title: GAHD, 38453

extract_protocol: Genomic DNA was extracted from whole blood using Proteinase K and phenol/chloroform with standard protocols.


title: SF

status: Public on Oct 01 2024

type: SRA

city: Hefe

first: sheng

last: zhang

state: Anhui Province

address: Shushan District

country: China

institute: anhui agriculture university

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw reads were aligned against the S. marcescens FY Lactobacillus plantarum FY1.Then, genome and counted by StarSolo. Sequencing data was further analyzed using the Scanpy software.
We initially reduced dimensionality of the dataset using principal components analysis (PCA), retaining 20 principal components.
Subsequent steps, like low-dimensional UMAP visualization and cell clustering via Leiden algorithm, were based on the initial PCA.
Finally, Wilcoxon rank sum was used to analyze the difference between different cluster cells.
Assembly: Serratia marcescens with the Genbank accession number CP053378 and Lactobacillus plantarum with the Genbank accession number KY038178
Supplementary files format and content: tsv files include gene counts for each Sample

molecule: total RNA

organism: Serratia marcescens

source_name: WT

extract_protocol:
Up to half a million cells were collected by centrifuging at 4000 rpm for 5 min at 4℃.The supernatant was removed and cell pellets were resuspended in 2 mL ice-cold 4% formaldehyde (Sigma, 47608) and incubated with shaking overnight at 4℃. The fixative was removed by centrifuging at 4000 rpm for 5 min at 4℃ and cells were washed twice by 1 mL PBS-TRI (1x PBS supplemented with 0.1% Tween-20 and 0.1 U/mL Murine RNase inhibitor (Vazyme, R 301)). The supernatant was removed and cells were resuspended in 200 μL PBS-TRI (1x PBS supplemented with 0.1% Tween-20 and 0.2 U/mL Murine RNase inhibitor (Vazyme, R 301)).
The cell suspensions were counted with a Moxi cell counter (ORFLO Technologies, Ketchum, Idaho) and diluted according to the manufacturer’s instructions to obtain 2000-4000 single-cell per sample. Random primers were added to amplify the full length of RNA, and the resulting cDNA fragment was added with adaptor. The microbeads with cell barcode, UMI, and the cDNA fragments linked to the adaptor were combined with the mixture of enzymes and extended in the microfluidic system to obtain the labeled cDNA chain. The beads were lysed and the cDNA was used as a template for PCR amplification. All products were pooled to construct a standard sequencing library.

tag: strain

value: Serratia marcescens FY

tag: cell type

value: WT

tag: treatment

value: bacteria and larvae were co-cultured


title: AT39 sRNA-Seq

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

country: Italy

institute: University of Turin

library_source: transcriptomic

data_processing:
After a quality check with FastQC tool, adapter sequences were trimmed using Cutadapt, which also removed sequences shorter than 16 nucleotides and longer than 30 nucleotides.
Reads were mapped using the STAR algorithm. Only reads that mapped unambiguously to the reference genome retrieved from miRBase 21 database (with at least 16 nucleotides aligned, and allowing a 10% mismatch) were used for the downstream analyses.
Raw counts from mapped reads were obtained using the htseq-count script from the HTSeq tools.
Assembly: hg38
Supplementary files format and content: Matrix table with the raw mature miRNA read counts for each sample

organism: Homo sapiens

source_name: Fibroblast

growth_protocol: Fibroblasts cell lines were obtained from skin biopsies and cultured in Dulbecco’s Modified Eagle Medium (DMEM, Sigma Aldrich, Italy) with 2 mMol Glutamine, 50 U/ml penicillin, 50 µg/ml streptomycin, 1 mMol Sodium Pyruvate, and 10% FBS.

extract_protocol:
RNA extraction was performed using miRNeasy Mini Kit (Qiagen) following the manufacturer’s standard protocol including the DNAse step.
Small RNA libraries were created for 6 fibroblast samples using TruSeq Small RNA Library PrepKit v2 (Illumina, San Diego, California RS-200-0012/24/36/48). The libraries were generated following manufacturer’s instruction starting from 35 ng of purified RNA. The High Sensitivity DNA (HS-DNA) kit (Agilent Technologies, Santa Clara, California, USA5067-4626) was used to quantify the libraries using Agilent Bioanalyzer (Agilent Technologies). The 24 DNA DNA libraries were combined in equal amount to create a libraries pool. The pooled libraries underwent size selection using magnetic beads (Agencourt, Beckman Coulter, Brea, California). They were then quantified using the HS-DNA Kit (Agilent Technologies), denatured, neutralized and combined with a Phix control library (standard library normalizator). A final concentration of 1.8 pM of pooled libraries was obtained and sequenced using the NextSeq 500/550 High Output Kit v2 (75 cycles) (Illumina, FC-404-2005) on the Illumina NextSeq500 platform.

value: Fibroblast

tag: Sex

value: Male

tag: age

tag: disease

value: AT patient


title: input-ARP1-KDM6A-H1146E

city: Gainesville

first: Alberto

last: Riva

state: FL

address: 2033 Mowry Rd

department: ICBR

country: USA

institute: University of Florida

library_source: genomic

data_processing:
Reads were trimmed with trimmomatic and quality control performed with FastQC and MultiQC.
Reads were mapped to the GRCh38 genome with Bowtie2.
Peak calling was performed with MACS v2.1.2
Additional processing and plots were performed with custom analysis scripts.
Assembly: GRCh38
Supplementary files format and content: Peak locations from MACS peak calling

molecule: genomic DNA

source_name: multiple myeloma

extract_protocol:
For crosslinking, cells were pelleted and resuspended in PBS containing 1% fresh formaldehyde for 8 min at room temperature with rotation. Crosslinking was quenched by addition of 1/10 volume of 1.25M glycine and incubated for 5 minutes at room temperature with rotation. For isolation of nuclei, cell pellets were washed once in ice-cold PBS and then resuspended in lysis buffer (10% glycerol, 1% Triton TX-100, 0.1 mM EDTA, 14mM NaCl 25mM Hepes pH 7.5) and incubated for 5 minutes on ice. Cell nuclei were pelleted and incubated 5 min in wash buffer (0.1 mM EDTA, 20mM NaCl, 2mM Tris-HCl pH 7.5). Cell nuclei were pelleted and resuspended in 1 ml sonication buffer (1 mM EDTA, 10mM Tris-HCl pH 7.5) at a concentration equivalent to 10x106 cells per ml. Samples were sonicated in 1ml in AFA fiber Covaris tubes using the Covaris E220 (Woburn, MA) for 30 minutes using the following settings: 15% Duty Cycle, 200 cycles/burst, and Peak incidence 140. Prior to immunoprecipitation, sheared chromatin was diluted 1:1 in 2X ChIP dilution buffer (2% Triton X-100, 2mM EDTA, 300mM NaCl, 30mM Tris-HCl pH 8). Sheared chromatin samples were block with 20 µl Protein A/G Dyna beads (Invitrogen) for 2h at 4°C with rotation. Immunoprecipitations were performed overnight (16 hours, 4°C, with rotation) with the following antibodies: H3K27Ac (Acitve Motif #39133), H3K27me3 (Cell Signaling Technologies #9733), KDM6A (Cell Signaling Technologies #33510). Samples were washed once with ChIP dilution buffer(1% Triton X-100, 1mM EDTA, 150mM NaCl, 15mM Tris-HCl pH 8), low salt wash buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 100mM NaCl, 20mM Tris-HCl pH 8), high salt wash buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 500mM NaCl, 20mM Tris-HCl pH 8), LiCl wash buffer (1% deoxycholate, 1% NP-40, 2mM EDTA, 250mM LiCl, 20mM Tris-HCl pH 8), and Tris buffer (10mM Tris-HCl pH 7.5). For library construction, beads were incubated in 15 µl Tagmentase buffer with 1µl Tagment enzyme (Illumina Nextera DNA library Prep kit #15028212) and incubated at 37°C for 10 min. Immediately after, beads were washed once in 1ml ChIP dilution buffer and in 1 ml TE (10mM Tris-HCl pH 7.5, EDTA 1mM) prior to incubation in reverse crosslinking buffer (300mM NaCl, 10 mM EDTA, 0.5% SDS, 20mM Tris-HCl pH 8) for 4 hours at 65°C with shaking. Finally, proteinase K digestion was performed for 1h at 55°C with shaking prior to DNA purification using Zymogen ChIP DNA Clean and Concentrator Kit (Zymo Research, D5205, Irvine, CA).
Libraries were generated by amplification of ChIP DNA using KAPA HiFi Hotstart Library Amp kit (Roche #07959028001, Indianapolis, IN) and size selected for between 200 bp and 700 bp using Ampure beads XP (Beckman Coulter, Brea, CA). Library were quantified and QC using D1000 high-sensitivity screen tape with 4200 TapeStation Instrument (Agilent Technologies, Santa Clara, CA) and sequenced on an Ilumina Hi-Seq 3000 with 150 bp pair-end reads.

tag: cell line

value: multiple myeloma

tag: genotype

value: KDM6A JmjD-dead

tag: ip antibody

value: input control


title: GAHD, 38452

type: genomic

city: Bethesda

first: Alexander

middle: Christian

last: Harris

state: Maryland

address: 50 South Drive

department: National Human Genome Research Institute

institute: National Institutes of Health

hyb_protocol: Resuspended DNA was loaded onto BeadChips arrays and hybridized overnight at at 48oC.  Single-base extension and allele-specific staining was performed by hand.

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing:
Image data was analyzed using GenomeStudio with GT module (Illumina).
genotypes AA, AB, BB, NC=no call

organism: Canis lupus familiaris

source_name: Whole Blood

label_protocol: 200ng of genomic DNA was amplified in an overnight reaction at 37oC. The amplified DNA was enzymatically fragmented, precipitated with isopropanol, and resuspended in hybridization buffer.

tag: breed

value: Galapagos Hunting Dog

tag: tissue

value: Whole Blood


title: neural progenitor cell, PRMT7knockdown-2, rep2

city: Changsha

first: Ting

last: Shen

address: Tongzhipo Road 172

institute: Central South University

data_processing:
FastQC v0.11.2 is firstly used to evaluate the quality of the sequencing data.
The low-quality reads are filtered via cutadapt v3.3
The remaining reads are aligned to the human reference genome Gencode GRCh38.p12 Release 29 using STAR-2.7.9a
The aligned reads are quantified through salmon-1.4.0 to obtain the original counts expression matrix.
Assembly: hg38
Supplementary files format and content: text file lincudes gene counts of all sample

source_name: neural progenitor cell

growth_protocol: The NPCs we used in this study were derived from the differentiation of human embryonic stem cell line H9 using Neural Induction Medium supplied by STEMCELL Technologies. The formed NPCs were cultured in Neural Progenitor Medium also supplied by STEMCELL Technologies.

extract_protocol:
The total RNA were extracted using the Trizol agent according to the manufacturer’s protocol.
The RNA library for RNA-seq  was constructed according to the instruction of Illumina TruSeq Stranded Total RNA kit.

value: neural progenitor cell

value: PRMT7 knockdown


title: GAHD, 38451


title: ATAC-ARP1-KDM6A-KO-rep3

extract_protocol:
Performed as described in Buenrostro et al, 2013
Libraries were size selected by SPRIselect, and library QC was performed by measuring the ratio of GAPDH promoter to a genomic desert region by qPCR prior to sequencing using a NextSeq 500 (Illumina)  (2 × 150 bp) to achieve approximately 60 million reads per sample.

value: KDM6A knock out

tag: biorep


title: GAHD, 38450


title: SF1

description: replicate=SF group biological replicate 1

data_processing:
For annotation, the genome of S. marcescens (GCF_013122155.1) and L. plantarum (GCF_032436005.1) was used as reference.
The significant differentially expressed genes were determined in different groups using the DESeq software, with the standards of P-value ≤0.05, and fold change |log2FC| ≥1.
KEGG B class database was used to classify the genes with significantly differential expression based on their functions using the tool Omicshare.
Assembly: Serratia marcescens with the Genbank accession number CP053378 and Lactobacillus plantarum with the Genbank accession number KY038178
Supplementary files format and content: txt files include gene count values for each Sample

source_name: Serratia marcescens FY

extract_protocol:
RNA was harvested using Bacteria RNA Extraction Kit (Vazyme). 1 ug of total RNA was used for the construction of sequencing libraries.
With Ribo-off rRNA Depletion Kit (Vazyme), the total bacterial RNA was subjected to rRNA removing to obtain mRNA.And then RNA libraries for RNA-seq were prepared using VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme) following manufacturer's protocols.


title: GAHD, 38449


title: neural progenitor cell, PRMT7knockdown-2, rep1


title: neural progenitor cell, PRMT7knockdown-1, rep2


title: ATAC-ARP1-KDM6A-KO-rep1


title: SF2

description: replicate=SF group biological replicate 2


title: neural progenitor cell, control, rep2


title: S1

description: replicate=S group biological replicate 1

value: single cultivation


title: THP1 Vec+VSV

city: Beijing

first: Ming

last: Kuang

address: Xueyuan Road 38 #, Haidian District

institute: Peking University

description: THP1 cells were collected for total RNA extraction with VSV infection for 6h.

data_processing:
The raw fastq files was trimmed to clean data by trim-galore software.
The clean data were aligned to human hg38 genome using subread, which produced the BAM type file directly.
The featureCounts command line tool was used to calculate the gene count matrix.
Then the count matrix was normalized with FPKM formula.
The GFOLD software was used to identify the differantially expressed genes.
Assembly: UCSC hg38 genome was used as reference genome.
Supplementary files format and content: Excel spreadsheet includes the FPKM value for each sample.

growth_protocol: THP1 Cells were cultured in 1640 medium supplemented with 10% FBS (Gibco) and 100U/ml Penicillin-Streptomycin in a humidified incubator at 37 °C with 5% CO2..

extract_protocol:
Total RNA was extracted using Trizol reagent.
The transcriptome library for sequencing was generated using VAHTSTM mRNA-seq v2 Library Prep Kit for Illumina® (Vazyme Biotech Co.,Ltd, Nanjing, China) following the manufacturer’s recommendations.

treatment_protocol: THP1 Cells were infected by VSV for 0 or 6 hours

value: Human epithelial cells

value: VSV infection

tag: time


title: ATAC-ARP1-KDM6A-KO-rep2


title: MAS98.12PR, Resistant, sample1

city: Oslo

first: Eivind Valen

last: Egeland

address: Ullernchausseen 70

department: Department of Tumor Biology, Institute for Cancer Research

country: Norway

institute: Oslo University Hospital

description: col S8 in raw_counts.txt

data_processing:
Fastq files were cropped to longest common read length, 75 bp, with Trimmomatic (v0.38).
Trimmed samples were aligned to grch38 with STAR (v2.7.8a), and transcript reference (GENECODE; v41) using default parameters.
Reads with better mapping to the mouse geneome (mm10) than grch38 were removed using XenoFilteR (v1.6)
Gene counts were retrieved with featureCounts from Subread.
Assembly: hg38
Supplementary files format and content: tab-delimited txt-file containes raw-counts from all Samples

source_name: triple negative breast cancer patient-derived xenograft

growth_protocol: Tumors were grown in Hsd: Athymic Nude-Foxn1nu

extract_protocol:
RNA was extracted with AllPrep DNA/RNA/miRNA Unviersal kit (Qiagen).
Libraries were prepared with Kapa RNA HyperPrep with dual index to generate cDNA, followed by Twist Human Comprehensive Exome for the mRNA capturing according to manufacturer's protocol. Amount of starting material 100 ng total RNA.

tag: paclitaxel sensitivity

value: Resistant

value: Untreated


title: neural progenitor cell, PRMT7knockdown-1, rep1


title: THP1 ZUFSP-knockdown+VSV

description: ZUFSP knockdown THP1 cells were collected for total RNA extraction with VSV infection for 6h.

value: ZUFSP knockdown


title: S4

description: replicate=S group biological replicate 4

value: Serratia marcescens FY

value: WT


title: MAS98.12, Sensitive, sample1

description: col S5 in raw_counts.txt

value: triple negative breast cancer patient-derived xenograft

value: Sensitive


title: S3

description: replicate=S group biological replicate 3


title: THP1 ZUFSP-knockdown

description: ZUFSP knockdown THP1 cells were collected for total RNA extraction without VSV infection.

value: no treatment


title: MUTT, 38445

value: Mixed Breed


title: GAHD, 38447

value: Galapagos Hunting Dog


title: GAHD, 38448

value: Whole Blood


title: S2

description: replicate=S group biological replicate 2


title: GAHD, 38446


title: neural progenitor cell, control, rep1

value: neural progenitor cell


title: 084NPC

type: RNA

city: Parkville

first: Alesha

middle: A

last: Thai

state: VIC

address: Department of Medical Oncology, 305 Grattan St

country: Australia

institute: Peter MacCallum Cancer Centre

hyb_protocol: Purified RNA was hybridized for 16 to 24 hours at 65°C in nCounter hybridization buffer with NanoString Reporter and Capture probes, using 8 μL Master Mix, 5 µL sample, and 2 µL Capture ProbeSet per sample.

scan_protocol: Once the hybridization reactions are removed from the thermal cycler, the samples are placed in the nCounter Prep Station for 3 hours. Next, the nCounter Digital Analyzer which is a multi-channel epifluorescence scanner collects raw data by taking images of the immobilized fluorescent reporters in the sample cartridge with a CCD camera through a microscope objective lens. Images are processed internally and the results are exported as a.csv file.

data_processing: The raw data as RCC files format were analyzed via the NanoString nCounter nSolver 4.0 software (MAN-C0019-08) with the NanoString Advanced Analysis 2.0 plugin (MAN-10,030-03) following the NanoString Gene Expression Data Analysis Guidelines (MAN-C0011-04). Both positive control and housekeeping normalization were used to normalize all sources of variation associated with the platform

label: biotin

source_name: pre treatment nasopharyngeal carcinoma biopsy

label_protocol: Per manufacturer recommendations, https://nanostring.com/products/ncounter-assays-panels/oncology/metabolic-pathways/.The purified RNA is diluted in nuclease-free water to 20 ng/uL. RNA (~100 ng) added for hybridization assay.

extract_protocol: RNA was extracted from tumour sections using the Roche High Pure FFPE RNA micro kit

treatment_protocol: Samples were not treated. Samples were collected at diagnosis, prior to treatment for NPC

value: F

tag: Stage

tag: survival


title: MUTT, 38444


title: THP1 Vec

description: THP1 cells were collected for total RNA extraction without VSV infection.


title: MUTT, 38443


title: Biotinylation-RNA-seq_Coilin_rep2_R1

city: Yokohama

first: Hidefumi

last: Suzuki

address: Fukuura 3-9

country: Japan

institute: Yokohama City University

data_processing:
For biotinylation-DNA-seq, adapter sequences were trimmed using Trim Galore (v 0.64_dev), and reads were mapped to human genome GRCH38 using the Bowtie2 alignment tool (version 2.3.5.1) with the default settings. The mapped reads from each in situ biotinylation-seq dataset were subjected to count per million (CPM) normalization and then used for downstream analysis. IP/input enrichment per gene was calculated with R (v. 4.0.2) and its package rtracklayer (version 1.48.0) using the Ensembl GRCH38.92 gene annotation model.
For biotinylation-RNA-seq, adapter sequences were trimmed using Trim Galore (v 0.64_dev), and reads were mapped to Ensembl gene annotation of human genome GRCh38.p13 using hisat2 (version). Read counts were obtained using Rsubread (version 2.2.6). Differential gene expression analysis was performed using R (v. 4.0.2) package DESeq2 (v. 1.28.1). Genes with an adjusted P-value <0.01 and absolute log2 fold-change >0.5 were included in the downstream analysis.
Assembly: GRCH38 and Drosophila melanogastergenome build5.41 from NCBI
Supplementary files format and content: BigWig files include normalized count data obtained from methods shown above.

molecule: nuclear RNA

source_name: HeLa

growth_protocol: HeLa cells  were cultured in Dulbecco’s modified Eagle’s medium (08458-45; Nacalai Tesque, Kyoto, Japan) with 10% foetal bovine serum and penicillin/streptomycin under 5% CO2 at 37 ºC.

extract_protocol:
For antibody-based in situ biotinylation-seq, HeLa cells cultured in 10 cm dish were fixed with 4% PFA and permeabilized with 0.5% Triton X-100. After blocking, cells were incubated with primary antibodies, and then incubated with HRP-labeled secondary antibodies. After washing, HRP-based in situ biotinylation was performed by incubating cells with biotinylation buffer. The cells were lysed in 1% SDS RIPA buffer and were sonicated for DNA fragmentation. The biotinylated chromatin was pulled-down using SoftLinkTM Soft Release Avidin Resin (Promega), and the chromatin DNA was purified.
The sequence libraries for in situ biotinylation DNA-seq were prepared using TruSeq ChIP Library Prep Kit (Illumina, San Diego, CA). The sequence libraries for in situ biotinylation RNA-seq were prepared using SMART-Seq Stranded Kit (Takara).

value: HeLa


title: Biotinylation-RNA-seq_Coilin_rep1_R1


title: Biotinylation-RNA-seq_Input_R1


title: SampleT-09

city: Toulouse

first: Leila

last: Khajavi

address: TOULOUSE

country: France

institute: INSERM

data_processing:
STAR  (v2.7.10a)
RSEM  (v1.3.1)
normalized via variance stabilizing transformation (vsd, DESeq2 function)
Assembly: Homo sapiens primary genome  sequence (Gencode: GRCh38, v27)
Supplementary files format and content: Expression matrix using RSEM

source_name: Lung tumor

extract_protocol:
RNA was extracted from FFPE slides with the “High Pure FFPE RNA Extraction Kit” from Roche.
The libraries were prepared with the KAPA RNA HyperPrep Kit with RiboErase (HMR) from Roche for whole transcriptome sequencin

value: Lung tumor

value: Stage  III


title: 162NPC

value: M


title: SampleT-10


title: a-LX-2 cells M3

city: Hefei

first: liangyun

last: li

address: 81 Meishan Road

institute: Anhui Medical University

data_processing:
ChIP-seq reads were aligned to the hg38 reference genome using Bowtie2(2.4.1)
Sam files were converted to Bam format using Samtools and used for peak calling
MACS2 (2.2.7.1) was used to call peaks with the sonicated input as a control and an initial threshold p-value of 0.001 as cutoff
Supplementary files format and content: GRCh38
Supplementary files format and content: bigwig files were generated using Deeptools(3.5.0)

growth_protocol: Culture with DMEM (Gibco, USA) and 10% fetal bovine serum (Gibco, USA)

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols. (non-default parameters: --max-n 0 --minimum-length 35) and Trimmomatic v0.38[2](non-default parameters: SLIDINGWINDOW:4:15 LEADING:10 TRAILING:10 MINLEN:35). Then FastQC[3](with default parameters) is used to ensure high reads quality. The clean reads were mapped to the mouse genome (assembly GRCm38) using the Bowtie2 v2.3.4.1[4](with default parameters) software. Duplicate reads were then removed using picard MarkDuplicates. Peak detection was performed using the MACS v2.1.2 [5](non-default parameters: -f BAMPE -g hs/mm -p 0.01) peak finding algorithm with 0.01 set as the p-value cutoff. Annotation of peak sites to gene features was performed using the ChIPseeker R package

tag: group

value: activated LX-2 Cells

value: Human hepatic stellate cells

tag: antibody


title: MUTT, 38441


title: SampleT-08

value: Stage  I


title: 065NPC


title: a-LX-2 cells M2

tag: cell type


title: SampleT-07

value: Stage  IV


title: 143NPCD1


title: MUTT, 38440


title: a-LX-2 cells M1


title: SampleT-06

value: Stage  II


title: 133NPC


title: SampleT-05


title: q-LX-2 cells N3

value: quiescent LX-2 Cells


title: 005NPC


title: MUTT, 38439


title: 160NPC


title: MUTT, 38438


title: SampleT-04


title: MUTT, 38442


title: 011NPC


title: MUTT, 38437


title: SampleT-03


title: q-LX-2 cells N1


title: MUTT, 38436


title: MUTT, 38435


title: CHLA06_Abema_REP_C

city: Tübingen

first: Daniel

middle: J.

last: Merk

address: Otfried-Müller-Str. 27

country: Germany

institute: Hertie-Institute for Clinical Brain Research

data_processing:
The libraries were sequenced as paired-end 50bp reads on an Illumina NovaSeq6000 (Illumina) with a sequencing depth of approximately 25 million clusters per sample.
Raw data QC and processing was performed using megSAP (version 0.2-135-gd002274) combined with ngs-bits package (version 2019_11-42-gflb98e63).
Reads were aligned using STAR v2.7.3a
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw read counts for each replicate.

source_name: tumor, central nervous system

growth_protocol: Cells were grown under optimized conditions in DMEM/F12 supplemented with B27, EGF, FGF (CHLA06) or RPMI supplemented with 10% FCS (BT16).

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 200ng of total RNA was used for the construction of sequencing libraries.
mRNA libraries were prepared using the NEB Next Ultra II Directional RNA Library Prep Kit

treatment_protocol: Cells were treated with 200nM abemaciclib or corresponding vehicle (DMSO).

value: tumor, central nervous system

value: atypical teratoid rhabdoid tumor

value: WT

tag: treatment

value: 200nM abemaciclib


title: SampleT-02


title: SampleT-01


title: CHLA06_Abema_REP_B


title: 142NPC

tag: Sex


title: MUTT, 38434

value: Mixed Breed

value: Whole Blood


title: MUTT, 38433


title: Sample-71


title: CHLA06_DMSO_REP_C

value: DMSO


title: Sample-72


title: 090NPC

tag: age


title: CHLA06_Abema_REP_A


title: 169NPC


title: 068NPC


title: MUTT, 38432


title: MUTT, 38431


title: 116NPC


title: Sample-70


title: Sample-69


title: q-LX-2 cells N2


title: 093NPC


title: CHLA06_DMSO_REP_A


title: BT16_Abema_REP_C


title: MUTT, 38429


title: MUTT, 38430


title: 058NPCD2


title: 167NPC


title: CHLA06_DMSO_REP_B


title: MUTT, 38428


title: Sample-67


title: BT16_Abema_REP_B


title: BT16_Abema_REP_A


title: 172NPC

value: F


title: MUTT, 38427


title: Sample-64

value: Lung tumor


title: Sample-66


title: 059NPC


title: 146NPC


title: BT16_DMSO_REP_C


title: MUTT, 38426


title: Sample-63


title: MUTT, 38425


title: BT16_DMSO_REP_A


title: 131NPC


title: Sample-68


title: 099NPC


title: BT16 C

growth_protocol: Cells were grown under optimized conditions in DMEM/F12 supplemented with B27, EGF, FGF (CHLA02, CHLA04, CHLA05, CHLA06), IMDM supplemented with 10% FCS and 1x IST (CHLA266, BT12), or RPMI supplemented with 10% FCS (BT16).

treatment_protocol: No treatment applied

value: atypical teratoid rhabdoid tumor (ATRT)


title: 180NPC

value: M


title: Sample-61


title: MUTT, 38424


title: Sample-59


title: BT16 A


title: Sample-60


title: 118NPC


title: BT16 B


title: MUTT, 38421


title: 051NPC


title: BT12 C


title: Sample-58


title: 177NPC


title: Sample-62


title: BT16_DMSO_REP_B


title: BT12 B


title: Sample-57

value: Stage  III


title: MUTT, 38418


title: MUTT, 38420


title: Sample-56A


title: MUTT, 38423


title: CHLA266 C


title: MUTT, 38417


title: MUTT, 38422


title: CHLA266 B


title: 117NPC


title: Sample-53


title: Sample-52


title: 143NPCD2


title: 054NPC


title: Sample-48


title: MUTT, 38419


title: CHLA266 A


title: MUTT, 38416


title: MUTT, 38414


title: 161NPC


title: 164NPC


title: CHLA06 C


title: Sample-47


title: 178NPC


title: CHLA06 B


title: BT12 A


title: Sample-46


title: 058NPCD1


title: Sample-45


title: MUTT, 38411


title: MUTT, 38412


title: 064NPC


title: MUTT, 38410


title: Sample-44


title: CHLA05 B


title: 066NPC


title: Sample-42


title: CHLA05 A


title: 055NPC


title: MUTT, 38409


title: Sample-40


title: MUTT, 38407


title: CHLA04 C


title: CHLA04 B


title: Sample-38


title: MUTT, 38406


title: CHLA06 A


title: CHLA04 A


title: Sample-37


title: 128NPC


title: MUTT, 38413


title: 077NPC


title: Sample-43


title: 105NPC


title: CHLA05 C


title: CHLA02 B


title: Sample-35


title: CHLA02 C


title: MUTT, 38415


title: Sample-32


title: MUTT, 38404


title: MUTT, 38403


title: 174NPC


title: CHLA02 A


title: 139NPC


title: MUTT, 38402


title: 017NPC


title: MUTT, 38401


title: Sample-29


title: MCF10A, F-YAP 5SA, serum-deprived, rep1

city: Daejeon

first: Daehee

last: Hwang

address: Yuseong-gu, Daehak-ro 291 Basic Science Bldg. (E6-6) #413

department: Biological Sciences

country: South Korea

institute: Korea Advanced Institute of Science and Technology

data_processing:
Raw reads were trimmed using TrimGalore (v0.6.7)
Index building and alignment were preformed using HISAT2 (v2.2.1)
Read counts were generated using FeatureCounts (v2.0.3)
DEGs were obtained by DESeq2 (v1.38.2)
Assembly: hg38
Supplementary files format and content: Raw CountMatrix file (.txt) obtained by FeatureCounts

growth_protocol: MCF10A cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM)-F12 (Welgene) supplemented with 5% horse serum (Invitrogen), epidermal growth factor (EGF, 20 ng/ml; Peprotech), insulin (10 μg/ml, Sigma), hydrocortisone (0.5 μg/ml, Sigma), cholera toxin (100 ng/ml, Sigma), and penicillin-streptomycin (Invitrogen). Cell culture incubator was set at 37℃ and 5% CO2

extract_protocol:
Harvested cell pellets were extracted using the RiboEx reagent (GeneAll) according to manufacturer's instructions
Library construction was performed using the TruSeq Stranded Total RNA Kit (Illumina)

treatment_protocol: Overnight serum-deprivation was performed by replacing growth medium with serum-free medium (same as growth medium, but without horse serum and EGF)

value: mammary epithelial

tag: expressing

value: F-YAP 5SA

value: Overnight (14 h) serum deprivation


title: MUTT, 38400


title: MUTT, 38405


title: MCF10A, F-YAP 5SA, rep2

tag: cell line


title: MUTT, 38399


title: 126NPC


title: Sample-28

tag: genotype

value: Stage  I


title: Sample-25

value: Stage  II


title: MCF10A, F-YAP 5SA, rep1


title: 061NPC


title: Sample-34


title: 063NPC


title: MUTT, 38398


title: MCF10A, Vec, serum-deprived, rep2

value: vector


title: MCF10A, Vec, serum-deprived, rep1


title: 145NPC


title: MUTT, 38396


title: Sample-31


title: 129NPC


title: 111NPC


title: Sample-24


title: MUTT, 38395


title: Sample-22


title: 154NPC


title: MCF10A, Vec, rep2


title: MCF10A, Vec, rep1


title: 135NPC


title: 150NPC


title: Sample-20


title: MUTT, 38394


title: 122NPC


title: Sample-19


title: MUTT, 38393


title: 60mins-48kd-r4_fadu

city: Heidelberg

first: Rebecca

middle: Emma

last: Wagner

address: Inf 280 im Neuenheimer Feld

department: Cell Biology and Tumor Biology

institute: DKFZ

description:
normalized_counts_TcRC.txt
normalized_counts_RC.txt
60mins-48kd-r4

data_processing:
Reads were aligned to the hs37d5 reference genome using STAR aligner
FeatureCounts was used for gene specific quantification fo reads on the appropriate gene annotation
Raw gene count values were then used as input for a differential gene expression analysis using DESeq2 within R
Bedtools were used to generate bedGraph files and bedGraphToBigWig was used to produce BigWig files.
Assembly: hs37d5
Library strategy: SLAM-seq

source_name: FaDu

growth_protocol: Keratinocytes were cultured with KBM-Gold (Lonza) medium  supplemented with 0.06mM CaCl and the essential growth factors supplied. FaDu cells were cultured with EMEM supplemented with 10% FBS and pen/strep. SCC25 cells were cultured in DMEM/F12 HEPES with 10% FBS and pen/strep. All cells were kept at 37 with 5% CO2

extract_protocol:
Total RNA was extracted using Trizol reagent, following manufacturer's instructions. DNA was purified using spin columns following manufacturer's instructions.
Total RNA from keratinocytes was rRNA depleted and RNA-sequencing libraries were prepped using NEB Ultra II directional kit (NEB). Total RNA from FaDu cells was used to prepare libraries using TruSeq stranded total RNA kit (Illumina). RNA from SCC25 cells and clones was used to generate RNA-sequencing libraries using stranded total RNA prep with Ribo-zero plus kit (Illumina). SLAM-sequencing libraries were prepared using Quant-seq 3' mRNA library prep kit (Lexogen). Libraries were prepared from purified DNA using the SimpleChIP, ChIP-seq DNA library prep kit for illumina (CST).

treatment_protocol: SRSF2 depletion was achieved by transfecting an siRNA pool using Lipofectamine RNAiMax

value: FaDu

value: squamous cell carcinoma cells

value: siRNA transfection + 4sU


title: Sample-18


title: 60mins-48kd-r5_fadu

description:
normalized_counts_TcRC.txt
normalized_counts_RC.txt
60mins-48kd-r5


title: MUTT, 38392

value: Mixed Breed


title: Sample-17

value: Stage  IV


title: 134NPC


title: Sample-23


title: MUTT, 38397

value: Whole Blood


title: 60mins-48kd-r3_fadu

description:
normalized_counts_TcRC.txt
normalized_counts_RC.txt
60mins-48kd-r3


title: 101NPC


title: MUTT, 38391


title: Sample-16


title: 60mins-48kd-r2_fadu

description:
normalized_counts_TcRC.txt
normalized_counts_RC.txt
60mins-48kd-r2


title: Sample-15


title: 60mins-48kd-r1_fadu

description:
normalized_counts_TcRC.txt
normalized_counts_RC.txt
60mins-48kd-r1


title: 032NPC


title: Sample-14


title: 60mins-ctr-r3_fadu

description:
normalized_counts_TcRC.txt
normalized_counts_RC.txt
60mins-ctr-r3


title: MUTT, 38388


title: Sample-12


title: 104NPC


title: 60mins-ctr-r2_fadu

description:
normalized_counts_TcRC.txt
normalized_counts_RC.txt
60mins-ctr-r2


title: 168NPC


title: MUTT, 38386


title: MUTT, 38387


title: Sample-10


title: Sample-04


title: 014NPC


title: 004NPC


title: MUTT, 38385


title: 30mins-48kd-r5_fadu

description:
normalized_counts_TcRC.txt
normalized_counts_RC.txt
30mins-48kd-r5


title: Sample-08


title: 60mins-ctr-r1_fadu

description:
normalized_counts_TcRC.txt
normalized_counts_RC.txt
60mins-ctr-r1


title: MUTT, 38389


title: MUTT, 38384


title: 30mins-48kd-r2_fadu

description:
normalized_counts_TcRC.txt
normalized_counts_RC.txt
30mins-48kd-r2


title: Sample-03


title: MUTT, 38390


title: 30mins-48kd-r3_fadu

description:
normalized_counts_TcRC.txt
normalized_counts_RC.txt
30mins-48kd-r3


title: MUTT, 38383


title: 153NPC

value: F


title: 109NPC


title: Sample-02

value: Lung tumor


title: 30mins-ctr-r5_fadu

description:
normalized_counts_TcRC.txt
normalized_counts_RC.txt
30mins-ctr-r5


title: MUTT, 38382


title: Sample-01


title: 136NPC


title: 034NPC


title: 047NPC


title: 30mins-ctr-r3_fadu

description:
normalized_counts_TcRC.txt
normalized_counts_RC.txt
30mins-ctr-r3


title: ChIP DSRCT3.INPUT

city: Charlestown

first: Rui

last: Dong

state: MA

address: 149 13th Street

institute: Massachusetts General Hospital

data_processing:
Reads were aligned to hg19 using bwa (Li and Durbin, 2009). Aligned reads were then filtered to exclude PCR duplicates.
Assembly: hg19
Supplementary files format and content: Aligned reads were extended to 200 bp to approximate fragment sizes. Density maps were generated by counting the number of fragments overlapping each position using igvtools, and normalized to 10 million reads.

source_name: INPUT

extract_protocol:
Chromatin from formaldehyde-fixed cells (2-5 x 10^6 cells per epitope) was fragmented to a size range of 200 - 700 bases with a Branson 250 Sonifier. Solubilized chromatin was immunoprecipitated with the indicated antibodies and Protein G-Dynabeads (Life Technologies). Immunoprecipitated DNA was extracted with AMP Pure beads(Beckman Coulter) after crosslink reversal, RNAse A and Proteinase K treatment.
ChIP DNA samples were used to generate Illumina sequencing libraries following standard protocols.

value: DSRCT

value: untreated


title: MUTT, 38380

extract_protocol: Genomic DNA was extracted from whole blood using Proteinase K and phenol/chloroform with standard protocols.


title: MUTT, 38379


title: ChIP DSRCT3.H3K9ac


title: 108NPC

value: M


title: 30mins-ctr-r2_fadu

description:
normalized_counts_TcRC.txt
normalized_counts_RC.txt
30mins-ctr-r2


title: 30mins-ctr-r1_fadu

description:
normalized_counts_TcRC.txt
normalized_counts_RC.txt
30mins-ctr-r1


title: 176NPC


title: MUTT, 38378


title: ChIP DSRCT3.H3K4me1


title: 001NPC


title: ChIP DSRCT3.H3K4me3


title: MUTT, 38377


title: 15mins-48kd-r4_fadu

description:
normalized_counts_TcRC.txt
normalized_counts_RC.txt
15mins-48kd-r4


title: 15mins-48kd-r5_fadu

description:
normalized_counts_TcRC.txt
normalized_counts_RC.txt
15mins-48kd-r5


title: 30mins-ctr-r4_fadu

description:
normalized_counts_TcRC.txt
normalized_counts_RC.txt
30mins-ctr-r4


title: 158NPC


title: MUTT, 38376


title: 166NPC


title: ChIP DSRCT3.H3K27me3


title: ChIP DSRCT3.H3K27ac


title: 15mins-48kd-r3_fadu

description:
normalized_counts_TcRC.txt
normalized_counts_RC.txt
15mins-48kd-r3


title: MUTT, 38381


title: MUTT, 38375


title: MUTT, 38374


title: 786-O, Non Target  siRNA, rep 3

city: Paris

first: Marco

last: PONTOGLIO

state: Choisir votre état

address: Inserm U1016, 24 rue du Faubourg Saint-Jacques

department: Growth and Signalling

institute: Inserm

description:
RSEM counts
siNT_3_S11

data_processing:
RNA-seq reads were aligned to the hg38 genome assembly using STAR version=2.7.0.d
Reads counts per genes were computed with RSEM and the Homo_sapiens.GRCh38.83.gtf annotation
A raw matrix contain the RSEM counts with the human gene names
Assembly: hg38
Supplementary files format and content: Reads counts by sample done by RSEM
Supplementary files format and content: A tab-delimited matrix that  include counts values for each sample

growth_protocol: 786-O cells were cultured in Roswell Park Memorial Institute (RPMI) medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin at 37C with 5% CO2.

extract_protocol:
Cells were collected in TRIzol and RNA was extracted following the manufacturer’s instructions.
Libraries were prepared from 250 ng of total RNA per sample using the Stranded mRNA Prep kit (Illumina).

treatment_protocol: HNF1B-siRNA or non-targeting-siRNA pools (Dharmacon) were transfected in 786-O cells using Lipofectamine RNAiMAX at a final concentration of 37.5 nM. Cells were collected in Trizol for RNA extraction 48 hours after transfection.

value: Human renal cell carcinoma

value: Non targeting siRNA

tag: cell cycle_stage

value: Asynchronous


title: Urostyle, stage 61, rep1

city: Cambridge

first: Gayani

last: Senevirathne

address: 11 Divinity Avenue

department: Human Evolutionary Biology

institute: Harvard University

data_processing:
Adapter sequences were trimmed from the raw paired end 100-bp files using NGmerge (Gaspar 2018) and the trimmed sequences were aligned to the X. tropicalis reference genome v. 9.1using Bowtie2.
Duplicated reads were removed from the subsequent analyses using Picard (http://broadinstitute.github.io/picard/)
Peaks were called using MACS2 (Zhang et al. 2008) (--nomodel --extsize 200 --shift -100 --nolambda) and Genrich (-e chrM -r -j).
Irreproducible discovery rate (IDR) <0.01 was used as the threshold to screen the replicate samples.
Assembly: Xenopus_tropicalis_v9.1

organism: Xenopus tropicalis

source_name: Urostyle

extract_protocol:
The tadpoles were anesthetized in MS-222, dissected on ice-cold 1X PBS and were mechanically crushed using a pestle (cleaned using 100% ethanol prior to this step) to obtain a homogenized sample.
The subsequent steps followed the OMNI-ATAC seq protocol (Buenrostro et al. 2015; Corces et al. 2017) with slight modifications using the Illumina Tagment DNA Enzyme and Buffer kit.

value: Urostyle


title: Urostyle, stage 65, rep1


title: 110NPC


title: 15mins-48kd-r2_fadu

description:
normalized_counts_TcRC.txt
normalized_counts_RC.txt
15mins-48kd-r2


title: 786-O, Non Target  siRNA, rep 2

description:
RSEM counts
siNT_2_S7


title: Urostyle, stage 56, rep1


title: MUTT, 38373

tag: breed


title: MUTT, 38372

tag: tissue


title: 15mins-48kd-r1_fadu

description:
normalized_counts_TcRC.txt
normalized_counts_RC.txt
15mins-48kd-r1


title: 15mins-ctr-r5_fadu

description:
normalized_counts_TcRC.txt
normalized_counts_RC.txt
15mins-ctr-r5


title: MSC 3

city: No. 94, Weijin Road, Nankai District, Tianjin

first: guoqiang

last: chen

state: Tianjin

institute: nankai university

data_processing:
Data filtering: The raw data was filtered with SOAPnuke (v1.6.5)  by 1) Removing reads containing adapters (adapter contamination); 2) Removing reads whose unknown base ('N' base) ratio is more than 1%; 3) Removing reads whose low-quality base ratio (Base quality less than or equal to 15) is more than 40%, afterwards clean reads were obtained and stored in FASTQ format. Reference genome mapping： The clean data were mapped to the reference genome by HISAT (v2.2.1) . Reference gene mapping: The clean data were mapped to the assembled unique gene by Bowtie2 (v2.4.5)  . The expression level of genes was calculated by RSEM (v1.3.1) . Gene Annotation: Using public database (KEGG, GO, etc.) to annotate the genes. Time Series and WGCNA analysis: Time Series analysis was performed by Mfuzz (v2.60.0) , and gene co-expression network analysis was performed by WGCNA (v1.71). Differential Gene Expression: Between-group differential gene analysis was performed using DEseq2/DEGSeq under the conditions of Fold Change ≥ 2 and Adjusted P value ≤ 0.001 (Depends on projects). PoissonDis was performed between-sample differential gene analysis under the conditions of Fold Change ≥ 2 and FDR ≤ 0.001 (Depends on projects). Using the pheatmap function on the differential gene set to draw a heatmap of differential gene clusters. According to the GO and KEGG annotation results and classifications, the differentially expressed genes were functionally classified, the phyper in R software was used for KEGG enrichment analysis, and the TermFinder package was used for GO Enrichment analysis. With a Q value of ≤ 0.05 as the threshold, candidate genes that met this condition were defined as significantly enriched.
Assembly: Homo sapiens(human:NCBI GCF 000001405.39 GRCh38.p13)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Mesenchymal stem cell

extract_protocol:
Total RNA was extracted from MSC and MSC aggregates using TRI Reagent (Merck Sigma Aldrich, Darmstadt, Germany); 1.3 ug of total RNA was used for the construction of sequencing libraries.
1 Sample QC Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 mRNA Isolation A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads. 3 mRNA Fragmentation The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented. 4 cDNA Synthesis Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA. 5 End Repair, Add A and Adaptor Ligation After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs. 6 PCR The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC The corresponding library quality control protocol will be selected depending upon product requirements. 8 Circularization Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested. 9 Sequencing Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

value: Mesenchymal stem cell

value: WT

value: Interferon-γ stimulation


title: 786-O, Non Target  siRNA, rep 1

description:
RSEM counts
siNT_1_S3


title: 15mins-ctr-r4_fadu

description:
normalized_counts_TcRC.txt
normalized_counts_RC.txt
15mins-ctr-r4

value: FaDu

value: squamous cell carcinoma cells


title: MUTT, 38370

value: Mixed Breed


title: 15mins-ctr-r3_fadu

description:
normalized_counts_TcRC.txt
normalized_counts_RC.txt
15mins-ctr-r3

value: siRNA transfection + 4sU


title: MSC 2

address: No. 94, Weijin Road, Nankai District, Tianjin


title: 786-O, HNF1B siRNA, rep 3

description:
RSEM counts
siB_3_S12

value: HNF1B siRNA


title: 786-O, HNF1B siRNA, rep 2

description:
RSEM counts
siB_2_S8


title: MUTT, 38369

value: Whole Blood


title: engineered MSC aggregates 3


title: engineered MSC aggregates 2


title: 786-O, HNF1B siRNA, rep 1

description:
RSEM counts
siB_1_S4


title: 15mins-ctr-r2_fadu

description:
normalized_counts_TcRC.txt
normalized_counts_RC.txt
15mins-ctr-r2


title: CIMA67_hp199b

city: NEWCASTLE UPON TYNE

first: David

last: Young

address: Centre For Life

country: United Kingdom

institute: Newcastle University

data_processing:
Kallisto was used for pseudo-alignment and quantification, against the human transcriptome.
Mapped transcripts were converted to a gene level using Tximport.
DESeq2 was used to calculate P-values and log2 fold-changes (logFC), using the Benjamini-Hochberg method to adjust for multiple testing.
Assembly: GRCh38

source_name: cartilage

extract_protocol:
RNA was extracted from the cells using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific), following the manufacturer’s protocol to isolate total RNA.
cDNA libraries generated using the Illumina TruSeq Stranded mRNA protocol

treatment_protocol: For the modulation of miR-199 levels in HAC, Dharmacon miRIDIAN hairpin inhibitor against miR-199a-5p or miR-199b-5p or Dharmacon miRIDIAN miRNA hairpin inhibitor nontargeting Control #2 (IN-002005-01) were transfected into 40%–50% confluent HAC using Dharmafect 1 lipid reagent (Horizon Discovery) at 100 nM final concentration.  24 hours later RNA was isolated following the miRVana protocol, quality assessed, and cDNA libraries generated

value: cartilage

value: chondrocyte


title: MUTT, 38368

data_processing:
Image data was analyzed using GenomeStudio with GT module (Illumina).
genotypes AA, AB, BB, NC=no call


title: hom2_r5_fadu

description:
normalized_counts_annotation_clones.txt
hom2_r5

data_processing:
Reads were aligned to the hs37d5 reference genome using STAR aligner
FeatureCounts was used for gene specific quantification fo reads on the appropriate gene annotation
Raw gene count values were then used as input for a differential gene expression analysis using DESeq2 within R
Bedtools were used to generate bedGraph files and bedGraphToBigWig was used to produce BigWig files.
Assembly: hs37d5

value: CrisprCas9 transfection and single cell sorting


title: CIMA67_hp199a


title: 65, coccyx, rep3

data_processing:
Sequence quality was checked using FastQC and, Adapter sequences were trimmed using Cutadapt (version 1.8.1)
Trimmed sequences were mapped to Xenopus_tropicalis_v9.1  to impelement a normal alignment using HTSeq v.0.13.5.
Read count extraction and normalization were performed using  HTSeq2
Assembly: Xenopus_tropicalis_v9.1
Supplementary files format and content: Tab deliminated text files with gene counts for each sample

source_name: Coccyx

extract_protocol:
RNA was harvested using Laser capture microdissection of targeted tissues which were frozen in OCT. RNA extractions followed the spatial transcriptomic protocol, Geo-seq using the TAKARA NucleoSpin® RNA XS kit.
cDNA and libraries were generated using the SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (with the number of amplification cycles set to 18).

value: Coccyx

value: stage 65


title: CIMA67_hpC


title: MUTT, 38366


title: hom2_r4_fadu

description:
normalized_counts_annotation_clones.txt
hom2_r4


title: MUTT, 38367


title: hom2_r3_fadu

description:
normalized_counts_annotation_clones.txt
hom2_r3


title: 65, hypochord, rep3

source_name: Hypochord

value: Hypochord


title: MUTT, 38365


title: CIMA64_hp199b


title: hom2_r2_fadu

description:
normalized_counts_annotation_clones.txt
hom2_r2


title: MUTT, 38364


title: CIMA64_hp199a


title: hom2_r1_fadu

description:
normalized_counts_annotation_clones.txt
hom2_r1


title: 61, coccyx, rep3

value: stage 61


title: 61, hypochord, rep3


title: CIMA64_hpC


title: CIMA56_hp199b


title: MUTT, 38363


title: hom1_r5_fadu

description:
normalized_counts_annotation_clones.txt
hom1_r5


title: MUTT, 38362


title: 56, coccyx, rep3

value: stage 56


title: MUTT, 38361


title: hom1_r4_fadu

description:
normalized_counts_annotation_clones.txt
hom1_r4


title: 65,coccyx, rep2


title: 56,Hypochord, rep3


title: hom1_r3_fadu

description:
normalized_counts_annotation_clones.txt
hom1_r3


title: 65,hypochord, rep2


title: CIMA56_hp199a


title: MUTT, 38360


title: CIMA56_hpC


title: MUTT, 38359


title: 65,hypochord, rep1


title: hom1_r2_fadu

description:
normalized_counts_annotation_clones.txt
hom1_r2


title: CIMA55_hp199b


title: hom1_r1_fadu

description:
normalized_counts_annotation_clones.txt
hom1_r1


title: 65,coccyx, rep1


title: CIMA55_hp199a


title: MUTT, 38358


title: MUTT, 38357


title: 61,hypochord, rep2


title: CIMA55_hpC


title: het_r4_fadu

description:
normalized_counts_annotation_clones.txt
het_r4


title: 61,coccyx, rep2


title: MUTT, 38356


title: MUTT, 38355


title: MUTT, 38354


title: 61,hypochord, rep1


title: het_r3_fadu

description:
normalized_counts_annotation_clones.txt
het_r3


title: 61,coccyx, rep1


title: HH27_H3K27me3-E009

city: Toyonaka

first: Takamasa

last: Ito

state: Osaka

address: 1-1 Machikaneyama

department: Biological Science

institute: Osaka University

data_processing:
The quality of the FASTQ files for ChIP-seq data was assessed using Trim Galore script. Paired-end sequencing reads were mapped to the galGal6 (GRCg6a) genome using the Bowtie2 tool with default parameters (Langmead, B. & Salzberg, S. L., 2012). The resulting BAM files were sorted and indexed using SAMtools (Li, H. et al., 2009). Duplicate reads were marked and removed using Picard (http://broadinstitute.github.io/picard/). RPKM and ChIP/Input values were calculated using the bamCompare tool from deepTools2, and bigwig files were generated.
Supplementary files format and content: bigwig

organism: Gallus gallus

source_name: whole embryo

growth_protocol: Eggs were incubated at 37.5°C. The cell culture medium dedicated to chickens was as follows: RPMI medium 1640 (Gibco), 10% fetal bovine serum, 1% chicken serum and 0.1% 2-mercaptoethanol.

extract_protocol:
or chromatin immunoprecipitation, antibodies against histones H3K9me3, H3K4me2 and H3K27me3 were used. These antibodies were kindly provided by Hiroshi Kimura, Tokyo Institute of Technology. Chromatin isolation and immunoprecipitation were performed as previously reported (Shang, WH et al., 2013). Briefly, 1.0 × 109 cells from DT40 cells and six HH27 embryos were washed twice with PBS and once with RSB (10 mM HEPES-NaOH at pH 7.4, 15 mM NaCl, 1.5 mM MgCl2). The recovered cells were then gently suspended in RSB with 1% Triton X-100 and left on ice for 5 min. The cell pellet was dissolved in Buffer A (15 mM HEPES-NaOH at pH 7.4, 15 mM NaCl, 60 mM KCl, 0.34 M sucrose, 0.5 mM spermidine, 0.15 mM spermine, 1 mM DTT, protease inhibitor without EDTA). The cells were mixed by inversion. The cell nuclear fraction was collected and digested with excess MNase (60 U/ml) (TaKaRa) at 37°C for 1 h, and then mixed with 200 µl of 0.5 M EDTA and divided into five small tubes. Collected cells were dissolved in 450 µl of 10 mM EDTA/tube and 50 µl of 5 M NaCl and placed on ice for 5min. They were then centrifuged (10,000 g, 4℃, 5 min) and mixed with the supernatant and 10 ml Buffer B (20 mM Tris-HCl at pH8.0, 5 mM EDTA, 500 mM NaCl, 0.2% Tween 20, protease inhibitor without EDTA) and 100 µl of Protein G-Sepharose conjugated with antibodies for H3K9me3, H3K4me2, or H3K27me3 (50% slurry) were mixed at 4°C for 2–4 h. The recovered beads were washed five times with 1 ml of Buffer B and once with 1 ml of TE buffer. Collected beads were dissociated in 300 µl TESS (10 µl of 1M Tris-HCl at pH 8.0, 60 µl of 5 M NaCl, 50 µl of 10% SDS, 10 µl of 0.5 M EDTA, 870 µl of distilled water) and 3 µl of 20 mg/ml ProK and incubated at 55°C, overnight (O/N).
DNA was extracted from immunoprecipitates and run on a HiSeq 2000 DNA sequencer (Illumina).

value: whole embryo


title: het_r1_fadu

description:
normalized_counts_annotation_clones.txt
het_r1


title: HH27_H3K27me3-E006


title: 58,coccyx, rep2

value: WT

value: stage 58


title: HH27_input-001

value: input


title: MUTT, 38353

city: Bethesda

first: Alexander

last: Harris

address: 50 South Drive

institute: National Institutes of Health


title: 58,hypochord, rep2


title: het_r2_fadu

description:
normalized_counts_annotation_clones.txt
het_r2

value: FaDu

value: squamous cell carcinoma cells


title: HH27_H3K27me3-E002


title: HH27_H3K9me3-x5Emix


title: empty_r5_fadu

description:
normalized_counts_annotation_clones.txt
empty_r5


title: MCF10A, F-YAP 5SA, serum-deprived, rep2

value: mammary epithelial

value: F-YAP 5SA

value: Overnight (14 h) serum deprivation


title: 56,hypochord, rep1


title: MUTT, 38351

value: Mixed Breed

value: Whole Blood


title: empty_r3_fadu

description:
normalized_counts_annotation_clones.txt
empty_r3

value: CrisprCas9 transfection and single cell sorting


title: het_r5_fadu

description:
normalized_counts_annotation_clones.txt
het_r5


title: empty_r4_fadu

description:
normalized_counts_annotation_clones.txt
empty_r4


title: HH27_H3K9me3-E004


title: 56,coccyx, rep1

value: Coccyx


title: MUTT, 38349


title: empty_r2_fadu

description:
normalized_counts_annotation_clones.txt
empty_r2


title: PET_100 mg/L

city: Jinju

first: June-Woo

last: Park

address: 17, Jegok-gil, Munsan-eup

department: Environmental Risk Research

institute: Korea Institute of Toxicology

data_processing:
NovaSeq Reagent Kit version: NovaSeq 6000 S4 Reagent Kit (300 cycles) 20012866Control Software version: NovaSeq Control Software v1.7 Real Time Analysis version: RTA3CASAVA(bcl2fastq) version: bcl2fastq v2.20.0.422
Sequence assembly was performed using the Trinity  v2.04 . The sequence assembly process of Trinity consists of three steps: Inchworm, Chrysalis, and Butterfly.
assembled UNIGENE and the predicted CDS based on it, a search method  Blast was used to search for DNA sequence homology.h, InterProScan was used to search for protein sequence homology.
the expression level by tissue was performed using the RSEM. RSEM uses Bowtie to align reads to transcripts and then measures the expression level of transcripts using a directed graph model
Genome_build: N/A
Supplementary_files_format_and_content: unprocessed sequence file
Supplementary_files_format_and_content: Assembled sequence file
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Cyprinodon variegatus

source_name: sheepshead minnow, 10d, PET 100 mg/L

growth_protocol: The sheepshead minnow larvae (72hpf) was exposed to PET microfibers (10, 100 mg/L), and surfactant control (tween80 0.001%) for 10days.

extract_protocol:
RNA was prepared using the RNeasy Mini kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). It was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: PET_100 mg/L

value: Whole body

tag: developmental stage


title: empty_r1_fadu

description:
normalized_counts_annotation_clones.txt
empty_r1


title: MUTT, 38348

source_name: Whole Blood


title: HH27_H3K9me3-E001


title: PET_10 mg/L

source_name: sheepshead minnow, 10d, PET 10 mg/L

value: PET_10 mg/L


title: MUTT, 38347


title: kd_48hr_r5_scc25

description:
normalized_counts_annotation_scc25.txt
kd_48hr_r5

value: siRNA transfection


title: Control

source_name: sheepshead minnow, 10d, no treatment

value: Control


title: kd_48hr_r4_scc25

description:
normalized_counts_annotation_scc25.txt
kd_48hr_r4


title: MUTT, 38352


title: Surfactant control

source_name: sheepshead minnow, 10d, tween 80, 0.001%

value: Surfactant control


title: HH27_H3K4me2-E005

value: whole embryo


title: kd_48hr_r3_scc25

description:
normalized_counts_annotation_scc25.txt
kd_48hr_r3


title: HH27_H3K4me2-E008


title: MUTT, 38346


title: GR245DS_6h_Rep3

city: beijing

first: jiayang

last: shi

address: No.1 House, West Beichen Road

institute: University of Chinese Academy of Sciences

data_processing:
The quality of raw sequencing reads in RNA-seq was assessed using fastp tool. Reads containing ambiguous nucleotides or with a length < 20 nt were filtered out by fastp.
RNA-seq raw reads were mapped to the S. bicolor reference genomeV3.1.1 annotation using HISAT2.
Gene expression was shown as fragments per kilobase of exon per million mapped fragments (FPKM) by using featureCounts.
The differentially expressed genes were analyzed using DESeq2 (version 1.22.1) with the P value being corrected by the Benjamini & Hochberg method. Genes with FDR < 0.05 and fold change > 2 were considered as differentially expressed genes.
Assembly: Sorghum_bicolor genome_v3.1.1
Supplementary files format and content: tab_delimited text file includes raw counts for each Sample
Supplementary files format and content: tab_delimited text file includes RPKM values for each Sample

organism: Sorghum bicolor

source_name: Roots

extract_protocol:
The plant total RNA was extracted using the RNAprep Pure Plant Kit (Tiangen, Beijing, China) according the instructions provided by the manufacturer. A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology (Shanghai) Co., Ltd.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: Roots


title: HH27_H3K9me3-E007


title: MUTT, 38345


title: MUTT, 38350


title: MUTT, 38344


title: kd_48hr_r2_scc25

description:
normalized_counts_annotation_scc25.txt
kd_48hr_r2


title: DT40_input

value: input


title: kd_48hr_r1_scc25

description:
normalized_counts_annotation_scc25.txt
kd_48hr_r1

value: squamous cell carcinoma cells


title: HH27_H3K4me2-E003


title: GR245DS_6h_Rep1


title: MUTT, 38343


title: DT40_H3K27me3


title: ctr_r5_scc25

description:
normalized_counts_annotation_scc25.txt
ctr_r5


title: GR245DS_6h_Rep2


title: HH27_H3K4me2-x5Emix


title: MUTT, 38342


title: ctr_r4_scc25

description:
normalized_counts_annotation_scc25.txt
ctr_r4


title: MUTT, 38341


title: DT40_H3K9me3


title: DT40_H3K4me2


title: GR245DS_3h_Rep2


title: ctr_r3_scc25

description:
normalized_counts_annotation_scc25.txt
ctr_r3


title: GR245DS_3h_Rep1


title: MUTT, 38340


title: ctr_r2_scc25

description:
normalized_counts_annotation_scc25.txt
ctr_r2


title: MUTT, 38339


title: GBA3_IR [GBA_UOX_Diabetic]

city: Esch sur Alzette

first: Alise

last: Zagare

state: Belval

address: 7 Avenue des Hauts-Fourneaux

country: Luxembourg

institute: University of Luxembourg

data_processing:
Reads were mapped with Bowtie2
Assembly: hg19
Supplementary files format and content: count_matrix.csv

source_name: Midbrain organoids

growth_protocol: Nickels, 2020

extract_protocol:
RNA was extracted using Qiazol (QIAGEN #79306). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries  were prepared using TruSeq stranded mRNA library prep kit (Illumina #20020594)

tag: subject status

value: insulin resistant healthy individual

value: Midbrain organoids

value: High insulin


title: MOCK_6h_Rep3


title: MOCK_6h_Rep2


title: GBA2_IS [GBA_KT16_LI]

value: insulin sensitive healthy individual

value: Low insulin


title: MOCK_6h_Rep1


title: MUTT, 38337

value: Mixed Breed

value: Whole Blood


title: 48kd_r5_fadu

description:
final_normalized_counts_annotation_fadu.txt
X48kd.r5

value: FaDu


title: GBA2_IR [GBA_KT16_Diabetic]


title: GR245DS_3h_Rep3


title: MUTT, 38336


title: 48kd_r2_fadu

description:
final_normalized_counts_annotation_fadu.txt
X48kd.r2


title: MOCK_3h_Rep2


title: MOCK_3h_Rep3


title: MUTT, 38335


title: GBA1_IS [GBA_309_LI]


title: MUTT, 38334


title: 48kd_r1_fadu

description:
final_normalized_counts_annotation_fadu.txt
X48kd.r1


title: GBA3_IS [GBA_UOX_LI]


title: GBA1_IR [GBA_309_Diabetic]


title: MOCK_3h_Rep1


title: MUTT, 38333


title: CTRL3_IR [CTRL23338_Diabetic]

value: wt/wt


title: phosphorus deficiency_7d_Rep3

description: Raw gene count.annot.txt

value: phosphorus deficiency_7d


title: CTRL3_IS [CTRL23338_LI]


title: ctr_r5_fadu

description:
final_normalized_counts_annotation_fadu.txt
ctr.r5

value: siRNA transfection


title: MUTT, 38338


title: ctr_r1_scc25

description:
normalized_counts_annotation_scc25.txt
ctr_r1


title: ctr_r4_fadu

description:
final_normalized_counts_annotation_fadu.txt
ctr.r4


title: phosphorus deficiency_7d_Rep2

description: Raw gene count.annot.txt


title: CTRL2_IS [CTRL56_LI]


title: ctr_r3_fadu

description:
final_normalized_counts_annotation_fadu.txt
ctr.r3


title: 48kd_r4_fadu

description:
final_normalized_counts_annotation_fadu.txt
X48kd.r4


title: phosphorus deficiency_7d_Rep1

description: Raw gene count.annot.txt


title: CTRL2_IR [CTRL56_Diabetic]


title: MUTT, 38331


title: MUTT, 38330


title: phosphorus deficiency_4d_Rep3

description: Raw gene count.annot.txt

value: phosphorus deficiency_4d


title: MUTT, 38329


title: CTRL4_IR [CTRL48_Diabetic]


title: MUTT, 38328


title: CTRL4_IS [CTRL48_LI]


title: CTRL3_IS [AZ_9_LowInsulin]

data_processing:
Reads were mapped with Bowtie2
Assembly: hg19
Supplementary files format and content: feature_counts_WTs.csv


title: MOCK_7d_Rep3

description: Raw gene count.annot.txt


title: healty control 7

city: Shanghai

first: Ye

last: Zhao

address: 197 Ruijin Er Road

institute: Ruijin Hospital

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

source_name: Human esophagus biopsy from healthy conrols

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer’s instructions. RNA integrity was assessed on the Agilent Bioanalyzer 2100 system. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease

value: healty control


title: MUTT, 38327


title: CTRL2_IS [AZ_8_LowInsulin]


title: healty control 6


title: CTRL1_IS [AZ_7_LowInsulin]


title: MUTT, 38326


title: MOCK_7d_Rep1

description: Raw gene count.annot.txt


title: healty control 5


title: MUTT, 38325


title: MUTT, 38332


title: CTRL3_IR [AZ_3_Ctrl]


title: healty control 4


title: MUTT, 38324


title: CTRL2_IR [AZ_2_Ctrl]


title: ctr_r1_fadu

description:
final_normalized_counts_annotation_fadu.txt
ctr.r1


title: MOCK_4d_Rep3

description: Raw gene count.annot.txt


title: healty control 3


title: MOCK_4d_Rep2

description: Raw gene count.annot.txt


title: phosphorus deficiency_4d_Rep2

description: Raw gene count.annot.txt


title: ctr_r2_fadu

description:
final_normalized_counts_annotation_fadu.txt
ctr.r2


title: phosphorus deficiency_4d_Rep1

description: Raw gene count.annot.txt


title: healty control 8


title: CTRL1_IR [AZ_1_Ctrl]


title: MOCK_7d_Rep2

description: Raw gene count.annot.txt


title: MOCK_4d_Rep1

description: Raw gene count.annot.txt


title: healty control 2


title: DN3(IK)-3day, H3K27me3, ChIP-seq, rep2

city: Hershey

first: Bing

last: He

state: PA

address: 500 University Dr

institute: Penn State University

data_processing:
Sequencing reads were mapped to the mouse genome (mm9) using Bowtie2 (v2.2.2) with default parameter setting
Samtools and PICARD were used for QC of mapped reads (MAPQ>30).
ChIP-Seq peaks were called by MACS2 using default parameter setting
Assembly: mm9
Supplementary files format and content: bigWig

organism: Mus musculus

source_name: JE131 cell line (DN3 cells)

growth_protocol: cells were cultured in RPMI1640 with 10% FBS at 37℃ with 5% CO2

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to instructions for Illumina ChIP-seq DNA sample prep kit or Quanta Bio sparQ DNA Library Prep Kit.

treatment_protocol: DN3 cells were transduced with retrovirus that contains HA-tagged wild-type murine Ikaros for 1 day, 2 days and 3 days.

value: JE131 cell line (DN3 cells)

value: an early T leukemia cell line that is derived from Ikaros knock-out mice

value: DN3 cells transduced with Ikaros for 3 days

tag: chip antibody


title: healty control 1


title: DN3(IK)-3day, H3K27me3, ChIP-seq, rep1


title: MUTT, 38321


title: MUTT, 38319


title: Brain, Parietal lobe ONT, PL

city: Rochester

first: Roberto

last: Cattaneo

state: MN

address: 222 3rd Ave SW

department: Molecular Medicine

institute: Mayo Clinic

description:
targeted RNA
cbDVG_refined_list_ont.txt

data_processing:
quality filtered with NanoFilt, alignment with minimap2 and a new pipeline for cbDVG detection
Assembly: https://github.com/jbloomlab/MeV_SSPE_Dynamics/blob/main/config/ref/MeVChiTok-SSPE.fa
Supplementary files format and content: tab-delimited text raw counts of cbDVG from ONT RNA seq samples

source_name: Brain

extract_protocol:
RNA was extracted from frozen brain specimens using Trizol extraction protocol.
Direct RNA library preparation was based on Oxford Nanopore Technologies (ONT) SQK-RNA004 kit
targeted RNA seq (ONT)

value: Brain

tag: agent

value: measles virus


title: Erosive Esophagitis 7

source_name: Human esophagus biopsy from patients with EE

value: Erosive Esophagitis


title: DN3(wt), H3K27me3, ChIP-seq, rep2

value: DN3 cells without transduction


title: Brain, Occipital lobe ONT, OL

description:
targeted RNA
cbDVG_refined_list_ont.txt


title: Erosive Esophagitis 6


title: MUTT, 38323


title: MUTT, 38318


title: L1_pC4_3xF_CLSY4_smRNAseq_flowerbuds

city: La Jolla

first: Laura

middle: M

last: Martins

email: jlaw@salk.edu, lmartins@salk.edu

state: CA

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

data_processing:
Illumina Casava software used for basecalling and demultiplexing.
Read Filtering, Mapping, and cluster calling: The adapters were removed from the de-multiplexed reads using cutadapt (v1.9.1) and trimmed reads longer that 15nt were mapped to the TAIR10 genome using ShortStack (v3.8.1) with the following options: --mismatches 1 and either --mmap f, to include multi-mapping reads, or --mmap n, to include only unique mapping reads. Only perfectly matched read or reads with a single 3’ mismatch were used to call smRNA clusters using ShortStack with the --mincov 20, --pad 100, --dicermin 21 and dicermax 24 options, to generate Tag Directories using the using the makeTagDirectory script from the HOMER with the -format sam -mis 1 and -keepAll options, and to make genome browser tracks specifically for the 24nt sized smRNAs using the makeUCSCfile script from HOMER with the -fragLength 24 and -norm 10000000 options.
Assembly: TAIR10
Supplementary files format and content: bedGraph file, including header and chr#, start position, end position and normalized value (rp10M).

organism: Arabidopsis thaliana

source_name: stage 12 and younger flower buds

growth_protocol: Growth conditions and tissue collection for 15 day old aerial rosettes (Ar) and 25 day old leaves (Lv) for all genotypes were as follows: seeds were sterilized with bleach and plated on half strength Linsmaier and Skoog medium (1/2 LS) supplemented with 1% agar. After three days stratification in the dark at 4℃, plants were grown in the Percival growth chamber (GCU-36L5) under 16h-light and 8h-dark cycle at 22℃ for 7 days and then were transplanted onto soil in Salk’s green house with long day conditions. At day 15 and day 25 of total growth, aerial rosette tissue (whole seedling without roots) or the first and second true leaves (without petioles) were collected from~40 plants as the Ar and Lv samples, respectively, immediately frozen in liquid nitrogen, and kept at -80°C until use.  Growth conditions and tissue collection for mature, unfertilized ovules (Ov) were as follows: seeds were grown from soil in Salk’s greenhouse with long day conditions and un-opened flower buds (stage 10-12) were dissected to obtain carpels using a tweezer and then fixed on a double-side tape on a glass slide. Subsequently, carpels were dissected under dissection microscope using a needle and ovules were collected with the vacuum-based micro-aspiration device as detailed below. After collection, ovules for RNA extraction were quickly mixed with 100 µL trizol (Invitrogen, Cat# 15596018), flash frozen in liquid nitrogen and preserved at -80℃ until use, while ovules for DNA preparation were preserved in the same way without trizol. For each genotype, > 300 carpels were dissected and over 10,000 ovules were collected.

extract_protocol:
Total RNAs were isolated using Trizol reagent (Life Tech, Cat# 15596018) following the manual and dissolved in 250μL RNase-free water. 2.0 µg of total RNA from Ar and Lv tissues, or ~0.5ug of total RNA from Ov, were used for smRNA enrichment through a polyethylene glycol (PEG) precipitation step. One volume of a 20% PEG 8000/2M NaCl solution was added to each RNA sample, mixed well and kept on ice for more than 30 minutes (min) and then centrifuged at 13,000rpm for 15min at 4°C. The supernatant, containing the small RNAs, was collected and precipitated with 1 volume of cold isopropanol, mixed and incubated on ice for 30min. Then the small RNA samples were recovered by centrifuged at 13,000rpm for 30min at 4°C. The resulting small RNA samples were run on 15% polyacrylamide-8M urea gels and performed size-selection of fragments from 17-29 nucleotide (nt) following the ZR-small RNA ladder (zymo research, Cat# R1090). The small RNAs in the gels were recovered by incubating with 0.3M NaCl overnight, filtering the gels and add 2.5 volumes of 100% ethanol and 3μL of glycogen for precipitation over 2 hours (h) at -80°C.
The small RNAs were used for library preparation with the NEBnext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, Cat# E7300) following the user’s manual. The final library products were further purified using an 8% polyacrylamide gel to excise 130-160nt products relative to the pBR322 DNA-MspI Digest ladder (New England Biolabs, Cat# E7323AA). The purified libraries were pooled and sequenced (single end 50 bp, SE50) on a HiSeq 2500 machine (Illumina).

value: stage 12 and younger flower buds

value: L1_pC4_3xF_CLSY4 clsy4_1

tag: molecule subtype

value: small RNA


title: DN3(IK)-3day, HDAC1, ChIP-seq, rep2


title: MUTT, 38316

value: Mixed Breed

value: Whole Blood


title: PUG, 38317

value: Pug


title: Brain, Temporal lobe ONT, TL

description:
targeted RNA
cbDVG_refined_list_ont.txt


title: DN3(IK)-3day, HDAC1, ChIP-seq, rep1


title: Erosive Esophagitis 5


title: Erosive Esophagitis 4


title: MUTT, 38322


title: Erosive Esophagitis 8


title: MUTT, 38315


title: L2_pC1_3xF_CLSY1_smRNAseq_flowerbuds

value: L2_pC1_3xF_CLSY1 clsy1_7


title: clsy1_7_smRNAseq_flowerbuds


title: DN3(IK)-1day, HDAC1, ChIP-seq, rep1

value: DN3 cells transduced with Ikaros for 1 day


title: DN3(wt), H3K27me3, ChIP-seq, rep1


title: Erosive Esophagitis 3


title: DN3(wt), HDAC1, ChIP-seq, rep2


title: Erosive Esophagitis 2


title: DN3(wt), HDAC1, ChIP-seq, rep1


title: MUTT, 38314


title: MUTT, 38320


title: Ctrl

city: Hangzhou

first: Xiaoyu

last: Li

state: Zhejiang

address: 866 Yuhangtang Road

department: SCHOOL OF BASIC MEDICAL SCIENCES

institute: Zhejiang University

description: Read1 file contains sample barcode

data_processing:
For batch paired-end reads of m5C-seq libraries, a sample-barcoded-sequence (Pos 1-6) and random-4-base (pos7-10) in Read1 and a 10nt unique molecular identifier (UMI) was included in the adaptor that ligates to the 3’end of cDNA so it locates in Read2 (Pos1-10). Firstly, m5C-seq batch libraries were demultiplexed into individual samples, using fastq-multx（with -m 1 parameters）that distributes reads into a sample FASTQ file(Read1.fq file and Read2.fq file) according to the sample-barcoded-sequence in Read1 (Pos 1-6). For every individual sample, only Read2 data with UMI was used for subsequent analyses. Illumina sequencing reads were first treated with trim_galore(version 0.6.4) for adapter removal and quality trimming. Work commands are as follows: trim_galore --fastqc --phred33 --length 30. We then used Seqkit (version 0.10.0) to deduplicate based on 10 bp UMI at the 5′ end of reads R2, key process parameters are as follows: seqkit rmdup -s. Finally, Fastp (version 0.23.2) was used to remove the 10 bp UMI in the deduplication read. 10 bases at the 3′ end of inserted sequences were also removed, using the key parameters: fastp -f 10 -t 10 -l 20.
Processed reads were mapped to reference genome (mouse mm10 reference) using HISAT2-3N (version 2.2.1-3n-0.0.3). The key parameters are as follows: hisat3n --base-change C,T --directional-mapping --repeat -p 20 -k 1. Considering a creditable m5C signal, the alignments are further filtering using python house-scripts, the alignments hosts >=3 C-to-T mismatches or >= 3 other type mismatches or the length of alignments < 20nt are filtered. Next, we parse BAM file using pysamstats (version 1.1.2), with commands as follow: pysamstats -D 100000 -S "nofilter" -t variation.
To identify the methyltransferase-dependent m5C sites, we calculated the C-to-T ratios for the m5C-TAC-seq-identified m5C sites in D0 and D6 samples.
Assembly: mm10
Supplementary files format and content: in tab file format

molecule: polyA RNA

source_name: Mouse embryonic stem cells

growth_protocol: The mESC cell line was cultured in a complete ESC culture medium, comprising Dulbecco's modified Eagle's medium (DMEM) supplemented with 15% heat-inactivated fetal bovine serum (FBS), 0.1 mM 2-mercaptoethanol, 2 mM L-glutamine, 0.1 mM non-essential amino acids, 1000 U/mL recombinant leukemia inhibitory factor (LIF), and 100 U/mL penicillin/streptomycin. For differentiation assays, mESC cells were cultured without LIF for six days. HeLa and HEK 293T cell lines were cultured in DMEM supplemented with 10% FBS and 100 U/mL penicillin/streptomycin.

extract_protocol:
Total RNA extraction from the cell lines was accomplished using the RNA isolater total RNA extraction reagent (Vazyme, R401-01). Prior to size selection, RNA underwent DNase I treatment at 37 ℃ for 15 min and subsequently was purified using RNA isolater extraction and ethanol precipitation (Vazyme, EN401-01). The small RNA fraction, characterized by a size of less than 200nt, was enriched from the total RNA utilizing the RNA Clean & Concentrator-25 Kit (Zymo, R1018). For mRNA purification, two successive rounds of poly(A)+ selection were performed employing oligo(dT)25 dynabeads (Life Technologies, 61005). Additionally, chromatin-associated RNA was isolated following subcellular fractionation assay, DNase I treatment, and rRNA depletion (Vazyme, N406-01). Modification-free control RNAs were prepared from HeLa or mESC mRNA, adhering to a previously published protocol (PMID: 34594034, 36593412).
The RNA samples were initially dephosphorylated using T4 polynucleotide kinase (Vazyme, N102-01) at 37℃ for 1 hour, followed by ethanol precipitation. Subsequently, they were ligated to the 3' RNA linker using T4 RNA ligase 2, truncated at 25°C for 2 hours, followed by an overnight incubation at 16°C (Beyotime, R0635L). To remove excess adaptors, the samples underwent treatment with 5´ Deadenylase (NEB, M0331S), RecJf (NEB, M0264S), and Proteinase K (NEB, P8102). RNA samples intended for group comparisons were pooled and then purified through Tris-phenol extraction followed by ethanol precipitation. The barcoded and pooled samples were labeled by 5-(2-azidoethyl)-1,3-indandione (AI) and subsequently subjected to a click reaction. The m5C-modified RNA was subjected to RNA pull-down to be enriched, followed by reverse transcription using the HiScript III RT SuperMix (Vazyme, R323-01). The excess reverse transcription primer was digested with exonuclease I (NEB, M0293S). The cDNA was purified by silane beads and then performed to 5′ adapter ligation on beads with T4 RNA ligase 1, high concentration (NEB, M0437M). cDNA was purified using silane beads (Invitrogen, 37002D), and subsequently, the purified cDNA was amplified using the KAPA HiFi HotStart ReadyMix (Roche, KK2602). Finally, PCR products were purified using 1.8X VAHTS DNA Clean Beads (Vazyme, N411-02) and 7% TBE gel.

value: Mouse embryonic stem cells

value: WT

value: control


title: Label

description: Read1 file contains sample barcode

value: TET2 oxidation and AI Labeling


title: MUTT, 38313


title: L1_pC3_CLSY3_3xF_smRNAseq_flowerbuds

value: L1_pC3_CLSY3_3xF clsy3_1


title: VCU-BC-002, Basal-like triple-negative breast cancer patient-derived xenograft

status: Public on Sep 30 2024

city: Richmond

first: Wright Center for Clinical and Translational Research

last: Bioinformatics Core

state: VA

address: 203 E Cary St

institute: Virginia Commonwealth University

data_processing:
Basecalling: BCL files were converted to fastq using bcl2fastq2 (v2.17.1.14)
QC: Fastq files containing the read were analyzed with FastQC >=v0.11.8 to identify any quality concerns with the raw data.
Alignment: Fastq files were aligned independently to the merged human/mouse hg19mm10 genome provided by 10X using CellRanger v6 "count" algorithm with the expected number of cells set to 5000.
Mouse Cell Removal: An in-house R script and the 10X-generated GEM file were used to identify and remove all mouse and multiplet cell barcodes from each PDX sample by using the CellRanger script "subset_bam".  The remaining reads were converted back to fastq files using the CellRanger script "bamtofastq".  These new filtered fastq files were then re-aligned independently to the GRCh38 human genome using the CellRanger "count" algorithm, however, this time the Force Cells option was set to the exact number of remaining human cells for each sample.
Cell-Level QC: An in-house R script using the Seurat v4 R package was used to identify barcodes associated with dead or poor quality cells.  The cell barcodes identified as having good quality are written to a "cells2keep" text file used to subset the experiment before merging.
Sample Merging: An in-hourse Rscript was utilized to merge samples using the R package Seurat's merge() method with Log2Normalization and scaling.  The 240705_Visvader-plus-PDX_MASTER_ALL_SimpleMerge_GRCh38_Seurat_LogNormalize_Annotated.cloupe Loupe Browser file contains the full merged dataset of all samples in this series after quality control, including normal and immune cells.
Malignent Cell Identification: The provided list of cancer cells only was generated by removing all cells from normal samples, all cells from non-normal samples that clustered with a normal sample, and all cells identified as immune cells.  The CancerCellsOnly processed files contain the list of cell barcodes used to create the Cancer Only merged Loupe Browser files included in this series where 011624_rerun_Visvader-plus-PDX_MASTER_CancerOnly.cloupe contains all cancer cells, 011624_Visvader-plus-PDX_MASTER_CancerTNOnly.cloupe contains cells from triple neagative breast cancer samples, and 011624_rerun_Visvader-plus-PDX_MASTER_CancerEROnly.cloupe file contains cancer cells from ER+ samples only.  Cancer cells were verified using inferCNV to ensure the CNV Z score was significantly different from that of the normal samples.
Assembly: GRCh38
Supplementary files format and content: The process data files include the 10X formatted features.tsv.gz, barcodes.tsv.gz, and matrix.mtx.gz files that can be imported directly into R using the Seurat package. These are provided as tar.gz files.
Supplementary files format and content: CancerOnly_TNBC-Samples.cloupe: A Loupe Cell Browser file that contains a subset of the CancerOnlyDataset file contain only TNBC samples.
Supplementary files format and content: CancerOnly_ERpositive-Samples.cloupe: A Loupe Cell Browser file that contains a subset of the CancerOnlyDataset file that contains only ER+ samples.
Supplementary files format and content: CancerOnlyDataset.cloupe: A Loupe Cell Browser file that contains the subset of identified malignant cells from the Master Merge file with all normal samples removed (the CancerCellsOnly processed data files contain a list of barcodes for each sample that are in this dataset).
Supplementary files format and content: MasterMerge_AllSamples.cloupe: A Loupe Cell Browser file that contains all 117 samples with human cells only.
Supplementary files format and content: WHIM30_PDX_PDXO_SamplesOnly.cloupe: A Loupe Cell Browser file that contains only the WHIM30 PDX and organoid samples.

source_name: PDX mammary tumor

growth_protocol: PDX tumors were grown orthotopically in NSG mice for 8 weeks.

extract_protocol:
10x Genomics Chromium kit
10x Genomics Chromium kit

treatment_protocol:
Carboplatin Resistant:  Mice with PDXs were grown and treated three times spaced out every 4 days with 40mg/kg of carboplatin. Once the tumors regrew they were passaged to new recipient mice and then treated with another set of carboplatin. This proceeded until the tumors no longer responded to carboplatin; at this point they were termed carboplatin-resistant.
Tamoxifen Resistant: Mice harboring PDX tumors were given tamoxifen citrate chow. These PDXs were passaged under tamoxifen citrate selection until no difference in growth rate between treated and untreated tumors was observed. These models were then termed "tamoxifen resistant."
Tamoxifen: Chow was replaced with Tamoxifen citrate chow from Envigo (600mg/kg) for 2 weeks prior to tumor excision.
Estradiol Withdrawal (EWD): Ovariectomy was performed and no exogenous estrogen pellet was provided.
Estrogen pellet (E2+): Two milligram slow-release estrogen pellets were implanted subcutaneously as an exogenous source of estrogen.
Ovariectomy (OVX): Both ovaries were surgically removed from mice to withdraw the primary source of estrogen.

value: PDX mammary tumor

value: PDX

tag: tumor type

value: TN

tag: source

value: Virginia Commonwealth University

value: Untreated

tag: total number_of_cells

tag: number of_cancer_cells


title: WHIM30CR-O_108805-9, Basal-like triple-negative breast cancer patient-derived xenograft

source_name: PDX organoid

value: PDX organoid

tag: cell type

value: Carboplatin Resistant

value: Washington University in St. Louis

tag: treatment


title: VCU-BC-001, Basal-like triple-negative breast cancer patient-derived xenograft


title: WHIM30-O_108793-4, Basal-like triple-negative breast cancer patient-derived xenograft

value: PDXO


title: WHIM30CR_108903, Basal-like triple-negative breast cancer patient-derived xenograft


title: DN3(IK)-2day, HDAC1, ChIP-seq, rep1

tag: cell line

value: JE131 cell line (DN3 cells)

value: an early T leukemia cell line that is derived from Ikaros knock-out mice

value: DN3 cells transduced with Ikaros for 2 days


title: VCU-BC-006_CMMC1416, Basal-like triple-negative breast cancer patient-derived xenograft


title: WHIM2_106361, Basal-like triple-negative breast cancer patient-derived xenograft


title: VCU-BC-024_CMMC1423, Basal-like triple-negative breast cancer patient-derived xenograft


title: WHIM30_108896, Basal-like triple-negative breast cancer patient-derived xenograft


title: WHIM2_106305, Basal-like triple-negative breast cancer patient-derived xenograft

value: Erlotinib


title: VCU-BC-003_CMMC1410, Basal-like triple-negative breast cancer patient-derived xenograft


title: SUM149, Basal-like triple-negative breast cancer patient-derived xenograft

source_name: Cell Line

value: Cell Line

value: The American Type Culture Collection (ATCC)


title: WHIM30_105954, Basal-like triple-negative breast cancer patient-derived xenograft


title: VCU-BC-004_CMMC1414, Basal-like triple-negative breast cancer patient-derived xenograft


title: UCD52, Basal-like triple-negative breast cancer patient-derived xenograft

value: University of Colorado Anschutz Medical Campus


title: HCC1143, Basal-like triple-negative breast cancer patient-derived xenograft


title: HCC1187, Basal-like triple-negative breast cancer patient-derived xenograft


title: BCM-2147_109176, Basal-like triple-negative breast cancer patient-derived xenograft

value: Baylor College of Medicine


title: BCM-2147CR_109178, Basal-like triple-negative breast cancer patient-derived xenograft

value: PDX mammary tumor


title: HCI-001_105983, Basal-like triple-negative breast cancer patient-derived xenograft

value: PDX

value: Huntsman Cancer Institute


title: HCI-013_109115, HCI-013_109115, ER+ breast cancer patient-derived xenograft

value: ER

value: Elacestrant (120 mg/kg/day)


title: C42B_oe_NR1D1

status: Public on Sep 25 2024

city: Sacramento

first: yatian

last: yang

institute: UC Davis

data_processing:
Sequencing was performed on an Illumina HiSeq 2000 Sequencer. The FASTQ-formatted sequence data were analyzed using a standard BWA-Bowtie-Cufflinks workflow.
Briefly, sequence reads were aligned to the reference human genome assembly (hg19) with BWA and Bowtie software. Subsequently, the Cufflinks package was applied for transcript assembly and quantification gene expression.
To avoid spurious fold levels due to low expression values, only subsets of genes that have expression value of FPKM (fragments per kilobase of exon model per million mapped reads) above 1 for either the vehicle treated cell, or the compound treated cells are included.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was isolated from cells using TRIzol™ Reagent
RNA-seq libraries from 1μg total RNA were prepared using Illumina Tru-Seq RNA Sample Prep Kit, according to the manufacturer’s instructions. Libraries were validated with an Agilent Bioanalyzer

value: prostate cancer

tag: genotype

value: WT

value: oe NR1D1

tag: time

value: 48 hours


title: C42B_sictrl_for_siFOXA1

value: sictrl


title: C42B_shNR1D1


title: myeloid cells, cko2

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw Data was processed with Perl scripts to ensure the quality of data used in further analysis. The adopted filtering criteria are as follows：1) Remove the adaptor-polluted reads. (Reads containing more than 5 adapter-polluted bases were regarded as adaptor-polluted reads and would be filtered out; 2) Remove the low-quality reads. Reads with the number of low quality bases (phred Quality value less than 19) accounting for more than 15% of total bases are regarded as low-quality reads; 3) Remove reads with number of N bases accounting for more than 5 %.
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was mapped to the reference genome using TopHat v2.0.12.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and RPKM (Reads Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: myeloid cells

extract_protocol:
Total RNA was harvested by Trizol reagent.2 ug of total RNA was used to construct sequencing libraries.
RNA libraries sequencing  was performed using standard Illumina protocols

value: myeloid cells

value: cko


title: myeloid cells, cko1


title: C42B_shcontrol

value: shcontrol


title: C42B_Veh_for_SR8278

value: Veh


title: Erosive Esophagitis 1

value: Erosive Esophagitis


title: Sample4: AA038_R1

status: Public on Sep 16 2024

city: Pamplona

first: Maite

last: Huarte

state: Navarra

address: c/ Avd Pio XII, 55

country: Spain

institute: Centro de Investigación Médica Aplicada

description: biol rep 4 (patient)

data_processing:
scRNA-seq sequencing data was preprocessed to generate the raw UMI count matrices with 1) Cell Ranger (v.3.0.1) and 2) Kallisto (v.0.46.1) followed by Bustools (v.0.40.0)
Assembly: hg38
Supplementary files format and content: mtx format matrix with barcode and gene information

source_name: Breast cancer biopsies

extract_protocol:
Sample tissues were disgregated and digested for cellular recovery. Single cells were captured in gel bead-in-emulsions.
Single cells were encapsulated with fixed Illumina Read 1 sequence, a cell-identifying 16 bp 10x Genomics barcode, a 12 bp Unique Molecular Identifier (UMI) and a poly-dT sequence. Upon cell lysis, reverse transcription yielded full-length, barcoded cDNA that was PCR-amplified. Fragmented cDNA was end-repaired, A-tailed and ligated to Illumina adaptors. A final PCR-amplification with barcoded primers allowed sample indexing.

treatment_protocol: Biopsies were directly processed for scRNA-seq library preparations

value: Breast cancer biopsies


title: Sample1: AA017_R1

description: biol rep 1 (patient)


title: MDA468, Basal-like triple-negative breast cancer patient-derived xenograft

value: Cell Line

value: TN

value: The American Type Culture Collection (ATCC)

value: Untreated


title: C42B_empty

value: empty


title: BCM-7482CR_109078, Basal-like triple-negative breast cancer patient-derived xenograft

value: PDX mammary tumor

value: Carboplatin Resistant

value: Baylor College of Medicine


title: C42B_5uM_SR8278

value: prostate cancer

value: WT


title: Sample5: AA051_R1

description: biol rep 5 (patient)


title: myeloid cells, wt1

value: wt


title: Sorted life cells, Bone Marrow, patient8, plate TM965

status: Public on Sep 13 2024

city: Utrecht

first: Arjan

last: Boltjes

address: Heidelberglaan 25

country: Netherlands

institute: Princess Máxima Center

description: Matrix column names (see plate_wellid) start with: TM965_

data_processing:
Raw data was processed with the Sharq pipeline as previously reported: https://www.biorxiv.org/content/10.1101/250811v2
Read mapping was performed using STAR (v2.6.1), on the hg38 Patch 10 human genome
Function featureCounts (v1.5.2) was used to assign reads based on GENCODE (v26) to generate count tables
Assembly: hg38 Patch 10 human genome
Supplementary files format and content: matrix.mtx.gz is a gzipped matrix file built from a sparse matrix in R – as is the usual case with this type of files, second row contains totals for 1. features, 2. cells, 3. non-zero values, third row and further contain 1. row index (features), 2. column index (plate and well ID, 3. counts
Supplementary files format and content: features.tsv.gz is a gzipped tab-delimited text file – this contains the row names of the original sparse matrix; the row indices in matrix.mtx refer to the rows in this file
Supplementary files format and content: plate_wellid.tsv.gz is a gzipped tab-delimited text file – this contains the column names of the original sparse matrix; the column indices in matrix.mtx refer to the rows in this file

source_name: Bone marrow including tumour

extract_protocol:
We have made use of the SORT-seq protocol, which is a partially robotized version of the CEL-seq2 protocol, for scRNA-seq. There is no RNA extraction in the classical sense: the cells within the wells are lysed by heat, and the aformentioned primers will hybridize to the poly-A tail of the mRNAs
The following steps take place after primer hybridization: reverse transcription & second-strand synthesis, pooling of wells (one cell per well), in vitro transcription, fragmentation and reverse transcription, PCR amplification of DNA, addition of sequencing adapters: cDNA libraries ready

treatment_protocol: Adrenal gland tissue was cut up and incubated with collagenase I, II and IV for up to one hour, filtered, washed, further dissociated with a dissociation kit. Bone marrow cells did not need dissociation, but were filtered and washed. Cells from both tissues were then FACS sorted into 384-well plates containing 10 μL of mineral oil, 50 nL of RT primers, deoxynucleotide triphosphates (dNTPs) and synthetic mRNA Spike-Ins. Plates were spun down, snap‐frozen on dry ice, and stored in ‐800C until further processing

value: Bone marrow including tumour

value: Mixed, but barcoded

value: None, directly ex vivo


title: Sample3: AA025_R1

description: biol rep 3 (patient)


title: Sample2: AA024_R1

description: biol rep 2 (patient)


title: Sorted life cells, Bone Marrow, patient8, plate TM963

description: Matrix column names (see plate_wellid) start with: TM963_


title: Sorted life cells, Bone Marrow, patient8, plate TM964

description: Matrix column names (see plate_wellid) start with: TM964_


title: Sorted life cells, Bone Marrow, patient8, plate TM968

description: Matrix column names (see plate_wellid) start with: TM968_


title: Sorted life cells, Bone Marrow, patient8, plate TM966

description: Matrix column names (see plate_wellid) start with: TM966_


title: Sorted life cells, Bone Marrow, patient9, plate TM492

description: Matrix column names (see plate_wellid) start with: TM492_


title: Sorted life cells, Bone Marrow, patient8, plate TM969

description: Matrix column names (see plate_wellid) start with: TM969_


title: Sorted life cells, Bone Marrow, patient9, plate TM491

description: Matrix column names (see plate_wellid) start with: TM491_


title: Sorted life cells, Bone Marrow, patient9, plate TM496

description: Matrix column names (see plate_wellid) start with: TM496_


title: Sorted life cells, Bone Marrow, patient2, plate TM977

description: Matrix column names (see plate_wellid) start with: TM977_


title: Sorted life cells, Bone Marrow, patient2, plate TM976

description: Matrix column names (see plate_wellid) start with: TM976_


title: Sorted life cells, Bone Marrow, patient4, plate TM972

description: Matrix column names (see plate_wellid) start with: TM972_


title: Sorted life cells, Bone Marrow, patient2, plate TM973

description: Matrix column names (see plate_wellid) start with: TM973_


title: Sorted life cells, Bone Marrow, patient9, plate TM497

description: Matrix column names (see plate_wellid) start with: TM497_


title: Sorted life cells, Bone Marrow, patient4, plate TM967

description: Matrix column names (see plate_wellid) start with: TM967_


title: Sorted life cells, Bone Marrow, patient1, plate TM958

description: Matrix column names (see plate_wellid) start with: TM958_


title: Sorted life cells, Bone Marrow, patient1, plate TM959

description: Matrix column names (see plate_wellid) start with: TM959_


title: Sorted life cells, Bone Marrow, patient2, plate TM975

description: Matrix column names (see plate_wellid) start with: TM975_


title: Sorted life cells, Bone Marrow, patient4, plate TM971

description: Matrix column names (see plate_wellid) start with: TM971_


title: Sorted life cells, Bone Marrow, patient2, plate TM978

description: Matrix column names (see plate_wellid) start with: TM978_


title: Sorted life cells, Bone Marrow, patient1, plate TM957

description: Matrix column names (see plate_wellid) start with: TM957_


title: Sorted life cells, Bone Marrow, patient7, plate TM921

description: Matrix column names (see plate_wellid) start with: TM921_


title: Sorted life cells, Bone Marrow, patient7, plate TM920

description: Matrix column names (see plate_wellid) start with: TM920_


title: Sorted life cells, Bone Marrow, patient4, plate TM970

description: Matrix column names (see plate_wellid) start with: TM970_


title: Sorted life cells, Bone Marrow, patient1, plate TM960

description: Matrix column names (see plate_wellid) start with: TM960_


title: Sorted life cells, Bone Marrow, patient7, plate TM919

description: Matrix column names (see plate_wellid) start with: TM919_


title: Sorted life cells, Bone Marrow, patient8, plate TM962

description: Matrix column names (see plate_wellid) start with: TM962_