title: wild-type_polyclonal_rep1

status: Public on Feb 18 2022

city: Freiburg

first: Yong

last: Li

address: Hugstetter Str. 49

department: Institute of Genetic Epidemiology

institute: Medical Center - University of Freiburg

data_processing:
Illumina Casava 1.8 software used for basecalling.
Remove reads containing adapters. Remove reads containing N > 10% (N represents the base cannot be determined). Remove reads containing low quality (Qscore<= 5) base which is over 50% of the total base.
Reads were then aligned to mouse reference genome GRCm38 using STAR 2.7.3a with default parameters.
RSEM v1.3.1 was used to calculate gene expression values.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample.

source_name: mIMCD-3 wild-type cells

growth_protocol: Cells were cultured with DMEM:F12 (LONZA, cat.no. BE12-719F), fetal bovine serum was added to a final concentration of 10% and penicillin/streptomycin (Sigma, P0781) with a final concentration of 1%.  Subculturing of cells was performed twice a week in a 1:10 ratio. Cells were maintained in a humidified incubator at 37°C and 10% CO2.

extract_protocol:
RNA Isolation was performed 4 days after full confluency according to manufacturer’s protocol using the RNeasy Plus Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were harvested using 0.25 % Trypsin-EDTA (Gibco)

value: polyclonal


title: wild-type_polyclonal_rep2

type: SRA

country: Germany

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: cell line

tag: treatment


title: wild-type_polyclonal_rep3


title: wild-type_polyclonal_rep4


title: HeyA8 siNT_3AB 1 nM (48 hours)

status: Public on Feb 16 2022

city: Chicago

first: Marcus

last: Peter

state: IL

address: 303 East Superior Street, Lurie 6-123

country: USA

institute: Northwestern University Feinberg School of Medicine

data_processing:
Sequenced reads were mapped to hg38 human genome using STAR aligner
raw counts were calculated by HTSeq
Genome_build: hg38
Supplementary_files_format_and_content: Txt file with raw read counts for each gene in each sample.

organism: Homo sapiens

source_name: Derived from from HEY-T30 ATCC CRL-3257

extract_protocol:
Total RNA was isolated with QIAGEN miRNeasy kit; dnase digestion was done
The quality and quantity of the RNA samples was checked using an Agilent bio-analyzer. RNA-SEQ libraries were generated using Illumina TruSEQ TotalRNA kits using the Illumina provided protocol.

treatment_protocol: PC# or HeyA8 were plated in 6-well plates and transfected with 1 nM of siRNA using RNAiMax. Total RNA was isolated afetr 24 or 48hrs.

tag: tissue

value: Ovaries

tag: treatment/infection

value: Transfected with 1 nM siNT1 for 48hrs

tag: genotype

value: wt


title: B16_P_44_CD8

status: Public on Mar 07 2022

city: Baltimore

first: Elana

middle: Judith

last: Fertig

state: MD

address: 670 W. Baltimore Street, 3rd floor

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore

data_processing:
Illumina Casava1.7 software used for basecalling.
Transcript counts calculated from Fastq files using Kallisto.
Transcript counts summarized to gene counts using tximport.
Abundance (logTPM) and estimated count measures from tximport normalized using TMM and filtered for expressed genes.
Genome_build: hg19
Supplementary_files_format_and_content: txt files include normalized values for each Sample.
Supplementary_files_format_and_content: txt files include filtered logTPM values for each Sample.

source_name: Tumor

extract_protocol:
Tumor infiltrating immune cells (TIICs) were obtained from a non-necrotic tumor piece at approximately 2 cm in diameter that could be spared for research purpose after the clinical specimens were prioritized and were dissected by pathologist. RPMI-1640 media were used to resuspend all the cells after disruption and homogenization. The cell suspension was filtered with a 70μm cell strainer and a layer of mononuclear cells that contained TIICs were then isolated using the Ficoll density gradient centrifugation with Ficoll-Paque™ PLUS (Cytiva) as described 39. TIICs were washed three times using 40 ml of the complete RPMI media each time. After the final wash with the RPMI media, isolated TIICs were cryopreserved in the liquid nitrogen freezer or subjected to cell sorting. Peripheral blood mononuclear cells were obtained from patient’s whole blood using the Ficoll-Paque™ PLUS gradient centrifugation to serve as the FACS staining control. TIICs and peripheral blood mononuclear cells were stained with the Zombie Green viability dye (Biolegend), anti-CD4-PE-CF594 (Biolegend), anti-CD8-APC (Biolegend), anti-CD19-PE (Biolegend), and anti-CD11b-BV421 (Biolegend) antibodies. After sorting with the BD FACSAria IIu Cell Sorter (Biosciences), bulk tumor RNA was extracted by using the All Prep DNA/RNA Micro Kit (Qiagen) according to the manufacturer’s instruction and sent to a commercial vendor (BGI Genomics) for whole transcriptomic RNA sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell type

tag: arm

value: A

tag: os

value: High

value: Low

value: Y


title: B3_P_26_CD4

value: B


title: HeyA8 siCAG_3AB 1 nM (48 hours)

source_name: Derived from from HEY-T30 ATCC CRL-3259

value: Transfected with 1 nM siCAG for 48hrs


title: Aorta_EC

status: Public on Mar 01 2022

city: Aarhus

first: Lin

last: Lin

address: Høegh-Guldbergs Gade 10

department: Department of Biomedicine

country: Denmark

institute: Aarhus University

data_processing: Cell Ranger 3.0.2 (10x Genomics) was used to process the raw sequencing data of polyA RNA libraries.

molecule: polyA RNA

organism: Sus scrofa domesticus

source_name: Aorta

growth_protocol: The aorta near to lung was separated and washed with PBS. 5 mL of digestion buffer was injected into the sealed aorta, and left the aorta into water bath at 37 ℃ for 30 mins. Next, the aorta was taken out, and digestion buffer was flowed out. The medium was transferred into a 15 mL Falcon tube and centrifuged at 300 x g for 5 min. The collected cells were washed with 5 mL PBS and centrifuged for culturing within 5 mL PAEC medium.

extract_protocol:
One leaf of pig lung was used for perfusion with PBS from the big vessel on top. After perfusion, the lung was squeezed and made the PBS out. 15 ml of the digestion buffer containing 0.1% collagenase II, 0.25% collagenase IV, 75 μl DNAse I in KnockOutTM DMEM medium was injected into the sealed pig lung. The opening site was closed by sealing clip, and leaved the bag into water bath at 37℃ for 30 mins. Next, the lung was taken out and the digestion buffer was flowed away. 20 mL of PBS was used to wash the lung for 3 times, and the medium was collected for filtering with 100 μm cell strainer afterwards. The medium was transferred into 10 mL Falcon tube and centrifuged at 300 x g for 5 mins. The cells were washed with 10 mL PBS and centrifuged for culturing into 5 mL PAEC medium (DMEM with 10% fetal calf serum, 1 x MEM-NEAA, 1 mM Sodium Pyruvate, 1 x Glutamax, 1 x Penicillin/Streptomycin) in CO2 incubator.
The ployA RNA libraries were prepared following the manufacturer’s instructions of GemCode Single Cell 3’ Gel Bead and Library kit (v3 Chemistry ) from 10x Genomics, Inc. (Pleasanton, CA).

value: Aorta


title: HeyA8 siNT_3AB 1 nM (24 hours)

source_name: Derived from from HEY-T30 ATCC CRL-3253

value: Transfected with 1 nM siNT1 for 24hrs


title: B1_P_26_CD11b


title: HeyA8 siMxy_3AB 1 nM (48 hours)

source_name: Derived from from HEY-T30 ATCC CRL-3258

value: Transfected with 1 nM siGGGGGC for 48hrs


title: HeyA8  mock (48 hours)

source_name: Derived from from HEY-T30 ATCC CRL-3256

value: Mock treated for 48hrs


title: PC3 mock (24 hours)

source_name: ATCC CRL-1435

value: Prostate

value: Mock treated for 24hrs


title: HeyA8 siCAG_3AB 1 nM (24 hours)

source_name: Derived from from HEY-T30 ATCC CRL-3255

value: Transfected with 1 nM siCAG for 24hrs


title: HeyA8 siMxy_3AB 1 nM (24 hours)

source_name: Derived from from HEY-T30 ATCC CRL-3254

value: Transfected with 1 nM siGGGGGC for 24hrs


title: PC3 siMxy_3AB 1 nM (48 hours)


title: SubfomicalOrgan_3

status: Public on Jan 21 2022

data_processing:
Cell Ranger 3.0.2 (10x Genomics) was used to process the raw sequencing data of polyA RNA libraries. The sequencing data from  nuclear RNA libraries was filtered, and the gene expression matrix was obtained using DNBelab C Series scRNA analysis software (MGI).
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: matrix files

molecule: nuclear RNA

extract_protocol:
The fresh tissues were collected, immediately placed on ice, and processed within 30 minutes.
The ployA RNA libraries were prepared following the manufacturer’s instructions of GemCode Single Cell 3’ Gel Bead and Library kit (v3 Chemistry ) from 10x Genomics, Inc. (Pleasanton, CA). The nuclear RNA library was operated on a DNBelab C4 device (MGI).

value: Subfomical Organ


title: SubfomicalOrgan_2


title: HeyA8 mock (24 hours)

source_name: Derived from from HEY-T30 ATCC CRL-3252

value: Ovaries


title: Spleen_2

value: Spleen


title: PC3 siNT_3AB 1 nM (48 hours)

value: Transfected with 1 nM siNT1 for 48hrs

value: wt


title: PC3 mock (48 hours)


title: PC3 siCAG_3AB 1 nM (48 hours)


title: OVoLT_4

value: OVoLT


title: Spleen_1


title: PC3 siCAG_3AB 1 nM (24 hours)


title: PC3 siMxy_3AB 1 nM (24 hours)


title: Spleen_3


title: OVoLT_3


title: SubfomicalOrgan_1


title: OVoLT_1


title: OVoLT_2


title: Liver_2

value: Liver


title: Liver_1


title: Kidney_4

value: Kidney


title: Kidney_2


title: PC3 siNT_3AB 1 nM (24 hours)


title: Liver_3


title: Kidney_1


title: Heart_4

value: Heart


title: Kidney_3


title: Heart_5


title: Heart_3


title: Heart_2


title: Heart_1


title: Cerebellum_8

value: Cerebellum


title: Cerebellum_7


title: Cerebellum_4


title: Cerebellum_3


title: Cerebellum_5


title: Cerebellum_2


title: Area_Postrema_3

value: Area Postrema


title: Cerebellum_1


title: Cerebellum_6


title: Area_Postrema_2


title: Area_Postrema_1


title: Pig-Brain

source_name: Pig-Brain

value: Brain


title: Pig-Intestine

source_name: Pig-Intestine

value: Intestine


title: PBMCs, YUNANCY, scRNA-seq

status: Public on Jan 13 2022

city: Stanford

first: Aaron

middle: M

last: Newman

state: California

address: 265 Campus Drive

department: Institute for Stem Cell Biology and Regenerative Medicine, Department of Biomedical Data Science

institute: Stanford University

description: Sample was prepared using the Chromium Single Cell 5’ kit, sequenced on Illumina NovaSeq, and aligned using Cell Ranger v5.0.1

data_processing:
Raw scRNA-seq reads were barcode-deduplicated and aligned to the hg38 reference genome using Cell Ranger v3.1.0 for the single-cell discovery cohort or Cell Ranger v5.0.1 otherwise, yielding sparse digital count matrices.
Sparse digital count matrices were analyzed to identify cell types and cellular states using Seurat v3.1.5, v3.2.1, or v4.0.1.
Outlier cells were identified and removed based on the following criteria: (i) >25% mitochondrial content or (ii) cells with less than 100 or greater than 1,500-3,000 expressed genes, depending on sample-level distributions.
Following normalization (NormalizeData) and variable feature identification (FindVariableFeatures with n = 2,000 features), we applied FindIntegrationAnchors (dims = 1:30) to identify anchors and IntegrateData (with default parameters) to perform batch correction.
Once integrated, we applied principal component analysis (PCA) and Uniform Manifold Approximation and Projection (UMAP) using the 2,000 most variable genes and the top 30 principal components. For unsupervised analysis, FindClusters was applied to identify cell types and cellular states with a resolution parameter set to 3.
Genome_build: hg38
Supplementary_files_format_and_content: *_counts.txt: Matrices with gene counts.
Supplementary_files_format_and_content: *_expression.txt: Matrices with normalized gene expression data for every gene and every cell following Seurat integration.
Supplementary_files_format_and_content: *_metadata.txt: Tab-delimited text files including cell barcodes, cell states, and corresponding patient IDs.

source_name: Peripheral blood

extract_protocol:
Single-cell suspensions from PBMC samples were obtained and prepared to a concentration of 700-1,200 viable cells/μl using a hemacytometer (Thermo Fisher Scientific, Waltham, MA) or Coulter Counter (Beckman Coulter Life Sciences, Indianapolis, IN) for cell counting, per the manufacturers’ instructions.
Chromium Single Cell 5’ Library Construction Kit (10x Genomics, Pleasanton, CA) following the manufacturer’s protocol.
Single-cell suspensions underwent library preparation for scRNA-seq using the 5’ transcriptome kit (10x Genomics, Pleasanton, CA) per the manufacturer’s instructions. Complementary DNA libraries were sequenced on a NovaSeq instrument (Illumina, San Diego, CA) with 2 x  92 bp paired-end reads targeting a mean of 20k reads per cell.

tag: patient

value: YUNANCY

value: Blood

tag: diagnosis

value: Melanoma

tag: Sex

value: Female

tag: age

tag: immunotherapy type

value: Combination

tag: highest irae grade

tag: cohort

tag: sequencing batch

value: B


title: Pig-Lung

source_name: Pig-Lung

value: Lung


title: Pig-Spleen

source_name: Pig-Spleen

value: Spleen


title: PBMCs, YUALOE, scRNA-seq

value: YUALOE

value: Male


title: Pig-Retina

source_name: Pig-Retina

value: Retina


title: PBMCs, YUHONEY, scRNA-seq

value: YUHONEY


title: Pig-Adipose-S

source_name: Pig-Adipose-S

value: Adipose-S


title: Pig-Adipose-V

source_name: Pig-Adipose-V

value: Adipose-V


title: PBMCs, YUVARDO, scRNA-seq

description: Sample was prepared using the Chromium Single Cell 5’ kit, sequenced on Illumina NovaSeq, and aligned using Cell Ranger v3.1.0

value: YUVARDO

value: Single-cell discovery

value: A


title: PBMCs, YUTORY, scRNA-seq

value: YUTORY


title: PBMCs, YUTHEA, scRNA-seq

value: YUTHEA

value: Blood


title: PBMCs, YUTAUR, scRNA-seq

value: YUTAUR

value: Melanoma


title: PBMCs, YUROD, scRNA-seq

value: YUROD

value: Combination


title: PBMCs, YUPIXEL, scRNA-seq

value: YUPIXEL


title: PBMCs, YUKEND, scRNA-seq

value: YUKEND

value: Female


title: PBMCs, YUHERN, scRNA-seq

value: YUHERN


title: PBMCs, YUGRUS, scRNA-seq

value: YUGRUS


title: PBMCs, YUFUB, scRNA-seq

value: YUFUB

value: Male


title: PBMCs, YUFURL, scRNA-seq

value: YUFURL


title: PBMCs, YUENZO, scRNA-seq

value: YUENZO

value: Single-cell discovery


title: PBMCs, YUCARD, scRNA-seq

value: YUCARD

value: A


title: siMxy-1 48hr

status: Public on Dec 31 2021

description: sequenced everything above 140nts

data_processing:
Sequenced reads were mapped to hg38 human genome using Tophat and bowtie2
raw counts were calculated by HTSeq
normalization and differential expression were calculated by DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: text sheet of raw counts for each sample and differential gene expression results

source_name: Derived from from Hey cells, ref: Buick, R. N., Pullano, R., and Trent, J. M. (1985). Comparative properties of five human ovarian adenocarcinoma cell lines. Cancer Res. 45: 3668 – 3676.

extract_protocol:
Total RNA was isolated with QIAGEN miRNeasy kit; dnase digestion was done
The quality and quantity of the RNA samples was checked using an Agilent bio-analyzer. RNA-SEQ libraries were generated using Illumina TruSEQ TotalRNA kits using the Illumina provided protocol.
RNA-Seq; sequenced on an Illumina HiSEQ4000 using Illumina provided reagents and protocols

treatment_protocol: HeyA8 cells were transfected with 10 nM of siRNA; total RNA was harvested 24 or 48 hrs after transfection

value: Parental ovarian cancer cell line HeyA8

value: Ovaries

tag: transfection

value: 10 nM siGGGGGC

tag: time point


title: siMxy-2 48hr

description: sequenced everything above 140nts

tag: cell line


title: Pig-PBMC

source_name: Pig-PBMC

tag: tissue

value: PBMC


title: Pig-Liver

source_name: Pig-Liver

value: Liver


title: si34a-1 48hr

description: sequenced everything above 140nts

value: 10 nM siGGCAGU


title: si34a-2 48hr

description: sequenced everything above 140nts


title: siMxy-2 24hr

description: sequenced everything above 140nts


title: siMxy-1 24hr

description: sequenced everything above 140nts


title: siNT1 S2'OM-1 48hr

description: sequenced everything above 140nts

value: 10 nM siNT1 S2'OM


title: siNT1 S2'OM-2 48hr

description: sequenced everything above 140nts


title: siNT1 S2'OM-2 24hr

description: sequenced everything above 140nts


title: DNAmeth_16h

status: Public on Dec 24 2021

city: Wuhan

first: Baibai

last: Gao

address: 1 Shizishan Street, Hongshan District

country: China

institute: National Key Laboratory of Crop Genetic Improvement

library_source: genomic

data_processing:
The sequence quality of the whole-genome bisulfite sequencing (WGBS) libraries was evaluated using FastQC, and the adapter sequences and low-quality reads were filtered using Trimmomatic
The cleaned reads were then mapped to the MH63 reference genome using BatMeth
The uniquely mapped reads were used for further analysis. Individual cytosines with coverage of at least 3 were considered for methylation-level calling.
The DNA methylation level of each cytosine was obtained by dividing the depth of methylated reads by the total coverage of individual cytosines
Genome_build: MH63
Supplementary_files_format_and_content: bigWig files

molecule: genomic DNA

organism: Oryza sativa

source_name: MH63 mature leaf

growth_protocol: Rice [Oryza sativa L. ssp. indica cv. Minghui 63 (MH63)] seeds were sown on May 19, 2017 in a paddy field. At 20 days after germination, the seedlings were transplanted into a paddy field of Huazhong Agricultural University at Wuhan, China, and grown under normal agricultural conditions. In the paddy field, the plants were transplanted at a density of one plant per 15 × 30 cm area.

extract_protocol:
Genomic DNA was extracted using a DNeasy plant mini kit according to the manufacturer’s instructions (QIAGEN, 69104).
Bisulfite conversion of DNA was conducted using the EZ DNA Methylation-GoldTM kit (ZYMO, D5005), and the bisulfite-treated DNA libraries were constructed using the Illumina TruSeq DNA sample prep kit, following the manufacturers’ instructions.

treatment_protocol: Fresh samples are frozen using liquid nitrogen.

value: mature leaf

tag: development stage

value: mature leaves harvested at 16:00 at floral induction stage

tag: cultivar

value: Minghui 63


title: CD71+ HSC/MPPs [SLX.17054.i729_i522]

status: Public on Dec 17 2021

city: Cambridge

first: Elisa

last: Laurenti

address: Jeffrey Cheah Biomedical Centre

department: Haematology

country: United Kingdom

institute: University of Cambridge

description:
SLX.17054.i729_i522
polyA mRNA

data_processing:
Reads were mapped to the Homo sapiens genome (EMSEMBL GRCh38 Release 81) and ERCC sequences using GSNAP (version 2015-09-29) with parameters: -A sam –B 5 –t 24 –n 1 –Q –N 1.
HTseq-count (PMID: 25260700) was used to count reads mapped to each gene, with parameters: –s no.
Genome_build: GRCh38
Supplementary_files_format_and_content: HTSeq_count.txt: HTSeq counts/gene counts.

source_name: Hematopoietic stem cells/ multipotent progenitor cells

extract_protocol: Single CD71+ phenotypic HSC/MPPs (CD19-CD34+CD38-CD45RA-CD71+CD34lo) from CD34+ enriched PB MNCs were directly sorted into lysis buffer, then libraries were prepared using the SmartSeq2 protocol.

value: Healthy

value: Adult

tag: marker

tag: cell type

value: HSC/MPPs


title: CD71+ HSC/MPPs [SLX.17054.i729_i521]

description:
SLX.17054.i729_i521
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i729_i520]

description:
SLX.17054.i729_i520
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i729_i515]

description:
SLX.17054.i729_i515
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i729_i516]

description:
SLX.17054.i729_i516
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i729_i518]

description:
SLX.17054.i729_i518
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i729_i513]

description:
SLX.17054.i729_i513
polyA mRNA


title: H3K27me3_ChIP_8h_rep1

data_processing:
Trimmomatic fitered the raw reads
ChIP-seq reads were aligned to the MH63 genome assembly using bwa mem
Data were filtered using the SAMTOOLS MAPQ30 and filter the duplication reads
peaks were called using MACS.2.2.1 with narrow parameters
Genome_build: MH63
Supplementary_files_format_and_content: bigWig by deepTools bamCoverage

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
ChIP-DNA was extracted with phenol:chloroform:isoamyl alcohol (Sigma–Aldrich, P3803), precipitated with ethanol, and resuspended in TE buffer. ChIP DNA libraries were prepared using an NEBNext® Ultra™ II DNA library prep kit for Illumina® (New England BioLabs, E7645). Briefly, ChIP DNA was end-repaired, ligated with an adaptor, and followed by 6–10 cycles of PCR amplification, per the manufacturer’s guidelines. Next, library fragments of 250–650 bp were selected using AMPure XP beads (Beckman, A63881). Finally, the DNA fragments were sequenced using an Illumina HiSeq X Ten system (paired-end 150-bp reads)

treatment_protocol: Tissues were cross-linked with 1% formaldehyde for 20 min and quenched with 0.2 M glycine at room temperature.

value: mature leaves harvested at 8:00 at floral induction stage

tag: chip antibody


title: CD71+ HSC/MPPs [SLX.17054.i729_i517]

description:
SLX.17054.i729_i517
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i728_i518]

description:
SLX.17054.i728_i518
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i728_i522]

description:
SLX.17054.i728_i522
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i728_i517]

description:
SLX.17054.i728_i517
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i728_i516]

description:
SLX.17054.i728_i516
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i728_i520]

description:
SLX.17054.i728_i520
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i728_i513]

description:
SLX.17054.i728_i513
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i727_i522]

description:
SLX.17054.i727_i522
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i728_i515]

description:
SLX.17054.i728_i515
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i727_i521]

description:
SLX.17054.i727_i521
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i727_i520]

description:
SLX.17054.i727_i520
polyA mRNA


title: siNT1 S2'OM-1 24hr

description: sequenced everything above 140nts


title: CD71+ HSC/MPPs [SLX.17054.i727_i516]

description:
SLX.17054.i727_i516
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i727_i513]

description:
SLX.17054.i727_i513
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i726_i520]

description:
SLX.17054.i726_i520
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i728_i521]

description:
SLX.17054.i728_i521
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i726_i522]

description:
SLX.17054.i726_i522
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i726_i516]

description:
SLX.17054.i726_i516
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i726_i513]

description:
SLX.17054.i726_i513
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i726_i517]

description:
SLX.17054.i726_i517
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i724_i518]

description:
SLX.17054.i724_i518
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i724_i520]

description:
SLX.17054.i724_i520
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i724_i521]

description:
SLX.17054.i724_i521
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i724_i522]

description:
SLX.17054.i724_i522
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i726_i515]

description:
SLX.17054.i726_i515
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i724_i516]

description:
SLX.17054.i724_i516
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i724_i515]

description:
SLX.17054.i724_i515
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i723_i522]

description:
SLX.17054.i723_i522
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i724_i513]

description:
SLX.17054.i724_i513
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i723_i521]

description:
SLX.17054.i723_i521
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i727_i518]

description:
SLX.17054.i727_i518
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i727_i517]

description:
SLX.17054.i727_i517
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i727_i515]

description:
SLX.17054.i727_i515
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i723_i517]

description:
SLX.17054.i723_i517
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i723_i515]

description:
SLX.17054.i723_i515
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i723_i516]

description:
SLX.17054.i723_i516
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i723_i513]

description:
SLX.17054.i723_i513
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i726_i518]

description:
SLX.17054.i726_i518
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i726_i521]

description:
SLX.17054.i726_i521
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i722_i522]

description:
SLX.17054.i722_i522
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i722_i521]

description:
SLX.17054.i722_i521
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i722_i520]

description:
SLX.17054.i722_i520
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i722_i518]

description:
SLX.17054.i722_i518
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i724_i517]

description:
SLX.17054.i724_i517
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i722_i513]

description:
SLX.17054.i722_i513
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i721_i522]

description:
SLX.17054.i721_i522
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i721_i521]

description:
SLX.17054.i721_i521
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i721_i518]

description:
SLX.17054.i721_i518
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i722_i515]

description:
SLX.17054.i722_i515
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i722_i516]

description:
SLX.17054.i722_i516
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i721_i517]

description:
SLX.17054.i721_i517
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i721_i515]

description:
SLX.17054.i721_i515
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i723_i518]

description:
SLX.17054.i723_i518
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i722_i517]

description:
SLX.17054.i722_i517
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i723_i520]

description:
SLX.17054.i723_i520
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i720_i522]

description:
SLX.17054.i720_i522
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i721_i516]

description:
SLX.17054.i721_i516
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i720_i521]

description:
SLX.17054.i720_i521
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i720_i520]

description:
SLX.17054.i720_i520
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i721_i513]

description:
SLX.17054.i721_i513
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i720_i515]

description:
SLX.17054.i720_i515
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i720_i516]

description:
SLX.17054.i720_i516
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i720_i518]

description:
SLX.17054.i720_i518
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i719_i522]

description:
SLX.17054.i719_i522
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i719_i521]

description:
SLX.17054.i719_i521
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i719_i520]

description:
SLX.17054.i719_i520
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i721_i520]

description:
SLX.17054.i721_i520
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i719_i516]

description:
SLX.17054.i719_i516
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i719_i515]

description:
SLX.17054.i719_i515
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i719_i517]

description:
SLX.17054.i719_i517
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i718_i522]

description:
SLX.17054.i718_i522
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i718_i518]

description:
SLX.17054.i718_i518
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i718_i517]

description:
SLX.17054.i718_i517
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i718_i520]

description:
SLX.17054.i718_i520
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i718_i521]

description:
SLX.17054.i718_i521
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i718_i515]

description:
SLX.17054.i718_i515
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i718_i513]

description:
SLX.17054.i718_i513
polyA mRNA


title: 9081858 Fast baseline

status: Public on Mar 31 2022

city: Toronto

first: Mohit

last: Kapoor

state: Ontario

address: 60 Leonard Ave

country: Canada

institute: Schroeder Arthritis Institute

data_processing:
Demultiplexing of .bcl files and conversion into Fastq files is performed, followed by quality assessment for each sample using the bcl2fastq conversion tool (v2.19.1.403).
UMI tags are extracted from raw files using UMI-tools software.
The first round of alignment using Bowtie1 is performed against human miRBase (v22.1), and then unaligned reads from this step are aligned to the human reference genome to obtain reads falling in miRBase chromosomal coordinates only.
Reads are collapsed according to associated UMI to remove PCR amplification bias.
UMI-based counts for each miRNA in a sample are generated from both alignments and summed to generate a final table of miRNA expression levels for each sample.
Inference is performed on the raw counts using a negative binomial regression estimated by quasi-likelihood with trended dispersion and normalized by total aligned sequences.
Genome_build: GRCh38
Supplementary_files_format_and_content: 1 combined excel spreadsheet (.xlsx) with two tabs having raw miRNA count values, one with baseline samples and other for 4-year follow-up samples.

source_name: plasma

growth_protocol: No growth

extract_protocol:
RNA is extracted from 200 µL of human plasma using the QIAcube following Qiagen's instructions for sample setup of the miRNeasy Serum/Plasma Advanced Kit (Cat #217204).
miRNA libraries are prepared using QIAseq miRNA Library Kit optimized for biofluid samples (QIAseq miRNA, Cat # 331505). Individual libraries are quantified using a fluorometric high-sensitivity dsDNA assay (Denovix). Library quality is assessed on a high sensitivity DNA chip on the Agilent 2100 Bioanalyzer system (Agilent).
Libraries are multiplexed and sequenced on Illumina NextSeq550 to generate 75bp SE UMI-tagged reads.

treatment_protocol: No treatment

tag: progressor

value: Fast

value: baseline


title: CD71+ HSC/MPPs [SLX.17054.i716_i522]

description:
SLX.17054.i716_i522
polyA mRNA

tag: diagnosis


title: CD71+ HSC/MPPs [SLX.17054.i718_i516]

description:
SLX.17054.i718_i516
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i716_i518]

description:
SLX.17054.i716_i518
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i716_i521]

description:
SLX.17054.i716_i521
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i716_i517]

description:
SLX.17054.i716_i517
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i720_i517]

description:
SLX.17054.i720_i517
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i716_i520]

description:
SLX.17054.i716_i520
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i716_i516]

description:
SLX.17054.i716_i516
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i716_i513]

description:
SLX.17054.i716_i513
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i712_i517]

description:
SLX.17054.i712_i517
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i719_i518]

description:
SLX.17054.i719_i518
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i712_i508]

description:
SLX.17054.i712_i508
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i712_i507]

description:
SLX.17054.i712_i507
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i712_i504]

description:
SLX.17054.i712_i504
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i712_i506]

description:
SLX.17054.i712_i506
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i712_i502]

description:
SLX.17054.i712_i502
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i711_i508]

description:
SLX.17054.i711_i508
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i711_i517]

description:
SLX.17054.i711_i517
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i711_i506]

description:
SLX.17054.i711_i506
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i719_i513]

description:
SLX.17054.i719_i513
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i711_i504]

description:
SLX.17054.i711_i504
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i711_i502]

description:
SLX.17054.i711_i502
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i710_i506]

description:
SLX.17054.i710_i506
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i710_i505]

description:
SLX.17054.i710_i505
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i711_i505]

description:
SLX.17054.i711_i505
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i710_i517]

description:
SLX.17054.i710_i517
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i710_i507]

description:
SLX.17054.i710_i507
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i710_i503]

description:
SLX.17054.i710_i503
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i710_i502]

description:
SLX.17054.i710_i502
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i710_i508]

description:
SLX.17054.i710_i508
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i716_i515]

description:
SLX.17054.i716_i515
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i709_i507]

description:
SLX.17054.i709_i507
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i709_i517]

description:
SLX.17054.i709_i517
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i709_i505]

description:
SLX.17054.i709_i505
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i710_i504]

description:
SLX.17054.i710_i504
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i709_i508]

description:
SLX.17054.i709_i508
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i708_i517]

description:
SLX.17054.i708_i517
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i708_i508]

description:
SLX.17054.i708_i508
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i712_i505]

description:
SLX.17054.i712_i505
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i709_i506]

description:
SLX.17054.i709_i506
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i708_i506]

description:
SLX.17054.i708_i506
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i712_i503]

description:
SLX.17054.i712_i503
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i709_i503]

description:
SLX.17054.i709_i503
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i711_i507]

description:
SLX.17054.i711_i507
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i708_i507]

description:
SLX.17054.i708_i507
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i709_i504]

description:
SLX.17054.i709_i504
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i708_i505]

description:
SLX.17054.i708_i505
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i707_i502]

description:
SLX.17054.i707_i502
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i709_i502]

description:
SLX.17054.i709_i502
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i711_i503]

description:
SLX.17054.i711_i503
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i706_i507]

description:
SLX.17054.i706_i507
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i706_i508]

description:
SLX.17054.i706_i508
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i708_i504]

description:
SLX.17054.i708_i504
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i708_i503]

description:
SLX.17054.i708_i503
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i706_i506]

description:
SLX.17054.i706_i506
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i707_i517]

description:
SLX.17054.i707_i517
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i707_i508]

description:
SLX.17054.i707_i508
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i707_i505]

description:
SLX.17054.i707_i505
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i707_i504]

description:
SLX.17054.i707_i504
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i705_i517]

description:
SLX.17054.i705_i517
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i706_i517]

description:
SLX.17054.i706_i517
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i707_i507]

description:
SLX.17054.i707_i507
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i705_i508]

description:
SLX.17054.i705_i508
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i705_i506]

description:
SLX.17054.i705_i506
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i706_i505]

description:
SLX.17054.i706_i505
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i706_i504]

description:
SLX.17054.i706_i504
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i706_i503]

description:
SLX.17054.i706_i503
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i707_i506]

description:
SLX.17054.i707_i506
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i708_i502]

description:
SLX.17054.i708_i502
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i706_i502]

description:
SLX.17054.i706_i502
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i705_i503]

description:
SLX.17054.i705_i503
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i705_i507]

description:
SLX.17054.i705_i507
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i707_i503]

description:
SLX.17054.i707_i503
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i705_i505]

description:
SLX.17054.i705_i505
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i705_i504]

description:
SLX.17054.i705_i504
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i705_i502]

description:
SLX.17054.i705_i502
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i704_i517]

description:
SLX.17054.i704_i517
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i704_i506]

description:
SLX.17054.i704_i506
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i704_i508]

description:
SLX.17054.i704_i508
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i704_i505]

description:
SLX.17054.i704_i505
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i704_i507]

description:
SLX.17054.i704_i507
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i704_i503]

description:
SLX.17054.i704_i503
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i704_i502]

description:
SLX.17054.i704_i502
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i703_i517]

description:
SLX.17054.i703_i517
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i720_i513]

description:
SLX.17054.i720_i513
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i703_i506]

description:
SLX.17054.i703_i506
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i703_i508]

description:
SLX.17054.i703_i508
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i703_i507]

description:
SLX.17054.i703_i507
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i703_i504]

description:
SLX.17054.i703_i504
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i703_i503]

description:
SLX.17054.i703_i503
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i703_i505]

description:
SLX.17054.i703_i505
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i702_i517]

description:
SLX.17054.i702_i517
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i702_i508]

description:
SLX.17054.i702_i508
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i702_i507]

description:
SLX.17054.i702_i507
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i702_i506]

description:
SLX.17054.i702_i506
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i702_i503]

description:
SLX.17054.i702_i503
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i702_i502]

description:
SLX.17054.i702_i502
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i702_i504]

description:
SLX.17054.i702_i504
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i701_i507]

description:
SLX.17054.i701_i507
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i701_i517]

description:
SLX.17054.i701_i517
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i701_i508]

description:
SLX.17054.i701_i508
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i704_i504]

description:
SLX.17054.i704_i504
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i701_i506]

description:
SLX.17054.i701_i506
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i701_i503]

description:
SLX.17054.i701_i503
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i702_i505]

description:
SLX.17054.i702_i505
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i701_i505]

description:
SLX.17054.i701_i505
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i701_i504]

description:
SLX.17054.i701_i504
polyA mRNA


title: CD71+ HSC/MPPs [SLX.17054.i701_i502]

description:
SLX.17054.i701_i502
polyA mRNA


title: E15.5_M_Snf5_Ctrl2

status: Public on Dec 15 2021

city: Sagamihara

first: Toshiaki

last: Ito

state: Kanagawa

address: 1-15-1, Kitasato, Minami-ku

department: Biosciences

country: Japan

institute: Kitasato university

data_processing:
Mapped by Tophat v 2.2.1
FPKM were calculated using Cuffmerge v2.1.1 and Cuffdiff v2.1.1
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Samples

extract_protocol:
RNA was harvested using RNeasy Micro Kit (Qiagen, Venlo, Netherland). The cDNA was synthesized from 10 ng of total RNA and was amplified with the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech, Palo Alto, CA).
RNA-seq libraries were prepared via the Nextera XT Kit (Illumina) using the amplified cDNA (150 pg for each sample).

treatment_protocol: Germ cells were sorted by Oct4-EGFP

tag: strain background

tag: genotype/variation

value: Snf5 Ctrl

tag: Sex

value: male

value: Germ cells sorted by using Oct4-EGFP


title: E15.5_M_Snf5_CKO2

value: Snf5 CKO


title: E15.5_M_Snf5_CKO1


title: E15.5_F_Snf5_CKO2

value: female


title: E15.5_F_Snf5_Ctrl2


title: CD71+ HSC/MPPs [SLX.17054.i703_i502]

description:
SLX.17054.i703_i502
polyA mRNA

tag: age


title: Gpr126_WT_3

status: Public on Nov 30 2021

city: Madrid

first: Jose Luis

last: de la Pompa

address: Melchor Fernández Almagro 3

country: Spain

institute: Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC).

data_processing:
Sequencing data were processed with RTA v1.18.66.3.
FastQ files for each sample were obtained using bcl2fastq v2.20.0.422 software (Illumina).
Sequencing adapter contaminations were removed using Cutadapt.
Reads were mapped on transcriptome and gene expression quantified using RSEM.
RSEM-estimated raw gene counts were normalized with Limma-Voom.
Genome_build: GRCm38 assembly, Ensembl gene build 91.
Supplementary_files_format_and_content: matrix_table.txt: Tab-delimited matrix table with normalized counts in each sample, for genes expressed with at least 1 CPM in at least 4 samples.

source_name: Heart ventricle

growth_protocol: Experiments were conducted with 4 pools of Gpr126+/+ (WT) and Gpr126Δ7/Δ7 (KO) embryonic ventricles at E12.5.

extract_protocol:
Total RNA was extracted from 4 pools of Gpr126+/+ (WT) and 4 pools of Gpr126Δ7/Δ7 (KO) mouse embryonic ventricles (4 ventricles per pool) at E12.5. The tissue was homogenized in TRI ReagentTM Solution (Invitrogen, AM9738) using steel beads in the TissueLyser LT Adapter for 5 minutes at 50 Hz. For RNA extraction, the PicoPureTM RNA Isolation kit (Applied Biosystems, KIT0204) was used according to the manufacturer’s instructions. RNA was quantified and its purity checked with a NanoDrop ND-1000 spectrophotometer (Thermo Scientific). RNA integrity was verified with an Agilent 2100 Bioanalyzer instrument (Agilent Technologies).
cDNA libraries were prepared with the NEBNext Ultra RNA Library Prep Kit (New England Biolabs).
Libraries were sequenced on a HiSeq 2500 system (Illumina) to generate 60 base single reads.

tag: genotype

value: WT

tag: developmental stage

value: Ventricle


title: Gpr126_WT_2


title: Gpr126_KO_5

value: Gpr126 KO


title: SC31-PDX-E2

status: Public on Dec 09 2021

city: Duarte

first: Shiuan

last: Chen

state: CA

address: 1500 E Duarte Rd

department: Cancer Biology-BRI

institute: City of Hope National Medical Center

data_processing:
Raw sequencing data were processed using the 10x Genomics Cell Ranger pipeline to generate FASTQ files
Sequences were aligned to hg19_and_mm10 genome to gene expression count using CellRanger's default settings
Gene expression level of Refseq coding genes were quantified using CellRanger (V3.1.0)'s default settings
Genome_build: hg19_and_mm10
Supplementary_files_format_and_content: text files containing the raw gene expression count

source_name: breast cancer

growth_protocol: Surgically resected chest wall metastasis tumor pieces were implanted into the 4th mammary fat pat of female NOD-scid/IL2Rγ-/- (NSG) mice, that were 6-8 weeks old, to establish PDX lines.

extract_protocol:
Cells were then loaded onto the Chromium Controller (10x Genomics) targeting 2000–5000 cells per lane.
The Chromium v2 single cell 3′ RNA-seq reagent kit (10x Genomics) was used to process samples into scRNA-seq libraries according to the manufacturer’s protocol. Libraries were sequenced with a Hiseq 2500 instrument (Illumina) with a depth of 50k–100k reads per cell.

treatment_protocol: After tumor volume reached approximately 200mm3, mice were randomized and implanted with an Placebo or E2 (1mg) or DHT (12.5mg) pellet on their backside. These treatments lasted 7 days for experiments on single cell analysis.

value: tumor

tag: treatment

value: SC31-PDX + E2 treatment


title: Gpr126_KO_3


title: Gpr126_WT_4


title: H-20820 P

status: Public on Nov 18 2021

city: Durham

first: Benjamin

last: Devlin

state: North Carolina

address: 210 Research Drive

department: Psychology and Neuroscience

institute: Duke University

description:
placenta_raw_counts.csv
placenta_tpm.csv

data_processing:
Adapter sequences were trimmed using Trimmomatic 0.38
FastQ files were merged across lanes and aligned using Bowtie2 against the Bowtie GRCh38_noalt_as human genome index.
Counts were generated using the Homo_sapiens.GRCh38.104 gtf from Ensembl.
Placenta and Brain samples were processed separately. Transcripts per million (TPM) was calculated using custom R script on the raw counts and used for all subsequent analyses
Gene inclusion was determined using EdgeR (threshold of 1)
Genome_build: hg38
Supplementary_files_format_and_content: comma separated value file including TPM values for each Sample
Supplementary_files_format_and_content: comma separated value file with raw gene counts for every gene and every sample

source_name: Fetal placental tissue

extract_protocol:
RNA was isolated using TRIzol RNA extraction reagent chloroform extraction
RNA libraries were prepared for sequencing using an Illumina TrueSeq RNA Exome kit and standard Illumina protocol

value: Fetal placental tissue

tag: fetal sex

value: Male

tag: log10 maternal decidual triglycerides

tag: brain serotonin (ng/ml)

tag: placental serotonin (ng/ml)


title: H-21027 P

tag: tissue


title: H-20819 P

value: Female


title: SC31-PDX-Placebo

value: SC31-PDX - E2 treatment


title: H-20748 P


title: H-20818 P


title: Gpr126_KO_2


title: Gpr126_WT_1


title: E15.5_M_Snf5_Ctrl1


title: H-20815 P


title: H-20442 P


title: E15.5_F_Snf5_CKO1


title: H-20381 P


title: H-19764 P


title: H-19931 P


title: H-20336 P


title: H-20385 P


title: E15.5_F_Snf5_Ctrl1


title: H-19125 P


title: H-19856 P


title: Gpr126_KO_4


title: H-19283 P


title: H-19600 P


title: H-18496 P


title: H-19124 P


title: H-17612 P


title: H-17410 P


title: H-17606 P


title: H-17417 P


title: H-17392 P


title: H-17394 P


title: H-17254 P


title: H-17255 P


title: H-16737 P


title: H-16849 P


title: H-16682 P


title: H-17257 P


title: H-17420 P


title: H-16681 P


title: H-17259 P


title: H-16730 P


title: H-16680 P


title: H-20820 B

description:
brain_raw_counts.csv
brain_tpm_TRIM_MBX.csv

source_name: Fetal brain tissue

value: Fetal brain tissue


title: H-21027 B


title: H-20818 B


title: H-20815 B


title: H-20819 B


title: H-20442 B


title: H-20748 B


title: H-20385 B


title: H-19931 B


title: H-19764 B


title: H-20381 B


title: H-19600 B


title: H-19856 B


title: H-20336 B


title: H-19283 B


title: H-19125 B


title: H-18496 B


title: H-19124 B


title: H-17612 B


title: H-17420 B


title: H-17606 B


title: H-17417 B


title: H-17394 B


title: H-17410 B


title: H-17259 B


title: H-17392 B


title: H-17257 B


title: H-17254 B


title: H-17255 B


title: H-16737 B


title: H-16681 B


title: H-16730 B


title: H-16849 B


title: H-16682 B


title: HT29_selumetinib_CCNB1_-ve_2

status: Public on Sep 12 2021

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

institute: The Babraham Institute

data_processing:
After adapter and quality trimming using Trim Galore (v0.5.0), RNAseq data was mapped to human genome GRCh38 using HISAT2 v2.1.0 by the Babraham Institute Bioinformatics Facility. Mapped data was imported into SeqMonk v1.47.0 (https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/) and normalised to total read count.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimed text files showing log2 values per gene for each sample

extract_protocol:
Cells grown in monolayers were harvested by trypsinization, centrifuged (300 x g for 5 minutes) and washed once with PBS prior to lysis in TRI reagent. For glyoxal fixation and staining, cell pellets were resuspended in 100 µL glyoxal fixation solution (2.8 ml water, 0.79 ml 100% ethanol, 0.31 ml 40% glyoxal and 30 µl acetic acid, pH 4-5) supplemented with 1:25 RNasin Plus RNase inhibitor (Promega, N261B) and incubated for 15 minutes on ice. The cell suspension was diluted in 1 mL PBS supplemented with 1:100 RNasin Plus RNase inhibitor and centrifuged at 2000  x g for 3 minutes at 4°C; the supernatant was discarded. All further centrifugation steps were carried out at similar conditions. Cells were permeabilized by adding 100 µL ice-cold methanol (100%, v/v) with 1:25 RNasin Plus RNase inhibitor drop by drop while gently vortexing cells, and incubated on ice for 30 minutes. The cell suspension was then diluted in 1 mL 1% bovine serum albumin (BSA) (Sigma, A7906) in PBS and centrifuged. For CCNB1 labelling, cells were incubated in 100 uL primary antibody (in this case CST 12231S - 1:200) diluted in 1% BSA in PBS with 1:25 RNasin Plus RNase inhibitor for 1 hour on ice. Following incubation, cells were washed once in 1mL 1% BSA in PBS. Secondary antibody staining was carried out in 100 μL Alexa Fluor 488 donkey anti-rabbit antibody (ThermoFisher Scientific, A21206) diluted 1:1000 in 1% BSA in PBS with 1:25 RNasin Plus RNase inhibitor and incubated on ice for 30 minutes in dark. Cells were washed once in 1 mL 1% BSA in PBS and the cell pellet resuspended in 200 µL 1% BSA in PBS with 1:100 RNasin Plus RNase inhibitor. Cells were incubated in 1 µg/mL DAPI. For collection of glyoxal-fixed cells that were stained with CCNB1 and flow sorted, cell suspension was pelleted by centrifugation at 2000 x g for 3 minutes at 4°C.
Cell pellets were lysed in 1 mL TRI reagent (Sigma, T9424) and mixed until a homogeneous lysate was obtained. For phase separation, 0.2 mL chloroform was added, mixed thoroughly and allowed to stand for 10 minutes prior to centrifugation at 12,000 × g for 15 min at 4 °C. The upper aqueous phase containing RNA was transferred to a fresh tube, and 0.5 mL 2-propanol per mL original lysate was then added, samples mixed and allowed to stand for 10 minutes. Samples were centrifuged (12,000 × g for 10 min at 4 °C), and RNA pellets washed with 1 mL 75% (v/v) ethanol (7,500 × g for 5 min at 4 °C). Pellets were air-dried for 5-10 minutes and resuspended in RNase-free water.
RNA prepared from flow sorted cells was quality controlled on a Bioanalyzer 2100 (Agilent) using RNA Pico 6000 chips (Agilent 5067-1513). mRNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB E7760S) with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490S), following the protocol provided by the manufacturer with the exception that two successive 0.9x AMPure purifications were performed on the final amplified libraries. All libraries were amplified using 12-14 PCR cycles. Library quality was assessed on a Bioanalyzer 2100 using High Sensitivity DNA chips (Agilent 5067-4626) and quantification performed with a KAPA Library Quantification Kit (Roche, KK4844). Libraries were sequenced by the Babraham Institute Next Generation Sequencing Facility on an Illumina HiSeq2500 in Rapid Run 50bp Single End mode.

value: colorectal cancer cell line

tag: growth media

value: RPMI-1640 + 1uM selumetinib (24 hours)

tag: cell line

tag: fixed/unfixed

value: Glyoxal fixed, stained for CCNB1 and sorted


title: H-16680 B


title: HT29_untreated_CCNB1_+ve_1

tag: cell type


title: HT29_selumetinib_CCNB1_-ve_1


title: P7_eWAT_SVF

status: Public on Aug 23 2021

first: Rana

middle: K

last: Gupta

address: Carmichael Building, 300 North Duke St.

department: Duke Molecular Physiology Institute

description: SVF from Postnatal day 7 eWAT

data_processing:
Data was analyzed using Cell Ranger (v3.1.0) to perform demultiplexing, aligning reads,
Cells with less than 200 genes and genes expressed less than 3 cells were removed; cells with mitochondria proportion greater than 25% were removed; cells with ribosome proportion less than 5% were removed; cells with abnormally high counts were removed.
Cells from different developmental stages were integrated and normalized using SCTransform from Seurat (v4.0.3)
Cell clusters were identified with the resolution of 1 using Seurat (v4.0.3) and were annotated with cell-specific marker genes
Genome_build: mm10
Supplementary_files_format_and_content: The processed data files contain the filtered barcodes, matrix, and genes.

source_name: epidydimal white adipose tissue

extract_protocol:
Both SVF and mesothelial cells were isolated from gonadal WAT as previously described (Hepler et al. Elife 2017).  The library was generated according to manufacturer's instructions (10X Genomics).
According to 10x Genomics’ protocol, sequenced R1=26cycles R2=58cycles, i7=8cycles

tag: strain

value: Postnatal day 7


title: HT29_selumetinib_CCNB1_+ve_2


title: HCT116 DicerKO.rep2

status: Public on Aug 22 2021

description: Single Read

data_processing:
Processing was done with the SPOROS pipeline: https://github.com/ebartom/SPOROS
Reads were trimmed with Trim_galore to remove all standard Illumina adapters and trimmed reads less than 6 bp in length
Reads were demultiplexed according to adaptor barcodes to separate into the individual samples listed below.
6 bp UMIs were removed with Trim_galore (4N before pull-down sequence and 2N after).  This resulted in the deposited fastq files.
Cleaned reads were sorted and uniq -c used to identify the total counts of all unique sequences
Reads were blasted against a set of processed miRNAs and the top blast hit retained as a putative source for the read.
Reads with hits against artificial and adapter sequences are removed from the table, as well as reads with a summed count < total number of samples
Genome_build: hg38
Supplementary_files_format_and_content: Excel sheet with read, seed (bp 2-7), cell viability based on seed, raw read counts for each sample, and putative source based on blast

source_name: Narry Kim, South Korea

extract_protocol:
Cells were subjected to pull down with a GW182 peptide bound to anti-FLAG M2 Magnetic beads RNA at a size of 19-35 nt was gel extracted and used to generate library
The quality and quantity of the RNA samples was checked using an Agilent bio-analyzer. Small RNA-SEQ libraries were generated using Illumina small RNA SEQ kits using the Illumina provided protocol containing library fragments 140-160 bp in size.
RNA-Seq; sequenced on an Illumina HiSEQ4000 using Illumina provided reagents and protocols

treatment_protocol: Cells were subjected to Ago pull down and smRNA Seq

value: Dicer knock out

value: Colon


title: HT29_untreated_CCNB1_-ve_2


title: HCT116 DroshaKO.rep2

description: Single Read

value: Drosha knock out


title: HT29_untreated_CCNB1_+ve_2


title: HT29_selumetinib_CCNB1_+ve_1


title: HT29_untreated_CCNB1_-ve_1


title: HCT116 WT.rep2

description: Single Read

source_name: ATCC CCL-247

value: WT


title: HCT116 DicerKO.rep1

description: Single Read


title: HCT116 DroshaKO.rep1

description: Single Read


title: HCT116 WT.rep1

description: Single Read


title: RH4_si-SCR_3

status: Public on Aug 03 2021

city: Rome

first: Francesca

last: Rossi

state: RM

address: Piazzale Aldo Moro, 5

department: Dipartimento di Biologia e Biotecnologie "Charles Darwin"

country: Italy

institute: Sapienza University of Rome

description: Total cell lysate

data_processing:
Raw sequencing data processing (format conversion and demultiplexing) was performed using Bcl2Fastq version 2.20.0.422.
Due to a laser intensity drop in the last cycles of the sequencing reaction, the last 20 based of reverse reads exhibited low Phred quality scores. Trimmomatic software was employed to cut reverse reads down to 130 nucleotides; a second Trimmomatic run, with parameters ILLUMINACLIP:path/to/adapter:2:30:10:8:true  MINLEN:35, allowed to remove adapter sequences (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4103590/).
Alignment to human GRCh38 genome and Ensembl 99 transcriptome was performed using STAR aligner version 2.5.2b with parameters --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --outSAMattrIHstart 0 --outSAMtype BAM SortedByCoordinate  --outFilterType BySJout –outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04.
Reads mapping to each gene were counted using htseq-count software with parameters -m intersection-strict -f bam -s reverse. Read count files were combined into a count matrix file, which was given as input to edgeR R package, after removing genes with a CPM value (Counts Per Million) less than 1 in at least 3 samples.
Gene-level FPKM values were calculated using rpkm function from the edgeR package.
Genome_build: GRCh38
Supplementary_files_format_and_content: FPKM values of expressed genes in each sample.

source_name: Alveolar rhabdomyosarcoma cell line (RH4)

growth_protocol: RH4 cells are cultured in DMEM high-glucose supplemented with 10% fetal bovine serum, 2 mM L-glutamine and 1x penicillin-streptomycin.

extract_protocol:
Total RNA was extracted with Direct-zol RNA Miniprep kit (Zymo Research) with a 30-minute DNase-I treatment according to the manufacturer’s protocol.
TruSeq Stranded mRNA kit

treatment_protocol: RH4 cells were transfected with 30 nM (final concentration) siRNA (Dharmacon) and Dharmafect-1 Transfection Reagent (Dharmacon) according to the manufacturer’s instructions. The medium was replaced 24 h after the transfection and cells were harvested after another 24 h.

value: Alveolar rhabdomyosarcoma cancer cells


title: C2C12-DamN44Ibeta-Rep2

status: Public on Aug 02 2021

city: La Jolla

first: Juliana

middle: S

last: Capitanio

address: 10010 N Torrey Pines Rd

department: molecular and call biology laboratory

institute: The Salk Institute for Biological Studies

data_processing:
Library strategy: DamID-seq
Basecalls performed using CASAVA version 1.8.2
Alignment was done using STAR (v02.02.01) against hg19 for both DAmID-seq and RNA-seq datasets.
DamID peaks were found by merging replicates and using the findPeaks program in HOMER with the following options "-style histone -o auto -size 2500 -minDist 2500 -tbp 0 -inputtbp 0 -fragLength 1 -inputFragLength 1 -F 2 -C 0 -ntagThreshold 100" using the Dam alone DamID experiments as background.
For RNA-seq experiments, reads were aligned with STAR against hg19 genome and HOMER was used to create tag directories and annotation. Reads Per Kilobase of exon per milion mapped reads were calculated using HOMER (http://homer.salk.edu/homer/) across annotated gene exons (RefSeq).
For filtering, all reads which uniquely map and has MAPQ>10 were selected for downstream analysis. Duplicates were removed using PICARD tools. The peaks overlapping blacklisted region of genome were also removed.
HOMER (v4.11) was used to process alignment files to generate normalized bedGraphs and bigwigs for the UCSC Genome Browser. For other coverage measurements, DeepTools, v3.1.3 (BamCoverage) was used.
Genome_build: hg19, mm10
Supplementary_files_format_and_content: bed files: (1) chr (2) start (3) end (4) peakName (5) peak score (6) strand.
Supplementary_files_format_and_content: RNA-seq: FPKM text file

source_name: C2C12 myotubes

growth_protocol: For NPC-DamID assay, cells were grown in 6 well plates with 70-80% confluency. Hela cells were grown in 5% FBS in DMEM media at 37 deg. C. IMR90 cells were grown in DMEM media supplemented with 15% FBS and 1X non-essential amino acid stock at 37 deg. C. mouse C2C12 cells were cultured in DMEM media supplemented with 20% FBS. In order to differentiate them to myotubes, C2C12 cells were grown to 100% conflency and then switched to differentiation media (DMEM with 2% horse serum). After 8 days myotubes were obtained for the experiemnts. U2OS cells were cultured in DMEM media suppplemented with 10% FBS.

extract_protocol:
Cells after NPC-DamID assay were scraped from 6 well plates and used for genomic DNA isolation. Qiagen gDNA isolation kit was used using the manufacturer’s protocol. DNA was eluted in 500 µl of water or elution buffer. The DNA was then concentrated using a rotatory evaporator if eluted in water otherwise precipitated with ethanol to dissolve in 50 μl of water so that concentration is about 500 ng/µl.
The genomic DNA was prepared for library preparation following the published protocol for DamID-seq(Marshall et al., 2016).  The library for DNA sequencing was prepared using Roche Kapa Hyper-prep DNA kit following the manufacturer’s protocol. The quality of the DNA libraries were checked using Tapestation bioanalyzer and Quibit. The libraries were usually sequenced with single-end 50 bp sequencing.

treatment_protocol: The media was washed 3X with 1X PBS at RT. After washing, cells were incubated with permeabilization buffer for 3 mins followed by digitonin permeabilization for 5 min at RT. Digitonin concentration ranged from 20-30 μg/ml for semi-permeabilization. The concentration was optimized for different cells through checking immunofluorescence for antibodies against lamin in semi-permeabilized cells. The digitonin was then washed by 3X wash with transport buffer for 3 min each. Then transport buffer with cocktail of proteins and SAM required for the assay was added, 5 units of Dam or Dam-fused proteins, 4 µM NTF2, Importinα (1 μM), 7.5 μM SAM. For assays with RanGDP/GTP, RanGDP (5 μM), and an energy regenerating system (2 mM GTP, 0.1 mM ATP, 4 mM creatine phosphate, and 20 µ/ml creatine kinase) was also added. The cells were incubated with transport mix for 20 min at RT with occasional gentle rocking to mix the reagents. After 20 min, the cells were washed with 1X PBS for 3X, 3 min each.

tag: protein

value: C2C12 myotubes


title: RH4_si-SCR_1

description: Total cell lysate


title: HeLa-RNA-Rep1

data_processing:
Basecalls performed using CASAVA version 1.8.2
Alignment was done using STAR (v02.02.01) against hg19 for both DAmID-seq and RNA-seq datasets.
DamID peaks were found by merging replicates and using the findPeaks program in HOMER with the following options "-style histone -o auto -size 2500 -minDist 2500 -tbp 0 -inputtbp 0 -fragLength 1 -inputFragLength 1 -F 2 -C 0 -ntagThreshold 100" using the Dam alone DamID experiments as background.
For RNA-seq experiments, reads were aligned with STAR against hg19 genome and HOMER was used to create tag directories and annotation. Reads Per Kilobase of exon per milion mapped reads were calculated using HOMER (http://homer.salk.edu/homer/) across annotated gene exons (RefSeq).
For filtering, all reads which uniquely map and has MAPQ>10 were selected for downstream analysis. Duplicates were removed using PICARD tools. The peaks overlapping blacklisted region of genome were also removed.
HOMER (v4.11) was used to process alignment files to generate normalized bedGraphs and bigwigs for the UCSC Genome Browser. For other coverage measurements, DeepTools, v3.1.3 (BamCoverage) was used.
Genome_build: hg19, mm10
Supplementary_files_format_and_content: bed files: (1) chr (2) start (3) end (4) peakName (5) peak score (6) strand.
Supplementary_files_format_and_content: RNA-seq: FPKM text file

source_name: HeLa

extract_protocol: RNA was extracted using Trizol (Ambion) and column purified using RNeasy kit (Qiagen). RNA-Seq strand-specific polyA+ libraries were generated from total RNA with polyA+ selection of mRNA using the TruSeq Stranded RNA LT Kit (Illumina).

value: HeLa

value: HeLa cell line


title: HeLa-RNA-Rep2


title: IMR90-RNA-Rep2

value: IMR90 cell line


title: HeLa-RNA-Rep3


title: IMR90-RNA-Rep1


title: C2C12-Dam-Rep1

value: Dam


title: C2C12-DamN44Ibeta-Rep1


title: C2C12-Dam-Rep2


title: Islets-DamN44Ibeta-Rep1

source_name: Pancreatic islets

value: Pancreatic islets


title: Islets-DamN44Ibeta-Rep2


title: Islets-Dam-Rep2


title: IMR90-DamN44Ibeta-RanGTP


title: IMR90-DamN44Ibeta-Rep1


title: Islets-Dam-Rep1


title: IMR90-DamN44Ibeta-Rep2


title: IMR90-DamIbeta-RanGTP

value: DamIbeta


title: RH4_si-SCR_2

description: Total cell lysate


title: IMR90-DamIbeta-Rep2


title: IMR90-DamIbeta-Rep1


title: IMR90-Dam-Rep1


title: IMR90-Dam-Rep2


title: HeLa-Ibeta

value: Ibeta


title: HeLa-DamIbeta-Rep3


title: HeLa-Dam-Rep2


title: HeLa-Dam-Rep1


title: HeLa-DamIbeta-Rep1


title: WT-4

status: Public on May 26 2021

data_processing:
Sequencing data were processed with RTA v1.18.66.3.
FastQ files for each sample were obtained using bcl2fastq v2.20.0.422 software (Illumina).
Sequencing adapter contaminations were removed using Cutadapt.
Reads were mapped on transcriptome and gene expression quantified using RSEM.
Genome_build: GRCz11 assembly, Ensembl gene build 99.
Supplementary_files_format_and_content: matrix_table.txt: Matrix table with RSEM-estimated raw gene counts for every gene and every sample.

organism: Danio rerio

source_name: Heart, cryoinjured ventricular apex

growth_protocol: Experiments were conducted with 7dpci hearts from zebrafish adult hearts with AB background.

extract_protocol:
Total RNA was extracted from 7 dpci ventricular adult tissue and it was collected from adult hearts by removing atrioventricular and aortic valves using QIAzol Lysis Reagent (Qiagen; CA; USA) and miRNeasy Mini Kit (Qiagen; CA; USA). RNA was quantified and purity checked using a NanoDrop ND-1000 (Thermo Scientific; MA; USA). RNA integrity was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies; CA; USA).
cDNA libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs).
Libraries were sequenced on a HiSeq 4000 system (Illumina) to generate 60 base single reads.

treatment_protocol: Cryoinjury of the ventricle.

tag: strain/background

value: AB

value: Adult

value: Ventricle

value: Cryoinjury of ventricle

tag: time point

value: 7 dpci


title: HeLa-DamIbeta-WGA


title: HeLa-DamIbeta-Rep2


title: KO-4

value: MDKA KO

tag: age


title: KO-2

tag: genotype


title: KO-3


title: WT-1


title: H3K4me3_293T_shNRSF

status: Public on Apr 14 2021

city: Shanghai

first: Yuanxiao

last: Tang

address: Dongchuan Road 800

institute: Shanghai Jiao Tong University

description: shRNA for NRSF transfected

data_processing:
Reads were sorted  using index
Reads were aligned to hg19 using bowtie2 for ChIP-Seq
The  peaks were called using the MACS for ChIP-Seq
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph were generated using Python

source_name: HEK293T cells

growth_protocol: HEC-1-B were cultured in MEM (Hyclone) , supplemented with 10% (v/v) FBS, 2 mM GlutaMAX (Gibco), 1 mM sodium pyruvate (Sigma), and 1% penicillin-streptomycin. HEK293T cells were cultured in DMEM/High glucose (Hyclone) , supplemented with 10% (v/v) FBSCells were maintained at 37 °C in a 5% (v/v) CO2 incubator.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
ChIP-Seq libraries were prepared according to the manual of VAHTSTM Universal DNA Library Prep Kit for Illumina® V2 (ND606). Briefly, DNA was end-repaired using End Prep Mix 3, ligated with index-contained adapters using Rapid DNA ligase in Rapid Ligation buffer, amplificated using PCR Primers and Amplification Mix for libraries. The library fragments of ~350 bp (insert plus adaptor and PCR primer sequences) were isolated  with Agencourt® AMPure® XP (Beckman Coulter®). Library DNAs were sequenced on an Illumina HiSeq platform.

treatment_protocol: The shGFP or shNRSF plasmid was transfected into HEK293T cells with the psPAX2 and pMD2.G helper plasmids (Addgene) using Lipofectamine 3000 to produce lentiviral particles. HEK293T cells or HEC-1-B cells were  infected with the virus in the presence of 8 μg/mL polybrene (Sigma). Puromycin (Sigma) was added to a final concentration of 2 μg/mL to select the infected cells. Fresh puromycin-containing medium was changed every other day. Cells were collected for assays at 5 days post infection.For monoclones, HEC-1-B cells or HEK293T cells at ~80% confluency was transfected with Cas9 (0.6 μg) and sgRNA (1.2 μg) expressing plasmids by Lipofectamine 3000 in a 12-well plate. 2 days post transfection, puromycin was added to a final concentration of 2 μg/mL. Four days later, cells were changed to fresh medium without puromycin and cultured for another ten days. The cells were diluted and plated in 96-well plates with approximately one cell per well. Two weeks later, single cell clones were screened for target deletion by PCR.

value: kidney

value: fetus

tag: chip antibody

value: H3K4me3 (Millipore, 17-614)


title: H3K4me3_M26

description: HS5-1 NRSE -/- monocolon


title: H3K4me3_M46

description: HS5-1 NRSE -/- monocolon

source_name: HEC-1-B cells

value: endometrium

tag: disease state

value: adenocarcinoma


title: SNZN7

status: Public on Apr 01 2021

data_processing:
libraries sequenced usign Genome Analyzer Iix and HiSeq 2500
base-calling was produced by Illumina RTA Software v 1.13.48
demultiplexed fastq files were generated from the bcl files using picard tools
sequencing adaptor contaminations were removed using cutadapt
reads were mapped and gene expression quantified using rsem 1.2.31
counts were normalized using voom from Limma R package
Genome_build: GRCh38 v78
Supplementary_files_format_and_content: tab separated file. Contains expected counts per gene aligned with RSEM and normalized using TMM and voom limma. Samples in columns, Genes in rows

source_name: Human aortic valve

extract_protocol:
Total RNA from fetal aortic valve leaflets was obtained using TRIzol LS (Invitrogen, Carlsbad, CA, USA)
RNA libraries were prepared for sequencing using TrueSeq RNASeq kit from Illumina

tag: developmental stage

value: Embryo

tag: disease

value: Aortic Valve

tag: Sex


title: SNZN8


title: H3K4me3_HEC_shNRSF

description: shRNA for NRSF transfected


title: HeLa-Dam-Rep3

value: HeLa

value: Dam

value: HeLa cell line


title: SNZN6


title: SNZN5


title: SNZN4


title: SNZN3


title: Control7

value: CTR

value: male


title: SNZN2


title: SNZN10


title: Control5

value: Adult


title: Control6


title: cBAV3

value: BicC

value: Aortic Valve with severe calcification and moderate stenosis

value: Female


title: SNZN13


title: Control4

value: female


title: cTAV6

value: TricC

value: Aortic Valve with severe calcification and stenosis


title: cTAV4


title: H3K4me3_M36

description: HS5-1 NRSE -/- monocolon

value: kidney

value: fetus

value: H3K4me3 (Millipore, 17-614)


title: WT-2

value: AB

value: WT

value: Ventricle

tag: treatment

value: Cryoinjury of ventricle

value: 7 dpci


title: cTAV5

tag: tissue


title: cBAV1


title: SK-TL

status: Public on Apr 30 2021

first: Loyal

middle: A

last: Goff

address: 733 N. Broadway Avenue

department: Institute of Genetic Medicine

institute: Johns Hopkins University

data_processing:
FASTQ sequence files were processed following a Kallisto Bustools workflow compatible with downstream RNA velocity calculations [kallisto == 0.46.1, bustools == 0.39.3] (Bray et al., 2016). References required for pseudo-alignment of transcripts were obtained using the get_velocity_files() functionality of BUSpaRSE (https://github.com/BUStools/BUSpaRse), with “L=98” for 10X Genomics v2.0 sequencing chemistry. Reads were pseudo-aligned to an index built from Ensembl 97 transcriptome annotation (Gencode vM22; GRCm38).
Barcodes within a Hamming distance of one to known 10X Genomics v2.0 barcodes were corrected. Reads were classified as “spliced” or “unspliced” by their complement to the target list of intronic sequences and exonic sequences, respectively, and subsequently quantified separately into expression count matrices. Spliced counts are used for all analyses.
scRNA-seq count matrices were analyzed using Monocle3. 11,123 high-quality cells were identified as meeting a 200 UMI minimum threshold with a mitochondrial read ratio of less than 20%; droplets that did not meet these criteria were excluded from the analysis. Mitochondrial counts were determined as the sum of reads mapping to 37 genes annotated to the mitochondrial genome. All genes with non-zero expression were included for downstream analysis.
Raw counts were first scaled by a cell-size scaling factor and subsequently log10 transformed with a pseudo-count of 1. Normalized values are used in place of raw counts unless otherwise noted.
Prior to UMAP dimensionality reduction, batch effects between the two biological replicates were assessed and corrected via the mutual nearest neighbors (MNN) algorithm as implemented by Batchelor in Monocle3 (50 principal components, with default k=20) (Haghverdi et al., 2018). 15 clusters of cells in the UMAP embedding were identified by Leiden community detection (resolu-tion = 1e -5, number of iterations = 5). 30 marker genes for each cluster were identified based on greatest pseudo R2 values and used for supervised annotation of cell types.
For further analysis into the MENs population, the full LM-MP dataset was subset to include only the 2,223 cells annotated as such. These cells were re-processed as above, but with a reduced PCA dimensionality of k=20 as input for the UMAP embedding. 5 clusters of cells in the UMAP embedding were identified by Leiden community detection (k= 10, resolution = 5e -4). The two samples showed a similar distribution of cells across the various cell clusters.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Raw aggregate gene single cell count matrix in csv format

source_name: dissociated, postnatal day 180, mouse small intestinal longitudinal muscle-myenteric plexus

growth_protocol: Experimental protocols were approved by The Johns Hopkins University’s Animal Care and Use Committee in accordance with the guidelines provided by the National Institutes of Health. Only male mice were used for the studies detailed in this report.

extract_protocol:
A laparotomy was performed, and the ileum was removed and lavaged with PBS containing penicillin-streptomycin (PS; Invitrogen), then cut into 1-cm-long segments and placed over a sterile plastic rod. A super-ficial longitudinal incision was made along the serosal surface and the LM-MP was peeled off from the underlying tissue using a wet sterile cotton swab (Kulkarni et al., 2017) and placed in Opti-MEM medium (Invitrogen) containing Pen-Strep (Invitrogen).  The tissues were then dissociated in Digestion Buffer containing 1 mg/ml Liberase (Sigma-Aldrich) in OptiMEM. Tissues from mouse 1 were dissociated in the Digestion buffer containing Liberase TH and tissues from mouse 2 were dissociated in the Digestion buffer containing Liberase TL. Dissociation was performed at 37°C for 30 minutes on a rotary shaker, after which the cells were centrifuged at 200g for 7 minutes, and the pellet was resuspended in ice cold ster-ile PBS. The cell suspension was passed through a 40 µm cell sieve and the resulting filtered cell suspension was again centrifuged at 200g for 7 minutes. This process of cell centrifugation and filtration was repeated two more times, after which the cells were resuspended in 1 ml ice cold sterile PBS. The repeated steps of serial cell washes and filtration removed clumps and debris and the viability of the resulting cell suspension was estimated to be >90% using Trypan Blue dye test.
The cells were then processed through 10X Genomics Chromium V2.0 system according to the manufacturer’s suggested workflow. The processing was done at the GRCF Core Facility at the Johns Hopkins University.
10x Genomics Chromium v2.0 3' gene expression assay

treatment_protocol: Mice were anesthetized with isoflurane and sacrificed by cervical dislocation.

tag: postnatal day


title: SK-TH

value: small intestinal longitudinal muscle-myenteric plexus


title: H3K4me3_M47

description: HS5-1 NRSE -/- monocolon

value: endometrium

value: adenocarcinoma


title: cTAV7

value: Adult

value: male


title: cBAV4

value: BicC


title: cTAV3


title: Control2

value: CTR

value: Aortic Valve


title: Control8


title: Control1


title: cBAV5

value: Aortic Valve with severe calcification and moderate stenosis


title: Control3


title: cBAV2

value: Aortic Valve with severe calcification and stenosis

value: female


title: COLO205_selumetinib_EdU_+ve

status: Public on Mar 23 2021

description:
gene_expression_data_sorts.txt
Cells grown in monolayers were harvested by trypsinization, centrifuged (300 x g for 5 minutes) and washed once with PBS prior to lysis in TRI reagent. For glyoxal fixation and staining, cell pellets were resuspended in 100 µL glyoxal fixation solution (2.8 ml water, 0.79 ml 100% ethanol, 0.31 ml 40% glyoxal and 30 µl acetic acid, pH 4-5) supplemented with 1:25 RNasin Plus RNase inhibitor (Promega, N261B) and incubated for 15 minutes on ice. The cell suspension was diluted in 1 mL PBS supplemented with 1:100 RNasin Plus RNase inhibitor and centrifuged at 2000  x g for 3 minutes at 4°C; the supernatant was discarded. All further centrifugation steps were carried out at similar conditions. Cells were permeabilized by adding 100 µL ice-cold methanol (100%, v/v) with 1:25 RNasin Plus RNase inhibitor drop by drop while gently vortexing cells, and incubated on ice for 30 minutes. The cell suspension was then diluted in 1 mL 1% bovine serum albumin (BSA) (Sigma, A7906) in PBS and centrifuged. For EdU staining, cells were incubated in a modified click reaction cocktail (221.5 µL PBS, 2.5 µL CuSO4, 25 µL 1 M sodium ascorbate, 1.25 µL Alexa Fluor 488) Click-iT™ EdU Alexa Fluor™ 488 Flow cytometry kit (Thermo Fisher Scientific, C10420) and incubated for 30 minutes on ice in dark. Following incubation, cells were washed in 1% BSA in PBS and 1:25 RNasin Plus and incubated in 1 µg/mL DAPI in PBS.  For CCNB1 labelling, cells were incubated in 100 uL primary antibody (in this case CST 12231S - 1:200) diluted in 1% BSA in PBS with 1:25 RNasin Plus RNase inhibitor for 1 hour on ice. Following incubation, cells were washed once in 1mL 1% BSA in PBS. Secondary antibody staining was carried out in 100 μL Alexa Fluor 488 donkey anti-rabbit antibody (ThermoFisher Scientific, A21206) diluted 1:1000 in 1% BSA in PBS with 1:25 RNasin Plus RNase inhibitor and incubated on ice for 30 minutes in dark. Cells were washed once in 1 mL 1% BSA in PBS and the cell pellet resuspended in 200 µL 1% BSA in PBS with 1:100 RNasin Plus RNase inhibitor. Cells were incubated in 1 µg/mL DAPI. For collection of glyoxal-fixed cells that were stained with EdU or CCNB1 and flow sorted, cell suspension was pelleted by centrifugation at 2000 x g for 3 minutes at 4°C.

data_processing:
After adapter and quality trimming using Trim Galore (v0.5.0), RNAseq data was mapped to human genome GRCh38 using HISAT2 v2.1.0 by the Babraham Institute Bioinformatics Facility. Mapped data was imported into SeqMonk v1.47.0 (https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/) and normalised to total read count.
Genome_build: GRCh38
tab delimited text files showing log2 values per gene for each sample

extract_protocol:
Cell pellets were lysed in 1 mL TRI reagent (Sigma, T9424) and mixed until a homogeneous lysate was obtained. For phase separation, 0.2 mL chloroform was added, mixed thoroughly and allowed to stand for 10 minutes prior to centrifugation at 12,000 × g for 15 min at 4 °C. The upper aqueous phase containing RNA was transferred to a fresh tube, and 0.5 mL 2-propanol per mL original lysate was then added, samples mixed and allowed to stand for 10 minutes. Samples were centrifuged (12,000 × g for 10 min at 4 °C), and RNA pellets washed with 1 mL 75% (v/v) ethanol (7,500 × g for 5 min at 4 °C). Pellets were air-dried for 5-10 minutes and resuspended in RNase-free water.
RNA prepared from flow sorted cells was quality controlled on a Bioanalyzer 2100 (Agilent) using RNA Pico 6000 chips (Agilent 5067-1513). mRNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB E7760S) with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490S), following the protocol provided by the manufacturer with the exception that two successive 0.9x AMPure purifications were performed on the final amplified libraries. All libraries were amplified using 12-14 PCR cycles. Library quality was assessed on a Bioanalyzer 2100 using High Sensitivity DNA chips (Agilent 5067-4626) and quantification performed with a KAPA Library Quantification Kit (Roche, KK4844). Libraries were sequenced by the Babraham Institute Next Generation Sequencing Facility on an Illumina HiSeq2500 in Rapid Run 50bp Single End mode.

value: colorectal cancer cell line

tag: growth media

value: RPMI-1640 + 1uM selumetinib (24 hours) + EdU (4 hours)

tag: cell line

value: Glyoxal fixed, stained for EdU and sorted


title: COLO205_selumetinib_EdU_-ve

tag: cell type

tag: fixed/unfixed


title: COLO205_selumetinib_CCNB1_-ve_3

value: RPMI-1640 + 1uM selumetinib (24 hours)

value: Glyoxal fixed, stained for CCNB1 and sorted


title: COLO205_selumetinib_CCNB1_-ve_2


title: COLO205_selumetinib_CCNB1_-ve_1


title: COLO205_selumetinib_CCNB1_+ve_2


title: COLO205_untreated_CCNB1_+ve_3


title: COLO205_selumetinib_CCNB1_+ve_1


title: COLO205_untreated_CCNB1_-ve_2


title: COLO205_untreated_CCNB1_+ve_1


title: COLO205_untreated_CCNB1_+ve_2


title: COLO205_48_hr_selumetinib_1

description:
gene_expression_data_timecourse.txt
Cells grown in monolayers were harvested by trypsinization, centrifuged (300 x g for 5 minutes) and washed once with PBS prior to lysis in TRI reagent. For glyoxal fixation and staining, cell pellets were resuspended in 100 µL glyoxal fixation solution (2.8 ml water, 0.79 ml 100% ethanol, 0.31 ml 40% glyoxal and 30 µl acetic acid, pH 4-5) supplemented with 1:25 RNasin Plus RNase inhibitor (Promega, N261B) and incubated for 15 minutes on ice. The cell suspension was diluted in 1 mL PBS supplemented with 1:100 RNasin Plus RNase inhibitor and centrifuged at 2000  x g for 3 minutes at 4°C; the supernatant was discarded. All further centrifugation steps were carried out at similar conditions. Cells were permeabilized by adding 100 µL ice-cold methanol (100%, v/v) with 1:25 RNasin Plus RNase inhibitor drop by drop while gently vortexing cells, and incubated on ice for 30 minutes. The cell suspension was then diluted in 1 mL 1% bovine serum albumin (BSA) (Sigma, A7906) in PBS and centrifuged. For EdU staining, cells were incubated in a modified click reaction cocktail (221.5 µL PBS, 2.5 µL CuSO4, 25 µL 1 M sodium ascorbate, 1.25 µL Alexa Fluor 488) Click-iT™ EdU Alexa Fluor™ 488 Flow cytometry kit (Thermo Fisher Scientific, C10420) and incubated for 30 minutes on ice in dark. Following incubation, cells were washed in 1% BSA in PBS and 1:25 RNasin Plus and incubated in 1 µg/mL DAPI in PBS.  For CCNB1 labelling, cells were incubated in 100 uL primary antibody (in this case CST 12231S - 1:200) diluted in 1% BSA in PBS with 1:25 RNasin Plus RNase inhibitor for 1 hour on ice. Following incubation, cells were washed once in 1mL 1% BSA in PBS. Secondary antibody staining was carried out in 100 μL Alexa Fluor 488 donkey anti-rabbit antibody (ThermoFisher Scientific, A21206) diluted 1:1000 in 1% BSA in PBS with 1:25 RNasin Plus RNase inhibitor and incubated on ice for 30 minutes in dark. Cells were washed once in 1 mL 1% BSA in PBS and the cell pellet resuspended in 200 µL 1% BSA in PBS with 1:100 RNasin Plus RNase inhibitor. Cells were incubated in 1 µg/mL DAPI. For collection of glyoxal-fixed cells that were stained with EdU or CCNB1 and flow sorted, cell suspension was pelleted by centrifugation at 2000 x g for 3 minutes at 4°C.

value: RPMI-1640 + 1uM selumetinib

value: Unfixed, processed direct for RNA


title: COLO205_48_hr_selumetinib_2


title: COLO205_24_hr_selumetinib


title: COLO205_8_hr_selumetinib


title: COLO205_untreated_CCNB1_-ve_3


title: COLO205_untreated_CCNB1_-ve_1


title: COLO205_2_hr_selumetinib


title: COLO205_4_hr_selumetinib


title: cTAV2

value: TricC


title: COLO205_single cell derived_Selumetinib resistant-5a

type: genomic

description: SAMPLE 15

hyb_protocol: Amplified and fragmented DNA samples were hybridised to BeadChips according to the instructions provided by the manufacturer (Illumina). See https://emea.support.illumina.com/downloads/infinium-cytosnp-850k-reference-guide-15046990.html

scan_protocol: BeadChips were scaned using the iScan system according to the instructions provided by the manufacturer (Illumina) See https://emea.support.illumina.com/downloads/infinium-cytosnp-850k-reference-guide-15046990.html

data_processing: The raw intensity data (.idat) files were converted to genotype call (.gtc) files using Beeline version 4.5 and then imported to BlueFuse multi version 4.5 and analysed using BlueFuse algorithm with default settings(10 contiguous markers for CNV and 500 contiguous markers for loss of heterozygosity (LOH)).Samples 1-8 processed on Illumina CytoSNP 850K v1.1 were analysed using the cluster file CytoSNP850Kv1-1_iScan_C1_ClusterFile.egt and manifest file CytoSNP-850Kv1-1_iScan_C1.bpm. Samples 9-16 processed on Illumina CytoSNP 850K v1.2 beadchips were analysed using the cluster file CytoSNP850Kv1-2_iScan_B1_ClusterFile.egt and CytoSNP-850Kv1-2_iScan_B3.bpm. The annotation file used for the analysis was BG_Annotation_Ens74_20180801.db (genome build 37).

label: Cy3 and Cy5

source_name: Colorectal cancer cell line

label_protocol: 200 ng of genomic DNA was amplified in a reaction mix containing multi-sample amplification Mix 1, multi-sample amplification mix 2 and multi- sample master mix according to the instructions provided by the manufacturer (Illumina).  See https://emea.support.illumina.com/downloads/infinium-cytosnp-850k-reference-guide-15046990.html

growth_protocol: Parental and selumetinib resistant  COLO205 cell lines were grown in RPMI-1640 media supplemented with 10% (v/v) foetal bovine serum, penicillin (100 U/mL), streptomycin (100 mg/mL) and 2 mM glutamine in the absence or presence of 1 µM selumetinib respectively at 37 °C in a humidified incubator with 5% (v/v) CO2.

extract_protocol: Cells grown in growth media were harvested by trypsinisation, centrifuged (300 x g for 3 minutes) and washed once in PBS. Genomic DNA from cells was extracted  using a a Qiagen DNeasy Blood and Tissue kit (Qiagen, 69504)

treatment_protocol: Cells were seeded in 25 cm2 flasks and treated with fresh growth media or media containing 1 µM selumetinib 24 hours later. Media and drug were changed weekly until colonies (>50 cells) of proliferating cells were formed in culture.

value: RPMI-1640 + 1µM selumetinib

tag: molecule

value: Genomic DNA


title: COLO205_single cell derived_Selumetinib resistant-5b

description: SAMPLE 16


title: cTAV1

value: Adult

value: male


title: COLO205_single cell derived_Selumetinib resistant-4d

description: SAMPLE 14


title: COLO205_untreated_1


title: COLO205_untreated_EdU_+ve

value: RPMI-1640 + 4 hour EdU


title: COLO205_single cell derived_Selumetinib resistant-4c

description: SAMPLE 13


title: COLO205_selumetinib_CCNB1_+ve_3


title: COLO205_single cell derived_Selumetinib resistant-4b

description: SAMPLE 12


title: COLO205_single cell derived_Selumetinib resistant-2b

description: SAMPLE 10


title: COLO205_Selumetinib resistant-f

description: SAMPLE 7


title: COLO205_Selumetinib resistant-c

description: SAMPLE 4


title: COLO205_Selumetinib resistant-g

description: SAMPLE 8


title: COLO205_single cell derived_Selumetinib resistant-2a

description: SAMPLE 9


title: COLO205_Selumetinib resistant-e

description: SAMPLE 6


title: COLO205_Selumetinib resistant-d

description: SAMPLE 5


title: COLO205_Selumetinib resistant-b

description: SAMPLE 3


title: COLO205_untreated_2


title: WT51 uninduced input 3 ChIP-seq

status: Public on Mar 15 2021

first: Sarah

last: Gillen

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

institute: Wellcome - MRC Cambridge Stem Cell Institute

data_processing:
For RNA-seq data, single-end 50-bp reads generated on the Illumina HiSeq 2000 were aligned to the human genome version GRCh37 and read counts were generated using STAR 2.5.1a, and data normalised using the RPKM method.
For ChIP-seq data, chIP-seq experiments were performed in at least biological triplicate. Reads were mapped to hg19 genome using Bowtie2 2.2.6. Aligned reads with mapping quality less than five were filtered out. The read alignments from three replicates were combined into a single library, and peaks were called with model based analysis for ChIP-seq 2 (MACS2) version 2.0.10.20131216 using sequences from SH-SY5Y chromatin extracts as a background input control.
Genome_build: hg19
Supplementary_files_format_and_content: RNA-seq raw counts: tab delimited file containing raw counts, quantified by gene (Ensembl gene ID version). Bigwig: Coverage track of ASCL1 ChIP-seq/input libraries, generated using Deeptools bamCoverage.

source_name: WT-ASCL1 inducible cells

growth_protocol: The Neuroblastoma cell line SH-SY5Y (kindly gifted by Prof. John Hardy, UCL) used in experiments was verified by submitting genomic DNA for short tandem repeat (STR) sequencing and compared to the Children’s Oncology Group Cell Line Identification database (http://www.cogcell.org/clid.php) to ensure it was genetically matched to standardised cell lines. SH-SY5Y cell line was cultured in DMEM/F-12 with GlutaMAX™ supplement, 10% tetracycline-free Fetal Bovine Serum (Clontech, cat# 631106), and 100 units/ml penicillin and 100 μg/ml streptomycin.

extract_protocol:
ChIP and ChIP-seq were performed as described previously (22,23 from prev. version). Antibodies used were anti-ASCL1 (Abcam, cat# ab74065), anti-P300 (Santa-Cruz, cat# sc-585), and anti-IgG (Abcam, cat# ab6706). ChIP-seq experiments were performed in two separate clones of each of WT and S-A SH-SY5Y tetracycline-inducible stable cell lines induced with 1 μg/ml doxycycline for 24 hours, before cross-linking with 1% formaldehyde.
ChIP-seq and the input libraries were prepared using the ThruPLEX® DNA-seq Kit (Rubicon Genomics, cat# R400406), following the manufacturers instructions.

treatment_protocol: Cells were induced with 1 µg/ml doxycycline for 24 hours before RNA extraction.

value: Uninduced

tag: clone

value: WT 2

tag: biological replicate


title: SA11 uninduced input 1 ChIP-seq

source_name: SA-ASCL1 inducible cells

value: S-A 2


title: SA11 uninduced input 3 ChIP-seq


title: WT51 uninduced input 2 ChIP-seq


title: SA11 induced 2 ChIP-seq

value: Dox


title: SA11 induced 4 ChIP-seq


title: WT51 uninduced input 1 ChIP-seq


title: SA11 induced 1 ChIP-seq


title: COLO205_Selumetinib resistant-a

description: SAMPLE 2


title: SA11 induced 3 ChIP-seq


title: WT51 induced 2 ChIP-seq


title: WT51 induced 4 ChIP-seq


title: SA31 induced 1 ChIP-seq

value: S-A 1


title: SA31 induced 3 ChIP-seq


title: WT51 induced 1 ChIP-seq


title: SA31 induced 4 ChIP-seq


title: SA31 induced 2 ChIP-seq


title: WT31 induced 4 ChIP-seq

value: WT 1


title: COLO205_single cell derived_Selumetinib resistant-4a

description: SAMPLE 11


title: COLO205_Parental

description: SAMPLE 1


title: WT51 induced 3 ChIP-seq


title: WT31 induced 3 ChIP-seq


title: SA11 induced 5 RNA-seq

extract_protocol:
Cultured cells were washed twice with cold PBS, and RNA was extracted using the RNeasy kit (Qiagen, cat# 74106).
RNA libraries were prepared using the TruSeq Stranded mRNA library prep kit (Illumina, cat# 20020594), following the manufacturers instructions.


title: SA11 uninduced input 2 ChIP-seq


title: SA11 induced 2 RNA-seq


title: SA11 induced 1 RNA-seq


title: SA31 induced 2 RNA-seq


title: SA31 induced 5 RNA-seq


title: SA31 induced 3 RNA-seq


title: SA31 induced 4 RNA-seq


title: WT31 induced 2 ChIP-seq


title: WT31 induced 1 ChIP-seq


title: SA11 induced 4 RNA-seq


title: WT51 induced 4 RNA-seq


title: WT51 induced 3 RNA-seq


title: SA31 induced 1 RNA-seq


title: WT51 induced 1 RNA-seq


title: SA11 induced 3 RNA-seq


title: WT31 induced 5 RNA-seq


title: WT31 induced 2 RNA-seq


title: WT51 uninduced 4 RNA-seq


title: WT31 induced 4 RNA-seq


title: WT31 induced 3 RNA-seq


title: WT51 uninduced 3 RNA-seq


title: WT51 uninduced 2 RNA-seq


title: WT31 induced 1 RNA-seq


title: WT51 uninduced 5 RNA-seq


title: WT51 uninduced 1 RNA-seq


title: WT51 induced 2 RNA-seq


title: WT51 induced 5 RNA-seq


title: 1366-S

status: Public on Feb 02 2021

first: Marcus

last: Peter

address: 303 East Superior Street, Lurie 6-123

institute: Northwestern University Feinberg School of Medicine

description:
Single Read
50bases

data_processing:
Reads were trimmed with Trim_galore to remove all standard Illumina adapters and trimmed reads less than 6 bp in length
Reads were demultiplexed according to adaptor barcodes to separate into the individual samples listed below.
6 bp UMIs were removed, including 4N before pulldown sequence and 2N after
Cleaned reads were sorted and uniq -c used to identify the total counts of all unique sequences
Counts were normalized to 1 million reads per sample, and reads with fewer than 6 normalized counts summed across all samples were discarded
Reads were blasted against a set of processed miRNAs and the top blast hit retained as a putative source for the read.
Genome_build: hg38
Supplementary_files_format_and_content: Excel sheet with normalized read counts for each sample comparison of interest, along with cell viability and blast-based annotations

source_name: Ovarian cancer patient

extract_protocol:
Tumor pieces or cells were lyzed and proteins were subjected to pull down with a GW182 peptide bound to anti-FLAG M2 Magnetic beads RNA at a size of 19-35 nt was gel extracted and used to generate library
The quality and quantity of the RNA samples was checked using an Agilent bio-analyzer. Small RNA-SEQ libraries were generated using Illumina small RNA SEQ kits using the Illumina provided protocol containing library fragments 140-160 bp in size.
RNA-Seq; sequenced on an Illumina HiSEQ4000 using Illumina provided reagents and protocols

treatment_protocol: Tumor pieces from ovarian cancer patients (either primry tumor (P) or recurrent tumor ('R))

tag: cancer tissue

value: Primary tumor from ovarian cancer patient  - Pt resistant

value: Ovaries


title: 842-S

description:
Single Read
50bases


title: 287-S

description:
Single Read
50bases


title: WT31 uninduced 2 RNA-seq


title: WT31 uninduced 3 RNA-seq


title: WT31 uninduced 1 RNA-seq


title: 1036-L

description:
Single Read
50bases

value: Primary tumor from ovarian cancer patient  - Pt sensitive


title: 21-KO-KO2: miR-34a KO 1

status: Public on Mar 08 2021

description: primary chondrocytes

data_processing:
Conversion of .bcl to .fastq files was performed for each sample using Illumina’s bcl2fastq2 conversion tool (v2.19.1.403)
Initial quality assessment of each sample revealed that the reads were of high quality (>Q30). Cutadapt (v1.18) software was used to maintain minimum read length of 25 bp post trimming of adapters (very few reads being contaminated=3%) as well as trimming of N’s.
Splice-aware alignment of reads using a Hierarchical Graph FM index (HGFM) method was performed using HISAT2 software (v2.1.0) with parameters (--rna-strandness FR –dta) against mouse reference genome (mm10).
To assemble the aligned reads into transcripts, StringTie software (v1.3.5) was used with parameters (--rf assuming it was a stranded library fr-firststrand).
To obtain the abundance of each of these transcripts based only on the known reference genome and transcriptome, StringTie was run again using different parameters (-e -B -G referencetranscripts.gtf) to generate output of Ballgown software compatible table files.
A script was provided by StringTie software named ‘prepDE.py’, which retrieves raw counts for genes and transcripts separately based on the table files, was used for Differential Expression Analysis (DEA).
For DEA, retain genes with at least 10 CPM in 2 samples and apply TMM normalization on remaining genes.
Assigned WT and KO groups and estimated dispersion.
Applied the exact test with trended dispersion in edgeR.
Retained genes with Benjamini-Hochberg adjusted FDR<0.05
Genome_build: mm10
Supplementary_files_format_and_content: 1 combined tab-delimited text file includes raw count values for each Sample ...

source_name: articular cartilage

growth_protocol: Cells were grown in 6-well plates in complete DMEM medium supplemented with 10% FBS and 1%Pen-Strep until confluent (approx. 1 week)

extract_protocol:
Articular cartilage was scraped from tibial plateau and femoral condyle surfaces in the knee joint as well as hip. Cartilage was incubated in 3mg/ml collagenase overnight at 37 degrees celsius in an incubator and filtered in a 70µm sterile filter. Filtrate was centrifuged and pellet was resuspended in complete medium. Cells were counted and plated. Primary chondrocytes were used for RNA extraction using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocol (TruSeq Stranded Total RNA, Cat # 20020596).

value: articular cartilage

tag: strain

tag: genotype

tag: model nomenclature

value: Mir34atm1.2 Mrl

tag: age

value: 5 weeks


title: 566-L

description:
Single Read
50bases


title: 377-S

description:
Single Read
50bases


title: 274-L

description:
Single Read
50bases


title: 1496-S

description:
Single Read
50bases

value: Primary tumor from ovarian cancer patient


title: 295-L

description:
Single Read
50bases


title: 18-WT-29RB: Wild-type 2

description: primary chondrocytes

value: wild type


title: 200/220-L

description:
Single Read
50bases


title: 22-KO-28LF: miR-34a KO 2

description: primary chondrocytes


title: 660-L

description:
Single Read
50bases


title: 706/723-S

description:
Single Read
50bases


title: 17-WT-30LF: Wild-type 1

description: primary chondrocytes


title: 1638-S

description:
Single Read
50bases


title: 285-L

description:
Single Read
50bases


title: 290-L

description:
Single Read
50bases


title: WT31 uninduced 5 RNA-seq


title: 20-WT-30RF: Wild-type 3

description: primary chondrocytes