title: untreated_MCF7_cells_0h_batch2 n8

type: RNA

city: Roma

first: Ivan

last: Arisi

address: viale Regina Elena 295

department: Bioinformatics Facility

country: Italy

institute: European Brain Research Institute

description: untreated MCF7 breast cancer cell line

hyb_protocol: One-color mixes of labelled cRNA pairs were hybridized to 8x60K whole human genome oligonucleotide microarray (Agilent grid ID 072363), at 65°C for 17 hours using Agilent’s Gene Expression Hybridization Kit. The hybridized microarrays were disassembled at room temperature in Agilent Gene Expression Wash Buffer 1. After the disassembly, the microarrays were washed in Gene Expression Buffer 1 for one minute at room temperature, followed by washing with Gene Expression Wash Buffer 2 for one minute at 37°C. The microarrays were then treated with acetonitrile for one minute at room temperature.

scan_protocol: Post-hybridization image acquisition was accomplished using the Agilent Scanner G2564C. Data extraction from the 20 bits TIFF images was accomplished by Agilent Feature Extraction (FE)  ver 12.0.3.1  software using the standard Agilent one-color gene expression extraction protocol (GE1_1200_Jan14 ).

data_processing: The “gProcessedSignal” data column of the Feature Extraction *.txt output file was used, containing the median signals corrected by spatial and multiplicative detrend. Data quality filtering was performed using R, discarding features with the Feature Extraction flag gIsWellAboveBG=0 in any sample, wich is a statistical method approximately equivalent to discarding features with a Signal/Noise ratio smaller than 2.0-3.0, where Signal = (median of the spot - median spot background level) and Noise is the Standard Deviation of the median spot background. Data were normalized to the 75th percentile in Log2 scale.  Differentially expressed genes were selected by a combination of fold change and moderated t-test thresholds (with FDR Pvalue correction) by the R-Bioconductor  tool limma (FDR<0.05; |Log2 fold-change ratio| >1.0 equivalent to 2.0 fold in linear scale).

source_name: MCF7 breast cancer cell line

label_protocol: For each sample 200ng of Poly A+RNA were labelled, using Cyanine 3-CTP (Agilent) in separate labelling reactions, with the Agilent Low Imput Linear Amplification Kit and purified with Qiagen’s RNeasy mini spin columns.

growth_protocol: The MCF7 luminal A phenotype breast cancer cells were grown at 37°C and 5% CO2 in complete DMEM (Dulbecco’s Modified Eagle Medium, GIBCO, 41966-029) high glucose supplemented with 10% foetal bovine serum (FBS).

extract_protocol: Total RNA were extracted from MCF7 treated with Doxorubicin for 24h and from control cells. Extraction was performed using RNeasy Mini Kit (QIAGEN, Germany, QG74104). Quality and integrity of RNA sample was assessed using the Agilent BioAnalyzer 2100: samples with a RNA Integrity Number (RIN) for all the samples was calculated and samples with a value lower than 8.0 were discarded.

treatment_protocol: MCF7 were treated with 30 µM Doxorubicin for 24 hours. Control samples correspond to untreated cells.

value: breast cancer

tag: array batch

tag: sample type

tag: time post treatment


title: single_cell TCR seq data of CSF from patient SMA1_4_nusinersen_6 months

status: Public on Mar 27 2024

type: SRA

city: Muenster

first: I-Na

last: Lu

state: NRW

address: Domagkstraße 20

department: Department of Pediatric Hematology and Oncology

country: Germany

institute: University Children's Hospital Münster

library_source: transcriptomic single cell

data_processing:
Processing of sequencing data was performed with the cellranger pipeline v6.1.0 (10X Genomics), according to the manufacturer’s instructions. Briefly, raw BCL files were de_multiplexed using the CellRanger mkfastq pipeline. Subsequent read alignments and transcript counting was done individually for each sample using the CellRanger count and CellRanger vdj pipelines with standard parameters.
Assembly: GRCh38
Supplementary files format and content: Standard cellranger output format
Supplementary files format and content: gene expression matrix h5
Supplementary files format and content: contig annotations

molecule: total RNA

organism: Homo sapiens

source_name: CSF

extract_protocol:
CSF cells were processed within 2 hours post lumbar puncture to ensure optimal sample quality. For processing, CSF was collected into round bottom polypropylene tubes and then centrifuged for 10 min at 300x g. CSF cell pellets were resuspended in 5 ml of X_Vivo15 media (Lonza) and stored on crushed ice. The samples were then transported with same day shipping on crushed ice to the laboratory. Cell suspensions were then centrifuged again for 5 min at 400 x g and resuspended in 50 μl of X_Vivo15 media. Out of this volume, 6 μl were used for cell counting and the remaining volume was entirely used for scRNA_seq.
Single cell suspensions were loaded onto the Chromium Controller (10X Genomics) using the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kits v3 and v3.1 (10X Genomics). For TCR sequencing, we applied a previously described technique to sequence antigen receptor information from the 3’ scRNA_seq libraries. In short, the method involves self_circulating the cDNA library, enriching the VDJ region and re_linearizing to remove the constant region of antigen receptors during enrichment, while maintaining their cell barcode and unique molecular identifier (UMI) information attached to the 3' of the cDNA molecules. Library preparation was performed according to manufacturer's instructions using AMPure beads (Beckman Coulter). Sequencing was carried out on a local Illumina Nextseq 500/2000 and Novaseq6000 with a 28_8_0_91 read setup.

treatment_protocol: Nusinersen was administered to SMA patients by lumbar puncture on days 1, 14, 28, and 63 followed by a repetitive application every 4 months according to the treatment guideline. Treatment was performed between the years 2017 - 2021 in the center in Essen. Before each nusinersen injection, the same amount (5 mL) of CSF was withdrawn to prevent excessive intra_CSF pressure.

tag: tissue

value: CSF leukocytes

tag: diagnosis

value: SMA

tag: treatment

value: nusinersen

tag: time point

value: 6 months


title: CRC-39-EV

city: Beijing

first: Zhi

middle: John

address: Shuangqing Road

department: School of Life Sciences

country: China

institute: Tsinghua University

description: RNA-seq of homo sapiens: colorectal cancer patient's EV RNA; Provided by Peking University First Affiliated Hospital;  Constructed by Detector-seq; Purpose: To explore novel plasma and extracellular RNA biomarkers for cancer diagnosis

library_source: transcriptomic

data_processing:
Adaptors and low-quality sequences in the raw sequencing data were trimmed using cutadapt version 2.3. Remeined reads were mapped to ERCC's spike-in sequences, NCBI's UniVec sequences and human rRNA sequences sequentially. GC oligos introduced in reverse transcription were trimmed off, after which reads shorter than 30 nt were discarded.
STAR (version 2.5.4a) was used to map clean reads to the hg38 genome index built with the GENCODE v38 annotation
Duplicates in the aligned reads were removed using umi_tools(v1.1.2)
The count matrix was constructed using featureCounts11 v1.6.2 with the GENCODE v38 annotation, circular RNA annotation from circBase, intron, intergenic regions frm UCSC Genome Browser. Reads mapped to mitochondrial RNAs were excluded.
Assembly: hg38
Supplementary files format and content: Matrix table of raw gene counts for each gene and sample

source_name: plasma

extract_protocol:
Cell-free RNAs in plasma were extracted using QIAzol Lysis Reagent (Qiagen, 79306). Cell-free RNAs in plasma extracellular vesicles (EVs) were extracted using exoRNeasy Midi Kit (Qiagen, 77144).
Detector-seq

value: plasma

tag: disease

value: colorectal cancer

tag: gender

value: male

tag: age

tag: Stage

value: IIIB


title: CRC-44-EV

value: female

value: IV


title: CRC-38-EV


title: PM154, Control, rep1

city: Chiba

first: Yasutaka

last: Yamada

state: MA

address: 1-8-1 Inohana, chuo-ku

department: Urology

country: Japan

institute: Graduate School of Medicine, Chiba University

data_processing:
RNA quantity and integrity were determined using the Qubit® Fluorometer and the Fragment Analyzer system with the PROSize 3.0 software (Agilent Technologies, Palo Alto, California, USA).
The RQN were ranging from 8.8 to 10 for all samples, which was considered sufficient. Illumina TruSEQ RNA library prep and sequencing reagents were used following the manufacturer’s recommendations using polyA-selected transcripts (Illumina, San Diego, CA, USA).
The samples were sequenced on the Illumina NovaSeq platform (2 x 150 bp, single index) and generated ~20 million paired-end reads for each sample.
Assembly: GRCh38
Supplementary files format and content: Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Below are the statistics of mapping the reads to the reference genome.
Supplementary files format and content: Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted. If a strand-specific library preparation was performed, the reads were strand-specifically counted.

growth_protocol: The medium for this cell lines is prostate specific media using advanced DMEM.

extract_protocol:
 Total RNA was extracted from each tissue by using Qiagen's ‘RNeasy’ RNA extraction kit (Qiagen).
RNA-sequencing was performed by GENEWIZ (South Plainfield, NJ, USA). RNA quantity and integrity were determined using the Qubit® Fluorometer and the Fragment Analyzer system with the PROSize 3.0 software (Agilent Technologies, Palo Alto, California, USA). The RQN were ranging from 8.8 to 10 for all samples, which was considered sufficient. Illumina TruSEQ RNA library prep and sequencing reagents were used following the manufacturer’s recommendations using polyA-selected transcripts (Illumina, San Diego, CA, USA). The samples were sequenced on the Illumina NovaSeq platform (2 x 150 bp, single index) and generated ~20 million paired-end reads for each sample.

tag: cell line

tag: cell type

value: Prostate cancer cell line

tag: genotype

value: Wild Type


title: ovary, VCD affected for 15 days, rep 3

city: 兰州市

first: Yi

last: Li

state: 甘肃

address: 甘肃省兰州市城关区东岗西路1号兰州大学第一医院

institute: Lanzhou University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) in a reference based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include readcount values for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Mus musculus

source_name: ovary

growth_protocol: Mice are kept in separate cages (Total six cages with five mice per cage) and have free to access food and water. The environment has a normal circadian rhythm and a constant temperature and humidity (24 ± 2°C/40%).

extract_protocol:
Ovarian tissues’ RNA extraction using TRLzol kit. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalentcationsunder elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: All the mice were treated intraperitoneally once a day for 15 days and starting the same day. The control group was injected with sesame oil and the experimental group had VCD dissolved in sesame oil at a concentration of 160 mg/kg.

value: ovary

tag: developmental stage

tag: Sex

value: Intraperitoneal Injection VCD

tag: time

value: 15 days


title: CRC-36-EV

value: I


title: single_cell TCR seq data of CSF from patient SMA1_2_nusinersen_10 months

value: 10 months


title: untreated_MCF7_cells_0h_batch2 n7

description: untreated MCF7 breast cancer cell line

value: breast cancer

tag: array batch

value: untreated


title: ovary, VCD affected for 15 days, rep 1

address: 甘肃省兰州市城关区东岗西路1号兰州大学第一医院


title: Ovary, control, rep 5

address: 甘肃省兰州市城关区东岗西路1号兰州大学第一医院

value: Intraperitoneal injection sesame oil


title: Doxorubicin_MCF7_cells_24h_batch2 n7

description: Doxorubicin treated MCF7 breast cancer cell line

value: Doxorubicin

tag: sample type

value: Doxorubicin treated


title: CRC-37-EV

value: plasma

value: colorectal cancer


title: Doxorubicin_MCF7_cells_24h_batch2 n6

tag: time post treatment


title: CRC-35-EV

tag: tissue

value: male

value: IIIB


title: Ovary, control, rep 4

address: 甘肃省兰州市城关区东岗西路1号兰州大学第一医院

value: female


title: single_cell TCR seq data of CSF from patient SMA1_2_nusinersen_6 months

value: CSF leukocytes

tag: diagnosis

value: SMA

value: nusinersen

value: 6 months


title: untreated_MCF7_cells_0h_batch2 n6

description: untreated MCF7 breast cancer cell line

tag: treatment


title: CRC-32-EV

value: IIA


title: single_cell TCR seq data of CSF from patient SMA1_1_nusinersen_10 months

tag: time point


title: Doxorubicin_MCF7_cells_24h_batch2 n8


title: single_cell TCR seq data of CSF from patient SMA1_3_nusinersen_6 months


title: Ovary, control, rep 3

address: 甘肃省兰州市城关区东岗西路1号兰州大学第一医院

value: ovary

value: 15 days


title: Doxorubicin_MCF7_cells_24h_batch2 n5

value: breast cancer


title: Ovary, control, rep 2

address: 甘肃省兰州市城关区东岗西路1号兰州大学第一医院


title: NC-50-plasma

description: RNA-seq of homo sapiens: healthy donor's plasma cell-free RNA; Provided by Peking University First Affiliated Hospital;  Constructed by Detector-seq; Purpose: To explore novel plasma and extracellular RNA biomarkers for cancer diagnosis

tag: disease

value: healthy donor

value: No stage (healthy donor)


title: Ovary, control, rep 1

address: 甘肃省兰州市城关区东岗西路1号兰州大学第一医院

value: Intraperitoneal injection sesame oil


title: NC-66-plasma

tag: gender


title: single_cell TCR seq data of CSF from patient SMA1_1_untreated

value: untreated


title: untreated_MCF7_cells_0h_batch1 n4

description: untreated MCF7 breast cancer cell line


title: PM154, Control, rep3

value: Prostate cancer cell line

value: Wild Type


title: Doxorubicin_MCF7_cells_24h_batch1 n4

value: Doxorubicin

value: Doxorubicin treated


title: NC-49-plasma

value: plasma

value: female

tag: age


title: MDA-MB-231 cells,150μg/ml,biol rep2

city: Chengdu

first: Yumei

last: Wang

address: 1166 LiuTai

institute: Chengdu University of TCM

data_processing:
Sequence reads were mapped to hg38 using hisat2 (v2.2.1)
HTSeq (v2.0.2) were used for sequence assembly and quantifying gene expression
Assembly: hg38

source_name: Breast; Mammary gland

growth_protocol: MDA-MB-231 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 100 units/mL streptomycin and penicillin in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA isolater Total RNA Extraction Reagent (Vazyme) was used for total RNA isolation.
RNA libraries for RNA-seq were prepared using NEBNext Ultra RNA Library Preparation Kit (NEB) following manufacturer's protocols.

treatment_protocol: DMSO as control, 75μg/ml and 150μg/ml AF-EAE were added in culture medium for 24 hours

value: Breast; Mammary gland

value: epithelial cell

value: WT

value: AF-EAE 150 ug/ml


title: Aged Diabetes

city: Houston

first: Rajasekaran

last: Mahalingam

state: TX

address: 6565 MD Anderson Blvd

department: Symptom Research

country: USA

institute: University of Texas MD Anderson Cancer Center

description: 10x Genomics

data_processing:
The demultplexing, barcoded processing, gene counting and aggregation wee made using the Cell Ranger v5.0.0
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Hindpaw

extract_protocol:
Both hindpaws were excised amputated at the ankle, and digested in a collagenase solution for 1.5-2 hours at 37°C, with agitation every 15 minutes. The resulting cell suspension and tissue remnants were filtered through a 70µm nylon filter, and the filter was rinsed to collect cells. After centrifugation and resuspension, the cells were sorted in FACS buffer (2% FBS + 0.5mM EDTA in PBS)
Library was performed according to the manufacture's instruction (single cell 3' v3 protocol, 10x Genomics)

value: Hindpaw

value: Immune cells

tag: disease state

value: Diabetes

value: Aged


title: NC-48-plasma

value: healthy donor

tag: Stage

value: No stage (healthy donor)


title: Aged Wild-type

description: 10x Genomics

tag: cell type

value: control


title: MDA-MB-231 cells,75μg/ml,biol rep2

tag: cell line

tag: genotype

value: AF-EAE 75 ug/ml


title: Young Diabetes

description: 10x Genomics

value: Young


title: untreated_MCF7_cells_0h_batch1 n3

description: untreated MCF7 breast cancer cell line

value: breast cancer

tag: Sex

value: untreated


title: NC-47-plasma

value: plasma


title: Doxorubicin_MCF7_cells_24h_batch1 n3

value: female

value: Doxorubicin

value: Doxorubicin treated


title: MDA-MB-231 cells,75μg/ml,biol rep1

value: Breast; Mammary gland

value: epithelial cell

value: WT


title: single_cell TCR seq data of CSF from patient SMA1_1_nusinersen_6 months

value: CSF leukocytes

value: SMA

value: nusinersen

value: 6 months


title: Young Wild-type

description: 10x Genomics

value: Hindpaw

value: Immune cells


title: Doxorubicin_MCF7_cells_24h_batch1 n2


title: NC-45-plasma

value: healthy donor

value: No stage (healthy donor)


title: MDA-MB-231 cells,DMSO,biol rep2

value: DMSO


title: untreated_MCF7_cells_0h_batch2 n5

description: untreated MCF7 breast cancer cell line

value: breast cancer

value: untreated


title: mBC replicate 3 scRNA

city: Pittsburgh

first: Jian

last: Ma

address: 5000 Forbes Ave

institute: Carnegie Mellon University

data_processing:
Demultiplexing using custom scripts
Alignment by BWA (version 0.7.17-r1188) for genomic DNA and by STAR (version 2.7.8a) for RNA
Deduplication using custom scripts
Contact calling by pairtools (version 0.3.1-dev.1)
RNA read count extraction by featureCounts (version 2.0.1)
Assembly: hg38; mm10
Supplementary files format and content: Tab-delimited text files include chromatin contact pairs for single cells
Supplementary files format and content: Tab-delimited text files include RNA reads and mapped genes for single cells

molecule: polyA RNA

source_name: Mouse brain cortex

extract_protocol:
GAGE-seq protocol
Hi-C and scRNA-seq

value: Mouse brain cortex


title: MDA-MB-231 cells,150μg/ml,biol rep1

value: AF-EAE 150 ug/ml


title: Doxorubicin_MCF7_cells_24h_batch1 n1

value: female

value: Doxorubicin

value: Doxorubicin treated


title: sphere_3

city: Dalian

first: Yuanyuan

last: Luo

address: No.457 Zhongshan Road

institute: Dalian institute of chemical physics

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
paired-end clean reads were aligned to the reference genome usinghisat2 (v2.0.5)
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: DMEM/F12. Cells were cultured at 37C at 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent. 0.4 ug of total RNA was used for the construction of sequencing libraries
RNA libraries were prepared for sequencing using standard Illumina protocols

value: epithelial cells

value: WT

value: no serum

tag: time

value: 7 d


title: NC-43-plasma

value: plasma


title: mBC replicate 2 scHi-C

library_source: genomic

molecule: genomic DNA


title: untreated_MCF7_cells_0h_batch1 n1

description: untreated MCF7 breast cancer cell line

tag: array batch


title: sphere_2


title: wild-type CG4 cells, proliferative, biological replicate 2 [RNA_S5131Nr12]

city: Erlangen

first: Michael

last: Wegner

state: Bavaria

address: Fahrstr. 17

department: Institut of Biochemistry

description:
edgeR_CG4diff-CG4prol.xlsx
RNA_S5131Nr12

data_processing:
RNA samples were quantified using Qubit 4.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked with RNA Kit on Agilent 5300 Fragment Analyzer (Agilent Technologies, Palo Alto, CA, USA).
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA), except for libraries S5131Nr10, S5131Nr12, S5131Nr22 which were prepared with TruSeq Stranded mRNA kit (Illumina)
Sequencing libraries were validated using NGS Kit on the Agilent 5300 Fragment Analyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 4.0 Fluorometer (Invitrogen, Carlsbad, CA).
The sequencing libraries were multiplexed and loaded on the flow cell on the Illumina NovaSeq 6000 instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150 Pair-End (PE) configuration v1.5, except for libraries S5131Nr10, S5131Nr12, S5131Nr22 which were sequenced using a 2x100 Pair-End (PE) configuration.
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Rattus norvegicus reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
DESeq2 was used for differential gene expression analysis between control and Nkx2.2 and Zfp488 expressing CG4 cells, respectively. EdgeR was used to determine differentially expressed genes in CG4 cells and rat oligodendoglia under proliferative and differentiating conditions.
Assembly: rn6
Supplementary files format and content: tab-delmited text files containing counts, DESeq2 results, and edgeR results

organism: Rattus norvegicus

growth_protocol: CG4 cells were grown in basal medium supplemented with bFGF and PDGF-AA. Rat oligodendroglia were grown in mixed glial cultures, separated via shake-off and kept in basal medium supplemented with bFGF and PDGF-AA.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit according to QIAGEN protocol.

treatment_protocol: CG4 cells and primary rat oligodendroglia were differentiated by switching to SATO medium supplemented with high T3/T4 and CNTF for three consecutive days. For proliferative conditions, CG4 cells and primary rat oligodendroglia were kept in basal medium supplemented with bFGF and PDGF-AA

value: CG4 cells, immortalized cell line derived from primary rat oligodendroglia derived from brain

value: wild-type

value: proliferative


title: wild-type CG4 cells, proliferative, biological replicate 1 [RNA_S5131Nr10]

description:
edgeR_CG4diff-CG4prol.xlsx
RNA_S5131Nr10


title: mBC replicate 2 scRNA


title: NC-46-plasma

value: healthy donor

value: male

value: No stage (healthy donor)


title: NC-41-plasma


title: MDA-MB-231 cells,DMSO,biol rep1

value: Breast; Mammary gland

value: epithelial cell

value: DMSO


title: mBC replicate 1 scHi-C

value: Mouse brain cortex


title: NC-44-plasma


title: primary rat oligodendroglia, 3d diff, biological replicate 4 [diff-cont4]

description:
edgeR_ratOPCdiff-ratOPCprol.xlsx
diff-cont4

source_name: primary rat oligodendroglia derived from brain

value: 3d differentiation


title: mBC replicate 3 scHi-C


title: Adh_3

value: with serum


title: mBC replicate 1 scRNA


title: NC-39-plasma

value: female


title: primary rat oligodendroglia, 3d diff, biological replicate 3 [diff-cont3]

description:
edgeR_ratOPCdiff-ratOPCprol.xlsx
diff-cont3

value: primary rat oligodendroglia derived from brain


title: untreated_MCF7_cells_0h_batch1 n2

description: untreated MCF7 breast cancer cell line

value: breast cancer

value: untreated

tag: sample type


title: Adh_2

value: epithelial cells

value: WT

value: 7 d


title: primary rat oligodendroglia, 3d diff, biological replicate 2 [diff-cont2]

description:
edgeR_ratOPCdiff-ratOPCprol.xlsx
diff-cont2

value: wild-type


title: KO_scRNAseq

city: Shanghai

first: Bei

last: Liu

address: 197 Rui Jin 2nd Road

institute: Ruijin Hospital, Shanghai Jiaotong University School of Medicine

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)  and Seurat v4.0.3 was used for downstream analysis.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: islet tissue

extract_protocol:
Cells were isolated per 10x Genomics manufacture instructions.
Cellular suspensions were loaded on the Chromiu Controller (10x Genomics, Pleasanton) to generate Gel Bead-In-Emulsions (GEMs). Barcoded sequencing libraries were conducted following the instruction manual of the Chromium Single Cell 3’ Reagent Kits v3 (10x Genomics).

value: islet tissue


title: wild-type CG4 cells, proliferative, biological replicate 3 [RNA_S5131Nr22]

description:
edgeR_CG4diff-CG4prol.xlsx
RNA_S5131Nr22

value: CG4 cells, immortalized cell line derived from primary rat oligodendroglia derived from brain

value: proliferative


title: NC-37-plasma

value: plasma

value: healthy donor

value: No stage (healthy donor)


title: NC-42-plasma

value: male


title: WT_scRNAseq

description: 10x Genomics


title: primary rat oligodendroglia, 3d diff, biological replicate 1 [diff-cont1]

description:
edgeR_ratOPCdiff-ratOPCprol.xlsx
diff-cont1

value: 3d differentiation


title: iHeps pD-1A day 13 (exp.11)

city: Madrid

first: Ramon

last: Garcia-Escudero

state: Madrid

address: Avda Complutense 40, Ed 70A

department: Biomedical Innovation

country: Spain

institute: CIEMAT

data_processing:
CLC Genomics Workbench v 11.0.1 / CLC Genomics Workbench v 12.0.3
Trimming. Quality trimming (quality limit: 0.01); Ambiguity trimming (ambigous limit: 2 nucleotides); Minimum number of nucleotides in reads: 30 nucleotides; Discard short reads
Trimmed sequence reads were mapped to the reference genome: Human (hg38). Parameters: Length fraction= 0.8; Similarity fraction= 0.8
The result of mapping served to determine the gene expression levels based on the TPM (Trancripts Per Kilobase Million per Million) and RPKM (Reads Per Kilobase MillionReads per Kilobase Million) methods
Differential gene expression analyses with TPM and RPKM values comparing human fibroblast starting samples with generated iHeps were performed using MultiExperimentViewer (MeV) (version 4.9.0) software. T-test (p<0.001) and LIMMA-test (p<0.001) were applied to both TPM and RPKM values of coding genes.
Gene set enrichment analyses were conducted with GSEA (version 4.1.0) software 74, using the TPM values of protein coding genes.
Assembly: hg38
Supplementary files format and content: "TPM_matrix.txt"
Supplementary files format and content: log2(TPM values), 0.0001 if value=0.
Supplementary files format and content: "RPKM_matrix.txt"
Supplementary files format and content: log2(RPKM values), 0.0001 if value=0.

source_name: Induced-hepatocytes

growth_protocol: Human fibroblasts were cultured in DMEM with GlutaMAX, 10% HyClone Research Grade Fetal Bovine Serum and 1% penicillin/streptomycin solution under normoxic conditions (37°C, 21% O2, 5% CO2 and 95% relative humidity).

extract_protocol:
Total RNA was extracted using TRIzol reagent (Thermo Fisher) and purified with RNeasy MinElute Cleanup Kit (Qiagen).
cDNA library was constructed using Kapa Stranded mRNA Library Preparation Kit and sequenced in the IlluminaHiSeq 4000 or Illumina Novaseq platform, using 150bp paired-end sequencing reads.

treatment_protocol:
Primary fibroblasts were immortalized by lentiviral transduction with a vector coding for the telomerase reverse transcriptase hTERT, the catalytic subunit of the telomerase enzyme (pLOX-TERT-iresTK, Addgene plasmid #12245). Healthy donor fibroblasts were also transduced with the lentiviral vector pCCL-Enh1mTTR:eGFP-wpre coding for the green fluorescent protein (eGFP) under the control of a synthetic promoter (Enh1mTTR) that was shown to restrict transgene expression to hepatocytes.
Hepatic transdifferentiation: For induced-hepatocyte (iHeps) generation, fibroblasts were transduced with four lentiviral vectors coding for selected  human hepatic transcription factors (FOXA2, HNF1α, HNF4α and TBX3) and cultured in hepatic-specific culture media. Two defined culture media were employed sequentially. Three-five days in endoderm induction medium (cDMEM supplemented with 4.99mM nicotinamide, 10ng/ml recombinant human FGF-basic, 20ng/ml recombinant human HGF, 0.10% DMSO, 2μM A-83-01 and 3μM CHIR99021). Then, in hepatic maturation medium until day 13 (cDMEM supplemented with 0.1μM dexamethasone, ITS (insulin, transferrin, sodium selenite) liquid media supplement, 640μM N-nitro-L-arginine methyl ester hydrochloride (L-NAME), 20ng/ml recombinant human HGF, 20ng/ml recombinant human oncostatin M, 0.10% DMSO, 2μM A-83-01 and 3μM CHIR99021).

value: Induced-hepatocytes

value: AGXT targeted knock-in

value: Hepatic transdifferentiation (FOXA2, HNF1a, HNF4a and TBX3 lentiviral overexpression and hepatic-specific culture media).


title: NC-36-plasma

value: female


title: Crypts, Low-fat diet, Sham

city: Ithaca

first: Kieran

last: Koch-Laskowski

state: NY

address: 618 Tower Road, VRT #T7006

department: Biomedical Sciences

institute: Cornell University

description: 10x Genomics

data_processing:
Demultiplexing, FASTQ generation and alignment, barcode/UMI processing, and gene counting were performed using Cell Ranger v.6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values (.tsv) and matrix (.mtx) files from raw and filtered feature-barcode matrices generated by Cell Ranger v.6.0.0

source_name: Small intestinal epithelial crypts

extract_protocol:
Small intestinal epithelial samples were freshly collected and flushed with ice-cold PBS to remove luminal contents. Intestinal segments were opened longitudinally and placed in individual tubes containing cold DMEM before immediate processing with a solution of 3mM EDTA in PBS for cell dissociation. During processing in the EDTA/PBS solution, the intestinal segments were manually scrapped and subsequently filtered through a 70 µm cell strainer to separate crypts from villi. For single-cell dissociation, the crypts and villi were resuspended separately in a cold solution of 0.04% bovine serum albumin (BSA)/PBS, followed by processing with 0.3 U/ml dispase/HBSS, DNAse1/FBS, and 0.04% BSA/PBS solutions. The viability of and number of dissociated crypt and villus cells were measured using the ThermoFisher ViCell counter, with an average viability of 71% for crypts and 66% for villus cells. Approximately 3.0 x 10^7 crypt cells and 3.5 x 10^7 villus cells from each sample were pooled (n=3 for LFD-sham and HFD-sham, n=2 for HFD-VSG) and diluted to a concentration of 1000 cells/µL.
Single-cell library preparation was performed using the 10x Genomics Chromium Next GEM 3' v3.1 kit following the manufacturer's instructions.

value: Small intestinal epithelial crypts

tag: diet

value: Low-fat diet

value: Sham

tag: strain

value: Wildtype C57BL/6J

value: Male

value: ~ 30-weeks-old


title: primary rat oligodendroglia, proliferative, biological replicate 4 [pro-control4]

description:
edgeR_ratOPCdiff-ratOPCprol.xlsx
pro-control4

value: primary rat oligodendroglia derived from brain

value: wild-type


title: iHeps pD-1A day 8 (exp.11)


title: primary rat oligodendroglia, proliferative, biological replicate 3 [pro-control3]

description:
edgeR_ratOPCdiff-ratOPCprol.xlsx
pro-control3

value: proliferative


title: Villi, Low-fat diet, Sham

description: 10x Genomics

source_name: Small intestinal epithelial villi

tag: tissue

value: Small intestinal epithelial villi


title: hFibros pD-1A

source_name: Skin

value: Skin

value: Fibroblasts


title: primary rat oligodendroglia, proliferative, biological replicate 2 [pro-control2]

description:
edgeR_ratOPCdiff-ratOPCprol.xlsx
pro-control2

tag: treatment


title: NC-38-plasma

value: plasma

value: healthy donor

value: male

value: No stage (healthy donor)


title: Crypts, High-fat diet, Vertical sleeve gastrectomy

description: 10x Genomics

value: High-fat diet

value: Vertical sleeve gastrectomy


title: NC-33-plasma


title: Villi, High-fat diet, Vertical sleeve gastrectomy

description: 10x Genomics


title: NC-31-plasma


title: NC-32-plasma


title: iHeps pA-1A day 13 (exp.11)

value: Induced-hepatocytes

value: AGXT targeted knock-in

value: Hepatic transdifferentiation (FOXA2, HNF1a, HNF4a and TBX3 lentiviral overexpression and hepatic-specific culture media).


title: iHeps pA-1A day 13 (exp.10)


title: Crypts, High-fat diet, Sham

description: 10x Genomics

value: Small intestinal epithelial crypts

value: Sham

value: Wildtype C57BL/6J

value: Male


title: iHeps pA-1A day 8 (exp.11)


title: Adh_1

value: epithelial cells

value: WT

value: with serum

value: 7 d


title: Villi, High-fat diet, Sham

description: 10x Genomics

value: Small intestinal epithelial villi

value: ~ 30-weeks-old


title: primary rat oligodendroglia, proliferative, biological replicate 1 [pro-control1]

description:
edgeR_ratOPCdiff-ratOPCprol.xlsx
pro-control1

value: primary rat oligodendroglia derived from brain

value: wild-type

value: proliferative


title: LC-41-plasma

description: RNA-seq of homo sapiens: lung cancer patient's plasma cell-free RNA; Provided by Peking University First Affiliated Hospital;  Constructed by Detector-seq; Purpose: To explore novel plasma and extracellular RNA biomarkers for cancer diagnosis

value: plasma

value: lung cancer

value: male

value: I


title: iHeps pA-1A day 8 (exp.10)

value: Induced-hepatocytes

value: AGXT targeted knock-in

value: Hepatic transdifferentiation (FOXA2, HNF1a, HNF4a and TBX3 lentiviral overexpression and hepatic-specific culture media).


title: NC-34-plasma

value: healthy donor

value: No stage (healthy donor)


title: CG4 cells expressing pCAG-T7-Nkx2.2-IRES-EGFP (Nkx2.2), 3d diff, biological replicate 3 [53-3-CG283-3]

description:
53_CG4diff_Nkx2-2_DESeq2.csv
53-3-CG283-3

value: CG4 cells, immortalized cell line derived from primary rat oligodendroglia derived from brain

value: 3d differentiation


title: CG4 cells expressing pCAG-T7-Nkx2.2-IRES-EGFP (Nkx2.2), 3d diff, biological replicate 2 [53-2-CG283-2]

description:
53_CG4diff_Nkx2-2_DESeq2.csv
53-2-CG283-2


title: PP5

city: Rotterdam

first: Mathijs

last: Verhagen

address: Doctor Molewaterplein 40

country: Netherlands

institute: Erasmus Medical Center

description: 10x Genomics

data_processing:
Cellranger count (v 6.0.1) was employed for demultiplexing, barcode processing, gene counting and aggregation of the samples
Downstream analysis was performed in Seurat (v 4.1.1) where cells were assigned to their mouse origin with HTODemux
Low quality cells were filtered from the data (mitochondrial genes > 10%, nFeature_RNA < 200 and nCount_RNA < 500)
Paneth Pools were integrated with Seurat using the single cell transform pipeline
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files, including counts of the merged data set as well as associated meta data

source_name: small intestine

growth_protocol: To activate the fluorescent reporter strains and induce mutations, mice received 3 intraperitoneal injections of 1 mg Tamoxifen.

extract_protocol:
The mouse small intestines were flushed with cold PBS, removed from fat and scraped with a glass slide to remove intestinal villi. Intestines were cut into 5-10 mm pieces and washed with cold PBS before incubation on rotator for 30 min at 4°C in cold PBS with 6 mM EDTA. Subsequently, crypts were de-attached from the muscle layer by 4 rounds of harsh pipetting with cold PBS. A single cell suspension was obtained by enzymatic dissociation with TryplE (3 min at 37°C). Cells were stained with fluorescent antibodies (Cd24 and cKit), and with hashing antibodies to enable de-multiplexing of samples. Paneth cells and Traced cells were enriched by FACS, and processed as Paneth Pool (PP) covering cells from 5-10 mice per run.
Libraries were made according to the manufacter’s instructions (Single Cell 3' v3 chemistry, 10x Genomics)

treatment_protocol: Where indicated, mice received 3% DSS for 7 days in the drinking water.

value: Intestinal epithelial cells

value: small intestine

value: various, Lyz1-Yfp/td-Tomato-Mut

value: 12-20 weeks old


title: LC-40-plasma


title: hFibros pA-1A

value: Skin

value: Fibroblasts


title: PP4

description: 10x Genomics


title: LC-38-plasma

value: plasma

value: female


title: iHeps pB-1C day 13 (exp.11)


title: LC-37-plasma

value: lung cancer

value: male


title: PP3

description: 10x Genomics


title: sphere_1

value: epithelial cells

value: WT

value: no serum

value: 7 d


title: CG4 cells expressing pCAG-T7-Nkx2.2-IRES-EGFP (Nkx2.2), 3d diff, biological replicate 4 [53-4-CG283-4]

description:
53_CG4diff_Nkx2-2_DESeq2.csv
53-4-CG283-4


title: CG4 cells expressing pCAG-myc-Zfp488-IRES-EGFP (Zfp488), 3d diff, biological replicate 4 [52-4-CG281-4]

description:
52_CG4diff_Zfp488_DESeq2.csv
52-4-CG281-4


title: iHeps pB-1C day 13 (exp.10)

value: Induced-hepatocytes

value: AGXT targeted knock-in

value: Hepatic transdifferentiation (FOXA2, HNF1a, HNF4a and TBX3 lentiviral overexpression and hepatic-specific culture media).


title: LC-36-plasma

value: I


title: CG4 cells expressing pCAG-myc-Zfp488-IRES-EGFP (Zfp488), 3d diff, biological replicate 3 [52-3-CG281-3]

description:
52_CG4diff_Zfp488_DESeq2.csv
52-3-CG281-3

value: CG4 cells, immortalized cell line derived from primary rat oligodendroglia derived from brain

value: 3d differentiation


title: LC-35-plasma


title: iHeps pB-1C day 8 (exp.11)


title: PP1

description: 10x Genomics

value: Intestinal epithelial cells

value: small intestine

value: various, Lyz1-Yfp/td-Tomato-Mut

value: 12-20 weeks old


title: PP2

description: 10x Genomics


title: CG4 cells expressing pCAG-myc-Zfp488-IRES-EGFP (Zfp488), 3d diff, biological replicate 2 [52-2-CG281-2]

description:
52_CG4diff_Zfp488_DESeq2.csv
52-2-CG281-2


title: iHeps pB-1C day 8 (exp.10)


title: LC-34-plasma

value: plasma


title: microglia-MRL/mpj3

city: Nanjing

first: Han

last: Xiaojuan

state: Jiangsu

address: Zhongshan Road 321

institute: Nanjing Drum Tower Hospital,  The Affiliated Hospital of Nanjing University Medical School

data_processing:
Paired-end reads were harvested from Illumina NovaseqTM 6000 sequencer, and were quality controlled by Cutadapt. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). The high quality trimmed reads were used to analyse circRNAs, LncRNAs and mRNAs
The high quality reads were aligned to the mouse reference genome (GRCm38) with hisat2 software (v2.0.4). Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (v2.2.1, part of cufflinks) was used to get the FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified.
And GO and Pathway analysis were performed on these target genes. GO and Pathway enrichment analysis were also performed based on the differentially expressed mRNAs.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: brain

extract_protocol:
Sorted microglia were collected, flash frozen on dry ice. Total RNA was isolated using trizol LS Reagent.
Total RNA was used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, USA) following the manufacturer's instructions. RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, USA).

value: brain

value: MRL/mpj

value: untreated


title: CG4 cells expressing pCAG-myc-Zfp488-IRES-EGFP (Zfp488), 3d diff, biological replicate 1 [52-1-CG281-1]

description:
52_CG4diff_Zfp488_DESeq2.csv
52-1-CG281-1


title: microglia-MRL/mpj2


title: CG4 cells expressing pCAG-T7-Nkx2.2-IRES-EGFP (Nkx2.2), 3d diff, biological replicate 1 [53-1-CG283-1]

description:
53_CG4diff_Nkx2-2_DESeq2.csv
53-1-CG283-1


title: iHeps GC-1C day 13 (exp.9)

value: AGXT c.853T>C mutation corrected


title: CG4 cells expressing GFP only (ctrl), 3d diff, biological replicate 4 [48-4-CG192-4]

description:
edgeR_CG4diff-CG4prol.xlsx
48-4-CG192-4

value: ctrl


title: LC-31-plasma

value: lung cancer

value: female


title: LC-32-plasma

value: male


title: hFibros pB-1C

value: Skin

value: Fibroblasts

value: AGXT targeted knock-in


title: CG4 cells expressing GFP only (ctrl), 3d diff, biological replicate 3 [48-3-CG192-3]

description:
edgeR_CG4diff-CG4prol.xlsx
48-3-CG192-3

value: CG4 cells, immortalized cell line derived from primary rat oligodendroglia derived from brain

value: 3d differentiation


title: LC-30-plasma

value: I


title: iHeps GC-1C day 8 (exp.9)

value: Induced-hepatocytes

value: Hepatic transdifferentiation (FOXA2, HNF1a, HNF4a and TBX3 lentiviral overexpression and hepatic-specific culture media).


title: CG4 cells expressing GFP only (ctrl), 3d diff, biological replicate 2 [48-2-CG192-2]

description:
edgeR_CG4diff-CG4prol.xlsx
48-2-CG192-2


title: microglia-MRL/lpr3

value: MRL/lpr


title: LC-29-plasma

value: plasma


title: microglia-MRL/lpr2

value: brain


title: iHeps GC-1A day 13 (exp.9)


title: LC-28-plasma


title: PT-00153875_NT_AA

type: genomic

city: BUFFALO

first: Eduardo

last: Cortes

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

hyb_protocol: Illumina Infinium HD Methylation

scan_protocol: Illumina iScan Control Software

data_processing:
Illumina GenomeStudio V1
m450K_Proc_Funnorm.tsv (Normalized Beta values from minfi’s preprocessFunnorm)
m450K_MatrixSignal.tsv (Unmethylated and methylated signal intensities)

label: Cy3, Cy5

source_name: Adjacent Tumor

label_protocol: Illumina Infinium HD Methylation

extract_protocol: QIAamp DNA mini Kit

value: prostate

tag: tissue region

value: Adjacent Tumor

tag: race

value: AA


title: microglia-MRL/lpr1

value: untreated


title: ETH_65 blood vessel

city: Fuzhou

first: Jun

last: Peng

state: Fujian

address: 1 Qiuyang Road, Minhou Shangjie

department: Academy of Integrative Medicine

institute: Fujian University of Traditional Chinese Medicine

description: SHR  with 10-week ETH(3.5mg/kg/d) treatment

data_processing:
Data were filtered using the following specifications fastq software. The filtering standards from raw data to clean reads are: check the sample for contamination and, if there is pollution, remove it if the reads contains a joint sequence, the joint sequence is cut off first a base having an average base mass of less than 15 on both ends of the readth window is cut with four base lengths as a sliding window, remove the number of threads with a high N content. If the N content in a read is more than 5%, the whole read is removed, and the read pair with high low-quality base content is removed. If the low-quality base in one read (the mass value is not higher than the base of 20) exceeds 30%, the whole pair of the reads is removed, if the truncated read length is less than 50 bp, the entire read is removedRemove unmatched reads  Q30，Q20 explanation：  Q30 indicates that the sequencing error rate of the base is 0.1%.  Q20 indicates that the sequencing error rate of the base is 1%.
Using String Tie for readcount and FPKM calculation.
Differential expression analyses were performed using the limma package.
Assembly: RGSC6.0/RN6 (UCSC)
Supplementary files format and content: tab_delimited text files include FPKM values for each sample

source_name: blood vessel

extract_protocol:
The abdominal aorta were dissected and  stored in RNA later.Total RNA was extracted with  TRIzol® Reagent (Invitrogen,Carlsbad, CA, USA). RNA integrity was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and RNA concentration was measured by Qubit RNA Assay Kit in a Qubit Fluorometer (Invitrogen, CA, USA).
A total amount of 1 μg RNA per sample was used. In brief, the NEBNext rRNA Depletion Kit was used to remove rRNA from the total RNA. The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB, Beijing, China) was used to construct the libraries for sequencing following the manufacturer's instructions.

treatment_protocol: The SHRs (n=12) were randomly divided into 2 groups: SHR, and SHR +ETH (3.5mg/kg/d) groups (n=6 for each group). WKY rats (n=6) were set as control. Rats in WKY and SHR groups were  intragastrically with double distilled water (dd H2O), while rats in  SHR + ETH (3.5mg/kg/d) group were intragastrically with 3.5 mg/kg/d of ETH for 10 weeks.

value: abdominal aorta

value: SHR

value: double distilled water

value: ETH

tag: group

value: SHR+ETH


title: iHeps GC-1A day 8 (exp.9)

value: AGXT c.853T>C mutation corrected


title: ETH_64 blood vessel


title: LC-27-plasma

tag: disease

value: lung cancer

tag: gender

value: male

tag: age


title: hFibros GC-1A

value: Skin

tag: cell type

value: Fibroblasts


title: PT-00153875_T_AA

source_name: Tumor

value: Tumor


title: microglia-MRL/mpj1

value: MRL/mpj


title: LC-26-plasma

value: plasma

value: female

tag: Stage

value: I


title: ETH_58 blood vessel

tag: genotype


title: iHeps PH1-1 day 13 (exp.11)

value: Induced-hepatocytes

value: PH1 / AGXT mutation:p.I244T (c.853T>C)

value: Hepatic transdifferentiation (FOXA2, HNF1a, HNF4a and TBX3 lentiviral overexpression and hepatic-specific culture media).


title: CG4 cells expressing GFP only (ctrl), 3d diff, biological replicate 1 [48-1-CG192-1]

description:
edgeR_CG4diff-CG4prol.xlsx
48-1-CG192-1

value: CG4 cells, immortalized cell line derived from primary rat oligodendroglia derived from brain

tag: cell line

value: ctrl

value: 3d differentiation


title: PT-00162955_NT_AA

value: prostate

value: Adjacent Tumor

value: AA


title: ETH_54 blood vessel

value: abdominal aorta

value: SHR

value: double distilled water

value: ETH

value: SHR+ETH


title: PT-00162955_T_AA

value: Tumor


title: iHeps PH1-1 day 13 (exp.10)


title: hFibros GC-1C

value: Skin

value: Fibroblasts

value: AGXT c.853T>C mutation corrected


title: LC-25-plasma

value: plasma

value: lung cancer

value: female


title: iHeps PH1-1 day 13 (exp.9)

value: Induced-hepatocytes

value: PH1 / AGXT mutation:p.I244T (c.853T>C)

value: Hepatic transdifferentiation (FOXA2, HNF1a, HNF4a and TBX3 lentiviral overexpression and hepatic-specific culture media).


title: ETH_2 blood vessel


title: LC-23-plasma

value: I


title: ETH_1 blood vessel


title: iHeps PH1-1 day 8 (exp.11)


title: LC-22-plasma


title: PT-00180319_T_AA

value: prostate

value: AA


title: SHR_60 blood vessel

description: SHR  with 10-week  double distilled water  treatment

value: abdominal aorta

value: SHR


title: iHeps PH1-1 day 8 (exp.10)


title: PT-00187338_NT_AA

value: Adjacent Tumor


title: iHeps PH1-1 day 8 (exp.9)


title: PT-00187338_T_AA


title: SHR_59 blood vessel

value: double distilled water


title: CRC-57-plasma

description: RNA-seq of homo sapiens: colorectal cancer patient's plasma cell-free RNA; Provided by Peking University First Affiliated Hospital;  Constructed by Detector-seq; Purpose: To explore novel plasma and extracellular RNA biomarkers for cancer diagnosis

value: colorectal cancer

value: IIA


title: CRC-56-plasma

value: male

value: IIIB


title: hFibros PH1-1

value: Skin

value: Fibroblasts


title: PT-00188738_T_AA

value: Tumor


title: SHR_41 blood vessel


title: LC-24-plasma

value: plasma

value: lung cancer

value: female


title: SHR_48 blood vessel


title: Primary human hepatocytes pool

source_name: Liver

value: Liver

value: Hepatocytes

value: control donor (pool from 20 control donors)


title: CRC-55-plasma

source_name: plasma


title: PT-00180319_NT_AA

value: prostate

value: AA


title: CRC-54-plasma


title: PT-00189562_T_AA


title: C666-1_RNAseq_rep3

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

institute: Chiba University

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
Read were aligned with HISAT v2.1.0.
Fragments per kilobase of exon model per million mapped fragments (FPKM) were calculated using Cufflinks v2.2.1. Command line options for cufflinks were '--max-bundle-flags 4000000' for RNA-seq
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.

source_name: EBV(+) nasopharyngeal carcinoma cell lines

growth_protocol: NP69T was cultured in keratinocyte serum-free medium (Gibco, Carlsbad, CA). C666-1 was cultured in RPMI-1640 medium with 10% FBS (HyClone SH30910.03, GE Healthcare, Chicago, IL) and Penicillin-Streptomycin (Sigma-Aldrich, St. Louis, MO). These cells were incubated in a humidified atmosphere containing 5% CO2 at 37 ℃.

extract_protocol:
Total RNA was collected using RNeasy (Invitrogen, Carlsbad, CA)
Libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina).


title: SHR_3 blood vessel

value: abdominal aorta

value: SHR


title: CRC-53-plasma

value: colorectal cancer


title: PT-00189570_T_AA


title: PT-00190334_NT_AA

value: Adjacent Tumor


title: SHR_40 blood vessel

value: double distilled water


title: C666-1_RNAseq_rep2

value: EBV(+) nasopharyngeal carcinoma cell lines


title: WKY_6 blood vessel

description: WKY with 10-week double distilled water treatment

value: WKY


title: CRC-52-plasma

value: I


title: LC-21-plasma

value: male


title: PT-00190334_T_AA

value: Tumor


title: WKY_5 blood vessel


title: PT-00190362_NT_AA


title: CRC-51-plasma

value: plasma


title: NP69T_RNAseq_rep3

source_name: nasopharyngeal epithelial cell lines

value: nasopharyngeal epithelial cell lines


title: WKY_4 blood vessel


title: NP69T_RNAseq_rep2


title: CRC-49-plasma

value: female

value: IIA


title: WKY_3 blood vessel


title: PT-00190362_T_AA


title: NP69T_RNAseq_rep1


title: CRC-48-plasma


title: PT-00190805_T_AA


title: C666-1_Hi-C

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
Hi-C reads were processed using HiC-Pro.
Assembly: hg19+NC007605.1
Supplementary files format and content: hic

extract_protocol: Hi-C experiment were conducted in biological replicates using MboI, according to the protocol published by Suhas S.P. Rao et al. Cell 2014 (PMID: 25497547).  DNA libraries were prepared during Hi-C protocol according to experimental procedures described in Suhas S.P. Rao et al. Cell 2014 (PMID: 25497547).

tag: restriction enzyme

value: MboI


title: CRC-47-plasma

data_processing:
Adaptors and low-quality sequences in the raw sequencing data were trimmed using cutadapt version 2.3. Remeined reads were mapped to ERCC's spike-in sequences, NCBI's UniVec sequences and human rRNA sequences sequentially. GC oligos introduced in reverse transcription were trimmed off, after which reads shorter than 30 nt were discarded.
STAR (version 2.5.4a) was used to map clean reads to the hg38 genome index built with the GENCODE v38 annotation
Duplicates in the aligned reads were removed using umi_tools(v1.1.2)
The count matrix was constructed using featureCounts11 v1.6.2 with the GENCODE v38 annotation, circular RNA annotation from circBase, intron, intergenic regions frm UCSC Genome Browser. Reads mapped to mitochondrial RNAs were excluded.
Assembly: hg38
Supplementary files format and content: Matrix table of raw gene counts for each gene and sample

extract_protocol:
Cell-free RNAs in plasma were extracted using QIAzol Lysis Reagent (Qiagen, 79306). Cell-free RNAs in plasma extracellular vesicles (EVs) were extracted using exoRNeasy Midi Kit (Qiagen, 77144).
Detector-seq


title: NPC-TW01-EBV-eGFP_4C_bait1_OriP

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
w4Cseq was used for demultiplexing, trimmning bait primer sequence, mapping to hg19 genome, and making bedgraph files from raw fastq files.
Assembly: hg19
Supplementary files format and content: bedgraph

source_name: EBV infected nasopharyngeal carcinoma cell lines

growth_protocol: C666-1 was cultured in RPMI-1640 medium with 10% FBS (HyClone SH30910.03, GE Healthcare, Chicago, IL) and Penicillin-Streptomycin (Sigma-Aldrich, St. Louis, MO). NPC-TW01-EBV-eGFP was cultured in minimal essential medium (Sigma-Aldrich, St. Louis, MO) supplemented with 10% FBS and penicillin/streptomycin. NP69T was cultured in keratinocyte serum-free medium (Gibco, Carlsbad, CA). These cells were incubated in a humidified atmosphere containing 5% CO2 at 37 ℃.

extract_protocol:
Cells were lysed, and cross-linked DNA was digested with the primary restriction enzyme. Next, digested DNA was subjected to proximity ligation using T4 DNA ligase (EL0013, Thermo Scientific), followed by cross-link removal using Proteinase K (P8107S, New England Biolabs), which resulted in 3C libraries. The 3C libraries were then subjected to a second restriction enzyme digestion, followed by a circularization reaction using T4 DNA ligase.
For the viewpoint of bait1 and 2, the 4C template was used to perform a scaled-up inverse nested PCR. Inverse primers were designed including appropriate adaptors and index sequences. For the viewpoint at the TSS of PLA2G4A, two-step PCR was performed. The first PCR were performed with the primer designed including TSS of PLA2G4A and adaptors. The second PCR was performed to add indexes.

tag: restricion enzymes

value: NlaIII, DpnII


title: CRC-45-plasma


title: C666-1_RNAseq_rep1


title: WKY_1 blood vessel


title: PT-00191716_T_EA

value: prostate

value: EA


title: NPC-TW01-EBV-eGFP_4C_bait2_EBER


title: PT-00190805_NT_AA

value: AA


title: PT-00191716_NT_EA


title: Wild Type Pig Kidney_L4

city: Birmingham

first: Rebecca

last: Asiimwe

state: Alabama

address: 1720 2nd Ave South

department: Surgery

institute: The University of Alabama at Birmingham

description:
C9_S33_L004
Fresh frozen Spatial transcriptome sequencing

data_processing:
library strategy: Spatial Transcriptomics
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to a hybrid human-pig reference genome to generate count matrices using Space Ranger’s default settings
Assembly: The human GRCh38 (GCA_000001405.28) or porcine Sus scrofa 11.1 (GCA_000003025.6)
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: high resolution image of tissue
Supplementary files format and content: tissue_lowres_image.png: low resolution image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots

organism: Sus scrofa

source_name: Kidney

extract_protocol:
Frozen biopsy OCT blocks were equilibrated to -10°C before use. Using a cryostat, a 10 μm section was placed onto a Visium Spatial Gene Expression Slide (10X Genomics) and processed according to the manufacturer’s protocol
Spatial transcriptome sequencing libraries were prepared with 10x Genomics Visium Spatial Gene Expression Slides and Reagent kit according to the manufacturer’s protocol

value: Kidney

value: wild type


title: PT-00192088_NT_AA

value: Adjacent Tumor


title: 22Rv1, CD276 knockout, rep3

data_processing:
RNA quantity and integrity were determined using the Qubit® Fluorometer and the Fragment Analyzer system with the PROSize 3.0 software (Agilent Technologies, Palo Alto, California, USA).
The RQN were ranging from 8.8 to 10 for all samples, which was considered sufficient. Illumina TruSEQ RNA library prep and sequencing reagents were used following the manufacturer’s recommendations using polyA-selected transcripts (Illumina, San Diego, CA, USA).
The samples were sequenced on the Illumina NovaSeq platform (2 x 150 bp, single index) and generated ~20 million paired-end reads for each sample.
Assembly: GRCh38
Supplementary files format and content: Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Below are the statistics of mapping the reads to the reference genome.
Supplementary files format and content: Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted. If a strand-specific library preparation was performed, the reads were strand-specifically counted.

source_name: Cell line

growth_protocol: The medium for this cell lines is RPMI-1640 Medium supplumented with 10% fetal bovine serum.

extract_protocol:
 Total RNA was extracted from each tissue by using Qiagen's ‘RNeasy’ RNA extraction kit (Qiagen).
RNA-sequencing was performed by GENEWIZ (South Plainfield, NJ, USA). RNA quantity and integrity were determined using the Qubit® Fluorometer and the Fragment Analyzer system with the PROSize 3.0 software (Agilent Technologies, Palo Alto, California, USA). The RQN were ranging from 8.8 to 10 for all samples, which was considered sufficient. Illumina TruSEQ RNA library prep and sequencing reagents were used following the manufacturer’s recommendations using polyA-selected transcripts (Illumina, San Diego, CA, USA). The samples were sequenced on the Illumina NovaSeq platform (2 x 150 bp, single index) and generated ~20 million paired-end reads for each sample.

value: Cell line

value: Prostate cancer cell line

value: CD276 knockout


title: Wild Type Pig Kidney_L2

description:
C9_S33_L002
Fresh frozen Spatial transcriptome sequencing


title: CRC-44-plasma

first: Zhi

last: Lu

value: colorectal cancer

value: IV


title: Wild Type Pig Kidney_L3

description:
C9_S33_L003
Fresh frozen Spatial transcriptome sequencing


title: 22Rv1, CD276 knockout, rep1

first: Yasutaka

last: Yamada


title: CRC-46-plasma

value: plasma

value: IIIB


title: CRC-42-plasma

value: female


title: PT-00192088_T_AA

value: Tumor


title: PT-00195211_T_AA


title: CRC-41-plasma

value: IIIC


title: Wild Type Pig Kidney_L1

description:
C9_S33_L001
Fresh frozen Spatial transcriptome sequencing


title: 22Rv1, Control, rep3

value: Wilde Type


title: M39_Lys_ApcKras_Ctrl

data_processing:
FASTQ files were preprocessed with the SOAPnuke pipeline
Reads were mapped with STAR (v2.7.9a) to the mouse mm10 reference genome with ensemble gene annotations
Read counts were extraced with Featurecounts (subread 2.0.3) and downstream analysis was performed with DESeq2 (1.36.0)
Assembly: mm10
Supplementary files format and content: DESeq2 processed tab delimited file includes variance stabilizing transformation (VST) values of the counts

extract_protocol:
Intestinal tumors were macro-dissected from intestinal tissues and cut into small fragments of 1-2 mm
RNA was isolated from cells using TRIzol Reagent (ThermoFisher Scientific) according to the manufacturer’s instructions
paired end RNA libraries were prepared according to DNBseq Library Preparation protocol

treatment_protocol: Mice were exposed to inflammatory stimulus (2% DSS, 7d) or given H2O (control). Subsequently, lineage specific mutations were induced by intraperitoneal injections of 1 mg tamoxifen.

value: small intestine

value: Lyz1 Apc Kras

value: Control

tag: time

value: 1-4 months


title: WKY_2 blood vessel

value: abdominal aorta

value: WKY

value: double distilled water


title: CRC-40-plasma


title: 22Rv1, Control, rep1

value: Cell line

value: Prostate cancer cell line


title: PT-00195338_NT_AA

value: prostate

value: Adjacent Tumor

value: AA


title: M27_Lys_ApcKras_Ctrl


title: CRC-39-plasma

value: plasma

value: colorectal cancer

value: male

value: IIIB


title: DNA methylation in 22Rv1 sgRB1 decitabine treated

data_processing:
restriction enzyme treatment
methylation library preparetion
bisulfite conversion
sequencing

growth_protocol: The medium for 22Rv1 cell lines is RPMI-1640 Medium supplumented with 10% fetal bovine serum for 22Rv1 cell line and for PM154 is prostate specific media using advanced DMEM.

extract_protocol:
Total genomic DNA was extracted from PDXs using QIAamp DNA Mini Kit (QIAGEN).
Illumina

value: decitabine treatment


title: PT-00195338_T_AA

value: Tumor


title: DNA methylation in 22Rv1 sgRB1 control

value: control


title: M25_Lys_ApcKras_Ctrl

value: small intestine

value: Lyz1 Apc Kras

value: Control


title: PT-00195907_NT_AA


title: CRC-38-plasma


title: M21_Lys_ApcKras_Dss

value: DSS

value: 1-4 months


title: CRC-37-plasma

value: female

value: IV


title: DNA methylation in 22Rv1 control


title: M12._Lys_ApcKras_Dss


title: M10._Lys_ApcKras_Dss


title: PT-00197746_NT_AA

value: prostate


title: CRC-35-plasma


title: DNA methylation in PM154 decitabine treated


title: PT-00195907_T_AA


title: PT-00197746_T_AA


title: DNA methylation in PM12 control


title: PT-00200672_NT_AA

value: Adjacent Tumor


title: DNA methylation in PM154 control


title: CRC-34-plasma

value: I


title: M9._Lys_Apc_Dss

value: Lyz1 Apc


title: PT-00200672_T_AA

value: AA


title: CRC-32-plasma

value: plasma

value: colorectal cancer

value: male

value: IIA


title: siRPL24_Input_03

city: New Haven

first: Karla

last: Neugebauer

state: Connecticut

address: 333 Cedar St

institute: Yale

data_processing:
FASTQC quality check
Reads trimmed with cutadapt
Reads aligned to reference genome hg38 using Bowtie2
Peaks called with MACS2, using input as a noIP control
Assembly: hg_38
Supplementary files format and content: pileup tracks in .bigWig format
Supplementary files format and content: peaks .narrowPeak

source_name: HeLa Kyoto

growth_protocol: Cells were grown in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal calf serum and pennicilin/streptomycin antibiotics at 37˚C with 5% CO2.

extract_protocol: Cells were crosslinked with 1% formaldehyde for 10 min at room temperature. After cell lysis, DNA was sheared to fragments of ~200bp and lysate was cleared by centrifugation. 25% of the supernatant was used as input and the remaiining part was used to precipitate coilin with Dynabeads Protein G coupled to goat anti-EGFP antibody. After stringent washing, the DNA was eluted and de-crosslinked by Proteinase K treatment. DNA fragments were purified by phenol-chlorophorm extraction.

treatment_protocol: HeLa cells were reverse transfected with ON-Target Plus siRNA mix in SMARTPool format and incubated for 72h before experimental assays.

tag: chip antibody

value: RPL24 siRNA, 72 hours

tag: sirna

value: L-011144-02, Horizon Discovery, ONTarget Plus


title: M7._Lys_Apc_Dss

tag: tissue

value: small intestine

value: Tumor


title: siRPL24_Input_02

tag: treatment


title: K562-NIH3T3 scHi-C

data_processing:
Demultiplexing using custom scripts
Alignment by BWA (version 0.7.17-r1188) for genomic DNA and by STAR (version 2.7.8a) for RNA
Deduplication using custom scripts
Contact calling by pairtools (version 0.3.1-dev.1)
RNA read count extraction by featureCounts (version 2.0.1)
Assembly: hg38; mm10
Supplementary files format and content: Tab-delimited text files include chromatin contact pairs for single cells
Supplementary files format and content: Tab-delimited text files include RNA reads and mapped genes for single cells

organism:
Homo sapiens
Mus musculus

extract_protocol:
GAGE-seq protocol
Hi-C and scRNA-seq


title: PT-00201372_NT_AA

tag: tissue region


title: M6._Lgr5_Apc_Dss

value: Lgr5 Apc

value: DSS


title: K562-NIH3T3 scRNA


title: CRC-36-plasma

city: Beijing

address: Shuangqing Road

institute: Tsinghua University


title: siRPL24_Pol2_03

value: Pol II antibody (Santa-Cruz sc-47701)


title: M5._Lgr5_Apc_Dss

value: 1-4 months


title: siRPL24_Pol2_02


title: PT-00208975_NT_AA

value: prostate

tag: race


title: M3._Lgr5_Apc_Ctrl

value: Control


title: PT-00214541_NT_AA

value: Adjacent Tumor


title: M4._Lgr5_Apc_Dss


title: M2._Lgr5_Apc_Ctrl


title: M1._Lgr5_Apc_Ctrl


title: c8086e2 tubular female control

city: Blacksburg

first: Alan

middle: D.

last: Ealy

state: VA

address: 175 W Campus Dr

institute: Virginia Tech

data_processing:
Data were generated from each sample submitted for sequencing (n = 12 ovoid, and n = 8 tubular conceptuses)
Paired-end reads were trimmed then aligned to the Bos taurus genome (ARS-UCD1.2 assembly) using HiSat2
Samtools was used to sort the aligned reads and filter out any samples with low quality reads
Picard was used for sorting and indexing aligned reads from samples with quality reads (http://broadinstitute.github.io/picard/).
Featurecounts was used for quantifying aligned reads against the Ensembl gene annotation (Bos taurusARS-UCD1.2.98) with duplicates removed
Assembly: ARS-UCD1.2
Supplementary files format and content: tab delineated read files

organism: Bos taurus

source_name: conceptus

extract_protocol:
TRIzol™ and Phasemaker™ Tubes (ThermoFisher) were used to extract high purity total RNA from whole, individual ovoid (n = 6, IL6-treated; n = 6, non-treated, control) and tubular (n = 4, IL6-treated; n = 4, non-treated, control) conceptuses.
Samples were further processed for RNA sequencing at Vanderbilt Technologies for Advanced Genomics (VUMC, Nashville, TN, USA) using the NEBNext® rRNA Depletion kit (New England BioLabs Inc., Ipswich, MA, USA).
A sequencing assay was carried out in a NovaSeq 6000 System (Illumina, Inc, San Diego, CA) to produce pair-end reads 150 nucleotides long.

treatment_protocol: On day 5 post IVF, recombinant bovine IL6 (100 ng/ml; KingFisher Biotech, St. Paul, MN, USA) or its carrier (SOF-BE1) were administered to embryos.  Embryos were kept in their treated culture drops until blastocyst assessment and collection on day 7.5 for embryo transfer or immunofluorescence.

value: conceptus

value: tubular

value: female

value: control


title: c9007e1 tubular female IL6


title: PT-00214592_NT_EA

value: EA


title: c8086e5 tubular male control

value: male


title: c6186e2 tubular female IL6


title: c9007e5 tubular male IL6


title: siRPL24_Coilin_03

value: coilin antibody (Abcam ab210785)

value: RPL24 siRNA, 72 hours


title: siRPL24_Coilin_02

value: L-011144-02, Horizon Discovery, ONTarget Plus


title: FBY2586_2_Y1F

city: Namur

first: Carlo

last: Yague-Sanz

address: 61 rue de Bruxelles

department: Medecine

country: Belgium

institute: Namur University

data_processing:
Reads were mapped to the S. pombe genome (version ASM294v2.26) with HISAT2 (Kim et al., 2015). Gene-level read quantification was made with featureCounts (Liao et al, 2014) with options -p -B -s 2 -P -d 0 -D 5000 -C -T 4. De novo transcript discovery was performed with stringtie (Pertea et al, 2015) using stringent options (-t -f 0.1 -c 5 --rf -s 5) that are better suited to the dense yeast genome than the default. The new transcript discovered in the S2A mutant were merged in the annotation if they did not overlap other transcripts on the same strand. Differential gene expression of mutant against WT was made with DESeq2 (Love et al, 2014). Based on DESeq2 size factors, we used deepTools to generate normalized coverage files (.bigwig) with options bamCoverage --samFlagExclude 256 --maxFragmentLength 5000 --scaleFactor [1/size_factor] -bs 1 -of --filterRNAstrand [fwd/rev] bigwig.
Assembly: ASM294v2.26
Supplementary files format and content: strand-specific genome coverage files in bigWig format are provided
Supplementary files format and content: CTD_couts_GEO.txt contains the raw read counts per gene.

organism: Schizosaccharomyces pombe

source_name: S. pombe cells

growth_protocol: Cells were grown in YES medium until mid-log phase (OD 0.5)

extract_protocol:
Total RNA was extracted by the hot-phenol method, as previously described (Duval et al., 2023). Briefly, yeast cells are first resuspended in 600 µl of TES solution (10 mM Tris-HCl [pH 7.5], 10 mM EDTA [pH8.0] and 0.5% SDS) and 600 µl of phenol-chloroform-Isoamyl alcohol (125:24:1 [pH 4.5]), and then incubated at 65°C for 60 min with vortexing every 10 min. The RNA was extracted once with 550 µl of phenol-chloroform-Isoamyl alcohol (125:24:1 [pH 4.5]) and once with 450 µl of chloroform-isoamyl alcohol (24:1), and precipitated with ethanol and 2 M NaCl.
rRNA-depleted RNA-seq libraries were prepared following manufacturer's instructions using the Illumina Truseq Stranded Total RNA-sequencing kit after ribodeletion with the RiboZero Yeast ribodepletion (Epicentre). RNA-seq libraries were sequenced in paired-end (2×100nt) using Illumina technologies (HiSeq 4000) at Genome Québec.

tag: strain

value: Y1F Rpb3-HA

value: h- rpb1 Y1F::kanMX6 Rpb3-3HA::hphMX6

value: S. pombe cells


title: PT-00201372_T_AA

value: Tumor

value: AA


title: siRPL24_Coilin_01


title: c6186e4 tubular male IL6


title: PT-00214592_T_EA

value: prostate


title: PT-00208975_T_AA


title: siRPL24_Pol2_01

value: Pol II antibody (Santa-Cruz sc-47701)


title: siRPL14_Input_03

value: RPL14 siRNA, 72 hours

value: L-012948-01, Horizon Discovery, ONTarget Plus


title: FBY2584_2_S7A

value: S7A Rpb3-HA

value: h- rpb1 S7A::kanMX6 Rpb3-3HA::hphMX6


title: c5036e2 tubular male control

value: conceptus

value: tubular

value: control


title: FBY2581_2_S2A

value: S2A Rpb3-HA

value: h- rpb1 S2A::kanMX6 Rpb3-3HA::hphMX6


title: PT-00216325_NT_EA

value: Adjacent Tumor

value: EA


title: PT-00216325_T_EA


title: PT-00214541_T_AA


title: siRPL14_Input_02


title: c5036e4 tubular male control

value: male


title: FBY2578_2_WT

value: WT Rpb3-HA

value: h- Rpb3-3HA::hphMX6

value: S. pombe cells


title: siRPL14_Input_01


title: siRPL14_Pol2_03


title: M8._Lys_Apc_Dss

value: small intestine

value: Tumor

value: Lyz1 Apc

value: DSS

value: 1-4 months


title: c9007e2 ovoid female IL6

value: ovoid

value: female


title: siRPL14_Pol2_02

value: Pol II antibody (Santa-Cruz sc-47701)

value: RPL14 siRNA, 72 hours

value: L-012948-01, Horizon Discovery, ONTarget Plus


title: PT-00216417_T_AA

value: prostate

value: AA


title: c6186e7 ovoid female IL6

value: conceptus


title: FBY2584_1_S7A

value: S7A Rpb3-HA

value: h- rpb1 S7A::kanMX6 Rpb3-3HA::hphMX6


title: PT-00216463_NT_AA

value: Adjacent Tumor


title: FBY2581_1_S2A

value: S2A Rpb3-HA

value: h- rpb1 S2A::kanMX6 Rpb3-3HA::hphMX6

value: S. pombe cells


title: c9007e3 ovoid female IL6


title: siRPL14_Pol2_01


title: PT-00216463_T_AA

value: Tumor


title: FBY2578_1_WT

value: WT Rpb3-HA

value: h- Rpb3-3HA::hphMX6


title: c6186e3 ovoid female IL6

value: ovoid


title: PT-00220025_NT_AA


title: c6186e5 ovoid male IL6

value: male


title: siRPL14_Coilin_02

value: coilin antibody (Abcam ab210785)


title: IPHA_FBY2581_2

data_processing:
Reads were mapped using HISAT2 (Kim et al, 2015) with option --no-splice-alignment on a concatenate genome containing the S. pombe (version ASM294v2.26) and S. cerevisiae chromosomes. Normalization factors were computed based on the proportion of reads mapped to the S. cerevisiae genome as previously described (Larochelle et al, 2018) while the average fragment size was estimated using MACS2 predicted function (Zhang et al, 2008). Based on the normalization factors and averaged fragment size, we used deepTools (Ramirez et al, 2016) to generate normalized coverage files (.bigwig) with options bamCoverage --smoothlength 20 --centerReads -e [average_fragment_size] --scaleFactor [size_factor] -bs 1 -of bigwig. If no spike-in was available (as it is the case for the Pcf11-myc and Set2-TAP ChIP data), the option --normalizeUsing RPKM was used instead of --scale factor.
Assembly: ASM294v2.26
Supplementary files format and content: genome coverage files in bigWig format are provided

growth_protocol: For each condition (IP), 50 mL of cell cultures were grown to an OD600nm of ∼0.5 at 30 °C in YES .

extract_protocol:
After quenching the solution with glycine (final concentration of 360 mM), cells were washed twice with a cold Tris-buffer saline (20 mM Tris-HCl [pH 7.5] and 150 mM NaCl) and frozen in liquid nitrogen. Cell pellets from 50 ml cultures were thawed and resuspended in 500 µL of cold lysis buffer (50 mM HEPES-KOH [pH 7.5], 140 mM NaCl, 1 mM EDTA pH 8.0, 1% Triton X-100 and 0.1% Na-deoxycholate) that was supplemented with a protease inhibitor cocktail (1X PMSF and 1X PLAAC) and disrupted vigorously with glass beads in a FastPrep-24TM (MP biomedical) for 3 cycles of 30 sec at 6.5 m/s. Then, 150 µL of cold lysis buffer with proteases was added to increase the volume and samples were sonicated for 12 cycles of 10 sec at 20% amplitude with a Branson digital sonifier. Sonicated chromatin was then incubated overnight at 4 °C with 50 µl of magnetic beads IgG Dynabeads (Life Technologies, 11041) in the case of TAP tagged proteins, or Dynabeads M-280 Sheep Anti-Rabbit IgG (Invitrogen, 11203D) beads coupled with 2 ug of rabbit anti-Histone H3 total (ab1791, abcam), H3K36me3 (ab9050, abcam) or H3K9ac (06-942, Millipore Sigma). Beads were then washed twice for 4 minutes at 4oC with 1 mL of cold lysis buffer, twice with 1 mL of cold lysis buffer with 500 mM NaCl, twice with 1 mL of cold wash buffer (10 mM Tris-HCl [pH 8.0], 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate and 1 mM EDTA), and once with 1 mL of cold Tris-EDTA (TE: 10 mM Tris-HCl [pH 8.0] and 1 mM EDTA [pH8.0]). Bound material was eluted by resuspending the beads in 50 µl elution buffer (50 mM Tris-HCl [pH 8.0], 10 mM EDTA and 1% SDS) at 65 °C for 15 min at 1200 rpm in an Eppendorf Thermomixer. After a short centrifugation, reverse-crosslinking was performed by incubating eluted chromatin with 120 µl of TE and 1% SDS or 5 µl of WCE in 165 µl of TE with 1% SDS at 65 °C overnight. For ChIP-Seq experiments, reverse-crosslinking was perfomed by incubating eluted chromatin with 20 µl of WCE in 150 µl of TE and 1% SDS. Samples were treated with a proteinase K mix (150 mg proteinase K, 60 mg glycogen in TE) and DNA was extracted twice with phenol-chloroform-isoamyl alcohol (25:24:1, [pH8.0], Invitrogen) and once with chloroform (Bioshop). Following ethanol precipitation, pellets were resuspended in 30 µl of TE plus 10 µg of RNAse A and incubated 1 h i at 37 °C. RNase-treated DNA was then purified with a QIAGEN PCR purification kit. The input DNA was diluted 400 times while the coimmunoprecipitated DNA was diluted 100 times in water. DNA were analyzed on a LightCycler 96 Instrument system (Roche) with the addition of the 2X SYBR Green in the presence of 0.15 μM of gene-specific oligonucleotide
ChIP-sequencing libraries were prepared using the SPARQ DNA Sample Prep Kit Illumina Platform (Quantabio) according to the manufacturer's instructions.

treatment_protocol: Cultures were cross-linked with 1% formaldehyde for 20 min at room temperature with manual shaking every 5 min.

tag: fraction

value: Rpb3-HA IP

tag: spike-in

value: 10 % S. cerevisiae Rpb3-HA strain mixed before the crosslink


title: siRPL14_Coilin_03

value: RPL14 siRNA, 72 hours

value: L-012948-01, Horizon Discovery, ONTarget Plus


title: c6186e1 ovoid male IL6

value: conceptus


title: PT-00220025_T_AA

value: prostate

value: AA


title: siRPL14_Coilin_01


title: PT-00224181_NT_AA

value: Adjacent Tumor


title: PT-00216417_NT_AA


title: WCE_FBY2581_2

value: S2A Rpb3-HA

value: input


title: siNT_Input_03

value: non-targeting siRNA, 72 hours

value: D-001810-10, Horizon Discovery, ONTarget Plus


title: c5036e5 ovoid male control

value: control


title: FBY2586_1_Y1F

value: Y1F Rpb3-HA

value: h- rpb1 Y1F::kanMX6 Rpb3-3HA::hphMX6

value: S. pombe cells


title: WCE_FBY2578_2

value: WT Rpb3-HA

value: h- Rpb3-3HA::hphMX6


title: c201e3 ovoid female control

value: ovoid

value: female


title: c201e4 ovoid female control


title: siNT_Input_01


title: IPHA_FBY2578_1

value: Rpb3-HA IP

value: 10 % S. cerevisiae Rpb3-HA strain mixed before the crosslink


title: PT-00227158_NT_AA

value: prostate


title: c201e1 ovoid male control

value: conceptus

value: male


title: PT-00228928_NT_EA

value: Adjacent Tumor

value: EA


title: siNT_Input_02

value: non-targeting siRNA, 72 hours


title: IPHA_FBY2581_1

value: S2A Rpb3-HA

value: h- rpb1 S2A::kanMX6 Rpb3-3HA::hphMX6


title: siNT_Pol2_03

value: Pol II antibody (Santa-Cruz sc-47701)

value: D-001810-10, Horizon Discovery, ONTarget Plus


title: PT-00228928_T_EA

value: Tumor


title: WCE_FBY2581_1

value: input

value: S. pombe cells


title: CON H3K9me3 whole cell extract

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
Libraries were sequenced on an Illumina NextSeq 500, generating 76 bp paired-end reads or Illumina NextSeq 2000 generating 66 bp paired-end reads.
Reads were aligned to the mouse genome mm10 by Rsubread with duplicates removed with Picard tools MarkDuplicates command
BigWig files were generated with BamCoverage from Deeptools with bamCoverage normalizeUsing RPGC, bs 10 and effectiveGenomeSize 2652783500.
Assembly: mm10
Supplementary files format and content: BigWig, a coverage track generated from the mapped read fragments. The coverage is calculated as the number of reads per 10 bp bin. Coverage was normalization by reads per genomic content (RPGC).

source_name: Thymus

extract_protocol:
ChIP-seq was performed as per (Lee et al. 2006) with amendments as follows: 1) sonication was performed using a Covaris S220 focused-ultrasonicator with the following settings to shear DNA to a size of 300-500 bp suitable for high-throughput sequencing: Fill Level 10, Duty Cycle 10, PIP 175, Cycles/Burst 200 for 60 seconds. 2) Immunoprecipitation was performed overnight at 4degC with rotation using ProteinG Dynabeads (50μL per IP) pre-coupled with antibody (5μL per IP) in 0.5% BSA/PBS for >5h. 3) Final immunoprecipitated DNA was purified using Zymo ChIP DNA Clean & Concentrator kit.
Illumina Tru-seq (1/2 reaction) library preparation was performed.

value: Thymus

value: CD4+CD8+ double positive thymocytes

tag: antibody

value: whole-cell extract

tag: Sex

value: Male


title: IPHA_FBY2578_2

value: WT Rpb3-HA

value: Rpb3-HA IP

value: 10 % S. cerevisiae Rpb3-HA strain mixed before the crosslink

value: h- Rpb3-3HA::hphMX6

tag: cell type


title: siNT_Pol2_02


title: c201e6 ovoid male control

value: conceptus

value: ovoid

tag: genotype

value: male

value: control


title: WCE_FBY2578_1


title: 839 cells,sgIFI35_2

city: Chapel Hill

first: Daqi

last: Li

address: 450 West Dr

institute: Univerity of North Carolina at Chapel Hill

data_processing:
The libraries were mixed in equimolar ratios and sequenced on MGISEQ-2000RS platform. ATAC-Seq raw reads were filtered to remove low-quality or adaptor sequences by SOAPnuke. Cleaned reads were mapped to the reference genome of hg38 with Bowtie2 and generated SAM files were converted to BAM files using Samtools using the view function. BAM files which were converted to BigWig files using Deeptools. MACS2 was used to call peaks for open chromatin regions. IDR was applied to measure the reproducibility of findings identified from replicate samples.
Assembly: hg38
Supplementary files format and content: CW839CONT_1_final_peaks.txt include peak genes of Sample CW839CONT_1
Supplementary files format and content: CW839CONT_2_final_peaks.txt include peak genes of Sample CW839CONT_2
Supplementary files format and content: CW839IFI35_1_final_peaks.txt include peak genes of Sample CW839IFI35_1
Supplementary files format and content: CW839IFI35_2_final_peaks.txt include peak genes of Sample CW839IFI35_2

source_name: glioblastoma

extract_protocol:
Cells were harvest and washed in ice-cold PBS followed by centrifugation at 500 g for 5 minutes. Cells were resuspended in 50 ul cold lysis buffer (10 mM Tris-HCl pH 7.5, 3 mM MgCl2, 10 mM NaCl, 0.1% Igepal CA-630) and mixed end over end. After centrifugation at 500 x g for 10 minutes, cell pellet was resuspended in transposition reaction mix (25 μl TD-Buffer, 2.5 μl Tn5, 22.5 μl water) and incubated at 37 °C for 30 min with gentle mixing.
Immediately following the transposition reaction, MinElute PCR Purification Kit (Qiagen) was used to purify transposed DNA. Finally, the PCR amplification was performed to amplify purified DNA and qPCR-based methods were used to quantify ATAC-seq libraries.

value: glioblastoma

tag: cell line

value: glioma stem cells


title: PT-00229031_NT_AA

data_processing:
Illumina GenomeStudio V1
m450K_Proc_Funnorm.tsv (Normalized Beta values from minfi’s preprocessFunnorm)
m450K_MatrixSignal.tsv (Unmethylated and methylated signal intensities)

extract_protocol: QIAamp DNA mini Kit

value: prostate

value: Adjacent Tumor

value: AA


title: 839 cells,sgIFI35_1


title: PT-00224181_T_AA

value: Tumor


title: siNT_Coilin_03

value: coilin antibody (Abcam ab210785)

value: non-targeting siRNA, 72 hours

value: D-001810-10, Horizon Discovery, ONTarget Plus


title: siNT_Coilin_02


title: c5036e6 ovoid female control

value: female


title: 839 cells,sgControl_2

value: sgControl


title: Dicerfl/fl_mESC, GFP-Cre, rep1

city: Fitzroy

first: Mark

last: Chong

state: Victoria

address: 9 Princes Street

institute: St Vincent's Institute of Medical Research

description:
Dicer_KO_rep1
creA
degseq_dicer_pileup_edgeR.txt

data_processing:
The raw reads were processed using the Trimmomatic program (version 0.38.0) to remove Illumina platform-specific adaptor sequences and low-quality bases (below 20 across 4 nt).
The processed reads were then aligned to the mouse reference genome GRCm38 (mm10) using RNA STAR with default parameters (version 2.7.8a).
The depth of Degradome-seq reads at each locus was determined by counting the number of reads starting at that locus.
We performed differential pile-up analysis between Drosha deficient and control ESCs or Dicer deficient and control ESCs using the edgeR package (version 3.26.1). A genomic locus with a log2 fold change (log2FC) < -1.5 and false discovery rate (FDR) < 0.05 were considered significant.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Tab-delimited edgeR output files, including the depth of reads starting at each genomic locus (normalized to RPM), statistics output from edgeR, and whether the locus is within an annotated gene.
Library strategy: Degradome-seq

source_name: embryonic stem cells

growth_protocol: All ESCs were cultured in KnockOut DMEM, supplemented with 10% heat-inactivated fetal bovine serum (FBS; GE Healthcare Life Sciences), 5% KnockOut Serum Replacement (Gibco), 1% sodium pyruvate (Gibco), 1% non-essential amino acids, 1% penicillin-streptomycin glutamine (PSQ; Gibco), 0.1 mM 2-mercaptoethanol and 103 U/mL LIF on a Mitomycin C-inactivated mouse embryonic fibroblasts.

extract_protocol:
Total RNA was harvested using TRIsure.
PolyA-tailed RNA was isolated from 75 μg of total RNA using the Dynabeads mRNA direct purification kit (Thermo Fisher) following the manufacturer’s instructions. An RNA linker (5’-CACGACGCUCUUCCGAUCU-3’) was ligated to the polyA RNA with T4 RNA ligase (Thermo Scientific) to capture RNAs with a 5’ monophosphate (5’P), a hallmark of RNase III cleavage. The ligation products were then purified with the Dynabeads mRNA direct purification kit and reverse transcription was performed using Superscript III reverse transcriptase (Invitrogen) and random hexamer primer attached to reverse adaptor sequence (5’-AGACGTGTGCTCTTCCGATCNNNNNN-3’). The cDNA was cleared of RNA by treating with RNase H (NEB). Half the cDNA was subjected to 2nd strand synthesis using Phusion high-fidelity DNA polymerase (NEB) with primers to the 5’ RNA linker and reverse adaptor (5’-ACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’ and 5’-GTGACTGGAGTTCAGAC-GTGTGCTCTTCCGATC-3’) using the cycling conditions: 98°C for 1 minute, (98°C for 30 seconds, 58°C for 30 seconds, 72°C for 1 minute) x7 cycles, and 72°C for 5 minutes. The resulting cDNA was resolved on a Low Melting Point agarose gel (Scientifix) and cDNA corresponding to 200–400 bp were gel purified. This cDNA library was then PCR barcoded with PCR Primer 1.0 (5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACG-3’) and a sample-specific barcode primer (5’-CAAGCAGAAGACGGCATACGAGATNNNNNNGTGACT-GGAGTTCAGACGTG-3’) using MyTaq Red Mix (Bioline) for 15 cycles. The resulting cDNA libraries were sequenced on the NextSeq 500 platform (Illumina).

treatment_protocol: Deletion of the floxed Drosha allele was achieved by adding 100 nM 4-hydroxytamoxifen (Sigma-Aldrich) to the Drosha fl/fl Gt(ROSA)26SorCreERT2 ESCs  for 72h. The medium was then replaced (without 4-hydroxytamoxifen) for a further 48h to completely deplete Drosha-dependent miRNAs before analysis. Deletion the floxed Dicer allele was achieved by transducing the Dicerfl/fl ESCs with Cre-expressing retrovirus. The virus also contained a GFP reporter that allowed for sorting of transduced cells. GFP+ ESCs were sorted 3 days after transduction, then cultured for a further 2 days before analysis.

value: embryonic stem cells

value: Dicer KO

value: GFP-Cre transduced


title: PT-00233979_T_EA

value: EA


title: PT-00235411_NT_AA


title: Dicerfl/fl_mESC, GFP, rep2

description:
Dicer_WT_rep2
gfpB
degseq_dicer_pileup_edgeR.txt

value: Dicer WT

value: GFP transduced


title: 839 cells,sgControl_1

value: glioblastoma


title: siNT_Pol2_01

value: Pol II antibody (Santa-Cruz sc-47701)


title: Ovarian granulosa cells-NOR_rep6

city: Jinan

first: li

last: dong

address: No. 42 Wen Hua Xi Road

institute: shandong university of traditional Chinese medcine

data_processing:
Illumina Casava1.7 software used for basecalling.
Cutadapt (v1.9) was used to remove the reads that contained adapter contamination, low quality bases and undetermined bases.
The sequence quality was verified using FastQC (v0.10.1).
The valid reads were mapped to the human reference genome (GRCh38) using HISAT software (v2.0.4).
The mapped reads of each sample were assembled using StringTie (v1.3.0) with default parameters. Then, all transcriptomes from samples were merged to reconstruct a comprehensive transcriptome using gffcompare.
After the final transcriptome was generated, StringTie was used to perform expression level for mRNAs by calculating fragments per kilobase of exon model per million mapped reads (FPKM).
Genome_build: Human reference genome (GRCh38)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Ovarian granulosa cells

extract_protocol:
Total RNA was isolated and purified using Trizol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity of each sample were analysis of Agilent Bioanalyzer 2100 and RNA Nano1000 Assay Kit with RIN number >7.0. Approximately 5 ug of total RNA was used to deplete ribosomal RNA according to the manuscript of the Ribo-Zero™ rRNA Removal Kit (Illumina, San Diego, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Ovarian

tag: age

value: untreated


title: Dicerfl/fl_mESC, GFP, rep1

description:
Dicer_WT_rep1
gfpA
degseq_dicer_pileup_edgeR.txt


title: Ovarian granulosa cells-NOR_rep4


title: PT-00235411_T_AA

value: prostate

value: AA


title: PT-00236614_NT_AA

source_name: Adjacent Tumor

value: Adjacent Tumor


title: PT-00227158_T_AA

value: Tumor


title: CON H3K9me3 replicate

value: Thymus

value: CD4+CD8+ double positive thymocytes

value: H3K9me3 Rabbit pAb (Abcam Cat#8898 Lot#GR3217836-1)

value: Male


title: Droshafl/fl_CreER_mESC, 4OHT, rep2

description:
Drosha_KO_rep2
tamB
degseq_drosha_pileup_edgeR.txt

value: embryonic stem cells

value: Drosha KO


title: PT-00229031_T_AA


title: Ovarian granulosa cells-NOR_rep3


title: PT-00236614_T_AA


title: Ovarian granulosa cells-NOR_rep2


title: Droshafl/fl_CreER_mESC, 4OHT, rep1

description:
Drosha_KO_rep1
tamA
degseq_drosha_pileup_edgeR.txt


title: PT-00233979_NT_EA

value: EA


title: Droshafl/fl_CreER_mESC, notreat, rep2

description:
Drosha_WT_rep2
wtB
degseq_drosha_pileup_edgeR.txt

value: Drosha WT

value: no treatment


title: Dicerfl/fl_mESC, GFP-Cre, rep2

description:
Dicer_KO_rep2
creB
degseq_dicer_pileup_edgeR.txt

value: Dicer KO

value: GFP-Cre transduced


title: siNT_Coilin_01

value: coilin antibody (Abcam ab210785)

value: non-targeting siRNA, 72 hours

value: D-001810-10, Horizon Discovery, ONTarget Plus


title: PT-00237623_NT_AA

value: prostate

value: AA


title: Ovarian granulosa cells-NOR_rep5

value: Ovarian

value: untreated


title: PT-00237623_T_AA

value: Tumor


title: Droshafl/fl_CreER_mESC, notreat, rep1

description:
Drosha_WT_rep1
wtA
degseq_drosha_pileup_edgeR.txt


title: NK_DMSO_7days_rep2

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

institute: University Heidelberg

description: Gene expression data after treatment

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 15, from SAS. Gene expression profiling was performed using arrays of Mouse Clariom D from Thermo Fischer Scientific. A Custom CDF Version 22 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label: Biotin

source_name: splenic NK cells, DMSO and IL-2, 7days

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: NK cells sorted as CD45+CD3-NK1.1+NKp46+TRAIL-CD200R- were cultured in RPMI-1640 medium supplemented with 10% FCS, 2 mM glutamine, 1% non-essential amino acids, 1 mM sodium pyruvate, 100 U/ml Penicillin/Streptomycin, 50 µM β-mercaptoethanol and 1700 U/ml recombinant human IL-2.

extract_protocol: RNA extraction was performed using RNeasy® Mini Kit (Qiagen). DNA was removed using TURBO DNA‐free™ kit (ThermoFisher)

treatment_protocol: NK cells were treated with 1uM all-trans retinoic acid or DMSO 0.01% v/v (as solvent control) for 7 days

value: adult

value: female+male

value: Rag 2 ko

value: spleen

value: sorted NK cells


title: PT-00238051_NT_AA

value: Adjacent Tumor


title: Ovarian granulosa cells-DOR_rep6


title: NK_atRA_7days_rep3

description: Gene expression data after treatment

source_name: splenic NK cells, atRA and IL-2, 7days


title: NK_DMSO_7days_rep3

description: Gene expression data after treatment


title: PT-00238051_T_AA

source_name: Tumor


title: P1_OSVZ_LS, rep3

city: Sant Joan d’Alacant

first: Lucia

last: Del-Valle-Anton

address: Av. Santiago Ramón y Cajal s/n

institute: Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas & Universidad Miguel Hernández

description: 10x Genomics Single Cell 3’ Reagent Kit v2

data_processing:
Genome alignment: Ferret gene annotation from Johnson et al., 2018, comprising Ensembl Mustela putorius furo annotation expanded using bulk RNAseq data, was further enriched with NCBI’s RefSeq mitochondrial genes from Mustela putorius furo annotation release 101 (Accession No. NC_020638.1), and transformed from a general feature format (GFF3) into gene transfer format (GTF) using Cufflinks-2.2.1. Johnson’s GenBank accessions were matched to RefSeq accessions through cthreepo-0.1.1 and gene_name and transcript_name attibutes were added to GTF rows where they were missing by appending gene_id and transcript_id entries. scRNA-seq reads were mapped to NCBI ferret reference genome (MusPutFur1.0/GCF_000215625.1) and Unique Molecular Identifiers (UMIs) were collapsed by STAR-2.7.3a adapting the parameters to v2 or v3 10x chemistry, depending on the sample.
Cell barcode filtering: Count matrices from each sample were loaded and cell-containing droplets were identified and distinguished from empty droplets retaining ambient RNA by DropletsUtils-1.6.1. Increased niters argument to 100,000 and decreased false discovery rate (FDR) to 0.1% were applied to all samples. A lower bound of 80 was implemented for replicates P1_VZ_LS_rep1 and E34_VZ_SG_rep1. Mitochondrial genes were removed before cell calling for replicates E34_VZ_LS_rep2, P1_VZ_SG_rep2, P1_VZ_LS_rep3, P1_OSVZ_SG_rep1 and P1_OSVZ_LS_rep1 to promote potential unhealthy cell removal. The automatic retention of droplets with large total UMI counts (determined by the knee point) was disabled for replicate P1_VZ_LS_rep3.
Assembly: MusPutFur1.0/GCF_000215625.1
Supplementary files format and content: Tab-separated values files from cell barcodes and genes (barcodes.tsv, genes.tsv) and matrix file (matrix.mtx) for each sample after genome alignment and cell barcode filtering.

organism: Mustela putorius

source_name: cerebral cortex

extract_protocol:
After microdissecting individual germinal zones from living cortical slices, tissue pieces were enzymatically dissociated for 20-30’ at 37ºC using MACS Neural Tissue Dissociation Kit P (Miltenyi Biotec) according to the manufacturer’s instructions. Cells were mechanically suspended using wide-tipped, fire-polished Pasteur pipettes (Fisher Scientific) followed by P1000 pipettes (Gilson). Cell suspensions were filtered to 2ml DNA LoBind tubes (Eppendorf) through 40 μm PluriStrainer Mini (PluriSelect) pre-wet with Hank’s Balanced Salt Solution (1X) without CaCl2/MgCl2/pH indicator (HBSS, Gibco). Cells were centrifuged (Spectrafuge 24D, Labnet) twice for 5min at 1000 rpm, and cell pellets were resuspended in 40μl of Phosphate Buffered Saline ph7.4 (1X) without CaCl2/MgCl2 (PBS, Gibco) containing 0.04% Bovine Serum Albumin (BSA, Sigma-Aldrich). Cell concentration from homogeneous suspensions was measured, and cell death was estimated twice using trypan blue 0.4% stain (Thermo Fisher Scientific): first on an automatic cell counter (Countess II FL, Thermo Fisher Scientific) and second using a hemocytometer (BLAUBRAND Neubauer, BRAND) on an inverted microscope (Leica DM IL). Debris-free suspensions with cell viability over 90% were used immediately for single-cell isolation.
Cell suspensions from 400 to 1200 cells/μl were loaded into the Chromium Single Cell Controller (10x Genomics) to target a recovery of 7k to 10k cells/sample. Single-cell Gel bead-in-EMulsions (GEMs) were generated, cells were lysed, and the released RNAs were retrotranscribed (RT) and barcoded inside the GEMs according to Single Cell 3’ Reagent Kits v2 and v3 (10x Genomics) protocols. Following GEMs break, barcoded cDNAs were pooled and cleaned from leftover RT reagents using DynaBeads MyOne Silane Beads (Invitrogen) and amplified (8 to 14 cDNA amplification cycles) following the Single Cell 3’ Reagent Kits v2 and v3 (10x Genomics) protocols. Enzymatic fragmentation, size selection and cleanup with SPRIselect Reagent kit (Beckman Coulter) were followed by library construction (total sample index cycles from 12 to 16 cycles), consistent with standard Illumina sequencing constructs and performed in line with Single Cell 3’ Reagent Kits v2 and v3 (10x Genomics) protocols. cDNA and library concentration and quality check were assessed using Bioanalyzer High Sensitivity DNA Kit (Agilent) and 2100 Expert Software (Agilent).

value: cerebral cortex

tag: litter

tag: region

value: lateral sulcus

tag: germinal zone

value: outer subventricular zone

tag: developmental stage

value: postnatal day 1

tag: sequencing flowcell