title: Experiment2_HOG1_KO_salt_1

city: Barcelona

first: Francesc

last: Posas

address: Baldiri Reixac 10

institute: IRB Barcelona

data_processing:
Sequencing reads were aligned to the S. cerevisiae genome (Ensembl, R64-1-1 v89) using HISAT2 (Kim et al. 2015) (v2.1.0) using the--rna-strandness parameter to account for strand-specific information, which differed between the libraries. The “R” and “F” labels were used to indicate single-end stranded and reversely stranded reads, respectively. For paired-end libraries, we used “RF” and “FR”. Reads were assigned to gene-level features (Ensembl, R64-1-1 v89 GTF) using featureCounts (Liao et al. 2014) (v1.5.1) in strand-specific mode (-s 1 for stranded and -s 2 for reversely stranded reads). Some of the samples generated in this study contain unique molecule identifiers (UMIs) that, for consistency, were not used for the analysis.
Genome_build: Ensembl, R64-1-1 v89
Supplementary_files_format_and_content: Raw read counts in tabular text format

molecule: polyA RNA

source_name: Yeast cells

growth_protocol: Biological triplicates BY4741 WT and hog1::KAN deletion strains were inoculated into 50 ml of YPD and allowed to grow overnight.  The next morning cells were subinoculated into fresh YPD media until exponential phase (OD660 = 0.6). Per each biological triplicate, a total of 15 ml of cells were harvested in the absence (control) or presence of osmotic stress (0.4M NaCl 15 mins), cells were pelleted and flash-frozen in liquid nitrogen.

extract_protocol:
Total RNA extraction was done with standard hot-phenol method. RNA integrity (RIN=8) was assessed by Bioanalyzer to ensure a RIN>8.
Experiment 1: A total of 1μg of RNA was used for library preparation using the TruSeq stranded mRNA v2 (Illuimna) following manufacturer instructions. Quality control of generated libraries was performed with bioanalyzer and library quantification was done using the KAP kit (KapaBiosystems) prior to sequencing on an Illumina HiSeq2500 with 50 bp single-end reads; Experiment 2: A total of 5 μg of total RNA were used to purify mRNA using the polyA RNA selection magnetic beads following the manufacturer’s instructions (Lexogen SKU: 039:100). Purified mRNA was used to generate strand-specific libraries using the total CORALL RNA kit (Lexogen SKU:  095.24). The number of library amplification cycles was determined by qPCR using a 1:10 dilution (PCR Add-on Lexogen, SKU: 020.96). Libraries were quantified by Qubit and Bioanalyzer. RNA-seq was performed on a pool containing all samples and triplicates and sequenced with 50 bp single-end read using an Illumina HiSeq2500.

treatment_protocol: 0.4 M NaCl for 15 min

tag: genotype

value: 0.4 M NaCl, 15 min


title: Pediatric acute lymphoblastic leukemia [16-106]

status: Public on Feb 14 2022

type: SRA

city: Montreal

first: Daniel

last: Sinnett

state: QC

address: 2900 Edouard Montpetit Blvd

country: Canada

institute: University of Montreal

description:
16-106
Strand-specific RNA-seq

library_source: transcriptomic

data_processing:
Raw reads were aligned to the GRCh37 genome reference using STAR v2.5.3a.
Expression counts were obtained using htseq-count v0.9.0 on the Ensembl Homo_sapiens.GRCh37.75.gtf.
Genome_build: GRCh37
Supplementary_files_format_and_content: *.counts.txt: Tab-delimited text files include raw expression counts.

molecule: total RNA

organism: Homo sapiens

source_name: Pediatric acute lymphoblastic leukemia

extract_protocol:
Mini AllPrep DNA/RNA kits from Qiagen.
Ribo-Zero Gold Kit according to Illumina's protocol.

tag: diagnosis

tag: tissue

value: peripheral blood

tag: gender

value: Female


title: Experiment2_HOG1_KO_salt_3

country: Spain

organism: Saccharomyces cerevisiae

tag: treatment


title: Experiment2_HOG1_KO_basal_3

value: untreated


title: D06_09_dist

city: Chicago

first: Cambrian

middle: Yangshao

last: Liu

state: IL

address: 5841 S Maryland Ave

department: Department of Medicine

country: USA

institute: The University of Chicago

data_processing:
Illumina Casava software was used for basecalling.
Abundance measurements (transcripts per million, tpm) were generated from pseudoalignment procedures in kallisto.
Genome_build: mm10
Supplementary_files_format_and_content: Comma-separated file includes tpm levels of individual transcripts for each sample.

organism: Mus musculus

source_name: rectal mucosa

growth_protocol: C57Bl/6 mice at 6 wks of age were purchased from Jackson Laboratory.

extract_protocol:
Colonic mucosal surfaces were cut and isolated from freshly dissected full-thickness colonic tissue, then placed into Trizol. RNA was precipitated with isopropanol and cleaned with multiple washes of 75% ethanol prior to resuspension in water.
Libraries were constructed using the Illumina Stranded mRNA library preparation kit to generate single-end reads 1x75bp on NextSeq High Output Runs.

treatment_protocol: Mice were exposed to 3% DSS for 6 d, beginning of experimental day (exp d) 0. On the indicated experimental days, 3-4 mice were euthanized from the larger cohort and their colons dissected for analysis.

tag: injury

value: DSS

value: dist


title: Experiment2_HOG1_KO_salt_2


title: Experiment2_WT_salt_2

value: WT


title: Experiment2_WT_basal_2


title: Pediatric acute lymphoblastic leukemia [16-105]

description:
16-105
Strand-specific RNA-seq

value: bone marrow


title: Experiment1_WT_salt_3


title: Bleomycin3G9_epithelial_226R

city: San Francisco

first: Vincent

last: Auyeung

state: CA

department: Medicine

institute: University of California, San Francisco

description: Tagged ribosome immunoprecipitated RNA

data_processing:
Alignment: STAR_2.5.2b
Genome_build: Ensembl Mouse GRCm38
Supplementary_files_format_and_content: Comma-separated file with read counts (rows) and samples (columns)

source_name: Lung epithelial Ribotag immunoprecipitation

extract_protocol:
Anti-HA immunoprecipitation followed by Rneasy Micro kit (Qiagen)
Lexogen Quantseq Forward kit

tag: mouse identifier

tag: mouse sex

value: F

tag: tissue compartment

value: Epithelium

tag: exposure

value: Bleomycin

tag: treatment type

tag: batch


title: Experiment1_WT_salt_2


title: Experiment2_HOG1_KO_basal_2


title: Pediatric acute lymphoblastic leukemia [16-114]

description:
16-114
Strand-specific RNA-seq

value: 9837/3 - Pre-T ALL (ETP)

value: Male


title: Pediatric acute lymphoblastic leukemia [16-099]

description:
16-099
Strand-specific RNA-seq


title: F_tar_leaf_1

city: Shanghai

first: Moyang

address: dongchuan road 800

department: School of Agriculture and Biology

country: China

institute: Shanghai Jiao Tong University

description:
Fagopyrum tataricum Gaertn.
F_tar_leaf_1

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house SOAPnuke. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2 and paired-end clean reads were aligned to the reference genome using CPC v0.9-r2.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, considering the effect of sequencing depth and gene length for the reads count at the same time.
Genome_build: http://www.mbkbase.org/Pinku1/
Genome_build: a FASTA file with all transcript sequences is available on the series record.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Fagopyrum tataricum

source_name: leaf

growth_protocol: Tartary buckwheat (XiQiao 2) were collected in 2016 at the experimental field of College of Life Science, Sichuan Agricultural University (Lat. 29°97’ N, 102°97’ E, Alt. 580 m), China. It had been introduced to the field and grown in the same ecoenvironmental and cultivation conditions for five years. We observed the development process. Samples were hand-collected at flowering stage.

extract_protocol:
Samples were sampled, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit  was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For the transcriptome sampling, samples were collected from the same individual, and samples with the same flowering stage from three plants comprised of three replicates. the collected samples were flash frozen in liquid nitrogen and stored at −80°c until further use.

tag: cultivar

value: XiQiao 2

tag: developmental stage

value: Flowering stage

value: leaf


title: Experiment2_HOG1_KO_basal_1


title: Pediatric acute lymphoblastic leukemia [16-104]

description:
16-104
Strand-specific RNA-seq


title: Experiment1_WT_salt_1


title: Experiment2_WT_salt_3


title: Experiment1_WT_basal_3


title: D03_07_anal

source_name: anus

value: anal


title: Experiment1_WT_basal_2


title: D06_08_dist


title: Pediatric acute lymphoblastic leukemia [16-102]

description:
16-102
Strand-specific RNA-seq


title: Pediatric acute lymphoblastic leukemia [16-100]

description:
16-100
Strand-specific RNA-seq


title: D03_07_prox

source_name: mucosa of mid-colon

value: prox


title: Experiment2_WT_basal_1


title: Experiment2_WT_salt_1

value: 0.4 M NaCl, 15 min


title: D03_06_prox


title: Experiment2_WT_basal_3


title: D06_08_anal


title: D03_07_dist


title: D03_06_dist


title: Experiment1_WT_basal_1


title: Pediatric acute lymphoblastic leukemia [16-094]

description:
16-094
Strand-specific RNA-seq

value: Female


title: Pediatric acute lymphoblastic leukemia [16-092]

description:
16-092
Strand-specific RNA-seq


title: D03_06_anal


title: Pediatric acute lymphoblastic leukemia [16-098]

description:
16-098
Strand-specific RNA-seq


title: Pediatric acute lymphoblastic leukemia [16-086]

description:
16-086
Strand-specific RNA-seq


title: Pediatric acute lymphoblastic leukemia [16-095]

description:
16-095
Strand-specific RNA-seq


title: D03_05_prox


title: Pediatric acute lymphoblastic leukemia [16-077]

description:
16-077
Strand-specific RNA-seq


title: Pediatric acute lymphoblastic leukemia [16-076]

description:
16-076
Strand-specific RNA-seq


title: D03_05_anal


title: Pediatric acute lymphoblastic leukemia [16-074]

description:
16-074
Strand-specific RNA-seq


title: D00_04_prox


title: Rapa 1

type: RNA

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

description: Gene expression data from Tsc2-/- ELT3 cells treated with 20 nM rapamycin in DMSO.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Rat Gene 2.0 ST for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez-Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray ragene20strnentrezgcdf R package (version 17.0.0).

label: biotin

organism: Rattus norvegicus

source_name: Tsc2-/- ELT3V cells

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

growth_protocol: Tsc2-deficient Eker rat uterine leiomyoma (ELT3V) cells were cultured using Dulbecco’s Modified Eagle’s medium (DMEM) containing 10% fetal bovine serum and incubated at 37°C in a humidified 5% CO2 atmosphere.

extract_protocol: RNA was extracted using Qiagen RNeasy Mini Kit (Catalog# 74004) following manufacturer's protocol.

treatment_protocol: ELT3V cells were serum starved for 16 hours and treated with DMSO, Syk-inhibitor (1µM) or rapamycin (20nM) for 24 hours.

value: 20 nM rapamycin in DMSO


title: 9_Input

city: Columbus

first: Amy

last: Hite

state: OH - Ohio

address: 1800 Cannon Drive 250 Lincoln Tower

department: Biomedical Informatics

institute: The Ohio State University

description: Input

library_source: genomic

data_processing:
Sequence reads were aligned to the reference genome Rn5, peak locations were identified using MACS2 algorithm and annotated based on UCSC RefSeq. Differential peak locations were called using SICER51. In-house shell and R scripts (https://www.r-project.org) were used for data integration. To summarize and cluster genomewide TSS coverage as heat maps, deepTools (PMID: 24799436) compute matrix and plotheatmap functions were utilized.
Genome_build: rn5 (Rnor_5.0)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include peaks for each Sample.
Supplementary_files_format_and_content: 0079Wis_SICER_intervals.xlsx: Excel file includes annotated SICER peaks.

molecule: genomic DNA

source_name: rat carotid

extract_protocol:
Tissue collection was performed at 7 days after balloon angioplasty. From the same animal, we collected the endothelial-damaged central segment of the balloon-injured common carotid artery (denoted as “injured” throughout this study) and the contralateral common carotid artery without angioplasty (sham control, denoted as “uninjured”). To preserve the artery “real-time” epigenetic information, the collected tissue samples were immediately snap-frozen in liquid N2. Artery tissues (injured or uninjured) from 50 rats were pooled for ChIPseq analysis at Active Motif per company standard procedures, and the sequencing raw data satisfactorily met quality control.
Chromatin was isolated after adding lysis buffer, followed by disruption with a Dounce homogenizer. Genomic DNA was sheared to an average length of 300–500 bp by sonicating the lysates, and the segments of interest were immunoprecipitated using an antibody (4 μg) against BRD4, H3K27ac, H3K27me3, or H3K4me1. The protein/DNA complexes eluted from beads were treated with RNase and proteinase K, crosslink was reversed, and the ChIP DNA was then purified for use in the preparation of Illumina sequencing libraries. Standard steps included end-polishing, dA-addition, adaptor ligation, and PCR amplification.

value: Carotid artery

tag: chip antibody


title: Rapa 3


title: Syk 2

description: Gene expression data from Tsc2-/- ELT3 cells treated with 1 uM R406 in DMSO.

value: 1 uM R406 in DMSO


title: Rapa 2


title: Syk 4


title: Syk 3


title: Pediatric acute lymphoblastic leukemia [16-070]

description:
16-070
Strand-specific RNA-seq


title: 8_Uninjured_H3K4me1

value: Uninjured


title: Rapa 4


title: Pediatric acute lymphoblastic leukemia [16-082]

description:
16-082
Strand-specific RNA-seq

value: bone marrow


title: D00_04_anal


title: D00_04_dist

value: dist


title: Syk 1


title: 7_Injured_H3K4me1

value: Injured


title: DMSO 4

description: Gene expression data from Tsc2-/- ELT3 cells treated with DMSO vehicle control.

value: DMSO vehicle control


title: 5_Injured_H3K27me3


title: D03_05_dist

value: DSS


title: DMSO 2


title: DMSO 1


title: Pediatric acute lymphoblastic leukemia [16-065]

description:
16-065
Strand-specific RNA-seq

value: Male


title: D00_03_prox


title: 4_Uninjured_H3K27Ac


title: 3_Injured_H3K27Ac


title: Pediatric acute lymphoblastic leukemia [16-059]

description:
16-059
Strand-specific RNA-seq


title: 6_Uninjured_H3K27me3


title: D00_03_dist


title: Pediatric acute lymphoblastic leukemia [16-057]

description:
16-057
Strand-specific RNA-seq


title: 1_Injured_BRD4


title: D00_03_anal


title: Pediatric acute lymphoblastic leukemia [16-056]

description:
16-056
Strand-specific RNA-seq


title: Retina_WT_sample4

city: Louisville

first: Jae Yeon

last: Hwang

state: Kentucky

address: 505 S. Hancock Street

department: Division of Medical Oncology & Hematology

institute: University of Louisville

data_processing:
RNA-Seq reads were trimmed to remove adapter at the end of reads
Trimmed reads were aligned to the rn6 genome assembly using STAR version 2.5.2b with the following configurations --runThreadN 16 --outSAMtype BAM SortedByCoordinate --outWigType wiggle read1_5p --outFilterMismatchNmax 2 --alignEndsType EndToEnd
Genome_build: rn6
Supplementary_files_format_and_content: wig files were generated using STAR aligner; Scores represent read counts RPM

source_name: retinal tissue

growth_protocol: Retinas were isolated and flash frozen in liquid nitrogen

extract_protocol:
Lysis of the retinas was performed using a lysis buffer with (sample 4) and without detergent (sample 3) in order to capture the membrane- associated and membrane-free ribosomes. Supernatants were collected and digested with RNaseI for 45 min at room temperature with rotation. Digestion was stopped using Superase-In. The digested lysate was loaded on MicroSpin S-400 HR column and eluted by centrifugation. RNA was extracted from the flow-through using Trizol LS (Life Technologies)
Libraries were prepared using the TruSeq Ribo Profile (Mammalian) Kit (Illumina, Cat# RPHMR12126), following manufacturer’s instructions.

value: retinal tissue

value: untreated

tag: age

value: 5 months old

value: WT


title: D00_02_dist


title: Retina_WT_sample3


title: Pediatric acute lymphoblastic leukemia [16-053]

description:
16-053
Strand-specific RNA-seq


title: D00_02_anal

value: anal


title: KO_polysome_rep1

city: Hong Kong

first: Yuwei

last: ZHANG

state: Hong Kong

address: Rm503, Li Ka Shing Medical Sciences Building, Prince of Wales Hospital, Shatin, NT, HK

department: Chemical Pathology

country: Hong Kong

institute: The Chinese University of Hong Kong

data_processing:
Library strategy: Ribo-seq
Adaptor sequence trimming, quality filtering (i.e. quality<38 and length<22) and duplication removal were first conducted.
Remaining reads were aligned to the mouse genome mm9 using HISAT2 software with the following parameters: --no-coverage-search; --mate-std-dev 60.
Cufflinks was then used to derive the fragments per kilobase per million (FPKM) values.
TE values were then calculated as the ratio between the abundance of polysome-associated RNAs (FPKM-polysome) and total cytoplasmic mRNAs (FPKM-total) in Ctrl and Lockd-KO conditions.
The fold change of TE upon Lockd deletion was further calculated as the average TE values in KO divided by average TEs in Ctrl cells.
Genome_build: mm9
Supplementary_files_format_and_content: *.fpkm_tracking: Tab-delimited files from Cufflinks containing FPKM values.

source_name: myoblast

growth_protocol: C2C12 myoblasts were grown in growth medium containing DMEM, 10% FBS and 1% pen/strep.

extract_protocol:
Total cytoplasmic RNA or RNA bound by more than 4 ribosomes were extracted using TRIzol LS reagent (Invitogen) following the manufacturer's instructions and then subjected to poly(A) selection by using mRNA purification beads (Ambion, 61006).
RNA libraries were prepared with 500 ng RNA according to the manufacturer's protocol (Illumina). The libraries were sequenced in 2 × 100 nt manner on HiSeq 2000 platform (Illumina).

treatment_protocol: C2C12 myoblasts were treated by 100 μg/ml of cycloheximide in culture medium and incubated at 37℃ for 10 min.

tag: cell type

value: myoblast

value: Lockd-KO

tag: molecule subtype

value: Polysome-associated RNA


title: KO_totalRNA_rep1

data_processing:
Adaptor sequence trimming, quality filtering (i.e. quality<38 and length<22) and duplication removal were first conducted.
Remaining reads were aligned to the mouse genome mm9 using HISAT2 software with the following parameters: --no-coverage-search; --mate-std-dev 60.
Cufflinks was then used to derive the fragments per kilobase per million (FPKM) values.
TE values were then calculated as the ratio between the abundance of polysome-associated RNAs (FPKM-polysome) and total cytoplasmic mRNAs (FPKM-total) in Ctrl and Lockd-KO conditions.
The fold change of TE upon Lockd deletion was further calculated as the average TE values in KO divided by average TEs in Ctrl cells.
Genome_build: mm9
Supplementary_files_format_and_content: *.fpkm_tracking: Tab-delimited files from Cufflinks containing FPKM values.

tag: genotype

value: Total RNA


title: Pediatric acute lymphoblastic leukemia [16-050]

description:
16-050
Strand-specific RNA-seq

tag: diagnosis

tag: tissue


title: WT_polysome_rep2


title: WT_polysome_rep1


title: D00_01_dist


title: 2_Uninjured_BRD4

value: Carotid artery


title: Tb-OB_3

city: Bethesda

first: Hong-wei

last: Sun

state: MD

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

data_processing:
[alignment, RNA-seq]  Raw sequencing data were processed with CASAVA 1.8.2 to generate FastQ files. Reads of 100 bases were mapped to mm10 using TopHat version 2.1.0.
[RPKM, RNA-seq]  Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek 6.6
Genome_build: mm10
Supplementary_files_format_and_content: Excel file reports RPKMs for TFs or all_plus_TFs

source_name: OB isolated from Tibia bone tissue

extract_protocol:
Mandible and tibia bones from P9 Col1a1*2,3-GFP mice were dissected. Three independent dissections, each pooling bone tissues from approximately fifty P9 mice, were carried out. Immediately after dissection and collagenase I digestion, GFP-positive cells were FACS-sorted. RNA was extracted using single cell RNA purification kit (Norgen). RNA quantification and integrity were performed with Bioanalyzer RNA (Agilent). Based on RNA quantification and RIN number, 3 experiments with RNA quantity ranging from 2 to 8ng were selected for RNAseq analysis.
RNAseq was performed by Oxford Gene Technology (OGT). Generation of cDNA was performed using SMART-Seq v4 Ultra Low Input RNA Kit (Takara) and processed with Illumina TruSeq RNA Sample Preparation kit (Illumina).
RNA seq data were generated on Illumina HiSeq 2000 sequencing instrument according to the manufacturer's instructions

value: Tibia bone tissue

value: osteoblasts

value: transgenic Col1a1*2,3-GFP

tag: description for exp id


title: Tb-OB_2


title: D00_02_prox

tag: injury

value: prox


title: Pediatric acute lymphoblastic leukemia [16-049]

description:
16-049
Strand-specific RNA-seq

value: bone marrow

tag: gender


title: Tb-OB_1


title: KO_polysome_rep2


title: D00_01_anal


title: Md-OB_3

source_name: OB isolated from Mandible bone tissue

value: Mandible bone tissue


title: WT_totalRNA_rep1


title: Md-OB_2


title: DMSO 3

tag: treatment

value: DMSO vehicle control


title: Pediatric acute lymphoblastic leukemia [16-052]

description:
16-052
Strand-specific RNA-seq

value: Male


title: Md-OB_1


title: D00_01_prox


title: F4749_E2S4

city: Brisbane

first: Brad

last: Balderson

state: QLD

address: Chemistry Bld, 68 Cooper Rd

department: The School of Chemistry and Molecular Bioscience

country: Australia

institute: The University of Queensland

description: ScRNA-seq run from E16.5 Control mouse hypothalamus

data_processing:
Base calling was performed using the Illumina BaseSpace application FASTQ Generation v1.0.0
Bam files and count matrices per sample were generated using the Illumina BaseSpace application SureCell RNA Single-Cell v1.2.0, using STAR (v2.5.2b) to align the cDNA reads to the mm10 genome (the second read mate, R2) and Samtools (v1.3) to append cell barcodes to aligned reads (derived from the first read mate, R1). Cell barcodes and UMIs in R1 are corrected and counted via the aforementioned Illumina Application.
Counts per cell in each sample were downloaded from Illumina Base Space and concatenated into a single count matrix to generate counts.txt.gz.
Genes with smaller than 10 counts across all cells and cells with counts/gene ratio smaller than 1.2, total UMIs <600, and detected genes <300 were filtered for QC.
To quantify intronic, exonic, and ambiguous reads for RNA velocity estimates, we modified the bam files generated above so the read tags were compatible with velocyto v0.17.17 using simplesam v0.1.3. In particular, XU tags were re-labelled as UB tags, XB tags were re-labelled as CB tags.
Intronic, exonic, and ambiguous read counts were then quantified using velocity v0.17.17 on the mm10 mouse genome by running 'velocyto run'.
Genome_build: mm10
Supplementary_files_format_and_content: counts_illumina.txt.gz, unspliced_counts_velocyto.txt.gz, spliced_counts_velocyto.txt.gz, ambiguous_counts_velocyto.txt.gz, sample_meta_data.txt

source_name: E16.5 Control mouse hypothalamus

growth_protocol: Mice were reared at normal 12:12h day:night cycle, on water and chow.

extract_protocol:
The hypothalamus of control and Eed-cKO embryos was dissected out in ice-cold RPMI-1640 medium (cat.no. 11530586, Thermo Fisher Scientific, Waltham, MA, USA). The dissected hypothalamis were further divided into 2-4 pieces before cell dissociation for single cell isolation using Papain Dissociation System (cat no. LK003150, Worthington Biochemical Corporation, Lakewood, NJ, USA). The tissues were incubated with papain solution at +37°C for 60 min. Isolated single cells were re-suspended in ice-cold 1xPBS, 0.1% BSA, to a final concentration of 2,500 cells/μl (+/- 10%). Cells were checked for viability using a Bio-Rad TC10 automated cell counter (Bio-Rad, Hercules, CA, USA).
Single cells and barcode beads were encapsulated into droplets using Bio-Rad ddSEQ Single-Cell Isolator for cell lysis and barcoding (cat.no. 12004336, Bio-Rad, Hercules, CA, USA). Subsequently, RNA-seq libraries were generated using Illumina SureCell WTA 3' Library Prep Kit for the ddSEQ System (6 cartridge version, cat.no. 20014280, Illumina, San Diego, CA, USA). Libraries were assessed for quality, using 1µl of undiluted cDNA, on an Agilent Technology 2100 Bioanalyzer using an Agilent High Sensitivity DNA chip (cat.no. 5067-4626, Agilent, Santa Clara, CA, USA) to determine fragment size and yield. Samples were stored at -20℃ until sequencing.
Libraries were pooled according to their molar concentration (yield), fragment size, and the unique Nextera i7 indices (8bp). Each sequencing run consisted of four samples with different Nextera i7 indices. The libraries were sequenced on an Illumina NextSeq 500, using NextSeq 500/550 High Output Kit v2.5 (150 Cycles, cat.no. 20024907, Illumina, San Diego, CA, USA), paired-end read type and Single-Index.

treatment_protocol: Control (Eed fl/fl) and Eed-cKO (Eed fl/fl; Sox1-Cre)

tag: Sex

value: M

tag: genotype/variation

value: Control (Eed fl/fl)

tag: timepoint


title: Pediatric acute lymphoblastic leukemia [16-039]

description:
16-039
Strand-specific RNA-seq

value: Female


title: WT_totalRNA_rep2

value: WT


title: Pediatric acute lymphoblastic leukemia [16-047]

description:
16-047
Strand-specific RNA-seq


title: Pediatric acute lymphoblastic leukemia [16-038]

description:
16-038
Strand-specific RNA-seq


title: F4748_E2S4

description: ScRNA-seq run from E15.5 Control mouse hypothalamus

source_name: E15.5 Control mouse hypothalamus


title: Pediatric acute lymphoblastic leukemia [16-037]

description:
16-037
Strand-specific RNA-seq


title: MK 1h rep3

city: Little Rock

first: Jia

state: AR

department: Microbiology and Immunology

institute: University of Arkansas for Medical Sciences

data_processing:
bcl2fastq v2.18.0.12 was used for demultiplexing, where TruSeq adapters were trimmed
The myxoma reference genome was concatenated to the Ensembl GRCh37 H. Sapien reference genome as the 23rd chromosome
Alignment was performed using STAR v2.7.6a and a "two-pass" method against the new dual genome reference
StringTie v2.1.4 was used to perform transcriptome reconstruction and quantification
Genome_build: GRCh37 / NC_001132.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Ensembl transcript ID for each sample as output from StringTie, suitable to import using tximport

organism:
Homo sapiens
Myxoma virus

source_name: THP1 cells from ATCC cat# TIB-202

growth_protocol: THP-1 cells are cultured in RPMI1640 supplemented with 10% FBS, antibiotics, L-glutamine, and 2-ME at 1^10(-5) uM.

extract_protocol:
THP-1 cells (106 cells per 3.5 cm dish) were differentiated in phorbol myristic acid (PMA) (Millipore-Sigma, )at 50 ng/mL for 48 hours before mock treated, transfection with ISD at 2 mg per dish using ViaFect (Promega, Madison, WI) at 3 mL per 1 mg of ISD based on manufacturer recommendations, or infected at an moi of 5 for either WT (vMyxGFP) or M062R-null MYXV.  At 8- hour post-transfection of ISD and at 1- and 8- hour post-viral infection cells were harvested, spun down in cell pellets, and then stored in -80°C until RNA extraction. RNA was extracted using the Quick DNA/RNA Mini-Prep Plus kit (catalog # D7003; Zymo, Irvine, CA, USA) with on-column DNase digestion. Purified RNA was assessed for mass concentration using the Qubit RNA BR Assay kit (catalog # Q10211; Invitrogen, Waltham, MA, USA) and for integrity using the Standard Sensitivity RNA Analysis kit on a Fragment Analyzer capillary electrophoresis system (catalog # DNF-471-0500; Agilent, Santa Clara, CA, USA).
A total of 250ng total RNA was used for each sample as input to the TruSeq Stranded Total RNA library prep kit with unique-dual indexing (catalog #s 20020598 & 2002371; Illumina, San Diego, CA, USA). Libraries were assessed for mass using the Qubit 1X dsDNA HS Assay kit (catalog # Q33231; Invitrogen, Waltham, MA, USA), for fragment size using the High Sensitivity NGS Fragment Analysis kit on a Fragment Analyzer capillary electrophoresis system (catalog # DNF-474-0500; Agilent, Santa Clara, CA, USA), and functional validation using the Universal Library Quantification kit (catalog # 07960140001; KAPA, Wilmington, MA, USA). Validated libraries were adjusted to 3nM before pooling, denaturing, and clustering. Paired-end (2X75) sequencing was performed to an average of 40 million reads per sample on a HiSeq 3000 (Illumina, San Diego, CA, USA).

treatment_protocol: Viral infection is conducted at a moi of 5-10 for one hour by on-ice incubation followed by PBS wash to rid of unbound virus before cells are cultured in normal growth medium. ISD transfection is performed using ViaFect transfection reagent following manufacturer's instruction. After 8 hours of treatment, cells are harvested for downstream applications.

tag: host cell line

value: mock

tag: hour


title: F4748_E2S3


title: MK 1h rep2


title: MK 1h rep1


title: 62KO 8h rep3


title: F4638_E2S5

value: F


title: F4748_E2S2


title: Pediatric acute lymphoblastic leukemia [16-033]

description:
16-033
Strand-specific RNA-seq


title: Pediatric acute lymphoblastic leukemia [16-035]

description:
16-035
Strand-specific RNA-seq


title: F4638_E2S2


title: Pediatric acute lymphoblastic leukemia [16-021]

description:
16-021
Strand-specific RNA-seq


title: F4842_E3S4

description: ScRNA-seq run from E13.5 Control mouse hypothalamus

source_name: E13.5 Control mouse hypothalamus


title: 62KO 8h rep2


title: 62KO 8h rep1


title: F4842_E2S2


title: F4842_E3S3


title: Pediatric acute lymphoblastic leukemia [16-015]

description:
16-015
Strand-specific RNA-seq


title: WT MYXV 8h rep2

value: wild type


title: WT MYXV 8h rep3


title: WT MYXV 8h rep1


title: F4840_E3S8

description: ScRNA-seq run from E12.5 Control mouse hypothalamus

source_name: E12.5 Control mouse hypothalamus


title: ISD 8h rep3

value: positive control for dsDNA induced gene expression


title: F4840_E3S7


title: F4842_E2S1


title: Pediatric acute lymphoblastic leukemia [16-002]

description:
16-002
Strand-specific RNA-seq

source_name: Pediatric acute lymphoblastic leukemia


title: F4840_E3S5


title: F4840_E3S3


title: F4840_E3S6


title: ISD 8h rep2


title: Pediatric acute lymphoblastic leukemia [16-001]

description:
16-001
Strand-specific RNA-seq


title: F4840_E3S4


title: F4840_E3S2


title: ISD 8h rep1


title: F4813_E2S4


title: F4813_E2S3


title: Pediatric acute lymphoblastic leukemia [16-017]

description:
16-017
Strand-specific RNA-seq


title: F4813_E1S2


title: BasL_169

city: Copenhagen Ø

first: Maria

last: Rossing

address: Blegdamsvej 9

department: Center for Genomic Medicine

country: Denmark

institute: Rigshospitalet

description: Gene expression data from human breast cancer

hyb_protocol: Following fragmentation, approx. 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. The arrays were washed and stained with phycoerytrin-conjugated streptavidin using the Affymetrix Fluidics Station 450.

scan_protocol: The Affymetrix GeneArray 3000 7G scanner was used to generate fluorescent images. Probe intensity files (.CEL files) were generated in the GeneChip Command Console Software (AGCC; Affymetrix, Santa Clara, CA, USA). These were anonymized using R v. 4.0.0 and modified functions from the affxparser package.

data_processing: CEL files were loaded into R 3.6.1 using justRMA from affy. For processing, the BrainArray Entrez Gene Custom CDF v. 24 was used, and otherwise default parameter settings were used. Entrez Gene IDs were subsequently translated to HGNC symbols using the BrainArray annotation from hgu133plus2hsentrezg.db. After filtering out data with missing HGNC annotation and control probes, expression data for 20,418 genes remained.

source_name: Breast cancer tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol for 12 ug total RNA.

extract_protocol: RNA was isolated using the AllPrep DNA/RNA purification kit (Qiagen, Hilden, Germany). The integrity of the RNA was measured using the Agilent RNA 6000 Nano Kit on an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA, USA).

treatment_protocol: Fresh tumor specimens, extracted during surgery, were inspected by pathologists, and tumor biopsies of around 100 mg were stored in RNALater (Thermo Fisher Scientific, Waltham, MA, USA).

value: Breast cancer

tag: citbcmst subtype

value: BasL

tag: sn status

value: Negative

tag: ihc er status


title: BasL_170

value: Positive


title: BasL_165


title: BasL_166


title: US22502553_252206068716_S01_CGH_1105_Oct12_1_1

type: genomic

city: Madrid

first: Gema

last: Moreno-Bueno

address: Arzobispo Morcillo 4

department: Biochemistry

institute: Instituto de Investigaciones Biomédicas "Alberto Sols" CSIC-UAM

hyb_protocol: Hybridization chamber type: SureHyb hybridization chamber (Agilent). Volume: 45 µL. Temperature (˚C): 67. Duration: 40 hours.

scan_protocol: Scanned on a G2565CA DNA microarray scanner (Agilent).

data_processing:
Microarray data were extracted and visualized using Feature Extraction software v10.7 and Agilent Genomic Workbench (AGW) software v7.0 (Agilent Technologies)
Copy number altered regions were detected using the Aberration Detection Method 2 (ADM-2) algorithm set as 6, with a minimum number of three consecutive probes
Please note that the *_p.txt files contain processed data.

source_name: human endometrial carcinoma tumors

label_protocol: Genomic DNA samples were processed with the SureTag DNA Labeling kit (Agilent Tech ref 5190-3399) according to the manufacturer instructions. Briefly, differential labeling of the genomic DNA samples was performed by the incorporation of  fluorescent-labeled nucleotides Cyanine 3-dUTP and cyanine 5-dUTP by the exo- Klenow fragment of DNA pol I during a random primer extension reaction. Labeled samples were purified by ultrafiltration on centrifugal filters.

extract_protocol: Total DNA was extracted with DNAeasy Blood & Tissue kit (Qiagen) following manufacturer's protocol

tag: tissue type

value: Tumour

source_name: DNA human reference (Agilent)

tag: sample type

value: wild type; refernce DNA


title: BasL_168


title: BasL_167


title: F4810_E3S4


title: F4810_E1S2


title: US22502553_252206068716_S01_CGH_1105_Oct12_1_3


title: US22502553_252206068717_S01_CGH_1105_Oct12_1_2

source_name: human endometrial carcinoma metastasis

value: Metastasis


title: US22502553_252206068716_S01_CGH_1105_Oct12_1_2


title: F4810_E1S1


title: BasL_164


title: BasL_163


title: US22502553_252206068703_S01_CGH_1105_Oct12_1_4


title: BasL_162


title: F4700_E2S7


title: US22502553_252206068702_S01_CGH_1105_Oct12_1_4


title: US22502553_252206068717_S01_CGH_1105_Oct12_1_1


title: US22502553_252206068703_S01_CGH_1105_Oct12_1_3


title: US22502553_252206068716_S01_CGH_1105_Oct12_1_4


title: US22502553_252206068703_S01_CGH_1105_Oct12_1_2


title: F4700_E2S4


title: F4700_E2S3


title: ctrl2_O

city: Baltimore

first: Matthew

middle: D

last: Smith

address: 600 N Wolfe Street

department: Neurology

institute: Johns Hopkins University

data_processing:
Estimated transcript level counts were calculated using Salmon (v1.4.0) with whole genome used as decoy sequence for selective alignment and gcBias flag enabled
Transcript level counts were improted into R with tximeta (v1.12.3) then aggregated to gene level counts, exported abundances (tpm) to csv and included as abundances.csv
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: quant files (.sf.txt, tab delimited) created by salmon showing estimated counts and abundances for each individual sample
Supplementary_files_format_and_content: csv files with gene level abundances (TPM) across all samples aggregated by tximeta

source_name: hESC Reporter OPC

extract_protocol:
Cells were lysed in RLT+ buffer then RNA was extracted with RNEasy Micro Plus Kit from Qiagen which includes gDNA removal column
Libraries prepared using Illumina Stranded Total RNA Prep with Ribo-Zero Plus Kit from Illumina

tag: cell type

value: hESC Reporter OPC

tag: group

value: media

tag: tnf+il1a stimulated

value: unstimulated

tag: batch

value: not applicable

tag: age


title: ctrl2_A

value: stimulated


title: BasL_160

tag: tissue


title: hc51292_A

value: control

value: Male


title: F4700_E1S6

value: F

value: Control (Eed fl/fl)


title: hc51292_O


title: F4700_E1S2


title: US22502553_252206068702_S01_CGH_1105_Oct12_1_3


title: US22502553_252206068703_S01_CGH_1105_Oct12_1_1


title: BasL_159


title: BasL_157


title: US22502553_252206068702_S01_CGH_1105_Oct12_1_2


title: hc51284_A

value: Female


title: US22502553_252206068701_S01_CGH_1105_Oct12_1_3


title: US22502553_252206068701_S01_CGH_1105_Oct12_1_2


title: hc51284_O


title: US22502553_252206068701_S01_CGH_1105_Oct12_1_4


title: F4700_E1S1


title: K562_P5k27_sc2for1_rep3_(20211206_DJ_Hs_K562_2for1)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: Single-cell K562 cell CnT2for1 replicate 3

data_processing:
Genome_build: UCSC hg19
1. We used Bowtie2 2.4.2 with options "--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the paired-end 25bp reads for each cell to hg19 Homo sapiens genomic sequence obtained from UCSC. 2. We extracted properly paired reads from the alignments to generate a bed files of aligned fragments for each cell and aggregated them into a single file.  3. We used bedtools genomecov to make a normalized count bedgraph file from the aggregate bed file. Normalized counts are the fraction of counts at each base pair scaled by the size of the reference sequence (3095693983) so that if the scaled counts were uniformly distributed there would be 1 at each position (Supplementary file normalized_counts.bedgraph.gz).

extract_protocol:
Single-cell CUT&Tag2for1 was performed using lightly fixed K562 and H1 nuclei. Frozen nuclei were thawed and aliquots containing 20,000 nuclei were centrifuged at 700 x g for 4 minutes at 4˚C. Nuclei were washed once with Wash buffer, centrifuged again, and then resuspended in Antibody buffer (10 mM HEPES pH 150 mM NaCl, 2 mM spermidine, 2 mM EDTA, 0.1% BSA, and Roche complete EDTA-free protease inhibitor) with primary anti-Pol2S5p antibody (Cell Signaling Technology cat. no. 13523, 1:50) and anti-H3K27me3 (Cell Signaling Technology cat. no. 9733, 1:100) in 0.6 mL PCR tubes. Primary antibody binding was performed overnight at 4oC. Samples were centrifuged at 700 x g for 4 minutes at 4˚C between incubation steps. and incubated for 1 hour at room temperature for the guinea pig anti-rabbit secondary antibody (Antibodies Online cat. no. ABIN101961 1:100) and for 1 hour at room temperature for pAG-Tn5 (Epicypher cat. no. 15-1117, 1:20) tethering. Samples were then centrifuged, washed with 300-wash buffer, pelleted by centrifugation, and then resuspended in 5 mM MgCl2, 10% hexanediol, 10 mM TAPS pH 8.5 for 20 min at 37˚C for tagmentaion. Reactions were stopped by adding EDTA to a final concentration of 1 mM, and kept at 4 ˚C until dispensation on the ICELL8 platform. Cells were processed on the ICELL8 instrument according to a previously optimized protocol for release of tagmented DNA in SDS, followed by a Triton X-100 neutralization step and PCR amplification (Janssens et al., 2021). Briefly, the volume of 10 mM TAPS Buffer pH 8.5 was adjusted to 65 uL per 20,000 nuclei to yield a concentration of ~300 nuclei/uL and nuclei were stained with 1X DAPI and 1X secondary diluent reagent (Takara Cat# 640196). The 8 source wells of the ICELL8 were loaded with 65 uL of the suspension of tagmented nuclei and dispensed into a SMARTer ICELL8 350v chip (Takara Bio, cat. no. 640019) at 35 nL per well. The chip was then sealed for imaging and spun down at 1200 x g for 1 min. Imaging on a DAPI channel confirmed the presence of single cells in specific wells. Non-single-cell wells were excluded from downstream reagent dispenses. A volume of 35 nL of 0.19% SDS in 10 mM TAPS Buffer pH 8.5 was dispensed into active wells and the chip was dried, sealed and spun down at 1200 x g for 1 min. The chip was placed in a thermocycler and held at 58oC for 1 hr to release tagmented chromatin. The chip was spun at 1200 x g for 1 min before opening, and 35 nL of 2.5% Triton X-100 in ddH20 was dispensed into all active wells. To index the whole chip, 72 × 72 i5/i7 primers containing unique indices (5,184 microwells total) were dispensed at 35 nL in wells that contained single cells, followed by two dispenses of 50 nL (100 nL total) KAPA PCR mix (2.775 X HiFi Buffer, 0.85 mM dNTPs, 0.05 U KAPA HiFi polymerase / µL, Roche Cat# 07958846001). The chip was sealed for heated incubation and spun down at 1200 x g for 1min after each dispense. PCR on the chip was performed with the following protocol: 5 min at 58 °C, 10 min at 72 °C and 2 min at 98°C, followed by 15 cycles of 15s at 98°C, 15s at 60°C and 10s at 72°C, with a final extension at 72 °C for 2 min. The contents of the chip were then spun out into a collection tube (Takara Cat# 640048) at 1200g for 3 min. Two rounds of SPRI bead cleanup at a 1.3 : 1 v/v ratio of beads to sample were performed to remove residual PCR primers and detergent. Samples were resuspended in 20 uL of 10 mM Tris-HCl pH 8.0. Library quality and concentration were evaluated by Agilent Tapestation capillary gel analysis, and single-cell CUT&Tag2for1 samples were then pooled with bulk libraries prepared using compatible barcodes. PE25 sequencing was performed on an Illumina HiSeq2500 by the Fred Hutch Genomics Shared Resource.
CUT&Tag2for1 was carried out using pA-Tn5-adapter-antibody conjugate complexes to integrate barcoded adapters via tagmentation directly to DNA for each antibody target on both sides of the insert, so that the DNA that is released is already a barcoded library.

tag: antibody

value: RNAP2Ser5P Cell Signaling Technology cat# 13523

value: H3K27me3 Cell Signaling Technology cat# 9733

value: K562 human immortalised myelogenous leukemia cell line


title: US22502553_252206068701_S01_CGH_1105_Oct12_1_1


title: Pediatric acute lymphoblastic leukemia [16-048]

description:
16-048
Strand-specific RNA-seq

tag: diagnosis

value: bone marrow

tag: gender


title: F4649_E4S4

tag: Sex

tag: genotype/variation

tag: timepoint


title: H1_P5k27_sc2for1_rep3_(20211206_DJ_Hs_H1_2for1)

description: Single-cell H1 ES cell CnT2for1 replicate 3

value: H1 human embryonic stem cell line


title: BasL_156

value: Breast cancer

tag: citbcmst subtype

value: BasL

value: Negative


title: F4648_E4S7

value: M


title: F4649_E1S5


title: KO_totalRNA_rep2

value: myoblast

tag: genotype

value: Lockd-KO

tag: molecule subtype

value: Total RNA


title: bq005_A

value: hESC Reporter OPC

value: ms

value: stimulated


title: F4648_E4S3

value: Control (Eed fl/fl)


title: bq007_O

value: unstimulated

value: Female


title: BasL_153

tag: sn status

tag: ihc er status


title: BasL_154

value: Positive


title: BasL_155


title: K562_P5k27_sc2for1_rep1_(20210528_KA_Hs_1990_K562_C241)

description: Single-cell K562 cell CnT2for1 replicate 1

value: RNAP2Ser5P Cell Signaling Technology cat# 13523

value: H3K27me3 Cell Signaling Technology cat# 9733

tag: cell type

value: K562 human immortalised myelogenous leukemia cell line


title: K562_P5k27_sc2for1_rep2_(20210818_KA_Hs_241_K562_2_1)

description: Single-cell K562 cell CnT2for1 replicate 2


title: H1_P5k27_sc2for1_rep2_(20210818_KA_Hs_241_H1_212_1)

description: Single-cell H1 ES cell CnT2for1 replicate 2

value: H1 human embryonic stem cell line


title: BasL_152

value: Breast cancer

value: BasL


title: F4648_E3S1

value: M


title: H1_P5k27_sc2for1_rep1_(20210528_KA_Hs_1992_H1_C241)

description: Single-cell H1 ES cell CnT2for1 replicate 1


title: US22502553_252206068702_S01_CGH_1105_Oct12_1_1

tag: tissue type

value: Tumour

tag: sample type

value: wild type; refernce DNA


title: F4553_E4S4


title: K562_PolS5p_CUTAC_rep2_(20210318+0323_SH_Hs_K5x_PolS5P_0315)

description: CUTAC in K562 cells for Pol2Ser5phosphate replicate 2

data_processing:
Genome_build: UCSC hg19
1. We used Bowtie2 2.4.2 with options "--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the paired-end 25bp reads to hg19 Homo sapiens genomic sequence obtained from UCSC. 2. We extracted properly paired reads from the alignments to generate a bed file of aligned fragments.  3. We used bedtools genomecov to make a normalized count bedgraph file. Normalized counts are the fraction of counts at each base pair scaled by the size of the reference sequence (3095693983) so that if the scaled counts were uniformly distributed there would be 1 at each position (Supplementary file normalized_counts.bedgraph.gz).

source_name: CUTAC

extract_protocol:
CUTnTag-direct_v3_Protocols.io.pdf
CUTAC was carried out using pA-Tn5-adapter-antibody conjugate complexes to integrate barcoded adapters via tagmentation directly to DNA for each antibody target on both sides of the insert, so that the DNA that is released is already a barcoded library. PMID 33191916


title: F4553_E3E6


title: K562_PolS5p_CUTAC_rep1_(20201229_SH_Hs_PolS5Hx_con_1221)

description: CUTAC in K562 cells for Pol2Ser5phosphate replicate 1


title: BasL_151

value: Negative


title: hc51282_A

value: hESC Reporter OPC

tag: group

value: control

tag: tnf+il1a stimulated

tag: batch


title: ctrl1_A

value: media

value: stimulated

value: not applicable

tag: age


title: ctrl1_O

value: unstimulated


title: F0787_E1S8

description: ScRNA-seq run from E13.5 Eed-cKO mouse hypothalamus

source_name: E13.5 Eed-cKO mouse hypothalamus

value: Eed-cKO (Eed fl/fl; Sox1-Cre/+)


title: bq005_O

value: ms

value: Male


title: BasL_149

tag: tissue

value: Positive


title: BasL_150


title: BasL_158


title: hc51282_O

value: Female


title: BasL_148

value: Breast cancer


title: F0787_E1S7


title: K562_PolS5p_CUTAC_linamp_hex_(20210318+0323_SH_Hs_K5x_PolS5Ph_lin_0315)

description: CUTAC in K562 cells for Pol2Ser5phosphate with linear amplification and hexanediol

tag: antibody

value: RNAP2Ser5P Cell Signaling Technology cat# 13523

value: K562 human immortalised myelogenous leukemia cell line


title: BasL_147

value: BasL


title: hc51313_O

tag: Sex


title: F0779_E1S6

value: M

tag: genotype/variation


title: K562_PolS5p_CUTAC_9cycles_(20210323_SH_Hs_K5xlin_PolS5P_9cy_0320)

description: CUTAC in K562 cells for Pol2Ser5phosphate with linear amplification


title: F0787_E1S3

tag: timepoint


title: bq008_A


title: K562_PolS5p_CUTAC_3cycles_(20210323_SH_Hs_K5xlin_PolS5P_3cy_0320)


title: F0779_E1S5


title: K562_PolS5p_CUTAC_6cycles_(20210323_SH_Hs_K5xlin_PolS5P_6cy_0320)


title: bq008_O


title: BasL_145

tag: citbcmst subtype

value: Negative


title: K562_PolS5p_CUTAC_hex_(20210318+0323_SH_Hs_K5x_PolS5Ph_0315)

description: CUTAC in K562 cells for Pol2Ser5phosphate with hexanediol


title: bq004_A

value: hESC Reporter OPC


title: K562_PolS5p_CUTAC_linamp_(20210318+0323_SH_Hs_K5x_PolS5P_lin_0315)


title: F0787_E1S4


title: K562_PolS5p_CUTAC_30min_(20201230_SH_Hs_PolS5_con30_1220)

description: CUTAC in K562 cells for Pol2Ser5phosphate


title: F0779_E1S2


title: bq004_O


title: K562_PolS5p_CUTAC_12cycles_(20210323_SH_Hs_K5xlin_PolS5P_12cy_0320)


title: BasL_142


title: hc51313_A

value: control


title: F0779_E1S1


title: BasL_143


title: BasL_146


title: F0764_E2S8

description: ScRNA-seq run from E15.5 Eed-cKO mouse hypothalamus

source_name: E15.5 Eed-cKO mouse hypothalamus


title: K562_PolS5p_CUTAC_10min_(20201230_SH_Hs_PolS5_con10_1220)


title: BasL_144


title: BasL_141


title: P7A

source_name: hiPSC astrocyte

value: hiPSC astrocyte


title: F0764_E2S7


title: BasL_140


title: K562_P5K27_CUTAC_rep2_(20210318+0323_SH_Hs_K5x_P5K27m_0315)

description: CUTAC in K562 cells for Pol2Ser5phosphate and H3K27me3 replicate 2

extract_protocol:
CUTnTag-direct_v3_Protocols.io.pdf
CUT&Tag2for1 was carried out using pA-Tn5-adapter-antibody conjugate complexes to integrate barcoded adapters via tagmentation directly to DNA for each antibody target on both sides of the insert, so that the DNA that is released is already a barcoded library.

value: H3K27me3 Cell Signaling Technology cat# 9733


title: P6O


title: K562_P5K27_CUTAC_rep1_(20201229_SH_Hs_P5K27mKx_con_1221)

description: CUTAC in K562 cells for Pol2Ser5phosphate and H3K27me3 replicate 1


title: P6A

value: stimulated


title: P7O

value: unstimulated


title: F0764_E2S3

value: Eed-cKO (Eed fl/fl; Sox1-Cre/+)


title: F0764_E1S6

value: F


title: C6O


title: BasL_138

description: Gene expression data from human breast cancer


title: F0764_E1S2


title: K562_P5K27_CUTAC_linamp_(20210318+0323_SH_Hs_K5x_P5K27m_lin_0315)

description: CUTAC in K562 cells for Pol2Ser5phosphate and H3K27me3 with linear amplification


title: K562_P5K27_CUTAC_linamp_hex_(20210318+0323_SH_Hs_K5x_P5K27mh_lin_0315)

description: CUTAC in K562 cells for Pol2Ser5phosphate and H3K27me3 with linear amplification and hexanediol


title: BasL_137


title: BasL_136


title: K562_P5K27_CUTAC_hex_(20210318+0323_SH_Hs_K5x_P5K27mh_0315)

description: CUTAC in K562 cells for Pol2Ser5phosphate and H3K27me3 with hexanediol


title: F0764_E1S1


title: BasL_139


title: BasL_135


title: K562_NPAT_CUTAC_(20210318_SH_Hs_K5x_NPAT_0315)

description: CUTAC in K562 cells for NPAT

value: NPAT Thermo Invitrogen cat# PA5-66839 lot# SL2495022A


title: F0753_E1S8


title: P5A

value: ms

value: Male


title: K562_NPAT_CUTAC_linamp_(20210318+0323_SH_Hs_K5x_NPAT_lin_0315)

description: CUTAC in K562 cells for NPAT with linear amplification


title: F0764_E2S4


title: C5O


title: K562_NPAT_CUTAC_linamp_hex_(20210318+0323_SH_Hs_K5x_NPATh_lin_0315)

description: CUTAC in K562 cells for NPAT with linear amplification and hexanediol


title: C6A

value: Female


title: C5A


title: F0753_E1S7


title: F0753_E1S4


title: P5O


title: P4O


title: F0753_E1S3


title: BasL_132

value: Breast cancer


title: BasL_133

value: Positive


title: K562_NPAT_CUTAC_hex_(20210318_SH_Hs_K5x_NPATh_0315)

description: CUTAC in K562 cells for NPAT with hexanediol

value: K562 human immortalised myelogenous leukemia cell line


title: BasL_161

value: BasL


title: K562_K27_CUTnTag_linamp_(20210427_SH_Hs_K27m3x_lin_0420)

description: CUT&Tag in K562 cells linear amplification

source_name: CUT&Tag

extract_protocol:
CUTnTag-direct_v3_Protocols.io.pdf
CUT&Tag uses tagmentation in which the barcoded adapters are integrated on both sides of the insert, so that the DNA that is released is already a barcoded library. PMID:31036827


title: F0748_E1S4

value: M


title: BasL_134

value: Negative


title: P4A


title: K562_K27_CUTnTag_5minhot_(20210427_SH_Hs_K27m3x_5m_0420)

description: CUT&Tag in K562 cells 5 min 98deg PCR denaturation


title: C4O

value: control


title: BasL_130


title: C4A

value: hiPSC astrocyte


title: K562_K27_CUTAC_rep2_(20210318+0323_SH_Hs_K5x_K27_0315)

description: CUTAC in K562 cells for H3K27me3 replicate 2

value: H3K27me3 Cell Signaling Technology cat# 9733


title: F0748_E1S2

description: ScRNA-seq run from E13.5 Eed-cKO mouse hypothalamus


title: F0748_E1S3


title: BasL_129


title: BasL_131


title: F0748_E1S1


title: P3A

value: stimulated


title: F0720_E1S4


title: K562_K27_CUTAC_linamp_(20210318+0323_SH_Hs_K5x_K27_lin_0315)

description: CUTAC in K562 cells for H3K27me3 with linear amplification


title: P3O

value: unstimulated


title: K562_K27_CUTAC_linamp_hex_(20210318+0323_SH_Hs_K5x_K27h_lin_0315)

description: CUTAC in K562 cells for H3K27me3 with linear amplification and hexanediol


title: BasL_128


title: BasL_127


title: F0720_E1S2

value: Eed-cKO (Eed fl/fl; Sox1-Cre/+)


title: C3O


title: BasL_126


title: K562_H3K27me3_CUTAC_9cycles_(20210323_SH_Hs_K5xlin_K27_9cy_0320)

value: RNAP2Ser5P Cell Signaling Technology cat# 13523


title: K562_K27_CUTAC_hex_(20210318+0323_SH_Hs_K5x_K27h_0315)

description: CUTAC in K562 cells for H3K27me3 with hexanediol


title: BasL_125


title: BasL_124


title: F0705_E3S8

value: F


title: K562_K27_CUTAC_rep1_(20201229_SH_Hs_K27meKx_con_1221)

description: CUTAC in K562 cells for H3K27me3 replicate 1


title: P2A

value: ms


title: BasL_122


title: BasL_123


title: K562_H3K27me3_CUTAC_6cycles_(20210323_SH_Hs_K5xlin_K27_6cy_0320)


title: F0705_E3S7


title: bq007_A

value: hESC Reporter OPC


title: C3A

value: Female


title: F0705_E3S6


title: C2A

value: Male


title: K562_H3K27me3_CUTAC_3cycles_(20210323_SH_Hs_K5xlin_K27_3cy_0320)


title: BasL_120

value: Breast cancer


title: F0720_E1S3

description: ScRNA-seq run from E15.5 Eed-cKO mouse hypothalamus


title: BasL_121


title: K562_H3K27me3_CUTAC_12cycles_(20210323_SH_Hs_K5xlin_K27_12cy_0320)

value: K562 human immortalised myelogenous leukemia cell line


title: BasL_119

value: BasL


title: P1A


title: F0705_E3S4


title: C2O


title: P1O


title: F0705_E3S3


title: H1_PolS5p_CUTAC_linamp_(20210318+0323_SH_Hs_H1x_PolS5P_lin_0315)

description: CUTAC in H1 ES cells for Pol2Ser5phosphate with linear amplification

value: H1 human embryonic stem cell line


title: H1_PolS5p_CUTAC_linamp_hex_(20210318+0323_SH_Hs_H1x_PolS5Ph_lin_0315)

description: CUTAC in H1 ES cells for Pol2Ser5phosphate with linear amplification and hexanediol


title: F0705_E1S2


title: BasL_118

description: Gene expression data from human breast cancer

value: Negative

value: Positive


title: P2O

value: hiPSC astrocyte


title: BasL_117


title: H1_PolS5p_CUTAC_hex_(20210318+0323_SH_Hs_H1x_PolS5Ph_0315)

description: CUTAC in H1 ES cells for Pol2Ser5phosphate with hexanediol


title: C1A

value: control


title: C1O


title: F0705_E3S5


title: BasL_116


title: H1_P5K27_CUTAC_(20210318+0323_SH_Hs_H1x_P5K27me_0315)

description: CUTAC in H1 ES cells for Pol2Ser5phosphate and H3K27me3

value: H3K27me3 Cell Signaling Technology cat# 9733


title: F0701_E2S4


title: Pediatric acute lymphoblastic leukemia [16-378]

description:
16-378
Strand-specific RNA-seq

data_processing:
Raw reads were aligned to the GRCh37 genome reference using STAR v2.5.3a.
Expression counts were obtained using htseq-count v0.9.0 on the Ensembl Homo_sapiens.GRCh37.75.gtf.
Genome_build: GRCh37
Supplementary_files_format_and_content: *.counts.txt: Tab-delimited text files include raw expression counts.

extract_protocol:
Mini AllPrep DNA/RNA kits from Qiagen.
Ribo-Zero Gold Kit according to Illumina's protocol.

tag: diagnosis

value: bone marrow

tag: gender


title: F0701_E2S3

value: Eed-cKO (Eed fl/fl; Sox1-Cre/+)


title: Pediatric acute lymphoblastic leukemia [16-376]

description:
16-376
Strand-specific RNA-seq


title: H1_P5K27_CUTAC_linamp_(20210318+0323_SH_Hs_H1x_P5K27me_lin_0315)

description: CUTAC in H1 ES cells for Pol2Ser5phosphate and H3K27me3 with linear amplification

value: RNAP2Ser5P Cell Signaling Technology cat# 13523


title: H1_PolS5p_CUTAC_(20210318+0323_SH_Hs_H1x_PolS5P_0315)

description: CUTAC in H1 ES cells for Pol2Ser5phosphate


title: H1_P5K27_CUTAC_linamp_hex_(20210318+0323_SH_Hs_H1x_P5K27hme_lin_0315)

description: CUTAC in H1 ES cells for Pol2Ser5phosphate and H3K27me3 with linear amplification and hexanediol


title: F0701_E2S2

value: F


title: Pediatric acute lymphoblastic leukemia [16-374]

description:
16-374
Strand-specific RNA-seq


title: BasL_114

tag: sn status


title: BasL_112

tag: ihc er status


title: F0701_E2S1


title: BasL_113


title: BasL_115


title: F0705_E1S1


title: H1_P5K27_CUTAC_hex_(20210318+0323_SH_Hs_H1x_P5K27hme_0315)

description: CUTAC in H1 ES cells for Pol2Ser5phosphate and H3K27me3 with hexanediol

tag: cell type


title: Pediatric acute lymphoblastic leukemia [16-372]

description:
16-372
Strand-specific RNA-seq


title: F0696_E3S8

value: M


title: F0696_E3S7


title: H1_NPAT_CUTAC_linamp_(20210318+0323_SH_Hs_H1x_NPAT_lin_0315)

description: CUTAC in H1 ES cells for NPAT with linear amplification

value: NPAT Thermo Invitrogen cat# PA5-66839 lot# SL2495022A


title: BasL_111


title: Pediatric acute lymphoblastic leukemia [16-367]

description:
16-367
Strand-specific RNA-seq

value: peripheral blood


title: BasL_110


title: BasL_109


title: Pediatric acute lymphoblastic leukemia [16-364]

description:
16-364
Strand-specific RNA-seq

value: Male


title: H1_NPAT_CUTAC_linamp_hex_(20210318+0323_SH_Hs_H1x_NPATh_lin_0315)

description: CUTAC in H1 ES cells for NPAT with linear amplification and hexanediol


title: F0696_E3S3

description: ScRNA-seq run from E13.5 Eed-cKO mouse hypothalamus


title: H1_NPAT_CUTAC_hex_(20210318_SH_Hs_H1x_NPATh_0315)

description: CUTAC in H1 ES cells for NPAT with hexanediol


title: Pediatric acute lymphoblastic leukemia [16-363]

description:
16-363
Strand-specific RNA-seq


title: Pediatric acute lymphoblastic leukemia [16-373]

description:
16-373
Strand-specific RNA-seq


title: F0696_E1S5


title: Pediatric acute lymphoblastic leukemia [16-362]

description:
16-362
Strand-specific RNA-seq

value: Female


title: BasL_108

value: Breast cancer


title: H1_K27_CUTnTag_linamp_(20210427_SH_Hs_H1_K27m3x_lin_0420)

description: CUT&Tag in H1 ES cells linear amplification


title: BasL_106

value: BasL


title: Pediatric acute lymphoblastic leukemia [16-359]

description:
16-359
Strand-specific RNA-seq


title: H1_NPAT_CUTAC_(20210318+0323_SH_Hs_H1x_NPAT_0315)

description: CUTAC in H1 ES cells for NPAT

value: H1 human embryonic stem cell line


title: BasL_107

value: Negative


title: F0696_E1S2


title: F0693_E2S6


title: Pediatric acute lymphoblastic leukemia [16-354]

description:
16-354
Strand-specific RNA-seq


title: H1_K27_CUTAC_(20210318+0323_SH_Hs_H1x_K27m_0315)

description: CUTAC in H1 ES cells for H3K27me3


title: H1_K27_CUTAC_linamp_(20210318+0323_SH_Hs_H1x_K27m_lin_0315)

description: CUTAC in H1 ES cells for H3K27me3 with linear amplification


title: F0693_E2S2


title: H1_K27_CUTAC_linamp_hex_(20210318+0323_SH_Hs_H1x_K27mh_lin_0315)

description: CUTAC in H1 ES cells for H3K27me3 with linear amplification and hexanediol


title: BasL_105


title: F0696_E1S6


title: Pediatric acute lymphoblastic leukemia [16-352]

description:
16-352
Strand-specific RNA-seq


title: F0693_E2S1


title: H1_K27_CUTAC_hex_(20210318+0323_SH_Hs_H1x_K27mh_0315)

description: CUTAC in H1 ES cells for H3K27me3 with hexanediol


title: Pediatric acute lymphoblastic leukemia [16-350]

description:
16-350
Strand-specific RNA-seq


title: F0677_E6S4


title: BasL_104


title: Pediatric acute lymphoblastic leukemia [16-348]

description:
16-348
Strand-specific RNA-seq


title: BasL_103

value: Positive


title: Pediatric acute lymphoblastic leukemia [16-347]

description:
16-347
Strand-specific RNA-seq


title: H1_K27_CUTnTag_5minhot_(20210427_SH_Hs_H1_K27m3x_5m_0420)

description: CUT&Tag in H2 ES cells 5 min 98deg PCR denaturation


title: F0677_E6S3


title: Pediatric acute lymphoblastic leukemia [16-346]

description:
16-346
Strand-specific RNA-seq


title: HOGD12 4

city: Atlanta

first: Bing

last: Yao

address: 615 Michael Street

department: Department of Human Genetics

institute: Emory University

data_processing:
Small RNA-seq data were mapped to miRNA database for miRNA quantification by miRge 2.0 to human miRNA database with the following parameter: “-sp human -ad AACTGTAGGCACCATCAAT -ai -gff -trf” [62].
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited file of DEseq2 result

source_name: HOG

growth_protocol: BE (2)-M17 human neuroblastoma (M17) cells were propagated in DMEM/F12 medium with 10% FBS (HyClone). For differentiation, M17 cells were incubated with DMEM/F12 medium supplemented with 10% FBS and 20 μm retinoic acid (RA, Sigma, r2625) for 10 days with medium changed every other day. HOG cells were propagated in DMEM medium (Invitrogen) supplemented with low glucose and 10% FBS. To induced differentiation, HOG cells were plated on to culture dishes coded with PDL (Sigma, P1524-25MG) in the differentiation DMEM medium with low glucose, containing 50 μg/ml transferrin, 0.5 μg/ml insulin, 30 nM triiodothyronine (T3), 30 nM selenium, 16.1 mg/L Putrescine, 0.5 mM IBMX (3-Isobutyl-1-methylxanthine) and 0.5 mM cAMP (all from sigma) for 13 days with medium change every other day.

extract_protocol:
Cultured cells were harvested then centrifuged at 1,500 g and cell pellets were used for RNA isolation. Cell pellet was homogenized in TRIzol using a hand-held pestle homogenizer and incubated in TRIzol for at least 5 minutes. Chloroform (1:5 ratio) was added, mixed well and incubated at room temperature for 15 minutes. Samples were then centrifuged at 12,000 g for 15 minutes at 4°C. The top aqueous layer was transferred to a clean tube, and the RNA was precipitated in 3 M NaAc pH 5.2 (10:1 ratio), 4 ml of glycogen (5 mg/ml), 100% isopropanol (1:1 ratio) overnight at -80°C. The next day, the samples were centrifuged at 20,000 g for 20 minutes at 4°C. The resulting RNA pellet was washed once in 75% ethanol, centrifuged at 7,500 g for 10 minutes at 4°C. The washed RNA pellet was dissolved in nuclease-free water. RNA was quantified by NanoDrop and the quality was confirmed by agarose gel.
For small RNA-seq library, total RNA sample quality was assessed by RNA ScreenTape (Agilent Technologies Inc., California, USA) and quantified by Qubit 2.0 RNA HS assay (ThermoFisher, Massachusetts, USA). All library construction was prepared according to the QIAseq miRNA Library (Qiagen, Hilden, Germany) per manufacturer’s instructions. Final libraries quantity was assessed by Qubit 2.0 (ThermoFisher, Massachusetts, USA) and quality was assessed by TapeStation HSD1000 ScreenTape (Agilent Technologies Inc., California, USA). Final library size was about 180 bp with an insert size of about 20 bp. Illumina® 8-nt single-indices were used. Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® HiSeq (Illumina, California, USA) with a read length configuration of 150 PE for 10M Single-ended reads per sample.

treatment_protocol: The HOG and M17 cell total RNA were subjected to poly (A) tailing and RNase R treatment as described in published method with modifications [31]. In brief, 3 μg of total RNA was subjected to poly (A) tailing in a 50 μL reaction using the poly (A) tailing kit (ThermoFisher AM1350) following manufacturer’s instructions. 2 μL E-PAP and 40 U RNase inhibitor (ThermoFisher Scientific N8080119) were also added to the reaction and incubated at 37 ºC for 1 hour. The RNAs were then purified by the RNA Clean & Concentrator-25 (Zymo R1018) kit and eluted in 25 μL nuclease-free water. The RNAs were then treated with 5 U RNase R in 30 μL reactions which contained 25 μL of all RNA samples from A-tailing reaction, 3 μL 10× RNase R Buffer (0.2 M Tris–HCl (pH 8.0), 1 mM MgCl2 and 1 M LiCl) and 1 μL RiboLock RNase Inhibitor (40 U/ μL) (ThermoFisher Scientific EO0381). Reactions were purified with RNA Clean & Concentrator-25 (Zymo Research R1018) according to the manufacturer’s instructions and the RNA was eluted in 30 μL nuclease-free water. Then the amount of RNAs (in 30 μL nuclease-free water) was used to prepare rRNA depleted RNA-seq library following the KAPA RNA HyperPrep Kit with RiboErase (HMR).

tag: treatment

value: untreated

tag: Stage

value: Differentiated


title: HOGD12 3


title: F0677_E6S2


title: HOGD12 2


title: BasL_102


title: Pediatric acute lymphoblastic leukemia [16-342]

description:
16-342
Strand-specific RNA-seq


title: HOGD0 4

value: Undifferentiated


title: BasL_100


title: HOGD0 3


title: Pediatric acute lymphoblastic leukemia [16-341]

description:
16-341
Strand-specific RNA-seq

value: bone marrow


title: F0671_E1S4

description: ScRNA-seq run from E15.5 Eed-cKO mouse hypothalamus

value: Eed-cKO (Eed fl/fl; Sox1-Cre/+)


title: F0671_E1S3


title: BasL_101

description: Gene expression data from human breast cancer


title: HOGD0 2


title: F0671_E1S2


title: Pediatric acute lymphoblastic leukemia [16-340]

description:
16-340
Strand-specific RNA-seq


title: Pediatric acute lymphoblastic leukemia [16-339]

description:
16-339
Strand-specific RNA-seq


title: BasL_096


title: BasL_098


title: BasL_099


title: BasL_097


title: BasL_095


title: F0671_E1S1


title: Pediatric acute lymphoblastic leukemia [16-343]

description:
16-343
Strand-specific RNA-seq


title: Pediatric acute lymphoblastic leukemia [16-338]

description:
16-338
Strand-specific RNA-seq


title: M17D10AR_2

data_processing:
Candidate circRNAs for each rRNA-depleted RNA-seq sample were first identified by CIRCexplorer2, CIRIquant, find_circ and MapSplice, individually. For CIRCexplorer2, reads were mapped to hg38 by TopHat2 version 2.1.0 with flag “--fusion-search --keep-fasta-order --no-coverage-search --library-type fr-unstranded”. The output bam files were used for “CIRCexplorer2 parse” with flag “--pe -t TopHat-Fusion”. CircRNA were then annotated by “CIRCexplorer2 annotate” with default parameter. CIRIquant was used to identify candidate circRNAs with default parameter with bwa version 0.7.17, HISAT2 version 2.1.0, StringTie version 2.0.3 and Samtools version 1.9. find_circ was used to identified candidate circRNAs following its instruction using Bowtie 2 version 2.3.5.1 and Samtools version 1.9. MapSplice was used for circRNA identification with flag “--bam --fusion-non-canonical --min-fusion-distance 200”. These four software and parameter are integrated in CARP now and could be automatically run using “CARP CIRCexplorer2”, “CARP CIRIquant”, “CARP findcirc” and “CARP MapSplice” with proper configuration file.
Candidate circRNAs identified by CIRCexplorer2, CIRIquant, find_circ and MapSplice from all A-tailing samples were pooled together and annotated to their host transcripts. By using “CARP PseudoRef”, a 248 bp “pseudo-reference” was constructed for each circRNA flanking its back splicing junction site (+/- 149 bp) with 8 bp center sequence as “seed sequence”. Reference for linear isoform quantification was also constructed using last exon of their host gene (referred as “last reference” hereafter) by “CARP PseudoRef”. Using “CARP Mapping”, reads from A-tailing and untreated library were mapped to “pseudo reference” and “last reference” by Bowtie 2 using default parameter. Reads mapped to “pseudo-reference” were compared with seed sequence by “CARP BSJreads” and mapped to genome and transcriptome by Bowtie 2 and TopHat2 using “CARP Remap”, respectively. Reads mapped to genome or transcriptome or could not exactly match 8 bp “seed sequence” were considered as linear isoform derived reads and were removed from downstream analysis. Using “CARP ReadsCount”, the remaining reads were used for circRNA identification and quantification while reads mapped to “last reference” were used for linear RNA quantification.  CircRNAs with reads count less than 2 was excluded and the ratio for reads count in A-tailing RNase R library and untreated library was calculated to differentiate RNase R-sensitive or resistant reads. Since linear RNAs, not circRNAs, can be degraded in A-tailing library, the ratio distribution for linear RNA and circRNA should display clear difference as shown in Fig. 1f. We defined a cutoff for A-tailing/Control ratio according to ratio distribution of linear RNAs to make sure ratio of >95% linear RNA which should be sensitive to A-tailing RNase R treatment are lower than this cutoff (Fig. 1f, dash line).  CircRNAs which have ratio higher than this cutoff were considered as confident circRNAs which should be resistant to A-tailing RNase R treatment. Therefore, we controlled the false discovery rate of confident circRNA to 0.05 by using this cutoff.
Differential analysis for individual circRNAs were conducted by a well-defined algorithm DESeq2 using normalized reads count integrated in “CARP DEcirc”. CircRNA share common 3’ donor site or 5’ acceptor site was defined as one circRNA cluster. Using “CARP CircCluster”, expression of circRNA cluster was calculated as total expression of each circRNA in this cluster. DE analysis of circRNA cluster was also conducted by DESeq2 and FDR < 0.05 was considered as significant circRNA cluster differential expression.
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited file of DEseq2 result

extract_protocol:
Cultured cells were harvested then centrifuged at 1,500 g and cell pellets were used for RNA isolation. Cell pellet was homogenized in TRIzol using a hand-held pestle homogenizer and incubated in TRIzol for at least 5 minutes. Chloroform (1:5 ratio) was added, mixed well and incubated at room temperature for 15 minutes. Samples were then centrifuged at 12,000 g for 15 minutes at 4°C. The top aqueous layer was transferred to a clean tube, and the RNA was precipitated in 3 M NaAc pH 5.2 (10:1 ratio), 4 ml of glycogen (5 mg/ml), 100% isopropanol (1:1 ratio) overnight at -80°C. The next day, the samples were centrifuged at 20,000 g for 20 minutes at 4°C. The resulting RNA pellet was washed once in 75% ethanol, centrifuged at 7,500 g for 10 minutes at 4°C. The washed RNA pellet was dissolved in nuclease-free water. RNA was quantified by NanoDrop and the quality was confirmed by agarose gel.
For rRNA-depleted RNA-seq library, sample quality was assessed by Bioanalyzer 2100 Eukaryote Total RNA Pico (Agilent Technologies, CA, USA) and quantified by Qubit RNA HS assay (ThermoFisher). Ribosomal RNA depletion was performed with Ribo-zero rRNA Removal Kit (Illumina Inc., San Diego, CA) followed by NEBNext® Ultra™ II Nondirectional RNA Library Prep Kit for Illumina® per manufacturer's recommendation. Library concentration was measured by qPCR and library quality evaluated by Tapestation High Sensitivity D1000 ScreenTapes (Agilent Technologies, CA, USA). Equimolar pooling of libraries was performed based on qPCR values. Libraries were sequenced on a HiSeq with a read length configuration of 150 PE targeting 80M total reads per sample (40M each direction).

value: A-tailing RNase R


title: F0677_E6S1

value: F


title: F0656_E6S4

value: M


title: Pediatric acute lymphoblastic leukemia [16-335]

description:
16-335
Strand-specific RNA-seq


title: F0656_E6S3


title: BasL_092


title: BasL_093


title: BasL_094


title: M17D10AR_3


title: M17D0AR_3


title: Pediatric acute lymphoblastic leukemia [16-328]

description:
16-328
Strand-specific RNA-seq


title: Pediatric acute lymphoblastic leukemia [16-326]

description:
16-326
Strand-specific RNA-seq


title: M17D0AR_2


title: F0656_E6S1


title: F0656_E6S2


title: M17D0AR_1


title: BasL_089


title: F0655_E5S4


title: BasL_090


title: Pediatric acute lymphoblastic leukemia [16-315]

description:
16-315
Strand-specific RNA-seq


title: Pediatric acute lymphoblastic leukemia [16-322]

description:
16-322
Strand-specific RNA-seq


title: F0655_E5S3


title: HOGD12AR_4


title: HOGD12AR_3


title: M17D10AR_1


title: BasL_091


title: HOGD12AR_2


title: BasL_087


title: Pediatric acute lymphoblastic leukemia [16-306]

description:
16-306
Strand-specific RNA-seq


title: HOGD0AR_3


title: BasL_088


title: Pediatric acute lymphoblastic leukemia [16-312]

description:
16-312
Strand-specific RNA-seq


title: Pediatric acute lymphoblastic leukemia [16-304]

description:
16-304
Strand-specific RNA-seq


title: F0616_E6S7


title: F0655_E5S1


title: BasL_085


title: HOGD0AR_4


title: F0655_E5S2


title: BasL_086


title: F0616_E6S8


title: HOGD0AR_2


title: Pediatric acute lymphoblastic leukemia [16-319]

description:
16-319
Strand-specific RNA-seq


title: M17D10_3


title: Pediatric acute lymphoblastic leukemia [16-296]

description:
16-296
Strand-specific RNA-seq


title: M17D10_2


title: F0616_E6S4


title: F0616_E6S3


title: F0616_E4S6


title: M17D10_1


title: BasL_082


title: Pediatric acute lymphoblastic leukemia [16-295]

description:
16-295
Strand-specific RNA-seq


title: BasL_084


title: F0616_E4S2


title: F0616_E4S5


title: Pediatric acute lymphoblastic leukemia [16-287]

description:
16-287
Strand-specific RNA-seq


title: M17D0_1


title: Pediatric acute lymphoblastic leukemia [16-294]

description:
16-294
Strand-specific RNA-seq


title: BasL_081


title: Pediatric acute lymphoblastic leukemia [16-293]

description:
16-293
Strand-specific RNA-seq


title: Pediatric acute lymphoblastic leukemia [16-286]

description:
16-286
Strand-specific RNA-seq


title: Pediatric acute lymphoblastic leukemia [16-291]

description:
16-291
Strand-specific RNA-seq


title: BasL_078


title: F0616_E4S1


title: M17D0_2


title: BasL_080


title: BasL_079


title: HOGD12_3


title: F4749_E1S2

description: ScRNA-seq run from E16.5 Control mouse hypothalamus

source_name: E16.5 Control mouse hypothalamus

value: Control (Eed fl/fl)


title: Pediatric acute lymphoblastic leukemia [16-282]

description:
16-282
Strand-specific RNA-seq


title: M17D0_3


title: Pediatric acute lymphoblastic leukemia [16-284]

description:
16-284
Strand-specific RNA-seq


title: BasL_083


title: F4749_E2S3


title: HOGD12_4


title: BasL_076


title: F4748_E2S1

description: ScRNA-seq run from E15.5 Control mouse hypothalamus

source_name: E15.5 Control mouse hypothalamus


title: Pediatric acute lymphoblastic leukemia [16-279]

description:
16-279
Strand-specific RNA-seq

value: peripheral blood


title: F4749_E1S1


title: BasL_074


title: HOGD12_2


title: HOGD0_2


title: BasL_075


title: HOGD0_4


title: SHSY-5Y-3

data_processing:
Paired end reads from rRNA depleted RNA-seq for untreated, RNase R (K+) treated, RNase R (Li+) treated, and A-tailing RNase R (Li+) treated library were mapped to human genome assembly version (GRCh38/hg38) using TopHat2 version 2.1.1 with default parameter. Bam files were sorted according to genome coordinate by “samtools sort” and converted to bed file by “bedtools bamtobed” with flag “-split”. Bed files were sorted by “sort -k 1,1 -k2,2n” according to instruction of bedtools. Genome coordinate of last exon of each gene were extract from gene structure annotation of hg38 downloaded from UCSC table by homemade perl script. Reads count for each last exon were counted by “bedtools coverage” with flag “-sorted -counts -split” from sorted bed file of each sample. Reads count for last exon were then normalized to total sequencing reads and exon length as RPKM to represent linear RNA expression level
Genome_build: hg38
Supplementary_files_format_and_content: RPKM for last exon

value: A-tailing RNaseR with LiCL


title: F4649_E4S7


title: Pediatric acute lymphoblastic leukemia [16-302]

description:
16-302
Strand-specific RNA-seq

value: Female


title: BasL_073

value: Breast cancer


title: BasL_071

value: BasL


title: Pediatric acute lymphoblastic leukemia [16-280]

description:
16-280
Strand-specific RNA-seq


title: F4649_E4S3


title: BasL_069


title: BasL_072


title: Pediatric acute lymphoblastic leukemia [16-272]

description:
16-272
Strand-specific RNA-seq


title: F4648_E4S4

description: ScRNA-seq run from E13.5 Control mouse hypothalamus


title: Pediatric acute lymphoblastic leukemia [16-273]

description:
16-273
Strand-specific RNA-seq

value: Male


title: F4553_E4S8


title: F4649_E1S1


title: SHSY-5Y-2

value: RNaseR with LiCL


title: BasL_070

value: Negative

value: Positive


title: Pediatric acute lymphoblastic leukemia [16-270]

description:
16-270
Strand-specific RNA-seq


title: F4648_E3S6


title: 293T-2


title: Pediatric acute lymphoblastic leukemia [16-269]

description:
16-269
Strand-specific RNA-seq


title: SHSY-5Y-1

value: untreated


title: BasL_067


title: SHSY-5Y-0

value: RNaseR with KCL


title: Pediatric acute lymphoblastic leukemia [16-268]

description:
16-268
Strand-specific RNA-seq

value: bone marrow


title: BasL_077


title: F4638_E4S4


title: Pediatric acute lymphoblastic leukemia [16-265]

description:
16-265
Strand-specific RNA-seq


title: 293T-3


title: Pediatric acute lymphoblastic leukemia [16-267]

description:
16-267
Strand-specific RNA-seq


title: F4499_E1S4


title: F4553_E3S1


title: F4497_E4S1


title: HOGD0_3

value: Undifferentiated


title: F4500_E3S8


title: BasL_068


title: 293T-1


title: Pediatric acute lymphoblastic leukemia [16-258]

description:
16-258
Strand-specific RNA-seq


title: Pediatric acute lymphoblastic leukemia [16-266]

description:
16-266
Strand-specific RNA-seq


title: BasL_063


title: 293T-0


title: F4499_E1S7


title: Pediatric acute lymphoblastic leukemia [16-090]

description:
16-090
Strand-specific RNA-seq


title: Pediatric acute lymphoblastic leukemia [16-089]

description:
16-089
Strand-specific RNA-seq


title: F4499_E1S2


title: BasL_066


title: Pediatric acute lymphoblastic leukemia [16-257]

description:
16-257
Strand-specific RNA-seq


title: BasL_064


title: BasL_065


title: Pediatric acute lymphoblastic leukemia [16-256]

description:
16-256
Strand-specific RNA-seq


title: F4650_E1S6


title: Pediatric acute lymphoblastic leukemia [16-044]

description:
16-044
Strand-specific RNA-seq


title: Pediatric acute lymphoblastic leukemia [16-261]

description:
16-261
Strand-specific RNA-seq


title: BasL_061


title: Pediatric acute lymphoblastic leukemia [16-253]

description:
16-253
Strand-specific RNA-seq


title: Pediatric acute lymphoblastic leukemia [16-252]

description:
16-252
Strand-specific RNA-seq


title: Pediatric acute lymphoblastic leukemia [16-042]

description:
16-042
Strand-specific RNA-seq


title: Pediatric acute lymphoblastic leukemia [16-249]

description:
16-249
Strand-specific RNA-seq


title: F4649_E4S8


title: F4648_E3S5


title: F4649_E1S2


title: BasL_060


title: F4648_E3S2


title: Pediatric acute lymphoblastic leukemia [16-027]

description:
16-027
Strand-specific RNA-seq


title: Pediatric acute lymphoblastic leukemia [16-025]

description:
16-025
Strand-specific RNA-seq


title: BasL_062


title: Pediatric acute lymphoblastic leukemia [16-245]

description:
16-245
Strand-specific RNA-seq


title: Pediatric acute lymphoblastic leukemia [16-244]

description:
16-244
Strand-specific RNA-seq


title: F4638_E4S3


title: BasL_056


title: BasL_058


title: BasL_059


title: Pediatric acute lymphoblastic leukemia [16-243]

description:
16-243
Strand-specific RNA-seq


title: BasL_055


title: Pediatric acute lymphoblastic leukemia [16-014]

description:
16-014
Strand-specific RNA-seq


title: F4553_E4S7


title: Pediatric acute lymphoblastic leukemia [16-022]

description:
16-022
Strand-specific RNA-seq


title: Pediatric acute lymphoblastic leukemia [16-242]

description:
16-242
Strand-specific RNA-seq


title: Pediatric acute lymphoblastic leukemia [16-029]

description:
16-029
Strand-specific RNA-seq


title: BasL_057


title: F4638_E2S1


title: Pediatric acute lymphoblastic leukemia [16-011]

description:
16-011
Strand-specific RNA-seq


title: Pediatric acute lymphoblastic leukemia [16-012]

description:
16-012
Strand-specific RNA-seq


title: Pediatric acute lymphoblastic leukemia [16-240]

description:
16-240
Strand-specific RNA-seq


title: Pediatric acute lymphoblastic leukemia [16-241]

description:
16-241
Strand-specific RNA-seq


title: Pediatric acute lymphoblastic leukemia [16-239]

description:
16-239
Strand-specific RNA-seq


title: BasL_053


title: Pediatric acute lymphoblastic leukemia [16-238]

description:
16-238
Strand-specific RNA-seq


title: Pediatric acute lymphoblastic leukemia [16-006]

description:
16-006
Strand-specific RNA-seq


title: F4500_E3S7


title: BasL_052


title: F4500_E3S6


title: BasL_054


title: Pediatric acute lymphoblastic leukemia [16-003]

description:
16-003
Strand-specific RNA-seq


title: Pediatric acute lymphoblastic leukemia [16-233]

description:
16-233
Strand-specific RNA-seq


title: BasL_049


title: F4500_E2S2


title: F4499_E1S1


title: Pediatric acute lymphoblastic leukemia [16-232]

description:
16-232
Strand-specific RNA-seq


title: Xenograft-C4-2-tet-shRB-DOX-T_tumor4

first: Changmeng

last: Cai

address: 100 William T Morrissey Blvd

institute: University of Massachusetts Boston

description: Xenograft_C4-2-tet-shRB_DOX_samples_count_table.txt

data_processing:
The sequence quality of raw reads was checked by FastQC (version 0.11.9).
Raw reads were aligned to the human reference genome (hg19) using STAR (version 2.7.2) followed by counting with featureCounts (version 1.6.4) from GRCh37 Ensembl reference.
Genome_build: hg19
Supplementary_files_format_and_content: txt file forraw counts of sequence reads

source_name: xenograft

extract_protocol:
RNA was extracted with Rneasy Mini Kit (QIAGEN) following manufacturer’s protocol.
RNA-seq libraries of xenograft C4-2-tet-shRB (without Dox) were performed by using TruSeq® Strnd Total RNA LT (Illumina). RNA-seq libraries of the rest of samples were performed by using TruSeq® Stranded mRNA (Illumina).

value: prostate cancer cell line

tag: cell line

value: 160mg/kg Depo-testosterone (daily), plus doxycycline


title: F4553_E4S3

value: M


title: BasL_048


title: Pediatric acute lymphoblastic leukemia [16-231]

first: Daniel

institute: University of Montreal

description:
16-231
Strand-specific RNA-seq


title: F4553_E3S5

value: Control (Eed fl/fl)


title: Xenograft-C4-2-tet-shRB-DOX-T_tumor3


title: Pediatric acute lymphoblastic leukemia [16-008]

description:
16-008
Strand-specific RNA-seq


title: BasL_050


title: BasL_051


title: F4499_E1S3

source_name: E13.5 Control mouse hypothalamus

value: F


title: BasL_047


title: Pediatric acute lymphoblastic leukemia [16-230]

description:
16-230
Strand-specific RNA-seq


title: Pediatric acute lymphoblastic leukemia [16-229]

description:
16-229
Strand-specific RNA-seq


title: Xenograft-C4-2-tet-shRB-DOX-Veh_tumor4

value: Corn oil (daily), plus doxycycline


title: BasL_046


title: F4497_E4S2


title: Xenograft-C4-2-tet-shRB-DOX-Veh_tumor3


title: Embryonic day E18.5 Hypothalamus, Eed-cKO, F0589_E1S4

description: ScRNA-seq run from E18.5 Mus musculus hypothalamus

data_processing:
Base calling was performed using the Illumina BaseSpace application FASTQ Generation v1.0.0
Bam files and count matrices per sample were generated using the Illumina BaseSpace application SureCell RNA Single-Cell v1.2.0, using STAR (v2.5.2b) to align the cDNA reads to the mm10 genome (the second read mate, R2) and Samtools (v1.3) to append cell barcodes to aligned reads (derived from the first read mate, R1). Cell barcodes and UMIs in R1 are corrected and counted via the aforementioned Illumina Application.
Counts per cell in each sample were downloaded from Illumina Base Space and concatenated into a single count matrix to generate counts.txt.gz.
Genome_build: mm10
Supplementary_files_format_and_content: counts.txt contains the read counts for each gene in each cell (rows are genes, columns are cells). The cell names are in the format: {sample_prefix}_{treatment}_{sex}_{day}_{}_{cell_barcode}.
Supplementary_files_format_and_content: sample_meta.txt contains meta-data related to each sample. Each row corresponds to a particular read pair, matches to the prefix of the fq files. Contains information about the sex (M for male, or F for female), the treatment (WT for wild-type, or KO for Eed-cKO), and the corresponding fastq file read mates; as well as checksums to make sure data is downloaded properly.

source_name: Embryonic day E18.5 Hypothalamus

extract_protocol:
The hypothalamus of control and Eed-cKO embryos was dissected out in ice-cold RPMI-1640 medium (cat.no. 11530586, Thermo Fisher Scientific, Waltham, MA, USA). The dissected hypothalamis were further divided into 2-4 pieces before cell dissociation for single cell isolation using Papain Dissociation System (cat no. LK003150, Worthington Biochemical Corporation, Lakewood, NJ, USA). The tissues were incubated with papain solution at +37°C for 60 min. Isolated single cells were re-suspended in ice-cold 1xPBS, 0.1% BSA, to a final concentration of 2,500 cells/μl (+/- 10%). Cells were checked for viability using a Bio-Rad TC10 automated cell counter (Bio-Rad, Hercules, CA, USA).
Single cells and barcode beads were encapsulated into droplets using Bio-Rad ddSEQ Single-Cell Isolator for cell lysis and barcoding (cat.no. 12004336, Bio-Rad, Hercules, CA, USA). Subsequently, RNA-seq libraries were generated using Illumina SureCell WTA 3' Library Prep Kit for the ddSEQ System (6 cartridge version, cat.no. 20014280, Illumina, San Diego, CA, USA). Libraries were assessed for quality, using 1µl of undiluted cDNA, on an Agilent Technology 2100 Bioanalyzer using an Agilent High Sensitivity DNA chip (cat.no. 5067-4626, Agilent, Santa Clara, CA, USA) to determine fragment size and yield. Samples were stored at -20℃ until sequencing.
Libraries were pooled according to their molar concentration (yield), fragment size, and the unique Nextera i7 indices (8bp). Each sequencing run consisted of four samples with different Nextera i7 indices. The libraries were sequenced on an Illumina NextSeq500 system, using NextSeq 500/550 High Output Kit v2.5 (150 Cycles, cat.no. 20024907, Illumina, San Diego, CA, USA), paired-end read type and Single-Index.

tag: genotype

value: Eed-cKO (Eed fl/fl; Sox1-Cre/+)

value: hypothalamus


title: Pediatric acute lymphoblastic leukemia [16-227]

description:
16-227
Strand-specific RNA-seq

source_name: Pediatric acute lymphoblastic leukemia


title: Embryonic day E18.5 Hypothalamus, Control, f4530_E2S4


title: Pediatric acute lymphoblastic leukemia [16-226]

description:
16-226
Strand-specific RNA-seq


title: Embryonic day E18.5 Hypothalamus, Control, F4530_E2S1


title: Embryonic day E18.5 Hypothalamus, Control, F4520_E2S1


title: Xenograft-C4-2-tet-shRB-DOX-T_tumor2


title: Xenograft-C4-2-tet-shRB-DOX-Veh_tumor1


title: Pediatric acute lymphoblastic leukemia [16-225]

description:
16-225
Strand-specific RNA-seq

value: Female


title: Xenograft-C4-2-tet-shRB-DOX-Veh_tumor2


title: BasL_043

source_name: Breast cancer tissue

value: Breast cancer

value: BasL


title: Pediatric acute lymphoblastic leukemia [16-223]

description:
16-223
Strand-specific RNA-seq

value: Male


title: Xenograft-C4-2-tet-shRB-T_tumor4

description: Xenograft_C4-2-tet-shRB_samples_count_table.txt

value: 160mg/kg Depo-testosterone (daily)


title: BasL_044

value: Negative


title: BasL_041


title: Xenograft-C4-2-tet-shRB-DOX-T_tumor1


title: Pediatric acute lymphoblastic leukemia [16-215]

description:
16-215
Strand-specific RNA-seq


title: BasL_045


title: Xenograft-C4-2-tet-shRB-T_tumor3


title: Embryonic day E18.5 Hypothalamus, Control, F4650_E2S4


title: Pediatric acute lymphoblastic leukemia [16-210]

description:
16-210
Strand-specific RNA-seq


title: Xenograft-C4-2-tet-shRB-T_tumor2


title: BasL_039


title: Embryonic day E18.5 Hypothalamus, Eed-cKO, F0652_E5S1


title: BasL_042

value: Positive


title: BasL_040


title: Embryonic day E18.5 Hypothalamus, Control, F4690_E3S2


title: Pediatric acute lymphoblastic leukemia [16-207]

description:
16-207
Strand-specific RNA-seq

value: bone marrow


title: Xenograft-C4-2-tet-shRB-T_tumor1


title: Pediatric acute lymphoblastic leukemia [16-205]

description:
16-205
Strand-specific RNA-seq


title: Embryonic day E18.5 Hypothalamus, Eed-cKO, F0582_E2S5


title: Xenograft-C4-2-tet-shRB-Veh_tumor4

value: Corn oil (daily)


title: BasL_037


title: Embryonic day E18.5 Hypothalamus, Eed-cKO, F0589_E1S7


title: Pediatric acute lymphoblastic leukemia [16-204]

description:
16-204
Strand-specific RNA-seq


title: BasL_038


title: Xenograft-C4-2-tet-shRB-Veh_tumor3

value: prostate cancer cell line


title: Xenograft-C4-2-tet-shRB-Veh_tumor2


title: BasL_036


title: Embryonic day E18.5 Hypothalamus, Control, F4690_E3S4


title: Embryonic day E18.5 Hypothalamus, Eed-cKO, F0571_E3S2


title: BasL_035


title: Pediatric acute lymphoblastic leukemia [16-201]

description:
16-201
Strand-specific RNA-seq

value: peripheral blood


title: BasL_034


title: P130-C4-2-tet-shRB-Dox_rep2

description:
C42shRb8_p130_dox.bw
C42shRb8_p130_dox_peaks.narrowPeak.gz

data_processing:
The sequence quality of raw reads was checked by FastQC (version 0.11.9).
Raw reads were mapped to the hg19 human genome using bwa (version 0.7.9a) with aln and samse sub-commands.
Samtools (version 1.2) was used to convert sam files to bam format.
MACS2 (version 2.1.0) was used to call peak on the bam files.
bedGraph files generated from MACS2 were converted into bigwig files with UCSC tools (version 369).
Genome_build: hg19
Supplementary_files_format_and_content: bw, narrowPeak

source_name: C4-2 cell

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were constructed using the SMARTer ThruPLEX DNA-Seq Prep Kit (Takara Bio USA).

tag: medium condition

value: In RPMI 1640 medium with 5% charcoal-stripped FBS (CSS)

value: 0.05μg/ml doxycycline for 3 days

tag: chip antibody

value: anti-RBL2 (Cell Signaling)


title: Embryonic day E18.5 Hypothalamus, Eed-cKO, F0652_E8S3

value: F

tag: tissue


title: BasL_033


title: Pediatric acute lymphoblastic leukemia [16-199]

description:
16-199
Strand-specific RNA-seq


title: P130-C4-2-tet-shRB-Dox_rep1


title: Pediatric acute lymphoblastic leukemia [16-192]

description:
16-192
Strand-specific RNA-seq


title: BasL_032


title: Pediatric acute lymphoblastic leukemia [16-189]

description:
16-189
Strand-specific RNA-seq


title: Embryonic day E18.5 Hypothalamus, Control, F4650_E1S1

value: Control (Eed fl/fl)


title: Embryonic day E18.5 Hypothalamus, Eed-cKO, F0582_E7S8

value: Eed-cKO (Eed fl/fl; Sox1-Cre/+)

value: hypothalamus


title: Pediatric acute lymphoblastic leukemia [16-202]

description:
16-202
Strand-specific RNA-seq

value: Female


title: P130-C4-2-tet-shRB-Ctrl_rep2

description:
C42shRb8_p130.bw
C42shRb8_p130_peaks.narrowPeak.gz

value: untreated


title: BasL_031

value: Breast cancer

value: BasL


title: P130-C4-2-tet-shRB-Ctrl_rep1


title: Pediatric acute lymphoblastic leukemia [16-186]

description:
16-186
Strand-specific RNA-seq

value: Male


title: Embryonic day E18.5 Hypothalamus, Control, F4520_E2S4


title: Embryonic day E18.5 Hypothalamus, Control, F4650_E2S8

value: M


title: MYC-C4-2-DHT_rep2

description:
C42_MYC_DHT.bw
C42_MYC_DHT_peaks.narrowPeak.gz

value: 10nM dihydrotestosterone (DHT) for 4 hours

value: anti-MYC (Cell Signaling)


title: Pediatric acute lymphoblastic leukemia [16-200]

description:
16-200
Strand-specific RNA-seq

value: bone marrow


title: Pediatric acute lymphoblastic leukemia [16-182]

description:
16-182
Strand-specific RNA-seq


title: BasL_028

value: Negative


title: Xenograft-C4-2-tet-shRB-Veh_tumor1

value: prostate cancer cell line

value: Corn oil (daily)


title: Embryonic day E18.5 Hypothalamus, Control, F4520_E4S8


title: BasL_030


title: BasL_029


title: BasL_027


title: Pediatric acute lymphoblastic leukemia [16-179]

description:
16-179
Strand-specific RNA-seq


title: MYC-C4-2-Veh_rep2

description:
C42_MYC_Veh.bw
C42_MYC_Veh_peaks.narrowPeak.gz

value: In RPMI 1640 medium with 5% charcoal-stripped FBS (CSS)


title: Embryonic day E18.5 Hypothalamus, Eed-cKO, F0571_E3S3


title: Pediatric acute lymphoblastic leukemia [16-177]

description:
16-177
Strand-specific RNA-seq


title: Embryonic day E18.5 Hypothalamus, Control, F4520_E2S3

value: F


title: Embryonic day E18.5 Hypothalamus, Eed-cKO, F0571_E3S4


title: Pediatric acute lymphoblastic leukemia [16-176]

description:
16-176
Strand-specific RNA-seq


title: MYC-C4-2-Veh_rep1


title: Embryonic day E18.5 Hypothalamus, Control, F4520_E2S2

value: Control (Eed fl/fl)


title: BasL_026


title: Pediatric acute lymphoblastic leukemia [16-174]

description:
16-174
Strand-specific RNA-seq


title: RB-C4-2-DHT_rep1

description:
RB_C42_DHT.bw
RB_C42_DHT_peaks.narrowPeak.gz

value: anti-RB (Cell Signaling)


title: Pediatric acute lymphoblastic leukemia [16-171]

description:
16-171
Strand-specific RNA-seq


title: MYC-C4-2-DHT_rep1


title: Pediatric acute lymphoblastic leukemia [16-068]

description:
16-068
Strand-specific RNA-seq


title: BasL_025


title: Pediatric acute lymphoblastic leukemia [16-164]

description:
16-164
Strand-specific RNA-seq


title: BasL_024

value: Positive


title: RB-C4-2-Veh_rep2

description:
RB_C42_VEH.bw
RB_C42_VEH_peaks.narrowPeak.gz


title: RB-C4-2-Veh_rep1


title: Pediatric acute lymphoblastic leukemia [16-162]

description:
16-162
Strand-specific RNA-seq


title: AR-C4-2-tet-shRB-Dox-DHT_rep2

description:
C42shRb8_AR_dox_DHT.bw
C42shRb8_AR_dox_DHT_peaks.narrowPeak.gz

value: 0.05μg/ml doxycycline for 3 days, then treat 10nM dihydrotestosterone (DHT) for 4 hours

value: anti-AR (abcam)


title: Pediatric acute lymphoblastic leukemia [16-158]

description:
16-158
Strand-specific RNA-seq


title: Embryonic day E18.5 Hypothalamus, Control, F4650_E2S7

value: hypothalamus


title: BasL_022

value: Breast cancer

value: BasL


title: Embryonic day E18.5 Hypothalamus, Control, F4520_E4S6

value: M


title: Embryonic day E18.5 Hypothalamus, Eed-cKO, F0652_E8S7

value: Eed-cKO (Eed fl/fl; Sox1-Cre/+)


title: AR-C4-2-tet-shRB-Dox-DHT_rep1


title: RB-C4-2-DHT_rep2

value: 10nM dihydrotestosterone (DHT) for 4 hours


title: BasL_021


title: BasL_020


title: Embryonic day E18.5 Hypothalamus, Eed-cKO, F0582_E7S3


title: BasL_019


title: Embryonic day E18.5 Hypothalamus, Eed-cKO, F0589_E1S3


title: AR-C4-2-tet-shRB-Dox-Veh_rep2

description:
C42shRb8_AR_dox.bw
C42shRb8_AR_dox_peaks.narrowPeak.gz

value: 0.05μg/ml doxycycline for 3 days


title: Embryonic day E18.5 Hypothalamus, Eed-cKO, F0588_E7S2


title: Embryonic day E18.5 Hypothalamus, Eed-cKO, F0588_E7S5


title: AR-C4-2-tet-shRB-Dox-Veh_rep1


title: BasL_023

value: Negative


title: BasL_018


title: Embryonic day E18.5 Hypothalamus, Eed-cKO, F502_E6S1


title: BasL_017


title: Pediatric acute lymphoblastic leukemia [16-144]

description:
16-144
Strand-specific RNA-seq

value: bone marrow

value: Male


title: Embryonic day E18.5 Hypothalamus, Eed-cKO, F0582_E7S7


title: BasL_016


title: AR-C4-2-tet-shRB-Ctrl-DHT_rep1

description:
C42shRb8_AR_DHT.bw
C42shRb8_AR_DHT_peaks.narrowPeak.gz

value: prostate cancer cell line

value: In RPMI 1640 medium with 5% charcoal-stripped FBS (CSS)


title: LR7-34

city: Tartu

first: Vijayachitra

last: Modhukur

address: L. Puusepa 8

country: Estonia

institute: University of Tartu

data_processing:
Adapted from Hagemann-Jensen et al. Small-seq for single-cell small-RNA sequencing. Nature Protocols.2018;13(10):2407-24.
Genome_build: hg38

source_name: Uterine fluid

extract_protocol:
RNA extraction using Guanidium based RLT plus Buffer
Hagemann-Jensen et al. Small-seq for single-cell small-RNA sequencing. Nature Protocols.2018;13(10):2407-24.

value: Uterine fluid

tag: study group

value: Recurrent implantation failure

tag: age

tag: bmi


title: Embryonic day E18.5 Hypothalamus, Eed-cKO, F0652_E5S6

tag: Sex

value: F

tag: timepoint


title: LR7-33

description: The data was removed during DESeq2  normalization


title: Pediatric acute lymphoblastic leukemia [16-152]

city: Montreal

description:
16-152
Strand-specific RNA-seq

tag: diagnosis

value: Female


title: Embryonic day E18.5 Hypothalamus, Control, F4530_E2S3

value: Control (Eed fl/fl)


title: AR-C4-2-tet-shRB-Ctrl-Veh_rep1

description:
C42shRb8_AR_Veh.bw
C42shRb8_AR_Veh_peaks.narrowPeak.gz

value: untreated

value: anti-AR (abcam)


title: LR7-32


title: BasL_014

description: Gene expression data from human breast cancer

value: Breast cancer

tag: citbcmst subtype

value: BasL


title: Pediatric acute lymphoblastic leukemia [16-155]

description:
16-155
Strand-specific RNA-seq

tag: gender


title: AR-C4-2-tet-shRB-Ctrl-Veh_rep2


title: AR-C4-2-tet-shRB-Ctrl-DHT_rep2


title: Embryonic day E18.5 Hypothalamus, Control, F4520_E4S5

value: M

value: hypothalamus


title: FOXA1-C4-2-tet-shRB-Dox_rep2

description:
FOXA1_C42_shRB8_DOX.bw
FOXA1_C42_shRB8_DOX_peaks.narrowPeak.gz

value: In RPMI 1640 medium with reduced steroid hormone [8% charcoal-stripped FBS (CSS) plus 2% regular FBS]

value: 0.05μg/ml doxycycline for 3 days

value: anti-FOXA1 (EMD Millipore)


title: FOXA1-C4-2-tet-shRB-Dox_rep1


title: LR7-30


title: FOXA1-C4-2-tet-shRB-Ctrl_rep2

description:
FOXA1_C42_shRB8.bw
FOXA1_C42_shRB8_peaks.narrowPeak.gz


title: LR7-29


title: BasL_013

tag: sn status

value: Negative

tag: ihc er status


title: Embryonic day E18.5 Hypothalamus, Control, F4690_E3S3


title: Embryonic day E18.5 Hypothalamus, Control, F4650_E1S2


title: BasL_010


title: FOXA1-C4-2-tet-shRB-Ctrl_rep1

tag: cell type

value: prostate cancer cell line

tag: treatment


title: BasL_011


title: Embryonic day E18.5 Hypothalamus, Control, F4520_E4S7


title: LR7-28


title: LR7-31


title: LR7-26


title: LR7-27


title: Embryonic day E18.5 Hypothalamus, Control, F4690_E3S1


title: BasL_009