title: ChIP-Exo, Abf1-Replicate2 [ChIP-exo-Seq] [PSU10707]

city: University Park

first: Bongsoo

last: Park

state: PA

address: 453 North Frear Building

institute: Penn State University

data_processing:
Library strategy: ChIP-exo-Seq
Basecalls performed using CASAVA version 1.7 for Illumina single reads, bcl2fastq ver 2.16 for NextSeq paired reads.
MNase-ChIP-Seq, MNase-Seq and ChIP-exo reads were aligned to the sg7(R55) genome assembly using bwa version 0.6.2 for single reads, and bwa mem version 0.7.9a for paired reads.
Peaks were called using GeneTrack (Albert I, et al. 2008) with the following setting: Smoothing(20) and Exclusion zone(147).
Genome_build: R55 (SGD)
Supplementary_files_format_and_content: Tab-delimited text files include enriched peak calls.

growth_protocol: For ChIP-exo, cells were grown to an O.D.600 of 0.8 - 1.0 at 25°C.

extract_protocol:
For ChIP-exo, lysates were clarified from sonicated nuclei and ABF1-DNA complexes were isolated with IgG antibody.
MNase-ChIP-Seq libraries were prepared for sequencing using standard Illumina protocols; Reference paper: http://www.sciencedirect.com/science/article/pii/B9780123919380000100
MNase-Seq libraries were prepared for sequencing using NEBNext standard Illumina protocols.
ChIP-exo libraries were prepared for sequencing using standard Illumina protocols; Reference paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3813302/

treatment_protocol:
For MNase-ChIP-Seq, cells were crosslinked with formaldehyde to a final concentration of 0.05%.
For MNase-Seq, cells were not crosslinked.
For ChIP-exo, cells were crosslinked with formaldehyde to a final concentration of 1.0%.

tag: sample type

value: in vivo

tag: genomic dna strain

value: MATa his3D1 leu2D0 met15D0 ura3D0 MSN2-T, S288C background

tag: histone source

value: Not applicable

tag: chip antibody

value: Abf1-TAP i5006


title: 133

status: Public on Aug 14 2016

type: SRA

city: Solna

first: Joakim

last: Lundeberg

address: Tomtebodavägen 23A

department: Gene Technology

country: Sweden

institute: KTH-Science for Life Laboratory

library_source: transcriptomic

data_processing:
Bcl to Fastq conversion was performed using bcl2Fastq v1.8.3 from the CASAVA software suite
The paired-end reads were trimmed with respect to quality and remaining adapter sequences using Trim Galore and aligned to the human genome reference hg19 with TopHat version 2.0.4
The aligned reads were assembled into transcripts using Cufflinks version 2.0.2
Genome_build: hg19, ENSEMBL v71
Supplementary_files_format_and_content: tab-delimited text files include output from Cufflinks for each Sample 1-33

molecule: total RNA

organism: Homo sapiens

source_name: skeletal muscle

extract_protocol:
Trizol® method
RNA libraries were prepared for sequencing using standard Illumina protocols for paired end sequencing and clustered on cBot

tag: tissue

value: skeletal muscle

tag: gender

value: male

tag: biopsy location

value: left leg

tag: exercise ststus

value: untrained

tag: time point

value: pre-training period 2

tag: original sample id


title: ChIP-Exo, Abf1-Replicate1 [ChIP-exo-Seq] [PSU10607]

country: USA

library_source: genomic

molecule: genomic DNA

organism: Saccharomyces cerevisiae


title: 117

value: post-training period 1


title: Reb1+ISW2+ISW1a+RSC-Replicate2 [MNase-Seq] [PSU56220]

data_processing:
Basecalls performed using CASAVA version 1.7 for Illumina single reads, bcl2fastq ver 2.16 for NextSeq paired reads.
MNase-ChIP-Seq, MNase-Seq and ChIP-exo reads were aligned to the sg7(R55) genome assembly using bwa version 0.6.2 for single reads, and bwa mem version 0.7.9a for paired reads.
Peaks were called using GeneTrack (Albert I, et al. 2008) with the following setting: Smoothing(20) and Exclusion zone(147).
Genome_build: R55 (SGD)
Supplementary_files_format_and_content: Tab-delimited text files include enriched peak calls.

value: in vitro

value: GRF88, MATa his4-38, S288C background

value: Drosophila embryo


title: Reb1+ISW2+ISW1a+RSC-Replicate3 [MNase-Seq] [PSU56221]


title: 125

value: right leg


title: 123

value: female


title: Abf1+ISW1a-Replicate8 [MNase-Seq] [PSU51315]


title: Abf1+ISW1a-Replicate9 [MNase-Seq] [PSU46527]


title: Abf1+ISW1a-Replicate5 [MNase-Seq] [PSU46520]


title: Abf1+ISW1a-Replicate6 [MNase-Seq] [PSU46521]


title: Reb1+ISW2+ISW1a-Replicate2 [MNase-Seq] [PSU56215]


title: 209


title: 210


title: Abf1+RSC-Replicate2 [MNase-Seq] [PSU51121]


title: 162


title: Abf1+ISW1a-Replicate4 [MNase-Seq] [PSU46519]


title: 204


title: Reb1+ISW2-Replicate3 [MNase-Seq] [PSU55216]


title: Abf1+ISW2-Replicate6 [MNase-Seq] [PSU46523]


title: 122

value: trained

value: post-training period 2


title: 106


title: Reb1+ISW2-Replicate2 [MNase-ChIP-Seq] [PSU53008]

data_processing:
Library strategy: MNase-ChIP-Seq
Basecalls performed using CASAVA version 1.7 for Illumina single reads, bcl2fastq ver 2.16 for NextSeq paired reads.
MNase-ChIP-Seq, MNase-Seq and ChIP-exo reads were aligned to the sg7(R55) genome assembly using bwa version 0.6.2 for single reads, and bwa mem version 0.7.9a for paired reads.
Peaks were called using GeneTrack (Albert I, et al. 2008) with the following setting: Smoothing(20) and Exclusion zone(147).
Genome_build: R55 (SGD)
Supplementary_files_format_and_content: Tab-delimited text files include enriched peak calls.

source_name: Reb1+ISW2, H3 ChIP

value: anti-H3 (Abcam, ab1791, lot no. GR150473-1)


title: isw1Δisw2Δchd1Δ WCE+ISW1a+Chd1 [MNase-ChIP-Seq] [PSU41613]

source_name: isw1Δisw2Δchd1Δ WCE+ISW1a+Chd1, H3 ChIP

value: anti-H3 (Abcam, ab1791, lot no. GR125637)


title: Abf1+ISW1a [MNase-Seq] [PSU51114]


title: Reb1+ISW2+ISW1a+RSC+ISW1b+Chd1-Replicate2 [MNase-Seq] [PSU55213]


title: isw1Δisw2Δchd1Δ WCE+ISW2 [MNase-ChIP-Seq] [PSU41607]

source_name: isw1Δisw2Δchd1Δ WCE+ISW2, H3 ChIP


title: Reb1+ISW2+ISW1a-Replicate3 [MNase-Seq] [PSU55219]


title: isw1Δisw2Δchd1Δ WCE+ISW1a [MNase-ChIP-Seq] [PSU41604]

source_name: isw1Δisw2Δchd1Δ WCE+ISW1a, H3 ChIP


title: 185


title: Reb1+ISW2+ISW1a [MNase-Seq] [PSU56213]


title: Reb1+ISW2+ISW1a+RSC [MNase-Seq] [PSU56219]


title: Reb1+ISW2 [MNase-Seq] [PSU56211]


title: Abf1+ISW2-Replicate3 [MNase-Seq] [LMU425]


title: Abf1+Chd1 [MNase-Seq] [PSU51119]


title: Abf1+ISW1b [MNase-Seq] [PSU51116]


title: 193


title: Abf1+RSC [MNase-ChIP-Seq] [PSU39311]

source_name: Abf1+RSC, H3 ChIP

value: anti-H3 (Abcam, ab1791, lot no. GR124580)


title: 161


title: Reb1 [MNase-Seq] [PSU56320]


title: Abf1+ISW2-Replicate5 [MNase-Seq] [PSU46522]


title: isw1Δisw2Δchd1Δ WCE+ISW1a+RSC [MNase-Seq] [LMU5222]

source_name: isw1Δisw2Δchd1Δ WCE+ISW1a+RSC


title: Abf1+ISW2 [MNase-ChIP-Seq] [PSU39310]

source_name: Abf1+ISW2, H3 ChIP


title: Abf1+ISW2+ISW1a-Replicate6 [MNase-Seq] [PSU46525]


title: isw1Δisw2Δchd1Δ WCE+ISW2 [MNase-Seq] [LMU06062015115]

source_name: isw1Δisw2Δchd1Δ WCE+ISW2


title: 114


title: isw1Δisw2Δchd1Δ WCE+INO80+ISW1a [MNase-Seq] [PSU51216]

source_name: isw1Δisw2Δchd1Δ WCE+INO80+ISW1a


title: INO80Arp8Δ [MNase-ChIP-Seq] [PSU39307]

source_name: INO80Arp8Δ, H3 ChIP


title: 153


title: Abf1+ISW1a-Replicate10 [MNase-Seq] [PSU53216]


title: 137


title: SGD-Replicate2 [MNase-ChIP-Seq] [PSU39301]

source_name: SGD, H3 ChIP


title: RSC-Replicate3 [MNase-ChIP-Seq] [PSU43205]

source_name: RSC, H3 ChIP

value: anti-H3 (Abcam, ab1791, lot no. GR103722)


title: Abf1+ISW1a-Replicate7 [MNase-Seq] [PSU53220]


title: isw1Δisw2Δchd1Δ WCE+ISW2+ISW1a [MNase-Seq] [LMU06062015121]

source_name: isw1Δisw2Δchd1Δ WCE+ISW2+ISW1a


title: isw1Δisw2Δchd1Δ WCE+ISW2+ISW1a [MNase-Seq] [LMU06062015120]


title: 203

value: skeletal muscle


title: Reb1+RSC [MNase-ChIP-Seq] [PSU53012]

source_name: Reb1+RSC, H3 ChIP


title: Abf1+ISW2+ISW1a-Replicate5 [MNase-Seq] [LMU5204]


title: 129


title: isw1Δisw2Δchd1Δ WCE+ISW2+ISW1a [MNase-Seq] [LMU06062015119]


title: 183

value: male


title: isw1Δisw2Δchd1Δ WCE+ISW2+ISW1a [MNase-Seq] [LMU06062015118]


title: ISW1b-Replicate2 [MNase-Seq] [PSU51304]


title: RSC-Replicate2 [MNase-ChIP-Seq] [PSU43204]


title: Abf1+ISW1a-Replicate2 [MNase-Seq] [PSU53221]


title: isw1Δisw2Δchd1Δ WCE+ISW2+ISW1a [MNase-Seq] [LMU06062015116]


title: 167

value: left leg


title: Reb1+ISW2+ISW1a+RSC+ISW1b+Chd1 [MNase-Seq] [PSU56321]


title: isw1Δisw2Δchd1Δ WCE+ISW2+ISW1a [MNase-Seq] [LMU5220]


title: Abf1+RSC-Replicate3 [MNase-Seq] [PSU53222]


title: 151

value: untrained


title: Abf1+ISW2+ISW1a+ISW1b+RSC+Chd1-Replicate2 [MNase-Seq] [PSU55202]


title: Chd1-Replicate2 [MNase-ChIP-Seq] [PSU45607]

source_name: Chd1, H3 ChIP


title: 175


title: Abf1+ISW2+ISW1a+ISW1b+RSC+Chd1 [MNase-Seq] [LMU5212]


title: SWI/SNF-Replicate2 [MNase-ChIP-Seq] [PSU42711]

source_name: SWI/SNF, H3 ChIP


title: 159

source_name: skeletal muscle

value: pre-training period 2


title: Abf1+ISW2+ISW1a-Replicate3 [MNase-Seq] [PSU53214]


title: 127


title: Abf1+ISW2+ISW1a-Replicate4 [MNase-Seq] [PSU56210]


title: Abf1+ISW1a-Replicate3 [MNase-ChIP-Seq] [PSU52903]

source_name: Abf1+ISW1a, H3 ChIP


title: ISW2-Replicate2 [MNase-ChIP-Seq] [PSU39305]

source_name: ISW2, H3 ChIP


title: Abf1+ISW2+ISW1a-Replicate2 [MNase-Seq] [PSU56209]


title: ISW1b [MNase-Seq] [PSU51103]


title: 111


title: isw1Δisw2Δchd1Δ WCE+INO80+ISW1a [MNase-Seq] [LMU5215]


title: Abf1+ISW2-Replicate4 [MNase-ChIP-Seq] [PSU52920]


title: isw1Δisw2Δchd1Δ WCE+INO80 [MNase-ChIP-Seq] [LMU214]

source_name: isw1Δisw2Δchd1Δ WCE+INO80, H3 ChIP


title: 190

value: post-training period 1


title: Abf1+ISW2-Replicate2 [MNase-ChIP-Seq] [PSU52923]

value: in vitro


title: Chd1 [MNase-Seq] [PSU51105]

value: GRF88, MATa his4-38, S288C background


title: isw1Δisw2Δchd1Δ WCE+ISW1a+ISW1b [MNase-ChIP-Seq] [PSU52916]

source_name: isw1Δisw2Δchd1Δ WCE+ISW1a+ISW1b, H3 ChIP

value: Drosophila embryo


title: ISW1a [MNase-Seq] [PSU51101]


title: 119


title: 221


title: RSC [MNase-ChIP-Seq] [PSU43203]


title: isw1Δisw2Δchd1Δ WCE+ISW1b [MNase-Seq] [LMU5214]

source_name: isw1Δisw2Δchd1Δ WCE+ISW1b


title: isw1Δisw2Δchd1Δ WCE+RSC [MNase-ChIP-Seq] [LMU215]

source_name: isw1Δisw2Δchd1Δ WCE+RSC, H3 ChIP


title: 103


title: Abf1 [MNase-ChIP-Seq] [PSU52925]

source_name: Abf1, H3 ChIP


title: isw1Δisw2Δchd1Δ WCE+ISW2 [MNase-ChIP-Seq] [PSU43216]

source_name: isw1Δisw2Δchd1Δ WCE+ISW2, H3 ChIP


title: SWI/SNF [MNase-ChIP-Seq] [PSU42710]


title: Abf1+ISW2+ISW1a [MNase-Seq] [PSU55218]


title: g-KO

city: Logroño

first: Laura

last: Ochoa-Callejero

state: La Rioja

address: C/Piqueras 98 SPAIN

country: Spain

institute: CIBIR

description: g-KO

data_processing:
Illumina base-calling was performed off-line with OLB v1.9.4
Sequenced reads were trimmed for adaptor sequence with Cutadapt and then mapped to mus musculus.GRCm38_71 whole genome using tophat v2.0.6.
Fragments Per Kilobase Of Exon Per Million Fragments Mapped (FPKM) were calculated using SeqSolve (Integromics). This analysis uses Cufflinks/Cuffdiff [38] in order to quantify gene expression and identify genes with a significant differential expression between different conditions.
Genome_build: mus musculus.GRCm38_71 (Ensembl)
Supplementary_files_format_and_content: tab-delimited text file including FPKM values for each Sample

organism: Mus musculus

source_name: lung endothelial cells

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq mRNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
mRNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: lung

tag: genotype

value: AM EC KO


title: rsc3-ts WCE+INO80 [MNase-Seq] [LMU06062015123]

source_name: rsc3-ts WCE+INO80


title: b-KO

description: b-KO


title: isw1Δisw2Δchd1Δ WCE+INO80 [MNase-ChIP-Seq] [PSU52910]


title: isw1Δisw2Δchd1Δ WCE+Chd1 [MNase-ChIP-Seq] [PSU43219]

source_name: isw1Δisw2Δchd1Δ WCE+Chd1, H3 ChIP


title: d-KO

description: d-KO


title: INO80+ISW2+RSC+ISW1a+ISW1b+Chd1 [MNase-ChIP-Seq] [PSU53002]


title: INO80+ISW2+RSC+ISW1a [MNase-ChIP-Seq] [PSU53004]

source_name: INO80+ISW2+RSC+ISW1a, H3 ChIP


title: SGD [MNase-Seq] [PSU51102]

source_name: SGD


title: isw1Δisw2Δchd1Δ WCE [MNase-Seq] [PSU51104]

source_name: isw1Δisw2Δchd1Δ WCE


title: SGD-Replicate3 [MNase-ChIP-Seq] [PSU52904]

source_name: SGD, H3 ChIP


title: e-WT

description: e-WT

value: wild type


title: f-WT

description: f-WT


title: c-WT

description: c-WT


title: ISW2 [MNase-ChIP-Seq] [PSU53206]


title: INO80 [MNase-ChIP-Seq] [PSU53006]

source_name: INO80, H3 ChIP


title: SGD [MNase-ChIP-Seq] [PSU43201]


title: a-WT

description: a-WT


title: isw1Δisw2Δchd1Δ WCE+ISW2+ISW1a [MNase-Seq] [PSU53204]

source_name: isw1Δisw2Δchd1Δ WCE+ISW2+ISW1a


title: TS543_scRNAseq

status: Public on Aug 13 2016

city: New York

first: Peter

last: Sims

state: NY

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

institute: Columbia University

description: TS543 cells were cultured in Complete NeuroCultTM Proliferation Medium (10% (v/v) NeuroCultTM NS-A Proliferation Supplement (Human) in NeuroCultTM NS-A Basal Medium (Human) with 20 ng/mL rh EGF, 10 ng/mL rh bFGF and 0.0002% (w/v) Heparin).

data_processing:
Read 1 and read 2 fastq files were generated on basespace.
Raw reads from  Read 1 were demultiplexed to obtain cell barcode and unique molecular identifier for each read.
Read 2 were pre-processed using faxtx_clipper to remove all poly(A) tails from the 3'-ends of each read. Any resulting fragment shorter than 25 nucleotides were discarded.
Pre-processed reads were then mapped to a concatenated human-murine transcriptome (hg19, UCSC known genes and mm10, UCSC known genes) using bwa-mem. We kept all reads with the correct strandedness that map uniquely to a specific gene with an alignment score that is greater than or equal 85% of the length of the fragment.
Cell barcodes were collapsed to account for PCR duplications. Unique molecular identifiers were collapsed to account for PCR duplications and errors that are associated with unique molecular identifier synthesis, PCR, and sequencing.
All fastq files were generated using Illumina's default pipeline on basespace. Read 1 is 26 bases long which contains cell barcode sequences (12 base long), unique molecular identifier sequences (8 base long) and 6-base long oligo(dT) sequences.Both cell barcode and unique molecular identifier are random sequences. Read 2 is 66 bases long which contains mRNA sequences.
Genome_build: hg19 and mm10
Supplementary_files_format_and_content: Tab-delimited text files that contain the gene expression counts of each individual cell.

molecule: polyA RNA

source_name: Brain

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

tag: cell line


title: 33-38_T9_RNAseq

city: Lausanne

first: Felix

last: Naef

address: Route Cantonale

department: Bioengineering

country: Switzerland

institute: École Polytechnique Fédérale de Lausanne

data_processing:
Paired end reads were aligned to the reference genome (mm10) index build with Ensembl annotation index using STAR with option --alignIntronMax 1000000
Using Ensembl annotations, we defined a gene body by merging all the respective transcripts using Bedtools(70). Under the exon-union model, a region is defined as exonic if it occurs in a least one of the transcripts while an intronic region has to be shared between all the transcripts. Using a custom Python script, we assigned uniquely mapping paired-reads to exonic region (reads that were mapped to the exon-exon junction) or intronic region (reads mapped to the intron-exon junction and complete intron reads) considering reads orientation. For the reads that were exclusively mapped within an exon, we used a probabilistic approach to assign the read to pre-mRNA or mRNA. After this step, the relative expression of mRNA and pre-mRNA was calculated for each time point under each temperature shift condition.
Reads count were normalized by the total number of exon-exon junction reads within the library and size of the sum of the respective intronic or exonic region. This is then used to quantify the expression level in the RPKM unit.
Genes that their expression undergo a change upon temperature variation were identified and further subdivided into col-inducible and heat-inducible genes.
The kinetics of mRNA and pre-mRNA accumulation was modelled using a dynamical model, and the model parameters were fitted to the measured expression for each gene.
Genome_build: mm10
Supplementary_files_format_and_content: Read counts categorized based on the position in which reads were mapped to the gene body.

source_name: NIH3T3 Total RNA

extract_protocol:
Total RNA was extracted from NIH 3T3 cells using the TRIzol Reagent (Ambion), precipitated in 1/10 volume of 3M NaOAc or 5M NaCl/ 2.5 volumes of EtOHabs at -70⁰C and treated with DNaseI (New England Biolabs) according to manufacturer’s instructions.
DNaseI-treated whole cell RNA samples were depleted of ribosomal RNA using the Ribo-Zero Gold rRNA removal kit (Illumina). Paired-end, strand-specific cDNA libraries of 50 bp inserts were prepared according to an in-house protocol of the iGE3 Genomics Platform, Geneva, Switzerland and sequenced using the Illumina HiSeq2500 platform.

tag: cell type

value: Fibroblast

value: Wild type


title: 33-38_T6_RNAseq


title: 33-38_T3_RNAseq


title: isw1Δisw2Δchd1Δ WCE+ISW1a [MNase-Seq] [PSU51213]

source_name: isw1Δisw2Δchd1Δ WCE+ISW1a


title: 33-38_T1_RNAseq


title: OX-OsbZIP23D-RNASeq

city: Austin

first: Wei

last: Zong

state: Texas

department: Molecular Biosciences

institute: University of Texas at Austin

description: RNA-Seq

data_processing:
For RNA-seq, Tophat (version 2.0.8) was used to align the clean tags filtered by Trimmomatic (version 0.32) to the reference genome of Nipponbare (RGAP version 7.0). edgeR (version 3.6.0) was used for identification of differentially expressed genes.
genome build: RGAP 7.0
processed data files format and content: text file with locus ID, FPKM and raw read number.

organism: Oryza sativa Japonica Group

source_name: ZH11-Four leaf stage seedling_OsbZIP23_overexpressed_drought

growth_protocol: Rice Zhonghua 11 (ZH11) (Oryza sativa ssp japonica) was used as the wild-type. The OsbZIP23-overexpression line and the osbzip23 mutant were from our previous study (Xiang et al., 2008). Seedlings were grown in sand/paddy (1:3) soil under natural conditions (14 h sun light/ 10 h dark) at July in Wuhan area. Seedlings at the four-leaf stage were used for drought stress treatments. The stressed plants were harvested until all of the leaves were rolled and the non-stressed samples were collected at the same time. For all of the samples, the above ground parts of the seedlings were harvested and frozen in liquid nitrogen for RNA isolation or immediately into 1% formaldehyde for chromatin isolation.

extract_protocol: Total RNAs used for RNA-Seq library construction were extracted from rice seedlings using TRIzol (Invitrogen) reagent.

treatment_protocol: Drought treatment was performed at four leaf stage. The stressed plants were harvested until all of the leaves were rolled and the non-stressed samples were collected at the same time.

value: above ground plant at four leaf stage

value: OsbZIP23 over expressed

tag: stress condition status

value: drought stress


title: 38-33_T9_RNAseq


title: 33-88_T0_RNAseq


title: 38-33_T6_RNAseq


title: WT WCE [MNase-Seq] [PSU46505]

source_name: WT WCE


title: OX-OsbZIP23N-RNASeq

description: RNA-Seq

source_name: ZH11-Four leaf stage seedling__OsbZIP23_overexpressed_normal

value: normal (no stress)


title: 38-33_T3_RNAseq


title: 38-33_T1_RNAseq


title: osbzip23D-RNASeq

description: RNA-Seq

source_name: ZH11-Four leaf stage seedling_OsbZIP23 mutant_drought

value: OsbZIP23 mutant


title: ZH11N-RNASeq

description: RNA-Seq

source_name: ZH11-Four leaf stage seedling_normal

tag: cultivar

value: Zhonghua 11 (ZH11)

value: wildtype


title: osbzip23N-RNASeq

description: RNA-Seq

source_name: ZH11-Four leaf stage seedling_OsbZIP23 mutant_normal


title: ZH11D-RNASeq

description: RNA-Seq

source_name: ZH11-Four leaf stage seedling_drought


title: OX-OsbZIP23N-OsbZIP23

description: Chromatin IP against OsbZIP23

data_processing:
For ChIP-seq, SOAP2 (version 2.1.0) was used to align the clean tags filtered by Trimmomatic (version 0.32) to the reference genome of Nipponbare (RGAP version 7.0). MACS (Version 1.4.2) was used for peak identification.
genome build: RGAP 7.0
processed data files format and content: tar archive with wig files of genome-wide signal, text files with MACS-called peaks.

source_name: ZH11-Four leaf stage seedling_OsbZIP23_overexpressed_normal

extract_protocol:
Seedlings were immediately cross-linking after harvest by 1% formaldehyde under vacuum. 3g of seedlings for each sample at the four-leaf stage were used for chromatin isolation. Isolated chromatin was sheared to approximately 100-500 bp by Diagenode® Bioruptor. For ChIP-Seq, the DNA was immunoprecipitated by anti-OsbZIP23 antibody (non-commercial antibody, generated by Abmart, Shanghai, China), and the precipitated DNA was purified and dissolved in distilled water.
The eluted ChIP DNA was used to generate Illumina sequencing libraries following the manufacturer's protocol. The eluted DNA from ChIP assay was used to generate Illumina sequencing libraries following the manufacturer's protocol.

tag: antibody

value: anti-OsbZIP23, Rabbit, Polyclonal


title: 38-33_T0_RNAseq


title: ZH11D-OsbZIP23

description: Chromatin IP against OsbZIP23


title: ZH11N-OsbZIP23

description: Chromatin IP against OsbZIP23


title: Veh_NS_Repl_2

city: Bethesda

first: Suman Kumar

last: Vodnala

state: MD

address: 10 Center Drive

department: Surgery Branch

institute: NCI

data_processing:
Sample reads were trimmed of adapters and low quality bases using Trimmomatic software.
Trimmed reads were aligned to the reference mouse genome mm9 using Tophat
FPKM values were calculated using Cufflinks and comapred between samples using Cuffdiff
Genome_build: mm9
Supplementary_files_format_and_content: Processed data files are tab-delimited text files containing FPKM values for each replicate RNA-Seq measurement

source_name: CD8+ T cells

growth_protocol: FACS purified CD8+, CD62L+, splenocytes, stimulated in distinct biological triplicates with 2 mcg /mL of anti CD3/28 for 48 hours in IL2 100 (IU/ml), then removed from anti CD3 and placed in media with IL2 100(IU/ml) for an additional 48 hours, rested overnight out of cytokine then restimulated on day 5

extract_protocol:
Total RNA was extracted using Qiagen RNeasy kits according to manufacturers instructions
mRNA samples were processed using the Clontech SMARTer Ultra low input RNA-v3 kit and sequenced using either an Illumina HiSeq 2500 (samples 1-12) or a Illumina HiSeq 2000 (samples 13-18)

treatment_protocol: On day 5 of culture, maintained in individual biologial triplicate cells were stimulated with immobilized anti-CD3/28 antibodies or kept in complete media (no stim) - with equivalent conditions treated with isotonic media containing elevated potassium as described in materials and methods

value: CD8+ T cells

value: male

tag: age

value: 8 weeks

tag: treatment

value: no stimulation

tag: media

value: vehicle


title: Veh_NS_Repl_0


title: K_NS_Repl_0

value: isotonic media containing elevated potassium


title: Veh_NS_Repl_1


title: K_NS_Repl_1


title: K_NS_Repl_2


title: K_Stim_Repl_2

value: stimulated with immobilized anti-CD3/28 antibodies


title: K_Stim_Repl_0


title: K_Stim_Repl_1


title: Veh_Stim_Repl_2


title: Veh_Stim_Repl_1


title: Veh_Stim_Repl_0


title: Atm null 2

first: Julian

last: Lange

address: 1275 York Avenue

department: Molecular Biology Program

institute: Memorial Sloan Kettering Cancer Center

description: SPO11-associated DNA oligonucleotides

data_processing:
Base calls were perfomed using HiSeq Control Software v.2.0.10.0 for samples sequenced on Illumina HiSeq 2500
Adaptors (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) were clipped from reads using fastx_clipper, part of the FASTX Toolkit 0.0.13.2, with parameters -l 15 -n -v -Q33 -i
First five bases (diffusion primer added in library prep) in each sequence were trimmed, and trimmed sequence was recorded in the FASTQ ID tag for downstream tracking
Clipped reads were mapped using gmapper-ls (2_1_1b) from the SHRiMP mapping package, with parameters -N 18 -U -g -1000 -q -1000 -m 10 -i -20 -h 100 -r 50% -n 1 -o 100001 -Q -E --sam- unaligned --strata
Sequences clipped from a read during mapping should be polyC on the 3′ end or polyG on the 5′ end. If clipped bases were not polyC or polyG the alignment score was corrected by deducting the mismatch score for each non-C,G base in the clipped sequence
Multi-mapped reads were assigned by imputation using version 2.4 of the CSEM method (Chung et al. 2011 PLoS Comput Biol) called as follows: sem-2.4/run-csem -- bam -p 12 --no-extending-reads --upper-bound 1000
Maps of 5' ends of sequence reads were compiled and analyzed in R versions 3.2.0 to 3.3.0
Genome_build: mm10
Supplementary_files_format_and_content: Seven txt files for each sample: (1) raw uniquely mapped reads at each non-zero base position in the genome, (2) raw imputed multi-mapped reads at each non-zero base position in the genome, (3) raw total mapped reads at each non-zero base position in the genome, (4) uniquely mapped RPM (per million uniquely mapped reads) at each non-zero base position in the genome, (5) uniquely mapped RPM (per million total mapped reads) at each non-zero base position in the genome, (6) imputed multi-mapped RPM (per million total mapped reads) at each non-zero base position in the genome, (7) total RPM (per million total mapped reads) at each non-zero base position in the genome

source_name: Spermatocytes

extract_protocol:
Based on Lange et al. 2011 Nature, with modifications. Testis lysates were prepared by Dounce-homogenization in lysis buffer (1% Triton X-100, 400 mM NaCl, 25 mM HEPES-NaOH at pH 7.4, 5 mM EDTA) and clarified by ultracentrifugation. Soluble protein was subjected to two successive rounds of affinity purification with a monoclonal anti-mSPO11 antibody and protein A-agarose beads. Protein was digested with proteinase K, and SPO11-associated oligonucleotides were recovered by ethanol precipitation.
Based on Pan et al. 2011 Cell, and Thacker et al. 2014 Nature, with modifications. Purified oligonucleotides were ribo-G-tailed on their 3′ ends using rGTP and terminal transferase, then tailed oligonucleotides were ligated to a duplex DNA adaptor with a 3′-CCCC overhang using T4 RNA ligase 2. The reverse complement of each oligonucleotide was synthesized by Klenow DNA polymerase, then purified by denaturing polyacrylamide gel electrophoresis. Purified complementary strands were ribo-G-tailed on their 3′ ends using rGTP and terminal transferase, then ligated to another duplex DNA adaptor using T4 RNA ligase 2. Ligated material was amplified with 14 cycles of PCR to add Illumina HiSeq adaptors.

value: Atm-/-

value: testis

value: adult (2-3 months)


title: Atm het

description: SPO11-associated DNA oligonucleotides

value: Atm+/-


title: U87_3T3_scRNAseq

description: U87 cells and 3T3 cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplimented with 10% (v/v) Fetal Bovine Serum (FBS).

organism:
Homo sapiens
Mus musculus

source_name: Brain and embyro


title: Atm wt

description: SPO11-associated DNA oligonucleotides

value: Atm+/+


title: B6

description: SPO11-associated DNA oligonucleotides

value: wild type


title: S2_NHS_RNA_seq

status: Public on Aug 12 2016

city: Cambridge

first: Fabiana

last: Duarte

state: MA

address: 7 Divinity Avenue

department: Stem Cell and Regenerative Biology

institute: Harvard University

description: processed data file: S2_NHS_30minHS_RNA_seq_FPKM_cuffnorm.txt

data_processing:
RNA-seq data processing: Illumina adapters were removed with the fastx_clipper tool (http://hannonlab.cshl.edu/fastx_toolkit/index.html) and sequencing reads shorter than 20 nucleotides were discarded. Reads were aligned to the Drosophila melanogaster dm3 reference genome/transcriptome using TopHat2 (Kim et al., 2013), with the following parameters: “--library-type fr-firststrand --no-novel-juncs”.
Genome_build: dm3
Supplementary_files_format_and_content: RNA-seq processed files: Table with the FPKM values for each gene in all samples and replicates. Values were generated using Cuffnorm (Trapnell et al., 2010), using the BAM files generated by TopHat2 as input.

organism: Drosophila melanogaster

source_name: S2 cell line

growth_protocol: Cells were grown in M3+BPYE media supplemented with 10% FBS

extract_protocol:
RNA extraction for RNA-seq: Cells were spun down, washed in cold 1x PBS once and total RNA was extracted using TRIzol reagent and then isolated from the aqueous phase using the E.Z.N.A. Total RNA Kit I (Omega Bio-tek).
RNA-seq library construction: PolyA+ RNA was isolated with the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). TruSeq-barcoded RNA-seq libraries were generated with the NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs). Each library was quantified with a Qubit 2.0 (dsDNA HS kit; Thermo Fisher Scientific) and the size distribution was determined with a Fragment Analyzer (Advanced Analytical) prior to pooling.

treatment_protocol: Cells were untreated or treated with double-stranded RNA against LacZ (control), GAF, HSF or M1BP. For the Heat Shock treatments, an equal volume of M3+BPYE medium (no serum) at 48°C was added to the cells, and the cultures were incubated at 37°C for the desired time.

tag: RNAi treatment

value: untreated

value: before heat shock (non-heat shock)


title: BCDGlu-2

city: Ansan

first: Se Kye

last: Kim

state: GYOENGGI-DO

address: 55 Hanyangdaehak-ro

department: Molecular and Life Science

country: South Korea

institute: Hanyang University ERICA

data_processing:
Illumina CASAVA v1.8.2 software was used for basecalling.
To avoid low-quality data, we clipped and trimmed the reads using Trimmomatic (v0.33)
For the analysis of differentially expressed genes, the data of quality-checked reads for each condition were processed with the Rockhopper (version 1.30) software based on reference genome sequence (Bacillus anthracis Sterne NC_005945)
Genome_build: Bacillus anthracis Sterne NC_005945
Supplementary_files_format_and_content: tab-delimited text files including normalized read counts for each sample

organism: Bacillus anthracis str. Sterne

source_name: codY gene (BAS3679) homologously replaced with kanamycin resistance cassette

growth_protocol: Cells were initially grown in rich brain heart infusion (Becton Dickinson, Franklin Lakes, NJ, USA) liquid media in 15 ml conical tubes, grown at 37°C with shaking for overnight. Cells were then inoculated to Ristroph medium (3.6 g yeast extract, 0.035 g tryptophan, 0.065 g glycine, 0.025 g cystine, 0.001 g thiamine, 0.0014 g uracil, 0.0021 g adenine sulfate, 2.5 g glucose, 0.0074 g CaCl2·H2O, 0.0099 g MgSO4·H2O, 3 g K2HPO4, 0.0009 g MnSO4·H2O, 8 g NaHCO3 in 1 L DW, pH 8.0) to OD600 of 0.05, grown at 37°C under 5% CO2 atmosphere.

extract_protocol:
RNA was extracted using RNAiso Plus (Takara, Shiga, Japan) and QIAGEN RNeasy® Mini kit (QIAGEN, Hilden, Germany) according to the manufacturer’s protocol. For RNA-Seq, RNA libraries were created from each group using the NEBNext® Ultra™ Directional RNA Library preparation kit from Illumina® (Illumina, San Diego, CA, USA). The first step in the workflow involved the removal of ribosomal RNA using the RNAMius™ Transcriptome Isolation kit (Life Technologies, Carlsbad, CA, USA).  Following purification, total RNA was fragmented into small pieces using divalent cations at elevated temperature. The cleaved RNA fragments were copied into first-strand cDNA using reverse transcriptase and random primers, followed by second-strand cDNA synthesis using DNA polymerase I and RNase H. The cDNA fragments were then processed through an end-repair reaction by the addition of a single ‘A’ base, followed by ligation of the adapters. The products of these reactions were then purified and enriched by PCR to create the final cDNA library. The cDNA fragments were sequenced using the Illumina HiSeq2000 (101 cycles PE lane)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For iron-depleted medium, Ristroph medium was treated with 450 μg 2,2'-dipyridyl (Sigma-Aldrich, St. Louis, MO, USA). For glucose starved condition, Ristroph medium was prepared without adding glucose. For CO2 depleted condition, Ristroph medium was prepared without adding NaHCO3 and grown under aerated atmosphere.

value: Sterne

tag: genotype/variation


title: S2_30minHS_RNA_seq

value: after 30min of heat shock


title: BCDGlu-3

value: codY gene (BAS3679) homologously replaced with kanamycin resistance cassette


title: BCDBic-2


title: 34F2Glu-3

source_name: wild-type 34F4

value: wild-type 34F4


title: 34F2Glu-1

source_name: wild-type 34F2

value: wild-type 34F2


title: 34F2Glu-2

source_name: wild-type 34F3

value: wild-type 34F3


title: BCDBic-1


title: 34F2Fe-1


title: BCDFe-2


title: 34F2Bic-1


title: 34F2Fe-3


title: BCDFe-1


title: BCDR-1


title: BCDFe-3


title: 34F2Fe-2


title: 34F2R-3


title: Atm null 1

description: SPO11-associated DNA oligonucleotides

tag: tissue


title: BCDR-2


title: BCDGlu-1


title: 34F2Bic-3


title: 34F2R-2


title: E12.5 Mutant rep3

city: London

first: Daniel

last: Dilg

address: 30 Guilford St

country: United Kingdom

institute: University College London

data_processing:
Illumina NextSeq 500
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using the Strand NGS 2.5 pipeline.
Genome_build: mm10
Supplementary_files_format_and_content: deseq_Dilg_E11.5cre_E11.5mut_differential_expression.tab: Fold change and z score at E11.5 between control and mutant
Supplementary_files_format_and_content: deseq_Dilg_E12.5cre_E12.5mut_differential_expression.tab: Fold change and z score at E12.5 between control and mutant
Supplementary_files_format_and_content: rpkm_values.csv: RPKM values for each Sample

source_name: E12.5 Mutant

extract_protocol:
Embryonic hearts were flash frozen and stored at -80 during genotyping. RNA extraction was done using QIAGEN
RNA libraries were prepared for sequencing using standard Illumina protocols

value: embryonic heart

value: embryonic stage 12.5


title: 34F2R-1


title: E12.5 Mutant rep2


title: BCDBic-3


title: BCDR-3


title: E11.5 Mutant rep3

source_name: E11.5 Mutant

value: embryonic stage 11.5


title: E11.5 Mutant rep2


title: 34F2Bic-2


title: E12.5 Mutant rep1


title: E12.5 Cre control rep3

source_name: E12.5 Cre control


title: E11.5 Mutant rep1


title: E12.5 Cre control rep2


title: E11.5 Cre control rep3

source_name: E11.5 Cre control


title: E11.5 Cre control rep1


title: ISW1a-Replicate2 [MNase-Seq] [PSU51302]

tag: sample type

value: in vitro

tag: genomic dna strain

value: GRF88, MATa his4-38, S288C background

tag: histone source

value: Drosophila embryo


title: CD11c- P3

city: Milwaukee

first: William

last: Drobyski

state: WI

address: 8701 Watertown Plank Road

department: Medicine

institute: Medical College of Wisconsin

data_processing:
Basecalls performed using Illumina software on HiSeq 2500
Sequenced reads were aligned to the mm9 genome using MapSplice version 2.1.4 and the pre-built mm9 Bowtie index with the following configurations: --fusion --bam
Mapped reads were sorted and indexed using samtools version 1.2
Reads were translated into transcirptome coordinates and filtered for indels, large insterts, and zero mapping quality
Transcirptome coordinates were inputted into RSEM version 1.1.13 with pre-built RSEM mm9 references and the following configurations: --paired-end --bam --estimate-rspd
Gene expression data was normalized to set the upper quartile count at 1000
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files including normalized gene expression data for each sample

source_name: T cells

extract_protocol:
Extracted using Qiagen RNEasy Micro Kit
Clontech SMARTer Ultra Low kit

treatment_protocol: Sorted two CD4+ T cell populations that were compared by RNA seq using flow cytometry

value: spleen, lymph nodes

tag: sample population


title: CD11c- P1


title: HIRA Input

data_processing:
Libraries were prepped using the NEB DNA Ultra kit, with bead bases size selection for an insert ~200bp
sequenced on the Illumina NextSeq 500, v2 chemistry
Data were aligned using Bowtiev2
peaks were called using MACS (P≤10^4)
Relevant peaks were validated by qChIP
Genome_build: mm10
Supplementary_files_format_and_content: Bed file of peaks under mm10

source_name: 30 E12.5 CD1 Wild Type hearts pooled

growth_protocol: 2 Wild type (CD1) plugged mice were culled on the same day and a total of 30 embryonic hearts were pooled

extract_protocol:
In parallel to sonication step, antibodies were coupled to magnetic beads (dynabeads InVitrogen, 112.03D, 112.01D) for at least 4 hours and washed 3 times in LB3. 10% of input was taken and protein–DNA complexes were selectively immunoprecipitated using WC15 antibody against HIRA, rolling overnight. Beads were then washed once with 20mM tris pH 8.0, 150mM NaCl, 0.1% SDS, 1% Triton, 2mM EDTA (WB1), once with 20mM Tris pH 8.0, 500mM NaCl, 0.1% SDS, 1% Triton, 2mM EDTA (WB2), once with 10mM Tris pH 8.0, 150mM LiCl, 1% NP-40, 1% DOC, 1mM EDTA, then TE 10:1, 50mM NaCl (WB3), and finally in TE 10:1. Samples were treated overnight with 50mM Tris pH 8.0, 10mM EDTA and 1% SDS at 65°C (elution buffer), to reverse cross-linking, then with RNAse (Qiagen, 19101) for an hour at 25°C and with PK for 2h at 56°C. DNA was purified with QIAGEN’s PCR purification kit (28104).
Libraries were prepped using the NEB DNA Ultra kit, with bead bases size selection for an insert ~200bp

treatment_protocol: 30 E12.5 hearts were pooled (equivalent to 10 million cells for ESC experiments), washed in PBS and cross-linked for 45 min with 1.5mM of EGS (Sigma, E3257), followed by 15min of 1% formaldehyde (from a freshly made filtered stock at 18.5%) at 37°C. The reaction was quenched by the addition of 125mM of Glycine, left for 15min at RT. Hearts/cells were lysed in 50mM Hepes-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton, 1X anti-protease cocktail (Roche, 04693132001), 1mM PMSF for 10 min at 4°C (LB1). The hearts/cells were briefly spun down resuspended in 10mM Tris-HCL pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, 1X anti-protease cocktail, 1mM PMSF for 10 min at 4°C (LB2). Finally the hearts/cells were resuspended in10mM Tris-HCL pH 8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% DOC, 0.5% N-Lauroylsarcosine, 1X anti-protease cocktail and 1mM PMSF rolling o/n at 4°C (LB3).

tag: strain

value: WT

value: heart

tag: chip antibody


title: S2_LacZ_RNAi_NHS_PRO_seq (from_M1BP_RNAi)

data_processing:
Library strategy: PRO-seq
PRO-seq data processing: Raw sequencing reads were processed using the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html). Illumina adapters were removed with the fastx_clipper tool and reads were trimmed to 26-mers using fastx_trimmer. Sequencing reads shorter than 15 nucleotides were discarded. fastx_reverse_complement was then used to generate the reverse complement of the sequencing reads, which correspond to the sense strand of nascent RNA in the nucleus. Reads were aligned uniquely to the Drosophila melanogaster dm3 reference genome using Bowtie (Langmead et al., 2009) with up to two mismatches. Replicates were highly correlated and were pooled for further analyses.
Genome_build: dm3
Supplementary_files_format_and_content: PRO-seq processed files: Normalized bedgraph files with the combined data for both replicates. Each entry in the bedgraph file represents the number of reads at each position with base-pair resolution. PRO-seq data is strand specific, so a ‘plus’ and a ‘minus’ strand file are provided for each sample. See the accompanying publication for a detailed description of the normalization method used.

extract_protocol:
Nuclei isolation for PRO-seq: Nuclei isolation was performed using standard protocols. Briefly, cells were spun down, washed in cold 1x PBS once and then resuspended in 1mL of cold Swelling buffer (10mM Tris-Cl pH 7.5, 10% glycerol, 3mM CaCl2, 2mM MgAc2, 0.5mM DTT). After incubation on ice for 10 minutes, cells were transferred to a dounce homogenizer and 9mL of cold Lysis buffer (10mM Tris-Cl pH 7.5, 300mM sucrose, 10mM NaCl, 3mM CaCl2, 2mM MgAc2, 0.1% TritonX-100, 0.5mM DTT) was added. After douncing, the cells were spun down, washed in 10mL of cold Lysis buffer and resuspended in 1mL of cold buffer D (50mM Tris-Cl pH 8.0, 25% glycerol, 5mM MgAc2, 0.1mM EDTA, 5mM DTT). Next, cells were spun down again, resuspended in buffer D and flash frozen in liquid nitrogen.
PRO-seq library construction: PRO-seq libraries were prepared as described previously (Kwak et al., 2013). Briefly, 2×10^7 nuclei were added to 2x Nuclear Run-On reaction mix (10mM Tris-Cl pH 8.0, 5mM MgCl2, 300mM KCl, 1% Sarkosyl, 1mM DTT, 0.05mM each of biotin-11-A/C/G/UTP (PerkinElmer), 0.4 u/µL RNase inhibitor) and incubated for 3 min at 30°C. Total RNA was extracted and fragmented by base hydrolysis in 0.2N NaOH on ice for 10 min, and neutralized by adding 1x volume of 1M Tris-Cl pH 6.8. Fragmented nascent RNA was purified using streptavidin beads, ligated with reverse 3' RNA adapter (5'p-GAUCGUCGGACUGUAGAACUCUGAAC-/3'InvdT/), and biotin-labeled products were enriched by another round of streptavidin bead binding and extraction. For 5' end repair, the RNA products were successively treated with tobacco acid pyrophosphatase (TAP, Epicentre) and polynucleotide kinase (PNK, New England Biolabs). 5' repaired RNA was ligated to reverse 5' RNA adapter (5'-CCUUGGCACCCGAGAAUUCCA-3') before being further purified by a third round of streptavidin bead binding and extraction. RNA was reverse transcribed using the Illumina RP1 primer. TruSeq-barcoded libraries were generated by PCR amplification and products greater than 120 bp were PAGE purified and pooled for sequencing.

tag: cell line

value: S2 cell line

value: LacZ-RNAi

tag: time point


title: S2_M1BP_RNAi_NHS_PRO_seq

value: before heat shock (non-heat shock)


title: E12.5 Cre control rep1

tag: genotype


title: HIRA ChIPSeq

value: WC15 HIRA Ab


title: TFH91_WGBS

city: Atlanta

first: Soojin

middle: V

last: Yi

state: GA

address: 950 Atlantic Dr

department: School of Biology

institute: Georgia Institute of Technology

description: Whole genome bisulfite sequencing

data_processing:
Quality and adaptor trimming was performed using TrimGalore! with default parameters
Reads were mapped to rheMac3 and methylation calling was done using Bismark or BSMap with default parameters
Duplicates were removed after mapping
Genome_build: rheMac3
Supplementary_files_format_and_content: *Bismark.bed = BED file with coordinates, methylated and total reads per CpG. Read mapped using Bismark.; *BsMap.bed = BED file with coordinates, methylated and total reads per CpG. Read mapped using BsMap.

organism: Macaca mulatta

source_name: Prefrontal Cortex

extract_protocol:
genomic DNA was extracted following the Qiagen DNeasy Blood & Tissue Kit
Paired-end BS-seq libraries for Illumina sequencing were constructed according to Lister et al.(2009) with minor modifications. In brief, 300 - 500 ng of genomic DNA was fragmented by sonication, end repaired and ligated to custom-synthesized methylated adapters (Eurofins MWG Operon, Huntsville, AL) according to manufacturer’s (Illumina, San Diego, CA) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (Qiagen, Valencia, CA) as outlined in the manufacturer’s instructions. Five to ten ng of bisulfite-converted libraries was PCR amplified with the following condition: 2.5 U of ExTaq DNA polymerase (Takara), 5 μl of 10X Extaq reaction buffer, 25 μM dNTPs, 1 μl Primer 1.1, 1 μl Primer 2.1 (50 μl final). The thermocyling was as follows: 95°C 3 min, then 10 cycles of 95°C 30 sec, 65°C 30 sec and 72°C 60 sec. The enriched libraries were purified twice with SPRI method using AMPure beads (Beckman Coulter, Inc. Brea CA).

value: Brain

tag: brain region

value: Prefrontal Cortex

tag: Sex

value: Male


title: CD11c- P2

tag: cell type


title: DIS3_RRP6_FRB_t60_ePAP

city: Los Angeles

first: Kevin

last: Roy

state: CA

address: 607 Charles E. Young Drive East

department: Chemistry and Biochemistry

institute: UCLA

description: RNA extracted from yeast cultures, Dnase I-treated, polyadenylated and rRNA subtracted

data_processing:
Reads were trimmed with TrimGalore v0.4.0 requiring a minimum final length of 15 nucleotides.
Trimmed reads were mapped using RNA-STAR v2.4.0k to the R64-2-1 version of the S.cerevisiae genome obtained from the Saccharomyces genome database (SGD) using default mapping parameters and allowing only uniquely mapped reads (Dobin et al., 2013).
5´ ends of reads at each chromosomal coordinate were aggregated to generate bedgraphs with the bedtools v2.25.0 genomecov function.
Mapped positions were first filtered for A/G richness in the immediate genomic region downstream.  Poly(A) sites with six genomically encoded A nucleotides downstream (with up to two G nucleotides) were flagged as potential internal oligo-dT mis-priming events and excluded from the analysis.
Analysis of the most abundant internal priming events by-passing this filter revealed that A-richness in across an 18 bp region explained internal priming events not flagged by the 6 bp filter.  Therefore, as an additional stringency filter, we excluded poly(A)-sites with 12 or more adenosines present in these downstream 18 nt. On the order of ~1% of sequencing reads involving long stretches of T’s, possibly due to priming internal to the poly(A) tail or due to a low level of contamination of the sequencer with Illumina Read 1 primer. As an additional quality control step, poly(A) sites were flagged if the preceding 15 or more nucleotides were adenosines.
The total reads for each bedgraph (both strands combined) remaining after filtering steps were normalized to 1 million.
Genome_build: R64-2-1 version of the S288C genome of S.cerevisiae (Saccharomyces genome database)
Supplementary_files_format_and_content: bedgraph with each strand separate

source_name: yeast cultures

growth_protocol: cultures were grown in YPD (1% yeast extract, 2% bacto-peptone, 2% dextrose) at 30°C at 200 rpm and harvested at OD 0.4 to 0.6

extract_protocol:
All cultures were harvested by centrifugation at 4000 rpm for 2 minutes, washed in deionized water, and spun down in microcentrifuge tubes. The supernatant was removed and pellets were flash-frozen in liquid nitrogen and stored at -80°C. RNA was extracted by standard phenol/chloroform extraction and DNase I-treated.
For the WT and rrp6Δ samples, libraries were prepared per the manufacturer’s protocol. For all other samples, the reverse transcription (RT) was performed at 42°C instead of 37°C to minimize imperfect priming between the oligo-dT primer and internal A-rich sequences. After denaturation and annealing of the RNA and the RT primer, the samples were kept on the heating block while 42°C pre-warmed RT enzyme solution was added to each sample. For samples with RT performed at 42°C, 15 PCR cycles instead of 12 were performed to compensate for decreased RT yields.
A subset of samples (labeled "ePAP") were treated with E.coli poly(A) polymerase in vitro prior to library preparation. 10 ug of total RNA was treated with ATP and E.coli poly(A) polymerase in a total volume of 20 ul at 37°C for 30 minutes, according to manufacturer’s recommendations (NEB #M0276L). After phenol/chloroform extraction and ethanol precipitation, 5 ug of RNA was subjected to rRNA depletion with Ribo-Zero Gold rRNA Removal Kit (Illumina, Inc.), prior to 3´-end poly(A)+  library preparation.

treatment_protocol: For anchor away experiments, WT HHY168 and FRB-tagged strains were treated for one hour with 0.1% v/v 1 mg/mL rapamycin (in 90% ethanol, 10% Tween-20) to yield a final concentration of 1 μg/mL.

tag: strain genotype

value: HHY168 fpr1Δ::hphMX4 DIS3-FRB::kanMX6 RRP6-FRB::His

tag: genetic background

value: W303 derivative

tag: mating type

value: alpha


title: E11.5 Cre control rep2

value: embryonic heart

tag: age

value: embryonic stage 11.5


title: S2_LacZ_RNAi_20minHS_PRO_seq (from_M1BP_RNAi)

tag: RNAi treatment

value: after 20min of heat shock


title: S2_M1BP_RNAi_20minHS_PRO_seq


title: CD11c+ P3

tag: tissue


title: TFH92_WGBS

description: Whole genome bisulfite sequencing


title: PilotDesign_SV40P_Plasmid_Rep2

first: Jason

last: Ernst

address: 615 Charles E Young Dr South

department: Biological Chemistry

description: Pilot Design 2 (30-bp steps), MPRA plasmid pool, replicate 2

data_processing:
To infer the tag copy numbers in each Tag-Seq library, all sequence reads were examined, regardless of their quality scores. If the first ten nucleotides of a read perfectly matched one of the 54K (pilot) or ~ 244K (scale-up) designed tags and the remaining nucleotides matched the expected upstream MPRA construct sequence, this was counted as one occurrence of that tag. All reads that did not meet this criterion were discarded.
Genome_build: hg19 for coordinates in *ScaleUpDesign*.counts.txt file
Supplementary_files_format_and_content: The first tab delimited column contains the construct ID, the second column the DNA sequence to which it corresponds, the third column all the barcode tag IDs in comma delimited form if more than one, the fourth column the corresponding counts for the tags also in comma delimited form if more than one. In the ScaleUpDesign construct IDs are of form CELLTYPE_STATE_REGIONINSTATE_TILEPOS_chr_center where CELLTYPE and STATE are the cell type and chromatin state based on which the regulatory region was selected, REGIONINSTATE is an ID among selections from the CELLTYPE and STATE combination, TILEPOS is the tile position and ranges from 0 to 30 where TILEPOS=0 is the first tile, and chr and center and the chromosome and coordinate of the center base (hg19) of the regulatory region being tiled. In the PilotDesign construct IDs are of the form GROUP_REGIONIDINGROUP_TILEPOS. GROUP is from the set {high,range,controlhigh} where high corresponds to regions selected based on being in candidate enhancer chromatin states in HepG2 with the strongest H3K27ac dip scores, range represents enhancers with a range of dip scores, and controlhigh are locations in candidate enhancers in K562 but not HepG2. REGIONIDINGROUP is an ID among selections in the GROUP. TILEPOS is the tile position and ranges from 0 to 8 where TILEPOS=0 is the first tile.

organism: Escherichia coli

source_name: Plasmid pool

extract_protocol:
Total RNA was isolated from cell lysates using RNeasy kits (Qiagen). mRNA was extracted from total RNA using MicroPoly(A)Purist™ kits (Ambion) and treated with DNase I using the Turbo DNA-free™ kit (Ambion).
First-strand cDNA was synthesized from 400-700 ng mRNA using High Capacity RNA-to-cDNA kits (Applied Biosystems). Tag-Seq sequencing libraries were generated directly from 12% of a cDNA reaction or 50 ng plasmid DNA by 26 cycle PCR using Pfu Ultra HS DNA polymerase 2x master mix (Agilent) and primers AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT and CAAGCAGAAGACGGCATACGAGATXXXXXXXXGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCGAGGTGCCTAAAGG (where XXXXXXXX is a library-specific index sequence). The resultant PCR products were size-selected using 2% agarose E-Gel EX (Invitrogen).

tag: source

value: plasmid

tag: promoter


title: CD11c+ P2

value: spleen, lymph nodes

tag: sample population


title: WT_HHY168_t60_ePAP

value: HHY168 fpr1Δ::hphMX4


title: CD11c+ P1


title: REB1_RRP6_FRB_t60

description: RNA extracted from yeast cultures and Dnase I-treated

value: HHY168 fpr1Δ::hphMX4 REB1-FRB::kanMX6 RRP6-FRB::His


title: K562_PilotDesign_SV40P_mRNA_Rep2

description: Pilot Design (30-bp steps), reporter mRNA, replicate 2

source_name: K562 cells


title: SEN1_RRP6_FRB_t60_rep1

value: HHY168 fpr1Δ::hphMX4 SEN1-FRB::kanMX6 RRP6-FRB::His


title: DIS3_RRP6_FRB_t60_rep2


title: DIS3_RRP6_FRB_t60_rep1


title: PilotDesign_SV40P_Plasmid_Rep1

description: Pilot Design 1 (30-bp steps), MPRA plasmid pool, replicate 1


title: K562_PilotDesign_SV40P_mRNA_Rep1

description: Pilot Design (30-bp steps), reporter mRNA, replicate 1


title: SEN1_RRP6_FRB_t60_rep2


title: HepG2_PilotDesign_SV40P_mRNA_Rep2

source_name: HepG2 cells


title: RRP6_FRB_t60_rep1

value: HHY168 fpr1Δ::hphMX4 RRP6-FRB::His


title: S2_20minHS_PRO_seq

data_processing:
library strategy: PRO-seq
PRO-seq data processing: Raw sequencing reads were processed using the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html). Illumina adapters were removed with the fastx_clipper tool and reads were trimmed to 26-mers using fastx_trimmer. Sequencing reads shorter than 15 nucleotides were discarded. fastx_reverse_complement was then used to generate the reverse complement of the sequencing reads, which correspond to the sense strand of nascent RNA in the nucleus. Reads were aligned uniquely to the Drosophila melanogaster dm3 reference genome using Bowtie (Langmead et al., 2009) with up to two mismatches. Replicates were highly correlated and were pooled for further analyses.
Genome_build: dm3
Supplementary_files_format_and_content: PRO-seq processed files: Normalized bedgraph files with the combined data for both replicates. Each entry in the bedgraph file represents the number of reads at each position with base-pair resolution. PRO-seq data is strand specific, so a ‘plus’ and a ‘minus’ strand file are provided for each sample. See the accompanying publication for a detailed description of the normalization method used.

value: untreated


title: RRP6_FRB_t60_rep2


title: WT_HHY168_t60_rep2


title: BDP1_RRP6_FRB_t60

value: HHY168 fpr1Δ::hphMX4 BDP1-FRB::kanMX6 RRP6-FRB::His


title: HepG2_PilotDesign_SV40P_mRNA_Rep1


title: WT_HHY168_t60_rep1


title: rrp6D_BMA64_rep2


title: autism-PFC-21900d [aut34]

city: Shanghai

first: Xiling

last: Liu

address: 320 Yue Yang Road

country: China

institute: Partner Institute for Computational Biology

description: RNA-seq data from post-mortem superior frontal gyrus of a autistic patient with age of 21900 days

data_processing:
The raw sequencing reads were mapped to each species’ reference genome and the splice junctions using Bowtie, allowing up to three mismatches.
Only uniquely mapped reads were used to calculate the gene expression levels.
Gene expression levels were calculated using the read coverage normalized by gene length and the total number of reads mapped to genes in a sample.
Genome_build: human: hg19; chimpanzee: panTro3.
Supplementary_files_format_and_content: tab-delimited text file shows RPKM values of each gene in each sample.

source_name: dissected human post-mortem superior frontal gyrus

extract_protocol:
Total RNA was isolated using Trizol® reagent (Invitrogen, Carlsbad, CA).
Sequencing libraries were prepared with TruSeq RNA Sample Preparation Kit (Illumina) according to manufacturer’s instruction.

treatment_protocol: PFC dissections were made from the frontal part of the superior frontal gyrus.

tag: sample group

value: autistic patient

tag: gender

value: male

value: superior frontal gyrus of the brain


title: autism-PFC-18980d [aut33]

description: RNA-seq data from post-mortem superior frontal gyrus of a autistic patient with age of 18980 days

value: female


title: S2_10minHS_PRO_seq

source_name: S2 cell line

tag: cell line

value: after 10min of heat shock


title: WT_BMA64_rep2

value: alpha


title: WT_BMA64_rep1


title: autism-PFC-18250d [aut32]

description: RNA-seq data from post-mortem superior frontal gyrus of a autistic patient with age of 18250 days


title: rrp6Δ::hphMX4 rep 1

data_processing:
Reads were mapped by SeqLL, LLC to the R64-2-1 version of the S.cerevisiae genome obtained from the Saccharomyces genome database (SGD) with the HeliSphere mapping pipeline using default parameters (minlen=15 minscore=4.3 bo=1 ga=none) and only uniquely mapped reads were allowed.
SeqLL, LLC provided bam files of mapped reads, which were converted to sam files with samtools view function.
5´ ends of reads at each chromosomal coordinate were aggregated to generate bedgraphs with the bedtools v2.25.0 genomecov function.
Mapped positions were first filtered for A/G richness in the immediate genomic region downstream.  Poly(A) sites with six genomically encoded A nucleotides downstream (with up to two G nucleotides) were flagged as potential internal oligo-dT mis-priming events and excluded from the analysis.
3´-end sequencing can only determine poly(A) sites to a precision based on the length of homo-adenosines encoded within the genome, so remaining poly(A) sites with the first sequenced nucleotide being an A were shifted to the nearest upstream non-adenosine.
The total reads for each bedgraph (both strands combined) remaining after filtering steps were normalized to 1 million.
Genome_build: R64-2-1 version of the S288C genome of S.cerevisiae (Saccharomyces genome database)
Supplementary_files_format_and_content: bedgraph with each strand separate

extract_protocol:
All cultures were harvested by centrifugation at 4000 rpm for 2 minutes, washed in deionized water, and spun down in microcentrifuge tubes. The supernatant was removed and pellets were flash-frozen in liquid nitrogen and stored at -80°C. RNA was extracted by standard phenol/chloroform extraction and DNase I-treated.
RNA was sequenced by directly loading onto oligo-dT flow cells, thus no library preparation is involved.
3´-end sequencing of poly(A)+ RNA

treatment_protocol: Cultures were harvested in log phase with no treatment.

value: MATa; ura3-1; trp1delta 2; leu2-3,112; his3-11,15; ade2-1; can1-100 rrp6delta::hphMX4


title: WT


title: ScaleUpDesign2_SV40P_Plasmid

description: Scale-up Design 2 (5-bp steps), MPRA plasmid pool, replicate 1 and 2


title: autism-PFC-17885d [aut31]

description: RNA-seq data from post-mortem superior frontal gyrus of a autistic patient with age of 17885 days


title: ScaleUpDesign2_minP_Plasmid

value: minimal TATA


title: S2_30secHS_PRO_seq

tag: time point

value: after 30sec of heat shock


title: S2_2minHS_PRO_seq

value: after 2min of heat shock


title: ScaleUpDesign1_minP_Plasmid

description: Scale-up Design 1 (5-bp steps), MPRA plasmid pool, replicate 1 and 2

value: plasmid


title: S2_NHS_PRO_seq

value: before heat shock (non-heat shock)


title: autism-PFC-14235d [aut29]

description: RNA-seq data from post-mortem superior frontal gyrus of a autistic patient with age of 14235 days


title: ScaleUpDesign1_SV40P_Plasmid


title: S2_5minHS_PRO_seq

value: after 5min of heat shock


title: autism-PFC-14235d [aut30]


title: chimpanzee-PFC-14564d [ptr38]

description: RNA-seq data from post-mortem superior frontal gyrus of a chimpanzee with age of 14564 days

organism: Pan troglodytes

source_name: dissected chimpanzee post-mortem superior frontal gyrus

value: chimpanzee; non-human primate


title: S2_HSF_RNAi_NHS_PRO_seq

value: HSF-RNAi


title: chimpanzee-PFC-15549d [ptr39]

description: RNA-seq data from post-mortem superior frontal gyrus of a chimpanzee with age of 15549 days


title: S2_GAF_RNAi_20minHS_PRO_seq

value: GAF-RNAi

value: after 20min of heat shock


title: chimpanzee-PFC-12592d [ptr36]

description: RNA-seq data from post-mortem superior frontal gyrus of a chimpanzee with age of 12592 days


title: chimpanzee-PFC-12784d [ptr37]

description: RNA-seq data from post-mortem superior frontal gyrus of a chimpanzee with age of 12784 days


title: chimpanzee-PFC-11826d [ptr35]

description: RNA-seq data from post-mortem superior frontal gyrus of a chimpanzee with age of 11826 days


title: rrp6D_BMA64_rep1


title: autism-PFC-10950d [aut27]

description: RNA-seq data from post-mortem superior frontal gyrus of a autistic patient with age of 10950 days

value: autistic patient


title: chimpanzee-PFC-11388d [ptr34]

description: RNA-seq data from post-mortem superior frontal gyrus of a chimpanzee with age of 11388 days

value: male


title: chimpanzee-PFC-11242d [ptr33]

description: RNA-seq data from post-mortem superior frontal gyrus of a chimpanzee with age of 11242 days

value: superior frontal gyrus of the brain


title: autism-PFC-10950d [aut28]


title: chimpanzee-PFC-10585d [ptr32]

description: RNA-seq data from post-mortem superior frontal gyrus of a chimpanzee with age of 10585 days


title: chimpanzee-PFC-10548d [ptr31]

description: RNA-seq data from post-mortem superior frontal gyrus of a chimpanzee with age of 10548 days


title: autism-PFC-10950d [aut26]


title: S2_LacZ_RNAi_20minHS_PRO_seq

value: LacZ-RNAi


title: autism-PFC-10585d [aut25]

description: RNA-seq data from post-mortem superior frontal gyrus of a autistic patient with age of 10585 days

value: female


title: autism-PFC-10585d [aut24]


title: S2_LacZ_RNAi_NHS_PRO_seq


title: chimpanzee-PFC-9636d [ptr29]

description: RNA-seq data from post-mortem superior frontal gyrus of a chimpanzee with age of 9636 days

value: 9636 days


title: S2_HSF_RNAi_20minHS_PRO_seq


title: chimpanzee-PFC-8796d [ptr27]

description: RNA-seq data from post-mortem superior frontal gyrus of a chimpanzee with age of 8796 days

value: 8796 days


title: ezh2-/-_replicate_2 + Hotair

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

data_processing:
Sequenced reads were trimmed for adaptor sequence, And  mapped to hg19 whole genome using  tophat_2.0.6, Method: Global alignment - No mismatch in seed alignment (of size 22), 3 mismatches in read length, Keep uniques best hits - Library type: Fr-firststr
reads count estimation with HTSeq-0.6.1
differential expression with R (R-3.2.0), Limma 3.24.13  packages, EdgeR 3.10.2 packages
Genome_build: hg19

source_name: MDA-MB-231 human breast cancer cell lines

extract_protocol:
RNA was extracted from cells resuspended in Trizol reagent. 1.5 ug of total RNA was used to prepare RNA library sequeced by Illumina HiSeq 2500.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: breast

tag: genotype

value: ezh2-/-; hotair overexpressed


title: autism-PFC-9855d [aut23]

description: RNA-seq data from post-mortem superior frontal gyrus of a autistic patient with age of 9855 days

value: 9855 days


title: chimpanzee-PFC-8724d [ptr26]

description: RNA-seq data from post-mortem superior frontal gyrus of a chimpanzee with age of 8724 days

value: 8724 days


title: ezh2-/-_replicate_1 + Hotair


title: chimpanzee-PFC-8286d [ptr25]

description: RNA-seq data from post-mortem superior frontal gyrus of a chimpanzee with age of 8286 days

value: 8286 days


title: chimpanzee-PFC-7848d [ptr24]

description: RNA-seq data from post-mortem superior frontal gyrus of a chimpanzee with age of 7848 days

value: 7848 days


title: wt_replicate_2 + Hotair

value: wild type; hotair overexpressed


title: autism-PFC-8030d [aut21]

description: RNA-seq data from post-mortem superior frontal gyrus of a autistic patient with age of 8030 days

value: 8030 days


title: S2_GAF_RNAi_NHS_PRO_seq

value: GAF-RNAi

value: before heat shock (non-heat shock)


title: wt_replicate_1 + Hotair


title: autism-PFC-8760d [aut22]

description: RNA-seq data from post-mortem superior frontal gyrus of a autistic patient with age of 8760 days

value: autistic patient

value: 8760 days


title: autism-PFC-7577d [aut20]

description: RNA-seq data from post-mortem superior frontal gyrus of a autistic patient with age of 7577 days

value: 7577 days

value: superior frontal gyrus of the brain


title: chimpanzee-PFC-7482d [ptr21]

description: RNA-seq data from post-mortem superior frontal gyrus of a chimpanzee with age of 7482 days

value: chimpanzee; non-human primate

value: female

value: 7482 days


title: chimpanzee-PFC-7811d [ptr23]

description: RNA-seq data from post-mortem superior frontal gyrus of a chimpanzee with age of 7811 days

value: 7811 days


title: autism-PFC-7300d [aut19]

description: RNA-seq data from post-mortem superior frontal gyrus of a autistic patient with age of 7300 days

value: male

value: 7300 days


title: chimpanzee-PFC-7774d [ptr22]

description: RNA-seq data from post-mortem superior frontal gyrus of a chimpanzee with age of 7774 days

value: 7774 days


title: chimpanzee-PFC-9892d [ptr30]

description: RNA-seq data from post-mortem superior frontal gyrus of a chimpanzee with age of 9892 days

value: 9892 days


title: chimpanzee-PFC-6752d [ptr19]

description: RNA-seq data from post-mortem superior frontal gyrus of a chimpanzee with age of 6752 days

value: 6752 days


title: ezh2-/-_replicate_2

value: breast


title: ezh2-/-_replicate_1


title: autism-PFC-6935d [aut18]

description: RNA-seq data from post-mortem superior frontal gyrus of a autistic patient with age of 6935 days

value: 6935 days


title: chimpanzee-PFC-6570d [ptr18]

description: RNA-seq data from post-mortem superior frontal gyrus of a chimpanzee with age of 6570 days

value: 6570 days


title: autism-PFC-6570d [aut17]

description: RNA-seq data from post-mortem superior frontal gyrus of a autistic patient with age of 6570 days


title: wt_replicate_2

value: wild type


title: chimpanzee-PFC-9308d [ptr28]

description: RNA-seq data from post-mortem superior frontal gyrus of a chimpanzee with age of 9308 days

value: 9308 days


title: wt_replicate_1


title: K562_ScaleUpDesign2_SV40P_mRNA_Rep2

description: Scale-up Design 2 (5-bp steps), reporter mRNA, replicate 2


title: chimpanzee-PFC-6132d [ptr16]

description: RNA-seq data from post-mortem superior frontal gyrus of a chimpanzee with age of 6132 days

value: 6132 days


title: autism-PFC-5236d [aut15]

description: RNA-seq data from post-mortem superior frontal gyrus of a autistic patient with age of 5236 days

value: autistic patient

value: 5236 days


title: autism-PFC-5475d [aut16]

description: RNA-seq data from post-mortem superior frontal gyrus of a autistic patient with age of 5475 days

value: 5475 days

value: superior frontal gyrus of the brain


title: chimpanzee-PFC-6059d [ptr15]

description: RNA-seq data from post-mortem superior frontal gyrus of a chimpanzee with age of 6059 days

value: chimpanzee; non-human primate

value: female

value: 6059 days


title: chimpanzee-PFC-7373d [ptr20]

description: RNA-seq data from post-mortem superior frontal gyrus of a chimpanzee with age of 7373 days

value: 7373 days


title: chimpanzee-PFC-4415d [ptr14]

description: RNA-seq data from post-mortem superior frontal gyrus of a chimpanzee with age of 4415 days

value: male

value: 4415 days


title: K562_ScaleUpDesign2_SV40P_mRNA_Rep1

description: Scale-up Design 2 (5-bp steps), reporter mRNA, replicate 1


title: chimpanzee-PFC-3978d [ptr13]

description: RNA-seq data from post-mortem superior frontal gyrus of a chimpanzee with age of 3978 days

value: 3978 days


title: autism-PFC-4015d [aut13]

description: RNA-seq data from post-mortem superior frontal gyrus of a autistic patient with age of 4015 days

value: 4015 days


title: K562_ScaleUpDesign1_SV40P_mRNA_Rep2

description: Scale-up Design 1 (5-bp steps), reporter mRNA, replicate 2


title: K562_ScaleUpDesign2_minP_mRNA_Rep2

value: minimal TATA


title: K562_ScaleUpDesign2_minP_mRNA_Rep1


title: chimpanzee-PFC-3796d [ptr12]

description: RNA-seq data from post-mortem superior frontal gyrus of a chimpanzee with age of 3796 days

value: 3796 days


title: chimpanzee-PFC-525d [ptr10]

description: RNA-seq data from post-mortem superior frontal gyrus of a chimpanzee with age of 525 days

value: 525 days


title: autism-PFC-3285d [aut10]

description: RNA-seq data from post-mortem superior frontal gyrus of a autistic patient with age of 3285 days

value: 3285 days


title: chimpanzee-PFC-2313d [ptr11]

description: RNA-seq data from post-mortem superior frontal gyrus of a chimpanzee with age of 2313 days

value: 2313 days


title: chimpanzee-PFC-6497d [ptr17]

description: RNA-seq data from post-mortem superior frontal gyrus of a chimpanzee with age of 6497 days

value: 6497 days


title: K562_ScaleUpDesign1_SV40P_mRNA_Rep1

description: Scale-up Design 1 (5-bp steps), reporter mRNA, replicate 1


title: autism-PFC-3224d [aut9]

description: RNA-seq data from post-mortem superior frontal gyrus of a autistic patient with age of 3224 days

value: autistic patient

value: 3224 days


title: chimpanzee-PFC-45d [ptr9]

description: RNA-seq data from post-mortem superior frontal gyrus of a chimpanzee with age of 45 days

value: 45 days

value: superior frontal gyrus of the brain


title: K562_ScaleUpDesign1_minP_mRNA_Rep2


title: input DNA, HaCaT

city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

department: Pathology

country: Japan

institute: University of Tokyo

description: Input genome, no wig and bed files available. This sample was also used as a control in GSE28427.

data_processing:
ChIP-seq reads were aligned to the hg18 genome assembly.
Peaks were called using MACS version 2.0.6 20110725 by 2-sample analysis. Following parameters were used: band width=300, genome size=2.7e+09, pvalue cutoff= 1e-5, control dataset was scaled towards ChIP dataset.
Genome_build: hg18
Supplementary_files_format_and_content: bed and wig files were generated using MACS.

source_name: HaCaT

growth_protocol: Human immortalized keratinocyte HaCaT cells were maintained in Dulbecco’s modified Eagle’s medium (Sigma) supplemented with 10% (v/v) fetal bovine serum (FBS) (HyClone) and 1% penicillin–streptomycin (Sigma).

extract_protocol:
ChIP were performed as described (Koinuma et al, Mol Cell Biol 29: 172-186, 2009). p63-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: Cells infected with adenoviral vectors were treated with 3 ng/ml of TGF-beta3 for 1.5 h.

value: Human immortalized keratinocyte (HaCaT)

tag: adenoviral infection

tag: histology

value: epidermal keratinocyte

tag: ChIP


title: p63 ChIP-seq, HaCaT, caRAS, with TGFB

tag: cell type

value: Ad-caRAS

value: anti-p63a (clone H-129, Santa Cruz Biotechnology, lot number not available)


title: p63 ChIP-seq, HaCaT, dnRAS, with TGFB

value: Ad-dnRAS


title: autism-PFC-2920d [aut8]

description: RNA-seq data from post-mortem superior frontal gyrus of a autistic patient with age of 2920 days

value: male

value: 2920 days


title: K562_ScaleUpDesign1_minP_mRNA_Rep1

value: minimal TATA


title: autism-PFC-2838d [aut7]

description: RNA-seq data from post-mortem superior frontal gyrus of a autistic patient with age of 2838 days

value: female

value: 2838 days


title: chimpanzee-PFC-39d [ptr8]

description: RNA-seq data from post-mortem superior frontal gyrus of a chimpanzee with age of 39 days

value: chimpanzee; non-human primate

value: 39 days


title: autism-PFC-4015d [aut14]

value: 4015 days


title: autism-PFC-3650d [aut12]

description: RNA-seq data from post-mortem superior frontal gyrus of a autistic patient with age of 3650 days

value: autistic patient

value: 3650 days


title: chimpanzee-PFC-34d [ptr7]

description: RNA-seq data from post-mortem superior frontal gyrus of a chimpanzee with age of 34 days

value: 34 days


title: p63 ChIP-seq, HaCaT, LacZ, with TGFB

value: Ad-LacZ


title: HepG2_ScaleUpDesign2_SV40P_mRNA_Rep2

description: Scale-up Design 2 (5-bp steps), reporter mRNA, replicate 2


title: HepG2_ScaleUpDesign2_SV40P_mRNA_Rep1

description: Scale-up Design 2 (5-bp steps), reporter mRNA, replicate 1


title: chimpanzee-PFC-32d [ptr6]

description: RNA-seq data from post-mortem superior frontal gyrus of a chimpanzee with age of 32 days

value: 32 days

value: superior frontal gyrus of the brain


title: autism-PFC-2610d [aut6]

description: RNA-seq data from post-mortem superior frontal gyrus of a autistic patient with age of 2610 days

value: 2610 days


title: p63 ChIP-seq, HaCaT, LacZ, without TGFB

value: Human immortalized keratinocyte (HaCaT)

value: epidermal keratinocyte

value: anti-p63a (clone H-129, Santa Cruz Biotechnology, lot number not available)


title: autism-PFC-3650d [aut11]

value: male


title: HepG2_ScaleUpDesign2_minP_mRNA_Rep1

value: minimal TATA


title: HepG2_ScaleUpDesign2_minP_mRNA_Rep2


title: chimpanzee-PFC-7d [ptr4]

description: RNA-seq data from post-mortem superior frontal gyrus of a chimpanzee with age of 7 days

value: 7 days


title: chimpanzee-PFC-7d [ptr3]

value: female


title: autism-PFC-1825d [aut3]

description: RNA-seq data from post-mortem superior frontal gyrus of a autistic patient with age of 1825 days

value: 1825 days


title: chimpanzee-PFC-8d [ptr5]

description: RNA-seq data from post-mortem superior frontal gyrus of a chimpanzee with age of 8 days

value: chimpanzee; non-human primate

value: 8 days


title: autism-PFC-2045d [aut5]

description: RNA-seq data from post-mortem superior frontal gyrus of a autistic patient with age of 2045 days

value: autistic patient

value: 2045 days


title: autism-PFC-1825d [aut4]


title: autism-PFC-1625d [aut2]

description: RNA-seq data from post-mortem superior frontal gyrus of a autistic patient with age of 1625 days

value: 1625 days


title: HepG2_ScaleUpDesign1_SV40P_mRNA_Rep2

description: Scale-up Design 1 (5-bp steps), reporter mRNA, replicate 2


title: autism-PFC-730d [aut1]

description: RNA-seq data from post-mortem superior frontal gyrus of a autistic patient with age of 730 days

value: 730 days


title: ESC_Hira_WT_H3gen

city: Dallas

last: Banaszynski

state: TX

address: 5323 Harry Hines Blvd

department: Green Center for Reproductive Biology Sciences

institute: UT Southwestern Medical Center

data_processing:
ChIP-seq reads were aligned at 36bp to the mm9 genome assembly using Bowtie.
duplicates removed using samtools
wig files made using igvtools and normalized based on read counts
Genome_build: mm9

source_name: Embryonic stem cells

growth_protocol: ESCs were cultured under standard conditions (KO-DMEM, 2 mM Glutamax, 15% ES grade fetal bovine serum, 0.1 mM 2-mercaptoethanol, and leukemia inhibitory factor (LIF)). For early passages, cells were maintained on an irradiated feeder layer. To remove feeders, cells were passaged at least two passages off of feeders onto gelatin-coated plates.

extract_protocol:
Native ChIP was performed as described (Goldberg et al. 2010). Briefly, ESCs were harvested and treated with Mnase, resulting in a population consisting mainly of mono- to trinucleosomes. Crosslinking ChIP was performed as described (Goldberg et al. 2010). Briefly, cell were harvested and crosslinked in 1% PFA or 1.5 mM EGS followed by 1% PFA. Chromatin was then sheared to 200-700 bp. For both procedures, chromatin was isolated and used for ChIP according to standard procedures.
Libraries were constructed according to the Illumina protocol.

tag: strain background

tag: genotype/variation

value: wild type

value: Embryonic stem cells (ESCs)

tag: antibody

value: anti-H3gen (Abcam; Ab1791)


title: ESC_Hira_null_H3gen

value: Hira-/-


title: HepG2_ScaleUpDesign1_minP_mRNA_Rep2


title: chimpanzee-PFC-0d [ptr1]

description: RNA-seq data from post-mortem superior frontal gyrus of a chimpanzee with age of 0 day

tag: age

value: 0 day

value: superior frontal gyrus of the brain


title: P3_Lin28Over_Polysome-seq

status: Public on Aug 11 2016

city: Seoul

first: Jin-Wu

last: Nam

address: Seongdong-Gu Hangdang-dong

department: Department of Life Science

institute: Hanyang University

description: Poly(A)-selected RNA

data_processing:
Library strategy: polysome-seq
To check sequence quality, RNA-seq and polysome-seq reads were mapped to the reference genomes (mm9) using Bowtie (version 1.0.0) with default parameter. We calculate mismatch rates across the position of mapped reads. If either end or both ends of the reads have shown mismatch rate higher than 10%, the corresponding positions of raw reads were trimmed off using Seqtk (version 1.0-r31). In addition, the trimmed reads with Phred base quality ≤ 20 were filtered using Sickle (version 1.200). Remaining reads were mapped to the reference genomes (mm9) using Tophat (version 2.0.6) with mapping parameters “-i 52 -I 240764 --min-segment-intron 52 --max-segment-intron 240764 -g 1 --library-type fr-firststrand”. Then, fragments per kilobase of transcript per million mapped reads (FPKM) was calculated using Cufflinks (v2.1.1) with parameters “-G RefSeq (version Seq-09-2013) --library-type fr-firststrand ”.
After all adaptors sequences of raw sRNA-seq data were removed, only reads of 18~26nt in length were mapped to mouse genome (mm9) using the BLAST with not allowing any mismatch. If the mapped loci is greater than five, the reads were excluded, otherwise the number of reads were normalized by the number of mapped loci. Based on the known miRNA annotations, sRNA reads whose 5' end are exactly matched to that of an annotated miRNA were used for measuring expression of the miRNA.
Genome_build: mm9
Supplementary_files_format_and_content: text file with FPKM or miRNA read count

source_name: Neural stem cells_Lin28 overexpression_P3_Polysome-seq

growth_protocol: NSCs isolated from mouse VM at embryonic day 10 were transduced with the lentiviruses expressing Lin28a (or mock control), and in vitro expanded with cell passages every 4 days. Gene expression anlayses were carried out on the VM-NSC cultures at passage 1 (P1) and P3.

extract_protocol:
Polysome profiling: Cells were washed twice with cold PBS, lysed with 1 ml polysome lysis buffer (20 mM HEPES pH 7.6, 5 mM MgCl2, 125 mM KCl, and 1% NP-40) supplemented with 2 mM DTT, 100   g/ml cycloheximide, a proteaseinhibitor cocktail (EDTA-free; Pierce), and RNasin (Thermo Scientific).After 15 min of agitation at 4  C, nuclei were pelleted (13,200 rpm for 15 min), and the protein contents of the supernatants were quantified. Anequal protein amount of each sample was fractionated by ultracentrifugation (35,000 rpm for 2 h 40 min; Beckman SW40 Ti rotor) on a 17.5 to 50 % linear sucrose gradient. Gradients were eluted with a gradient fractionator (Brandel) and monitored with a UA-5 detector (ISCO). Fractions wereprepared for protein and RNA analyses by acetone precipitation and TRIZOL.
RNA extraction: Total RNA were extracted using Trizol reagent (Invitrogen,Carlsbad, CA) according to the manufacturer's instructions.
Libraries were constructed with TruSeq Stranded Total RNA Library Prep Kit

tag: cell-type

value: Neural stem cells

tag: background strain

value: ICR

tag: tissue

value: ventral midbrain at embryonic day 10

tag: passage

value: Passage 3


title: P3_Lin28Over_sRNA-seq

description: small RNAs

data_processing:
To check sequence quality, RNA-seq and polysome-seq reads were mapped to the reference genomes (mm9) using Bowtie (version 1.0.0) with default parameter. We calculate mismatch rates across the position of mapped reads. If either end or both ends of the reads have shown mismatch rate higher than 10%, the corresponding positions of raw reads were trimmed off using Seqtk (version 1.0-r31). In addition, the trimmed reads with Phred base quality ≤ 20 were filtered using Sickle (version 1.200). Remaining reads were mapped to the reference genomes (mm9) using Tophat (version 2.0.6) with mapping parameters “-i 52 -I 240764 --min-segment-intron 52 --max-segment-intron 240764 -g 1 --library-type fr-firststrand”. Then, fragments per kilobase of transcript per million mapped reads (FPKM) was calculated using Cufflinks (v2.1.1) with parameters “-G RefSeq (version Seq-09-2013) --library-type fr-firststrand ”.
After all adaptors sequences of raw sRNA-seq data were removed, only reads of 18~26nt in length were mapped to mouse genome (mm9) using the BLAST with not allowing any mismatch. If the mapped loci is greater than five, the reads were excluded, otherwise the number of reads were normalized by the number of mapped loci. Based on the known miRNA annotations, sRNA reads whose 5' end are exactly matched to that of an annotated miRNA were used for measuring expression of the miRNA.
Genome_build: mm9
Supplementary_files_format_and_content: text file with FPKM or miRNA read count

source_name: Neural stem cells_Lin28 overexpression_P3_sRNA-seq


title: P1_Lin28Over_sRNA-seq

description: small RNAs

source_name: Neural stem cells_Lin28 overexpression_P1_sRNA-seq

extract_protocol:
Polysome profiling: Cells were washed twice with cold PBS, lysed with 1 ml polysome lysis buffer (20 mM HEPES pH 7.6, 5 mM MgCl2, 125 mM KCl, and 1% NP-40) supplemented with 2 mM DTT, 100   g/ml cycloheximide, a proteaseinhibitor cocktail (EDTA-free; Pierce), and RNasin (Thermo Scientific).After 15 min of agitation at 4  C, nuclei were pelleted (13,200 rpm for 15 min), and the protein contents of the supernatants were quantified. Anequal protein amount of each sample was fractionated by ultracentrifugation(35,000 rpm for 2 h 40 min; Beckman SW40 Ti rotor) on a 17.5 to 50 % linear sucrose gradient. Gradients were eluted with a gradient fractionator (Brandel) and monitored with a UA-5 detector (ISCO). Fractions wereprepared for protein and RNA analyses by acetone precipitation and TRIZOL.
RNA extraction: Total RNA were extracted using Trizol reagent (Invitrogen,Carlsbad, CA) according to the manufacturer's instructions.
Libraries were constructed with TruSeq Stranded Total RNA Library Prep Kit

value: Passage 1


title: P3_Lin28Over_RNA-seq

description: Poly(A)-selected RNA

source_name: Neural stem cells_Lin28 overexpression_P3_RNA-seq


title: P3_Control_RNA-seq

description: Poly(A)-selected RNA

source_name: Neural stem cells_control_P3_RNA-seq

extract_protocol:
Polysome profiling: Cells were washed twice with cold PBS, lysed with 1 ml polysome lysis buffer (20 mM HEPES pH 7.6, 5 mM MgCl2, 125 mM KCl, and 1% NP-40) supplemented with 2 mM DTT, 100   g/ml cycloheximide, a proteaseinhibitor cocktail (EDTA-free; Pierce), and RNasin (Thermo Scientific).After 15 min of agitation at 4  C, nuclei were pelleted (13,200 rpm for 15 min), and the protein contents of the supernatants were quantified. Anequal protein amount of each sample was fractionated by ultracentrifugation(35,000 rpm for 2 h 40 min; Beckman SW40 Ti rotor) on a 17.5 to 50 % linear sucrose gradient. Gradients were eluted with a gradient fractionator(Brandel) and monitored with a UA-5 detector (ISCO). Fractions wereprepared for protein and RNA analyses by acetone precipitation and TRIZOL.
RNA extraction: Total RNA were extracted using Trizol reagent (Invitrogen,Carlsbad, CA) according to the manufacturer's instructions.
Libraries were constructed with TruSeq Stranded Total RNA Library Prep Kit


title: P1_Lin28Over_RNA-seq

description: Poly(A)-selected RNA

source_name: Neural stem cells_Lin28 overexpression_P1_RNA-seq


title: P1_Control_sRNA-seq

description: small RNAs

source_name: Neural stem cells_control_P1_sRNA-seq


title: chimpanzee-PFC-1d [ptr2]

description: RNA-seq data from post-mortem superior frontal gyrus of a chimpanzee with age of 1 day

tag: sample group

value: chimpanzee; non-human primate

value: female

value: 1 day


title: HepG2_ScaleUpDesign1_SV40P_mRNA_Rep1

description: Scale-up Design 1 (5-bp steps), reporter mRNA, replicate 1

tag: promoter


title: HIRAsiRNA ChIP-Seq

first: Zhexin

last: Zhu

institute: Chinese Academy of Sciences

data_processing:
1.CASAVA1.8.2 convert per-cycle *.bcl files into FASTQ files
2. Fastqcv0.10.1  evaluate the quality statistics of FASTQ
3. Reads were mapped to human genome with bowtie2. Peaks is called with SICER.
4. The reads were extended and counted every 50bp bin.
5. The count of the reads for the bin was corrected for sequencing depth to 10 million reads. The coverage was clustered with k-means.
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text file; first column is peak id (see peaks_genomics_position.bed for genomic position of each id); table includes 80 bins of peaks for NT, PHB, and HIRA.

source_name: H3.3B-HA tagged human embryonic stem cells

growth_protocol: hESCs were culture in conditioned medium onhESC-qualified Matrix coated cell culture plates at 37oC, 5% CO2.

extract_protocol:
Cells were cross-linked with 1% formaldehyde (Sigma) for 15 minutes at 37oC and then quenched with 0.125 M glycine (Sigma) for 5 minutes at room temperature. Cells were scraped and transferred into Eppendorf tubes with cold PBS supplemented with 1×PIC, and then centrifuged to remove supernatant. Cell pellet was suspended in 1% SDS FA cell lysis buffer comprised of 50 mM HEPES- KOH (Sigma), pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, and 1% SDS supplemented with 1×PIC. After rotating for 15 minutes at 4oC, the suspension mixture was centrifuged at 15,000×g for 45 minutes and supernatant was discarded. The pellet was suspended in 1 ml of 0.1% SDS FA cell lysis buffer supplemented with 1×PIC and 1× PMSF, and then sonicated at 50% amplitude (30S ON, 30S OFF) for 40 cycles using Sonics (UibraCELL) at 4oC, followed by centrifugation at the maximum speed for 12 minutes in a cold room. One percent of the supernatant was used as the input. The remaining supernatant was precleaned and incubated with specific antibody overnight at 4oC. On the next day, 100 μl of the Protein A and Protein G Dynabead mixture were employed to pull down antibody-precipitated protein-DNA complexes for 15 minutes at room temperature, followed by gentle wash with a low salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris-HCl; pH8.1), a high salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 500 mM NaCl, 20 mM Tris-HCl; pH8.1), a LiCl wash buffer (0.25M LiCl, 1% NP40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl; pH8.1), and a TE buffer (10 mM Tris-HCl, 1 mM EDTA; pH8.1). Chromatin was dissociated from proteins by 200 μl freshly prepared elution buffer (1% SDS, 0.1 M NaHCO3) and decross-linked by adding 8 μl NaCl and 1 μl of 10 μg/μl RNase A (Roche) at 65oC for no longer than 16 hours, followed by the treatment with 4 μl of 0.5 M EDTA, 8 μl of 1 M Tris-HCl (pH6.5) and 1 μl of 20 mg/ml protease K (Sigma). DNA was purified by a QIAquick PCR Purification Kit as instructed. Thirty ng of DNA was used for CHIP-Seq (Shanghai Biotechnology Corporation).
The ChIP-enriched DNA samples were treated with end-repair of the DNA, adding ‘‘A” bases to the DNA, ligating sequencing adapters to DNA fragments, amplifying adapter-modified DNA by PCR and gel purification for ChIPseq using NEBNext Ultra DNA Library Prep Kit for Illumina. Purified libraries were sequenced on Illumina HiSeq2500 platforms.

treatment_protocol: For high knock down efficiency, reverse transfection method was performed to deliver siRNA into hESCs. A mixture containing 4 μl DharmaFECT1, 391 μl Opti-MEM I and 5 μl siRNA (20 μM) was incubated at room temperature for 20 to 30 minutes. 5× 105 hESCs in 1600 μl conditioned medium supplemented with 10 μM Y-27632 was added to each well. Fresh conditioned medium was supplied daily. After 4 days of culture, cells were collected for further analysis.

value: human embryonic stem cells

tag: passages

tag: chip antibody

value: HA (Abcam, ab9110)


title: Input NTsiRNA ChIP-Seq


title: PHBsiRNA ChIP-Seq


title: NTsiRNA ChIP-Seq


title: 6-20-14_231_Input

first: Xiaoyu

last: Wang

address: ND3 200, 6001 Forest Park Rd

department: Cancer Center

institute: Ut Southwestern Medical Center

description: ChIP-SEQ Input

data_processing:
Sequencing reads were aligned to human genome (hg19) by bowtie2 (version 2.2.3)
After mapping reads to human genome (hg19) by bowtie2 (version 2.2.3) with parameter “--sensitive”,perform filtering by (1) removing alignments with mapping quality less than 10, (2) removing duplicate reads identified by Picard Mark Duplicates (version 1.92, http://broadinstitute.github.io/picard).
The enriched regions (peaks) were identified using MACS2 (version 2.0.10.20131216), with a q-value cut-off of 0.05. Peak regions was annotated by HOMER.
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak

source_name: Breast cancer cell line

growth_protocol: MCFDCIS cells were grown in 5% horse serum, 20 ng/ml EGF, 0.5 ug/ml hydrocortisone, 100 ng/ml cholera toxin, and 10 ug/ml recombinate human insulin in DME-F12.  MDA-MB-231 cells were grown in 10% FBS-RPMI

extract_protocol:
Cells were crosslinked with 1% formaldhyde for 15 min. at room temperature, quenched with 0.125 M glycine, lysed with PIPES hypotonic buffer for 30 min and RIPA buffer for overnight at 4C.  Samples were then sonicated using a Bioruptor Sonicator, pre-cleared with blocked sepharose beads and then incubated overnight with respective antibodies.  Samples where then incubated with blocked beads for two hours, washed with ChIP wash buffers, incubated with ProteinaseK and RNAse then decrosslinked overnight at 65C.  DNA was cleaned up using the Qiagen QiaQuick PCR Purification Kit (cat no. 28104).
Library was constructed with KAPA HTP Library Prepartion kit.

tag: cell line

value: MDA-MB-231 cells


title: 6-25-14_DCIS_p63

description: p63 ChIP-SEQ

value: MCFDCIS cells

value: p63 antibody (Santa Cruz, H129)


title: Input HIRAsiRNA ChIP-Seq


title: 6-20-14_DCIS_Input

description: ChIP-SEQ Input


title: HepG2_ScaleUpDesign1_minP_mRNA_Rep1

value: minimal TATA


title: Input PHBsiRNA ChIP-Seq


title: 6-20-14_DCIS_p63

description: p63 ChIP-SEQ


title: P3_Control_Polysome-seq

description: Poly(A)-selected RNA


title: P3_Control_sRNA-seq

description: small RNAs

source_name: Neural stem cells_control_P3_sRNA-seq


title: Adrenalectomy 300 ug/kg corticosterone_6

city: Boston

first: Richard

middle: G.

last: Hunter

state: Massachusetts

address: 100 William Morrissey Blvd.

department: Psychology

institute: University of Massachusetts Bo

description: Sample name: Sample 12

data_processing:
Sequenced .fastq files were transferred via File Transfer Protocol from MGH to the R.G.H. laboratory local galaxy server. Quality scores were converted to Sanger format with the Fastq Groomer tool (v1.0.4) using default settings. The rn5 mitochondrial DNA sequence was downloaded from the University of California, Santa Cruz genome table browser and indexed with Bowtie2 (v0.6) and default settings. The paired-end groomed files were mapped to this index using Tophat (v0.9), After read mapping, the accepted-hits.bam files were run through Cufflinks (v2.2.1.0) to identify transcripts, using the ensembl annotation .gtf file to identify mitochondrial genes. The cufflinks transcripts were merged with the cuffmerge tool (v2.2.1.0) with default settings, and Cuffdiff (v2.2.1.3) was used to look for differences between the two groups.
Genome_build: rn5 mitochondrial DNA sequence from University of California, Santa Cruz genome table browser
Supplementary_files_format_and_content: bed, tabular, differentially expressed transcripts between corticosterone treated and control animals.

organism: Rattus norvegicus

growth_protocol: Rats were group housed and maintained under standard conditions for one week prior to surgery. Rats were ordered from Charles-River Laboratories.

extract_protocol:
RNA-seq was performed on rats (n = 6) adrenalectomized and treated with either 300 μg/kg corticosterone or vehicle (as in the GR ChIP-seq process described in GSE84202). Rats were killed 1 h after treatment, and their hippocampi were harvested and flash frozen before RNA extraction, using Qiagen RNAeasy Kits. RNA was processed for RNA-seq by the Massachusetts General Hospital (MGH) Next-Generation Sequencing Core on an Illumina HiSeq sequencer.
Standard Illumina Hiseq Protocol

tag: strain

value: Sprague-Dawley

tag: Sex

value: Male

value: brain

tag: brain region

value: hippocampus

value: 8 weeks


title: Adrenalectomy plus vehicle control_5

description: Sample name: Sample 9


title: Adrenalectomy plus vehicle control_6

description: Sample name: Sample 11


title: Adrenalectomy 300 ug/kg corticosterone_5

description: Sample name: Sample 10


title: P1_Control_RNA-seq

description: Poly(A)-selected RNA

source_name: Neural stem cells_control_P1_RNA-seq

extract_protocol:
Polysome profiling: Cells were washed twice with cold PBS, lysed with 1 ml polysome lysis buffer (20 mM HEPES pH 7.6, 5 mM MgCl2, 125 mM KCl, and 1% NP-40) supplemented with 2 mM DTT, 100   g/ml cycloheximide, a proteaseinhibitor cocktail (EDTA-free; Pierce), and RNasin (Thermo Scientific). After 15 min of agitation at 4  C, nuclei were pelleted (13,200 rpm for 15 min), and the protein contents of the supernatants were quantified. Anequal protein amount of each sample was fractionated by ultracentrifugation (35,000 rpm for 2 h 40 min; Beckman SW40 Ti rotor) on a 17.5 to 50 % linear sucrose gradient. Gradients were eluted with a gradient fractionator(Brandel) and monitored with a UA-5 detector (ISCO). Fractions wereprepared for protein and RNA analyses by acetone precipitation and TRIZOL.
RNA extraction: Total RNA were extracted using Trizol reagent (Invitrogen,Carlsbad, CA) according to the manufacturer's instructions.
Libraries were constructed with TruSeq Stranded Total RNA Library Prep Kit

value: Neural stem cells

value: ICR

value: ventral midbrain at embryonic day 10


title: Adrenalectomy plus vehicle control_3

description: Sample name: Sample 4


title: Adrenalectomy plus vehicle control_2

description: Sample name: Sample 3


title: Adrenalectomy plus vehicle control_1

description: Sample name: Sample 2


title: Adrenalectomy 300 ug/kg corticosterone_1

description: Sample name: Sample 1


title: Adrenalectomy 300 ug/kg corticosterone_3

description: Sample name: Sample 6


title: 6-20-14_231_p63

description: p63 ChIP-SEQ


title: 6-25-14_DCIS_Input

description: ChIP-SEQ Input


title: Adrenalectomy 300 ug/kg corticosterone_4

description: Sample name: Sample 7


title: Adrenalectomy 300 ug/kg corticosterone_2

description: Sample name: Sample 5


title: exp_3

first: Abbie

last: Groff

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology;

description: GFP RNA

data_processing:
Casava 1.8.2 was used to call bases
Reads containing barcodes with a perfect match to a designed barcode and originating from a read with GFP sequence were counted.
analysis scripts were run in R, and are provided in supplemental material for the paper
Supplementary_files_format_and_content: a tab-delimited processed file showing normalized counts for tags associated to lincp21 genomic sequence and all relevent annotation information

extract_protocol:
C2C12 cells were harvested in TRIzol.
Libraries were generated from cDNA using indexed primers against the tag-containing GFP.

tag: tissue type

value: mouse myoblast cells (C2C12)


title: exp_2

description: GFP RNA


title: Adrenalectomy plus vehicle control_4

description: Sample name: Sample 8


title: exp_1

description: GFP RNA


title: linc-p21_L27-10_KO-M_E14.5 Lung

description: Lung.tab

data_processing:
Casava 1.8.2 was used to call bases
Reads were aligned to mm10 using tophat2 (--no-coverage-search --max-multihits 10 -p 8)
Bams were quantified using cuffquant and a modified verson of the GENCODE M2 transcriptome (--no-update-check -p 8)
Differential analysis was performed using cuffdiff2 (-p 8)
Genome_build: mm10
Supplementary_files_format_and_content: Final measurements are reported in FPKMs.

source_name: Lung

extract_protocol:
E14.5 organs were harvested and homogenized in TRIzol.
Standard illumina protocols were used to make libraries (TruSeq RNA Sample Preparation Kit v2)

tag: lncrna previous name

tag: background

tag: official strain name

tag: genotype

value: KO

value: M

tag: litter

value: Lung


title: linc-p21_L27-3_WT-M_E14.5 Liver

description: Liver.tab

source_name: Liver

value: WT

tag: age

value: Liver


title: linc-p21_L27-7_KO-M_E14.5 Lung

description: Lung.tab

tag: tissue


title: linc-p21_L28-7_KO-F_E14.5 Lung

description: Lung.tab

value: F


title: linc-p21_L27-5_WT-M_E14.5 Lung

description: Lung.tab


title: linc-p21_L27-7_KO-M_E14.5 Liver

description: Liver.tab


title: linc-p21_L27-3_WT-M_E14.5 Lung

description: Lung.tab


title: linc-p21_L28-2_WT-F_E14.5 Lung

description: Lung.tab


title: linc-p21_L25-7_KO-F_E14.5 Liver

description: Liver.tab


title: linc-p21_L27-5_WT-M_E14.5 Liver

description: Liver.tab


title: linc-p21_L27-10_KO-M_E14.5 Liver

description: Liver.tab


title: linc-p21_L25-2_WT-F_E14.5 Liver

description: Liver.tab