspondent parameters for paired-end and strand-specific reads whenever necessary. Multiple mapping to several locations in the genome was allowed unless otherwise stated.
Genome_build: hg19, panTro4, rheMac2 (Mmul_051212), mm10
Supplementary_files_format_and_content: Cufflinks output (isoforms.fpkm_tracking) containing abundance measurements and transcript assembly coordinates

organism: Pan troglodytes

source_name: Testis

extract_protocol:
Total RNA was extracted using a miRNeasy Mini kit.
Libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit v2 according to the manufacturer’s protocol.  Poly (A)-positive RNA was purified from 250-500 mg of total RNA using streptavidin-coated magnetic beads (AMPure XP) and subsequently fragmented to ~300 bp. cDNA was synthesized using reverse transcriptase (SuperScript II, Invitrogen) and random primers. The strand-specific RNA-Seq library preparation was based on the incorporation of dUTP in place of dTTP in the second strand of the cDNA. Double-stranded DNA was further used for library preparation. Such dsDNA was subjected to A-tailing and ligation of the barcoded Truseq adapters. Library amplification was performed by PCR on the size selected fragments using the primer cocktail supplied in the kit. Final libraries were analyzed using Agilent DNA 1000 chip to estimate the quantity and check size distribution, and they were quantified by qPCR using the KAPA Library Quantification Kit (KapaBiosystems). Sequencing was done with a Illumina HiSeq 2000 sequencer in a paired-end design according to the manufacturer’s instructions.

value: Testis

value: 14 weeks

tag: protocol

value: dUTP stranded protocol


title: chimp ts 1

value: Male

value: 46 weeks


title: chimp ht 2

source_name: Heart

value: Heart

value: 18 weeks


title: chimp lv 2

source_name: Liver

value: Liver


title: ZH-11-9D embryo

city: shanghai

first: yijing

last: zhang

address: 2005 Songhu Road

institute: Fudan University

data_processing:
MeDIP-seq reads were aligned to the japonica genome (version 7.0, http://rice.plantbiology.msu.edu/) using BOWTIE2 with default settings.
The duplicated reads were removed, and only alignments with MAPQ score > 20 were kept for further analysis.
Enriched regions of DNA methylation were identified using MACS14.
Genome_build: the japonica genome (version 7.0, http://rice.plantbiology.msu.edu/)
Supplementary_files_format_and_content: peak files

organism: Oryza sativa

source_name: Oryza sativa embryo

growth_protocol: Rice variety Zhonghua11 (Oryza sativa spp. Japonica) and 93-11 (Oryza sativa spp. indica) were cultivated in a phytotron with a light (12h, 28℃)/dark(12h, 22℃) cycle.

extract_protocol:
DNA was extracted from the embryo and endosperm of rice seeds. Methylated DNA was isolated with  anti 5-mc antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. 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 Hiseq2000 following the manufacturer's protocols.

treatment_protocol: Embryo of 3,6,9 days after pollination (DAP) and endosperm of 2,3,6,9 DAP were manually selected under the dissecting scope. Selected embryo and endosperm were transferred to the eppendorf tube, rinsed with ethanol and placed on ice in the 100% ethanol.

value: embryo

value: 9 DAP

tag: cultivar


title: ZH-11-3D endosperm

source_name: Oryza sativa endosperm

value: endosperm

value: 3 DAP


title: ZH-11-6D endosperm

value: 6 DAP


title: chimp ht 1


title: NeuroD2 ChIP-SEQ from embryonic cortex 1

value: cerebral cortex

value: NeuroD2 antibody, vendor:Abcam, cat#:ab168932, lot#:GR161014-2


title: ZH-11-9D endosperm


title: chimp lv 1


title: ZH-11-2D endosperm

value: 2 DAP


title: 93-11-9D endosperm


title: ZH-11-3D embryo


title: chimp br 2

source_name: Brain

value: Brain


title: chimp br 1


title: MB151_9

data_processing:
Raw reads aligned using lifescope to hg19 reference genome containing IUPAC ambiguity codes for SNPs listed in dbSNP 135.
Whole gene and isoform expression generated by cufflinks version 2.1.1 using multiread correction and without effective length correction.  Whole gene expression estimated by summation of isoform expression of measurments with status "OK".
SNP calling was performed through samtools mpileup specifically for known heterozygous SNP locations confirmed by SNP chip genotyping generating allele counts.  These allele counts are used to make allelic expression ratio calculations.
Genome_build: hg19 with IUPAC codes for dbSNP 135

source_name: raphae nuclei

value: nonsmoker

value: male


title: MB151_8

source_name: cerebellum


title: 93-11-6D endosperm


title: 93-11-6D embryo


title: ZH-11-6D embryo


title: 93-11-9D embryo


title: Cyto-mCherry-input-24A

city: Berkeley

first: James

last: Craig

state: CA

address: 341A Koshland Hall

department: Plant & Microbial Biology

institute: UC Berkeley

description:
chromatin immuno precipitated DNA
2015_04_14_SD2_MACS_output_&_Nearby_genes.xlsx

data_processing:
reads were aligned with Bowtie2
MACS
genes surrounding the identified peaks were annotated
Genome_build: aligned to Neurospora crassa genome version 12 mitochondria version 10
Supplementary_files_format_and_content: tab delimited spreadsheet of the MACS output with the nearest genes surrounding the peak annotated

organism: Neurospora crassa

source_name: whole tissue

growth_protocol: Neurospora crassa was grown on Vogel's Mininal Media for 16 hrs with Sucrose as the carbon source

extract_protocol:
Cells were ground in liquid nitrogen and DNA sheared by sonication, the chromatin was immunoprecipitated by antibody to epitope-tagged transcription factors
Libraries were prepared according to Illumina's instructions for the Genomic DNA Prep Kit, adapters were diluted 1:20, and PCR amplification was carried out to 24 cycles.

treatment_protocol: The filamentous fungus was washed and transferred to fewsh Vogel's Media with Avicel, Xylan, or Sucrose as the carbon source

value: Neurospora crassa OR74A (FGSC2489)

value: mCherry


title: Cyto-GFP-ab-24A

description:
mock immunoprecipitated DNA (no antibody control)
2015_04_14_SD2_MACS_output_&_Nearby_genes.xlsx

value: his-3::p_ccg1::GFP, matA

value: GFP


title: MB151_7

source_name: posterior putamen


title: Cyto-GFP-input-24A


title: 93-11-3D embryo


title: MB151_6

source_name: hippocampus


title: Cyto-mCherry-ab-24A


title: clr1-V5-4A-39

value: clr1-V5::HygR, mat'a', deltamus51::bar


title: ccg1-xlr1-gfp-4X-64


title: ccg1-xlr1-gfp-4X-63


title: MB151_3


title: MB151_4

source_name: insula


title: ccg1-xlr1-gfp-4A-68


title: ccg1-xlr1-gfp-4A-67


title: MB151_2


title: MB052_8


title: ccg1-clr2-mC-4A-40


title: ccg1-xlr1-gfp-4A-66


title: MB151_1