title: MRC_NSph_chemicals

description:
MRC-iPSC-derived neurosphere (NSph) with mixed exposure to 5 chemicals (DEP, cotinine, S-421, Hg, and Se)
MRC_NSph_5all

source_name: chemical exposed MRC-NSph

value: male


title: SCD-SC184

status: Public on Dec 06 2023

type: SRA

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

country: USA

institute: UCLA

library_source: transcriptomic single cell

data_processing:
For single cell RNA-seq, libraries were then sequenced on the Illumina NovaSeq 6000 sequencer to generate 150 bp paired-end reads. Data processing including quality control, read alignment (hg38), and gene quantification was conducted using the 10X Cell Ranger software. The samples were then merged into a single expression matrix using the cellranger aggr pipeline. For spatial-seq, the reads were aligned to the human genome (hg38), and the expression matrix was extracted using the spaceranger pipeline.
Assembly: hg38
Supplementary files format and content: merged raw count expression matrix for scRNA-seq and spaceranger output for spatial-seq

molecule: total RNA

organism: Homo sapiens

source_name: Skin

extract_protocol:
Generation of single-cell suspensions for scRNA-seq was performed as follows: Skin biopsies were incubated overnight in 0.4% dispase (Life Technologies) in Hank’s Balanced Saline Solution (Gibco) at 4°C. Epidermis and dermis were separated. Epidermis was digested in 0.25% Trypsin-EDTA (Gibco) with 10U/mL DNase I (Thermo Scientific) for 1 hour at 37°C, quenched with FBS (Atlanta Biologicals), and strained through a 70μM mesh. Dermis was minced, digested in 0.2% Collagenase II (Life Technologies) and 0.2% Collagenase V (Sigma) in plain medium for 1.5 hours at 37°C and strained through a 70μM mesh. For spatial-seq, skin samples were frozen in OCT medium and stored at -80°C until sectioning. Optimization of tissue permeabilization was performed on 20 μm sections using Visium Spatial Tissue Optimization Reagents Kit (10X Genomics, Pleasanton, CA, USA), which established an optimal permeabilization time to be 9 minutes. Samples were mounted onto a Gene Expression slide (10X Genomics), fixed in ice-cold methanol, stained with hematoxylin and eosin, and scanned under a microscope (Keyence, Itasca, IL, USA). Tissue permeabilization was performed to release the poly-A mRNA for capture by the poly(dT) primers that are precoated on the slide and include an Illumina TruSeq Read, spatial barcode, and unique molecular identifier (UMI).
For single cell RNA-seq, for the samples collected from the University of Pittsburgh, epidermal and dermal cells were combined in 1:1 ratio. For three of the samples collected from the University of Michigan, the epidermal and dermal cells were prepared in different libraries that were constructed by the University of Michigan Advanced Genomics Core on the 10X Chromium system with chemistry v3.  For the remaining samples the epidermis and dermis were combined in 1:1 ratio.  Libraries were then sequenced on the Illumina NovaSeq 6000 sequencer to generate 150 bp paired-end reads. For spatial-seq, Visium Spatial Gene Expression Reagent Kit (10X Genomics) was used for reverse transcription to produce spatially barcoded full-length cDNA and for second strand synthesis followed by denaturation to allow a transfer of the cDNA from the slide into a tube for amplification and library construction. Visium Spatial Single Cell 3ʹ Gene Expression libraries consisting of Illumina paired-end sequences flanked with P5/P7 were constructed after enzymatic fragmentation, size selection, end repair, A-tailing, adaptor ligation, and PCR. Dual Index Kit TT Set A (10X Genomics) was used to add unique i7 and i5 sample indexes and generate TruSeq Read 1 for sequencing the spatial barcode and UMI and TruSeq Read 2 for sequencing the cDNA insert, respectively. Libraries were then sequenced on the Illumina NovaSeq 6000 sequencer to generate 150 bp paired end reads.

tag: tissue

value: Skin

tag: experiment type

value: scRNA-seq

tag: cell type

value: Epidermis and dermis cell

tag: disease

value: Scleroderma skin


title: SCD-SC169


title: SCD-SC164


title: SCD-SC160


title: SCD-SC159


title: SK-HEP-1 S

city: Hangzhou

first: Jiongjie

last: Yu

state: Zhejiang

address: Kaixuan Road

country: China

institute: Zhejiang University

library_source: genomic

data_processing:
Raw Reads were filtered to remove adapters (the Cutadapt software was used to remove the adapters and remove reads less than 35bp in length)and low quality reads (including Reads with N ratio greater than 10% were removed, and Reads with bases quality value Q≤10 accounting for more than 50% of the entire Read were removed), and then high-quality Clean Reads provided in FASTQ format were obtained for subsequent information analysis
The Bowtie2 software was used to compare the high-quality Reads obtained from the sequencing of each sample with the reference genome to obtain the alignment efficiency of the sample Reads and the position information of the Reads on the genome. DeepTools v2.07 was used to map the density distribution of sequencing Read in the 3 kb of interval upstream and downstream of the TSS of each gene, and the results were presented as heat maps
The Reads abundance in the whole genome was statistically analyzed by the sliding window method,taking 10kb as the unit length of interval and dividing chromosomes into multiple small Windows.The Mapped Reads landed in each window were counted as Reads abundance, and the Pearson correlation coefficient of normalized Reads abundance was calculated. Sample correlation clustering heat map was made.
MACS2 v2.1.1 software was used to perform peak extraction.   MACS2 contained four steps:   (1) removing redundant Reads, (2) adjusting the Read position, (3) calculating Peak enrichment , (4) estimating the empirical false detection rate (FDR). Finally, FDR<0.05 was selected as the identified peak
The ChIPseeker package was used for functional annotation of genome-wide Peak. The average Peak number of the TSS region was counted. According to the distance relationship between the Peak region and the functional elements of each gene on the genome, the Peak region was annotated as to whether the Peak region was in the TSS, Exon, 5 'UTR, 3' UTR, Intronic or Intergenic region. The proportion of Reads falling into different gene functional elements was calculated to demonstrate the distribution characteristics and patterns of Reads.
Assembly: hg38
Supplementary files format and content: BED, peak file for each sample

molecule: genomic DNA

extract_protocol:
50000 cells were centrifuged using 4℃,5 min and 500 g centrifuging parameters, and then the supernatant was removed. The cells were washed with cold PBS once. Using 4℃,5min and 500 g centrifuging parameters the supernatant was removed.The cells were suspended with cold lysis buffer. Using 4℃,10 min and 500 g centrifuging parameters the supernatant was removed. The transposing reaction system was configured with the Tn5 Transposase. The cell nucleus were suspended with the transposing reaction system, and the DNA were purified after incubating at 37℃ for 30 minutes.
The PCR reaction system was configured with the purified DNA ,and then the PCR amplification reaction was performed. Purify amplified library using Qiagen MinElute PCR Purification Kit.

tag: cell line

value: hepatocellular carcinoma cell line

tag: treatment

value: sirolimus


title: BxPC3-CRISPRi-GW-p63-FACS-high

city: Cold Spring Harbor

first: Diogo

last: Maia e Silva

state: NY

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

data_processing:
For RNA-seq, sequencing reads were mapped onto reference human genome hg38 using STAR v2.7.9a with default settings. HTSeq-counts was used to generate raw gene counts, and DESeq2 was then used to perform differential expression analysis.
For ChIP-Seq, reads were mapped to hg38 with bowtie2 2.4.2 with very-sensitive setting. Bam files are then sorted with Samtools 1.11 with default settings, and used to call peaks with MACS2. Bedtools 2.30.0 was used to intersect and merge peaks
Deeptools v3.5.0 was used to generate BigWig files that were then visualized in the UCSC genome browser with the hg38 genome. HOMER v4.11 was used to assign the closest annotated ORFs to each peak and for motif discovery.
For CRISPR amplicon sequencing, raw reads were aligned to each sgRNA library to generate count files with MAGeCK.
For scRNA-seq experiments, data was genetically demultiplexed using cellsnp-lite 1.2.3 and Vireo 0.5.8, aligned to the human genome and assigned to cells using Cell Ranger 7.1.0, and downstream analyzed using Seurat 4.3.0.1.
Assembly: hg38
Supplementary files format and content: Htseq-count matrix for RNA-Seq. H5 Seurat files for scRNA-seq. Bigwig files for ChIP-Seq. Mageck count files for CRISPR libraries.
Library strategy: CRISPR

growth_protocol: Human cancer cell lines were cultured according to vendor recommendations in RPMI or DMEM 10% FBS supplemented with pen-strep.

extract_protocol:
For RNA-seq experiments, total RNA was isolated using TRIzol (Thermo Fisher, 15596026) according to the manufacturer’s instructions. For scRNA-seq experiments, cells were single cell captured and barcoded using the 10X Chromium chemistry. For ChIP-seq experiments, lysates were clarified from crosslinked, sonicated nuclei and protein-DNA complexes were immunoprecipitated with specific antibodies. For CRISPR libraries, genomic DNA was isolated using phenol-chloroform extraction and directly used for library preparation.
RNA-seq and ChIP-seq ibraries were constructed using  Illumina TruSeq RNA library prep kit v2 (Illumina, RS-122-2001) or  Illumina TruSeq ChIP library prep kit (Illumina, IP-202-1012) based on the manufacturer’s instructions. scRNA-seq libraries were biult using 10X Genomics NextGEM Single-Cell 3' Library Kit. CRISPR libraries were prepared using sgRNA flanking primers described in the article and 1 step PCR amplification.

value: human pancreatic cancer cell line

tag: genotype

value: CRISPRi-GW

tag: time

tag: facs antibody

value: p63-alpha, CST, D2K8X


title: SCD-SC163


title: BxPC3-CRISPRi-GW-p63-FACS-low


title: KLM1-CRISPRi-GW-p63-FACS-high


title: KLM1-CRISPRi-GW-p63-FACS-low


title: SCD-925YJ2

value: Dermis cell


title: SK-HEP-1 NC

value: control


title: T3M4-SEL120_250nM-48h-rep2

library_source: transcriptomic

data_processing:
For RNA-seq, sequencing reads were mapped onto reference human genome hg38 using STAR v2.7.9a with default settings. HTSeq-counts was used to generate raw gene counts, and DESeq2 was then used to perform differential expression analysis.
For ChIP-Seq, reads were mapped to hg38 with bowtie2 2.4.2 with very-sensitive setting. Bam files are then sorted with Samtools 1.11 with default settings, and used to call peaks with MACS2. Bedtools 2.30.0 was used to intersect and merge peaks
Deeptools v3.5.0 was used to generate BigWig files that were then visualized in the UCSC genome browser with the hg38 genome. HOMER v4.11 was used to assign the closest annotated ORFs to each peak and for motif discovery.
For CRISPR amplicon sequencing, raw reads were aligned to each sgRNA library to generate count files with MAGeCK.
For scRNA-seq experiments, data was genetically demultiplexed using cellsnp-lite 1.2.3 and Vireo 0.5.8, aligned to the human genome and assigned to cells using Cell Ranger 7.1.0, and downstream analyzed using Seurat 4.3.0.1.
Assembly: hg38
Supplementary files format and content: Htseq-count matrix for RNA-Seq. H5 Seurat files for scRNA-seq. Bigwig files for ChIP-Seq. Mageck count files for CRISPR libraries.


title: MRC_NSph_untreated

type: genomic

city: Miyazaki

first: Yoshikazu

last: Arai

department: Faculty of Agriculture

country: Japan

institute: University of Miyazaki

description:
Untreated MRC-iPSC-derived neurosphere (NSph)
MRC_NSph_Non

hyb_protocol: bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: GenomeStudio software V2011.1

label: Cy3 and Cy5

source_name: untreated MRC-NSph

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from neurosphere samples using Qiagen DNeasy Blood & Tissue Kit according to standard instructions

tag: gender

tag: sample type

value: iPSC-derived neurosphere

tag: disease state

value: normal


title: RPMI8226 cells, STAT1 KO, MBP-PTR1, 6 h, rep3

city: Madison

first: Hae Yeun

last: Chang

state: WI

address: 1111 Highland ave., WIMR II

institute: UW-Madison

data_processing:
Raw sequence data (.bcl files) generated from the Illumina instrument was converted into fastq files and de-multiplexed using Illumina bcl2fastq 2.20 software.
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.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2
Assembly: Homo sapiens GRCh38 reference genome on ENSEMBL
Supplementary files format and content: txt file including raw counts for all samples

growth_protocol: RPMI8226 (WT or STAT1 KO) cells were cultured at 37°C/5% CO2 in RPMI1640 containing 10% FBS, 2% glutamax (Gibco) + 1% penicillin/streptomycin.

extract_protocol:
RNA extraction and sample QC was conducted at GENEWIZ, LLC./Azenta US, Inc (South Plainfield, NJ, USA) as follows:  Total RNA was extracted using Qiagen RNeasy Plus Universal kit following manufacturer’s instructions (Qiagen, Hilden, Germany). The RNA sample extracted was quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) and RNA integrity was checked using TapeStation (Agilent Technologies, Palo Alto, CA, USA).
The RNA sequencing library was prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (New England Biolabs, Ipswich, MA, USA).

treatment_protocol: RPMI8226 (WT or STAT1 KO) cells were treated with 100 nM MBP-PTR1 or MBP control for 6 hours in 3 biological replicates.

value: Multiple myeloma

value: STAT1 KO

value: MBP-PTR1 100 nM, 6 h


title: SCD-604YJ1

value: Epidermis cell


title: SCD-604YJ2

value: Skin


title: SCD-925YJ1

value: scRNA-seq


title: SK-HEP-1 NC1

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp (https://github.com/OpenGene/fastp) with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml) software. The mapped reads of each sample were assembled by StringTie (https://ccb.jhu.edu/software/stringtie/) in a reference-based approach.
To identify DEGs (differential expression genes) between two different samples/groups, the expression level of each gene was calculated according to the transcripts per million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances. Essentially, differential expression analysis was performed using the DESeq2/DEGseq/edgeR/Limma/NOIseq, DEGs with |log2 (foldchange)| ≥ 1 and P-adjust ≤ 0.05 (DESeq2/edgeR/Limma) / P-adjust ≤ 0.001 (DEGseq) / Prob > 0.8 (NOIseq) were considered to be significantly different expressed genes. In addition, functional-enrichment analysis including GO (Gene Ontology, http://www.geneontology.org) and KEGG (Kyoto Encycloedia of Genes and Genomes, http://www.genome.jp/kegg/) were performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at P-adjust ≤ 0.05  compared with the whole-transcriptome background. GO functional enrichment and KEGG pathway analysis were carried out by Goatools (https://github.com/tanghaibao/Goatools) and KOBAS (http://kobas.cbi.pku.edu.cn/home.do)
All the alternative splice events that occurred in our samples were identified by using recently releases program rMATS (http：//rnaseq-mats.sourceforge.net/index.html). Only the isoforms that were similar to the reference or comprised novel splice junctions were considered, and the splicing differences were detected as exon inclusion, exclusion, alternative 5′, 3′, and intron retention events.
Assembly: hg38
Supplementary files format and content: txt files

extract_protocol:
RNA was extracted by Qiagen kit. 1 ug RNA was used for library construction.
RNA library for RNA sequencing was prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocol.

value: hepatocellular carcinoma

value: NC


title: RPMI8226 cells, STAT1 KO, MBP-PTR1, 6 h, rep2


title: T3M4-SEL120_250nM-48h-rep1


title: SCD-547YJ1

value: Scleroderma skin


title: SCD-547YJ2


title: RPMI8226 cells, STAT1 KO, MBP-PTR1, 6 h, rep1


title: SCD-404YJ2


title: T3M4-SEL120_250nM-12h-rep2


title: SCD-404YJ1


title: SCD-1909116


title: Edom_NSph_chemicals

description:
Edom-iPSC-derived neurosphere (NSph) with mixed exposure to 5 chemicals (DEP, cotinine, S-421, Hg, and Se)
Epi_NSph_5all

source_name: chemical exposed Edom-NSph

value: female


title: RPMI8226 cells, STAT1 KO, MBP, 6 h, rep3

value: MBP 100 nM, 6 h


title: Edom_NSph_untreated

description:
Untreated Edom-iPSC-derived neurosphere (NSph)
Epi_NSph_Non

source_name: untreated Edom-NSph


title: RPMI8226 cells, STAT1 KO, MBP, 6 h, rep2


title: T3M4-SEL120_250nM-12h-rep1

value: human pancreatic cancer cell line


title: MRC_NSph_solvent

description:
Solvent (EtOH and HNO3) exposed MRC-iPSC-derived neurosphere (NSph)
MRC_NSph_EH

source_name: solvent exposed MRC-NSph

value: male


title: SCD-1908205

value: Dermis cell


title: Pt. 15 Lesional

city: Aarhus

first: Hakim

last: Ben Abdallah

state: Denmark

address: Palle Juul-Jensens Boulevard 45

department: Dermatology and Venerology

country: Denmark

institute: Aarhus University Hospital

description: 2x150 Sequence mode to obtain at approx. 20 million read pairs

data_processing:
R package Subread (version 2.10.3)
Raw reads were aligned to the human reference genome (GRCh38.p14 primary assembly)
Gene counts were obtained by uniquely aligned unambiguous reads
Assembly: GRCh38.14 primary assembly
Supplementary files format and content: xlsx

extract_protocol:
Total RNA was isolated using the SV 96 Total RNA Isolation System (Promega) according to the manufacturer’s instructions
RNA sequencing library was prepared with 100 ng of total RNA using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina

tag: subject status

value: hidradenitis suppurativa patient

tag: subject id

tag: tissue type

value: Lesional


title: T3M4-SEL120_2.5uM-48h-rep1


title: SCD-1908204


title: T3M4-SEL120_2.5uM-48h-rep2


title: RPMI8226 cells, STAT1 KO, MBP, 6 h, rep1


title: Pt. 15 Non-Lesional

value: Non-Lesional


title: RPMI8226 cells, WT, MBP-PTR1, 6 h, rep3

value: Multiple myeloma

value: WT


title: Pt. 14 Lesional


title: Pt. 13 Lesional


title: Pt. 13 Non-Lesional


title: Pt. 14 Non-Lesional


title: T3M4-SEL120_2.5uM-12h-rep2


title: RPMI8226 cells, WT, MBP-PTR1, 6 h, rep2

value: MBP-PTR1 100 nM, 6 h


title: Pt. 12 Lesional


title: T3M4-SEL120_2.5uM-12h-rep1


title: RPMI8226 cells, WT, MBP-PTR1, 6 h, rep1


title: T3M4-DMSO-48h-rep2

value: DMSO


title: Pt. 12 Non-Lesional

value: Skin


title: RPMI8226 cells, WT, MBP, 6 h, rep3


title: RPMI8226 cells, WT, MBP, 6 h, rep2


title: Pt. 11 Non-Lesional


title: Pt. 9 Non-Lesional

value: Pt. 9


title: T3M4-DMSO-12h-rep2


title: Pt. 9 Lesional


title: T3M4-DMSO-12h-rep1


title: RPMI8226 cells, WT, MBP, 6 h, rep1


title: T3M4-DMSO-48h-rep1


title: Pt. 10 Lesional


title: PLCγ2 S707Y HOMO, replicate 3

city: London

first: Daniel

last: Bull

address: Gower Street

country: United Kingdom

institute: ARUK UCL Drug Discovery Institute

data_processing:
Libraries were prepared and sequenced at a minimum of 25 million paired-end reads (75 bp) per sample by UCL genomics
Assembly: hg38
Supplementary files format and content: file includes the raw counts for each Sample

extract_protocol:
RNA was extracted from PLCγ2 WT and S707Y hiPSC-derived microglia through TRIzol (Invitrogen) separation in accordance with the manufacturer's instructions
Libraries were prepared using the KAPA RNA HyperPrep Kit in accordance with the manufacturer's instructions

value: hiPSC

value: PLC{gamma}2 S707Y HOMO


title: Pt. 7 Lesional

value: Pt. 7


title: Pt. 7 Non-Lesional


title: Pt. 10 Non-Lesional


title: Pt. 8 Lesional

value: Pt. 8


title: Pt. 8 Non-Lesional


title: PLCγ2 S707Y HOMO, replicate 2


title: T3M4-AS2863619_250nM-48h-rep2


title: Pt. 6 Lesional

value: Pt. 6


title: T3M4-AS2863619_250nM-48h-rep1

value: human pancreatic cancer cell line


title: PLCγ2 S707Y HOMO, replicate 1


title: T3M4-AS2863619_250nM-12h-rep1


title: Pt. 4 Lesional

value: Pt. 4


title: Pt. 6 Non-Lesional


title: Pt. 11 Lesional


title: T3M4-AS2863619_250nM-12h-rep2


title: Pt. 5 Lesional

value: Pt. 5


title: PLCγ2 S707Y HET, replicate 3

value: PLC{gamma}2 S707Y HET


title: Pt. 5 Non-Lesional

value: hidradenitis suppurativa patient


title: PLCγ2 S707Y HET, replicate 2


title: Pt. 4 Non-Lesional

value: Non-Lesional


title: Pt. 3 Non-Lesional

value: Pt. 3


title: T3M4-AS2863619_2.5uM-12h-rep2


title: Pt. 1 Non-Lesional

value: Pt. 1


title: T3M4-AS2863619_2.5uM-12h-rep1


title: T3M4-AS2863619_2.5uM-48h-rep2


title: Pt. 3 Lesional

value: Lesional


title: T3M4-AS2863619_2.5uM-48h-rep1


title: PLCγ2 WT, replicate 3

value: PLC{gamma}2 WT


title: HTR-h-3

city: Ningbo

first: Jiaqing

last: Zhou

address: Haishu

institute: Ningbo First Hospital

data_processing:
Based on preliminary judgment and recognition, paired-end reads were obtained from an Illumina NovaSeq 6000 sequencer.
The sequencing quality of the reads was evaluated by FastQC software, and cutadapt was used to remove the 3' and 5' joints. LncRNAs, circRNAs, and mRNAs were analyzed using high-quality pruned read segments by comparing them to the reference genome (GRCh37) using HISAT2 software.
Supplementary files format and content: Tne floders include raw counts and FPKM values for each example

source_name: placenta

growth_protocol: The human chorionic trophoblast cell line HTR-8/Svneo was cultivated in media that also contained 1% and 10% penicillin‒streptomycin and fetal bovine serum. They were cultivated in a typical, humidified tissue culture chamber (normoxic) at 37 °C, 21% O2, and 5% CO2.

extract_protocol:
RNA was extracted from control and hypoxic HTR-8/SVneo cells using TRIzol reagent (Invitrogen, Carlsbad, CA, USA)24 hours after culture according to the manufacturer's instructions. The concentration of total RNA was determined by a NanoDrop ND-1000 spectrophotometer (Thermo, Waltham, MA, USA).RNA Integrity and gDNA contamination test by denaturing agarose gel electrophoresis(concentration of agarose gel is 1%, and 0.5 µg/ml ethidium bromide to help it visualized).
The library was constructed with a KAPA Stranded RNA-Seq Library Prep Kit (Illumina) after total RNA samples were stranded by oligo dT enrichment (rRNA removal). In the process of library construction, double-stranded cDNA was synthesized using the dUTP method combined with subsequent high-fidelity PCR polymerase action, which made the resulting RNA sequencing library have chain specificity.

treatment_protocol: Cells were cultivated in an anoxic chamber that was humidified (made by Forma Scientific, Marietta, Ohio, USA) at 37 °C, 1% O2 and 5% CO2.

value: placenta

value: human chorionic trophoblast


title: PLCγ2 S707Y HET, replicate 1

value: hiPSC


title: Pt. 2 Lesional

value: Skin

value: Pt. 2


title: Pt. 2 Non-Lesional


title: Pt. 1 Lesional


title: HTR-h-1


title: PLCγ2 WT, replicate 2


title: D6 T3M4-sgROSA26-sgNT-D6-rep3


title: HTR-S-3


title: PLCγ2 WT, replicate 1


title: HTR-S-2


title: D6 T3M4-sgROSA26-sgNT-D6-rep2


title: HTR-S-1


title: prostatic hyperplasia,2 [S4-2]

city: Nanchang

first: Xing

last: Wang

state: Jiangxi

address: No. 1 Minde Road

institute: The Second Affiliated Hospital of Nanchang University

data_processing:
Assessing the quality of sequencing data: including the statistics of data volume, comparison rate, and sequencing error rate, the primary process is to remove the low-quality data and get the high quality and standard data, called "clean reads."
The obtained CircRNA "clean reads" were compared to the reference genome, and then the circRNAs were identified by CIRI and find_circ , and the results of both software were combined to perform qualitative and quantitative analysis of circRNAs
The differentially expressed circRNAs were identified using DESeq2  based on the negative binomial distribution
In this experiment, a differential ploidy of 2-fold or more and a p-value of less than 0.05 were set as the screening conditions for differential RNAs.
The differentially expressed circRNAs were subjected to enrichment analysis such as GO enrichment of source genes, KEGG enrichment analysis and prediction of miRNA binding sites and miRNA binding site prediction, etc.

source_name: prostatic hyperplasia

extract_protocol:
Total RNA was extracted from the test samples by Trizol method, and the samples were firstly analyzed for DNA contamination and integrity by agarose gel electrophoresis; then the RNA concentration and purity (OD260/280) were detected by Nanodrop, and if the OD260/280 values were in the range of 1.8-2.1, the RNA purity was qualified; next, the RNA purity was detected by Agilent 2100. Agilent 2100 was used to detect the purity and integrity of the total RNA. The sequencing of the test RNA samples was entrusted to Shanghai Jikai Gene Technology Co
5ug of each sample was prepared for library preparation. Ribosomal rRNA was removed using the Ribo-zero™ rRNA Removal Kit (Epicentre, USA), then eliminated linear RNA using RNase Rase. The remaining circRNA was broken into short fragments of 250-300 bp, which were used as a template to synthesize the second strand of cDNA using random oligonucleotides as primers to synthesize the first strand of cDNA, followed by dNTPs (dUTP, dATP, dGTP, dCTP) as raw materials to synthesize the second strand of cDNA. The purified double-stranded cDNAs were end-repaired, A-tailed, and sequenced, and AMPure XP beads were used to screen 350-400 bp cDNAs in length. cDNAs containing U were degraded with USER enzymes, and PCR amplified to obtain libraries. The fragment size and purity of the library were checked using Agilent 2100 to ensure the quality of the library. Illumina PE150 double-end sequencing was performed after passing quality control.

value: prostatic hyperplasia

tag: age

value: 79 years old


title: D6 T3M4-sgROSA26-sgNT-D6-rep1

value: human pancreatic cancer cell line


title: D6 T3M4-sgMED13-sgMED13L-2-D6-rep3


title: Kl_FGF23_24h_3

city: Zurich

first: Ganesh

last: Pathare

state: Zürich

address: Winterthurerstrasse 190

department: Institute of Anatomy

country: Switzerland

institute: University of Zurich

data_processing:
In brief, amplified cDNA samples were subjected to different quality control standards. RNA sample was used for library preparation using NEB Next® Ultra RNA Library Prep Kit for Illumina®.
Indices were included to multiplex multiple samples. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis.
The library was ready after end repair, A-tailing, adapter ligation, and size selection. After amplification and purification, the insert size of the library was validated on an Agilent 2100 and quantified using quantitative qPCR.
. Libraries were then sequenced on Illumina NovaSeq 6000 S4 flow cell with PE150 according to results from library quality control and expected data volume.
Assembly: mm10
Supplementary files format and content: .xls files included raw counts for each sample

source_name: Kidney-epithelial

growth_protocol: HEK293 cells were cultured at 5% CO2 in a growth medium consisting of Modified Eagle’s Medium MEM, supplemented with 10% heat-inactivated FBS and 100 U/ml penicillin, and 100 µg/ml streptomycin.

extract_protocol:
RNA was isolated using a Nucleospin kit
RNA sample was used for library preparation using NEB Next® Ultra RNA Library Prep Kit for Illumina®.

treatment_protocol: Recombinant human FGF23 was treated 0.5 nM for 1 hour and 10 nM for 24 hours

value: Kidney-epithelial

value: Stable Klotho

value: Kl


title: prostatic hyperplasia,1 [S4-1]

value: 67 years old


title: Kl_FGF23_24h_1


title: Prostate cancer tissue, T4,3 [S3-3]

source_name: Prostate cancer

value: Prostate cancer

value: 63 years old


title: Kl_FGF23_24h_2


title: D6 T3M4-sgMED13-sgMED13L-2-D6-rep2


title: Kl_Ctrl_24h_3

value: Ctrl


title: Liver, KO3

city: Kent

first: Manabu

last: Kurowaka

state: OH

address: 800 E Summit St

department: Biological Sciences

institute: Kent State

data_processing:
Data analysis was performed by BGI Genomics using their standard pipeline.
Assembly: mm10
Supplementary files format and content: DEseq2 analyzed data file produced by BGI Genomics

organism: Mus musculus

source_name: Liver

growth_protocol: Mice were maintained on 5P00 ProLab® RMH 3000 (LabDiet) chow diet ad libitum for 1 year before harvesting livers.

extract_protocol:
Promega SV Total RNA Isolation System was used according to manufactuter's instructions
Library construction performed by BGI Genomics using their standard pipeline.
RNAseq was performed by BGI Genomics using their standard pipeline.

value: Liver

value: Liver-specific Huwe1 KO


title: D6 T3M4-sgMED13-sgMED13L-2-D6-rep1


title: Kl_Ctrl_24h_2


title: HTR-h-2

value: placenta


title: Prostate cancer tissue, T4,2 [S3-2]


title: prostatic hyperplasia,3 [S4-3]

value: 74 years old


title: Liver, KO1


title: Kl_Ctrl_24h_1


title: Prostate cancer tissue, T3,3 [S2-3]

value: 73 years old


title: D6 T3M4-sgMED13-sgMED13L-1-D6-rep2


title: WT_FGF23_24h_3

value: WT


title: Prostate cancer tissue, T3,2 [S2-2]

value: 70 years old


title: D6 T3M4-sgMED13-sgMED13L-1-D6-rep1


title: WT_FGF23_24h_2


title: Liver, KO4


title: Liver, WT3


title: Prostate cancer tissue, T1-T2, 3 [S1-3]

value: 64 years old


title: WT_FGF23_24h_1


title: D6 T3M4-sgMED12-ROSA26-2-D6-rep2


title: WT_Ctrl_24h_3


title: Prostate cancer tissue, T3,1 [S2-1]


title: Prostate cancer tissue, T4,1 [S3-1]


title: Prostate cancer tissue, T1-T2, 2 [S1-2]

value: 66 years old


title: D6 T3M4-sgMED12-ROSA26-2-D6-rep3

value: human pancreatic cancer cell line


title: WT_Ctrl_24h_2

value: Kidney-epithelial


title: Liver, WT1


title: Prostate cancer tissue, T1-T2, 1 [S1-1]


title: WT_Ctrl_24h_1


title: D6 T3M4-sgMED13-sgMED13L-1-D6-rep3


title: D6 T3M4-sgMED12-sgMED12L-2-D6-rep3


title: Liver, KO2


title: Liver, WT4


title: HA-ripply1-injected embryos at 6hpf replicate 2

city: Hang Zhou

first: Tao

last: cheng

state: Zhe Jiang

address: 886 Yuhangtang Road

department: Institute of genetics

data_processing:
Illumina sequencing reads were first treated by Cutadapt v4.5 to remove adapters and trim reads using the following parameters “-m 18 -q 30,30 --max-n=0.05 -e 0.2 -n 2”.
The trimmed reads were then aligned to zebrafish genome (danRer11) through Bowtie2 v2.5.2 using the following parameters “--end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700”.
Samtools v1.18 and BEDtools v2.31.0 were then use¬d for post-alignment processing to covert file formats in preparation for the peak calling and visualization.
SEACR was used to call “non stringent” peaks for wild-type and HA-ripply1-injected samples using merged HA-ripply1-injected samples without primary antibody as control.
Assembly: danRer11
Supplementary files format and content: *.bw: bigWig files give the normalized coverage of DNA fragments across the genome in reads per million.

organism: Danio rerio

source_name: zebrafish cells

growth_protocol: Embryos were incubated in a Petri dish coated with 2% agarose filled with 0.3x Danieau buffer.

extract_protocol:
The library construction steps were included in the CUT&Tag protocol of Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme, TD904).
CUT&Tag

treatment_protocol: HA-ripply1 mRNA was injected into zebrafish embryo at 1-cell stage. All embryos were incubated in 0.3x Danieau buffer until 6 hpf.

tag: strain

value: AB

value: embryonic cells

tag: antibody

value: HA-Tag Rabbit mAb;Goat Anti-Rabbit IgG H&L

value: HA-ripply injection at 1-cell stage


title: D6 T3M4-sgMED12-sgMED12L-2-D6-rep2


title: D6 T3M4-sgMED12-sgMED12L-2-D6-rep1


title: Kl_FGF23_1h_3

tag: tissue

value: Stable Klotho

value: Kl


title: nTg male 2

city: New York

first: Hina

last: Chaudhry

state: USA

department: Cardiology

institute: Mount Sinai Hospital

description: 10x Genomics

data_processing:
Single-nucleus RNA sequencing (SnRNA-seq) reads, genes counting and aggregation were made using the Cell Ranger software from 10x Genomics, with default parameters applied to each individual sample. This involved various steps, including various steps, including alignment to a reference, collapsing of unique molecular identifiers, counting, and initial quality control procedures.
Assembly: mm10
Supplementary files format and content: Tab seperated values files and barcodes/features files

molecule: nuclear RNA

source_name: Adult heart

extract_protocol:
Tissue was homogenized and resuspended in the lysis buffer, followedby resuspension in the nuclei extraction buffer. Nuclei quality was assessedbefore proceeding to single nuclei RNA-seq ensuring well-resolvededges without debris or clumping or deformation.
The library was performed according to the manifactor's instructors (10x Genomics)

value: Adult heart

tag: Sex

value: Male

tag: cell type

value: Cardiac cells

value: WT- non Tg


title: Tg male 1

description: 10x Genomics


title: Tg male 2

description: 10x Genomics


title: Kl_FGF23_1h_2

tag: cell line


title: Liver, WT2

value: Liver

tag: treatment


title: Wild-type embryos at 6hpf replicate 2


title: Wild-type embryos at 6hpf replicate 1


title: nTg male 1

description: 10x Genomics

tag: genotype


title: D6 T3M4-sgMED12-ROSA26-2-D6-rep1

tag: time


title: Tg Female 2

description: 10x Genomics

value: Female


title: Kl_FGF23_1h_1


title: Kl_Ctrl_1h_3

value: Ctrl


title: Tg Female 1

description: 10x Genomics


title: D6 T3M4-sgMED12-ROSA26-1-D6-rep2


title: HA-ripply1-injected embryos at 6hpf w/o primary antibody replicate 1

description: No primary antibody in CUT&Tag experiment

value: Goat Anti-Rabbit IgG H&L


title: HA-ripply1-injected embryos at 6hpf w/o primary antibody replicate 2


title: Kl_Ctrl_1h_2


title: Kl_Ctrl_1h_1


title: nTg Female 2

description: 10x Genomics


title: GFP_ChIP_control

city: Beijing

first: Weifeng

last: Zhang

address: Zhongguancun Street

institute: Tsinghua University

data_processing:
Illumina RTA software was used for basecalling.
Reads were aligned to the TAIR10 genome using bowtie2.
For ssDRIP-seq and ATH ChIP-seq,reads coverage was normalized to RPKM (Reads Per Kilobase Million)
For DEtail-seq,reads coverage was normalized to RPGC (Reads Per Genomic Content)
Assembly: TAIR10

organism: Arabidopsis thaliana

source_name: leaf

growth_protocol: Surface-sterilized seeds were sown on 1/2 MS medium and incubated at 4˚C for 2 days for stratification. The plants were grown in the chamber under long-day conditions (day/night cycle of 16/8 h) at 22°C in white light and 18°C in the dark. All plant materials are used from 21-day-old seedling leaves that grew on 1/2 MS medium.

extract_protocol:
For ssDRIP-seq, the chloroplasts were extracted by grounding plant leaves in 20 ml ice-cold CIB buffer. The homogenate was filtrated through two layers of Miracloth and centrifuged at 200 g/4°C for 3 min. Then the supernatant was transferred to new 50 ml tubes and centrifuged for 10 min at 1200 g/4°C. The chloroplasts were then suspended with cold CIB buffer and was ready for use. The chloroplasts were lysed in chloroplast DNA extraction buffer (CIB with 1% SDS and proteinase K) at 37°C overnight with shaking, and then SDS was removed by adding 20 µM KAc. Chloroplast DNA was purified by phenol/chloroform/isoamyl alcohol (25:24:1, v/v/v) and precipitated with an equal volume of isopropyl alcohol at -20°C overnight. The chloroplast DNA was fragmented with 5 U of DdeI (NEB, R0175V), MseI (NEB, R0525S), RsaI (NEB, R0167V), and AluI (NEB, R0137V) at 37°C for 12 h and then purified. 2 µg of purified fragment DNA with or without RNase H treatment was incubated with 10 µg of S9.6 antibody overnight at 4°C. Samples were further incubated with 50 µl Protein G beads (Invitrogen, 10004D) for 4 h at 4°C. The immunoprecipitated DNA was purified as mentioned above.
For ATH ChIP-seq, the chloroplasts were cross-linked with 1% formaldehyde for 10 min, and the cross-linking reaction was stopped by adding 150 µl 1 M glycine and incubating for 10 min. Then the cross-linked chloroplasts were washed twice with CIB and lysed in lysis buffer (50 mM Tris-HCl (pH 7.6), 0.15 M NaCl, 1 mM EDTA (pH 8.0), 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate). Chloroplast DNA was sheared with sonication into fragments of ∼500bp. The supernatant was incubated with an anti-GFP antibody (abcam, ab290) overnight at 4°C.
For DEtail-seq, the chloroplasts were embedded in low-melting-point agarose and lysed in lysis buffer as described above. Agarose plugs were then washed in 1x TE buffer 4 times at 37°C, with the first two washes containing 1 mM PMSF. Then, agarose plugs were cut into small pieces and lysed in 10 μg/ml RNase A at 37°C overnight. The lysed agarose pieces were then washed in 1x TE buffer 5 times at 37°C, followed by two washes with 300 μl 1x CutSmart (NEB, B7204S) at 37°C. The agarose pieces were then incubated with 3 μl I-CeuI (NEB, R0699S) in 150 μl 1x CutSmart Buffer at 37°C for 12 h and washed 3 times with 1x TE buffer. Then the T7 ligation process was conducted by adding 65 μl (T7 Buffer 8 μl, T7 Adapter 5 μl, T7 Enzyme Mix Ⅱ 6 μl, Low-EDTA TE 46 μl) T7 Tailing & Ligation solution (ABclonal, RK20228) and incubating at 37°C for 12 h. The DNA in agarose was purified using a DNA gel purification kit (Magen, D2111-02), and fragmented to ~250 bp using a focused ultrasonicator (Covaris, S220).
The library preparation steps were conducted according to the manual (ABclonal, RK20228). Briefly, the first adapter was ligated to the 3’ end of the ssDNA using Adaptase via a highly efficient, proprietary reaction that only tails 3’ ends of ssDNA and ligates the first truncated adapter to 3’ ends simultaneously. This method avoids the bias inherent in random primer-based methods, as it ligates adapters in a sequence-independent manner. The extension step was performed using the primer paired to the first adapter, followed by a ligation reaction to add the second truncated adapter to the 5’ ends. An indexing PCR step was performed to add the indexed sequence, and the library was amplified.

value: leaf

value: chloroplast

value: Col-0 WT

value: GFP


title: D6 T3M4-sgMED12-ROSA26-1-D6-rep1

value: human pancreatic cancer cell line


title: D6 T3M4-sgMED12-sgMED12L-1-D6-rep3


title: D6 T3M4-sgMED12-sgMED12L-1-D6-rep2


title: WT_FGF23_1h_3

value: Kidney-epithelial

value: WT


title: nTg Female 1

description: 10x Genomics


title: ATH_ChIP_rep2

value: trangenic line


title: 100 ng/ml IFNy 24h - 10 ng/ml TGFb 24h [13_24h_ifny_24h_tgfb]

city: Amsterdam

first: Maarten

last: Slagter

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Reads were aligned paired-end, strand and transcriptome aware, with hisat
Counts per gene were made using itreecount (https://github.com/NKI- GCF/itreecount) and annotated using ensembl gtf version 87
Assembly: GRCm38
Supplementary files format and content: itreecount count output

source_name: NMM

growth_protocol: Cells were cultured at 37°C/ 5% CO2 in IMDM (Gibco) supplemented with 10% FCS (Sigma), 100 U/ml penicillin (Roche), 100 μg/ml streptomycin (Roche), and GlutaMax (Gibco, 1x).

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (74106, Qiagen), including an on-column DNase digestion (79254, Qiagen)
Total RNA samples having RIN values>8 were subjected to xGen™ mRNA library preparation, according to the manufacturer's instructions (xGen™ RNA Lib Prep 96rxn, CAT 10009814)
Stranded mRNA libraries were analyzed on a 2100 Bioanalyzer instrument, following the manufacturer’s protocol “Agilent DNA 7500 kit” (G2938-90024, Agilent Technologies), diluted to 10nM and pooled equimolar into multiplex sequencing pools for sequencing on NovaSeq 6000 instrument (Illumina).

treatment_protocol: Cells were treated with various cytokines (IFNy,TGFb or medium control) for different durations (2, 6, 12, 24 hours of continuous stimulation). Cells were washed 5x with PBS and were subsequently stimulated with a a second cytokine or combination of cytokines (IFNg, TGFb, mix or medium control) for 24 hours

value: NMM

value: Mouse melanoma

value: NRAS mutant

value: 100 ng/ml IFNy 24h - 10 ng/ml TGFb 24h

tag: primary stimulus

value: 100 ng/ml IFNy

tag: secondary stimulus

value: 10 ng/ml TGFb

tag: primary stimulus_duration

value: 24h continuous

tag: secondary stimulus_duration


title: D6 T3M4-sgMED12-sgMED12L-1-D6-rep1


title: D6 T3M4-sgMED12-ROSA26-1-D6-rep3


title: 100 ng/ml IFNy 24h - Unstimulated 24h [14_24h_ifny_24h_medium]

value: 100 ng/ml IFNy 24h - Unstimulated 24h

value: Unstimulated


title: WT_FGF23_1h_2


title: WT_FGF23_1h_1


title: HA-ripply1-injected embryos at 6hpf replicate 1

value: AB

value: embryonic cells

value: HA-Tag Rabbit mAb;Goat Anti-Rabbit IgG H&L

value: HA-ripply injection at 1-cell stage


title: D6 T3M4-sgCDK8-sgCDK19-3-D6-rep2

value: human pancreatic cancer cell line


title: 10 ng/ml TGFb 24h - Unstimulated 24h [16_24h_tgfb_24h_medium]

value: 10 ng/ml TGFb 24h - Unstimulated 24h


title: WT_Ctrl_1h_3

value: Kidney-epithelial

value: WT

value: Ctrl


title: D6 T3M4-sgCDK8-sgCDK19-3-D6-rep1


title: WT_Ctrl_1h_2


title: D6 T3M4-sgCDK8-sgCDK19-1-D6-rep3


title: WT_Ctrl_1h_1


title: Unstimulated 24h - 100 ng/ml IFNy 10 ng/ml TGFb 24h [18_24h_medium_24h_mix]

value: NMM

value: Mouse melanoma

value: 100 ng/ml IFNy 10 ng/ml TGFb


title: atrnh1c_rep1_ssDRIP

value: leaf

value: chloroplast

value: atrnh1c mutant


title: 35S_ATH_GFP_in_acs1_rep2_DEtail

value: trangenic line


title: Unstimulated 24h - 100 ng/ml IFNy 24h [20_24h_medium_24h_ifny]

value: NRAS mutant

value: Unstimulated 24h - 100 ng/ml IFNy 24h

value: Unstimulated

value: 100 ng/ml IFNy

value: 24h continuous


title: D6 T3M4-sgCDK8-sgCDK19-1-D6-rep2

value: human pancreatic cancer cell line


title: Unstimulated 24h - 10 ng/ml TGFb 24h [19_24h_medium_24h_tgfb]

value: Unstimulated 24h - 10 ng/ml TGFb 24h

value: 10 ng/ml TGFb


title: Si2-3

city: Zhengzhou

first: Simin

last: Zheng

address: Huanghe Road, Jinshui District, Zhengzhou City, Henan Province

institute: Henan Provincial People's Hospital

data_processing:
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Trimmomatic (v0.30) to be high quality clean data.
Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis used the DESeq Bioconductor package, a model based on the negative binomial distribution. After adjusted by Benjamini and Hochberg’s approach for controlling the false discovery rate, P-value of genes were setted <0.05 to detect differential expressed ones.
FPKM, short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairssequenced, was used to estimate gene expression levels, which takes into account the effects of both sequencing depth and gene length oncounting of fragments(Trapnell, Cole, et al., 2010).
Assembly: Hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample, log2foldchange, pvalue, qvalue

growth_protocol: cells were maintained in DMEM (Biological Industries, #01-052-1ACS; Beit Haemek, Israel) supplemented with 10% fetal bovine serum (FBS, Biological Industries, #04-001-1A; Beit Haemek, Israel) and 1% penicillin-streptomycin (Biological Industries, #03-031-1BCS，Beit Haemek, Israel).  Cells were cultured in a humidified incubator at 37 °C and 5% CO2.

extract_protocol:
RNA was extracted using TRIzol™ Reagent(Catalog number:  15596026,ThermoFisher Scientific) according to the manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MDA-MB-231 cells were seeded in 6-well plate (1.5X10^5/well). Transfections were performed after 24h by using Lipofectamine™ 3000 Transfection Reagent (Thermo Fisher, L3000-015) according to the manufacturer’s instructions.In this study,we used two different PLANE siRNAs, Si1-1 &Si1-2 & Si1-3 were transfacted with siRNA1, and  Si2-1 & Si2-2 & Si2-3 were transfacted with siRNA2, NC was used for siRNA control

value: triple-negative breast cancer

value: transfected with  MILIP siRNA (siRNA2)


title: ATH_ChIP_rep1

value: GFP


title: D6 T3M4-sgCDK8-sgCDK19-1-D6-rep1


title: Si2-2


title: 35S_ATH_GFP_in_acs1_rep1_DEtail


title: Unstimulated 24h - Unstimulated 24h [17_24h_medium_24h_medium]

value: NMM

value: Mouse melanoma

value: Unstimulated 24h - Unstimulated 24h


title: Si2-1


title: D6 T3M4-sgCDK1-sgROSA26-D6-rep3


title: DRIP_control

value: leaf

value: chloroplast


title: 100 ng/ml IFNy 12h - 10 ng/ml TGFb 24h [9_12h_ifny_24h_tgfb]

value: 100 ng/ml IFNy 12h - 10 ng/ml TGFb 24h

value: 12h continuous


title: D6 T3M4-sgCDK8-sgCDK19-3-D6-rep3


title: D6 T3M4-sgCDK1-sgROSA26-D6-rep2


title: Si1-3

value: transfected with  MILIP siRNA (siRNA1)


title: 100 ng/ml IFNy 12h - Unstimulated 24h [10_12h_ifny_24h_medium]

value: NRAS mutant

value: 100 ng/ml IFNy 12h - Unstimulated 24h

value: Unstimulated


title: D6 T3M4-sgCDK1-sgROSA26-D6-rep1

value: human pancreatic cancer cell line


title: Si1-2


title: atrnh1c_rep2_ssDRIP

value: atrnh1c mutant


title: acs1_rep2_DEtail

value: acs1 mutant


title: 35S_ATH_FLAG_in_Col-0_rep1_DEtail

value: trangenic line


title: 10 ng/ml TGFb 12h - 100 ng/ml IFNy 24h [11_12h_tgfb_24h_ifny]

value: 10 ng/ml TGFb 12h - 100 ng/ml IFNy 24h

value: 10 ng/ml TGFb

value: 100 ng/ml IFNy

value: 24h continuous


title: acs1_rep1_Detail


title: D6 T3M4-sgCCNC-sgROSA26-2-D6-rep3


title: Si1-1

value: triple-negative breast cancer


title: atrnh1c_rep2_DEtail

value: leaf


title: 10 ng/ml TGFb 12h - Unstimulated 24h [12_12h_tgfb_24h_medium]

value: NMM

value: Mouse melanoma

value: 10 ng/ml TGFb 12h - Unstimulated 24h


title: 10 ng/ml TGFb 24h - 100 ng/ml IFNy 24h [15_24h_tgfb_24h_ifny]

value: 10 ng/ml TGFb 24h - 100 ng/ml IFNy 24h


title: NC3

value: transfected with  negtive control siRNA


title: 35S_ATH_FLAG_in_Col-0_rep2_DEtail

value: chloroplast


title: Unstimulated 12h - 100 ng/ml IFNy 24h [21_12h_medium_24h_ifny]

value: NRAS mutant

value: Unstimulated 12h - 100 ng/ml IFNy 24h

value: Unstimulated

value: 12h continuous


title: atrnh1c_rep1_DEtail

value: atrnh1c mutant


title: NC2


title: D6 T3M4-sgCCNC-sgROSA26-2-D6-rep1

value: human pancreatic cancer cell line


title: Col-0_rep2_Detail

value: Col-0 WT


title: NC1


title: Col-0_rep1_Detail


title: D6 T3M4-sgCCNC-sgROSA26-1-D6-rep3


title: Unstimulated 12h - Unstimulated 24h [23_12h_medium_24h_medium]

value: Unstimulated 12h - Unstimulated 24h


title: 100 ng/ml IFNy 6h - 10 ng/ml TGFb 24h [5_6h_ifny_24h_tgfb]

value: 100 ng/ml IFNy 6h - 10 ng/ml TGFb 24h

value: 100 ng/ml IFNy

value: 10 ng/ml TGFb

value: 6h continuous

value: 24h continuous


title: WT_Leu_2

city: Tianjin

first: Jingen

last: Li

address: Xiqi Dao 32, Tianjin Airport Economic Area

institute: Tianjin institute of industrial biotechnology,Chinses Academy of Sciences

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with NGSQCToolkit (v2.3).
Clear reads were mapped to Neurospora crassa OR74A genome using Tophat (version 2.0.8b) with parameters -i 10 -g 1 --segment-length 24 --b2-very-sensitive --no-convert-bam --library-type fr-unstranded.
The counts of reads uniquely mapped to only one gene for each gene were calculated by HTseq-count(version 0.13.5).
Assembly: Neurospora crassa OR74A (https://fungidb.org/fungidb/app/downloads/release-61/NcrassaOR74A/)
Supplementary files format and content: tab-delimited text files including Reads count for each sample.

organism: Neurospora crassa

growth_protocol: Precultured mycelium from N. crassa WT strain or ∆clr5 strain  were shifted into 1× No-nitrogen Vogel’s salt with 2% Avicel, and 50mM Leucine  for the induciton of additional 8 h.

extract_protocol:
Mycelia were harvested by vacuum filtration with Whatman filter paper, frozen immediately in liquid nitrogen. Total RNA from frozen samples was isolated using TRIzol reagent and an additional clean-up was performed for DNA degradation using the RNeasy mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: FGSC 2489

value: Mycelium


title: PDO27 and CAF co-culture SPLiT-seq experiment sublibrary 2

first: James

last: Opzoomer

address: 72 Huntley Street

department: Department of Oncology

institute: University College London Cancer Institute

data_processing:
zUMIs v2.9.7
Assembly: GRCh38
Supplementary files format and content: .h5ad-formatted hdf5 file containing Scanpy AnnData object of processed SPLiT-seq data per sublibrary

source_name: Colorectal cancer

growth_protocol: PDOs were dissociated into single cells on day 0, and expanded in 12-well plates in Growth Factor Reduced Matrigel (Corning 354230) with Advanced DMEM F/12 (Thermo 12634010) containing 2 mM L-glutamine (Thermo 25030081), 1 mM N-acetyl-L-cysteine (Sigma A9165), 10 mM HEPES (Sigma H3375), 1X B-27 Supplement (Thermo 17504044), 1X N-2 Supplement (Thermo 17502048), 50 ng ml−1 EGF (Thermo PMG8041), 10 nM Gastrin I (Sigma SCP0152), 10 mM Nicotinamide (Sigma N0636), 500 nM A83-01 (Generon 04-0014), 10 μM SB202190 (Avantor CAYM10010399-10) and 1X HyClone Penicillin-Streptomycin Solution (Fisher SV30010) at 5% CO2, 37 °C for 4 days.

extract_protocol:
On day 9, organoids were dissociated into single cells using TrypLE and incubated for 10 minutes at 37 °C on a heated orbital shaker at 300 rpm. Sample preparation was then performed based on the SPLiT-seq protocol.
Single-cell RNA-seq libraries were prepared using the SPLiT-seq protocol

treatment_protocol: On day 5, PDOs were starved in Reduced media (Advanced DMEM F/12 containing only 2 mM L-glutamine, 1 mM N-acetyl-L-cysteine, 10 mM HEPES, 1X B-27 Supplement, 1X N-2 Supplement, 10 mM Nicotinamide, and 1X HyClone-Penicillin Streptomycin Solution) at 5 % CO2, 37 °C. In parallel, CAFs were starved in 2 % FBS DMEM with 1X Hyclone-Penincillin Streptomycin Solution. PDOs and CAFs were seeded on day 6 in 96-well plates (Helena Biosciences 92696T) in 50 μL Matrigel stacks with 300 μL of reduced media. PDO monocultures are seeded at a density of ∼ 1.5 x10^3 organoids/well, and CAFs at 2.5 x 10^5 cells/well, co-cultures were mixed in Matrigel on ice at the densities described, and seeded together on the plates for polymerization. After 72 hours of co-culture, and 48-hours of treatment (day 9), cultures were processed for scRNAseq.

value: Colorectal cancer

tag: culture

value: PDO monocultures, CAF monocultures, and co-cultures


title: D6 T3M4-sgCCNC-sgROSA26-1-D6-rep1

data_processing:
For RNA-seq, sequencing reads were mapped onto reference human genome hg38 using STAR v2.7.9a with default settings. HTSeq-counts was used to generate raw gene counts, and DESeq2 was then used to perform differential expression analysis.
For ChIP-Seq, reads were mapped to hg38 with bowtie2 2.4.2 with very-sensitive setting. Bam files are then sorted with Samtools 1.11 with default settings, and used to call peaks with MACS2. Bedtools 2.30.0 was used to intersect and merge peaks
Deeptools v3.5.0 was used to generate BigWig files that were then visualized in the UCSC genome browser with the hg38 genome. HOMER v4.11 was used to assign the closest annotated ORFs to each peak and for motif discovery.
For CRISPR amplicon sequencing, raw reads were aligned to each sgRNA library to generate count files with MAGeCK.
For scRNA-seq experiments, data was genetically demultiplexed using cellsnp-lite 1.2.3 and Vireo 0.5.8, aligned to the human genome and assigned to cells using Cell Ranger 7.1.0, and downstream analyzed using Seurat 4.3.0.1.
Assembly: hg38
Supplementary files format and content: Htseq-count matrix for RNA-Seq. H5 Seurat files for scRNA-seq. Bigwig files for ChIP-Seq. Mageck count files for CRISPR libraries.

extract_protocol:
For RNA-seq experiments, total RNA was isolated using TRIzol (Thermo Fisher, 15596026) according to the manufacturer’s instructions. For scRNA-seq experiments, cells were single cell captured and barcoded using the 10X Chromium chemistry. For ChIP-seq experiments, lysates were clarified from crosslinked, sonicated nuclei and protein-DNA complexes were immunoprecipitated with specific antibodies. For CRISPR libraries, genomic DNA was isolated using phenol-chloroform extraction and directly used for library preparation.
RNA-seq and ChIP-seq ibraries were constructed using  Illumina TruSeq RNA library prep kit v2 (Illumina, RS-122-2001) or  Illumina TruSeq ChIP library prep kit (Illumina, IP-202-1012) based on the manufacturer’s instructions. scRNA-seq libraries were biult using 10X Genomics NextGEM Single-Cell 3' Library Kit. CRISPR libraries were prepared using sgRNA flanking primers described in the article and 1 step PCR amplification.


title: PDO27 and CAF co-culture SPLiT-seq experiment sublibrary 1


title: WT_Leu_1


title: 100 ng/ml IFNy 6h - Unstimulated 24h [6_6h_ifny_24h_medium]

value: NMM

value: Mouse melanoma

value: NRAS mutant

value: 100 ng/ml IFNy 6h - Unstimulated 24h


title: D6 T3M4-sgCCNC-sgROSA26-2-D6-rep2


title: D3 T3M4-sgROSA26-sgNT-D3-rep3


title: ∆clr5_Leu_1


title: 10 ng/ml TGFb 6h - 100 ng/ml IFNy 24h [7_6h_tgfb_24h_ifny]

value: 10 ng/ml TGFb 6h - 100 ng/ml IFNy 24h


title: D3 T3M4-sgROSA26-sgNT-D3-rep2

value: human pancreatic cancer cell line


title: 10 ng/ml TGFb 6h - Unstimulated 24h [8_6h_tgfb_24h_medium]

value: 10 ng/ml TGFb 6h - Unstimulated 24h

value: Unstimulated


title: PDO21 and CAF co-culture SPLiT-seq experiment sublibrary 1


title: ∆clr5_Leu_2


title: D3 T3M4-sgROSA26-sgNT-D3-rep1


title: WT_His_2

growth_protocol: Precultured mycelium from N. crassa WT strain or ∆clr5 strain  were shifted into 1× No-nitrogen Vogel’s salt with 2% Avicel, and 50 mM Histidine for the induciton of additional 8 h.


title: Unstimulated 12h - 10 ng/ml TGFb 24h [22_12h_medium_24h_tgfb]

value: Unstimulated 12h - 10 ng/ml TGFb 24h

value: 12h continuous


title: slide_2_P88-81 | 024 | CD31

city: Brisbane

first: Akhilandeshwari

last: Ravichandran

state: Queensland

address: 60 Musk Avenue

country: Australia

institute: Queensland University of Technology

description:
FFPE Spatial transcriptomics
qcdata.csv
normdata.csv

data_processing:
*library strategy: GeoMx Seq
Adapter trimming with trim galore,  trimGaloreOpts = " --hardtrim5 26 --dont_gzip"
If paired-end, merge overlapping R1 and R2 with flash2, flash2Opts = " -m 26 -e 26 -f 26 -s 1 -r 27”
Extract UMIs in bowtie2, umiExtractOpts = " --bc-pattern=NNNNNNNNNNNNNN"
Align RTS_IDs (probe barcodes) using bowtie2, bowtie2Opts = " --end-to-end -L 4 --trim5 0 --trim3 0 --norc"
Deduplication using UMI-tools, umiDedupOpts = " --edit-distance-threshold=1“
Assembly: sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform, see attached NanoString GeoMx Hs_R_NGS_WTA_v1.0 file
Supplementary files format and content: Processed data files format and content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode)
Supplementary files format and content: rawdata: raw count data, normdata: normalised count data

source_name: Breast

extract_protocol:
Samples were incubated with DNA-oligo barcoded RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with fluorescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Each collection of oligo tags from one well (representing an AOI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR. After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio.

value: Breast

tag: cell

value: Endothelial cell

value: Normal-adjacent

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: area


title: D3 T3M4-sgCDK8-sgCDK19-5-D3-rep3

first: Diogo

last: Maia e Silva

tag: cell type

tag: cell line

tag: genotype

tag: time


title: slide_2_P88-81 | 023 | CD31

tag: tissue

tag: tissue type


title: D6 T3M4-sgCCNC-sgROSA26-1-D6-rep2


title: Unstimulated 6h - 10 ng/ml TGFb 24h [28_6h_medium_24h_tgfb]

tag: treatment

value: Unstimulated 6h - 10 ng/ml TGFb 24h

tag: primary stimulus

tag: secondary stimulus

value: 10 ng/ml TGFb

tag: primary stimulus_duration

value: 6h continuous

tag: secondary stimulus_duration

value: 24h continuous


title: slide_2_P88-81 | 022 | CD31

tag: cell

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads


title: Unstimulated 6h - 100 ng/ml IFNy 24h [27_6h_medium_24h_ifny]

tag: cell line

value: NMM

tag: cell type

value: Unstimulated 6h - 100 ng/ml IFNy 24h

value: 100 ng/ml IFNy


title: WT_His_1

tag: strain

value: FGSC 2489

value: Mycelium


title: Unstimulated 6h - Unstimulated 24h [29_6h_medium_24h_medium]

value: Mouse melanoma

tag: genotype

value: NRAS mutant

value: Unstimulated 6h - Unstimulated 24h


title: D3 T3M4-sgCDK8-sgCDK19-5-D3-rep2

value: human pancreatic cancer cell line

tag: time


title: D3 T3M4-sgCDK8-sgCDK19-5-D3-rep1


title: ∆clr5_His_2


title: slide_2_P88-81 | 021 | CD31

tag: tissue

tag: tissue type

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: area


title: ∆clr5_His_1


title: D3 T3M4-sgCDK8-sgCDK19-4-D3-rep3


title: 100 ng/ml IFNy 2h - 10 ng/ml TGFb 24h [1_2h_ifny_24h_tgfb]

tag: treatment

value: 100 ng/ml IFNy 2h - 10 ng/ml TGFb 24h

tag: primary stimulus

tag: secondary stimulus

tag: primary stimulus_duration

value: 2h continuous

tag: secondary stimulus_duration


title: WT_Avicel_2

growth_protocol: Precultured mycelium from N. crassa WT strain or ∆clr5 strain  were shifted into 1×Vogel’s salt with 2% Avicel for the induciton of additional 8 h.


title: PDO21 and CAF co-culture SPLiT-seq experiment sublibrary 2

value: Colorectal cancer

tag: cell line

tag: culture

value: PDO monocultures, CAF monocultures, and co-cultures


title: slide_2_P88-81 | 020 | CD31

value: Breast

tag: cell

value: Endothelial cell

value: Normal-adjacent

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads


title: 100 ng/ml IFNy 2h - Unstimulated 24h [2_2h_ifny_24h_medium]

tag: cell type

tag: genotype

value: 100 ng/ml IFNy 2h - Unstimulated 24h

value: Unstimulated

value: 24h continuous


title: D3 T3M4-sgCDK8-sgCDK19-4-D3-rep2

tag: time


title: WT_Avicel_1

tag: strain


title: ∆clr5_Avicel_2


title: D3 T3M4-sgCDK8-sgCDK19-4-D3-rep1


title: 10 ng/ml TGFb 2h - Unstimulated 24h [4_2h_tgfb_24h_medium]

value: NMM

tag: treatment

value: 10 ng/ml TGFb 2h - Unstimulated 24h

tag: primary stimulus

value: 10 ng/ml TGFb


title: ∆clr5_Avicel_1

value: Mycelium


title: slide_2_P88-81 | 017 | CD31

tag: tissue

tag: tissue type

value: Tumor

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: area


title: D3 T3M4-sgCDK8-sgCDK19-3-D3-rep3

tag: cell line


title: Unstimulated 2h - 100 ng/ml IFNy 24h [24_2h_medium_24h_ifny]

value: Mouse melanoma

value: NRAS mutant

value: Unstimulated 2h - 100 ng/ml IFNy 24h

tag: secondary stimulus

value: 100 ng/ml IFNy

tag: primary stimulus_duration

tag: secondary stimulus_duration


title: D3 T3M4-sgCDK8-sgCDK19-3-D3-rep2

tag: cell type

value: human pancreatic cancer cell line


title: slide_2_P88-81 | 016 | CD31

tag: cell

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads


title: D3 T3M4-sgCDK8-sgCDK19-3-D3-rep1

tag: genotype

tag: time


title: Unstimulated 2h - Unstimulated 24h [26_2h_medium_24h_medium]

tag: treatment

value: Unstimulated 2h - Unstimulated 24h

tag: primary stimulus

value: 2h continuous


title: slide_2_P88-81 | 015 | CD31

tag: tissue

value: Breast

value: Endothelial cell

tag: tissue type

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: area


title: D3 T3M4-sgCDK8-sgCDK19-1-D3-rep3

tag: cell type

tag: cell line


title: RNA-seq_3KO 7h post sporulation induction, replicate 2

city: Warsaw

first: Agata

middle: L.

last: Starosta

address: Pawińskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics Polish Academy of Sciences

description:
3KO7m_2
countsRAW_CDSandUTR_mRNA.xlsx
countsRAW_CDS_mRNA.xlsx
countsTPM_CDSandUTR_mRNA.xlsx
countsTPM_CDS_mRNA.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_mRNA.xlsx

data_processing:
FastQC reports were utilized to assess raw data quality.
Following this step, the removal of adapters and low-quality sequences was performed using TrimGalore! software
The Bowtie tool was employed to eliminate sequences corresponding to tRNA and rRNA using genome reference data.
After preprocessing, the FastQC tool was used for quality control.
The clean and trimmed data was mapped to the genome using STAR, with a tolerance of up to 4% mismatch in read length and exclusion of splicing. The resulting BAM files were sorted and indexed using the sambamba software. Unique mapped reads were counted using featureCounts, employing gene and UTR annotations from the BSGatlas database, with a minimum overlap of 4 nucleotides.
Subsequently, the normalization of read counts was carried out using the Transcripts Per Million (TPM) method for CDS, UTR, and combined data.
Differential gene expression analysis was carried out on RNA-seq and RIBO-seq data using the DEBrowser tool and the DESeq2 library.
Assembly: NC_000964.3
Supplementary files format and content: XLSX files include raw counts for each sample (CDS and UTRs)
Supplementary files format and content: XLSX files include raw counts for each sample (CDS only)
Supplementary files format and content: XLSX files include TPM values for each sample (CDS and UTRs)
Supplementary files format and content: XLSX files include TPM values for each sample (CDS only)
Supplementary files format and content: XLSX file includes differential expression results between 3KO and WT for each time-point

organism: Bacillus subtilis

source_name: strain 168

growth_protocol: The B. subtilis 168 strain served as the wild type, and other strains were derived from it. The strains were cultured overnight in LB medium at 30 °C with shaking, then diluted to OD600=0.1 in CH medium. They were grown until OD600 reached 0.5 – 0.6 at 37 °C with shaking. Sporulation was induced by changing the medium to sporulation medium, following the method by Sterlini and Mandelstam (1968), with the modification that cells were harvested by filtration. Filters were then transferred into the culture flasks, and the sporulation medium was supplemented with 3% v/v of the culture in the CH medium at OD600=0.5-0.6 to promote sporulation.

extract_protocol:
RNA was isolated from sporulating WT and 3KO strains. Cultures were harvested hourly for seven hours into sporulation, beginning at T0 (prior to sporulation induction), resulting in a total of eight timepoints. Before harvesting, cultures were treated with 0.3 mM chloramphenicol. Cells were collected by filtration and flash frozen in liquid nitrogen. Purification of mRNA, ribosomal footprint isolation and library preparation was performed as described earlier. Briefly, frozen pellets were ground using mortar and pestle with the addition of aluminum oxide and lysis buffer. The extracted total RNA was used for purification of mRNA and ribosomal footprint isolation. rRNA depletion was performed to yield mRNA which was then fragmented by alkaline hydrolysis. Ribosomal footprint isolation was performed by MNase digestion of the total RNA followed by size selection using polyacrylamide gel electrophoresis.
The obtained mRNA fragments and ribosomal footprints were end-repaired (dephosphorylation of 3'ends followed by phosphorylation of 5' ends) and used for preparation of cDNA sequencing libraries with NEBNext Multiplex Small RNA Library Prep Set for Illumina, according to the manufacturer's guidelines. Sequencing was performed on an Illumina NextSeq500 by Genomed S.A. (Warsaw, Poland) and Genome Facility at CeNT (Warsaw, Poland); single-end 50bp reads were sequenced.

tag: strain

value: strain 168

tag: library type

value: RNA-seq


title: RNA-seq_3KO 6h post sporulation induction, replicate 2

description:
3KO6m_2
countsRAW_CDSandUTR_mRNA.xlsx
countsRAW_CDS_mRNA.xlsx
countsTPM_CDSandUTR_mRNA.xlsx
countsTPM_CDS_mRNA.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_mRNA.xlsx


title: RNA-seq_3KO 7h post sporulation induction, replicate 1

description:
3KO7m_1
countsRAW_CDSandUTR_mRNA.xlsx
countsRAW_CDS_mRNA.xlsx
countsTPM_CDSandUTR_mRNA.xlsx
countsTPM_CDS_mRNA.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_mRNA.xlsx


title: WTM2

first: Yanni

last: Lv

address: Yongwai street No. 17

institute: The First Affiliated Hospital of Nanchang University

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

molecule: polyA RNA

source_name: brain

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: brain

tag: group

value: Wild-type mice following MCAO/R


title: D3 T3M4-sgCDK8-sgCDK19-1-D3-rep2

city: Cold Spring Harbor

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory


title: RNA-seq_3KO 6h post sporulation induction, replicate 1

description:
3KO6m_1
countsRAW_CDSandUTR_mRNA.xlsx
countsRAW_CDS_mRNA.xlsx
countsTPM_CDSandUTR_mRNA.xlsx
countsTPM_CDS_mRNA.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_mRNA.xlsx


title: WTM1


title: 10 ng/ml TGFb 2h - 100 ng/ml IFNy 24h [3_2h_tgfb_24h_ifny]

value: NMM

value: 10 ng/ml TGFb 2h - 100 ng/ml IFNy 24h

tag: secondary stimulus

tag: primary stimulus_duration

tag: secondary stimulus_duration

value: 24h continuous


title: D3 T3M4-sgCDK8-sgCDK19-1-D3-rep1

tag: genotype

tag: time


title: slide_2_P88-81 | 019 | CD31

tag: tissue

tag: cell

value: Normal-adjacent

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads


title: slide_2_P88-81 | 018 | CD31

tag: tissue type

value: Tumor

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: area


title: slide_2_P88-81 | 012 | CD31


title: WTC3

tag: group

value: Wild-type mice following sham surgery


title: RNA-seq_3KO 5h post sporulation induction, replicate 2

description:
3KO5m_2
countsRAW_CDSandUTR_mRNA.xlsx
countsRAW_CDS_mRNA.xlsx
countsTPM_CDSandUTR_mRNA.xlsx
countsTPM_CDS_mRNA.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_mRNA.xlsx

tag: strain

tag: genotype

tag: library type


title: slide_2_P88-81 | 011 | CD31

tag: tissue

tag: cell


title: D3 T3M4-sgCDK1-sgROSA26-D3-rep3

tag: cell type

tag: cell line

tag: time


title: RNA-seq_3KO 5h post sporulation induction, replicate 1

description:
3KO5m_1
countsRAW_CDSandUTR_mRNA.xlsx
countsRAW_CDS_mRNA.xlsx
countsTPM_CDSandUTR_mRNA.xlsx
countsTPM_CDS_mRNA.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_mRNA.xlsx


title: slide_2_P88-81 | 010 | CD31

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads


title: D3 T3M4-sgCDK1-sgROSA26-D3-rep2


title: WTC2


title: Unstimulated 2h - 10 ng/ml TGFb 24h [25_2h_medium_24h_tgfb]

value: Mouse melanoma

value: NRAS mutant

tag: treatment

value: Unstimulated 2h - 10 ng/ml TGFb 24h

tag: primary stimulus

value: Unstimulated

tag: secondary stimulus

value: 10 ng/ml TGFb

tag: primary stimulus_duration

tag: secondary stimulus_duration


title: slide_2_P88-81 | 014 | CD31

value: Breast

tag: tissue type

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: area


title: RNA-seq_3KO 4h post sporulation induction, replicate 2

description:
3KO4m_2
countsRAW_CDSandUTR_mRNA.xlsx
countsRAW_CDS_mRNA.xlsx
countsTPM_CDSandUTR_mRNA.xlsx
countsTPM_CDS_mRNA.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_mRNA.xlsx

tag: strain

tag: genotype

tag: library type


title: WTC1

tag: tissue

tag: group


title: RNA-seq_3KO 4h post sporulation induction, replicate 1

description:
3KO4m_1
countsRAW_CDSandUTR_mRNA.xlsx
countsRAW_CDS_mRNA.xlsx
countsTPM_CDSandUTR_mRNA.xlsx
countsTPM_CDS_mRNA.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_mRNA.xlsx


title: slide_2_P88-81 | 013 | CD31

tag: cell

value: Endothelial cell

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads


title: D3 T3M4-sgCDK1-sgROSA26-D3-rep1

tag: cell type

value: human pancreatic cancer cell line

tag: cell line

tag: time


title: KOM5

value: Lrg1 knockout mice following MCAO/R


title: D3 T3M4-sgCCNC-sgROSA26-3-D3-rep3


title: D3 T3M4-sgCCNC-sgROSA26-3-D3-rep2


title: KOM2

value: brain


title: slide_2_P88-81 | 008 | CD31

tag: tissue type

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads


title: RNA-seq_3KO 3h post sporulation induction, replicate 2

description:
3KO3m_2
countsRAW_CDSandUTR_mRNA.xlsx
countsRAW_CDS_mRNA.xlsx
countsTPM_CDSandUTR_mRNA.xlsx
countsTPM_CDS_mRNA.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_mRNA.xlsx

tag: strain

value: strain 168

tag: genotype

tag: library type

value: RNA-seq


title: RNA-seq_3KO 3h post sporulation induction, replicate 1

description:
3KO3m_1
countsRAW_CDSandUTR_mRNA.xlsx
countsRAW_CDS_mRNA.xlsx
countsTPM_CDSandUTR_mRNA.xlsx
countsTPM_CDS_mRNA.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_mRNA.xlsx


title: D3 T3M4-sgCCNC-sgROSA26-3-D3-rep1


title: KOM1

tag: tissue

tag: group


title: RNA-seq_3KO 2h post sporulation induction, replicate 2

description:
3KO2m_2
countsRAW_CDSandUTR_mRNA.xlsx
countsRAW_CDS_mRNA.xlsx
countsTPM_CDSandUTR_mRNA.xlsx
countsTPM_CDS_mRNA.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_mRNA.xlsx


title: D3 T3M4-sgCCNC-sgROSA26-2-D3-rep3


title: KOC5

value: Lrg1 knockout mice following sham surgery


title: slide_2_P88-81 | 007 | CD31

tag: cell

tag: aoisurfacearea

tag: aoinucleicount

tag: sequencingsaturation

tag: area


title: slide_2_P88-81 | 006 | CD31

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads


title: RNA-seq_3KO 2h post sporulation induction, replicate 1

description:
3KO2m_1
countsRAW_CDSandUTR_mRNA.xlsx
countsRAW_CDS_mRNA.xlsx
countsTPM_CDSandUTR_mRNA.xlsx
countsTPM_CDS_mRNA.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_mRNA.xlsx


title: slide_2_P88-81 | 004 | CD31

tag: tissue type

tag: alignedreads


title: KOC2


title: D3 T3M4-sgCCNC-sgROSA26-2-D3-rep2

tag: cell type

tag: cell line

tag: time


title: RNA-seq_3KO 1h post sporulation induction, replicate 2

description:
3KO1m_2
countsRAW_CDSandUTR_mRNA.xlsx
countsRAW_CDS_mRNA.xlsx
countsTPM_CDSandUTR_mRNA.xlsx
countsTPM_CDS_mRNA.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_mRNA.xlsx

tag: strain

tag: genotype


title: KOC1

tag: tissue


title: D3 T3M4-sgCCNC-sgROSA26-2-D3-rep1


title: slide_2_P88-81 | 003 | CD31

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads


title: RNA-seq_3KO 1h post sporulation induction, replicate 1

description:
3KO1m_1
countsRAW_CDSandUTR_mRNA.xlsx
countsRAW_CDS_mRNA.xlsx
countsTPM_CDSandUTR_mRNA.xlsx
countsTPM_CDS_mRNA.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_mRNA.xlsx

tag: library type


title: Rete testis cell, 3

city: Moscow

first: Valeru

last: Mun

address: st. Vavilova, 26

country: Russia

institute: IDB RAS

description:
RT3
gene_count_matrix.csv

data_processing:
bcl2fastq v2.20 Conversion Software (Illumina) was used to obtain FASTQ files
Sequence reads were trimmed using Trim Galore and Cutadapt
Reads were mapped using the HiSat2 algorithm
Read summarization was performed using FeatureCounts v.2.0.1
The R package EdgeR v.3.42.4 was used for normalization of data and differential expression analysis
Assembly: GRCm38
Supplementary files format and content: Comma Separated Spreadsheet includes raw counts for each sample

source_name: Rete testis cell culture

extract_protocol:
Total RNA was extracted using ExtractRNA kit (Evrogen). Samples were treated with recombinant duplex-specific nuclease (Eurogen) to remove genomic DNA impurities.
Poly(A) enrichment of the total RNA, cDNA synthesis and preparation of cDNA libraries were performed using TruSeq mRNA Stranded (Illumina).

value: Rete testis cell culture

value: WT


title: D3 T3M4-sgCCNC-sgROSA26-1-D3-rep3


title: Rete testis cell, 2

description:
RT2
gene_count_matrix.csv


title: D3 T3M4-sgCCNC-sgROSA26-1-D3-rep1


title: slide_2_P88-81 | 001 | CD31

tag: cell

value: Tumor

tag: aoisurfacearea

tag: aoinucleicount

tag: sequencingsaturation


title: RNA-seq_3KO 0h, prior to sporulation induction, replicate 2

description:
3KO0m_2
countsRAW_CDSandUTR_mRNA.xlsx
countsRAW_CDS_mRNA.xlsx
countsTPM_CDSandUTR_mRNA.xlsx
countsTPM_CDS_mRNA.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_mRNA.xlsx


title: RNA-seq_3KO 0h, prior to sporulation induction, replicate 1

description:
3KO0m_1
countsRAW_CDSandUTR_mRNA.xlsx
countsRAW_CDS_mRNA.xlsx
countsTPM_CDSandUTR_mRNA.xlsx
countsTPM_CDS_mRNA.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_mRNA.xlsx


title: slide_2_P88-81 | 002 | CD31

description:
FFPE Spatial transcriptomics
qcdata.csv
normdata.csv

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: area


title: Slide_1_P91-72 | 024 | CD31

tag: tissue type

value: Normal-adjacent

tag: alignedreads


title: RNA-seq_WT 7h post sporulation induction, replicate 2

description:
WT7m_2
countsRAW_CDSandUTR_mRNA.xlsx
countsRAW_CDS_mRNA.xlsx
countsTPM_CDSandUTR_mRNA.xlsx
countsTPM_CDS_mRNA.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_mRNA.xlsx

tag: strain


title: D6 T3M4-sgROSA26-rep3

tag: cell type

tag: cell line

tag: genotype

tag: time


title: Rete testis cell, 1

description:
RT1
gene_count_matrix.csv


title: Slide_1_P91-72 | 023 | CD31

tag: tissue

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads


title: D6 T3M4-sgROSA26-rep2


title: Sertoli cell, 2

description:
SC2
gene_count_matrix.csv

source_name: Sertoli cell culture

value: Sertoli cell culture


title: Sertoli cell, 3

description:
SC3
gene_count_matrix.csv


title: D6 T3M4-sgROSA26-rep1


title: slide_2_P88-81 | 005 | CD31

tag: cell

tag: aoisurfacearea

tag: aoinucleicount


title: RNA-seq_WT 7h post sporulation induction, replicate 1

description:
WT7m_1
countsRAW_CDSandUTR_mRNA.xlsx
countsRAW_CDS_mRNA.xlsx
countsTPM_CDSandUTR_mRNA.xlsx
countsTPM_CDS_mRNA.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_mRNA.xlsx

tag: library type


title: Slide_1_P91-72 | 022 | CD31

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: sequencingsaturation


title: RNA-seq_WT 6h post sporulation induction, replicate 2

description:
WT6m_2
countsRAW_CDSandUTR_mRNA.xlsx
countsRAW_CDS_mRNA.xlsx
countsTPM_CDSandUTR_mRNA.xlsx
countsTPM_CDS_mRNA.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_mRNA.xlsx

tag: strain


title: Slide_1_P91-72 | 021 | CD31

tag: tissue type

tag: alignedreads

tag: area


title: Sertoli cell, 1

description:
SC1
gene_count_matrix.csv

tag: cell type

tag: genotype


title: D6 T3M4-sgNT-4-rep3

tag: cell line

tag: time


title: RNA-seq_WT 6h post sporulation induction, replicate 1

description:
WT6m_1
countsRAW_CDSandUTR_mRNA.xlsx
countsRAW_CDS_mRNA.xlsx
countsTPM_CDSandUTR_mRNA.xlsx
countsTPM_CDS_mRNA.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_mRNA.xlsx


title: D6 T3M4-sgNT-4-rep2


title: M_3, replicate 3, scRNAseq

city: Nanjing

first: Meng

last: Cao

state: Jiangsu Province

address: Hongshan road 100#

institute: Affiliated Hospital of Integrated Traditional Chinese and Western Medicine

data_processing:
Celescope was used to base-calling, alignment, filtering and generation of normalized abundance measurements.
Read 1: contains the 24bp GEXSCOPE barcode and the 12bp UMI (bases 25-36). Read 2 contains the cDNA information.
Assembly: GRCm38
Supplementary files format and content: matrix files

source_name: MC38 tumor-bearing mouse

extract_protocol:
The tumor tissues of MC38 tumor-bearing mice were collected, and the tissue dissociation solution was used to form single-cell suspension, and CD45+ cells were sorted by magnetic beads
We used GEXSCOPETM Single Cell RNA Library Kit Tissue (Singleron Biotechnologies) to barcode single cells, capture mRNA from isolated single cells, and generate cDNA libraries for scRNA-seq. Then, individual libraries were diluted to 4 ng/μl, and pooled for sequencing on a HiSeq X platform (Illumina, San Diego, USA) with 150 bp paired-end reads.

tag: tissue

value: Subcutaneous tumor

tag: age

value: 6-8 weeks old

tag: treatment

value: PBS, Intraperitoneal injection


title: RNA-seq_WT 5h post sporulation induction, replicate 2

description:
WT5m_2
countsRAW_CDSandUTR_mRNA.xlsx
countsRAW_CDS_mRNA.xlsx
countsTPM_CDSandUTR_mRNA.xlsx
countsTPM_CDS_mRNA.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_mRNA.xlsx


title: Slide_1_P91-72 | 020 | CD31

tag: cell

tag: aoisurfacearea

tag: aoinucleicount

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads


title: M_2, replicate 2, scRNAseq

tag: strain


title: D6 T3M4-sgNT-4-rep1


title: Slide_1_P91-72 | 019 | CD31

tag: tissue type

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: sequencingsaturation


title: RNA-seq_WT 5h post sporulation induction, replicate 1

description:
WT5m_1
countsRAW_CDSandUTR_mRNA.xlsx
countsRAW_CDS_mRNA.xlsx
countsTPM_CDSandUTR_mRNA.xlsx
countsTPM_CDS_mRNA.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_mRNA.xlsx

tag: genotype

tag: library type


title: Slide_1_P91-72 | 018 | CD31

tag: tissue

tag: alignedreads

tag: area


title: M_1, replicate 1,scRNAseq

tag: cell line

tag: age

tag: treatment


title: D6 T3M4-sgNT-3-rep3

tag: cell type

tag: time


title: G_3, replicate 3, scRNAseq

value: GDNPs, Intraperitoneal injection


title: RNA-seq_WT 4h post sporulation induction, replicate 2

description:
WT4m_2
countsRAW_CDSandUTR_mRNA.xlsx
countsRAW_CDS_mRNA.xlsx
countsTPM_CDSandUTR_mRNA.xlsx
countsTPM_CDS_mRNA.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_mRNA.xlsx


title: Slide_1_P91-72 | 017 | CD31

value: Breast

tag: cell

tag: aoisurfacearea

tag: aoinucleicount

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads


title: D6 T3M4-sgNT-3-rep2


title: RNA-seq_WT 4h post sporulation induction, replicate 1

description:
WT4m_1
countsRAW_CDSandUTR_mRNA.xlsx
countsRAW_CDS_mRNA.xlsx
countsTPM_CDSandUTR_mRNA.xlsx
countsTPM_CDS_mRNA.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_mRNA.xlsx

tag: strain


title: RNA-seq_WT 3h post sporulation induction, replicate 2

description:
WT3m_2
countsRAW_CDSandUTR_mRNA.xlsx
countsRAW_CDS_mRNA.xlsx
countsTPM_CDSandUTR_mRNA.xlsx
countsTPM_CDS_mRNA.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_mRNA.xlsx

tag: genotype


title: Slide_1_P91-72 | 016 | CD31

value: Endothelial cell

tag: tissue type

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: sequencingsaturation


title: D6 T3M4-sgNT-3-rep1

value: human pancreatic cancer cell line

tag: cell line


title: G_2, replicate 2, scRNAseq

tag: tissue

tag: age

tag: treatment


title: Slide_1_P91-72 | 015 | CD31

tag: cell

tag: alignedreads

tag: area


title: D6 T3M4-sgMED12-4-rep3

tag: cell type

tag: time


title: G_1, replicate 1, scRNAseq


title: D6 T3M4-sgMED12-4-rep2


title: NC3

city: Taichung

first: Yu-Jung

last: Cheng

state: OTH

address: Road NaN-Tong, sec 1, 152-8, 8F

department: Physical Therapy

country: Taiwan

institute: China Medical University

data_processing:
The sequence was determined using Illumina's sequencing-by-synthesis (SBS) technology (Illumina, USA).
Sequencing data (FASTQ reads) were generated using Welgene Biotech's pipeline based on Illumina's basecalling program bcl2fastq v2.20.
Alignment Tool: HISAT2

source_name: gastrocnemius muscle

extract_protocol:
Total RNA was extracted using Trizol® Reagent (Invitrogen, USA) according to the instruction manual. Purified RNA was quantified at OD260nm using a ND-1000 spectrophotometer (Nanodrop Technology,USA) and qualitated by using a Bioanalyzer 2100 (Agilent Technology, USA) with RNA 6000 LabChip kit (Agilent Technology, USA).
All RNA sample preparation procedures were carried out according to the Illumina's official protocol. SureSelect XT HS2 mRNA Library Preparation kit (Agilent, USA) was used for library construction followed by AMPure XP beads (Beckman Coulter, USA) size selection.

value: gastrocnemius muscle


title: NC2


title: Slide_1_P91-72 | 014 | CD31

tag: aoisurfacearea

tag: aoinucleicount

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads


title: Slide_1_P91-72 | 013 | CD31

tag: tissue type

tag: roicoordinatex

tag: roicoordinatey


title: RNA-seq_WT 2h post sporulation induction, replicate 2

description:
WT2m_2
countsRAW_CDSandUTR_mRNA.xlsx
countsRAW_CDS_mRNA.xlsx
countsTPM_CDSandUTR_mRNA.xlsx
countsTPM_CDS_mRNA.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_mRNA.xlsx

tag: strain

tag: genotype

tag: library type


title: D6 T3M4-sgMED12-4-rep1

tag: cell line


title: RNA-seq_WT 2h post sporulation induction, replicate 1

description:
WT2m_1
countsRAW_CDSandUTR_mRNA.xlsx
countsRAW_CDS_mRNA.xlsx
countsTPM_CDSandUTR_mRNA.xlsx
countsTPM_CDS_mRNA.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_mRNA.xlsx


title: Slide_1_P91-72 | 012 | CD31

tag: tissue

tag: cell

tag: rawreads

tag: sequencingsaturation


title: Dis3

tag: treatment

value: immobilized for 7 days


title: RNA-seq_WT 1h post sporulation induction, replicate 2

description:
WT1m_2
countsRAW_CDSandUTR_mRNA.xlsx
countsRAW_CDS_mRNA.xlsx
countsTPM_CDSandUTR_mRNA.xlsx
countsTPM_CDS_mRNA.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_mRNA.xlsx

value: strain 168


title: D6 T3M4-sgMED12-3-rep2

tag: cell type

tag: time


title: NC1


title: D6 T3M4-sgMED12-3-rep3


title: Slide_1_P91-72 | 011 | CD31

tag: aoisurfacearea

tag: aoinucleicount

tag: alignedreads

tag: deduplicatedreads

tag: area


title: RNA-seq_WT 1h post sporulation induction, replicate 1

description:
WT1m_1
countsRAW_CDSandUTR_mRNA.xlsx
countsRAW_CDS_mRNA.xlsx
countsTPM_CDSandUTR_mRNA.xlsx
countsTPM_CDS_mRNA.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_mRNA.xlsx

value: RNA-seq


title: Dis2


title: D6 T3M4-sgMED12-3-rep1


title: Dis1


title: Slide_1_P91-72 | 009 | CD31

tag: tissue type

tag: roicoordinatex

tag: roicoordinatey

tag: trimmedreads

tag: stitchedreads


title: RNA-seq_WT 0h, prior to sporulation induction, replicate 2

description:
WT0m_2
countsRAW_CDSandUTR_mRNA.xlsx
countsRAW_CDS_mRNA.xlsx
countsTPM_CDSandUTR_mRNA.xlsx
countsTPM_CDS_mRNA.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_mRNA.xlsx

tag: strain

tag: genotype

tag: library type


title: Slide_1_P91-72 | 010 | CD31

tag: tissue

tag: cell

tag: rawreads

tag: sequencingsaturation


title: D6 T3M4-sgMED12-2-rep3

tag: cell type

tag: cell line

tag: time


title: C3

tag: treatment

value: non-immonilized, from the contraleral leg of immobilization group


title: RNA-seq_WT 3h post sporulation induction, replicate 1

description:
WT3m_1
countsRAW_CDSandUTR_mRNA.xlsx
countsRAW_CDS_mRNA.xlsx
countsTPM_CDSandUTR_mRNA.xlsx
countsTPM_CDS_mRNA.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_mRNA.xlsx


title: Slide_1_P91-72 | 008 | CD31

tag: aoisurfacearea

tag: aoinucleicount

tag: alignedreads

tag: deduplicatedreads

tag: area


title: RNA-seq_WT 0h, prior to sporulation induction, replicate 1

description:
WT0m_1
countsRAW_CDSandUTR_mRNA.xlsx
countsRAW_CDS_mRNA.xlsx
countsTPM_CDSandUTR_mRNA.xlsx
countsTPM_CDS_mRNA.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_mRNA.xlsx


title: D6 T3M4-sgMED12-2-rep2


title: 3KO 7h post sporulation induction, replicate 1

description:
3KO7r_1
countsRAW_CDSandUTR_Ribo.xlsx
countsRAW_CDS_Ribo.xlsx
countsTPM_CDSandUTR_Ribo.xlsx
countsTPM_CDS_Ribo.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_Ribo.xlsx

library_source: other

data_processing:
FastQC reports were utilized to assess raw data quality.
Following this step, the removal of adapters and low-quality sequences was performed using TrimGalore! software
The Bowtie tool was employed to eliminate sequences corresponding to tRNA and rRNA using genome reference data.
For RIBO-seq data, filtering was applied, retaining only sequences between 15-32 nucleotides in length.
After preprocessing, the FastQC tool was used for quality control.
Length distribution plots were created to analyze the read length distribution of the RIBO-seq data.
The clean and trimmed data was mapped to the genome using STAR, with a tolerance of up to 4% mismatch in read length and exclusion of splicing. The resulting BAM files were sorted and indexed using the sambamba software. Unique mapped reads were counted using featureCounts, employing gene and UTR annotations from the BSGatlas database, with a minimum overlap of 4 nucleotides.
Subsequently, the normalization of read counts was carried out using the Transcripts Per Million (TPM) method for CDS, UTR, and combined data.
Differential gene expression analysis was carried out on RNA-seq and RIBO-seq data using the DEBrowser tool and the DESeq2 library.
Assembly: NC_000964.3
Supplementary files format and content: XLSX files include raw counts for each sample (CDS and UTRs)
Supplementary files format and content: XLSX files include raw counts for each sample (CDS only)
Supplementary files format and content: XLSX files include TPM values for each sample (CDS and UTRs)
Supplementary files format and content: XLSX files include TPM values for each sample (CDS only)
Supplementary files format and content: XLSX file includes differential expression results between 3KO and WT for each time-point
Library strategy: RIBO-seq

molecule: other

value: RIBO-seq

value: bacterial cells


title: 3KO 7h post sporulation induction, replicate 2

description:
3KO7r_2
countsRAW_CDSandUTR_Ribo.xlsx
countsRAW_CDS_Ribo.xlsx
countsTPM_CDSandUTR_Ribo.xlsx
countsTPM_CDS_Ribo.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_Ribo.xlsx


title: C2


title: D6 T3M4-sgMED12-1-rep3


title: D6 T3M4-sgMED12-2-rep1


title: 3KO 6h post sporulation induction, replicate 2

description:
3KO6r_2
countsRAW_CDSandUTR_Ribo.xlsx
countsRAW_CDS_Ribo.xlsx
countsTPM_CDSandUTR_Ribo.xlsx
countsTPM_CDS_Ribo.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_Ribo.xlsx


title: Slide_1_P91-72 | 007 | CD31

description:
FFPE Spatial transcriptomics
qcdata.csv
normdata.csv

tag: tissue type

tag: roicoordinatex

tag: roicoordinatey

tag: trimmedreads

tag: stitchedreads


title: C1

tag: strain

tag: tissue


title: D3 T3M4-sgTP63-87e10-rep3

tag: genotype


title: PD fluid1

city: Guangzhou

first: Si

last: Zekun

state: Guangdong

address: Guangdong,China

department: Division of Nephrology

institute: Nanfang Hospital, South Medical University

description: PD fluid_1

data_processing:
to get high quality clean reads, reads were further filtered by fastp (version 0.18.0). The parameters were as follows:  1) removing reads containing adapters;  2) removing reads containing more than 10% of unknown nucleotides(N);  3) removing low quality reads containing more than 50% of low quality (Q-value＜20) base
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Assembly: Ensembl_release107
Supplementary files format and content: txt file including count values and FPKM values for all samples

source_name: Peritoneal tissue

extract_protocol:
Isolate primary peritoneal endothelial cells by CD31+ magnetic activated cell sorting
Total RNA was extracted using Trizol reagent kit according to the manufacturer’s protocol. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina. The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters. The ligation reaction was purified with the AMPure XP Beads(1.0X).And polymerase chain reaction (PCR) amplified.The resulting cDNA library was sequenced using Illumina Novaseq6000.

value: Peritoneal tissue

tag: cell type

value: Endothelial

value: WT

value: mouse intra-peritoneally injected with PD fluid for 6 weeks


title: 3KO 6h post sporulation induction, replicate 1

description:
3KO6r_1
countsRAW_CDSandUTR_Ribo.xlsx
countsRAW_CDS_Ribo.xlsx
countsTPM_CDSandUTR_Ribo.xlsx
countsTPM_CDS_Ribo.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_Ribo.xlsx

tag: library type


title: Slide_1_P91-72 | 005 | CD31

tag: cell

value: Tumor

tag: rawreads

tag: sequencingsaturation


title: 3KO 5h post sporulation induction, replicate 1

description:
3KO5r_1
countsRAW_CDSandUTR_Ribo.xlsx
countsRAW_CDS_Ribo.xlsx
countsTPM_CDSandUTR_Ribo.xlsx
countsTPM_CDS_Ribo.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_Ribo.xlsx

tag: treatment


title: D6 T3M4-sgMED12-1-rep1

tag: cell line

tag: time


title: Saline3

value: mouse intra-peritoneally injected with Saline for 6 weeks


title: Slide_1_P91-72 | 004 | CD31

tag: aoisurfacearea

tag: aoinucleicount

tag: alignedreads

tag: deduplicatedreads

tag: area


title: D6 T3M4-sgMED12-1-rep2


title: Slide_1_P91-72 | 002 | CD31

tag: tissue type

tag: roicoordinatex

tag: roicoordinatey

tag: trimmedreads

tag: stitchedreads


title: PD fluid2

description: PD fluid_2

tag: tissue

tag: cell type

tag: genotype


title: D3 T3M4-sgTP63-87e10-rep2


title: 3KO 5h post sporulation induction, replicate 2

description:
3KO5r_2
countsRAW_CDSandUTR_Ribo.xlsx
countsRAW_CDS_Ribo.xlsx
countsTPM_CDSandUTR_Ribo.xlsx
countsTPM_CDS_Ribo.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_Ribo.xlsx

tag: strain

tag: library type


title: 3KO 4h post sporulation induction, replicate 2

description:
3KO4r_2
countsRAW_CDSandUTR_Ribo.xlsx
countsRAW_CDS_Ribo.xlsx
countsTPM_CDSandUTR_Ribo.xlsx
countsTPM_CDS_Ribo.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_Ribo.xlsx

tag: treatment


title: Slide_1_P91-72 | 003 | CD31

tag: cell

tag: rawreads

tag: sequencingsaturation


title: NCI-H1975_siFRA1_DMSO_rep3

first: Michael

last: Hottiger

department: DMMD

data_processing:
For the analysis, demultiplexing was performed using the Illumina bcl2fastq Conversion Software. Individual library sizes ranged from 22.5 million to 39.2 million reads. RNA sequencing analysis was performed using the SUSHI framewor, encompassing the following steps: Read quality was inspected using FastQC, and sequencing adaptors were removed using fastp; Alignment of the RNA-Seq reads using the STAR aligner and with the GENCODE human genome build GRCh38.p13 (Release 37) as the referenc; the counting of gene-level expression values using the ‘featureCounts’ function of the R package Rsubread; differential expression using the generalized linear model as implemented by the DESeq2 Bioconductor R package, and; GO term pathway analysis using both the hypergeometric over-representation test via the ‘enricher’ function and gene-set enrichment analysis via the ‘GSEA’ function, of the clusterProfiler Bioconductor R package. For the GSEA-based pathway analysis, we included a gene set from the MSigDB Hallmark, KEGG, and Wiki pathways. All R functions were executed on R version 4.1.2 (R Core Team, 2020) and Bioconductor version 3.14
Assembly: GRCh38.p13 (Release 37)
Supplementary files format and content: DESeq2 computed mean of normalized count of all samples based on sequencing depth

source_name: lung

growth_protocol: NCI-H1975 cells were grown in complete DMEM medium supplemented with 10% FCS and 1% P/S. 2x10^5 cells were seeded into 6-well plates.

extract_protocol:
Total RNA was extracted from quadruplicate experiments using the RNAeasy Plus Mini Kit (Qiagen) according to the manufactures protocol.
The quality of the isolated RNA was determined with a Fragment Analyzer (Agilent). The TruSeq Stranded mRNA kit (Illumina) was used in the succeeding steps. Briefly, total RNA samples (100-1000ng) were poly-A enriched and then reverse-transcribed into double-stranded cDNA. The cDNA samples were fragmented, end-repaired, and adenylated before the ligation of TruSeq adapters containing unique dual indices (UDI) for multiplexing. Fragments containing TruSeq adapters on both ends were selectively enriched with PCR. The quality and quantity of the enriched libraries were validated using the Fragment Analyzer (Agilent). The product is a smear with an average fragment size of approximately 260bp. The libraries were normalized to 10nM in Tris-Cl 10 mM pH=8.5 with 0.1% Tween20. According to standard protocol, the Novaseq 6000 (Illumina) was used for cluster generation and sequencing. The sequencing configuration was single-end 100bp.

treatment_protocol: NCI-H1975 cells were reverse transfected with the control siRNA (siSCR, 10uM) or a siRNA targeting FRA1 (10uM) using RNAiMAX (Thermo Fisher). To avoid cytotoxicity, the medium was exchange 12h following the transfection. 42h after the transfection DMSO or RBN-2397 (100uM) were added to the respective samples for 6h.

value: lung

tag: cell line

value: non-small cell lung cancer

value: FRA1 knockdown

value: siFRA1 48h,DMSO 6h


title: D3 T3M4-sgTP63-87e10-rep1

value: human pancreatic cancer cell line

tag: time


title: Slide_1_P91-72 | 001 | CD31

value: Breast

value: Endothelial cell

tag: aoisurfacearea

tag: aoinucleicount

tag: alignedreads

tag: deduplicatedreads

tag: area


title: 3KO 3h post sporulation induction, replicate 1

description:
3KO3r_1
countsRAW_CDSandUTR_Ribo.xlsx
countsRAW_CDS_Ribo.xlsx
countsTPM_CDSandUTR_Ribo.xlsx
countsTPM_CDS_Ribo.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_Ribo.xlsx

value: strain 168


title: 3KO 4h post sporulation induction, replicate 1

description:
3KO4r_1
countsRAW_CDSandUTR_Ribo.xlsx
countsRAW_CDS_Ribo.xlsx
countsTPM_CDSandUTR_Ribo.xlsx
countsTPM_CDS_Ribo.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_Ribo.xlsx


title: Saline2


title: Slide_1_P91-72 | 006 | CD31

tag: tissue type

tag: roicoordinatex

tag: roicoordinatey

tag: trimmedreads

tag: stitchedreads


title: Saline1

tag: tissue

tag: cell type

tag: genotype


title: D3 T3M4-sgTP63-51e1-rep3


title: C2

first: Huiyun

last: Ye

address: 1838 North Guangzhou Ave

institute: Southern Medical University

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0 mapping to reference genome
count counting
Assembly: mm10
Supplementary files format and content: TXT file contain counts for each sample

source_name: kidney

extract_protocol:
Total RNA was extracted from the samples by Trizol reagent (Invitrogen) separately
mRNA libraries were prepared for sequencing using standard Illumina protocols

value: kidney

tag: treatment

value: control

tag: strain

value: PCOS mouse

tag: strain background


title: 3KO 2h post sporulation induction, replicate 1

description:
3KO2r_1
countsRAW_CDSandUTR_Ribo.xlsx
countsRAW_CDS_Ribo.xlsx
countsTPM_CDSandUTR_Ribo.xlsx
countsTPM_CDS_Ribo.xlsx
DESeq2_betweenConditions_CDS_batchCorrected_Ribo.xlsx

tag: library type

value: RIBO-seq

value: bacterial cells