title: MCF-7 CTCF ChIP-Seq sample 1

city: Grand Rapids

first: Gerry

last: Coetzee

state: MI

address: 333 Bostwick Ave NE

department: Center for Neurodegenerative Science

institute: Van Andel Research Institute

description:
Coetzee_CTCF_IDR830.xlsx
MCF7_CTCF.bed
chip_mcf7_ctcf.bw

data_processing:
RNA-seq: Following sequencing, fastq files were trimmed using Trimmomatic V0.36 and the settings: ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
RNA-seq: Trimmed fastq files were aligned to HG19 using STAR v2.5 (Dobin and Gingeras, 2015).
RNA-seq: Alignments (bam files) were converted to feature counts using HTSeq v0.6.0 referenced against the ENSEMBLE annotation of HG19: Homo_sapiens.GRCh37.87.gtf counting against the feature “exon”, grouped by “gene_id”, and using the strand parameter “reverse”.  This set included exon locations for 57,905 genomic entities including pseudogenes, lncRNAs, and 20,356 protein coding genes.
RNA-seq: The resulting gene_id map counts included 2 technical replicates for each sample. The 2 replicates were combined to generate 8 total samples which were normalized using edgeR (TMM) and tested for significant differential expression (either between 2 WT MCF-7 batches generated here or compared to existing HMEC expression data) with Limma and Voom, in R (v3.3.1) (Law et al., 2014; Ritchie et al., 2015; Robinson and Oshlack, 2010).
RNA-seq: The normalized count data for all 8 datasets revealed, through principle component analysis (PCA) and other comparisons (DE included), that there was no distinction between the 2 groups of 8 WT MCF-7. Therefore, the datasets were combined for analysis. An expression threshold of at least 0.1 CPM a minimun of 3 samples was imposed.  The log2 FC and p-value for DE, as well as normalized log2CPM were derived for each gene.
ChIP-seq: Two biological replicates with 2 technical replicates each were used for input and ChIP for both H3K27Ac and CTCF. Following sequencing, fastq files were aligned to the HG19 genome assembly using default setting for BWA v0.7.15 (Li and Durbin, 2009).
ChIP-seq: Aligned reads were merged with Samtools and peaks were called using MACS2 v2.1 using a liberal FDR cutoff of 0.1 (Zhang et al., 2008).
ChIP-seq: Narrowpeaks were aligned and an irreproducible discovery rate (IDR) of >830 was used for filtering (Li et al., 2011). H3k27Ac Chip-Seq was ranked by p.value, CTCF ChIP-Seq was ranked by signal. Peaks greater than 1000 bp from gene tss were annotated as enhancers.
Genome_build: hg19
Supplementary_files_format_and_content: .txt, htseq output feature count of each ensembl_gene_id for 16 RNA-seq samples (2 technical replicates per clone).
Supplementary_files_format_and_content: .xlsx, excel contains differential expression metrics and expression values for RNA-seq or IDR values for ChIP-Seq
Supplementary_files_format_and_content: .bed, bed file contains chromosome, start, stop coordinates, and name for ChIP-Seq high IDR peaks or highly expressed exons for RNA-Seq (11,310 genes expressed in MCF-7 at at-least 1 count per million).
Supplementary_files_format_and_content: .bw bigwig file contains merged signal strength for ChIP-Seq fragment pileups

source_name: MCF-7 (ATCC HTB-22)

growth_protocol: MCF-7 cells were obtained from ATCC and cultured in DMEM (ATCC, cat # 30-2003) supplemented with 10% FBS and 0.01 mg/ml human recombinant insulin (Gibco, ref # 12585-014). They were incubated in a humidified 37°C, 5% CO2 incubator. For routine passaging, cells were grown in T25 and T75 culture flasks and passaged using 0.25% Trypsin/EDTA.

extract_protocol:
100 ug of sonicated chromatin was used for immunoprecipitation and 1 ug (1%) was used for the input control.
Libraries for input and IP samples were prepared by the Van Andel Genomics Core from 10 ng of input material and all available IP material using the KAPA Hyper Prep Kit (v5.16) (Kapa Biosystems, Wilmington, MA USA). Prior to PCR amplification, end-repaired and Atailed DNA fragments were ligated to Bio Scientific NEXTflex Adapters (Bio Scientific, Austin, TX, USA). The quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.), QuantiFluor dsDNA System (Promega Corp., Madison, WI, USA), and Kapa Illumina Library Quantification qPCR assays (Kapa Biosystems). Sequencing (75 bp, single end) was performed on an Illumina NextSeq 500 sequencer using a 75-bp sequencing kit (v2) (Illumina Inc., San Diego, CA, USA). Base calling used Illumina NextSeq Control Software (NCS) v2.0, and the output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.9.0.
RNA was isolated using a Qiagen RNeasy mini kit (Cat # 74104). Paired-end mRNA libraries were then prepared.
Libraries were prepared by the Van Andel Research Institute Genomics Core from 1 μg of material using the KAPA Stranded mRNAseq Kit (v4.16) (Kapa Biosystems, Wilmington, MA USA). RNA was sheared to 250–300 bp. Prior to PCR amplification, cDNA fragments were ligated to Bio Scientific NEXTflex Adapters (Bioo Scientific, Austin, TX, USA). The quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.), QuantiFluor dsDNA System (Promega Corp., Madison, WI, USA), and Kapa Illumina Library Quantification qPCR assays (Kapa Biosystems).

treatment_protocol: For ChIP we followed previously published protocols from Rhie et al (20) with slight modifications. Roughly 30-40 x 106 cells were used per ChIP. Upon reaching 70-80% confluency, cells were directly fixed in T75 flasks by adding 16% formaldehyde to the culture medium to a final concentration of 1%. The reaction was quenched for 5 minutes at room temperature with 10X (1.15 M) glycine. Using a Bioruptor Pico (Diagenode, Cat # B01060001) the isolated chromatin was sonicated for 30 second on and 30 second off cycles to yield DNA fragments between 200 and 500 base pairs. 100 ug of sonicated chromatin was used for immunoprecipitation and 1 ug (1%) was used for the input control. To probe for CTCF or H3K27ac, samples were incubated at 4 °C overnight with a primary antibody [CTCF: Cell Signaling monoclonal (D31H2), Cat# 3418; H3K27ac: Active Motif, Cat #39133] or an IgG control (Sigma, Cat # R9133). A/G magnetic beads (Pierce, Cat # 88802) were then incubated with the samples for 2 hours at 4 °C. Following this incubation, the beads were washed with a series of buffers of varying salt concentrations before overnight elution at 67 °C. The ChIP, IgG, and Input samples were all purified using a QIAprep Spin Miniprep Kit (Qiagen, Cat # 27104).

tag: general

value: luminal epithelial breast cancer line; ER+, PR+/-, HER2-

value: female

tag: sample type

value: WT

value: CTCF


title: MCF-7 H3k27Ac ChIP-Seq sample 2

status: Public on May 09 2019

type: SRA

middle: A.

country: USA

description:
Coetzee_H3k27Ac_IDR850.xlsx
MCF7_enhancers.bed
chip_mcf7_h3k27ac.bw

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: Sex

tag: passages

tag: antibody


title: MCF-7 CTCF ChIP-Seq sample 2


title: MCF-7 H3k27Ac ChIP-Seq sample 1


title: Input for Etv5-Flag ChIP

city: Cambridge

first: Susanne

last: Bornelöv

address: Tennis Court Road

department: WT-MRC Cambridge Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

data_processing:
ChIP-seq reads aligned to mm10 using bowtie2 (version  2.0.6) with extra parameters (-k 2 -N 1).
bigWig density profiles were created with in-house script incorporating UCSC's wigToBigWig utility.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig – read density profile

organism: Mus musculus

source_name: ESCs

extract_protocol:
ChIP-DNA was eluted with Qiagen MinElute PCR purification kit
Ev5-ChIP-Seq libraries were generated   using NEB Next ChIP-Seq Library Prep Master Mix Set for Illumina (NEB. For H3K4me3 ChIP-seq libraries DNA samples were prepared for sequencing by end repair of 20 ng DNA as measured by Qubit (Invitrogen). Adaptors were ligated to DNA fragments, followed by size selection (∼300 bp) and 14 cycles of PCR amplification. Cluster generation and sequencing (36 bp) was performed with the Illumina Genome Analyzer IIx (GAIIx) platform according to standard Illumina protocols

tag: cell type

value: ESCs

tag: genotype/variation

value: RGd2 1903.4 parental

tag: growth

value: Input for Flag-ChIP

tag: line

tag: ChIP

value: input


title: HUVECs siCont+DF rep3

type: RNA

city: Houston

first: Jun-ichi

last: Abe

state: Texas

address: 2121 W Holcombe Blvd. IBT8 803e

institute: University of Texas MD Anderson Cacer Center

hyb_protocol: Following fragmentation and labeling, 5.2 ug of labeled ss-cDNA were hybridized for 16 hrs at 45 degree on GeneChip Mouse Transcriptome arrays. Arrays were washed and stained in Affymetrix Fluidics station 450.

scan_protocol: Arrays were scanned using Affymetrix GCS3000 scanner

data_processing:
The array data were incorporated into the Transcriptome Analysis Console 3.0 software program (Affymetrix), and GeneChip data were normalized using Tukey’s biweight average algorithm and represented as a biweight average on a log2 scale.
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

label: biotin

molecule: total RNA

source_name: HUVECs siCont disturbed flow (DF) 24 hrs

label_protocol: Fragmented and biotinylated labeled ss-cDNA were prepared according to standard Affymetrix WT Plus protocol (P/N 703174) from 100 ng total RNA

growth_protocol: HUVECs were either obtained from human collagenase-digested umbilical cord veins and cultured in M200 medium supplemented with LSGS (Cascade Biologics, Portland, OR, USA), 2% fetal bovine serum (Atlanta Biologicals, Flowery Branch, GA, USA), and 1% penicillin/streptomycin. HUVECs were cultured in dishes precoated with 0.2% gelatin type A (#901771; MP Biomedicals, Solon, OH, USA).

extract_protocol: Total RNA was extracted by using an RNeasy Plus Mini Kit (catalog #74134; QIAGEN)  according to the manufacturer's instructions.

treatment_protocol: HUVECs were transfected by control siRNA or MAGI1 siRNA, and after 48 hrs of transfection HUVECs were exposed to disturbed flow (d-flow). After 24 hrs of disturbed flow RNA was extracted for futher microarray processing.

value: HUVECs

tag: transfection

value: Control siRNA

tag: protocol

value: disturbed flow (d-flow)


title: RGd2_2i

value: 2i- negative control for Flag-ChIP


title: MCF-7 RNA-seq sample 6

description:
Booms_Coetzee_Pierce_MCF7_wt_htseq_raw_count_matrix.txt
WT1_exp2
Supplemental_table_5.xlsx
expressed_MCF7.bed

library_source: transcriptomic

molecule: polyA RNA


title: HUVECs siCont rep3

source_name: HUVECs siCont static 24 hrs

value: static


title: Etv5-3xFlag Knock-in (KI)-32 N16h

value: RGd2 Etv5-3xFlag knock-in

value: withdrawn from 2i for 16h

value: clonal line 32


title: MCF-7 RNA-seq sample 7

description:
Booms_Coetzee_Pierce_MCF7_wt_htseq_raw_count_matrix.txt
WT3_exp2
Supplemental_table_5.xlsx
expressed_MCF7.bed


title: MCF-7 RNA-seq sample 5

description:
Booms_Coetzee_Pierce_MCF7_wt_htseq_raw_count_matrix.txt
WT_E5g23C
Supplemental_table_5.xlsx
expressed_MCF7.bed

value: WT, treated with CRISPR/Cas9 -> no insertion


title: HUVECs siCont rep2


title: HUVECs siCont+DF rep2


title: HUVECs siCont rep1


title: Etv5-3xFlag Knock-in (KI)-20 N16h

value: RGd2 Etv5-3xFlag knock-in c

value: clonal line 20


title: MCF-7 RNA-seq sample 4

description:
Booms_Coetzee_Pierce_MCF7_wt_htseq_raw_count_matrix.txt
WT_E3g14C
Supplemental_table_5.xlsx
expressed_MCF7.bed

value: luminal epithelial breast cancer line; ER+, PR+/-, HER2-

value: female


title: RbpJ-KO.N-16h.21

data_processing:
Trim Galore! was used to remove Illumina sequencing adapter and reads shorter than 20 nt.
TopHat2 was used to align the reads to the mm10 reference genome with ERCC spike-ins.
Gencode M14 gene models were used to guide alignment and for read counts.
featureCounts was used to calculate read counts per gene and spike-in.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files with read counts for each sample per gene or spike-in

extract_protocol:
RNA-seq was performed in triplicates per condition, including three independently derived clonal lines per genetic knock-out, and two RGd2 lines as wild type controls. RGd2-2 is a clonal line derived from the parental RGd2 line (RGd2-1903). Total RNA was extracted with ReliaPrep RNA Miniprep System (Promega) and was processed with Ribo-Zero capture probes (Illumina).
Libraries were produced using NEXTflex Rapid Directional qRNA-Seq Kit (Bioo Scientific).

tag: clonal id

tag: culture condition

tag: genotype

value: RGd2-RbpJ KO


title: MCF-7 RNA-seq sample 8

description:
Booms_Coetzee_Pierce_MCF7_wt_htseq_raw_count_matrix.txt
WT9_exp2
Supplemental_table_5.xlsx
expressed_MCF7.bed

value: WT


title: RbpJ-KO.N-16h.20


title: RbpJ-KO.2i.28


title: MCF-7 RNA-seq sample 2

description:
Booms_Coetzee_Pierce_MCF7_wt_htseq_raw_count_matrix.txt
WT_D3g14C
Supplemental_table_5.xlsx
expressed_MCF7.bed


title: MCF-7 RNA-seq sample 3

description:
Booms_Coetzee_Pierce_MCF7_wt_htseq_raw_count_matrix.txt
WT_D9g14C
Supplemental_table_5.xlsx
expressed_MCF7.bed


title: RbpJ-KO.N-16h.19


title: P56 Rad21cKO US+CS1

city: Evanston

first: Yue

last: Yang

state: IL

address: 2200 Campus Dr

department: Neurobiology

institute: Northwestern University

data_processing:
RNA-Seq, ChIP-Seq, DHS, HiC, and PLAC-Seq data was analyzed using HISAT2/Bowtie2 on the public server at usegalaxy.org or bwa mem for genome alignment, MACS2 for peak calling, MAPS for PLAC-Seq analyses, Juicebox for visualizing HiC and PLAC-Seq datasets
Genome_build: mm10
Supplementary_files_format_and_content: .bigwig files were generaed for RNA-Seq and ChIP-Seq datasets
Supplementary_files_format_and_content: .hic files were generated for HiC and PLAC-Seq datasets

source_name: anterior dorsal cerebellar vermis

extract_protocol:
Cerebella were removed and microdissected. For ChIP, lysates were purified from sonicated nuclei and histone-DNA complexes were isolated with the indicated antibodies. For HiC and PLAC-Seq, lysates of nuclei digested with MboI and re-ligated with biotin fill-in were sonicated and subjected to ChIP (PLAC) and biotin-IP. RNA was fractionated and harvested with Trizol. For DHS, nuclei were digested with DNase I and DNA fragments smaller than 500bp were purified.
ChIP-Seq, HiC, and PLAC-Seq libraries were prepared with the NEBNext Ultra™ II DNA Library Prep Kit. RNA libraries were prepared with the NEBNext Ultra™ Directional RNA Library Prep Kit. DHS libraries were prepared with the Illumina DNA Sample Prep Kit.

tag: developmental stage

value: 6-8 weeks

tag: tissue

value: cerebellum

tag: behavior

value: unconditioned stimulus and conditioned stimulus

tag: drugs/virus

value: AAV9 Rad21 gRNA injection


title: P56 Rad21cKO US+CS5


title: P56 Rad21cKO US+CS3


title: Etv5-KO.N-16h.18

value: RGd2-Etv5 KO


title: Etv5-3xFlag Knock-in (KI)-20 2i

value: ESCs

value: RGd2 Etv5-3xFlag knock-in c20


title: Etv5-3xFlag Knock-in (KI)-32 2i

value: RGd2 Etv5-3xFlag knock-in c32


title: P56 ctrl US+CS5

value: AAV9 control gRNA injection


title: Etv5-KO.2i.27


title: P56 ctrl US+CS4


title: P56 Rad21cKO US+CS4


title: P56 ctrl US+CS2


title: Etv5-KO.2i.26


title: RGd2_N16h

value: RGd2 1903.4 parental

value: 16h-negative control for Flag-ChIP


title: RbpJ-KO.2i.29


title: Etv5-KO.2i.25


title: ETR-tKO.N-p5.15

value: N2B27, passage 5

value: RGd2-Triple KO (Etv5, Tcf3, RbpJ)


title: P56 Rad21cKO US+CS2


title: MCF-7 RNA-seq sample 1

description:
WT_B7g23C
Booms_Coetzee_Pierce_MCF7_wt_htseq_raw_count_matrix.txt
Supplemental_table_5.xlsx
expressed_MCF7.bed

tag: general

value: luminal epithelial breast cancer line; ER+, PR+/-, HER2-

tag: Sex

tag: sample type

value: WT, treated with CRISPR/Cas9 -> no insertion


title: ETR-tKO.N-p5.14


title: ETR-tKO.N-p5.13


title: P56 Rad21cKO home2

value: homecage


title: P56 ctrl home1

value: WT


title: ER-dKO.CH-p5.12

value: Chiron, passage 5

value: RGd2-Double KO (Etv5, RbpJ)


title: P56 ctrl home2

value: 6-8 weeks

value: cerebellum


title: ER-dKO.CH-p5.11


title: ER-dKO.CH-p5.10


title: P56 CB rotarod4

description: CB-rotarod.bigwig

source_name: cerebellum

value: rotarod


title: Control.N-72h.9

value: RGd2 1903.4-2 clonal


title: P56 CB rotarod2

description: CB-rotarod.bigwig


title: P56 CB rotarod3

description: CB-rotarod.bigwig


title: P56 ctrl US+CS3

value: unconditioned stimulus and conditioned stimulus


title: Etv5-KO.N-16h.17

value: RGd2-Etv5 KO


title: Control.N-72h.8


title: Control.N-72h.7


title: P56 CB home3

description: CB-homecage.bigwig


title: P56 CB rotarod1

description: CB-rotarod.bigwig


title: P56 CB home4

description: CB-homecage.bigwig


title: P56 ctrl US+CS1

value: AAV9 control gRNA injection


title: Control.N-16h.24


title: P56 CB home2

description: CB-homecage.bigwig


title: Control.N-16h.22

value: RGd2 1903.4 parental


title: P56 L6 US d3-3

source_name: lobule VI

value: unconditioned stimulus only


title: P56 Rad21cKO home1

value: AAV9 Rad21 gRNA injection


title: Control.CH-p2.6

value: Chiron, passage 2


title: Control.CH-p2.4


title: Control.CH-p2.5


title: P56 CB home1

description: CB-homecage.bigwig


title: P56 L6 US d3-2


title: P56 L6 US+CS d3-2


title: Control.2i-p5.1

value: 2i, passage 5


title: Control.N-16h.23


title: Control.2i.33


title: P56 L6 US d7-5


title: Control.2i.32


title: P56 L6 US+CS d3-1


title: P56 L6 US+CS d7-5


title: Control.2i.31


title: P56 L6 US d7-3


title: P56 L6 US d7-4


title: P12_BRG1_RNAseq_cKO3

city: Chapel hill

first: Terry

last: Magnuson

state: NC

address: 120 Mason Farm Road, Genetics Medicine Bldg.,

department: Genetics

institute: University of North Carolina at Chapel Hill

description:
kallisto_counts.txt
3cKO3

data_processing:
Read counts were quantified using Kallisto (v0.42.5)
Transcript levels were summarized per gene using tximport
Summarized count table was imported into edgeR to perform differential analysis of gene expression
Low abundance genes (counts per million <1 across 4 replicates) were filtered out in edgeR
Genome_build: mm9
Supplementary_files_format_and_content: txt file with read counts per gene

source_name: Spermatogenic cells from P12 Brg1 cKO testes

extract_protocol:
Spermatogenic cells were isolated from P12  testes which were digested with collagnease and trypsin followed by filteration through a 40 micron sieve.  Cells were flash frozen in liquid nitrogen and stored at -80 C until RNA extraction.  RNA was extracted in Trizol reagent and purified using Zymo RNA clean and concentrator kit (cat # 11-352).
Libraries were generated from 0.5 ug of RNA using Kapa stranded mRNA-seq kit library kit for Illumina sequencing

tag: strain

value: Mixed background

tag: age

value: testes

tag: cell type

value: spermatogenic cells


title: P12_BRG1_RNAseq_cKO2

description:
kallisto_counts.txt
2cKO2


title: Control.2i-p5.2


title: P12_BRG1_RNAseq_cKO4

description:
kallisto_counts.txt
4cKO4


title: P56 L6 US+CS d7-3

value: WT


title: P56 L6 US d7-2


title: P12_BRG1_RNAseq_WT4

description:
kallisto_counts.txt
8WT4

source_name: Spermatogenic cells from P12 Brg1 WT testes


title: P56 L6 US+CS d7-2


title: P12_BRG1_RNAseq_WT3

description:
kallisto_counts.txt
7WT3


title: P12_BRG1_RNAseq_cKO1

description:
kallisto_counts.txt
1cKO1


title: P56 L6 US d7-1


title: P12_BRG1_RNAseq_WT2

description:
kallisto_counts.txt
6WT2


title: Control.2i-p5.3


title: 25h Rex1-high H3K4me3 (FACS-sorted)

value: ESCs

tag: genotype/variation

value: RGd2_clone 6

tag: growth

value: withdrawn from 2i for 25h, Rex1-high population

tag: line

value: RGd2 clonal line 6


title: P56 L6 US d3-1

value: 6-8 weeks

value: cerebellum


title: P56 L6 home4

value: homecage


title: P56 L6 US+CS d7-4

value: unconditioned stimulus and conditioned stimulus


title: P56 L6 home2


title: P12_H3K27ac_ChIPseq_cKO1

description:
Mnase digested chromatin
H3K27ac.lostPeaks.Macs2diffPeak.bed
H3K27ac.gainedPeaks.Macs2diffPeak.bed
H3K27ac.commonPeaks.Macs2diffPeak.bed
H3K27ac.Chp_Inp.cKO.merge.depthNorm1xCov.bw

data_processing:
Alignment to the mm9 genome was performed using bowtie1 (BRG1 ChIP-seq)/bowtie2 (Histone ChIP-seq). BAM files were generated using samtools.
For H2AK119ub1 and H3K27ac ChIP-seq,  PCR duplicates were filtered out using Picard tools, MarkDuplicates
BAM files were converted to bigWig format, representing log2(ChIP/Input) ratio, using Deeptools (version 2.5.2) bamCompare -bs 1 -bl mm9-blacklist.bed --normalizeto1x --scaleFactors --extend reads =150
Replicates were merged using UCSC tools  bigWigMerge
Peaks called using macs2 call peak --broad --broad-cutoff 0.05.  Differential peak analysis performed using macs2 bdgdiff
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files of log2(ChIP/Input) tracks and bed files of ChIP peaks.

extract_protocol:
Spermatogenic cells were isolated from P12 and P18 testes which were digested with collagnease and trypsin followed by filteration through a 40 micron sieve. Cells were fixed in 0.3% formaldehyde at 4 C for 30 min. The resulting chromatin was digested with Mnase prior to immunoprecipitation with antibody.
Libraries were created using Kapa hyperprep DNA library kit for Illumina sequencing

tag: chip antibody

value: Active Motif (39133)


title: P56 L6 home3


title: P56 L6 home1


title: P12_H3K27ac_ChIPseq_WT2

description:
Mnase digested chromatin
H3K27ac.lostPeaks.Macs2diffPeak.bed
H3K27ac.gainedPeaks.Macs2diffPeak.bed
H3K27ac.commonPeaks.Macs2diffPeak.bed
H3K27ac.Chp_Inp.WT.merge.depthNorm1xCov.bw


title: H3K27ac_H2AK119ub1_Input_DNA

description: Mnase digested chromatin

source_name: Spermatogenic cells from P12 Brg1WT and cKO testes

value: Brg1WT and cKO


title: P56 L6 free2

value: freewheel, naïve


title: P56 L6 free1


title: P12_H2AK119ub1_ChIPseq_WT2

description:
Mnase digested chromatin
H2AK119ub1.Chp_Inp.WT.merge.depthNorm1xCov.bw

value: Millipore -E6C5 (05-678)


title: P56 ADCV US d3-3

value: unconditioned stimulus only


title: P12_H3K27ac_ChIPseq_WT1

value: Mixed background


title: P12_H2AK119ub1_ChIPseq_cKO2

description:
Mnase digested chromatin
H2AK119ub1.Chp_Inp.cKO.merge.depthNorm1xCov.bw

value: testes


title: P56 ADCV US d3-2


title: P12_H2AK119ub1_ChIPseq_cKO1

value: spermatogenic cells


title: P56 ADCV US+CS d3-3

value: WT


title: Y490_IP

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

data_processing:
Aligned to mm10 using STAR spliced read aligner
Count read using HT-seq and using mm10 RefSeq as reference
Normalization (TMM), quantitation (logCPM) and differential expression analysis using edgeR and limma voom.
Genome_build: mm10
Supplementary_files_format_and_content: logCPM values

extract_protocol:
Total RNA was extracted using RNeazy kit (Qiagen) accordance with the prescribed protocol provided with the kit.
Libraries prepared using the Illumina TruSeq Stranded RNA (100 ng) + RiboZero Gold Library Prep Kit  and sequenced on an Illumina HiSeq4000 sequencer using strand-specific

treatment_protocol: We overexpressed either a control protein or a protein that suppresses calcium signals named hPMCA2w/b in astrocytes of the mouse striatum.

value: RiboTag mice (B6 background) crossed with Aldh1l1-Cre/ERT2 mice (FVB background but backcrossed with C57BL/6N for more than 9 generations)

tag: fraction

value: IP

tag: treatment


title: P12_H2AK119ub1_ChIPseq_WT1

tag: genotype


title: P56 ADCV US d3-1

tag: developmental stage


title: P56 ADCV US+CS d3-1

tag: tissue


title: P56 ADCV US+CS d3-2

tag: behavior


title: Y490_input

value: input


title: Y489_IP


title: P12_BRG1_RNAseq_WT1

description:
kallisto_counts.txt
5WT1


title: P56 ADCV US d7-5


title: P56 L6 US+CS d3-3


title: P56 ADCV US+CS d7-5


title: Y487_input


title: P56 ADCV US d7-4


title: P56 ADCV US+CS d7-4


title: Y487_IP


title: P56 ADCV US d7-3


title: Y486_input


title: Y486_IP


title: P56 ADCV US+CS d7-3


title: P56 ADCV US d7-2


title: Y485_input

value: Control


title: Y485_IP


title: P56 ADCV US+CS d7-1

value: 6-8 weeks


title: Y483_IP


title: Y482_IP


title: P56 ADCV US d7-1

value: cerebellum


title: P56 ADCV US+CS d7-2


title: Y483_input


title: P56 ADCV home4

description: ADCV-homecage.bigwig

value: homecage


title: P56 ADCV home3

description: ADCV-homecage.bigwig


title: Y481_IP


title: Y481_input


title: Y482_input


title: P56 ADCV home2

description: ADCV-homecage.bigwig


title: Y295IP

treatment_protocol: We overexpressed either a control protein or a protein that suppresses calcium signals named hPMCA2w/b together with Rpl22-HA in astrocytes of the mouse striatum.

value: C57BL/6N mice


title: P56 ADCV home1

description: ADCV-homecage.bigwig


title: Y295input


title: P56 ADCV free2


title: Y489_input


title: Y259IP


title: P56 ADCV free1


title: Y259input


title: P56 muscimol US+CS3

value: unconditioned stimulus and conditioned stimulus

tag: drugs/virus

value: muscimol injection


title: Y257IP


title: P56 muscimol US+CS4


title: Y257input


title: P56 muscimol US+CS1


title: P56 L6 US+CS d7-1


title: P56 muscimol US+CS2


title: Y225IP


title: P56 saline US+CS4

value: saline injection


title: Y225input


title: P12_H3K27ac_ChIPseq_cKO2

value: Active Motif (39133)


title: Y223IP


title: RbpJ-KO.2i.30

tag: clonal id

tag: culture condition

value: RGd2-RbpJ KO


title: T210-50 rep2

city: Yangzhou

first: Shuangyi

last: Yin

address: 88 daxue south road

country: China

institute: Yangzhou University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to B73 RefGen_v3 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) were calculated using Cuffdiff.
Genome_build: B73 RefGen_v3
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Zea mays

source_name: kernel

extract_protocol:
Maize ears were sampled at 10, 20, 30, 40, and 50 days after pollination (DAP). At each time point, seeds in the middle of each ear were removed. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 50 days after pollination


title: primary tumor sample [51156]

type: genomic

city: Leipzig

first: Edith

last: Willscher

address: Haertelstraße 16-18

country: Germany

institute: IZBI

description:
Gene expression data from cerebral tumor
51156

hyb_protocol: Illumina

scan_protocol: glioma samples were arrayed using the Illumina HumanMethylation450 BeadChip according to the manufacturer’s instructions at the DKFZ

data_processing: From beta-values, CpG IDs were mapped to the promoter region of each gene ranging from 2kb upstream to 200bp downstream of the transcription start site using RefSeq mRNA annotation. DNA methylation beta‐values of the respective CpGs were averaged to get one mean methylation beta‐value for each gene promoter available. Genes located on Chr. X and Y were excluded from analyses. Resulted M-values were quantile‐normalized and transformed into log10‐scale.

source_name: Human Brain, cerebral tumor sample

label_protocol: Mutational analyses of the IDH1, IDH2, TERT, BRAF and H3F3A genes were carried out by Sanger sequencing or pyrosequencing. The MGMT promoter methylation status was determined by methylation-specific PCR.

extract_protocol: DNA was extracted by ultracentrifugation from deep-frozen tissue samples. High quality of extracted DNA was assured by spectrophotometric analysis and agarose gel electrophoresis.

treatment_protocol: Tumor samples were shock-frozen after resection and stored at -80 °C. Only specimens with a histologically estimated tumor cell content of 80% or more were used for molecular analyses. All tumors were subjected to central pathology review and classified according to the 2016 WHO classification of tumors of the central nervous system

tag: diagnosis

tag: idh mutation (1 yes, 0 no)

tag: chr1_loss (1 yes, 0 no)

tag: chr19_loss (1 yes, 0 no)


title: primary tumor sample [33206]

description:
Gene expression data from cerebral tumor
33206


title: primary tumor sample [31806]

description:
Gene expression data from cerebral tumor
31806


title: P56 saline US+CS2


title: Y223input

tag: strain


title: P56 saline US+CS1


title: T210-40 rep2

value: 40 days after pollination


title: primary tumor sample [50926]

description:
Gene expression data from cerebral tumor
50926


title: P56 NucCyto-Seq 150min opto2

description:
nucleocytoplasmic RNA
none

value: Atoh1-CRE; Ai32 fl/fl

value: optogenetic stimulation

tag: timepoint

value: 150 minutes after stimulation


title: primary tumor sample [50240]

description:
Gene expression data from cerebral tumor
50240


title: primary tumor sample [53522]

description:
Gene expression data from cerebral tumor
53522


title: T210-50 rep1


title: primary tumor sample [53548]

description:
Gene expression data from cerebral tumor
53548


title: primary tumor sample [48112]

description:
Gene expression data from cerebral tumor
48112


title: primary tumor sample [50228]

description:
Gene expression data from cerebral tumor
50228


title: primary tumor sample [40490]

description:
Gene expression data from cerebral tumor
40490


title: Y222IP

value: IP


title: primary tumor sample [53806]

description:
Gene expression data from cerebral tumor
53806


title: T210-40 rep1


title: P56 NucCyto-Seq 150min opto1

description:
nucleocytoplasmic RNA
none


title: primary tumor sample [67816]

description:
Gene expression data from cerebral tumor
67816


title: primary tumor sample [53802]

description:
Gene expression data from cerebral tumor
53802


title: primary tumor sample [53788]

description:
Gene expression data from cerebral tumor
53788


title: primary tumor sample [67818]

description:
Gene expression data from cerebral tumor
67818


title: primary tumor sample [50222]

description:
Gene expression data from cerebral tumor
50222


title: Y222input

value: input


title: primary tumor sample [57448]

description:
Gene expression data from cerebral tumor
57448


title: Y221IP

value: Control


title: T210-30 rep2

value: 30 days after pollination


title: primary tumor sample [30608]

description:
Gene expression data from cerebral tumor
30608


title: P56 NucCyto-Seq 60min opto2

description:
nucleocytoplasmic RNA
none

value: 6-8 weeks

value: cerebellum

value: 60 minutes after stimulation


title: Y221input

value: C57BL/6N mice


title: T210-30 rep1


title: primary tumor sample [67600]

description:
Gene expression data from cerebral tumor
67600


title: primary tumor sample [56208]

description:
Gene expression data from cerebral tumor
56208


title: P56 NucCyto-Seq 20min opto2

description:
nucleocytoplasmic RNA
none

value: 20 minutes after stimulation


title: Y219IP


title: Y219input


title: primary tumor sample [40590]

description:
Gene expression data from cerebral tumor
40590


title: primary tumor sample [67614]

description:
Gene expression data from cerebral tumor
67614


title: P56 NucCyto-Seq 20min opto1

description:
nucleocytoplasmic RNA
none


title: MT rep3

city: Corvallis

first: Chih-Ning

last: Chang

state: OR

address: 1601 SW Jefferson Ave., RM 115

department: Pharmacy

institute: Oregon State University

data_processing:
Casava pipeline version 1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using TopHat version 2.1.0 default parameters.
HTseq was used to create count tables from tophat2 aligned reads.
DEseq2 was used to calculate differential gene expression between genotypes using a cutoff of reads > 200, p < 0.05 (Benferroni correction), and a fold change cutoff of ± 0.5.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: MT

extract_protocol:
Mice were euthanized at postnatal day 30. Tibialis anterior of both legs were collected, grinded in Next Advance bullet blender in presence of 0.5mm zirconium oxide beads and RNA was harvested using Qiagen mini kit.
Library preparation was prepared using Kapa Biosystems Stranded mRNA-seq Kit.

value: ICR

value: Tibialis anterior muscle

tag: age

value: post natal day 30

value: MCKcre Pitx2 fl/z


title: T210-20 rep2

value: 20 days after pollination


title: T210-20 rep1


title: T210-10 rep2

value: 10 days after pollination


title: T210-10 rep1


title: primary tumor sample [50944]

description:
Gene expression data from cerebral tumor
50944


title: primary tumor sample [50230]

description:
Gene expression data from cerebral tumor
50230


title: P56 NucCyto-Seq 0min home1

description:
nucleocytoplasmic RNA
none

value: Ai32 fl/fl

value: homecage

value: unstimulated


title: P56 NucCyto-Seq 0min home2

description:
nucleocytoplasmic RNA
none


title: MT rep2


title: MT rep1


title: T209-50 rep2

value: 50 days after pollination


title: primary tumor sample [67806]

description:
Gene expression data from cerebral tumor
67806


title: P56 Chrom-Seq 150min opto2

description:
chromatin-bound RNA
none

value: Atoh1-CRE; Ai32 fl/fl

value: optogenetic stimulation

value: 150 minutes after stimulation


title: primary tumor sample [67586]

description:
Gene expression data from cerebral tumor
67586


title: T209-50 rep1


title: Control rep3

source_name: Control

value: Pitx2 fl/z


title: P56 Chrom-Seq 150min opto1

description:
chromatin-bound RNA
none

value: 6-8 weeks

value: cerebellum


title: primary tumor sample [53544]

description:
Gene expression data from cerebral tumor
53544


title: P56 saline US+CS3

value: WT

value: unconditioned stimulus and conditioned stimulus

value: saline injection


title: T209-40 rep2

value: 40 days after pollination


title: P56 Chrom-Seq 60min opto2

description:
chromatin-bound RNA
none

value: 60 minutes after stimulation


title: Control rep1

value: ICR

value: Tibialis anterior muscle

value: post natal day 30


title: P56 Chrom-Seq 60min opto1

description:
chromatin-bound RNA
none


title: Control rep2


title: T209-40 rep1


title: P56 Chrom-Seq 20min opto2

description:
chromatin-bound RNA
none

value: 20 minutes after stimulation


title: T209-30 rep2

value: 30 days after pollination


title: Sample_15

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

institute: Leibniz Institute on Aging - FLI

data_processing:
Sequence information was extracted in FastQ format using Illumina's CASAVA v1.8.2 (Sample_01, 05, 09-11, 15, 17) and bcl2fastq software v1.8.3 (Sample_02-04, 06-08, 12-14, 16)
The processing and annotation of small RNA-Seq raw data was performed using the R programming language (version 3.0.2) and the ShortRead Bioconductor package (Morgan et al., 2009). First, raw data were pre-processed with the following parameters: Quality filtering, eliminating all reads containing an “N”; Adapter trimming, by use of the function trimLRPatterns(), allowing up to 2 mismatches and using as adapter sequence "TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC".
Size filtering removed all the reads with length shorter 18 and longer 33 nucleotides.
Reads were aligned, resulting in a direct annotation and quantification. The alignment was divided in two steps, to allow the recognition and the annotation of the reads exceeding reference length. In fact, the algorithm of Bowtie 1.1.2 does not allow aligning longer reads to shorter references. Specifically, first we performed alignment against the reference (Danio rerio, miRBase v21) with up to 2 mismatches. In this step the reference used was the mature sequence of microRNAs. Each read was aligned using these criteria with Bowtie 1.0.0 (settings: “-q", "--threads 8 --best", "—norc”). The remaining reads, which could not align in the previous step, were used as reference for a second alignment step with Bowtie 1.1.2 (settings: -f", "-a", "--threads 8 --norc"). In this case, the annotated mature microRNAs were aligned against the reads.
The information obtained in the two alignment phases was conveyed in one single table, containing a list of all the retrieved sequences and their relative counts. Read counts were normalized to RPM (reads per million mappable reads).
Genome_build: Danio rerio, miRBase v21;
Supplementary_files_format_and_content: Excel file, containing samples metadata information, mapping statistics and RPMs of each sample

organism: Iconisemion striatum

source_name: whole embryos

extract_protocol:
Extraction was done as described in Baumgart et al. 2012. (PMID:22487494)
library preparation was done using Illumina's TruSeq small RNA sample preparation kit following the manufacturer's instructions.

tag: life style

value: non-anual

tag: Stage

value: somite

tag: diapause

value: no


title: T209-30 rep1


title: T209-20 rep2

value: 20 days after pollination


title: Sample_17

organism: Rivulus cylindraceus


title: P56 Chrom-Seq 20min opto1

description:
chromatin-bound RNA
none

tag: genotype

value: Atoh1-CRE; Ai32 fl/fl

value: optogenetic stimulation


title: P56 Chrom-Seq 0min home2

description:
chromatin-bound RNA
none

value: Ai32 fl/fl

tag: developmental stage

value: 6-8 weeks

value: cerebellum

value: homecage

value: unstimulated


title: T209-20 rep1


title: P56 Chrom-Seq 0min home1

description:
chromatin-bound RNA
none

tag: tissue


title: Bookmarked replicate 4

city: Seattle

first: Dana

last: Miller

state: United States (1)

address: 1705 NE Pacific St. HSB J-587 Box 357350

department: Biochemistry

institute: University of Washington

data_processing:
STAR (v2.5.0) alignment: outSAMattributes NH NM MD  outSAMtype BAM SortedByCoordinate  outSAMunmapped Within  outSAMmapqUnique 50  readFilesCommand zcat  outFilterType BySJout  outSJfilterCountUniqueMin -1 2 2 2  outSJfilterCountTotalMin -1 2 2 2  outFilterIntronMotifs RemoveNoncanonical  twopassMode Basic
featureCounts (v1.6.2)
edgeR (3.24.3) differential expression analysis
Genome_build: UCSC ce10
Supplementary_files_format_and_content: DE_analysis_16_28-30_edgeR.csv

organism: Caenorhabditis elegans

source_name: Whole animal

growth_protocol: Short-lay synchronized animals grown to L4 at 20C

extract_protocol:
Wash worms with M9 and spin down for 1 minute at 3220 rcf. Flash freeze samples in liquid nitrogen. Store samples in -80C until ready for extraction. Perform standard Trizol RNA extraction.
NEBNext Ultra RNA Lib Prep Kit, Unstranded

treatment_protocol: Unexposed: Grown in standard atmosphere ("house air").  Naïve: Grown in house air to L4, then exposed to >150 ppm hydrogen sulfide 1h prior to collection. Bookmarked: Exposed to 50-60 ppm hydrogen sulfide 8-12 h starting at L1, returned to house air ~24h, then exposed to >150 ppm hydrogen sulfide 1h prior to collection.

tag: agent

value: exposed to approx. 50 ppm hydrogen sulfide for approx 8 hr as embryos) exposed to 1 hr high hydrogen sulfide


title: primary tumor sample [32226]

description:
Gene expression data from cerebral tumor
32226


title: Bookmarked replicate 3


title: T209-10 rep2

value: 10 days after pollination


title: Bookmarked replicate 2


title: P56 NucCyto-Seq 60min opto1

description:
nucleocytoplasmic RNA
none

tag: behavior

value: 60 minutes after stimulation


title: P56 NucCyto-Seq opto3

description:
nucleocytoplasmic RNA
ADCV-opto_nuccyto(+).bigwig
ADCV-opto_nuccyto(-).bigwig


title: T191-50 rep2

value: 50 days after pollination


title: primary tumor sample [53556]

description:
Gene expression data from cerebral tumor
53556


title: primary tumor sample [50220]

description:
Gene expression data from cerebral tumor
50220


title: T209-10 rep1


title: primary tumor sample [53554]

description:
Gene expression data from cerebral tumor
53554


title: P56 NucCyto-Seq opto4


title: primary tumor sample [30094]

description:
Gene expression data from cerebral tumor
30094


title: T191-40 rep2

value: 40 days after pollination


title: P56 NucCyto-Seq home4

description:
nucleocytoplasmic RNA
ADCV-home_nuccyto(+).bigwig
ADCV-home_nuccyto(-).bigwig


title: P56 NucCyto-Seq opto1


title: Sample_11

organism: Austrofundulus leohoignei


title: primary tumor sample [30100]

description:
Gene expression data from cerebral tumor
30100


title: primary tumor sample [30086]

description:
Gene expression data from cerebral tumor
30086


title: primary tumor sample [53800]

description:
Gene expression data from cerebral tumor
53800


title: Naïve replicate 4

value: 1 hr high (>150 ppm) hydrogen sulfide


title: primary tumor sample [53566]

description:
Gene expression data from cerebral tumor
53566


title: T191-40 rep1


title: T191-50 rep1


title: P56 NucCyto-Seq home3


title: Naïve replicate 2


title: T191-30 rep2

value: 30 days after pollination


title: P56 NucCyto-Seq opto2


title: Bookmarked replicate 1


title: P56 NucCyto-Seq home2


title: Naïve replicate 3


title: P56 NucCyto-Seq home1


title: primary tumor sample [30528]

description:
Gene expression data from cerebral tumor
30528


title: T191-30 rep1


title: primary tumor sample [50690]

description:
Gene expression data from cerebral tumor
50690


title: primary tumor sample [50210]

description:
Gene expression data from cerebral tumor
50210


title: Unexposed replicate 3


title: Unexposed replicate 4


title: primary tumor sample [40610]

description:
Gene expression data from cerebral tumor
40610


title: T191-20 rep2


title: P56 Chrom-Seq opto4

description:
chromatin-bound RNA
ADCV-opto_chromatin(+).bigwig
ADCV-opto_chromatin(-).bigwig


title: Unexposed replicate 2


title: P56 Chrom-Seq opto3


title: T191-20 rep1


title: Unexposed replicate 1


title: P56 Chrom-Seq opto2


title: T191-10 rep2


title: primary tumor sample [30508]

description:
Gene expression data from cerebral tumor
30508


title: P56 Chrom-Seq opto1


title: T191-10 rep1


title: C.13.0601_NS9

city: Columbus

first: Hatice Gulcin

last: Ozer

state: OH

address: 1800 Cannon Dr

department: Biomedical Informatics

institute: The Ohio State University

hyb_protocol: The tagged lncRNAs product were denatured 5 minutes at 85°C and aliquots of 10ul were combined with 20 ul of Reported Probes in hybridization buffer and 5 ul of Capture probes. The overnight hybridization (16 to 20 hours) at 65°C allowed hybridization of probes with specific targets. Probes excess were removed using two-step magnetic beads based purification on an automated fluidic handling system (nCounter Prep Station) and target/probe complexes were immobilized on the cartridge for data collection.

scan_protocol: The nCounter Digital Analyzer collected the data by taking images of immobilized fluorescent reporters in the sample cartridge with a CCD camera through a microscope objective lens. For each cartridge, a high-density scan encompassing 600 fields of view (FOV) has been performed. RLF file, containing all the key info about the ProbeSet used (such as barcodes info for each specific target miR, Positives controls, Negatives Controls and Housekeeping genes) was uploaded to the Scanner. A CDF file with the experiment informations (sample ID, Data, RLF file needed to be used, FOVs) was uploaded to the Digital Analyzer before to scan the cartridge. RCC files (Reporter Code Count) were collected once the scan was done.

data_processing: OSU CCC Genomics Shared Resource provided counts on probes after performing technical normalization using internal positive controls. Then we performed geometric mean normalization using all probes. These normalized counts were used for further analysis.

source_name: CN-AML blasts

label_protocol: 200ngs of total RNA were annealed with multiplexed DNA tags and bridged to target-specific tags. LncRNAs were bound to specific tags using a Ligase enzyme and all the tags in excess were removed by an enzume clean-up step.

growth_protocol: Patient samples were thawed and directly used for RNA extraction. No cytokines or cell culture techniques were used to expand leukemic blasts.

extract_protocol: On average, 20 million leukemic blasts isolated from cryopreserved samples were thawed and subjected to total RNA extraction using the Trizol reagent and previously published protocols

value: CN-AML blasts

tag: batch

tag: nanostring cartridge


title: C.93.0031_NS9


title: P56 Chrom-Seq home4

description:
chromatin-bound RNA
ADCV-home_chromatin(+).bigwig
ADCV-home_chromatin(-).bigwig


title: T147-50 rep1


title: primary tumor sample [51182]

description:
Gene expression data from cerebral tumor
51182

tag: diagnosis


title: T147-40 rep2


title: P56 Chrom-Seq home2


title: T147-50 rep2


title: C.12.5922_NS9


title: C.05.2039_NS9


title: primary tumor sample [67820]

description:
Gene expression data from cerebral tumor
67820

tag: idh mutation (1 yes, 0 no)


title: C.99.1970_NS9


title: primary tumor sample [53564]

description:
Gene expression data from cerebral tumor
53564

tag: chr1_loss (1 yes, 0 no)


title: P56 HiC Rad21cKO2

value: Gabra6-CRE; Cas9 fl/+

value: unconditioned stimulus and conditioned stimulus

tag: drugs/virus

value: AAV9 Rad21 gRNA injection


title: primary tumor sample [50216]

description:
Gene expression data from cerebral tumor
50216

tag: chr19_loss (1 yes, 0 no)


title: P56 Chrom-Seq home1


title: C.13.0574_NS9


title: T147-30 rep1


title: P56 HiC Rad21cKO1


title: 93.C.0196_NS9


title: T147-30 rep2


title: T147-20 rep2

value: 20 days after pollination


title: 93.C.0185_NS9


title: primary tumor sample [53520]

description:
Gene expression data from cerebral tumor
53520


title: P56 HiC ctrl2

value: AAV9 control gRNA injection


title: primary tumor sample [50218]

description:
Gene expression data from cerebral tumor
50218


title: primary tumor sample [67592]

description:
Gene expression data from cerebral tumor
67592


title: primary tumor sample [31886]

description:
Gene expression data from cerebral tumor
31886


title: T147-20 rep1


title: C.93.0010_NS9


title: Naïve replicate 1


title: T147-10 rep2


title: primary tumor sample [40468]

description:
Gene expression data from cerebral tumor
40468


title: primary tumor sample [29302]

description:
Gene expression data from cerebral tumor
29302


title: primary tumor sample [51158]

description:
Gene expression data from cerebral tumor
51158


title: P56 HiC opto3

value: Atoh1-CRE; Ai32 fl/fl

value: 6-8 weeks

value: optogenetic stimulation


title: P56 HiC opto2

value: cerebellum


title: primary tumor sample [55098]

description:
Gene expression data from cerebral tumor
55098


title: C.13.1651_NS9


title: NC87.1-NC58.1_slug_b

city: Bath

first: Atahualpa

last: Castillo Morales

address: Claverton Down

department: Biology and Biochemistry

institute: University of Bath

data_processing:
Reads were trimmed and filtered using Skewer v0.2.2 (min. length of 20bp, mean Quality score of 20). Chimerism genes are then defined as those that are significantly up-regulated in chimeric slugs (FDR adjusted p-value < 0.05).
Segmental duplication specific to AX4 on chromosome 2 between bases 3002337 and 375508 was masked from the reference genome prior to mapping.
Reads were pseudo-aligned to D. discoideum transcripts obtained from Ensembl Protists database release 36 and quantified using Kallisto v0.43.0.  One hundred bootstrap samples were generated for each replicate to compute uncertainty estimates for the expression levels.
Genes with less than 5 reads in at least 47% of the libraries were discarded.
Estimates of expression were then normalized and summarized to gene level using sleuth v0.29.0
Wald test for differential expression was conducted using sleuth v0.29.0
Genome_build: Genome assembly: dicty_2.7
Supplementary_files_format_and_content: tab-delimited text files include estimated counts and transcripts per million for each Sample

organism: Dictyostelium discoideum

source_name: Slug stage of 1:1 mixture of Dictyostelium discoideum NC87.1 and NC58.1

growth_protocol: Cells of each strain were grown in association with Klebsiella aerogenes, before washing by centrifugation in KK2 buffer. Washed cells were then plated on non-nutrient L28 purified agar (agar) at a density of x cells/cm2. For chimeric combinations we mixed equal numbers of cells from each strain. Aggregations were harvested after fourteen hours of development, when slugs had formed.

extract_protocol:
Ten agar plates per sample were pooled for RNA extraction using Trizol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Slug


title: P56 HiC opto1


title: C.13.1496_NS9


title: P56 Chrom-Seq home3

value: Ai32 fl/fl

value: homecage


title: primary tumor sample [67602]

description:
Gene expression data from cerebral tumor
67602


title: primary tumor sample [53568]

description:
Gene expression data from cerebral tumor
53568


title: T147-10 rep1

value: 10 days after pollination


title: T147-40 rep1

value: 40 days after pollination


title: NC87.1-NC58.1_slug_a


title: P56 HiC home3


title: C.05.2039_NS8.2


title: primary tumor sample [53546]

description:
Gene expression data from cerebral tumor
53546


title: C.93.0031_NS8


title: P56 HiC home2


title: primary tumor sample [67604]

description:
Gene expression data from cerebral tumor
67604


title: P56 HiC home1


title: NC34.2-NC87.1_slug_a

source_name: Slug stage of 1:1 mixture of Dictyostelium discoideum NC34.2 and NC87.1


title: NC34.2-NC87.1_slug_b


title: NC34.2-NC58.1_slug_b

source_name: Slug stage of 1:1 mixture of Dictyostelium discoideum NC34.2 and NC58.1


title: P56 PLAC-Seq opto2

data_processing:
Library strategy: PLAC-Seq
RNA-Seq, ChIP-Seq, DHS, HiC, and PLAC-Seq data was analyzed using HISAT2/Bowtie2 on the public server at usegalaxy.org or bwa mem for genome alignment, MACS2 for peak calling, MAPS for PLAC-Seq analyses, Juicebox for visualizing HiC and PLAC-Seq datasets
Genome_build: mm10
Supplementary_files_format_and_content: .bigwig files were generaed for RNA-Seq and ChIP-Seq datasets
Supplementary_files_format_and_content: .hic files were generated for HiC and PLAC-Seq datasets

tag: chip antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #


title: primary tumor sample [67598]

description:
Gene expression data from cerebral tumor
67598


title: C.13.0601_NS8


title: C.13.0574_NS8


title: primary tumor sample [53804]

description:
Gene expression data from cerebral tumor
53804


title: NC34.2-NC58.1_slug_a


title: P56 PLAC-Seq opto1


title: C.12.5922_NS8


title: P56 PLAC-Seq home2


title: C.05.2039_NS8.1


title: P56 input opto


title: NC87.1_slug_a

source_name: Slug stage of Dictyostelium discoideum NC87.1 grown clonally


title: PS87.0052_NS9


title: C.13.0884_NS8


title: primary tumor sample [56206]

description:
Gene expression data from cerebral tumor
56206


title: P56 input home

source_name: anterior dorsal cerebellar vermis


title: primary tumor sample [50938]

description:
Gene expression data from cerebral tumor
50938


title: C.12.6543_NS8


title: NC87.1_slug_b


title: NC34.2_slug_b

source_name: Slug stage of Dictyostelium discoideum NC34.2 grown clonally


title: P56 HiC ctrl1


title: C.12.2111_NS8


title: primary tumor sample [67596]

description:
Gene expression data from cerebral tumor
67596


title: P56 Rad21 opto


title: P56 PLAC-Seq home1


title: NC58.1_slug_b

source_name: Slug stage of Dictyostelium discoideum NC58.1 grown clonally


title: primary tumor sample [51710]

description:
Gene expression data from cerebral tumor
51710


title: NC34.2_slug_a


title: P56 Rad21 home


title: C.12.0618_NS8


title: P56 CTCF opto4

value: CTCF

value: Millipore


title: primary tumor sample [33474]

description:
Gene expression data from cerebral tumor
33474


title: Sample_05

organism: Nothobranchius furzeri

tag: life style

value: anual

tag: Stage

value: somite

tag: diapause

value: yes


title: C.09.4525_NS8

tag: tissue

value: CN-AML blasts


title: Sample_01


title: P56 CTCF opto3

tag: genotype

tag: developmental stage


title: spt20del_Sgf73-5xFLAG_HS_ChIP-seq

city: Daejeon

first: Minhoo

last: Kim

address: Basic Science Bld Rm418, 291 Daehak-ro, Yuseong-gu, KAIST

department: Department of Biological Sciences

country: South Korea

institute: KAIST

description: Cells subjected to heat shock at 42degrees for 20min

data_processing:
Sequenced reads were mapped to Saccharomyces cerevisiae genome (sacCer3) and processed using Bowtie2 and SAMtools, respectively.
Significant peaks were identified and annotated using HOMER.
Quantification analyses and average plots were generated using Deeptools.
Genome_build: sacCer3
Supplementary_files_format_and_content: bigwig files were prepared using Deeptools.

organism: Saccharomyces cerevisiae

growth_protocol: Yeast cells were cultured at 30degrees to mid-log phase, unless indicated otherwise.

extract_protocol:
Cells were fixed using formaldehyde (1% final concentration) for 15min at RT and lysates were prepared by beadbeating. Chromatin was sheared by sonication and DNA-protein complexes were silated by anti-FLAG immunoprecipitation.
Libraries were prepared according to the manufacturer’s instructions (Bioo Scientific Corporation, 5143-02).


title: C.93.0031_NS7.1

tag: batch


title: P56 CTCF opto2

tag: behavior


title: primary tumor sample [67812]

description:
Gene expression data from cerebral tumor
67812

tag: diagnosis


title: rpt2-1_Sgf73-5xFLAG_HS_ChIP-seq


title: C.13.0601_NS7

tag: nanostring cartridge


title: C.13.0574_NS7


title: wt_Sgf73-5xFLAG_HS_ChIP-seq

source_name: wildtype

value: wildtype


title: primary tumor sample [53534]

description:
Gene expression data from cerebral tumor
53534

tag: idh mutation (1 yes, 0 no)

tag: chr1_loss (1 yes, 0 no)


title: P56 CTCF home4


title: primary tumor sample [30930]

description:
Gene expression data from cerebral tumor
30930

tag: chr19_loss (1 yes, 0 no)


title: NC58.1_slug_a

tag: strain


title: primary tumor sample [56194]

description:
Gene expression data from cerebral tumor
56194


title: primary tumor sample [67808]

description:
Gene expression data from cerebral tumor
67808


title: primary tumor sample [53792]

description:
Gene expression data from cerebral tumor
53792


title: primary tumor sample [67588]

description:
Gene expression data from cerebral tumor
67588


title: C.12.6475_NS8


title: P56 CTCF home3

tag: chip antibody


title: rpt2-1_Sgf73-5xFLAG_noHS_ChIP-seq

description: Before heat shock


title: primary tumor sample [48570]

description:
Gene expression data from cerebral tumor
48570


title: P56 CTCF home2

value: Atoh1-CRE; Ai32 fl/fl

tag: chip antibody vendor


title: C.12.5922_NS7


title: C.09.1913_NS7


title: primary tumor sample [67814]

description:
Gene expression data from cerebral tumor
67814


title: wt_Sgf73-5xFLAG_noHS_ChIP-seq

description: Before heat shock


title: C.05.2039_NS7


title: primary tumor sample [47612]

description:
Gene expression data from cerebral tumor
47612


title: P56 CTCF home1

value: 6-8 weeks

tag: chip antibody cat. #


title: primary tumor sample [53794]

description:
Gene expression data from cerebral tumor
53794


title: sgf73del_Rpb3-5xFLAG_ChIP-seq


title: P56 H2A.z opto3

value: optogenetic stimulation


title: P56 H2A.z opto2

value: cerebellum


title: rpt2-1_Rpb3-5xFLAG_ChIP-seq


title: C.05.1079_NS7


title: wt_Rpb3-5xFLAG_ChIP-seq


title: primary tumor sample [40554]

description:
Gene expression data from cerebral tumor
40554


title: C.01.1926_NS7


title: sgf73del_Yra1-5xFLAG_ChIP-seq


title: C.01.1564_NS7


title: C.04.2323_NS7


title: P56 H2A.z opto1


title: P56 H2A.z home3


title: rpt2-1_Yra1-5xFLAG_ChIP-seq


title: primary tumor sample [52836]

description:
Gene expression data from cerebral tumor
52836


title: spt20del_Sgf73-5xFLAG_noHS_ChIP-seq

description: Before heat shock


title: primary tumor sample [31142]

description:
Gene expression data from cerebral tumor
31142


title: C.93.0031_NS7.2


title: P56 H2A.z home2


title: C.06.3957_NSR

value: NSR


title: P56 CTCF opto1


title: primary tumor sample [48266]

description:
Gene expression data from cerebral tumor
48266


title: primary tumor sample [48224]

description:
Gene expression data from cerebral tumor
48224


title: wt_Yra1-5xFLAG_ChIP-seq


title: primary tumor sample [67800]

description:
Gene expression data from cerebral tumor
67800


title: P56 H2A.z home1

value: Ai32 fl/fl


title: R.02.0228_NSR


title: C.10.0444_NSR


title: rpt2-1_Sua7-5xFLAG_ChIP-seq


title: P56 H3K27me3 opto2


title: C.05.2881_NSR


title: wt_Sua7-5xFLAG_ChIP-seq


title: sgf73del_Sgf11-5xFLAG_ChIP-seq


title: P56 H3K27me3 opto3


title: primary tumor sample [50232]

description:
Gene expression data from cerebral tumor
50232


title: P56 H3K27me3 opto1


title: C.06.2271_NSR


title: sgf73del_Sua7-5xFLAG_ChIP-seq


title: P56 H3K27me3 home2

value: homecage


title: rpt2-1_Sgf11-5xFLAG_ChIP-seq


title: primary tumor sample [56198]

description:
Gene expression data from cerebral tumor
56198


title: primary tumor sample [48056]

description:
Gene expression data from cerebral tumor
48056


title: C.02.0572_NSR


title: R.02.0307_NSR


title: primary tumor sample [55096]

description:
Gene expression data from cerebral tumor
55096


title: P56 H3K27me3 home3


title: wt_Sgf11-5xFLAG_ChIP-seq


title: P56 H3K27me3 home1


title: rpt2-1_Sgf73-5xFLAG_ChIP-seq


title: P56 H3K27ac opto2


title: wt_Sgf73-5xFLAG_ChIP-seq


title: C.00.0652_NSR


title: C.00.1607_NSR


title: wt_WCE


title: P56 H3K27ac opto1


title: C.02.0053_NS6


title: primary tumor sample [48584]

description:
Gene expression data from cerebral tumor
48584


title: primary tumor sample [53570]

description:
Gene expression data from cerebral tumor
53570


title: P56 H3K27ac home2


title: P56 H3K4me3 opto2


title: C.01.0924_NS6


title: C.01.1564_NS6


title: P22 DHS wt2

source_name: cerebellum

value: WT


title: primary tumor sample [53540]

description:
Gene expression data from cerebral tumor
53540


title: P56 H3K27ac home1


title: C.00.2312_NS6


title: P18_Input_DNA_rep1

description: Mnase digested chromatin

source_name: Spermatogenic cells from P18 testes

tag: age

value: testes

value: wild type

tag: cell type

value: spermatogenic cells


title: P56 H3K4me3 opto1

value: Abcam


title: primary tumor sample [50238]

description:
Gene expression data from cerebral tumor
50238


title: P56 H3K4me3 home2


title: P18_Input_DNA_rep2

description: Mnase digested chromatin


title: C.00.2304_NS6


title: C.00.1844_NSR


title: P18_BRG1_ChIPseq_rep2

description:
Mnase digested chromatin
P18BRG1.merged.macs2Peaks.bed
P18merge_Chp_Inp_scaledNrm1x.bw


title: P56 H3K4me3 home1


title: C.00.1844_NS6


title: primary tumor sample [30514]

description:
Gene expression data from cerebral tumor
30514


title: primary tumor sample [51178]

description:
Gene expression data from cerebral tumor
51178


title: P18_BRG1_ChIPseq_rep1


title: FATP2 KO cells, replicate 3 [KO.3]

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing:
RNA-seq data was aligned using bowtie2 against mm10 version of the human genome and RSEM v1.2.31 software was used to estimate raw read counts and FPKM values using transcriptome information from Ensemble v84 set
DESeq2 was used to estimate significance of differential expression between groups
Genome_build: mm10
Supplementary_files_format_and_content: Prosessed files contains the raw counts for each gene as estimated by RSEM

source_name: FAPT2 KO mouse spleen derived Ly6G+ cells

extract_protocol:
PMN-MDSC cells were isolated from mouse spleen using Ly6G beads
Lexogen Quantseq RNA-Seq Library Preparation Kit was used for library preparation and ran in a 75bp single end run on Illumina NextSeq 500

tag: genotype/variation

value: FATP2 KO

value: spleen

value: Polymorphonuclear myeloid derived suppressor cells (PMN-MDSC)


title: primary tumor sample [53538]

description:
Gene expression data from cerebral tumor
53538

source_name: Human Brain, cerebral tumor sample


title: primary tumor sample [46540]

description:
Gene expression data from cerebral tumor
46540


title: P12_Input_DNA_rep2

description: Mnase digested chromatin

source_name: Spermatogenic cells from P12 testes

tag: tissue


title: FATP2 KO cells, replicate 2 [KO.2]


title: C.00.1607_NS6

value: CN-AML blasts


title: C.00.0652_NS6


title: P12_Input_DNA_rep1

description: Mnase digested chromatin

tag: genotype


title: FATP2 KO cells, replicate 1 [KO.1]


title: C.06.3957_NS6


title: primary tumor sample [64098]

description:
Gene expression data from cerebral tumor
64098


title: P12_BRG1_ChIPseq_rep2

description:
Mnase digested chromatin
P12BRG1.merged.macs2Peaks.bed
P12merge_Chp_Inp_scaledNrm1x.bw


title: FATP2 WT cells, replicate 3 [WT.3]

source_name: FAPT2 WT mouse spleen derived Ly6G+ cells

value: FATP2 WT


title: U.00.233_NS6


title: primary tumor sample [53798]

description:
Gene expression data from cerebral tumor
53798


title: primary tumor sample [51166]

description:
Gene expression data from cerebral tumor
51166


title: P12_BRG1_ChIPseq_rep1


title: FATP2 WT cells, replicate 2 [WT.2]


title: P22 DHS wt1

tag: developmental stage


title: FATP2 WT cells, replicate 1 [WT.1]


title: Spinal motor neuron GFP neg, replicate 2 [SC2_neg]

city: Stockholm

first: Eva

last: Hedlund

address: Svante Arrhenius v. 16C

department: Department of Biochemistry and Biophysics

country: Sweden

institute: Stockholm University

data_processing:
Base-calling using Illumina Cassava 1.7
Alignment to the mouse genome (mm10) performed using HISAT2 version 2.0.3 using the main Galaxy server
Raw read counts were extracted using the GenomicAlignments package in R, with the function SummarizeOverlaps, mode set to "Union"
Differential gene expression analysis was performed on the read counts using DESeq2 version 1.12.4. Only genes with reads in 4 samples or more were considered in the analysis.
Normalized abundance measurements (RPKMs) were generated manually, using transcript lengths from the the Ensembl GRCm38 (version 87) annotation file.
Genome_build: mm10
Supplementary_files_format_and_content: One data file is added providing normalized abundance measurements (RPKM) organized as a matrix for the samples (tab-delimited txt).

source_name: Spinal motor neuron GFP neg

growth_protocol: mESCs were cultured and patterned towards OMN or SC motor neurons with appropriate morphogens as embriod bodies for 5 days. GFP positive and negative fractions were purified using FACS and collected as bulk for RNAseq.

extract_protocol:
Cells were lysed in the presence of RNAse inhibitor and immediately frozen down. Library preparation occurred in the lysis buffer directly, without RNA-extraction.
Libraries for RNA-seq were prepared by using SMART-seq2 combined with Tn5-based tagementation.

treatment_protocol: Specification of mESCs into spinal motor neurons was conducted by exposing embryo bodies to the Smoothened Agonist SAG (500 nM) and retinoic acid (RA, 100 nM)  while oculomotor neurons were patterned by SAG (250 nM) and Fgf8 (100 ng/ml) both for 5 days.

tag: source cell type

value: Stem cell-derived motor neuron

tag: disease status

value: Control

tag: cell preparation

value: bulk culture preparation, FACS purified


title: P2ten

city: New Orleans

first: Samir

middle: S

last: El-Dahr

state: LA

address: 1430 Tulane Ave

department: Pediatrics

institute: Tulane University School of Medicine

description: ATAC-seq

data_processing:
Concatenate paired-end reads run across multiple lanes for each sample such that there exist one forward (_1.fastq.gz) and one reverse (_2.fastq.gz) reads file for each sample.
Assess quality of reads using FASTQC(v0.11.7)
Aligned paired-end Fastq files to mm10 using Bowtie2
Samtools to remove Mitochondrial reads
Picard tools v1.77 to remove Duplicates
Call narrow peaks using MACS2
Bedtools to generate sorted bdg and bigwig files for viewing in IGV
HOMER to annotate files and find Motifs
GREAT analysis for gene ontology (C.Y. McLean et al., 2010)
Genome_build: mm10
Supplementary_files_format_and_content: fastq.gz and Bigwig files

source_name: Postnatal Kidneys

extract_protocol:
Corces et al., 2017
Buenrostro et al., 2013
Omni-ATAC

tag: develomental stage


title: Spinal motor neuron GFP pos, replicate 2 [SC2]

source_name: Spinal motor neuron GFP pos


title: P2nine

description: ATAC-seq


title: Spinal motor neuron GFP neg, replicate 1 [SC1_neg]


title: P2two

description: ATAC-seq


title: Spinal motor neuron GFP pos, replicate 1 [SC1]


title: P0L3

description: ATAC-seq

source_name: Neonatal Kidneys


title: Oculomotor neuron GFP neg, replicate 3 [OMN3_neg]

source_name: Oculomotor neuron GFP neg


title: P0L2

description: ATAC-seq


title: R.02.0228_NS5

source_name: CN-AML blasts

tag: batch

tag: nanostring cartridge


title: primary tumor sample [50702]

description:
Gene expression data from cerebral tumor
50702

tag: diagnosis

tag: idh mutation (1 yes, 0 no)

tag: chr1_loss (1 yes, 0 no)

tag: chr19_loss (1 yes, 0 no)


title: primary tumor sample [48298]

description:
Gene expression data from cerebral tumor
48298


title: PS87.0154_NS5


title: C.99.0479_NS5


title: primary tumor sample [30502]

description:
Gene expression data from cerebral tumor
30502


title: C.99.1664_NS5


title: R.02.0307_NS6


title: Oculomotor neuron GFP pos, replicate 3 [OMN3]

source_name: Oculomotor neuron GFP pos


title: P0L1

description: ATAC-seq

tag: strain


title: C.99.1285_NS5


title: C.99.1113_NS5


title: C.98.1331_NS5


title: primary tumor sample [30910]

description:
Gene expression data from cerebral tumor
30910


title: primary tumor sample [57450]

description:
Gene expression data from cerebral tumor
57450


title: P0H3

description: ATAC-seq


title: Oculomotor neuron GFP neg, replicate 2 [OMN2_neg]


title: P0H2

description: ATAC-seq


title: Oculomotor neuron GFP pos, replicate 2 [OMN2]


title: C.98.0778_NS5


title: P0H1

description: ATAC-seq


title: Oculomotor neuron GFP neg, replicate 1 [OMN1_neg]


title: C.10.0444_NS5


title: C.98.0453_NS5


title: primary tumor sample [32232]

description:
Gene expression data from cerebral tumor
32232


title: primary tumor sample [30914]

description:
Gene expression data from cerebral tumor
30914


title: primary tumor sample [53526]

description:
Gene expression data from cerebral tumor
53526


title: Oculomotor neuron GFP pos, replicate 1 [OMN1]


title: E16WTc

description: ATAC-seq

source_name: Embryonic Kidneys


title: Spinal motor neuron GFP neg, replicate 4 [SC4_neg]


title: C.09.5209_NS4


title: primary tumor sample [53550]

description:
Gene expression data from cerebral tumor
53550


title: Sample_16

organism: Aplocheilus lineatus

source_name: whole embryos

tag: life style

value: non-anual

tag: Stage

value: somite

tag: diapause

value: no


title: C.09.4551_NS4

tag: tissue


title: E16WTb

description: ATAC-seq

tag: genotype


title: Sample_14


title: E16WTa

description: ATAC-seq


title: primary tumor sample [67608]

description:
Gene expression data from cerebral tumor
67608


title: Sample_08

value: GRZ x MZZW

value: anual

value: yes (2 months)


title: Sample_13


title: E13WTA

description: ATAC-seq


title: C.09.3606_NS4


title: C.09.2442_NS4


title: E13WT

description: ATAC-seq


title: Sample_06

value: yes (2 weeks)


title: C.09.1438_NS4


title: Sample_12


title: cKO 3

city: Pohang

first: Sin-Hyeog

last: Im

state: Gyeongsangbuk-do

address: POSTECH Biotech Center Rm. 428-431, Pohang University of Science and Technology (POSTECH), 77 Cheongam-ro, Nam-gu, Pohang, Republic of Korea

department: Academy of Immunology and Microbiology

institute: Institute for Basic Science

data_processing:
The quality of the sequenced reads was determined using the FastQC tool, and contaminated adaptor sequences were trimmed using the Cutadapt tool.
The trimmed sequence reads were aligned to the mouse reference genome mm9 using Bowtie2.
The abundance of transcripts was estimated using the Tuxedo protocol (Tophat and Cufflinks). Fragments per kilobase of transcript per million mapped reads (FPKM), which is normalized expression level, was generated with Cuffnorm and differentially expressed genes (DEGs) were identified using Cuffdiff.
DEGs were defined as the genes that were differentially expressed, showing less than a false discovery rate (FDR)-adjusted p-value cutoff of 0.05.
We further discarded genes showing less than 1.5-fold changes of up- or down-regulated genes between conditions.
Genome_build: mm9

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with Ribospin II RNA purification kit (GeneAll, Korea)
TruSeqStranded mRNA  Sample Preparation Kit


title: Sample_04


title: primary tumor sample [51180]

description:
Gene expression data from cerebral tumor
51180


title: Gi4_DSN

city: Jerusalem

first: Iddo

middle: Z.

last: Ben-Dov

address: Ein Kerem

department: Nephrology and Hypertension

country: Israel

institute: Hadassah Medical Center

description:
The cDNA library of sample 4 was cleaved with duplex specific nuclease (DSN), re-amlified and re-sequenced
Gia_DNS-26_78

data_processing:
HiSeq 2500 standard base-calling
miRDeep2
Each non-cleaved and duplex-specific-nuclease-cleaved small RNA library pairs were combined to a single FASTQ file and the resulting 5 files were processed by miRDeep2's mapper.pl
Genome_build: GiardiaDB-37_GintestinalisAssemblageAWB_Genome.fasta file (2018-04-19) from GiardiaDB
Supplementary_files_format_and_content: Excel worksheet: Mapping of collapsed reads to the GiardiaDB-37_GintestinalisAssemblageAWB_Genome.fasta file (2018-04-19) from www.GiardiaDB.org
Supplementary_files_format_and_content: The collapsed_read_id column incorporates the source library (Gi1-Gi5), followed by the unique read id, and lastly the number of collapsed reads (e.g. x341354)

organism: Giardia duodenalis

source_name: trophozoite cells

growth_protocol: Trophozoites were grown in Polystyrene Cell Culture Tubes, Greiner bio-one in a presence of TYDK medium enriched in FCS 10% in 37°C in anaerobic conditions. Every 3 days the trophozoites were separated by cooling with ice, collecting, centrifugation and fluidization in 1 ml of TYDK medium.

extract_protocol:
mirVana miRNA isolation kit (Ambion, AM1561)
ligation & gel-based small RNA cDNA library (see PMID: 24489795)

tag: isolate

value: WB cl.6

tag: bei resources cat. #

tag: barcode

tag: 3' adapter sequence

value: TGATGTCGTATGCTGTCCTCTGTGGAA


title: C.06.4476_NS4


title: Sample_03


title: Gi3_DSN

description:
The cDNA library of sample 3 was cleaved with duplex specific nuclease (DSN), re-amlified and re-sequenced
Gia_DNS-26_77

value: SUG

value: TATCATCGTATGCTGTCCTCTGTGGAA


title: Sample_02


title: cKO 2


title: C.05.2881_NS4


title: Gi5_DSN

description:
The cDNA library of sample 5 was cleaved with duplex specific nuclease (DSN), re-amlified and re-sequenced
Gia_DNS-26_79

value: TGTGTTCGTATGCTGTCCTCTGTGGAA


title: cKO 1


title: Gi2_DSN

description:
The cDNA library of sample 2 was cleaved with duplex specific nuclease (DSN), re-amlified and re-sequenced
Gia_DNS-26_76

value: Mario

value: TAGGATCGTATGCTGTCCTCTGTGGAA


title: Sample_07

value: yes (1 month)


title: primary tumor sample [40478]

description:
Gene expression data from cerebral tumor
40478


title: Control 3


title: HH31 scRNA-seq

city: Berlin

first: Christian

last: Feregrino

address: Ihnestraße 63

institute: MPI - Molecular Genetics

data_processing:
Base calling, adaptor trimming, joint sequencing runs mapping, de-multiplexing and of the gene / cell count matrices generation using the Cell Ranger software v2 (10X Genomics).
Base calling, adaptor trimming, mapping, de-multiplexing and of the gene / cell count matrices generation using the DropSeq pipeline v1 (https://github.com/broadinstitute/Drop-seq/releases).
Cells with an UMI count of more than 4 times the sample mean or less than 20% of the sample median were filtered out, cells with a mitochondrial or ribosomal contribution to UMI count of more than 10% were also filtered out.
Genome_build: ENSEMBL Gallus gallus 5.0
Supplementary_files_format_and_content: Tab delimited text files. UMI count tables where cells are rows and genes are columns, additional meta-data columns

organism: Gallus gallus

source_name: Developing hindlimb

extract_protocol:
Cells were dissociated using trypsin 0.25%. Single cells suspensions were fed into Chromium 10x or DropSeq systems
DropSeq
10x v2

tag: dissection

value: Tip of digit 4

tag: protocol

tag: protocol notes

value: Two combined sequencing runs.


title: C.06.3358_NS4

value: CN-AML blasts

tag: batch

tag: nanostring cartridge


title: Gi1_DSN

description:
The cDNA library of sample 1 was cleaved with duplex specific nuclease (DSN), re-amlified and re-sequenced
Gia_DNS-26_75

value: TAGAGTCGTATGCTGTCCTCTGTGGAA


title: Control 2


title: Gi5_noDSN

value: TAATATCGTATGCTGTCCTCTGTGGAA


title: C.06.2271_NS4


title: primary tumor sample [47622]

description:
Gene expression data from cerebral tumor
47622

tag: diagnosis

tag: idh mutation (1 yes, 0 no)

tag: chr1_loss (1 yes, 0 no)


title: Control 1

tag: strain


title: primary tumor sample [50226]

description:
Gene expression data from cerebral tumor
50226

tag: chr19_loss (1 yes, 0 no)


title: primary tumor sample [53560]

description:
Gene expression data from cerebral tumor
53560


title: primary tumor sample [30920]

description:
Gene expression data from cerebral tumor
30920


title: C.06.2110_NS3


title: Gi4_noDSN

value: TAACGTCGTATGCTGTCCTCTGTGGAA


title: RE2

city: Yangling District

first: Lei

last: Zhang

state: Province, State or Region

address: No.22 Xinong Road,  Yangling District

department: College of Animal Science and Technology

institute: Northwest A&F University

description:
circRNA
Sample name: GE706_T_count

data_processing:
Prior to reference genome mapping, the raw data (raw reads) were processed to remove low quality reads.
Firstly the RNA-seq clean reaps (valid data) were mapped to the goat reference genome (http://www.ncbi.nlm.nih.gov/genome/?term=goat) using a publicly available program Tophat 2 (http://ccb.jhu.edu/software/tophat/index.shtml).
Second, TopHat-Fusion (http://ccb.jhu.edu/software/tophat/fusion_index.shtml) is an enhanced version of TopHat with the ability to align reads across fusion points, which results from the breakage and re-joining of two different chromosomes, or from rearrangements within a chromosome. The reads, unmapped with TopHat but mapped with TopHat-Fusion on the same chromosome in a noncolinear ordering (back-spliced ordering), were extracted as candidate back-spliced junction reads.
Last, the circRNAs were identified from back-spliced junction reads based on structural and splice sites characters of circRNAs: (1) the two ends of splice sites must be GU/AG, (2) mismatch≤ 2, (3) back-splice junction reads ≥ 1, (4) if there were more than 2 splice sites, they were on the same chromosome and not too wide apart from each other more than 100 kb.
The aligned read files were processed by Cufflinks, which uses the normalized RNA-seq fragement counts to measure the relative abundances of the transcripts [43], the unit of the measurement is Fragment Per Kilobase of exon per Million fragments mapped (FPKM
Genome_build: http://www.ncbi.nlm.nih.gov/genome/?term=goat
Supplementary_files_format_and_content: excel files with circRNA counts, fpkm (S2 File. circRNA expression in goat endometrium. (XLS).xlsx) and other analysis.

organism: Capra hircus

source_name: receptive endometrium

growth_protocol: A total of 20 healthy 24-month-old multiparous dairy goats (Xinong Saanen) were induced to estrous synchronization for this study.

extract_protocol:
Total RNA was extracted from the six samples using the TRIzol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The quantity and purity of total RNA were analyzed with Bioanalyzer 2100 (Agilent, CA, USA) and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number> 7.0. At the same time, a new library was constructed by mixing all the six total RNAs with equal amount, and it was used to decrease false positive dentification of circRNA. Approximately 10 ug of total RNA representing a specic adipose type was used to deplete ribosomal RNA according to the manuscript of the Epicentre Ribo-Zero Gold Kit (Illumina, San Diego, USA). Following purication, the RNAs were treated with RNase R for 20 min at 37 ℃ (Epicentre Technologies, Madison, WI), and then the poly (A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature.
Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the RNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 250 bp (±50 bp).  Paired-end sequencing on an Illumina Hiseq2500 (LC Sceiences, USA) following the vendor's recommended protocol.

treatment_protocol: The first day of mating was considered to be Day 0 of pregnancy. Gestational days 5 and 15 were important time points for the embryo implantation in goats. The experimental goats were observed 3 times daily to ascertained estrous sign and mated naturally twice in estrus. And then the goats were euthanized when the goats lost consciousness caused by intravenous injection of barbiturate (30mg/kg) at gestational day 5 (pre-receptive endometrium) and gestational day 15 (receptive endometrium).

tag: breed

value: Xinong Saanen

value: endometrium

tag: endometrium status

value: receptive

tag: gestational day

value: at gestational day 15


title: RE1

description:
circRNA
Sample name: GE592_T_count

tag: tissue


title: C.09.1388_NS4


title: C.06.0865_NS3


title: primary tumor sample [67802]

description:
Gene expression data from cerebral tumor
67802


title: primary tumor sample [52452]

description:
Gene expression data from cerebral tumor
52452


title: C.06.0770_NS3


title: PE2

description:
circRNA
Sample name: GE990_C_count

source_name: pre-receptive endometrium

value: pre-receptive

value: at gestational day 5


title: Gi2_noDSN

tag: isolate

tag: bei resources cat. #

value: TCTGATCGTATGCTGTCCTCTGTGGAA


title: primary tumor sample [56196]

description:
Gene expression data from cerebral tumor
56196


title: primary tumor sample [50236]

description:
Gene expression data from cerebral tumor
50236


title: C.06.0074_NS3


title: primary tumor sample [32244]

description:
Gene expression data from cerebral tumor
32244


title: Gi1_noDSN

tag: barcode

tag: 3' adapter sequence

value: TCACTTCGTATGCTGTCCTCTGTGGAA


title: PE1

description:
circRNA
Sample name: GE258_C_count


title: H3.1K36M#2_2_RNA

city: Hangzhou

first: Dong

last: Fang

state: Zhejiang

address: 866 Yuhangtang Road

department: Life Sciences Institute

institute: Zhejiang University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequencing reads were cleaned with trim-galore and aligned to the human genome, hg19, using bowtie2. PCR duplicated reads were removed by SAMtools
ChIP-seq peaks were identified by MACS2 with the parameter of narrow peak for H3K36M peaks, and broad peak calling for H3K36 and H3K27 methylations. For spike-in ChIP-seq results, the sequencing reads were aligned and normalized according to previous published procedures (Orlando et al., 2014). In brief, human (hg19) and drosophila (dm6) genome sequences were combined to produce a reference genome. Cleaned sequencing reads were aligned to the reference genome by bowtie2 with default parameters. The mapped reads were then separated into human and drosophila reads, where the reads mapped to the drosophila genome were used to determine the normalization factor. The number of reads in each sequencing results was counted and normalized by the normalization factor.
For RNA sequencing. Sequence reads were cleaned with trim-galore and then aligned to the human genome hg19 using STAR. The mapped reads were annotated to Refseq genes using TopHat and the FPKM of genes was calculated by Cufflinks. Cuffdiff was used to identify and analyze the differential gene expression using false discovery rate (FDR) < 0.05 as the cutoff.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated, scores represent the normalization Reads Per 10 Million.
Supplementary_files_format_and_content: txt files are tab-delimited text files include reads counts values for each gene

source_name: Astrocyte

growth_protocol: T/C28a2 cell, which was the immortalized human juvenile costal chondrocyte, was cultured in DMEM supplemented with 10% FBS.

extract_protocol:
Total RNA was extracted using RNeasy plus kit (Qiagen) according to the manufacturer’s instructions.
The poly-A containing mRNA was purified by poly-T oligo-attached magnetic beads, and then fragmented by divalent cations under elevated temperature. The cleaved RNA was reverse transcript into cDNA with random primers, followed by second strand cDNA synthesis with DNA Polymerase I and RNase H. These single 'A' base added cDNAs were ligated to adapter, amplified and then purified as single strand DNA circle, which was used to generated DNA nanoballs (DNBs) by rolling circle replication PCR.
Then DNBs were sequenced with read of 100bp on the BGISEQ-500 platform.

tag: cell line

value: immortalized juvenile costal chondrocyte cell line T/C 28a2

tag: genotype/variation

value: hetero K36M mutation at HIST1H3D


title: CP18

city: Torun

first: CHANDRA

middle: SHEKHAR

last: PAREEK

state: Kuj. Pom.

address: ul. Wilenska 4

department: Centre for Modern Interdisciplinary Technologies

country: Poland

institute: Nicolaus Copernicus University

description:
young bull
fpkm calculated using cufflinks

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to UMD cattle genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
fpkm calculated using cufflinks
Genome_build: UMD Bos Taurus plus y-chromosome
Supplementary_files_format_and_content: tab-delimited text files with option of excel file format, include RPKM values for each Sample ...

organism: Bos taurus

source_name: Pituitary gland tissue

extract_protocol:
Total RNA isolation from bovine pituitary gland tissues of three cattle breeds were harvested using Trizol reagent. Illumina TruSeq mRNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Polish-HF

tag: age

value: Pituitary gland tissue


title: CP17


title: primary tumor sample [51168]

description:
Gene expression data from cerebral tumor
51168

data_processing: From beta-values, CpG IDs were mapped to the promoter region of each gene ranging from 2kb upstream to 200bp downstream of the transcription start site using RefSeq mRNA annotation. DNA methylation beta‐values of the respective CpGs were averaged to get one mean methylation beta‐value for each gene promoter available. Genes located on Chr. X and Y were excluded from analyses. Resulted M-values were quantile‐normalized and transformed into log10‐scale.

source_name: Human Brain, cerebral tumor sample


title: H3.1K36M#2_1_RNA


title: Gi3_noDSN

value: SUG

value: TTAAGTCGTATGCTGTCCTCTGTGGAA


title: C.05.3092_NS3

value: CN-AML blasts

tag: batch

tag: nanostring cartridge


title: H3.1K36M#1_2_RNA


title: Rattus_norvegicus_D84_Liver_CCl4_treated_3

city: Kitakatsushika-gun

first: Kyosuke

last: Yamashita

state: Saitama

address: Sugito-machi Shimotakano1600

department: Tokyo

country: Japan

institute: Chemicals Evaluation and Research Institute Japan

description: Gene expression on day 84 after CCl4 treatment

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 uL containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 uL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Rat GE 8x60K Microarray Toxplus ver.2 for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60K array slides (Scan Area 61 x 21.6 mm, Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 045522_D_F_20130222) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Rattus norvegicus

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low RNA Input Quick Amplification Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: five-week-old male F344/NSlc rats were purchased from Japan SLC, Inc. (Hamamatsu, Japan) and acclimatized to a basal diet (CRF-1; Oriental Yeast Co., Ltd., Tokyo, Japan) and tap water ad libitum for one week. They were housed in plastic cages with paper chip bedding in a barrier-maintained animal room on a 12 h light-dark cycle and conditioned at 23 ± 2°C with a relative humidity of 55 ± 15%.

extract_protocol: Total RNA was purified with an miRNeasy Mini Kit (Qiagen) following the manufacturer's protocol.

treatment_protocol: Animals were fed a basal diet (untreated controls) or treated with DEN (4 mg/5 mL/kg body weight, dissolved in saline) or CCl4 (100 mg/5 mL/kg body weight, dissolved in corn oil) daily by gavage for 28  or 84 days.

value: F344 rat

value: Liver

tag: gender

value: male

tag: timepoint/treatment

value: day 84 after CCl4 treatment


title: C.05.2525_NS3


title: primary tumor sample [33156]

city: Leipzig

first: Edith

last: Willscher

address: Haertelstraße 16-18

institute: IZBI

description:
Gene expression data from cerebral tumor
33156

extract_protocol: DNA was extracted by ultracentrifugation from deep-frozen tissue samples. High quality of extracted DNA was assured by spectrophotometric analysis and agarose gel electrophoresis.

tag: diagnosis

tag: idh mutation (1 yes, 0 no)

tag: chr1_loss (1 yes, 0 no)


title: C.05.0518_NS3


title: CP16

tag: breed


title: primary tumor sample [33210]

description:
Gene expression data from cerebral tumor
33210

tag: chr19_loss (1 yes, 0 no)


title: primary tumor sample [57464]

description:
Gene expression data from cerebral tumor
57464


title: C.05.1670_NS3

tag: tissue


title: H3.1K36M#1_1_RNA


title: Rattus_norvegicus_D84_Liver_CCl4_treated_2

tag: strain


title: CP15


title: H3.3K36M#2_2_RNA

value: hetero K36M mutation at H3F3B


title: H3.3K36M#2_1_RNA


title: CP14


title: CP13


title: Rattus_norvegicus_D84_Liver_CCl4_treated_1


title: Rattus_norvegicus_D84_Liver_DEN_treated_3

description: Gene expression on day 84 after DEN treatment

value: day 84 after DEN treatment


title: Rattus_norvegicus_D84_Liver_DEN_treated_1


title: H3.3K36M#1_2_RNA


title: Rattus_norvegicus_D84_Liver_DEN_treated_2


title: CP12

value: Polish-Red


title: CP11


title: C.09.3990_NS1


title: CP10


title: H3.3K36M#1_1_RNA


title: Rattus_norvegicus_D84_Liver_Vehicle_3

description: Gene expression on day 84 after control treatment

value: day 84 after control treatment


title: HH25 scRNA-seq

tag: Stage

tag: dissection

value: Whole autopod

tag: protocol

tag: protocol notes

value: Two combined sequencing runs.


title: C.04.3132_NS3


title: WT_1_RNA

tag: cell line

value: immortalized juvenile costal chondrocyte cell line T/C 28a2

tag: genotype/variation

value: WT


title: WT_2_RNA


title: C.01.0617_NS1

tag: batch


title: C.09.1830_NS1

tag: nanostring cartridge


title: CP09

tag: age


title: C.04.1814_NS3


title: Rattus_norvegicus_D84_Liver_Vehicle_2

tag: gender

tag: timepoint/treatment


title: Rattus_norvegicus_D28_Liver_CCl4_treated_3

description: Gene expression on day 28 after CCl4 treatment

value: day 28 after CCl4 treatment


title: C.02.0572_NS3


title: C.04.3570_NS1


title: primary tumor sample [31996]

description:
Gene expression data from cerebral tumor
31996

tag: diagnosis

tag: idh mutation (1 yes, 0 no)


title: Sample_18

data_processing:
Sequence information was extracted in FastQ format using Illumina's CASAVA v1.8.2 (Sample_01, 05, 09-11, 15, 17) and bcl2fastq software v1.8.3 (Sample_02-04, 06-08, 12-14, 16)
The processing and annotation of small RNA-Seq raw data was performed using the R programming language (version 3.0.2) and the ShortRead Bioconductor package (Morgan et al., 2009). First, raw data were pre-processed with the following parameters: Quality filtering, eliminating all reads containing an “N”; Adapter trimming, by use of the function trimLRPatterns(), allowing up to 2 mismatches and using as adapter sequence "TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC".
Size filtering removed all the reads with length shorter 18 and longer 33 nucleotides.
Reads were aligned, resulting in a direct annotation and quantification. The alignment was divided in two steps, to allow the recognition and the annotation of the reads exceeding reference length. In fact, the algorithm of Bowtie 1.1.2 does not allow aligning longer reads to shorter references. Specifically, first we performed alignment against the reference (Danio rerio, miRBase v21) with up to 2 mismatches. In this step the reference used was the mature sequence of microRNAs. Each read was aligned using these criteria with Bowtie 1.0.0 (settings: “-q", "--threads 8 --best", "—norc”). The remaining reads, which could not align in the previous step, were used as reference for a second alignment step with Bowtie 1.1.2 (settings: -f", "-a", "--threads 8 --norc"). In this case, the annotated mature microRNAs were aligned against the reads.
The information obtained in the two alignment phases was conveyed in one single table, containing a list of all the retrieved sequences and their relative counts. Read counts were normalized to RPM (reads per million mappable reads).
Genome_build: Danio rerio, miRBase v21;
Supplementary_files_format_and_content: Excel file, containing samples metadata information, mapping statistics and RPMs of each sample

organism: Epiplatys dageti monroviae

tag: life style

value: non-anual

value: somite

tag: diapause

value: no


title: Rattus_norvegicus_D84_Liver_Vehicle_1

tag: tissue


title: CP08

tag: breed

value: Pituitary gland tissue


title: Rattus_norvegicus_D28_Liver_CCl4_treated_2

tag: strain

value: F344 rat


title: Rattus_norvegicus_D28_Liver_DEN_treated_3

description: Gene expression on day 28 after DEN treatment

value: Liver

value: day 28 after DEN treatment


title: CP07


title: C.00.2213_NS1

organism: Homo sapiens

value: CN-AML blasts


title: CP05

value: Hereford


title: CP04


title: C.05.3055_NS1


title: C.06.4460_NS1


title: Sample_10

organism: Nematolebias papilliferus

value: anual

tag: Stage

value: yes


title: CP03


title: Sample_09

organism: Callopanchax occidentalis


title: C.01.0171_NS1


title: C.05.2227_NS1


title: C.01.2154_NS1


title: C.00.2070_NS1


title: CP02


title: adjacent skin normal tissue circRNA 3

city: Jinan

first: Cong

last: Fu

state: Shandong

address: No. 324, jingwu Road, Huaiyin Dist

institute: Shandong provincial hospital

description:
circRNA
circRNA expression data from Homo sapiens skin

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software package. The circRNAs that at least 4 out of 8 samples have flags in P or M (“All Targets Value”) were retained for further differential analyses. Differentially expressed circRNAs with statistical significance between the two groups were identified through Volcano Plot filtering.

source_name: adjacent skin normal tissue

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Tissues from IH surgury were immersed overnight in RNAlater at 4 ℃ and preserved at -80 ℃.

value: adjacent normal skin tissue

value: male

value: 4 months


title: gmcsf_donor2

city: Cambridge

first: Brian

last: Hie

state: MA

address: 77 Massachusetts Ave

institute: MIT

data_processing:
Raw sequencing data was converted to demultiplexed FASTQ files using bcl2fastq2 based on Nextera N700 indices corresponding to individual samples/arrays.
Reads were then aligned to the hg19 genome using the Galaxy portal maintained by the Broad Institute for Drop-Seq alignment using standard settings.
Individual reads were tagged according to the 12-bp barcode sequence and the 8-bp UMI contained in Read 1 of each fragment. Following alignment, reads were binned onto 12-bp cell barcodes and collapsed by their 8-bp UMI.
Digital gene expression matrices for each sample were obtained from quality filtered and mapped reads, with an automatically determined threshold for cell count.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited cell-by-gene expression matrix with digital gene expression values corresponding to unique molecule counts

source_name: GM-CSF derived macrophages

growth_protocol: Human monocytes were isolated from human buffy coats purchased from the Massachusetts General Hospital blood bank using a standard Ficoll gradient and subsequent CD14+ cell positive selection (Stemcell Technologies).

extract_protocol:
SeqWell analysis was performed as described in Gierahn et al. (Nature Methods, 2017) Briefly, at the respective timepoint, cells were detached using trypsin, spun down, and counted. Approximately 12,000 cells were loaded on each array for each timepoint and condition to minimize doublet-loading. The arrays were sealed with a semi-permeable membrane prior to cell lysis and hybridization to single-cell beads. Beads were subsequently pooled for reverse transcription and whole transcriptome amplification.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Selected monocytes were cultured in ultra low-adherence flasks (Corning) for 6 days with RPMI media (Invitrogen) supplemented with 10% FBS (Invitrogen) and 50 ng/mL human GM-CSF (Biolegend).

tag: adapter

value: TCCTGAGC

tag: donor

tag: sequencing run


title: C.00.0305_NS1

data_processing: OSU CCC Genomics Shared Resource provided counts on probes after performing technical normalization using internal positive controls. Then we performed geometric mean normalization using all probes. These normalized counts were used for further analysis.


title: gmcsf_donor1

value: AGGCAGAA


title: CP01


title: adjacent skin normal tissue circRNA 4

value: female

value: 7 months


title: Rattus_norvegicus_D28_Liver_DEN_treated_2


title: infantile hemangioma (IH) tumor tissue circRNA 3

description:
circRNA
circRNA expression data from infantile hemangioma (IH) tumor tissue

source_name: infantile hemangioma (IH) tumor tissue

value: infantile hemangioma (IH) tumor tissue


title: infantile hemangioma (IH) tumor tissue circRNA 4


title: Rattus_norvegicus_D28_Liver_Vehicle_1

description: Gene expression on day 28 after control treatment

value: day 28 after control treatment


title: adjacent skin normal tissue circRNA 1

value: 5 months


title: Rattus_norvegicus_D28_Liver_Vehicle_2

value: F344 rat


title: Rattus_norvegicus_D28_Liver_Vehicle_3

value: Liver


title: Rattus_norvegicus_D28_Liver_DEN_treated_1

value: day 28 after DEN treatment


title: adjacent skin normal tissue circRNA 2


title: infantile hemangioma (IH) tumor tissue circRNA 1


title: infantile hemangioma (IH) tumor tissue circRNA 2