title: C-BEAS-2B_2

city: Wuhan

first: Xue

last: Zhou

state: Hubei

address: 13 Hangkong Road

department: Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College

institute: Huazhong University of Science and Technology

description: circRNA

data_processing:
libraries were sequenced on illumina Hiseq X ten platform and 150 bp paired-end reads were generated.
Raw data(raw reads) of fastq format were firstly processed through in-house perlscripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads on containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using bowtie2 v2.2.8 and paired-end clean reads were aligned to the reference genome using Bowtie.
The circRNA were detected and identified, using find_circ and CIRI2.
The raw counts were first normalized using TPM. Normalized expression level =(readCount*1,000,000)/libsize (libsize is the sum of circRNA readcount).
Differential expression analysis of two conditions groups was performed using the DESeq R package (1.10.1). DESeq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted  using the Benjamini and Hochberg's approach for controlling the false discovery rate. Genes with an adjusted P-value found by DESeq were assigned as  differentially expressed.
Genome_build: hg19
Supplementary_files_format_and_content: The file contains average TPM value, fold-change, and p-value for each group.

growth_protocol: cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) with 10% fetal bovine serum. The cells were grown in an incubator at 37C with a humidified atmosphere containing 5% CO2.

extract_protocol:
RNA was extracted with TRIzol.
A total amount of 5μg RNA per sample was used as input material for the RNA sample preparations. Firstly, ribosomal RNA was removed by Epicentre Ribo-  zero rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, the linear RNA was digested with 3 U of RNase R (Epicentre, USA) per ug of RNA. The sequencing libraries were generated by NEBNext Ultra' Directional RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations. Briefly, fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. In the reaction buffer, dNTPs with dTTP were replaced by dUTP. Remaining overhangs were converted into blunt ends vial exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μI USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: After seeded on plates for 6 hours, cells were treated with 0.0 or 2.0 μM cadmium.  Subculture was done every 3 days.

value: lung

value: human bronchial epithelial cells

value: treat with 0.0μM cadmium for twenty weeks


title: C-BEAS-2B_3

status: Public on Jan 26 2024

type: SRA

country: China

description: circRNA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: cell line

tag: cell type

tag: treatment


title: cKO_3_contralateral

city: Blacksburg

first: Alicia

last: Pickrell

state: VA

address: 970 Washington Street SW

department: Neuroscience

country: USA

institute: Virginia Tech

data_processing:
Bases with quality scores less than 30 and adapters were trimmed from raw sequencing reads by Trim Galore (v 0.6.4)
After trimming, only reads with length greater than 30bp were mapped to mm10 by STAR (v 2.7.1a).
Raw counts and normalized counts for each gene were outputted by RSEM (v1.2.28).
The raw counts were used to identify differentially expressed genes by DESeq2 (v 1.36.0)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw count and TPM values for each Sample

organism: Mus musculus

source_name: contralateral cortical tissue

extract_protocol:
RNA was isolated with Trizol and cleaned up with RNA mini plus kit (Qiagen)
Illumina TruSeq stranded mRNA kit

value: contralateral cortical tissue

tag: genotype

value: CX3CR1cre-er/+ STING fl/fl

value: CCI

tag: time

value: 2 hr


title: 208F

city: Freising

first: Frank

last: Johannes

state: Bavaria

address: Emil-Ramann str. 4

department: Department of Molecular Life Sciences

country: Germany

institute: Technical University of Munich

library_source: genomic

data_processing:
fastq files were analyzed using the Methylstar pipeline (Shahryary et al.2020).
Assembly: METHimpute (Taudt et al., 2018)
Supplementary files format and content: Methylation status calls and levels for all cytosines in the genome

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: Aerial rosette

growth_protocol: All plants were sown in the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) fully automatic phenotyping facility for small plants in long day (16h light, 8h dark ) conditions.

extract_protocol:
Genomic DNA was extracted from each sample using the DNAeasy plant mini kit from Qiagen
At least 1 μg of DNA were submitted to the Beijing Genome Institute where they were prepared for WGBS libraries.

treatment_protocol: Aerial rosette tissue 27 days after sowing (DAS) was harvested.

value: Aerial rosette

tag: line

value: epiHybrid

value: Harvested at 27 days after sowing (DAS)


title: RNA_S4142Nr3

city: Hamburg

first: Karoline

last: Hack

address: Martinistraße 52

department: Children's Cancer Center Hamburg

institute: University Medical Center Hamburg-Eppendorf

data_processing:
Pre-processing was started by checking RNA sequencing read quality using FASTQC (v0.11.9) and subsequently aligned to the human reference genome assembly (GRCh38.106) using STAR aligner (v2.7.10a) in default 1-pass mode.
Mapped reads were quantified using featureCounts (v1.6.0) as part of the Subread software package. The “isPairedEnd” parameter was specified in default “unstranded” read counting mode.
Assembly: GRCh38.106
Supplementary files format and content: The count matrix is provided as non-normalized and unfiltered raw read counts.

source_name: Spinal ependymoma (FFPE tissue)

extract_protocol:
RNA of SP-EPN was isolated from FFPE tissues using the Maxwell® RSC RNA FFPE Kit (Promega). Concentrations were measured with a Qubit 2.0 Fluorometer (Thermo Fisher Scientific) and RNA integrity was analyzed using the RNA 6000 Nano Kit on a 2100 Bioanalyzer (Agilent Technologies).
Library preparation  was conducted using the SMART-Seq Stranded Kit (Takara Bio)

value: Spinal ependymoma (FFPE tissue)


title: T-BEAS-2B_3

description: circRNA

value: treat with 2.0μM cadmium for twenty weeks


title: RNA_S4142Nr21


title: 207F


title: RNA_S4142Nr23


title: C-BEAS-2B_1

description: circRNA


title: RNA_S4142Nr20


title: 204F


title: RNA_S4142Nr2


title: T-BEAS-2B_1

description: circRNA


title: cKO_2_contralateral


title: cKO_1_contralateral


title: E9.5 GATA DKO mouse placenta

city: Kansas City

first: Soumen

last: Paul

state: KS

address: Hemenway Building 3901 Rainbow Boulevard

department: Department of Pathology & Laboratory Medicine

institute: University of Kansas Medical Center

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The data was analyzed using the 10x Genomics Chromium Single Cell software suite (cellranger-3.0.2).
The demultiplexing and conversion of Illumina base call files (BCL) to raw FASTQ files was done using "cellranger mkfastq" with default parameters.
The sequencing reads were aligned to the mouse reference mm10 and analyzed using "cellranger count".
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Placenta

growth_protocol: Time pregnant female mice (Gata2f/fGata3f/f) mated with cre driver males (Gata2f/+Gata3f/+ Gcm1Cre) were euthanized on day 9.5 after conception and the embryos were isolated.

extract_protocol:
Placenta from control and GATA DKO embryos were isolated and pooled. They were then made into a single cell suspension as per the protocol mentioned in the publication "Trophoblast paracrine signaling regulates placental hematoendothelial niche", Home et al.(bioRxiv preprint first posted online Nov. 13, 2019)
The RT reaction to generate 10X barcoded single stranded cDNA, in the single cell containing GEMs, is performed using an Eppendorf MasterCycler Pro thermal cycler. Post GEM-RT Cleanup is conducted by breaking the GEMS with 10X Recovery Agent to separate the aqueous phase from the Recovery Agent and Partitioning oil. A cleanup of the sscDNA containing aqueous phase is completed using Dynabeads MyOne Silane beads (Life Technologies 37002D). The second strand cDNA amplification is performed using the cDNA Amplification Mix on the Eppendorf MasterCycler Pro. The 3’ gene expression library construction is initiated with fragmentation, end repair and A-tailing of the dscDNA followed by adapter ligation and a sample index PCR using the Illumina compatible indexed adapters in the Chromium i7 Multiplex kit (10X Genomics 120262). Validation of the single cell library is conducted using the Agilent Tapestation 4200 ScreenTape assay (Agilent 5067-5576).
Single Cell RNA-seq (10X Genomics Chromium Single Cell 3' v3)

treatment_protocol: no treatment

value: Single cells obtained from mouse placenta

value: Placenta

tag: age

value: embryonic day 9.5

value: GATA DKO


title: RNA_S4142Nr19


title: 203F


title: d4_2_R1_ATACseq

city: Naples

first: Antonio

last: Baldini

state: Naples

address: Via Sergio Pansini 5

department: Department of Molecular Medicine and Medical Biotechnology

country: Italy

institute: University of Naples Federico II

data_processing:
The quality of  paired-end (PE) reads were assessed using FastQC.
The low-quality and short PE reads were filtered out and the universal Illumina adapters were trimmed out using cutadapt  with following settings: -q 30 -m 30.
The PE sequences were alignedto the mouse genome (mm10) containing only canonical chromosomes with Bowtie2, setting the options -q -t --end-to-end --very-sensitive -X 1000
Reads mapping to the mitochondrial chromosome were removed and after that, duplicates and reads mapping to multiple positions were removed using sambamba with -F "[XS] == null and not unmapped and not duplicate"
ATAC peaks were called for each sample using MACS2 with the option -BAMPE –nomodel –shif100 –extsize 200 and then were removed those peaks overlapping the mm10 blacklist regions
Assembly: mm10

growth_protocol: ES-E14TG2a mESCs (ATCC CRL-1821) were cultured without feeders and maintained undifferentiated on gelatin-coated dishes in GMEM (Sigma Cat# G5154) supplemented with 10^3  U/ml ESGRO LIF (Millipore, Cat# ESG1107), 15% fetal bovine serum (ES Screened Fetal Bovine Serum, US Euroclone Cat# CHA30070L), 0.1 mM non-essential amino acids (Gibco, Cat# 11140-035), 0.1 mM 2-mercaptoethanol (Gibco, Cat# 31350-010), 0.1 mM L-glutamine (Gibco, Cat# 25030081), 0.1 mM Penicillin/Streptomycin (Gibco, Cat# 10378016), and 0.1 mM sodium pyruvate (Gibco, Cat# 11360-070). The cells were passaged every 2–3 days using 0.25% Trypsin-EDTA (1X) (Gibco, Cat# 25200056) as the dissociation buffer.

extract_protocol:
mESCs were collected at day2 and day4  and then washed two times in PBS, harvested, counted using a hemacytometer chamber and pelleted. 15.000 cells/sample for mESC were treated with Tagment DNA Buffer 2x reaction buffer with Tagment DNA Enzyme (Illumina) according to the manufacturer’s protocol. After washes in PBS, cells were suspended in 50 mL of cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and immediately spun down at 500 × g for 10 min at 4°C. Fresh nuclei were treated with Transposition mix and Purification (Illumina #FC121-130), the nuclei were incubated at 37°C in Transposition Reaction Mix (25 µL reaction buffer, 2.5 µL Transposase, 22.5 µL Nuclease free water), purified using Qiagen MinElute PCR Purification Kit (catalog no./ID: 28006) and eluted in 10 µL of nuclease free water.
Sequencing library was prepared from the fragmented amplified tagmented DNA. Fragmentation size was evaluated using the Agilent 4200 TapeStation. Two biological replicates for each condition were sequenced using Illumina NextSeq500 system to obtain paired-end (PE) reads of 60 bp.

treatment_protocol: For differentiation, E14-Tg2a mESCs were dissociated with Trypsin-EDTA and cultured at 75,000 cells/ml in serum-free media: 75% Iscove’s modified Dulbecco’s media (Cellgro Cat# 15-016-CV) and 25% HAM F12 media (Cellgro #10-080-CV), supplemented with N2 (GIBCO #17502048) and B27 (GIBCO #12587010) supplements, penicillin/streptomycin (GIBCO #10378016), 0.05% BSA (Invitrogen Cat#. P2489), L-glutamine (GIBCO #25030081), 5 mg/ml For differentiation, E14-Tg2a mESCs were dissociated with Trypsin-EDTA and cultured at 75,000 cells/ml in serum-free media: 75% Iscove’s modified Dulbecco’s media (Cellgro Cat# 15-016-CV) and 25% HAM F12 media (Cellgro #10-080-CV), supplemented with N2 (GIBCO #17502048) and B27 (GIBCO #12587010) supplements, penicillin/streptomycin (GIBCO #10378016), 0.05% BSA (Invitrogen Cat#. P2489), L-glutamine (GIBCO #25030081), 5 mg/ml ascorbic acid (Sigma A4544) and 4.5 × 10^4 M monothioglycerol (Sigma M-6145). After 48h in culture, the EBs were dissociated using the Embryoid Body dissociation kit (cod. 130-096-348 Miltenyi Biotec) according to the manufacturer’s protocol and reaggregated for 40h in serum-free differentiation media with the addition of 8 ng/ml human Activin A (R&D Systems Cat#. 338-AC), 0.5 ng/ml human BMP4 (R&D Systems Cat# 314-BP), and 5 ng/ml human VEGF (R&D Systems Cat#. 293-VE). The 2-day-old EBs were dissociated and 6 × 10^4  cells were seeded onto individual wells of a 24-well plate coated with 0.1% gelatin in EC Induction Medium consisting of StemPro-34 medium (Gibco #10639011), supplemented with SP34 supplement, L-glutamine, penicillin/streptomycin, 200 ng/ml human-VEGF, and 2 μM Forskolin (Abcam, ab120058). The Induction Medium was renewed after one day. On day six of differentiation, the cells were dissociated and replated on gelatin 0.1% -coated dishes at a density of 25,000 cells/cm^2  in EC Expansion Medium, consisting of StemPro-34 supplemented with 50 ng/ml human-VEGF. Stem cell derived endothelial cells were maintained until they reached confluency (about 2-3 days). EC Expansion Medium was replaced every other day.

value: Mouse embryonic stem cells

value: WT

value: cardiogenic differentiation

tag: time point


title: RNA_S4142Nr22


title: E9.5 mouse placenta

description: 10x Genomics


title: RNA_S4142Nr17


title: RNA_S4142Nr16


title: 19F


title: 18F


title: RNA_S4142Nr15


title: d2_1_R1_ATACseq


title: Q405_24_1

city: kunming

first: le

last: 杨

state: 校内

address: cuihubeilu

institute: yunnan university

data_processing:
The data from high-throughput sequencing were analyzed using the Majorbio tools, a free online platform for data analysis (www.majorbio.com).
Supplementary files format and content: HiSat2 and StringTie
Supplementary files format and content: xlsx file includes tpm value for each sample

organism: Orbilia oligospora

growth_protocol: The wild-type and  mutant strains were cultured on potato dextrose agar (PDA) medium at 28°C.

extract_protocol:
Total RNA was extracted from tissue samples, the concentration and purity of the extracted RNA were detected by Nanodrop2000, RNA integrity was detected by agarose gel electrophoresis, and RIN value was determined by Agilent2100.
A single library construction requires that the total amount of RNA is ≥1ug, the concentration is ≥35ng/μL, OD260/280 is 1.8 - 2.2, and OD260/230≥1.0.
The libraries were prepared for sequencing using standard Illumina protocols.

value: Fungal hyphae cells

value: mutant strain

value: C. elegans induced


title: Q405_24_3


title: Q405_24_2


title: AGO IP, Dicer N1, SINV-GFP MOI 0.02 24 hpi, rep2

city: Strasbourg

first: Sébastien

last: Pfeffer

address: 2 allée Konrad Roentgen

department: UPR 9002 - Architecture et Réactivité de l'ARN

country: France

institute: CNRS - Institut de Biologie Moléculaire et Cellulaire (IBMC)

description: Homo sapiens and Sindbis-GFP virus

library_source: other

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.20.0.422.
Sequencing reads of sRNA-seq libraries were processed and analyzed with the following workflow.
Cutadapt v1.16 was first run to trim the 3' adapter (command: cutadapt -a TGGAATTCTCGGGTGCCAAGG -e 0.1 --no-indels -O 6 -m 18 --discard-untrimmed -o <sample>-cutadapt.fastq <sample>.fastq) and an additional filter was applied to only keep 18- to 32-nt long trimmed reads for further analyses.
Sample quality checks were performed before and after these preprocessing steps using FastQC v0.11.8.
Preprocessed reads were then mapped simultaneously to the human (GENCODE Human (GRCh38.p13) release 41) and SINV-GFP (private sequence derived from NC_001547.1) genomes, using Bowtie v1.3.1. (command: bowtie -q --phred33-quals -v 2 -y -a --best --strata -m 30 -x hg38coreGencodeSINVGFP <sample>-preprocessed.fastq <sample>-hg38coreGencodeSINVGFP.bwtmap).
Only alignments from the lowest mismatch stratum with at most 2 mismatches were reported for each read, provided that their number was not exceeding 30.
For each library, small RNA reads deriving solely from SINV-GFP were computationally extracted and further characterized.
Furthermore, expressed human miRNAs (miRBase v22.1), among which known mirtrons, were also identified and quantified in each library using BEDTools v2.30.0 by comparing their genomic coordinates to those of the original aligned reads and by counting only reads overlapping miRs on at least 80% of their size (command: bedtools intersect -a <sample>-hg38coreGencodeSINVGFP.bwtmap.bed -b hsa-matmir.bed -f 0.80 -wa -wb -s). Multiple mapped reads were weighted by the number of mapping sites in other miRNAs, and the final counts obtained for each miR were rounded down before further analysis.
Differential miRNA expression analysis between the two AGO-IP conditions was then performed with the DESeq2 package by using an adjusted p-value < 0.05 and an absolute log2 fold change > 1 as thresholds to define statistical significance.
Assembly: GRCh38.p13 + private sequence derived from NC_001547.1
processed data files format and content: xxx-2mmMax-onlyViral-stats.txt: tab-delimited text files with properties of reads mapping only against the SINV-GFP genome in each sample
processed data files format and content: xxx-onlyViral-22nt-anyali-anymm-POS.norm.bw: bigWig files with the normalized distribution (per 100000 only viral reads) of 22-nt long only viral reads along the positive strand of SINV-GFP genome for each sample
processed data files format and content: xxx-onlyViral-22nt-anyali-anymm-NEG.norm.bw: bigWig files with the normalized distribution (per 100000 only viral reads) of 22-nt long only viral reads along the negative strand of SINV-GFP genome for each sample
processed data files format and content: hsa-matmir_rawcounts.txt:  tab-delimited text file with our pipeline quantification of human mature miRs in each sample
processed data files format and content: hsa-matmir_deseq2_normcounts.txt:  tab-delimited text file with DESeq2 normalized human mature miR counts in each AGO IP sample

molecule: other

organism:
Homo sapiens
Sindbis virus

growth_protocol: NoDice FHA:DICER WT #4 or N1 #6 cells were plated in P150mm petri dishes at 25 000 000 cells per dish and infected the following day with SINV-GFP at an MOI of 0.02 for 24 h. Cells were maintained in Dulbecco’s modified Eagle medium supplemented with 10 % fetal bovine serum in a humidified atmosphere with 5 % CO2 at 37°C.

extract_protocol:
Cells were collected in 1.3 mL of ice-cold lysis buffer (50 mM Tris-HCl pH 7.5, 150 mM NaCl, 5 mM EDTA, 1 % NP-40, 0.5 mM DTT, 0.1 U/mL of RNase inhibitor and protease inhibitor cocktail (complete Mini, Merck, Sigma Aldrich)). Cells were lysed by putting the extract on ice for 15 min. First, human AGO proteins were immunoprecipitated from whole extract to enrich for loaded small-RNAs. AGO-IP was done following the protocol described in (Hauptmann et al., 2015). Briefly, 50 µL of magnetic Dynabeads coupled to G protein (Invitrogen, Fisher Scientific) were coupled to anti-Flag M2 antibody (F1804, Merck, Sigma Aldrich) overnight at 4°C under rotation. The day after, Flag-TNRC6B WT or mutant (with Tryptophans mutated to Alanines; called TNRC6B Ala) peptides were incubated with the coupled beads for 3 h at 4°C under rotation. Meanwhile, lysates were cleared with a centrifugation step at 10 000 g for 10 min at 4°C and 100 µL were kept as INPUT (20 µL for proteins and 80 µL for RNAs). Then, lysates were divided in two and put on the beads coupled to the peptides and incubated at 4°C for 3 h under rotation. After 4 washing steps with 300 µL of ice-cold washing buffer, beads were split: 280 µL were eluted with 1 mL of TRI Reagent solution (Invitrogen, Fisher Scientific) and RNAs were isolated according to the manufacturer’s instructions
Illumina TruSeq small RNA library preparation kit was used according to the manufacturer’s protocol (RS-200-0012, Illumina).

treatment_protocol: Cells were infected with a modified version of Sindbis virus expressing GFP (SINV-GFP) at an MOI of 0.02 for 24 h. Cells were maintained in Dulbecco’s modified Eagle medium supplemented with 10 % fetal bovine serum in a humidified atmosphere with 5 % CO2 at 37°C.

value: Human embryonic kidney

value: NoDice FHA:DICER N1 #6

tag: viral infection_conditions


title: 189F

value: Aerial rosette


title: RNA_S4142Nr14


title: d4_2_RNAseq

data_processing:
The quality of  paired-end (PE) reads were assessed using FastQC.
The low-quality and short PE reads were filtered out and the universal Illumina adapters were trimmed out using cutadapt  with following settings: -q 30 -m 30.
The PE reads were aligned to mm10/GRCm38 reference genome using STAR aligner with  following two steps: i) Generation of Ensembl mm10 referencenome index (release 102) setting the parameters --sjdbGTFfile 100 --sjdbOverhang 100 ii) Alignment of PE reads to the reference genome (--sjdbOverhang 100 --quantMode GeneCounts --outSAMtype BAM SortedByCoordinate).
The gene expression levels (raw counts) were quantified using featureCounts in R using the sorted BAM files as input and  the mm10 primary assembly annotation file in GTF format as reference annotation
Assembly: mm10
Supplementary files format and content: raw counts

growth_protocol: ES-E14TG2a mESCs (ATCC CRL-1821) were cultured without feeders and maintained undifferentiated on gelatin-coated dishes in GMEM (Sigma Cat# G5154) supplemented with 10^3   U/ml ESGRO LIF (Millipore, Cat# ESG1107), 15% fetal bovine serum (ES Screened Fetal Bovine Serum, US Euroclone Cat# CHA30070L), 0.1 mM non-essential amino acids (Gibco, Cat# 11140-035), 0.1 mM 2-mercaptoethanol (Gibco, Cat# 31350-010), 0.1 mM L-glutamine (Gibco, Cat# 25030081), 0.1 mM Penicillin/Streptomycin (Gibco, Cat# 10378016), and 0.1 mM sodium pyruvate (Gibco, Cat# 11360-070). The cells were passaged every 2–3 days using 0.25% Trypsin-EDTA (1X) (Gibco, Cat# 25200056) as the dissociation buffer.

extract_protocol:
Total RNA was isolated with QIAzol lysis reagent (Qiagen #79306), according to the manufacturer’s protocol. RNA concentration was estimated using a Nanodrop spectrophotometer 1000.
Libraries were prepared according to the Illumina strand specific RNA-seq protocol. Libraries were sequenced on the NextSeq 500, in paired end, 75 bp reads.

treatment_protocol: For differentiation, E14-Tg2a mESCs were dissociated with Trypsin-EDTA and cultured at 75,000 cells/ml in serum-free media: 75% Iscove’s modified Dulbecco’s media (Cellgro Cat# 15-016-CV) and 25% HAM F12 media (Cellgro #10-080-CV), supplemented with N2 (GIBCO #17502048) and B27 (GIBCO #12587010) supplements, penicillin/streptomycin (GIBCO #10378016), 0.05% BSA (Invitrogen Cat#. P2489), L-glutamine (GIBCO #25030081), 5 mg/ml ascorbic acid (Sigma A4544) and 4.5 × 10^4 M monothioglycerol (Sigma M-6145). After 48h in culture, the EBs were dissociated using the Embryoid Body dissociation kit (cod. 130-096-348 Miltenyi Biotec) according to the manufacturer’s protocol and reaggregated for 40h in serum-free differentiation media with the addition of 8 ng/ml human Activin A (R&D Systems Cat#. 338-AC), 0.5 ng/ml human BMP4 (R&D Systems Cat# 314-BP), and 5 ng/ml human VEGF (R&D Systems Cat#. 293-VE). The 2-day-old EBs were dissociated and 6 × 10^4  cells were seeded onto individual wells of a 24-well plate coated with 0.1% gelatin in EC Induction Medium consisting of StemPro-34 medium (Gibco #10639011), supplemented with SP34 supplement, L-glutamine, penicillin/streptomycin, 200 ng/ml human-VEGF, and 2 μM Forskolin (Abcam, ab120058). The Induction Medium was renewed after one day. On day six of differentiation, the cells were dissociated and replated on gelatin 0.1% -coated dishes at a density of 25,000 cells/cm^2  in EC Expansion Medium, consisting of StemPro-34 supplemented with 50 ng/ml human-VEGF. Stem cell derived endothelial cells were maintained until they reached confluency (about 2-3 days). EC Expansion Medium was replaced every other day.


title: 188F

value: epiHybrid


title: d4_1_RNAseq


title: Q405_12_1


title: 185F

value: Harvested at 27 days after sowing (DAS)


title: Q405_12_2


title: 184F


title: d4_1_R1_ATACseq


title: RNA_S4142Nr12

value: Spinal ependymoma (FFPE tissue)


title: 200F


title: d2_2_R1_ATACseq


title: EPEN_SPEPN_00OCU_00000023_DR


title: RNA_S4142Nr11


title: Q405_6_3


title: d2_1_RNAseq


title: Ctrl_x_dox_b

city: Aachen

first: Mingbo

last: Cheng

state: North Rhine-Westphal

address: Pauwelsstr. 19

institute: Uniklinik RWTH Aachen

data_processing:
scRNA: The Cell Ranger Software Suite (version 3.1.0) was used for processing sequencing information and single cell barcodes.
scRNA: Seurat (version 3.2.3) was used to integrate the scRNA-seq data and predict cell labels.
Assembly: scRNA: mm10 RNA_tdTomato
Supplementary files format and content: barcodes: barcodes present in input data
Supplementary files format and content: matrix: a count matrix with Market Exchange Format (MEX). The first line contains the type code and the second line includes format and cell-ranger versions. Number of peaks, barcodes, and non-zero entries can be found in the third line.  The rest of the lines represent  nonzero entries with the first two numbers corresponding to peak and barcode indices and the last one corresponding to  the number of cut sites.
Supplementary files format and content: genes: a bed file contains genes corresponding to row indices. For each gene, its gene ID and name are stored in the first and second column of the gene.tsv file, respectively

source_name: Mouse Kidney

extract_protocol: All protocols to generate scRNA-seq data on the 10x Chromium platform, including sample prep, library prep, instrument and sequencing settings, are available here: https://support.10xgenomics.com/single-cell-gene-expression

value: Kidney

tag: Stage

value: Control with dox


title: 171F


title: Q405_6_1


title: 176F


title: EPEN_SPEPN_00OCU_00000022_DR


title: Ctrl_x_dox_a


title: RNA_S4142Nr13


title: Q405_12_3


title: Q405_6_2


title: Q405_0_3


title: EPEN_SPEPN_00OCU_00000021_DR


title: d2_2_RNAseq


title: 16F


title: Q405_0_1


title: Hour8_c


title: EPEN_SPEPN_00OCU_00000016_DR


title: week4_a

value: Week 4


title: 160F


title: Hour8_a


title: 161F


title: 158F


title: Hour48_R_c

value: Hour48 Right


title: AO_24_2

value: wild type


title: Hour8_b


title: T-BEAS-2B_2

description: circRNA

value: lung

value: human bronchial epithelial cells

value: treat with 2.0μM cadmium for twenty weeks


title: AO_24_1

value: Fungal hyphae cells


title: AO_24_3


title: Hour48_R_b


title: EPEN_SPEPN_00OCU_00000012_DR


title: EPEN_SPEPN_00OCU_00000013_DR


title: EPEN_SPEPN_00OCU_00000009_DR


title: week4_b


title: 17F


title: EPEN_SPEPN_00OCU_00000014_DR


title: Q405_0_2

value: mutant strain


title: EPEN_SPEPN_00OCU_00000008_DR


title: AO_12_3

value: C. elegans induced


title: 152F


title: Hour48_R_a


title: 153F


title: AO_12_2


title: 157F


title: EPEN_SPEPN_00OCU_00000004_DR


title: 168F


title: Hour48_L_c

value: Hour48 Left


title: AO_12_1


title: EPEN_SPEPN_00OCU_00000003_DR


title: 150F


title: AO_6_3


title: Hour48_L_b


title: 146F


title: EPEN_SPEPN_00OCU_00000002_DR


title: AO_6_2


title: Hour48_L_a


title: EPEN_SPEPN_00OCU_00000001_DR


title: 141F


title: Hour24_c


title: AO_6_1


title: EPEN_SPEPN_000UT_00003915_DR


title: 13F


title: Hour24_b


title: AO_0_3


title: EPEN_SPEPN_000UT_00003759_DR


title: 139F


title: Hour24_a


title: EPEN_SPEPN_000UT_00003680_DR


title: 136F


title: 131F


title: AO_0_1


title: EPEN_SPEPN_000UT_00003488_DR


title: Day6_b


title: EPEN_SPEPN_000UT_00003309_DR


title: Day6_a


title: EPEN_SPEPN_000UT_00003246_DR


title: Day12_b


title: Day12_c


title: 12F


title: 125F


title: AO_0_2


title: EPEN_SPEPN_000UT_00002413_DR


title: EPEN_SPEPN_000UT_00002846_DR


title: Day6_c


title: organoids_2-months-old C6_PTCC_rep3

type: genomic

city: Heidelberg

first: Haikun

last: Liu

address: INF 581

institute: DKFZ

description:
Organoid
This sample was used only for producing a PCA on raw data from IDAT. Signal intensities are therefore not provided.

scan_protocol: DNA methylation array analyses were then performed with Infinium HumanMethylation450 BeadChip kit (Illumina) according to the manufacturer’s instructions by the microarray unit of the DKFZ Genomics and Proteomics Core Facility

data_processing: The PCA plot was drawn with the Factoextra R package using raw data

label: Cy5 and Cy3

extract_protocol: The DNA was extracted with DNeasy Blood & Tissue Kit (Qiagen, Hilden, Germany, Cat# 69504) following the manufacturer’s protocol

value: PTCC

value: organoid


title: 120F

value: Aerial rosette

value: epiHybrid


title: Day12_a


title: Control_c

value: Control


title: organoids_2-months-old C6_PTCC_rep2

hyb_protocol: DNA methylation array analyses were then performed with Infinium HumanMethylation450 BeadChip kit (Illumina) according to the manufacturer’s instructions


title: 118F

value: Harvested at 27 days after sowing (DAS)


title: organoids_2-months-old C6_PTN_rep3

label_protocol: DNA methylation array analyses were then performed with Infinium HumanMethylation450 BeadChip kit (Illumina) according to the manufacturer’s instructions

value: PTN


title: 126F


title: EPEN_SPEPN_000UT_00001980_DR

value: Spinal ependymoma (FFPE tissue)


title: EPEN_SPEPN_000UT_00000814_DR


title: organoids_2-months-old C6_PT_rep3

value: PT


title: EPEN_SPEPN_000UT_00000517_DR


title: Control_b

value: Kidney


title: 10F


title: organoids_2-months-old C6_PTN_rep1


title: Control_a


title: 107F


title: 128F


title: EPEN_SPEPN_000SK_14355578_DR


title: EPEN_SPEPN_000SK_14166906_DR


title: 106F


title: organoids_2-months-old C6_PT_rep1


title: organoids_2-months-old C6_WT_rep2

value: WT


title: organoids_2-months-old C6_WT_rep1


title: 104F


title: 102F


title: 103F


title: EPEN_SPEPN_000SK_14129474_DR


title: RH4_PFI90_1uM_24h_PAX3FOXO1_Rep4

city: Bethesda

first: Javed

last: Khan

state: MD

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

data_processing:
RNA-seq was mapped using STAR with hg19 as reference.
RNA-seq read abundance for each gene counted (TPM) using RSEM
RNA-seq raw reads normalized using DESeq2
ChIP-seq was mapped using BWA with hg19 as reference.
ChIP-seq peaks were called using MACS2. https://github.com/CBIIT/ChIP_seq.
Assembly: hg19/GRCh37
Supplementary files format and content: ChIP-seq peak files are tab delimited bed text files for each sample.
Supplementary files format and content: RNA-seq processed files are quantification matrices of TPM (transcripts per million) at the gene level.

source_name: muscle

growth_protocol: Cells were maintained in DMEM with 10% FBS and Penn/Strep at 37 °C incubation.

extract_protocol:
Bulk RNA is extracted using QIAGEN Rneasy Plus Mini Kit. ChIP samples were fixed with 1% formaldehyde for 15 mins, sonicated, immunoprecipitated using antibody, washed, eluted, and reverse crosslinked.
Illumina TruSeq Stranded mRNA and Total RNA library prep, Illumina TruSeq ChIP Library Prep

treatment_protocol: Cells were treated with either DMSO or compound of interest for the specified amount of time.

value: muscle

value: Rhabdomyosarcoma

value: wt

tag: antibody

value: PAX3-FOXO1 (in house)

value: 24 hr


title: RH4_DMSO_24h_KDM3B

value: KDM3B (Cell Signaling, 3100)

value: DMSO


title: RH4_DMSO_24h_HP1_Rep2

value: HP1 (Cell Signaling, 2616)


title: RH4_PFI90_1uM_24h_HP1_Rep2


title: EPEN_SPEPN_000DK_98430159_DR


title: iPSCs_C6_PTN_rep3

description:
iPSCs
This sample was used only for producing a PCA on raw data from IDAT. Signal intensities are therefore not provided.

value: iPSC


title: RH4_PFI90_1uM_24h_PAX3FOXO1_Rep3


title: HepG2 shBRD4 +dox2

first: LI

last: NENG

department: Biochemistry and Molecular Biology

description:
BRD4-KD_featureCounts_raw reads.txt
BRD4-KD_changed genes.txt

data_processing:
Raw reads were first filtered with Trim-Galore
Reads were aligned by STAR to human hg38 assembly with the Gencode V39 genome annotation.
Alignments with MAPQ > 10 were kept
Bam file were then further filtered with 'RmDup' to remove PCR duplicate
Gene-level counts were generated with featureCounts and further analyzed for gene differential expression with DeSeq2 with default parameters
Assembly: hg38
Supplementary files format and content: gene_level Counts by "featureCounts"
Supplementary files format and content: Differentially regulated genes

growth_protocol: All cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) (Gibco #12800-082) supplemented with 10% fetal bovine serum (FBS)(PAN, Germany. #ST30-3302). All cell lines were maintained in 37 °C incubator with 5% CO2.

extract_protocol:
Cells were then collected into TRNzol (TIANGEN Cat# DP424) in RNAase-free EP tubes for subsequent RNA extraction. Total RNA was extracted as recommended by the manufacturer.
Sample processing and sequencing were performed by BIG.inc (Shenzhen China). Briefly, messenger RNA was purified with magnetic beads conjugated with Oligo-dT and then fragmented with fragmentation buffer. Then first-strand cDNA was synthesized with random primer. After second-strand cDNA synthesis, A-tailing and RNA index adapters were added. The cDNA fragments were amplified by PCR and products were purified by Ampure XP Beads. The product was analyzed on the Agilent Technologies 2100 bioanalyzer for quality control. The PCR product was heat-denatured and circularized by the splint oligo sequence to get the final library. The final library was amplified with Phi29 DNA Polymerase to make DNA nanoball (DNB) which had more than 300 copies of one molecular. Pair-end 150 bases reads were generated on MGISEQ-2000RS platform (BGI, Shenzhen, China).

treatment_protocol: HepG2 cells were transduced with lentivirus carrying doxycycline inducible USP1-shRNA and BRD4-shRNA respectively. 48 hours after lentivirus infection, cells were divided into 6cm dishes. Puromycin (InvivoGen #ANT-PR-1) was added at a final concentration of 1 μg/ml after 12 hours. Cells were selected with puromycin for 3 days and then divided into 6 cm dishes. The next day, cells were either left untreated or treated with 1 μg/ml Doxycycline for three days. Culture medium was replenished every two days.

value: Hepatocellular Carcinoma


title: iPSCs_C6_PTN_rep2


title: EPEN_SPEPN_000SK_14047380_DR


title: RH4_PFI90_1uM_24h_KDM3B


title: HepG2 shBRD4 +dox1


title: EPEN_SPEPN_000DK_82513943_DR


title: iPSCs_C6_PTN_rep1


title: RH4_DMSO_24h_PAX3FOXO1_Rep4


title: HepG2 shBRD4 control2


title: organoids_2-months-old C6_WT_rep3

value: organoid


title: EPEN_SPEPN_000DK_80726857_DR


title: iPSCs_C6_PTCC_rep3

value: PTCC


title: iPSCs_C6_PTCC_rep2


title: RH4_DMSO_24h_PAX3FOXO1_Rep3


title: RH4_PFI90_1uM_24h_H3K9me2_Rep5

value: H3K9me2 (Abcam, ab1220)


title: HepG2 shBRD4 control1


title: EPEN_SPEPN_000DK_80195944_DR

value: Spinal ependymoma (FFPE tissue)


title: HepG2 shUSP1 +dox2

description:
USP1-KD_featureCounts_raw reads.txt
USP1-KD_changed genes.txt


title: iPSCs_C6_PTCC_rep1


title: RH4_PFI90_1uM_24h_H3K9me2_Rep3


title: HepG2 shUSP1 +dox1


title: EPEN_SPEPN_000DK_72588778_DR


title: RH4_DMSO_24h_H3K9me2_Rep5


title: EPEN_SPEPN_000DK_92897825_DR


title: HepG2 shUSP1 control2


title: EPEN_SPEPN_000DK_71536856_DR


title: EPEN_SPEPN_000DK_72083382_DR


title: iPSCs_C6_PT_rep2

value: PT


title: HepG2 shUSP1 control1


title: RH4_DMSO_24h_H3K9me2_Rep3


title: EPEN_SPEPN_000DK_68720552_DR


title: iPSCs_C6_PT_rep1


title: RH4_PFI90_1uM_24h_H3K27ac_Rep4

value: H3K27ac (Active Motif, 39133)


title: EPEN_SPEPN_000DK_64091354_DR


title: RH4_PFI90_1uM_24h_H3K27ac_Rep2


title: iPSCs_C6_WT_rep3

value: WT


title: Biotriplicates 22,23,24

city: Copenhagen

first: Morten

last: Petersen

address: Ole Maaløes Vej 5

country: Denmark

institute: University of Copenhagen

data_processing:
The reads obtained from the instrument were base called using the instrument manufacturer’s base calling software.
The reads were aligned against the Arabidopsis thaliana reference genome (TAIR10 release) with STAR version 2.5.1b using 2-pass alignment mode.
The Araport11 annotation was used in both mapping and read counting.
Assembly: TAIR 10
Supplementary files format and content: xls file includes raw counts and annotaion of genes in all samples
Supplementary files format and content: xls file includes normalized counts and annotaion of genes in all samples

source_name: above ground plant

growth_protocol: Plants were grown in 9×9cm or 4×5cm pots at 21°C with 8/16hrs light/dark regime for 6 weeks

extract_protocol:
Total RNA from above ground plant tissue were extracted using the NucleoSpin® RNA Plant kit, 1μg RNA was used for library construction
RNA library was prepared by BGI to fit BGISEQ-500

treatment_protocol: Above ground tissue were collected for RNA extraction

value: above ground plant


title: Biotriplicates 19,20,21


title: EPEN_SPEPN_000DK_62304557_DR


title: iPSCs_C6_WT_rep2


title: Biotriplicates 16,17,18


title: iPSCs_C6_PT_rep3


title: RH4_DMSO_24h_H3K27ac_Rep2

value: muscle

value: Rhabdomyosarcoma


title: Biotriplicates 13,14,15


title: EPEN_SPEPN_000DK_55635427_DR


title: iPSCs_GFP_PTN_rep3

value: PTN


title: RH4_DMSO_24h_H3K27ac_Rep4

value: wt

value: 24 hr


title: iPSCs_C6_WT_rep1


title: EPEN_SPEPN_000DK_41126053_DR


title: Biotriplicates 10,11,12


title: iPSCs_GFP_PTN_rep2


title: EPEN_SPEPN_000DK_53825772_DR


title: RH4_PFI90_1uM_24h_H3K4me3_Rep3

value: H3K4me3 (Active Motif, 39159)


title: Biotriplicates 7,8,9


title: EPEN_SPEPN_000DK_40730599_DR


title: iPSCs_GFP_PTN_rep1


title: Biotriplicates 4,5,6


title: EPEN_SPEPN_000DK_37768453_DR


title: iPSCs_GFP_PT_rep3


title: Biotriplicates 1,2,3


title: RH4_PFI90_1uM_24h_H3K4me3_Rep4


title: iPSCs_GFP_PT_rep2


title: EPEN_SPEPN_000DK_29522364_DR


title: dorsal, Pig ID 52-5, 5 months

city: Boston

first: Christiane

last: Fuchs

state: MA

address: 40 Blossom Street

department: Wellman Center for Photomedicine

institute: Massachusetts General Hospital / Harvard Medical School

data_processing:
Reads were aligned to the pig transcriptome using Salmon and transcript counts were converted to gene counts using tximport.
Assembly: Ensembl Sus scrofa version 98
Supplementary files format and content: CSV of gene counts

organism: Sus scrofa

source_name: skin

extract_protocol:
4mm biopsies were taken from different skin sites (flank, snout, dorsal foot and volar foot skin) and immediately put in RNA later for storage at -20℃. RNA was isolated using the Qiagen Rneasy Fibrous Tissue Mini Kit (#74704) and tissue homogenization was performed using the Qiagen Tissue Lyser II. RNA concentration was measured using Nanodrop and final quality control via visualization of 18S & 28S rRNA bands was done before sending samples to sequencing core facility.
TruSeq Stranded mRNA Prep with minor modifications to the protocol for automation on liquid handling systems.

treatment_protocol: samples were stored in RNA later until further processing

value: skin

tag: breed

value: Yorkshire

tag: harvest date

tag: Sex

value: female


title: Rh4_PLX1

molecule: polyA RNA

value: 6 hr

value: PLX1 BRD4 inhibitor


title: EPEN_SPEPN_000DK_15275547_DR


title: Rh4_DMSO

value: DMSO


title: iPSCs_GFP_PTCC_rep3

value: PTCC

value: iPSC


title: volar, Pig ID 52-5, 5 months


title: iPSCs_GFP_PT_rep1

value: PT


title: RH4_DMSO_24h_H3K4me3_Rep4


title: iPSCs_GFP_PTCC_rep2


title: flank, Pig ID 52-5, 5 months

value: WT


title: EPEN_SPEPN_000DK_14325313_DR

value: Spinal ependymoma (FFPE tissue)


title: RH4_shBRD4

value: muscle

value: 72 hr


title: EPEN_SPEPN_000DK_11845200_DR


title: EPEN_SPEPN_000DK_14554425_DR


title: EPEN_SPEPN_00OCU_00000010_DR


title: RH4_PFI90_1uM_24h_Rep4

value: Rhabdomyosarcoma


title: snout, Pig ID 52-5, 5 months


title: RH4_scramble

value: wt

value: scramble shRNA


title: dorsal, Pig ID 142-24, 6 months


title: RH4_DMSO_24h_H3K4me3_Rep3

value: H3K4me3 (Active Motif, 39159)

value: 24 hr


title: RH4_PFI90_1uM_24h_Rep3


title: L7205

city: Leiden, The Netherlands

first: Siddh

last: van Oost

address: Albinusdreef 2

department: Pathology

country: Netherlands

institute: Leiden University Medical Center

data_processing:
Raw RNA-seq data was processed by the RNA-seq BioWDL pipeline using default settings, developed by the SASC (https://biowdl.github.io/, LUMC, Leiden, the Netherlands)
Reads were aligned against hg38 with STAR and expression quantification was performed using HTseq-count
Assembly: hg38
Supplementary files format and content: Tab-delimited tsv file with raw counts for each sample

source_name: bulk tumour

extract_protocol:
RNA was isolated from tissue sections (thickness = 20 µm) in TRIzol (15596018, Ambion) according to manufacturer’s instructions. RNA purification was performed using RNaesy mini kit (74104, Qaigen) and included DNAse treatment according to manufacturer’s instructions
The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina was used to process the samples.

tag: disease

value: Chordoma

value: bulk tumour

tag: anatomical location

value: Sacrococcygeal


title: iPSCs_GFP_WT_rep3

tag: tissue


title: L6787

value: Mobile Spine

tag: neoadjuvant radiotherapy

value: Yes


title: iPSCs_GFP_WT_rep2


title: RH4_PFI63_10uM_24h_Rep4

tag: cell line

tag: cell type


title: L4716


title: iPSCs_GFP_PTCC_rep1

tag: genotype

value: PTCC


title: RH4_PFI63_10uM_24h_Rep3

tag: time

tag: treatment


title: snout, Pig ID 142-24, 6 months

value: skin

value: Yorkshire

value: female


title: L3382

value: Skull base


title: iPSCs_GFP_WT_rep1

value: WT

value: iPSC


title: RH4_DMSO_24h_060123_Rep4

value: muscle

value: Rhabdomyosarcoma

value: DMSO


title: SP-EPN 173

hyb_protocol: not provided

scan_protocol: not provided

data_processing: Methylation data were processed using minfi and noob normalization. CpG sites associated with SNPs and sex chromosomes were excluded.

label: Cy3 and Cy5

source_name: Spinal ependymoma

label_protocol: not provided

extract_protocol: DNA was extracted from FFPE tissue using the ReliaPrep™ FFPE gDNA Miniprep System (Promega). About 100-500 ng DNA were used for bisulfite conversion by the EZ DNA Methylation Kit (Zymo Research). The DNA Clean & Concentrator-5 (Zymo Research) and the Infinium HD FFPE DNA Restore Kit (Illumina) were employed to clean and restore the converted DNA.

value: Spinal ependymoma (FFPE tissue)

tag: array type

tag: material type

value: FFPE


title: dorsal, Pig ID 78-1, 7 months


title: RH4_DMSO_24h_040623_Rep3

value: wt

value: 24 hr


title: L7234

value: Chordoma

value: bulk tumour

value: Sacrococcygeal


title: SP-EPN 145


title: L7231


title: volar, Pig ID 78-1, 7 months


title: flank, Pig ID 78-1, 7 months


title: SP-EPN 172


title: H358,Comb,rep2

city: Montreal

first: Sidong

last: Huang

address: McIntyre Medical Sciences Building 3655 promenade Sir-William-Osler

country: Canada

institute: McGill University

data_processing:
Sequencing files were trimmed with trimmoatic and mapped to the reference human genome sequence (hg38) with STAR (2.6.1c). Gene expressions were calculated by Homer with Gencode gene annotation GTF file. Differential expression genes were identified with DESeq2 (version 1.19.38) and visualized in pheatmap (1.0.12) using R package.
Assembly: HG38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: Lung

growth_protocol: H358 cells were cultured in Roswell Park Memorial Institute 1640 Medium (RPMI, Thermo Fisher Scientific, Cat# 11875-093; no pyruvate) with 6% fetal bovine serum (Sigma, Cat# F1051), 1% penicillin/streptomycin (Thermo Fisher Scientific, Cat# 15140-122), and 2 mM L-glutamine (Thermo Fisher Scientific, Cat# 25030-081). Cells were maintained in a humidified 5% CO2-containing incubator at 37°C and regular Mycoplasma test was performed using Mycoalert Detection Kit (Lonza, Cat# LT07-318).

extract_protocol:
Total RNA was extracted with the RNeasy Mini Kit (Qiagen, Hilden, Germany). 1ug total RNA was used for the library construction.
RNA libraries for RNA-Seq were prepared using the SMARTER mRNA-Seq library.

value: Lung

value: Lung Adenocarcinoma cells

value: Combination


title: SP-EPN 144


title: H358,Comb,rep3


title: L6617

value: Mobile Spine


title: snout, Pig ID 78-1, 7 months

value: skin

value: Yorkshire

value: female


title: volar, Pig ID 142-24, 6 months

value: WT


title: SP-EPN 143

value: Cryo


title: flank, Pig ID 142-24, 6 months


title: H358,Comb,rep1


title: dorsal, Pig ID 81-8, 8 months


title: L6371


title: H358,IBET726,rep3


title: SP-EPN 141


title: volar, Pig ID 81-8, 8 months


title: L7232

value: Skull base


title: H358,IBET726,rep2


title: flank, Pig ID 81-8, 8 months


title: H358,IBET726,rep1


title: L5651

value: Yes


title: SP-EPN 138

value: Spinal ependymoma (FFPE tissue)


title: H358,Palbociclib,rep3

value: Palbociclib


title: L6737


title: snout, Pig ID 81-8, 8 months


title: L5343


title: SP-EPN 135


title: SP-EPN 139


title: L3770


title: H358,Palbociclib,rep1


title: SP-EPN 132


title: flank, Pig ID 98-6, 4 months


title: H358,Ctrl,rep3

value: Ctrl


title: H358,Palbociclib,rep2


title: volar, Pig ID 98-6, 4 months


title: L3519

value: Chordoma


title: SP-EPN 131


title: organoids_2-months-old C6_PT_rep2

value: PT

value: organoid


title: SP-EPN 140


title: H358,Ctrl,rep2

value: Lung


title: SP-EPN 129


title: SP-EPN 128


title: H358,Ctrl,rep1

value: Lung Adenocarcinoma cells


title: L3356

value: bulk tumour

value: Sacrococcygeal


title: dorsal, Pig ID 98-6, 4 months

value: skin


title: organoids_2-months-old C6_PTN_rep2

value: PTN


title: organoids_2-months-old C6_PTCC_rep1

value: PTCC


title: SNB1_48h_biolrep3

city: Szeged

first: Zsolt

last: Merényi

state: Csongrad-Csanad

address: Temesvári krt. 62, 5. emelet 519. szoba (vagy az épület főportája)

department: Biochemistry

country: Hungary

institute: Biological Research Centre

data_processing:
Reads were trimmed using bbduk.sh (part of BBMap/BBTools; http://sourceforge.net/projects/bbmap/) with the following parameters: trimq = 30 minlen = 50.
A two-pass STAR alignment (Veeneman et al., 2016) was performed against the reference genome (CopciAB 2.0)
Read count data was normalized using EdgeR (Robinson et al., 2010)
Expression values were calculated as fragments per kilobase of transcript per million mapped reads (FPKM).
Assembly: CopciAB 2.0 (DNA seq file:CopciAB_new_jgi_20220113.fasta, Annot file:CopciAB_new_annot_CDS_20220425m2_newIds_isoforms_mancur_filtered.gtf)
Supplementary files format and content: comma-separated text file with the raw count matrix
Supplementary files format and content: comma-separated text file with the FPKM matrix

organism: Coprinopsis cinerea

source_name: stage 1 primordia

growth_protocol: To obtain fruiting bodies from the same developmental stages, we followed a previously described method (Muragachi et al., 2015.) Briefly, C. cinerea strains (d=5mm mycelial plugs) were inoculated in the centre of YMG with half glucose content (0.2% w/v) and incubated for 6.5 days at 28°C in the dark. Once the agar was almost completely colonised by mycelium, we initiated fruiting body development by exposing the colony to white light for 2 hours, then placing them back in dark for 24-hours. This was followed by a 12-hour light/12-hour dark period at 28°C.

extract_protocol:
Total RNA was extracted by using the Zymo Quick-RNA Mini-Prep Kit (R1055) following the manufacturer's instructions.
Strand-specific cDNA libraries were constructed from poly(A)-captured RNA using the Illumina TruSeq Stranded RNA-Seq library preparation kit, and sequenced on the Illumina Novaseq 6000 (S4) PE150

treatment_protocol: Before RNA extraction, samples were washed thrice with 1 ml of diethyl pyrocarbonate-treated distilled water and then homogenised with micropestles using liquid nitrogene.

value: stage 1 primordia

tag: strain

value: AmutBmut1 pab1-1 #326

value: SNB1 knockout


title: snout, Pig ID 98-6, 4 months

value: Yorkshire

value: WT

value: female


title: SP-EPN 126

value: Spinal ependymoma (FFPE tissue)

value: Cryo


title: L7230

value: Chordoma

value: Mobile Spine


title: SNB1_48h_biolrep2


title: SNB1_48h_biolrep1


title: Sample_PBS_83_pool3C1

city: Bonn

first: Jiangyan

last: Yu

address: Carl-Troll-Str. 31

institute: University of Bonn

data_processing:
Sequencing reads were mapped to the mouse reference genome mm10 using STAR alignment from the Drop-seq pipeline (v2.0.0) as previously described (Macosko, Cell, 2015). Next, we assess the quality of our libraries and excluded cells with low quality (<500 genes per cell), doublets (>3000 genes per cell), or dead cells (>10% of mitochondrial content). All genes expressed in less than 5 cells were filtered out.
Cell clustering analysis was performed using the Seurat package (v4.1.1) according to instructions (Hao et al., 2021). In brief, the expression data was log normalized with a scale factor of 10,000. After scaling, PCA was performed using the top 3,000 variable genes for a linear dimensional reduction. The first 15 PCA components were used to cluster cells by the Louvain algorithm. To obtain an optimal cluster resolution, we set the resolution parameter in the FindClusters function as 0.25 to generate 5 major clusters, which were visualized after non-linear dimensional reduction with UMAP. Differentially expressed genes (DEGs) in each cluster were identified by using the default Wilcoxon rank sum test in the FindAllMarkers function, and were defined with logfc.threshold >0.25 and min.pct >0.25.
Assembly: mm10
Supplementary files format and content: R seurat object includes raw counts and normalized counts for each cell

source_name: Lung BALF

extract_protocol:
Cells of the bronchoalveolar space were harvested by flushing the lungs with 3x 1 ml ice cold 1x PBS containing 10 mM EDTA. After centrifugation with 1350 rpm for 5 min at 4°C, cell pellets were resuspended in antibody mix and stained for 35 min at 4°C. After washing with FACS buffer (1x PBS, 2 mM EDTA, 0.5% BSA (SERVA))
Seq-Well libraries were generated as described by Gierahn et al. (Gierahn et al., 2017). Briefly, 110000 barcoded mRNA-capture beads in Bead Loading Buffer were loaded onto the array. Afterwards, the Bead Loading Buffer was replaced by RPMI 1640 medium (Gibco) with 10% FCS (Sigma-Aldrich) and incubated for 10 min. The medium was discarded, 20000 to 30000 BALF cells were loaded and rocked for 10 min. The loaded arrays were washed 5x with PBS, soaked in RPMI 1640 und sealed by polycarbonate membranes under mild vaccum. The sealed arrays were incubated for 37°C for 30 min in Agilent clamps (Agilent) and then incubated in a guanidinium-based lysis buffer for 20 min. After incubation in hybridization buffer, the mRNA capture beads were washed from arrays and collected. Reverse transcription was performed on the bead pellet using a Maxima Reverse Transcriptase reaction (ThermoFisher) for 30 min at room temperature with end-over-end rotation followed by 90 min incubation at 52°C with end-over-end rotation. The reaction was stopped by washing with TE buffer supplemented with 0.01% Tween-20 or 0.5% SDS. Excess primers were digested by exonuclease ExoI (New England Biolabs). Beads were counted and the reverse transcribed cDNA libraries were amplified in a PCR reaction. After PCR, 20000 – 40000 beads were pooled and cleaned using AMPure XP beads (Beckman Coulter). The library integrity was assessed using a High Sensitivity D5000 assay (Agilent) for Tapestation 4200 (Agilent).

treatment_protocol: Mice were anesthetized by intraperitoneal injection of ketamine/xylazine and intranasally inoculated with endotoxin-free 1x PBS (EMD Millipore) or 0.2 mg β-glucan from Candida albicans

value: Lung BALF

value: BALF cells

value: PBS

tag: age

value: 8-12 weeks

value: Male


title: Sample_PBS_83_pool3C2


title: L6473

value: bulk tumour

value: Sacrococcygeal


title: SP-EPN 125


title: SP-EPN 124


title: L6325

value: Yes


title: Sample_PBS_83_pool2B2


title: SNB1_24h_biolrep3

source_name: secondary hyphal knot

value: secondary hyphal knot

value: AmutBmut1 pab1-1 #326


title: SP-EPN 122


title: Sample_PBS_83_pool2B1


title: L3034


title: SNB1_24h_biolrep1

value: SNB1 knockout


title: Gata3 knock Down ST cell (replicate 1)

data_processing:
Illumina bcl2fastq2 conversion software used for basecalling.
reads were aligned using the STAR (2.6.1c) software.
raw read counts were obtained using RSEM-1.3.1
differential expression was obtained using DESeq2
Assembly: GRCh38.rel92
Supplementary files format and content: tab-delimited text files of raw count values for each Sample

source_name: cell line

growth_protocol: Cell culture protocol was published earlier (Saha et al. Proc Natl Acad Sci U S A. 2020 Jul 28;117(30):17864-17875. doi: 10.1073/pnas.2002449117)

extract_protocol:
For RNA extraction we used Qiagen RNeasy Kit (Catalog#74104) following manufacturer's protocol. For each experimental conditions, 1 million cells were used to isolate total RNA.
For sequencing, libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech) designed for transcriptome analysis from samples as small as a single cell.  For library preparation, the mRNA fraction was enriched, fragmented, sized, reverse transcribed into cDNA and ligated with the appropriate adaptors. Finally, deep sequencing was performed using the Illumine NovaSeq 6000 sequencing system at the University of Kansas Genome Sequencing Facility to generate pair-end reads with read length 101 bp.

value: Placenta

value: human trophoblast stem cells

value: Gata2 knock down


title: WT_48h_biolrep3

value: stage 1 primordia

value: wild type


title: SP-EPN 121

value: Spinal ependymoma (FFPE tissue)

value: FFPE


title: SP-EPN 120


title: WT_48h_biolrep2


title: SP-EPN 119


title: Control ST cell (replicate 2)

value: Control


title: WT_48h_biolrep1


title: SP-EPN 118


title: Sample_PBS_40_pool3C1

value: Lung BALF

value: BALF cells

value: WT

value: PBS


title: SP-EPN 117


title: Sample_PBS_40_pool2B2

value: 8-12 weeks

value: Male


title: Control ST cell (replicate 1)


title: WT_24h_biolrep3

value: secondary hyphal knot


title: SNB1_24h_biolrep2

value: AmutBmut1 pab1-1 #326


title: Sample_PBS_40_pool2B1


title: SP-EPN 116


title: GATA3 (pooled samples)

description:
Sample_Gata3
Placenta

data_processing:
Illumina bcl2fastq2 conversion software used for basecalling.
nf-core/chipseq v1.2.2 with Nextflow v22.04.5, FastQC v0.11.9, Trim Galore! v0.6.4_dev, BWA v0.7.17-r1188, Samtools v1.10, BEDTools v2.29.2, BamTools v2.5.1, deepTools v3.4.3, Picard v2.23.1, R v3.6.3, Pysam v0.15.3, MACS2 v2.2.7.1, featureCounts v2.0.1, Preseq v2.0.3, MultiQC v1.9
Assembly: UCSC hg38 (iGenomes illumina)
Supplementary files format and content: *.bed: Peaks call files generated by nf-core chipseq pipeline.
Library strategy: CUT&RUN

source_name: CT27 cell line

growth_protocol: Cell culture protocol was published earlier (Okae H, Toh H, Sato T, Hiura H, Takahashi S, Shirane K, Kabayama Y, Suyama M, Sasaki H, Arima T. Derivation of Human Trophoblast Stem Cells. Cell Stem Cell. 2018 Jan 4;22(1):50-63.e6. doi: 10.1016/j.stem.2017.11.004. Epub 2017 Dec 14. PMID: 29249463).

extract_protocol:
Cut&Run experiments will be performed according to the published protocol (1, 2). hTSC were cultured in the stem condition following published protocol (3). When cells reached about 70% confluency, cells were washed with room temperature PBS and trypsinized to get single cell suspension. 500,000 hTSC cells were used per condition. Briefly, 500,000 hTSC cells were washed, then mixed with Concanavalin A beads. The immobilized cells were incubated with the primary antibody GATA2 (Rabbit Abcam ab109241 and GATA3 (Mouse BD Pharmingen 558686) or IgG (Rabbit ab46540, Abcam) in a binding buffer containing digitonin. Immobilized cells on concanavalin A beads were washed with DIG wash buffer and then incubated with protein A/G-MNase (homemade). After washing these cells, MNase was activated by treatment with Ca2+ at 4°C for 30 minutes. Reactions were stopped by adding stop buffer containing RNase A and Glycogen blue. DNA fragments diffuse out of the cell, reaction mix were incubated at 37°C for 10 minutes without agitation. The soluble DNA fragments were transferred into a fresh tube to incubate with proteinase K at 55°C for 30 minutes. Finally, DNA fragments were purified and used directly for library preparation using the Illumina TruSeq ChIP.
1. Skene PJ, Henikoff JG, Henikoff S. Targeted in situ genome-wide profiling with high efficiency for low cell numbers. Nat Protoc. 2018 May;13(5):1006-1019. doi: 10.1038/nprot.2018.015. Epub 2018 Apr 12. PMID: 29651053.
2. Meers MP, Bryson TD, Henikoff JG, Henikoff S. Improved CUT&RUN chromatin profiling tools. Elife. 2019 Jun 24;8:e46314. doi: 10.7554/eLife.46314. PMID: 31232687; PMCID: PMC6598765.
3. Okae H, Toh H, Sato T, Hiura H, Takahashi S, Shirane K, Kabayama Y, Suyama M, Sasaki H, Arima T. Derivation of Human Trophoblast Stem Cells. Cell Stem Cell. 2018 Jan 4;22(1):50-63.e6. doi: 10.1016/j.stem.2017.11.004. Epub 2017 Dec 14. PMID: 29249463.
For library preparation TruSeq RNA Library Prep Kit v2 was used. Finally, deep sequencing was performed using the Illumina NovaSeq 6000 sequencing system at the University of Kansas Genome Sequencing Facility to generate pair-end reads with read length 101 bp.

treatment_protocol: No

value: Human trophoblast stem cells

tag: antibody


title: GATA2 (pooled samples)

description:
Sample_Gata2
Placenta


title: Sample_PBS_83_pool1A2


title: SP-EPN 115


title: Sample_PBS_40_pool1A2


title: Sample_PBS_83_pool1A1


title: Gata2 knock Down ST cell (replicate 1)

value: Placenta


title: placenta_HET_hom_F_rep5

city: Clayton

first: Patrick

middle: S

last: Western

state: VIC

address: 27-31 Wright Street

department: Centre for Reproductive Health

country: Australia

institute: Hudson Institute of Medical Research

description:
2243-2
PE150

data_processing:
Adaptor and low quality sequences of raw reads were trimmed using trimmomatic (v0.39) with following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20.
Clean reads were mapped to mouse reference genome (GRCm38) using STAR (v2.7.5c) with following settings: --outFilterMismatchNoverLmax 0.03 --alignIntronMax 10000.
Raw counts for mouse reference genes (ensembl-release-101) were calculated using STAR (v2.7.5c) with parameter "--quantMode GeneCounts" whening doing genome alignment.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab delimited text file including raw reads counts for mouse reference genes in all samples

source_name: E17.5 Female Placenta

growth_protocol: Eedfl/fl mice were crossed with ZP3Cre transgenic mice, facilitating oocyte specific deletion from the primary follicle oocyte stage. For production of placental samples, females producing wild type (Eedfl/fl), heterozygous (Eedwt/del) of homozygous (Eeddel/del) oocytes were mated to isogenic wild type C57bl6 males to produce wild type or heterozygous offspring from oocytes that developed with wild type, heterozygous or homozygous null EED function. These offspring were produced from females producing Eed-wt, Eed-het or Eed-hom oocytes to generate wild type or heterozygous offspring as previously described by Prokopuk, L. et al. Clinical Epigenetics 10, 95 (2018). Heterozygous offspring generated from Eed heterozygous oocytes (HET-het offspring) or from Eed homozygous null oocytes (HET-hom offspring) are isogenic. However, the HET-hom offspring were generated from oocytes that completely lacked functional EED. In contrast, the HET-het offspring were generated from oocytes that had one functional copy of EED. As they are isogenic and heterozygous, comparison of HET-hom with HET-het offspring allowed the identification of differences that resulted from a loss of EED-dependent oocyte programming in the absence of confounding genetic differences. In addition, wild type offspring generated from Eed-het and Eed-wt oocytes allowing the comparison of WT-wt and WT-het offspring with HET-het and HET-hom offspring. This provided controls for differences generated as a result of Eed heterozygosity in offspring. The mouse lines used were obtained from the following sources: Zp3Cre mice (C57BL/6-Tg 93knw/J; Jackson Labs line 003651, constructed and shared by Prof Barabara Knowles), Eed floxed mice (Eedfl/fl) (B6; 129S1-Eedtm1Sho/J; Jackson Labs line 0022727; constructed and shared by Xie, H. et al. Cell Stem Cell 14, 68-80 (2014). The Eed line was backcrossed to a pure C57BL6/J and shared with us by Associate Professor Rhys Allen and Professor Marnie Blewitt, Walter and Eliza Hall Institute for Medical Research, Melbourne. All subsequent breeding and oocyte collection was performed by the authors at the Hudson Institute of Medical Research / Monash Medical Centre, Clayton, Victoria, Australia. Mice were housed at Monash Medical Centre Animal Facility using a 12-hour light-dark cycle as previously reported by Prokopuk, L. et al. Clinical Epigenetics 10, 95 (2018). Food and water were available ad libitum with room temperature maintained at 21-23°C with controlled humidity. All animal work was undertaken in accordance with Monash University Animal Ethics Committee (AEC) approvals.

extract_protocol:
Placentas were isolated at E17.5, weighed and bisected. Half of the placenta was rinsed in PBS, snap-frozen on dry ice and stored at -80°C for RNA analysis. Growth plate and placental RNA was extracted from 4-5 samples / genotype using NucleoSpin RNA Plus columns. RNA quality was assessed on an Agilent Bioanalyser and samples with RIN >7.5 used for library preparation and sequencing on the BGI Genomics platform (placentae, BGI Genomics, Hong Kong).
Placental libraries were constructed using the BGI DNBseq protocol followed by 150bp PE sequencing on the BGI DNBSeq Eukaryotic Transcriptome Resequencing platform (Beijing Genomics)

treatment_protocol: Refer to growth protocol for mouse strain information. Mice were crossed to produce genotypes described for each sample.

value: Eed.fl.Zp3Cre on C57BL/6 background


title: SP-EPN 65

value: Cryo


title: IgG (pooled samples)

description:
Sample_IgG
Placenta

value: IgG


title: placenta_HET_hom_F_rep4

description:
2243-1
PE150


title: Sample_Glucan_84_pool3C2

value: Glucan


title: WT_24h_biolrep2

value: wild type


title: Sample_Glucan_84_pool3C1


title: organoids_4-month-old-PTN

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg19
Supplementary files format and content: Tab-separated values files

source_name: PTN organoid

extract_protocol:
The single cells from the organoids were isolated with Neural dissociation kit (P) (Miltenyi) following the manufacturer’s protocol
The libraries were constructed with 10x Genomics Chromium Single Cell 3′ Kit v3.1

value: PTN organoid


title: organoids_4-month-old-PTCC

description: 10x Genomics

source_name: PTCC organoid

value: PTCC organoid

value: PTCC:PTEN-/-; TP53-/-; CDKN2A-/-;  CDKN2B-/-


title: Sample_PBS_40_pool3C2

value: Lung BALF

value: BALF cells


title: placenta_HET_hom_F_rep3

description:
2226-3
PE150


title: Control ST cell (replicate 3)

value: human trophoblast stem cells

value: Control


title: placenta_HET_hom_F_rep2

description:
2226-1
PE150


title: Sample_Glucan_84_pool2B2

value: WT

value: 8-12 weeks

value: Male


title: SP-EPN 61

value: Spinal ependymoma (FFPE tissue)


title: organoids_4-month-old-WT

description: 10x Genomics

source_name: WT organoid

value: WT organoid


title: placenta_HET_hom_F_rep1

description:
2185-1
PE150

value: Placenta

value: Eed.fl.Zp3Cre on C57BL/6 background


title: SP-EPN 60

value: Cryo


title: organoids_1-month-old-PTN

description: 10x Genomics


title: Sample_PBS_40_pool1A1

value: PBS


title: WT_24h_biolrep1

value: secondary hyphal knot

value: AmutBmut1 pab1-1 #326

value: wild type


title: SP-EPN 59


title: Sample_Glucan_84_pool2B1

value: Glucan


title: Sample_Glucan_84_pool1A2

value: Lung BALF


title: SP-EPN 64


title: organoids_1-month-old-PTCC

description: 10x Genomics

value: PTCC organoid

value: PTCC:PTEN-/-; TP53-/-; CDKN2A-/-;  CDKN2B-/-


title: SP-EPN 62


title: placenta_HET_het_F_rep3

description:
2178-3
PE150


title: SP-EPN 58


title: placenta_HET_het_F_rep2

description:
2178-2
PE150


title: Sample_Glucan_84_pool1A1

value: BALF cells


title: organoids_4-month-old-PT

description: 10x Genomics

source_name: PT organoid

value: PT organoid


title: SP-EPN 56


title: placenta_HET_het_F_rep1

description:
2167-8
PE150


title: Sample_Glucan_41_pool3C2

value: WT

value: 8-12 weeks


title: organoids_1-month-old-WT

description: 10x Genomics


title: SP-EPN 57

value: Spinal ependymoma (FFPE tissue)


title: organoids_1-month-old-PT

description: 10x Genomics


title: placenta_HET_het_F_rep4

description:
2221-4
PE150


title: totalRNA_6037FLAG_exponential

city: Gießen

first: Gabriele

last: Klug

address: Heinrich-Buff-Ring 26-32

department: Molecular- and Microbiology

institute: Justus-Liebig University Gießen

data_processing:
All reads were trimmed for adaptor sequences using trim-galore (version 0.6.3), low-quality reads have been rejected in the same data processing step. Options were set to -q 10 --length 15 -j 8
Reads were mapped to the Rhodobacter sphaeroides 2.4.1 whole genome (NC_007493.2, NC_007494.2, NC_009007.1, NC_007488.2, NC_007489.1, NC_007490.2, and NC_009008.1) using the READemption pipeline (version 0.4.3) subcommand align with the integrated mapper segemehl (version 0.2.0)
Assembly: Genome_build: GCF_000012905.2 ASM1290v2
Supplementary files format and content: wiggle format

organism: Cereibacter sphaeroides

source_name: Total RNA from Rhodobacter sphaeroides expressing CcaF1-3xFLAG grown under phototrophic conditions to mid exponential growth phase

growth_protocol: Cells were grown anaerobically, illuminated with 80 W*m^2 white light in malate minimal medium  (phototrophic conditions).

extract_protocol:
Total RNA and immunoprecipated RNA were isolated as published (Grützner et al., 2021, Nucleic Acids Res. 49(6), doi: 10.1093/nar/gkab146)
RNA was processed as published (Grützner et al., 2021, Nucleic Acids Res. 49(6), doi: 10.1093/nar/gkab146); NEBnext Multiplex Small RNA Library Prep Set

treatment_protocol: Cells were harvested either during exponential growth phase of after 48h of growth.

value: expressing CcaF1-3xFLAG


title: placenta_WT_wt_F_rep4

description:
2229-2
PE150

value: Placenta

value: Eedfl/fl


title: Sample_Glucan_41_pool2B2

value: Male


title: placenta_WT_wt_F_rep3

description:
2220-4
PE150

value: Eed.fl.Zp3Cre on C57BL/6 background


title: Sample_Glucan_41_pool3C1


title: Sample_Glucan_41_pool2B1


title: CoIP_6037FLAG_exponential

source_name: Immunoprecipitated RNA from Rhodobacter sphaeroides expressing CcaF1-3xFLAG grown under phototrophic conditions to mid exponential growth phase


title: totalRNA_6037FLAG_48h

source_name: Total RNA from Rhodobacter sphaeroides expressing CcaF1-3xFLAG grown under phototrophic conditions for 48h


title: placenta_WT_wt_F_rep2

description:
2136-2
PE150


title: placenta_WT_wt_F_rep1

description:
2074-1
PE150


title: CoIP_6037FLAG_48h

source_name: Immunoprecipitated RNA from Rhodobacter sphaeroides expressing CcaF1-3xFLAG grown under phototrophic conditions for 48h


title: Sample_Glucan_41_pool1A1


title: E15.5, MERFISH,region0

status: Public on Jan 25 2024

type: RNA

city: Jamaica Plain

first: Xiaoran

last: Zhang

address: 14 Perkins Square, Apt 11

department: Cardiology

institute: Boston Children's Hospital

description: A 300-genes gene panel was used which includes 296 MERFISH probes and 4 sequential probes. Then the probe hybridization, imaging, segmentation and decoding were performed by Vizgen MERSCOPE platform.

hyb_protocol: Performed by Vizgen MERSCOPE platform.

scan_protocol: Performed by Vizgen MERSCOPE platform.

data_processing:
Cellular segmentation and gene decoding were performed by Vizgen MERSCOPE platform, and the Vizgen Data Output which includes the List of detectable transcripts (.CSV), Mosaic images (.TIFF), Tanscripts per cell matrix (.CSV), Cell metadata (.CSV), Cell boundaries (.HDF5) was furhter processed by Scanpy (F. Alexander et al., 2018), Squidpy (Giovanni et al., 2022) and Seurat (Hao et al., 2021).
Processed data contains detected transcript number

source_name: whole embryo

label_protocol: Performed by Vizgen MERSCOPE platform.

extract_protocol: Performed by Vizgen MERSCOPE platform.

value: whole embryo

tag: developmental stage

tag: molecule subtype

value: targeted RNA


title: E9.5, MERFISH,region1

value: wild type


title: E9.5, MERFISH,region0


title: SP-EPN 45

city: Hamburg

first: Karoline

last: Hack

address: Martinistraße 52

institute: University Medical Center Hamburg-Eppendorf

source_name: Spinal ependymoma

value: FFPE


title: ATAC-seq on purified Müller cells from 6-month-old db/db mice - rep2

city: Munich

first: Antje

last: Grosche

address: Grosshaderner Str. 9

institute: Ludwig-Maximilian University Munich

data_processing:
ENCODE ATAC-seq pipeline
Assembly: mm10
Supplementary files format and content: narrowPeak

source_name: retina

extract_protocol:
Müller cells were purified using the MACS protocol and subjected to the omni-ATAC protocol with slight modification [PMID: 28846090]. Briefly, 100.000 viable, pelleted cells were resupended in cold ATAC resuspension buffer (10mM Tris-HCl pH 7.5 (Invitrogen, catalog nr 15567027), 10mM NaCl (Invitrogen, catalog nr AM9760G), 5mM MgCl2 (Invitrogen, catalog nr AM9530G), 0.1% IgePAL (Sigma Aldrich, catalog nr I3021-50ML), 0.1% Tween-20 (Sigma Aldrich, catalog nr P9416-50ML), 0.01% Digitonin (Promega, catalog nr G9441)) and incubated on ice for 3min. Lysed cells were washed with cold ATAC wash buffer (10mM Tris-HCl pH 7.5, 10mM NaCl, 5mM MgCl2, 0.1% Tween-20) and nuclei pelleted 10min at 500g. Nuclei were resuspended in 25uL of transposition mix (12.5ul 2x TD buffer, 1.25ul transposase (Illumina, catalog nr 20034197), 8.25ul PBS, 0.25ul 1% Digitonin, 0.25ul 10% Tween-20, 2.5ul nuclease-free water (Invitrogen, catalog nr AM9937)) and incubated at 37ºC for 30min, 1000RPM.
Transposed fragments were purified using a Zymo Clean and Concentrator5 kit (Zymo, catalog nr R1013), followed by amplification (Ultra II Q5, NEB, catalog nr M0544L) and double size selection of 100-1000bp fragments with AMPure XP beads (Beckman Coulter, catalog nr A63881). Library was sequenced using 2x50bp reads.

value: retina

value: Muller glia

value: db/db


title: ATAC-seq on purified Müller cells from 6-month-old WT mice - rep2


title: ATAC-seq on purified Müller cells from 6-month-old db/db mice - rep1


title: ATAC-seq on purified Müller cells from 6-month-old WT mice - rep1


title: WT-Te3

city: Shanghai

first: Yiwei

last: Lin

address: No.1630 Dongfang Road, Shanghai

institute: Renji Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
Quality control: The quality of raw reads was first assessed using the FastQC. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Reads were mapped to mouse genome assembly GRCm38 (ftp://ftp.ensembl.org/pub/release-83/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz) using HISAT2.
Stringtie(v1.3.0)was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:https://ftp://ftp.ensembl.org/pub/release-102/gtf/mus_musculus/Mus_musculus.GRCm38.102.gtf.gz.
Assembly: GRCm38
Supplementary files format and content: FileincludeCountandFPKMvaluesforeachsample

source_name: CD8+ T effector cells

growth_protocol: The spleens from WT and scd-1-/- mice were extracted, pulverized in PBS, and subsequently passed through a 70 μm filter. After being spun at 1500 rpm for 5 min, the cells were suspended in 2–3 mL buffer to lyse the red blood cells, left to incubate at 0°C for 6 min, and then washed twice. A MojoSort Mouse CD8 T Cell Isolation Kit (BioLegend) was used to screen the acquired CD8+ T cells. The cells were resuspended in complete medium (RPMI medium 1640 with 10% FBS, 1% penicillin/streptomycin, 2.5% HEPES, 1% sodium pyruvate, 1% nonessential amino acids, and 0.1% 2-ME) at a concentration of 1.5 × 106 cells/mL and placed in a 24-well plate at 1 mL per well. The cells were stimulated with 5 μg/mL of anti-CD3 and 0.5 ug/mL of anti-CD28 in a 37℃, 5% CO2 incubator for three days. In addition, 100 U/mL IL-2 was also added to the samples.

extract_protocol:
After 6 days, removed the medium and directly add 800μL Trizol into the 24-well plate to harvest samples. Total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® (Vazyme, China) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Teff cells were obtained by stimulating the cells with CD3/28 for three days followed by washing with PBS to eliminate the CD3/28. Then, IL-2 was induced for an additional three days. Cell counting was performed daily and the complete medium was replaced on a daily basis.

value: CD8+ T effector cells

value: The differentiation of effector CD8+ T cells


title: Sample_Glucan_41_pool1A2

source_name: Lung BALF

value: Lung BALF

value: BALF cells

value: WT

value: Glucan

tag: Sex


title: WT-Te2


title: SCD-1KO-Te3

value: Scd-1 knockout


title: SP-EPN 44

value: Spinal ependymoma (FFPE tissue)


title: SCD-1KO-Te1


title: WT-Te1


title: Gene expression Library, multiplexed

city: Leiden

first: Max

last: Fernkorn

address: Einsteinweg 55

department: Leiden Academic Centre for Drug Research (LACDR)

institute: University Leiden

description: Multiplexed sample, containing gene expression data

data_processing:
Demultiplexing to the individual samples, based on the cell multiplexing barcode and alignment to the mouse genome mm10 (GENCODE vM23/Ensembl 98, obtained from 10x Genomics) was performed with CellRanger (version 7.1.0, 10x Genomics).
Assembly: mm10 (GENCODE vM23/Ensembl 98, obtained from 10x Genomics)
Supplementary files format and content: For every demultiplexed sample: matrix.mtx: count matrix of genes and barcodes in Market Exchange Format (MEX); features.tsv: table of corresponding Ensemble Ids (first column) and Gene Ids (second column), corresponding to rows in matrix.mtx; barcodes.tsv: table of cell barcodes, corresponding to columns in matrix.mtx

source_name: mESCs

growth_protocol: Cells were seeded at a density of 3.5 * 104 cells/cm2 in 6-well plates in 2i + LIF and grown overnight.

extract_protocol:
For sequencing, cells were washed three times with PBS and detached with Accutase. Accutase was removed by centrifugation and 1 * 106 cells per sample were resuspended in PBS + 0.04 % BSA and immediately used for multiplexing labeling following the protocol of 10x Genomics for samples with a viability above 80 % (Cell Multiplexing Oligo Labeling for Single Cell RNA Sequencing Protocols with Feature Barcode technology, CG000391). Briefly, cells were spun down once again, resuspended with individual cell multiplexing oligos (CMO no. 301 to 310) and incubated for 5 min at RT. Cells were washed twice with PBS + 1 % BSA and passed through a cell strainer (FALCON, mesh size 35µm). A total of 1.2 * 105 single cells from all samples were pooled at equal ratios, and 4 * 104 were used for droplet generation, corresponding to a target number of 2.4 * 104 cell-containing droplets.
Droplet generation, lysis, mRNA and cell barcode capture, and generation of both the gene expression library as well as the cell multiplexing library was performed following the instructions by 10x genomics (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index) with Feature Barcode technology for Cell Multiplexing, CG000388). Specifically, we chose 11 PCR cycles for cDNA amplification and 10 cycles for the sample index PCR.
Multiplexed (CellPlex) 10x genomics single-cell RNA sequencing

treatment_protocol: Induction in 2i + LIF + dox was first started in the mutant clones, and 4 h later in the wild-type lines. After 8h and 4 h, respectively, Induction was stopped by washing once with N2B27, followed by 20 h of differentiation in N2B27. Controls for each cell line were continuously kept in 2i + LIF.

value: mESCs


title: Cell multiplexing Library, multiplexed

description: Cell multiplexing library for demultiplexing samples


title: Gata3 knock Down ST cell (replicate 2)

city: Kansas City

first: Soumen

last: Paul

address: Hemenway Building 3901 Rainbow Boulevard

institute: University of Kansas Medical Center

source_name: cell line

value: Placenta

value: human trophoblast stem cells

value: Gata3 knock down


title: SCD-1KO-Te2


title: Med12 mutant, N2B27, rep1

data_processing:
Alignment to genome with hisat2, version 2.1.0
Probe definition using RNA-seq quantitation pipeline in Seqmonk, version 1.48.1. Parameters: Transctipt features mRNA; Library type Non-strand specific; Libraries are paired end TRUE; Merge transcript isoforms TRUE; Generate Raw Counts TRUE; all others: FALSE
Read count quantification using Read Count Quantification in Seqmonk, version 1.48.1. Parameters for Raw Counts: Count reads on strand: Opposite Strand to Probe; Correct for total read count FALSE; Correct for probe length FALSE; Log Transform Count FALSE; Count duplicated reads only once FALSE
Parameters for TPMs: Count reads on strand: Opposite Strand to Probe; Correct for total read count TRUE; Correct to what? Per Million Reads; Count total only within probes FALSE; Correct for probe length FALSE; Log Transform Count FALSE; Count duplicated reads only once FALSE
Assembly: GRCm39, release 108
Supplementary files format and content: All_Probes_Raw_Counts.txt: Contains raw counts per sample (columns) for each gene (rows) including gene information (e.g. genomic location, strand, ID, etc.)
Supplementary files format and content: All_Probes_TPMs.txt: Contains TPMs per sample (columns) for each gene (rows) including gene information (e.g. genomic location, strand, ID, etc.)

source_name: Spry4:H2B-mVenus reporter

growth_protocol: Spry4H2B-Venus/+-reporter cells and Med12 mutant cells of this line were seeded at 35k cells/cm2 and grown in 2i for 14 h.

extract_protocol:
Trizol-based total RNA extraction
Strand-specific, Poly-A-enriched

treatment_protocol: Wild-type and Med12 mutant cells were differentiated in N2B27 or kept in 2i as controls for 24 h

value: Spry4:H2B-mVenus reporter

value: Med12 mutant

value: Differentiation


title: Med12 mutant, 2i, rep3


title: Med12 mutant, N2B27, rep2


title: Med12 mutant, N2B27, rep3


title: OX.NAC61_Thompson Seedless_rep3

city: VR

first: Alessandra

last: Amato

address: strada le grazie 15

institute: University of Verona

hyb_protocol: For microarray analysis on Thompson Seedless leaves transiently overexpressing VviNAC61, the hybridization and washing reactions have been conducted according to the Agilent Microarray-Based Gene Expression Analysis Guide (V 6.5).

scan_protocol: Scanning and Feature Extraction were performed by using an Agilent Scanner following the settings and parameters indicated in the instruction manual.

data_processing: Feature extraction and statistical analysis of the microarray data was conducted by using the Limma package in R

organism: Vitis vinifera

source_name: OX.NAC61 leaves of Vitis vinifera cv. Thompson Seedless

label_protocol: For microarray analysis on Thompson Seedless leaves transiently overexpressing VviNAC61, the cDNA synthesis and labeling reactions have been conducted according to the Agilent Microarray-Based Gene Expression Analysis Guide (V 6.5).

growth_protocol: For the transient overexpression of VviNAC61 in grapevine, plantlets of Vitis vinifera cv. Thompson Seedless were in vitro micropropagated and cultivated in growth chamber at 25°C with a 16-h photoperiod.

extract_protocol: Total RNA was isolated from ~100 mg of the ground grapevine leaves tissue using the Spectrum™ Plant Total RNA kit (Sigma-Aldrich).

treatment_protocol: For transient transformation of Vitis vinifera cv. Thompson Seedless, the 35S:VviNAC61 construct was transferred to Agrobacterium tumefaciens strain C58C1 by electroporation. As control, Agrobacterium was also transformed with an empty pK7WG2 containing a non-coding sequence. Seven in vitro six-week-old plants of grapevine cv. Thompson Seedless for overexpression and five for the control were immersed in each bacterial suspension and vacuum infiltrated (2 X 2 min at 90kPa).

tag: cultivar

value: cv. Thompson Seedless

value: Thompson Seedless OX

value: Young leaves


title: OX.NAC61_Thompson Seedless_rep1


title: CTRL_Thompson Seedless_rep1 [OX.NAC61]

source_name: Control leaves of Vitis vinifera cv. Thompson Seedless

value: Thompson Seedless control


title: wt, N2B27, rep3

value: wt

value: Pluripotency


title: CTRL_Thompson Seedless_rep3 [OX.NAC61]


title: CTRL_Thompson Seedless_rep2 [OX.NAC61]


title: Med12 mutant, 2i, rep2


title: Med12 mutant, 2i, rep1


title: wt, N2B27, rep2


title: wt, N2B27, rep1


title: wt, 2i, rep1


title: wt, 2i, rep2


title: wt, 2i, rep3


title: mESCs, stimulated, 6h 40 ng/ml FGF4

data_processing:
Alignment to genome with hisat2, version 2.1.0
Probe definition using RNA-seq quantitation pipeline in Seqmonk, version 1.48.1. Parameters: Transctipt features mRNA; Library type Non-strand specific; Libraries are paired end TRUE; Merge transcript isoforms TRUE; Generate Raw Counts TRUE; all others: FALSE
Read count quantification using Read Count Quantification in Seqmonk, version 1.48.1. Parameters for Raw Counts: Count reads on strand: Opposite Strand to Probe; Correct for total read count FALSE; Correct for probe length FALSE; Log Transform Count FALSE; Count duplicated reads only once FALSE
Parameters for TPMs: Count reads on strand: Opposite Strand to Probe; Correct for total read count TRUE; Correct to what? Per Million Reads; Count total only within probes FALSE; Correct for probe length FALSE; Log Transform Count FALSE; Count duplicated reads only once FALSE
Assembly: GRCm39, release 97
Supplementary files format and content: All_Probes_Raw_Counts.txt: Contains raw counts per sample (columns) for each gene (rows) including gene information (e.g. genomic location, strand, ID, etc.)
Supplementary files format and content: All_Probes_TPMs.txt: Contains TPMs per sample (columns) for each gene (rows) including gene information (e.g. genomic location, strand, ID, etc.)

growth_protocol: E14 Fgf4-mutant mESCs were seeded at 45k cells/cm2 were grown in N2B27 + Chiron + LIF for 18 h

treatment_protocol: Stimulation with 0, 0.625, 1.25, 2.5, 5, 10, 20 or 40 ng/ml FGF4 in N2B27 + 1 μg/ml heparin for 6 h

value: 40 ng/ml FGF


title: mESCs, stimulated, 6h 10 ng/ml FGF4

value: 10 ng/ml FGF


title: Fgf4 mutant mESCs, stimulated with 40 ng/ml FGF4 for 6h, clone 1, rep3

data_processing:
Alignment to genome with hisat2, version 2.1.0
Probe definition using RNA-seq quantitation pipeline in Seqmonk, version 1.48.1. Parameters: Transctipt features mRNA; Library type Non-strand specific; Libraries are paired end TRUE; Merge transcript isoforms TRUE; Generate Raw Counts TRUE; all others: FALSE
Read count quantification using Read Count Quantification in Seqmonk, version 1.48.1. Parameters for Raw Counts: Count reads on strand: All Reads; Correct for total read count FALSE; Correct for probe length FALSE; Log Transform Count FALSE; Count duplicated reads only once FALSE
Parameters for TPMs: Count reads on strand: All Reads; Correct for total read count TRUE; Correct to what? Per Million Reads; Count total only within probes FALSE; Correct for probe length FALSE; Log Transform Count FALSE; Count duplicated reads only once FALSE
TPMs filtered for features with a raw count above 50 in one of the samples
Assembly: GRCm39, release 108
Supplementary files format and content: All_Probes_Raw_Counts.txt: Contains raw counts per sample (columns) for each gene (rows) including gene information (e.g. genomic location, strand, ID, etc.)
Supplementary files format and content: Probes_with_raw_count>50_TPMs.txt: Contains log2(TPMs) per sample (columns) for each gene with over 50 raw counts over all samples (rows) including gene information (e.g. genomic location, strand, ID, etc.)

growth_protocol: 55k cells/cm2 of Fgf4-mutant cells and Fgf4 Med12 double-mutant cells were seeded into N2B27 + Chiron + LIF and grown for 18h.

extract_protocol:
Trizol-based total RNA extraction
Poly-A-enriched

treatment_protocol: Stimulation with or without 40 ng/ml FGF4 in N2B27 + 1 μg/ml heparin for 6 h.

value: N2B27 + 40 ng/ml FGF4


title: mESCs, stimulated, 6h 20 ng/ml FGF4

value: 20 ng/ml FGF


title: mESCs, stimulated, 6h 1.25 ng/ml FGF4

value: mESCs

value: 1.25 ng/ml FGF


title: mESCs, stimulated, 6h 5 ng/ml FGF4

value: 5 ng/ml FGF


title: Fgf4 mutant mESCs, stimulated with 40 ng/ml FGF4 for 6h, clone 1, rep2


title: Fgf4 Med12 double mutant mESCs, unstimulated, clone 3, rep1


title: Fgf4 mutant mESCs, unstimulated, clone 1, rep1


title: mESCs, unstimulated

value: 0 ng/ml FGF


title: Fgf4 Med12 double mutant mESCs, stimulated with 40 ng/ml FGF4 for 6h, clone 3, rep1


title: Fgf4 Med12 double mutant mESCs, stimulated with 40 ng/ml FGF4 for 6h, clone 2, rep1


title: Fgf4 Med12 double mutant mESCs, stimulated with 40 ng/ml FGF4 for 6h, clone 1, rep3


title: Fgf4 Med12 double mutant mESCs, unstimulated, clone 1, rep3


title: mESCs, stimulated, 6h 2.5 ng/ml FGF4

value: 2.5 ng/ml FGF


title: Fgf4 Med12 double mutant mESCs, stimulated with 40 ng/ml FGF4 for 6h, clone 1, rep2


title: Fgf4 Med12 double mutant mESCs, unstimulated, clone 1, rep1


title: Fgf4 mutant mESCs, unstimulated, clone 1, rep3


title: OX.NAC61_Thompson Seedless_rep2


title: KR158 DCs PD1 biol rep 5 [S21_1_val]

city: Gainesville

first: Duane

last: Mitchell

state: Florida

address: 1333 Center Drive, BSB B1-150

institute: University of Florida

description: CD45+ immune cell were selected from GBM tumor microenvironment following tissue dissociation and positive cell selection. Celero™ EZ DNA-Seq, 24 reactions kit (Tecan Genomics) was utilized to generate sequencing libraries following the manufacturer’s instructions. RNA-sequencing was performed using Illumina NovaSeq 6000, SP 2 x 50.

data_processing:
Sequence reads were trimmed and for adaptor sequence and low quality reads by trimgalore 0.6.5 (--stringency 5)
Bulk RNA seq fastq data was aligned and quantifies using RSEM 1.3.3
Read count extraction and normalization were applied using RSEM 1.3.3
Assembly: gencode.vM24_GRCm38 (mm10)
Supplementary files format and content: Processed .tsv file contains TPM values for each sample

source_name: brain tumor

extract_protocol:
RNA was extracted using Zymo mini/midi RNA extraction kit.
Celero™ EZ DNA-Seq, 24 reactions kit (Tecan Genomics) was utilized to generate sequencing libraries following the manufacturer’s instructions. RNA-sequencing was performed using Illumina NovaSeq 6000, SP 2 x 50.

value: brain tumor

value: Day 21 post implantation

value: immune cells

value: WT

value: Kluc antigen loaded DCs+ aPD-1 ab


title: Fgf4 Med12 double mutant mESCs, unstimulated, clone 1, rep2


title: Fgf4 mutant mESCs, stimulated with 40 ng/ml FGF4 for 6h, clone 1, rep1


title: immune cells mix 1

description: CD45+ immune cell were selected from GBM tumor microenvironment following tissue dissociation and positive cell selection.  The Chromium Next GEM Single Cell 3 Reagent Kits v3.1 (Dual Index, 10x Genomics) was utilized to construct the cDNA sequencing libraries. The samples were multiplexed and prepared as per the manufacturer's instructions and sequenced by Illumina Novaseq 6000.

data_processing:
BCL files were demultiplexed to fastq data using Cellranger 7.0 makefastq and were aligned to a customized Luciferase-mm10 mouse genome and counted using Cellranger 7.0 multi. Cells were further demultiplexed using Seurat 4.0 HTOdemux.
Cells with over than 250 genes, 500 UMIs, 0.8 Complexity (log10 gene counts/ log10 UMI count), and less than 5% mitochondrial genes were selected using Seurat 4.0.
SingleR with built-in Immgen dataset was applied for cell type identification.
Assembly: gencode.vM24_GRCm38 (mm10)
Supplementary files format and content: Processed files contains demultiplexing barcode information and gene expression for each sample. The files for samples immune cells mix 1, 2, and 3 are the same and processed into one.
Supplementary files format and content: The files for samples immune cells mix 1, 2, and 3 are the same and processed into one.

extract_protocol:
RNA was extracted using Zymo mini/midi RNA extraction kit.
Chromium Next GEM Single Cell 3 Reagent Kits v3.1 (Dual Index, 10x Genomics) was utilized to construct the cDNA sequencing libraries. The samples were multiplexed and prepared as per the manufacturer's instructions and sequenced by Illumina Novaseq 6000.


title: immune cells mix 2


title: immune cells mix 3


title: tumor cells mix

value: tumor cells and normal brain cellss


title: Fgf4 Med12 double mutant mESCs, stimulated with 40 ng/ml FGF4 for 6h, clone 1, rep1


title: KR158 DCs PD1 biol rep 3 [S19_1_val]


title: KR158 DCs PD1 biol rep 2 [S18_1_val]


title: KR158 DCs PD1 biol rep 4 [S20_1_val]


title: KR158 DCs IgG biol rep 4 [S16_1_val]

value: Kluc antigen loaded DCs+ IgG ab


title: KR158 DCs PD1 biol rep 1 [S17_1_val]


title: KR158 DCs IgG biol rep 3 [S15_1_val]


title: Fgf4 Med12 double mutant mESCs, unstimulated, clone 2, rep1


title: Ctrl DCs PD1 biol rep 3 [S11_1_val]

value: unloaded DCs+ aPD-1 ab


title: Ctrl DCs PD1 biol rep 2 [S10_1_val]


title: Ctrl DCs PD1 biol rep 4 [S12_1_val]


title: Ctrl DCs IgG biol rep 3 [S7_1_val]

value: unloaded DCs + IgG ab


title: Ctrl DCs IgG biol rep 4 [S8_1_val]


title: Ctrl DCs IgG biol rep 2 [S6_1_val]


title: Ctrl DCs IgG biol rep 1  [S5_1_val]


title: KR158 DCs IgG biol rep 1 [S13_1_val]


title: Ctrl DCs PD1 biol rep 1 [S9_1_val]


title: Untreated biol rep 4 [S4_1_val]


title: Untreated biol rep 3 [S3_1_val]


title: Untreated biol rep 2 [S2_1_val]


title: Untreated biol rep 1 [S1_1_val]


title: GL261 DCs PD1 biol rep 5 [GP 5]

value: GL261 antigen loaded DCs+ aPD-1 ab


title: GL261 DCs PD1 biol rep 2 [GP 2]


title: GL261 DCs PD1 biol rep 4 [GP 4]


title: GL261 DCs PD1 biol rep 1 [GP 1]


title: KR158 DCs IgG biol rep 2 [S14_1_val]


title: GL261 DCs IgG biol rep 4 [GI 4]

value: GL261 antigen loaded DCs+ IgG ab


title: GL261 DCs IgG biol rep 3 [GI 3]


title: Ctrl DCs PD1 biol rep 5 [CP 5]


title: Ctrl DCs PD1 biol rep 3 [CP 3]


title: GL261 DCs IgG biol rep 1 [GI 1]


title: GL261 DCs IgG biol rep 2 [GI 2]


title: Ctrl DCs IgG biol rep 6 [CI 6]


title: Ctrl DCs PD1 biol rep 2 [CP 2]


title: Ctrl DCs IgG biol rep 2 [CI 2]


title: Ctrl DCs IgG biol rep 1 [CI 1]


title: Untreated biol rep 4 [Un 4]


title: Tongue CCL28 Candida-infected_rep2

city: Milwaukee

first: Anna

middle: R

last: Huppler

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

description:
deseq/Differential_Expression__DESeq2__compare_2_groups__on_CCL28_Infected_on_CCL28_Sham.diffexpr.w_symbols.txt
deseq/Differential_Expression__DESeq2__compare_2_groups__on_CCL28_Infected_on_WT_infected.diffexpr.w_symbols.txt

data_processing:
(1) Remove reads containing adapters.
(2) Remove reads containing N > 10% (N represents the base cannot be determined).
(3) Remove reads containing low quality (Qscore<= 5) base which is over 50% of the total base.
Original image data file from high-throughput sequencing is transformed into sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw data are stored in FASTQ(fq) format files, which contain sequences of reads and corresponding base quality
Genome_build: mm10

source_name: tongue

extract_protocol:
tongues were removed, flash frozen on dry ice, and RNA was harvested using Qiagen Rneasy mini kit. The concentration was measured with Nanodrop 2000c. RNA samples then were sent on dry ice to Novogene for library preparation and sequecing. Contract ID is H202SC20072776 . Batch ID is X202SC20072776-Z01-F001. Illumina TruSeq RNA Sample Prep Kit (Cat# FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
After enrichment, mRNAs are fragmented randomly in fragmentation buffer and the first-strand cDNA is synthesized using random hexamer primers and M-MuLV Reverse Transcriptase (RNase H-). The second strand is subsequently generated by dNTPs, DNA polymerase I and RNase H. Double-stranded cDNA molecules are purified by AMPure XP beads and overhanging ends are repaired to blunt ends by exonuclease/polymerase. After 5’ phosphorylation and 3’ adenylation, the cDNAs are ligated with P5/P7 sequencing adapters to prepare for hybridization. In order to select the insert fragment of preferentially 150~200 bp in length, the modified libraries are purified with AMPure XP system (Beckman Coulter, Beverly, USA). The final library is ready after PCR amplification and products purification by AMPure XP beads.

tag: infection

value: Candida albicans, strain CAF2-1

tag: day after infection

value: whole tongue


title: Tongue CCL28 Candida-infected_rep1

tag: tissue


title: Tongue CCL28 Candida-infected_rep3


title: Tongue CCL28 Candida-infected_rep4


title: Untreated biol rep 3 [Un 3]


title: Untreated biol rep 2 [Un 2]


title: Untreated biol rep 1 [Un 1]


title: Tongue CCL28 sham-infected_rep3

description:
deseq/Differential_Expression__DESeq2__compare_2_groups__on_CCL28_Infected_on_CCL28_Sham.diffexpr.w_symbols.txt
deseq/Differential_Expression__DESeq2__compare_2_groups__on_CCL28_Sham_on_WT_Sham.diffexpr.w_symbols.txt

value: sham


title: Tongue CCL28 sham-infected_rep4


title: Tongue CCL28 sham-infected_rep1


title: Tongue CCL28 sham-infected_rep2


title: RNAseq,TamPos,E15.5,EC,rep3

data_processing:
RNA-seq mapping and quantitation was done using STAR v. 2.6.147 with a hg38 STAR index.
The mapped reads were further analyzed by HTSeq-count v.0.11.2 and annotated using a RefSeq database.
The reads count were normalized by DEseq2
Assembly: mm10
Supplementary files format and content: tab-delimited text files include normalized readscount values for each Sample

extract_protocol:
Cellular samples were treated with TRIzol reagent then total RNA was purified with RNA Clean & Concentrator-5 Kit (Zymo). Genomic DNA disgestion was performed with Dnase I on column treatment.
Completely followed the protocol of NEBNext Ultra II RNA Library Prep Kit for use with NEBNext rRNA Depletion Kit v2.

value: whole embryo

value: Endothelial cell

value: wild type

value: tamoxifen gavage


title: L5327

data_processing:
Raw RNA-seq data was processed by the RNA-seq BioWDL pipeline using default settings, developed by the SASC (https://biowdl.github.io/, LUMC, Leiden, the Netherlands)
Reads were aligned against hg38 with STAR and expression quantification was performed using HTseq-count
Assembly: hg38
Supplementary files format and content: Tab-delimited tsv file with raw counts for each sample

source_name: bulk tumour

extract_protocol:
RNA was isolated from tissue sections (thickness = 20 µm) in TRIzol (15596018, Ambion) according to manufacturer’s instructions. RNA purification was performed using RNaesy mini kit (74104, Qaigen) and included DNAse treatment according to manufacturer’s instructions
The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina was used to process the samples.

tag: disease

value: Chordoma

value: bulk tumour

tag: anatomical location

value: Sacrococcygeal

tag: neoadjuvant radiotherapy

value: Yes


title: RNAseq,TamPos,E15.5,EC,rep4

tag: cell type

tag: genotype