title: H1, D, day 13, biol repl 3, run 1

description: 10x Genomics


title: 177, M, day 40, biol repl 1, run 2

status: Public on Nov 20 2024

type: SRA

city: Vienna

first: Julia

last: Naas

address: Dr. Bohr Gasse 9

department: Max Perutz Labs

country: Austria

institute: University of Vienna

description: 10x Genomics

library_source: transcriptomic

data_processing:
Sequencing was performed on Illumina NextSeq High Output 75 cycle lanes and Illumina Novaseq S1 100 cycle lanes and reads combined. Reads were preprocessed using umi2index (Lexogen) to add the UMI sequence to the read identifier, and trimmed using BBDuk v38.06 (ref=polyA.fa.gz,truseq.fa.gz k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20). Reads mapping to abundant sequences included in the iGenomes UCSC hg38 reference (human rDNA, human mitochondrial chromosome, phiX174 genome, adapter) were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCh38/hg38 assembly obtained from Homo sapiens Ensembl release 94. Reads were aligned to the genome using star v2.6.0c, alignments were processed using collapse_UMI_bam (Lexogen) and reads in genes were counted with featureCounts (subread v1.6.2) using strand-specific read counting (-s 1).
Assembly: GRCh38
Supplementary files format and content: sample-wise RDS files: raw counts (rows: genes)

molecule: total RNA

organism: Homo sapiens

source_name: brain organoid tissue

extract_protocol:
RNA samples were extracted from organoids collected in Buffer RLT (Qiagen, cat. # 79216) using the RNA isolation kit provided by VBC core facilities. The kit uses carboxylate-modified Sear-Mag Speed beads and was applied using the Kingfisher instrument (Thermo).
Lexogen’s Quantseq kit was used, including the UMI extension (Lexogen, cat# 015.384, 081.96). All kits were used according to manufacturers’ instructions.

tag: tissue

value: brain organoid tissue

tag: cell line

value: Human induced pluripotent stem cell (HipSci) line SCCF-177J clone#8 (177)

tag: Sex

value: female

tag: time

value: day 40

tag: treatment

value: midbrain protocol (M)


title: dcm-/dam- lambda phage DNA [LMD_dC]

city: Munich

first: Raheleh

last: Salehi

state: Bavaria

address: Würmtalstraße 201

department: Chemisty

country: Germany

institute: LMU

library_source: genomic

data_processing:
css-reads.bam data processing step:  call hifi reads with kenetics from ccsmeth package
extract_features.tsv processing step: call extract with kenetics from ccsmeth package
modification_frequency.bed processing step: call modification frequency with kenetics from ccsmeth package
Assembly: GCF_000840245.1_ViralProj14204_genomic
Supplementary files format and content: extract_features.tsv, TSV-files format, containing kmer sequence, poylmerase kenetics i.e. IPD and PWD from DNA forward and reverse strands
Supplementary files format and content: modification_frequency.bed, bedMethy file containing location, coverage and methylation frequency of a given CpG
Library strategy: Pacbio Sequel IIe Hifi-Sequencing

molecule: genomic DNA

organism: Escherichia phage Lambda

source_name: phage

growth_protocol: unmodifed DNA was obtained from whole-genome amplification of lambda DNA/genome.

extract_protocol:
Lambda DNA dcm-/dam- was purchased from Thermo Fisher, catalog number: SD0021
Libraries for the Sequel IIe were prepared according to PacBio's SMRTbell express template prep kit 2.0 (PN: 100-938-900). Briefly, for DNA-repair and A-tailing, 300 ng - 1 µg DNA (1 kb) in 46 µl nuclease free water, 8 µl repair buffer, 4 µl end repair mix and 2 µl DNA repair mix were mixed by pipetting and incubated at 30°C for 30 min. The reaction was inactivated by incubating at 65°C for 5min. Next, 4 µl SMRTbell barcoded adapter (Barcoded overhang adapter kit 8B, PN: 101-628-500), 30 µl ligation mix and 1 µl ligation enhancer were mixed by pipetting. 31µl of the ligation mix was directly added to the A-tailed DNA. The reaction was incubated for 30 min at 20°C and subsequently purified using SMRTbell cleanup beads. Non-SMRTbell-DNA was depleted by nuclease treatment. The concentration of the final library was determined using the Qubit dsDNA-HS-Assay-Kit (ThermoFisher: cat. no. Q32851).

treatment_protocol: WGA DNA was either kept unmodifed, or subjected to M.SssI methylation for the generation of a mdC model genome (mdC in CpG context) or subjected to M.SssI + hpTet3 treatment for the generation of a cadC model genome (cadC in CpG context).

value: phage

value: Control


title: D53_1input

city: Xi`an

first: Chen

middle: Hao

last: Ren

state: Shannxi

address: No. 620, West Chang'an Street, Chang'an District, Xi'an City

department: College of Life Sciences

country: China

institute: Shannxi Normal University

data_processing:
Data preprocessing. Remove the junction sequence, contamination sequence, and low-quality bases to obtain clean data sequence, and conduct relevant data statistics
Clean data is located on the reference genome, resulting in a BAM file, which is then de-duplicated and retained as a unique a sequence for comparison
Perform peak detection on the BAM file to obtain information about the enriched region, and perform peak mapping on the gene function.Distribution of functional elements, recent gene search and motif prediction.
Statistical analysis of the distribution of peaks, GO and KEGG functional annotation and enrichment of the most recent gene in the peak,transcription factor prediction, etc.
Assembly: Gossypium_hirsutum_v2.1

organism: Gossypium hirsutum

source_name: leaves

extract_protocol:
Chromatin immunoprecipitation assays were performed according to the previously described by Wuhan IGENEBOOK Biotechnology Co.,Ltd (http://www.igenebook.com) . Briefly, XXX g samples were washed twice in cold PBS buffer and cross-linked with 1% formaldehyde for 10 minutes at room temperature and then quenched by addition of glycine (125 mmol/L final concentration) .Afterwards, samples were lysed with 50mM Tris-HCl (pH 8.0), 10mM EDTA, 1%SDS, 1×protease inhibitor cocktail, and chromatins were obtained on ice. Chromatins were sonicated to get soluble sheared chromatin (average DNA length of 200–500 bp). 20ul chromatin was saved at –20°C for input DNA, and 100ul chromatin was used for immunoprecipitation. 10 μg of antibody was used in the immunoprecipitation reactions at 4 °C overnight. The next day, 30 μL of protein beads was added and the samples were further incubated for 3 h. The beads were next washed once with 20 mM Tris/HCL (pH 8.1), 50 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS; twice with 10 mM Tris/HCL (pH 8.1), 250 mM LiCl, 1 mMEDTA, 1% NP-40, 1% deoxycholic acid; and twice with TE buffer 1× (10 mM Tris-Cl at pH 7.5. 1 mM EDTA). Bound material was then eluted from the beads in 300 μL of elution buffer (100 mM NaHCO3, 1% SDS), treated first with RNase A (final concentration 8 μg/mL) during 6 h at 65°C and then with proteinase K (final concentration 345 μg/mL) overnight at 45°C
Immunoprecipitated DNA was used to construct sequencing libraries following the protocol provided by the I NEXTFLEX® ChIP-Seq Library Prep Kit for Illumina® Sequencing（NOVA-5143-02，Bioo Scientific） and sequenced on Illumina Novaseq 6000 with PE 150 method.

value: leaves

value: control DNA

tag: chip-antibody

value: flag


title: 178, V, day 120, biol repl 3, run 1

description: 10x Genomics

value: Human induced pluripotent stem cell (HipSci) line SCCF-178J clone#5 (178)

value: male

value: day 120

value: ventral protocol (V)


title: 178, V, day 80, biol repl 3, run 1

description: 10x Genomics

value: day 80


title: D53_1ip

value: DNA from each immunoprecipitated sample


title: 177, M, day 120, biol repl 1, run 2

description: 10x Genomics


title: 178, V, day 25, biol repl 3, run 1

description: 10x Genomics

value: day 25


title: 177, M, day 80, biol repl 1, run 2

description: 10x Genomics

value: brain organoid tissue


title: 178, V, day 13, biol repl 3, run 1

description: 10x Genomics

value: day 13


title: 177, D, day 120, biol repl 1, run 2

description: 10x Genomics

value: Human induced pluripotent stem cell (HipSci) line SCCF-177J clone#8 (177)

value: female

value: dorsal protocol (D)


title: 177, D, day 80, biol repl 1, run 2

description: 10x Genomics


title: B_2ip


title: 178, pluripotent, day 0, biol repl 3, run 1

description: 10x Genomics

value: day 0


title: 177, M, day 16, biol repl 1, run 2

description: 10x Genomics

value: day 16

value: midbrain protocol (M)


title: 178, M, day 40, biol repl 3, run 1

description: 10x Genomics

value: day 40


title: 177, D, day 40, biol repl 1, run 2

description: 10x Genomics


title: 178, V, day 40, biol repl 3, run 1

description: 10x Genomics


title: 177, D, day 25, biol repl 1, run 2

description: 10x Genomics


title: KO2

city: Suzhou

first: Rui

middle: xing

last: Hou

state: Jiangsu

address: No.5, Tayun Road, Wuzhong District

department: Key Laboratory of Hand Surgery

institute: Suzhou Ruihua Orthopedic Hospital

data_processing:
The raw sequencing data was filtered with SOAPnuke to obtain clean data.
Expression levels of genes were calculated by RSEM (v1.3.1).
Assembly: Mus_musculus, NCBI GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

organism: Mus musculus

source_name: epidermal stem cells

growth_protocol: Epidermal stem cells were isolated from the skin of Angptl4 knockout (KO) and wild-type (WT) mice and cultured with KGM2 in a 37℃, 5% CO2 incubator.

extract_protocol:
Total RNA was extracted from Angptl4 KO and WT EpSCs using TRIzol reagent (Invitrogen).
RNA libraries for RNA-seq were prepared by BGI Genomics Co. Ltd (Shenzhen, China).

tag: strain

tag: genotype

value: Angptl4 knockout

tag: cell type

value: epidermal stem cells

value: Male

value: 8 weeks


title: B_2input

value: leaves

value: control DNA

value: flag


title: 178, D, day 120, biol repl 3, run 1

description: 10x Genomics

value: Human induced pluripotent stem cell (HipSci) line SCCF-178J clone#5 (178)

value: male

value: day 120


title: 178, M, day 80, biol repl 3, run 1

description: 10x Genomics

value: brain organoid tissue

value: day 80


title: KO1


title: 178, M, day 16, biol repl 3, run 1

description: 10x Genomics


title: 178, S, day 16, biol repl 3, run 1

description: 10x Genomics

value: striatum protocol (S)


title: 178, D, day 40, biol repl 3, run 1

description: 10x Genomics

value: dorsal protocol (D)


title: 176, V, day 120, biol repl 1, run 2

description: 10x Genomics

value: Human induced pluripotent stem cell (HipSci) line SCCF-176J clone#1 (176)

value: female

value: ventral protocol (V)


title: 178, D, day 25, biol repl 3, run 1

description: 10x Genomics

value: day 25


title: 177, D, day 13, biol repl 1, run 2

description: 10x Genomics

value: Human induced pluripotent stem cell (HipSci) line SCCF-177J clone#8 (177)

value: day 13


title: WT2

value: wild type

value: epidermal stem cells

value: Male

value: 8 weeks


title: 177, V, day 120, biol repl 3, run 1

description: 10x Genomics


title: 176, V, day 40, biol repl 1, run 2

description: 10x Genomics

value: day 40


title: 177, V, day 80, biol repl 3, run 1

description: 10x Genomics


title: WT1


title: 176, V, day 80, biol repl 1, run 2

description: 10x Genomics


title: 177, V, day 40, biol repl 3, run 1

description: 10x Genomics


title: WT3


title: KT2440-NYL_Ahx, rep2

city: Jülich

first: Tom

last: Luthe

address: Wilhelm-Johnen-Strasse

institute: Forschungszentrum Jülich

data_processing:
CLC Genomics Workbench v 20.0.4
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomics workbench (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to the P. putida YA101 genome using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.9 similarity fraction: 0.9)
Read count extraction and normalization were performed using CLC genomics workbench
Assembly: P. putida YA101
Supplementary files format and content: tab-delimited txt file includes TPM values for each sample

organism: Pseudomonas putida

source_name: bacterial

growth_protocol: Strains of P. putida were pre-cultured in MSM with adpic acid (AA) or 6-aminohexanoic acid (Ahx) for 16 h

extract_protocol:
RNA was extracted using the Quick-RNA Microprep Kit (Zymo Research)
Library was constructed by Genewiz, Germany

treatment_protocol: Fresh cultures were inoculated with a starting OD600 of 0.1 and harvested after entering the mid-exponential phase

value: bacterial


title: 176, V, day 25, biol repl 1, run 2

description: 10x Genomics


title: 177, V, day 13, biol repl 3, run 1

description: 10x Genomics


title: 178, D, day 13, biol repl 3, run 1

description: 10x Genomics

value: Human induced pluripotent stem cell (HipSci) line SCCF-178J clone#5 (178)

value: male


title: 177, S, day 120, biol repl 3, run 1

description: 10x Genomics

value: brain organoid tissue

value: day 120


title: KT2440-NYL_Ahx, rep1


title: 177, V, day 25, biol repl 3, run 1

description: 10x Genomics


title: 178, M, day 120, biol repl 3, run 1

description: 10x Genomics

value: midbrain protocol (M)


title: 177, S, day 16, biol repl 3, run 1

description: 10x Genomics

value: day 16

value: striatum protocol (S)


title: 177, pluripotent, day 0, biol repl 3, run 1

description: 10x Genomics

value: female

value: day 0


title: 176, S, day 120, biol repl 1, run 2

description: 10x Genomics

value: Human induced pluripotent stem cell (HipSci) line SCCF-176J clone#1 (176)


title: 176, V, day 13, biol repl 1, run 2

description: 10x Genomics

value: day 13

value: ventral protocol (V)


title: 177, M, day 120, biol repl 3, run 1

description: 10x Genomics

value: Human induced pluripotent stem cell (HipSci) line SCCF-177J clone#8 (177)


title: KT2440-NYL_AA, rep2


title: 176, S, day 80, biol repl 1, run 2

description: 10x Genomics

value: day 80


title: 177, M, day 16, biol repl 3, run 1

description: 10x Genomics


title: 176, S, day 40, biol repl 1, run 2

description: 10x Genomics


title: 177, M, day 40, biol repl 3, run 1

description: 10x Genomics


title: 177, M, day 80, biol repl 3, run 1

description: 10x Genomics


title: PP_2884∆3_Ahx, rep2


title: 177, D, day 120, biol repl 3, run 1

description: 10x Genomics

value: dorsal protocol (D)


title: PP_2884∆3_Ahx, rep1


title: 177, D, day 40, biol repl 3, run 1

description: 10x Genomics

value: day 40


title: 177, D, day 25, biol repl 3, run 1

description: 10x Genomics

value: day 25


title: PP_2884∆3_AA, rep2

value: bacterial


title: 176, pluripotent, day 0, biol repl 1, run 2

description: 10x Genomics


title: 177, D, day 80, biol repl 3, run 1

description: 10x Genomics


title: 177, D, day 13, biol repl 3, run 1

description: 10x Genomics


title: 176, V, day 80, biol repl 3, run 1

description: 10x Genomics


title: 176, S, day 16, biol repl 1, run 2

description: 10x Genomics


title: 176, V, day 40, biol repl 3, run 1

description: 10x Genomics


title: 176, S, day 120, biol repl 3, run 1

description: 10x Genomics


title: 176, M, day 40, biol repl 1, run 2

description: 10x Genomics


title: 176, M, day 16, biol repl 1, run 2

description: 10x Genomics


title: 176, S, day 40, biol repl 3, run 1

description: 10x Genomics


title: 176, S, day 16, biol repl 3, run 1

description: 10x Genomics


title: 176, M, day 80, biol repl 1, run 2

description: 10x Genomics


title: 176, D, day 80, biol repl 1, run 2

description: 10x Genomics


title: 176, M, day 40, biol repl 3, run 1

description: 10x Genomics


title: 176, M, day 80, biol repl 3, run 1

description: 10x Genomics


title: Donor16, SIC, RNA-seq

city: wuhan

first: Mingjie

last: Li

address: union hospital

institute: Huazhong University of Science and Technology

description: H20-1A, H20-4A

data_processing:
For RNA-seq analysis, the raw sequencing data were filtered with SOAPnuke (v1.4.0) to obtain clean data in FASTQ format and then mapped to the reference genome using HISAT (v2.1.0). The clean data were mapped to the assembled unique gene by Bowtie2 (v2.2.5), and the expression level of genes was calculated by RSEM (v1.2.8). Differential expression analysis was performed using DESeq with a Q value corrected (Q value < 0.05) by Bonferroni correction. The Dr.Tom online platform of BGI was used for data analysis (https://biosys.bgi.com).
Assembly: mm10
Supplementary files format and content: tab-delimited text fles include FPKM values for each Sample

source_name: PBMCs

extract_protocol:
Human PBMC samples were lysed with TRIzol reagent (Invitrogen, CA, USA) and sent for transcriptome sequencing in liquid nitrogen (BGI, Shenzhen, China). Total RNA was extracted from PBMC. RNA quantification and integrity were measured by an Agilent 2100 Bioanalyzer (Agilent RNA 6000 Nano Kit).
The mRNA was purified using oligo (dT) -attached magnetic beads and DNA probes to eliminate contamination from other nucleic acids. The mRNA was then fragmented and reverse transcribed into cDNA for the construction of the final library. The RNA-seq libraries were prepared for sequencing at BGI Genomics (Shenzhen, China).

value: PBMCs

value: SIC

value: SCRT followed by immunochemotherapy


title: 176, V, day 13, biol repl 3, run 1

description: 10x Genomics

value: brain organoid tissue


title: PP_2884∆3_AA, rep1


title: 176, V, day 120, biol repl 3, run 1

description: 10x Genomics

value: day 120


title: 176, M, day 120, biol repl 1, run 2

description: 10x Genomics

value: midbrain protocol (M)


title: Donor15, SIC, RNA-seq

description: H16-1A, H16-4A


title: 176, D, day 40, biol repl 1, run 2

description: 10x Genomics

value: female


title: 176, pluripotent, day 0, biol repl 3, run 1

description: 10x Genomics

value: day 0


title: 176, D, day 120, biol repl 3, run 1

description: 10x Genomics

value: Human induced pluripotent stem cell (HipSci) line SCCF-176J clone#1 (176)


title: Donor14, SIC, RNA-seq

description: H11-1A, H11-4A


title: 176, M, day 120, biol repl 3, run 1

description: 10x Genomics


title: 176, M, day 16, biol repl 3, run 1

description: 10x Genomics

value: day 16


title: 176, D, day 80, biol repl 3, run 1

description: 10x Genomics


title: 178, D, day 80, biol repl 3, run 1

description: 10x Genomics

value: Human induced pluripotent stem cell (HipSci) line SCCF-178J clone#5 (178)

value: male


title: Organoid_PAAD_meta_liver_2_v2

type: genomic

city: Berlin

first: Mihnea

middle: P.

last: Dragomir

state: Berlin

address: 1 Charitéplatz

department: Pathology

institute: Charité - Universitätsmedizin

hyb_protocol: Samples were hybridized to Infinium Human Methylation EPIC BeadChips (Illumina) v1 and v2 according to the manufacturer’s protocol.

scan_protocol: Arrays were scanned on Iscan (Illumina)

data_processing: We performed FunNorm (Minfi R package) and BMIQ (WateRmelon R package) normalization. We filtered probes non-cg probes, probes corresponding to SNPs, probes that align to multiple locations, and probes on sex chromosomes.

label: Cy5 and Cy3

source_name: Organoid PAAD metastasis in the liver

label_protocol: Supplier protocol (Illumina)

extract_protocol: Semi-automated DNA extraction was performed according to the manufacturer’s instructions (Maxwell RSC FFPE Plus DNA Purification Kit, Custom, Promega)

tag: tissue type

value: organoid

tag: illumina methylation epic assay version


title: 176, D, day 25, biol repl 1, run 2

description: 10x Genomics

value: dorsal protocol (D)


title: Donor12, SIC, RNA-seq

description: H8-1A, H8-4A


title: 176, D, day 40, biol repl 3, run 1

description: 10x Genomics

value: day 40


title: 176, V, day 25, biol repl 3, run 1

description: 10x Genomics

value: day 25

value: ventral protocol (V)


title: Donor13, SIC, RNA-seq

description: H9-1A, H9-4A

value: PBMCs


title: 176, D, day 13, biol repl 1, run 2

description: 10x Genomics

value: day 13


title: 176, D, day 13, biol repl 3, run 1

description: 10x Genomics


title: XUJA_2, V, day 120, biol repl 2, run 1

description: 10x Genomics

value: Human induced pluripotent stem cell (HipSci) line Xuja_2


title: 176, D, day 25, biol repl 3, run 1

description: 10x Genomics

value: brain organoid tissue


title: Donor11, SIC, RNA-seq

description: H2-1A, H2-4A

value: SIC

value: SCRT followed by immunochemotherapy


title: Donor10, SIC, RNA-seq

description: H35-1A, H35-4A


title: XUJA_2, V, day 25, biol repl 2, run 1

description: 10x Genomics

value: female


title: 176, D, day 120, biol repl 1, run 2

description: 10x Genomics

value: day 120


title: Donor8, SIC, RNA-seq

description: H18-1A, H18-4A


title: XUJA_2, V, day 80, biol repl 2, run 1

description: 10x Genomics

value: day 80


title: XUJA_2, V, day 13, biol repl 2, run 1

description: 10x Genomics


title: KT2440-NYL_AA, rep1

value: bacterial


title: XUJA_2, S, day 120, biol repl 2, run 1

description: 10x Genomics

value: striatum protocol (S)


title: Donor7, SIC, RNA-seq

description: H14-1A, H14-4A


title: XUJA_2, S, day 80, biol repl 2, run 1

description: 10x Genomics


title: XUJA_2, V, day 40, biol repl 2, run 1

description: 10x Genomics


title: Donor9, SIC, RNA-seq

description: H22-1A, H22-4A


title: XUJA_2, S, day 40, biol repl 2, run 1

description: 10x Genomics


title: Donor6, SIC, RNA-seq

description: H12-1A, H12-4A


title: P22

city: Oklahoma City

first: Chao

last: Xu

state: Oklahoma

address: 801 N. E. 13th Street

department: Biostatistics and Epidemiology

country: USA

institute: University of Oklahoma Health Sciences Center

data_processing:
Human mRNA sequencing of the samples was performed using NovaSeq-PE150 (Novogene, Sacramento, CA) with 40M reads. The raw sequencing data has been quality controlled by removing reads based on adapter sequences, low quality nucleotides (base quality less than 5) constitute more than 50 percent of the read, and   uncertain nucleotides constitute more than 10 percent of either read (N > 10%).
The reads passed quality control were aligned to reference genome (hg38) using HISAT2.
Gene expression level was estimated by FPKM  (the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced).
Assembly: GRCh38 (hg38)
Supplementary files format and content: Excel file with genes in rows and read counts for subjects in columns. Gene name, location, and decription were added as additional columns.
Supplementary files format and content: Excel file with genes in rows and FPKM for subjects in columns. Gene name, location, and decription were added as additional columns.

source_name: Blood

growth_protocol: Primary chronic lymphocytic leukemia (CLL) cells were purified from CLL patients' blood and cultured in AIM-V (serum-free) media (GIBCO) as needed

extract_protocol:
Total RNA was extracted and purified using the TRIZOL method
Novogene library preparation protocol.

treatment_protocol: No treatment

value: Blood

value: Primary cells

value: B cell chronic lymphocytic leukemia cells

value: WT

tag: patient


title: P22_JAK

value: JAK2 knockdown


title: P21_JAK


title: P21


title: XUJA_2, S, day 16, biol repl 2, run 1

description: 10x Genomics

value: day 16


title: XUJA_2, pluripotent, day 0, biol repl 2, run 1

description: 10x Genomics

value: day 0


title: P63


title: Donor5, LC, RNA-seq

description: H7-1A, H7-4A

value: PBMCs

value: LC

value: LCRT sequential chemotherapy


title: XUJA_2, M, day 120, biol repl 2, run 1

description: 10x Genomics

value: brain organoid tissue

value: Human induced pluripotent stem cell (HipSci) line Xuja_2

value: midbrain protocol (M)


title: XUJA_2, M, day 80, biol repl 2, run 1

description: 10x Genomics

value: female


title: Donor4, LC, RNA-seq

description: H19-1A, H19-4A


title: XUJA_2, M, day 40, biol repl 2, run 1

description: 10x Genomics

value: day 40


title: P53


title: XUJA_2, D, day 120, biol repl 2, run 1

description: 10x Genomics

value: day 120

value: dorsal protocol (D)


title: Organoid_PAAD_meta_liver_1_v2

value: organoid


title: Donor2, LC, RNA-seq

description: H5-1A, H5-4A


title: Donor3, LC, RNA-seq

description: H13-1A, H13-4A


title: XUJA_2, D, day 40, biol repl 2, run 1

description: 10x Genomics


title: P53_JAK

value: Blood

value: Primary cells


title: XUJA_2, D, day 25, biol repl 2, run 1

description: 10x Genomics

value: day 25


title: P23

value: B cell chronic lymphocytic leukemia cells

value: WT


title: P63_JAK

value: JAK2 knockdown


title: XUJA_2, D, day 13, biol repl 2, run 1

description: 10x Genomics

value: day 13


title: ROZH_5, V, day 80, biol repl 2, run 1

description: 10x Genomics

value: Human induced pluripotent stem cell (HipSci) line Rozh_5

value: day 80

value: ventral protocol (V)


title: ROZH_5, V, day 120, biol repl 2, run 1

description: 10x Genomics

value: brain organoid tissue


title: Donor1, LC, RNA-seq

description: H4-1A, H4-4A

value: PBMCs

value: LC

value: LCRT sequential chemotherapy


title: P23_JAK


title: ROZH_5, V, day 40, biol repl 2, run 1

description: 10x Genomics

value: female

value: day 40


title: Organoid_PAAD_3_v2

source_name: Organoid primary PAAD

value: organoid


title: ADRCs, LymphREG, sample 10, scRNAseq

city: Odense M

first: Charlotte Harken

middle: Harken

last: Jensen

address: Campusvej 55

department: Clinical Biochemistry/Clinical Research

country: Denmark

institute: Odense University Hospital/University of Southern Denmark

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
BAMboozle was used to anonymize patient samples (BAM files)
Single-cell count-matrices were generated using CellRanger (version 7.2.0). First, raw data was demultiplexed using CellRanger mkfastq. Reads were aligned and counted by CellRanger count using the GRCh38 reference genome
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: subcutaneous adipose tissue

extract_protocol:
ADRCs were isolated from human lipoaspirates using an automated processing Celution® 800/IV device (Lorem Cytori Therapeutics)To enable single-cell RNA sequencing (scRNA-seq), at least 106 ADRCs from each of 10 subjects (all female) were methanol-fixed and stored at -80°C. Briefly, the cells were resuspended in 500 µl PBS with 1% BSA and 1 U/µl RNAsin PLUS RNase Inhibitor (Promega) and incubated on ice for 5 min to ensure the integrity of the RNA in the cells. The cells were passed through a 40 µm Flowmi® Cell strainer (VWR) to create a single-cell suspension. The cells were centrifuged at 400g for 3 min at 4°C, and washed in 1 ml RNase-free PBS and subsequently centrifuged at 400g for 3 min at 4°C, before the cell pellet was resuspended in 200 µl RNase-free PBS and 800 µl ice-cold methanol gently added dropwise to the cells. The cells were fixed for 30 min at -20°C and subsequently stored at -80°C until use.
Immediately following rehydration, 8,000 cells were loaded onto the 10x Genomics Chromium controller (10X Genomics). Libraries were prepared according to the instructions of the manufacturer using the 10x Genomics Single-Cell 3’ v3, Chromium Single Cell B Chip Kit, 48 runs (10X Genomics) and sequenced on an Illumina NovaSeq 6000 System (10X Genomics).

value: subcutaneous adipose tissue

value: adipose derived regenerative cells/stromal vascular fraction

tag: age

value: adult


title: ROZH_5, V, day 13, biol repl 2, run 1

description: 10x Genomics


title: PAAD_meta_lymph_node_V2

source_name: PAAD metastasis lymph node, technical cohort

value: metastasis


title: ROZH_5, V, day 25, biol repl 2, run 1

description: 10x Genomics

value: day 25


title: Faslpr4

city: Shanghai

first: Yingying

last: Luan

address: 130 Dong'an road

institute: Fudan University

data_processing:
The raw data was filtered with SOAPnuke (v1.6.5)Removing reads containing adapters (adapter contamination); 2) Removing reads whose unknown base ('N' base) ratio is more than 1%; 3) Removing reads whose low-quality base ratio (Base quality less than or equal to 15) is more than 40%, afterwards clean reads were obtained and stored in FASTQ format.
The clean data were mapped to the reference genome by HISAT (v2.2.1)
The clean data were mapped to the assembled unique gene by Bowtie2 (v2.4.5)
The expression level of genes was calculated by RSEM (v1.3.1)
Assembly: GCF_000001635.27_GRCm39
Supplementary files format and content: gene_expression.txt

source_name: B220+CD3+ cells, spleen

extract_protocol:
Total RNA was extracted from tissues using TRIzol (Invitrogen, Carlsbad, California, USA) according to manual instruction.
RNA Library Preparation (DNBSEQ) used optimal Dual-mode mRNA Library Prep Kit according to manufacturer's protocols

value: B220+CD3+ cells, spleen


title: ROZH_5, S, day 120, biol repl 2, run 1

description: 10x Genomics

value: day 120

value: striatum protocol (S)


title: ADRCs, LymphREG, sample 09, scRNAseq

description: 10x Genomics


title: XUJA_2, M, day 16, biol repl 2, run 1

description: 10x Genomics

value: Human induced pluripotent stem cell (HipSci) line Xuja_2

value: day 16

value: midbrain protocol (M)


title: Organoid_PAAD_2_v2


title: PAAD_meta_peritoneal_carcinomatosis_V2

source_name: PAAD metastasis peritoneum, technical cohort


title: ROZH_5, S, day 40, biol repl 2, run 1

description: 10x Genomics

value: brain organoid tissue

value: Human induced pluripotent stem cell (HipSci) line Rozh_5


title: ROZH_5, S, day 80, biol repl 2, run 1

description: 10x Genomics

value: day 80


title: ADRCs, LymphREG, sample 08, scRNAseq

description: 10x Genomics

value: female


title: Faslpr1


title: ROZH_5, pluripotent, day 0, biol repl 2, run 1

description: 10x Genomics

value: day 0


title: ADRCs, LymphREG, sample 07, scRNAseq

description: 10x Genomics


title: Faslpr2


title: ROZH_5, M, day 120, biol repl 2, run 1

description: 10x Genomics


title: EAF2Faslpr4


title: EAF2Faslpr3


title: ADRCs, LymphREG, sample 06, scRNAseq

description: 10x Genomics


title: PAAD_meta_spleen_V2

source_name: PAAD metastasis spleen, technical cohort


title: Faslpr3


title: ADRCs, LymphREG, sample 05, scRNAseq

description: 10x Genomics


title: P969

city: COLUMBIA

first: HAO

last: JI

state: SC

address: 715 SUMTER ST CLS RM 109

department: College of Pharmacy

institute: University of South Carolina

data_processing:
Indexed sequences were checked quality by Fastqc
Indexed sequences were trimmed adaptor sequence by TrimGalore-0.4.5
Sequences were aligned to the Sus scrofa reference genome 11.1 (GCA_000003025.6) using STAR v2.7.2b with default parameters (generation of sam files)
Convert .sam files to .bam files using samtools | version: 1.5 with parameters -bh -F 3840 -q 255
Read counts over annotated genes were obtained using featureCount (subreads | version: 1.5.3) with parameters -p -B -M -O --fraction -T 10
Assembly: Sus_scrofa.Sscrofa11.1.dna.toplevel.fa
Supplementary files format and content: tab-delimited text file includes CPM values for each Samples , treatment group avarage CPM and DEG values.

molecule: polyA RNA

organism: Sus scrofa

source_name: heart

extract_protocol:
Total RNA was extracted using  Qiagen RNeasy Fibrous Tissue Mini Kit Qiagen, Cat #74104 as per manufacturer recommendations (Qiagen) and RNA quality was validated on RNA-1000 chip using Bioanalyzer (Agilent)
Sequencing libraries were generated using NEBNext Ultra II Directional RNA Library prep Kit

treatment_protocol: Aortic cuff placemnt and inflation to induce pressure overload

value: heart

tag: group

value: LV Pressure Overload


title: P1002


title: ROZH_5, S, day 16, biol repl 2, run 1

description: 10x Genomics


title: ROZH_5, M, day 80, biol repl 2, run 1

description: 10x Genomics


title: ROZH_5, M, day 16, biol repl 2, run 1

description: 10x Genomics


title: P967


title: P1018

value: Referent Control


title: ROZH_5, M, day 40, biol repl 2, run 1

description: 10x Genomics

value: day 40


title: ADRCs, LymphREG, sample 04, scRNAseq

description: 10x Genomics

value: subcutaneous adipose tissue

value: adipose derived regenerative cells/stromal vascular fraction

value: adult


title: EAF2Faslpr1

value: B220+CD3+ cells, spleen


title: PAAD_meta_liver_V2

source_name: PAAD metastasis liver, technical cohort

value: metastasis


title: ADRCs, LymphREG, sample 02, scRNAseq

description: 10x Genomics


title: EAF2Faslpr2


title: ROZH_5, D, day 120, biol repl 2, run 1

description: 10x Genomics

value: day 120

value: dorsal protocol (D)


title: V134


title: ADRCs, LymphREG, sample 01, scRNAseq

description: 10x Genomics


title: nmoD15c scRNA-seq

city: Guangzhou

first: Cheng

last: Chen

state: Guangdong

address: Kaiyuan Ave 190

institute: Guangzhou Institute of Biomedicine and Health, Chinese Academy of Science

description: DNBelab C4

data_processing:
The barcoded processing, gene counting,  and aggregation were made using  the DNBelab_C_Series_HT_scRNA-analysis-software v1.0 (https://github.com/MGI-tech-bioinformatics/DNBelab_C_Series_HT_scRNA-analysis-software) The allele calling of amplicons was made using the Cassiopeia 2.0.0 software (https://github.com/YosefLab/Cassiopeia)
Assembly: mm10/GRCh38
Supplementary files format and content: normalized UMI counts (mtx), gene names (tsv), and cellIDs (tsv); molecular table containing filtered lineage tracer calls (csv).

source_name: in vitro organoid

extract_protocol:
Mouse neuromesodermal organoids were dissociated by Papain dissociation kit (Worthington). In brief, embryoid bodies were incubated in 1 ml Enzyme A along with 20 μl DnaseI at 37℃ for 20-25 min, following by gentle blowing every 5 minutes with wide-bore tips. After washing and filtering, a suitable volume of PBS with 0.04% BSA was added to resuspend the cells to achieve the cell concentration of 2x106 /ml.
Single-cell RNA libraries were prepared using DNBelab C4 kit (BGI-MGI) according to the user’s guide. The main steps of library preparation include droplet formation, demulsification, reverse transcription, second-strand synthesis, cDNA and oligo product amplification following size selection. Each obtained cDNA pool was divided into two parts. One part of cDNA was prepared by fragmentation, end repair, adaptor ligation and PCR to get a cDNA library for scRNA-seq. Another part of cDNA was used for amplicon sequencing. Corresponding oligo libraries were generated by PCR amplification from oligo products.In order to better capture information on target site, we divided the obtained  cDNA into two portions. One portion was used for normal transcriptome sequencing, while the other portion was used for amplicon sequencing.

value: in vitro organoid

value: organoid

value: nmpD0-D3+4-OHT, nmoD2-D8 +Dox


title: ROZH_5, D, day 40, biol repl 2, run 1

description: 10x Genomics

source_name: brain organoid tissue

value: brain organoid tissue

value: Human induced pluripotent stem cell (HipSci) line Rozh_5


title: P970


title: ROZH_5, D, day 25, biol repl 2, run 1

description: 10x Genomics

value: female

value: day 25


title: P965

value: heart

value: LV Pressure Overload


title: ADRCs, LymphREG, sample 03, scRNAseq

description: 10x Genomics


title: P964


title: ROZH_5, D, day 13, biol repl 2, run 1

description: 10x Genomics

value: day 13


title: nmoD15a scRNA-seq

description: DNBelab C4


title: HCC827 cells, SI1

city: Beijing

first: Ye-guang

address: Tsinghua Road, Medical Building

department: School of life science

institute: Tsinghua University

data_processing:
RNA-seq reads were aligned to the reference genome hg38 using the STAR software.
Then the differential expression analysis was effectuated employing DESeq2 software.
Differentially expressed genes that meets the established criteria of a false discovery rate (FDR) of < 5% and a fold change of > 2.0 were selected for further analysis.
Assembly: hg38
Supplementary files format and content: gene_expression.xlsx
Supplementary files format and content: fpkm, tpm ,readcounts

source_name: human lung

growth_protocol: The HCC827 cells transfected with SPIN1 siRNAs or negative control for 48h were used for RNA sequencing.

extract_protocol:
The total RNA was extracted from HCC827 cells using TRIzol reagent (Takara, Japan) and the RNA integrity was validated further.
The RNA sequencing process was performed with MGI2000 platform (MGI-Wuhan).

value: human lung

value: HCC827 cells

value: Non-small cell lung cancer cells

value: Transfected with SPIN1 siRNAs


title: nmoD30 scRNA-seq

description: DNBelab C4

value: nmoD0-D10 +4OHT,nmoD20-D30 +Dox


title: nmpD3 scRNA-seq

description: DNBelab C4


title: nmoD30 amplicon-seq

description: DNBelab C4


title: HCC827 cells, SI3

value: HCC837 cells


title: H9, V, day 120, biol repl 2, run 1

description: 10x Genomics

value: Human embryonic stem cell (hESCs) line WA09 (H9)

value: day 120

value: ventral protocol (V)


title: P966


title: HCC827 cells, NC3

value: Negative control


title: P963

value: Referent Control


title: H9, V, day 80, biol repl 2, run 1

description: 10x Genomics

value: brain organoid tissue

value: day 80


title: HCC827 cells, NC2


title: P962


title: MARC145 cells,PRRSV SD16-2, 36 h (anti m6A)

city: ZHENG ZHOU

first: Yunyun

last: zhai

address: China Henan Zhengzhou Agricultural Road No. 63 (450002)

institute: Henan Agricultural University

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.number of fragments per kilobase of transcript sequence per millions base pairs (FPKM) method to estimate the expression level of each gene. FPKM values were calculated based on the length of the gene and the number of reads mapped to the gene.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Library strategy: m6A-seq

organism: Chlorocebus sabaeus

growth_protocol: MARC145 cells were maintained in DMEM  Medium supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.
RNA libraries for RNA-seq were prepared for sequencing using standard Illumina protocols.

treatment_protocol: MARC145 cells were infected with the PRRSV SD16 strain (MOI=0.5), with uninfected cells serving as the control group. Two biological replicates were conducted for each group, and cells were collected for RNA extraction after 36 hours.

value: epithelial cell

value: PRRSV SD16_infected

tag: library type


title: HCC827 cells, SI2


title: HCC827 cells, NC1


title: H9, V, day 40, biol repl 2, run 1

description: 10x Genomics

value: female

value: day 40


title: P961

value: heart


title: MARC145 cells,mock-2, 36 h (anti m6A)

value: PRRSV SD16_uninfected


title: Cdk8i-cycCi-Med12i scRNA-seq

city: New Orleans

first: Jun-yuan

last: Ji

state: LA

address: 1700 Tulane Avenue

department: Department of Biochemistry and Molecular Biology

institute: Tulane University

description: 10x Genomics

data_processing:
Alignment was performed using CellRanger 3.0.2 (Zheng et al., 2017), followed by further processing of the count data with Seurat (Butler et al., 2018). The scripts used in Seurat is available on Github athttps://github.com/YJulyXing/scRNA-seq.
Assembly: Dmel r6.35
Supplementary files format and content: csv, Differential expression gene list in nub+ cells comparing GFP positive and negative cells

organism: Drosophila melanogaster

source_name: L3 wing imaginal disc

extract_protocol:
100-120 wing imaginal discs were dissected and dissociated in 500 μL 0.25% Trypsin-EDTA (ThermoFisher) at 37°C for 10 min. The resulting cell suspension underwent two washes with PBS and was then passed through a 35 μm filter (Deng et al., 2019).
The filtered cells were resuspended and sent to Texas A&M Health Science Center TIGSS Molecular Genomics Core for standard 10X Genomics library prep and subsequential sequencing.

value: L3 wing imaginal disc

value: ap-Gal4>GFP/+; UAS-Cdk8i-cycCi-Med12i/+


title: MARC145 cells,mock-1, 36 h (anti m6A)


title: H9, V, day 25, biol repl 2, run 1

description: 10x Genomics

value: day 25


title: H9, S, day 120, biol repl 2, run 1

description: 10x Genomics

value: striatum protocol (S)


title: H9, V, day 13, biol repl 2, run 1

description: 10x Genomics

value: Human embryonic stem cell (hESCs) line WA09 (H9)

value: day 13


title: MARC145 cells,PRRSV SD16-2, 36 h (m6A input)


title: Med12i scRNA-seq

description: 10x Genomics

value: ap-Gal4>GFP/+; UAS-Med12i/+


title: Hep3B cells, PD-L1-KO-nPD-L1 A2

city: Changsha

first: zhi

last: yang

address: No.87 Xiangya Road

institute: Xiangya Hospital Central South University

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. 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 N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
Total RNA from Hep3B-PD-L1-KO-vector and Hep3B-PD-L1-KO-nPD-L1 cells was isolated using TRIzol™ Plus RNA Purification Kit (Invitrogen).
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols

value: liver cancer cell

value: PD-L1 knock out, nPD-L1 overexpressed


title: Cdk8i-cycCi scRNA-seq

description: 10x Genomics

value: ap-Gal4>GFP/+; UAS-Cdk8i-cycCi/+


title: MARC145 cells,PRRSV SD16-1, 36 h (anti m6A)


title: Hep3B cells, PD-L1-KO-nPD-L1 A1


title: MARC145 cells,PRRSV SD16-1, 36 h (m6A input)


title: Control scRNA-seq

description: 10x Genomics


title: H9, S, day 80, biol repl 2, run 1

description: 10x Genomics

value: brain organoid tissue

value: day 80


title: MARC145 cells,mock-2, 36 h (m6A input)

value: epithelial cell


title: Hep3B cells, PD-L1-KO-vector C3

value: PD-L1 knock out


title: ROZH_5, D, day 80, biol repl 2, run 1

description: 10x Genomics

value: Human induced pluripotent stem cell (HipSci) line Rozh_5

value: female

value: dorsal protocol (D)


title: H9, S, day 40, biol repl 2, run 1

description: 10x Genomics

value: day 40


title: Hep3B cells, PD-L1-KO-nPD-L1 A3


title: MARC145 cells,mock-1, 36 h (m6A input)

value: PRRSV SD16_uninfected


title: Hep3B cells, PD-L1-KO-vector C1


title: H9, S, day 16, biol repl 2, run 1

description: 10x Genomics

value: day 16


title: MARC145 cells,PRRSV SD16-2, 36 h

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.number of fragments per kilobase of transcript sequence per millions base pairs (FPKM) method to estimate the expression level of each gene. FPKM values were calculated based on the length of the gene and the number of reads mapped to the gene.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

value: PRRSV SD16_infected

value: RNA-seq


title: H9, pluripotent, day 0, biol repl 2, run 1

description: 10x Genomics

data_processing:
Sequencing was performed on Illumina NextSeq High Output 75 cycle lanes and Illumina Novaseq S1 100 cycle lanes and reads combined. Reads were preprocessed using umi2index (Lexogen) to add the UMI sequence to the read identifier, and trimmed using BBDuk v38.06 (ref=polyA.fa.gz,truseq.fa.gz k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20). Reads mapping to abundant sequences included in the iGenomes UCSC hg38 reference (human rDNA, human mitochondrial chromosome, phiX174 genome, adapter) were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCh38/hg38 assembly obtained from Homo sapiens Ensembl release 94. Reads were aligned to the genome using star v2.6.0c, alignments were processed using collapse_UMI_bam (Lexogen) and reads in genes were counted with featureCounts (subread v1.6.2) using strand-specific read counting (-s 1).
Assembly: GRCh38
Supplementary files format and content: sample-wise RDS files: raw counts (rows: genes)

value: Human embryonic stem cell (hESCs) line WA09 (H9)

value: day 0


title: H9, M, day 120, biol repl 2, run 1

description: 10x Genomics

value: day 120

value: midbrain protocol (M)


title: sample11

city: Fukuoka

first: Ryosuke

last: Tsurui

address: 3-1-1 Maidashi Higashi-ku

department: Department of Orthopaedic Surgery

country: Japan

institute: Graduate School of Medical Sciences, Kyushu University

data_processing:
FastQC v 0.11.7
Low quality (< 20) bases and adapter sequences were trimmed by Trimmomatic software (Version 0.38).
The trimmed reads were aligned to the reference genome using RNA-seq aligner HISAT2 (Version 2.1.0).
The HISAT2-resultant .sam files were converted into .bam files with Samtools (Version1.9).
The .bam files were used to estimate the abundance of uniquely mapped reads with featureCounts (Version 1.6.3).
Assembly: Grch38.107
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: blood

growth_protocol: PBMCs were cultured with recombinant human IL-7 in culture medium (RPMI 1640 with 10% fetal bovine serum, 500 units/ml penicillin, 500 µg/ml streptomycin, and 0.1 µM 2-mercaptoethanol) at 37°C up to 14 days without or with RASF.

extract_protocol:
Flow cytometric cell sorting was performed on a FACSAria Fusion cell sorter (BD Biosciences). Total RNA was purified using the SMART-seq HT Plus kit (Takara Bio).
Barcoded cDNA libraries were generated by the Nextera XT DNA Library Preparation kit (Illumina).

value: blood

value: Healthy controls(human)

value: T lymphocyte

value: IL-7-Tph with RASF


title: MARC145 cells,mock-2, 36 h

value: epithelial cell


title: K562, delEX2, H3K27me3, rep1

city: Mexico city

first: Hober

last: Nuñez

state: CDMX

address: Cto. Exterior s/n

department: Molecular Genetics

country: Mexico

institute: IFC-UNAM

data_processing:
Sequencing reads were trimmed for adaptor sequence using Trim Galore
Trimmed sequencing reads were mapped to GRCh37/hg19 using Bowtie2
Read filtering and peak calling were performed using NGSUtils and MACS2, respectively.
Assembly: hg19
Supplementary files format and content: Normalized raw signal in bigwig format

source_name: Hematopoietic

growth_protocol: K562 cells were grown in ISCOVE supplemented with 10% fetal bovine serum (FBS) and penicillin-streptomycin in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 minutes. Chromatin was sheared by sonication. Immunoprecipitation was performed overnight with the corresponding primary antibody. DNA was purified from A/G beads using phenol-chloroform.
ChIP-seq libraries were prepared using NEBNext Ultra Library Prep Kit for Illumina according to the manufacturer's conditions.

value: Hematopoietic

value: chronic myelogenous leukemia

tag: chip antibody


title: K562, delEX2, H3K4me1, rep2


title: MARC145 cells,PRRSV SD16-1, 36 h


title: K562, delEX2, H3K27ac, rep2


title: K562, delEX2, H3K27ac, rep1


title: H9, M, day 80, biol repl 2, run 1

city: Vienna

first: Julia

last: Naas

address: Dr. Bohr Gasse 9

institute: University of Vienna

description: 10x Genomics

extract_protocol:
RNA samples were extracted from organoids collected in Buffer RLT (Qiagen, cat. # 79216) using the RNA isolation kit provided by VBC core facilities. The kit uses carboxylate-modified Sear-Mag Speed beads and was applied using the Kingfisher instrument (Thermo).
Lexogen’s Quantseq kit was used, including the UMI extension (Lexogen, cat# 015.384, 081.96). All kits were used according to manufacturers’ instructions.

value: brain organoid tissue

value: female

value: day 80


title: Hep3B cells, PD-L1-KO-vector C2

value: liver cancer cell

value: PD-L1 knock out


title: MARC145 cells,mock-1, 36 h

value: PRRSV SD16_uninfected

value: RNA-seq


title: H9, M, day 40, biol repl 2, run 1

description: 10x Genomics

value: Human embryonic stem cell (hESCs) line WA09 (H9)

value: day 40


title: sample10


title: sample9


title: K562, delEX2, H3K4me1, rep1


title: sample12


title: H9, M, day 16, biol repl 2, run 1

description: 10x Genomics

value: day 16

value: midbrain protocol (M)


title: K562, delEX2, H3K4me3, rep1


title: H9, D, day 120, biol repl 2, run 1

description: 10x Genomics

value: day 120

value: dorsal protocol (D)


title: sample7

source_name: Synovial fluid

value: Synovial fluid

value: RA patients(human)

value: T lymphocyte

value: RA-Tph


title: sample8

value: blood

value: Healthy controls(human)

value: naive CD4 Tcell


title: K562, delEX2, H3K4me3, rep2

value: Hematopoietic

value: chronic myelogenous leukemia


title: BB8_16_1

city: Oslo

first: Parmeshwar

middle: Bajirao

last: Katare

state: Oslo

address: Gydas vei 8

department: Section for Pharmacology and Pharmaceutical Biosciences, Department of Pharmacy,

country: Norway

institute: University of Oslo

data_processing:
The library preparation and RNA-seq analysis were carried out at Novogene Co., LTD. (Milton, United Kingdom). To identify differential genes and perform enrichment analysis, we utilized the Novomagic (https://magic.novogene.com) online platform, which is specifically designed for data analysis. This allowed us to test for statistical enrichment of differentially expressed genes at the functional level. We considered p-values less than 0.05 as statistically significant. For a comprehensive understanding of the analytical methods used, please refer to the Supporting information in the Supplementary Material.
Excel file with sellected pathways
Assembly: hg38
Supplementary files format and content: The list of identified mRNA sequences in each sample and kegg enrich mRNA: gene_fpkm_group.txt, BBvsAA.all_KEGGenrich.txt

source_name: skeletal muscle

growth_protocol: Human satellite cells were isolated from muscle biopsy samples from musculus vastus lateralis as previously described (Lund et al., 2018). Isolation of satellite cells was performed based on the method of (Henry et al., 1995) with the modifications described by (Gaster et al., 2001). In brief, satellite cells were isolated from muscle biopsies, decontaminated of fibroblasts and grown to 3-6 passages. The isolated cells were cultured and proliferated in DMEM-GlutaMAX (5.5 mM glucose) supplemented with 10% FBS, HEPES (25 mM), gentamicin (50 ng/ml), penicillin (25 IU), streptomycin (25 μg/ml), amphotericin B (1.25 μg/ml), hEGF (10 ng/ml), dexamethasone (0.39 μg/ml) and 0.05% BSA. Differentiation of myoblasts into myotubes was induced at 80-90% confluence by changing the medium to DMEM-GlutaMAX (5.5 mM glucose) supplemented with 2% FBS and 25 pM insulin. Proteomic analysis confirmed that cells from all donors expressed markers of myotubes. This indicated that the myotubes from both groups were well differentiated and exhibited the basic characteristics of skeletal muscle cells. The cells were cultured at 37°C in a humidified atmosphere containing 5% CO2, and the medium was changed regularly every 2-3 days. Experiments were carried out 7–8 days after the induction of cell differentiation.

extract_protocol:
RNA isolation and high-throughput RNA sequencing were conducted in myotubes from biopsies harvested before and after krill oil intervention. The total RNA was extracted using the RNeasy mini kit, adhering to the manufacturer's guidelines. Subsequently, the quantity and quality of the RNA were assessed.
The RNA library preparation and transcriptome sequencing processes were outsourced to Novogene Co., LTD. (Milton, United Kingdom), utilizing their Illumina platform for paired-end sequencing.

treatment_protocol: Human participants received a daily supplement of krill oil (1 g/day), over a 7-week period. Skeletal muscle biopsies were obtained from the musculus vastus lateralis on both the first and last days of the study, and these muscle biopsies underwent processing to isolate satellite cells.

value: skeletal muscle

value: Skeletal mucle cell

value: after a 7-week krill oil


title: MSC_young_mouse_2

city: Heidelberg

first: Jonas

last: Metz

address: Im Neuenheimer Feld 580

institute: DKFZ

data_processing:
Sequence information was converted to FASTQ format using bcl2fastq2 v2.20.0
Reads were aligned to the mouse reference (GRCm39) using STAR version 2.7.10.
Uniquely mapped fragments were quantified with the featureCounts function of the subread software v.1.6.5 based on the Ensembl genome annotation v.108 (Mus_musculus.GRCm39.108.gtf).
Assembly: GRCm39
Supplementary files format and content: Comma delimited text file includes read counts of all sample.

source_name: Bone marrow

extract_protocol:
MSCs (CD45- Ter119- CD31- CD51+ PDGFRa+ Sca1-) were FACsorted and RNA was extracted according to the method described by Picelli, S. et al. (10.1038/nmeth.2639).
For library preparation 2 µl cDNA was tagmented using the Illumina DNA Prep Kit according to manufacturers intructions.

value: Bone marrow

value: MSCs

value: wild-type

value: C57BL/6J (30 years inbred in-house)

value: male


title: MSC_young_mouse_3


title: MSC_young_mouse_4


title: H9, D, day 80, biol repl 2, run 1

description: 10x Genomics

value: brain organoid tissue

value: Human embryonic stem cell (hESCs) line WA09 (H9)

value: female

value: day 80

value: dorsal protocol (D)


title: sample6

source_name: blodd

value: blodd

value: Healthy controls(human)

value: T lymphocyte


title: BB7_14_1


title: H9, D, day 40, biol repl 2, run 1

description: 10x Genomics

value: day 40


title: sample5

value: blood


title: H9, D, day 25, biol repl 2, run 1

description: 10x Genomics

value: day 25


title: BB6_12_1

value: skeletal muscle

value: Skeletal mucle cell

value: after a 7-week krill oil


title: BB5_10_1


title: H9, D, day 13, biol repl 2, run 1

description: 10x Genomics

value: day 13


title: K562, delEX2, H3K27me3, rep2

value: Hematopoietic

value: chronic myelogenous leukemia


title: sample4

value: naive CD4 Tcell


title: BB4_8_1


title: sample2

value: Synovial fluid

value: RA patients(human)

value: RA-Tph


title: DN2a, Del_TE, scRNAseq

city: Seattle

first: Hao Yuan

last: Kueh

state: WA

address: 3720 15th Ave NE

institute: University of Washington

description: singe cell combinatorial indexing RNA-seq 3

data_processing:
Sequencing reads were processed as described in (Cao et al., 2019).
Assembly: mm9
Supplementary files format and content: Tab-separated files and matrix files

molecule: nuclear RNA

source_name: bone marrow derived

extract_protocol:
Bone marrow progenitors attached to OP9-DL1 stromal cells were washed three times with PBS before scraping in HBH buffer and passing through a 70uM mesh filter to minimize OP9-DL1 stromal cell contamination. Cells were then washed with PBS and fixed in 4% paraformaldehyde for 15 minutes on ice. After fixation, cells were pelleted at 500xg for 3 minutes at 4°C before resuspending in 1mL of PBSR [PBS, pH 7.4, 1% BSA, 1% SUPERase-In RNase Inhibitor (ThermoFisher Scientific), and 1% 10mM DTT], pelleting again at 500xg for 5 minutes at 4°C and resuspending in PBSR. Thawed nuclei were permeabilized with 0.2% TritonX-100 (in nuclei wash buffer) for 3 min on ice, and briefly sonicated (Diagenode, 12 sec on low power mode) to reduce nuclei clumping. The nuclei were then washed once with nuclei wash buffer and filtered through 1 ml Flowmi cell strainer. Filtered nuclei were spun down at 500×g for 5 min and resuspended in nuclei wash buffer.
Libraries were prepared and sequenced as described in (Cao et al., 2019).
scRNA-seq (sciRNA-seq3)

value: bone marrow derived

value: DN2a T cell progenitor


title: DN2b, Del_TE, scRNAseq

value: DN2b T cell progenitor


title: H1, V, day 120, biol repl 2, run 1

description: 10x Genomics

value: brain organoid tissue

value: Human embryonic stem cell (hESCs) line WA01 (H1)

value: male

value: day 120

value: ventral protocol (V)


title: H1, V, day 80, biol repl 2, run 1

description: 10x Genomics

value: day 80


title: BB3_6_1

value: skeletal muscle

value: Skeletal mucle cell

value: after a 7-week krill oil


title: sample1

value: T lymphocyte


title: DN2b, WT, scRNAseq

value: WT


title: DN2a, WT, scRNAseq


title: BB2_4_1


title: MSC_young_mouse_1

value: Bone marrow

value: MSCs

value: wild-type

value: C57BL/6J (30 years inbred in-house)


title: H1, V, day 40, biol repl 2, run 1

description: 10x Genomics

value: day 40


title: BB1_2_1


title: DN1, WT, scRNAseq

value: bone marrow derived

value: DN1 T cell progenitor


title: AdGC-11

city: Nankang

first: Jean

last: Lu

state: Taipei

address: 128 Academia Road, Section 2, IBMS, N401F

department: Genomics Research Center

country: Taiwan

institute: Academia Sinica

data_processing:
RNA-seq samples were pseudoaligned to the Ensembl GRCh38 human transcriptome release 90 using Kallisto, version 0.46.2.
Transcript abundance was quantified with 100 bootstraps using default k-mer length 31, mean fragment length 250, and sd 50.
Assembly: GRCh38
Supplementary files format and content: xlsx files include fold change values between disease group and control group.
Supplementary files format and content: xlsx files include fold change values between normal group and control group.

source_name: cumulus GC

extract_protocol:
Total RNA were extracted with TRIzol™ Reagent and then RNAs were cleaned and concentrated with kit (Zymo research, R1015).
RNA libraries for RNA-seq were prepared using Stranded RNA (Poly-A) method.

treatment_protocol: Human iPSC-derived granulosa cells are collacted at differentiation day 14.

value: cumulus GC

value: Normal 46XX

value: Normal


title: H1, V, day 25, biol repl 2, run 1

description: 10x Genomics

value: brain organoid tissue

value: Human embryonic stem cell (hESCs) line WA01 (H1)

value: male

value: day 25

value: ventral protocol (V)


title: AdGC-10


title: H1, V, day 13, biol repl 2, run 1

description: 10x Genomics

value: day 13


title: AA8_15_1

value: skeletal muscle

value: Skeletal mucle cell

value: before a 7-week krill oil


title: DN1, Del_TE, scRNAseq


title: AdGC-9


title: AA7_13_1


title: sample3

value: blood

value: Healthy controls(human)

value: T lymphocyte

value: naive CD4 Tcell


title: AdGC-8


title: AA6_11_1


title: H1, S, day 120, biol repl 2, run 1

description: 10x Genomics

value: day 120

value: striatum protocol (S)


title: H1, S, day 80, biol repl 2, run 1

description: 10x Genomics

value: day 80


title: Be6

first: pei

last: xia

address: No. 74, Zhongshan 2nd Road, Yuexiu District, Guangzhou City, Guangdong Province

institute: Sun Yat-Sen University

data_processing:
RNA quantification and qualification: Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Library preparation for Transcriptome sequencing: Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.
Quality Control: In order to ensure the quality of the library, the library needs to be tested. After the construction of the library, the library was initially quantified by Qubit2.0 Fluorometer, then diluted to 1.5ng/ul, and the insert size of the library is detected by Agilent 2100 bioanalyzer. After insert size meets the expectation, qRT-PCR is used to accurately quantify the effective concentration of the library (the effective concentration of the library is higher than that of 2nM) to ensure the quality of the library.
Clustering and sequencing: After the library is qualified, the different libraries are pooling according to the effective concentration and the target amount of data off the machine, then being sequenced by the Illumina NovaSeq 6000. The end reading of 150bp pairing is generated. The basic principle of sequencing is to synthesize and sequence at the same time (Sequencing by Synthesis). Four fluorescent labeled dNTP, DNA polymerase and splice primers were added to the sequenced flowcell and amplified. When the sequence cluster extends the complementary chain, each dNTP labeled by fluorescence can release the corresponding fluorescence. The sequencer captures the fluorescence signal and converts the optical signal into the sequencing peak by computer software, so as to obtain the sequence information of the fragment to be tested.
Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level: featureCounts (v1.5.0-p3) 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. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genes with counts < 5 in more than 70% of samples were classified as low-expression genes and excluded from further analysis. Normalization of the reads and the analysis of differentially expressed genes (DEGs) were performed using DESeq2 (version 1.40.2) in R. DEGs were selected with a cutoff value of p < 0.05.
Assembly: ensembl_107_mus_musculus_c57bl6nj_c57bl_6nj_v1_toplevel
Supplementary files format and content: Excel files include counts for each Sample

source_name: ACC brain tissue samples

extract_protocol:
ACC brain tissuer samples were harvested from mice in each group. RNA extraction was carried out using the RNAeasy Plus Universal Kit (Qiagen).
The samples underwent library construction by the NEBNext Ultra RNA Library Prep Kit for Illumina, and were loaded onto an Illumina NovaSeq 6000 for 150 bp paired-end sequencing.

treatment_protocol: MC38 tumor cells implantation

value: ACC brain tissue samples

value: Brain tissue cells

value: WT

value: Chemogenetic regulation of ACC brain regions in colorectal cancer mice


title: TS2-6

source_name: fibroblast

value: fibroblast

value: human iPSCs

value: iPSC-derived GC

value: Aneupoidy 45X

value: Disease


title: Be5


title: AA5_9_1

value: skeletal muscle

value: Skeletal mucle cell

value: before a 7-week krill oil


title: Be4


title: H1, S, day 40, biol repl 2, run 1

description: 10x Genomics

value: brain organoid tissue

value: Human embryonic stem cell (hESCs) line WA01 (H1)

value: male

value: day 40


title: TS2-4


title: Be3


title: AA4_7_1


title: TS1-2


title: Be2


title: TS1-1


title: H1, pluripotent, day 0, biol repl 2, run 1

description: 10x Genomics

value: day 0


title: Be8

value: ACC brain tissue samples


title: AA3_5_1


title: AA2_3_1


title: Be1

value: Brain tissue cells


title: H1, M, day 120, biol repl 2, run 1

description: 10x Genomics

value: day 120

value: midbrain protocol (M)


title: WT4-4

value: fibroblast

value: Normal 46XX

value: Control


title: BC6

value: WT

value: Colorectal cancer


title: H1, M, day 80, biol repl 2, run 1

description: 10x Genomics

value: day 80


title: AA1_1_1

value: skeletal muscle

value: Skeletal mucle cell


title: BC5


title: WT2-10

value: human iPSCs

value: iPSC-derived GC


title: H1, M, day 40, biol repl 2, run 1

description: 10x Genomics

value: brain organoid tissue

value: Human embryonic stem cell (hESCs) line WA01 (H1)

value: male


title: H1, M, day 16, biol repl 2, run 1

description: 10x Genomics

value: day 16


title: REEP6-2

city: Shiyan

first: Qin

last: Shanshan

address: Renmin Road 30, Maojian District

institute: Institute of Basic Medical Sciences, School of Basic Medical Sciences, Hubei University of Medicine

data_processing:
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. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to human genome assembly GRCh38 (ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) using HISAT2 with default parameters.
HTSeq v0.13.5 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:ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_29/gencode.v29.annotation.gtf.gz.
Assembly: GRCh38
Supplementary files format and content: FileincludeCount and FPKM valuesforeachsample

growth_protocol: The human OSCC cell line SCC-15 was purchased from the Shanghai Cell Bank of Chinese Academy of Sciences (Shanghai, China). The OSCC cell line were cultured in DMEM medium containing 10% fetal bovine serum (FBS), 100 U/mL penicillin, 100 U/mL streptomycin and 0.03% glutamine at 37 oC in 5% CO2.

extract_protocol:
After 48 hours, remove the medium and directly add 800μL Trizol into the 6-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 NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: The SCC-15 cells were seeded into 6-well plates and grown overnight. The next day, when the cell plating density reached 20%-30%, OSCC cells were transfected with letivirus (Genechem) to establish REEP6-overexpression cell line. After validation of the overexpression efficiency of REEP6, cells were harvested for RNA sequencing.

value: OSCC cell line


title: BC4

value: ACC brain tissue samples

value: Brain tissue cells


title: H1, D, day 120, biol repl 2, run 1

description: 10x Genomics

value: day 120

value: dorsal protocol (D)


title: BC3


title: REEP6-1


title: H1, S, day 16, biol repl 2, run 1

description: 10x Genomics

value: striatum protocol (S)


title: HPASMC, S1-miR637

city: Suzhou

first: Jie

last: Zhou

address: NO.242, Guangji Road

institute: Suzhou Municipal Hospital

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: Excel files include count and FPKM values for each Sample

source_name: HPASMC

growth_protocol: HPASMC cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with hypoxia (1% O2 and 5% CO2) at 37 °C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Cells were plated in 6-well plates and grown to a cell density of 50%, and RNA were transfected by Lipofectamine 2000 according to the manufacturer’s instructions.

value: HPASMC

value: Pulmonary artery smooth muscle cells

value: overexpressing miR637 overexpression

value: hypoxia (1% O2 and 5% CO2)


title: BC2

value: WT

value: Colorectal cancer


title: HPASMC, O3-miR661

value: overexpressing miR661 overexpression


title: H1, D, day 80, biol repl 2, run 1

description: 10x Genomics

value: brain organoid tissue

value: day 80


title: HPASMC, O2-miR661


title: NC3

value: Sham operation


title: H1, D, day 40, biol repl 2, run 1

description: 10x Genomics

value: Human embryonic stem cell (hESCs) line WA01 (H1)

value: male

value: day 40


title: NC4

value: ACC brain tissue samples

value: Brain tissue cells


title: A549, CHX, rep1

city: Moscow

first: Dmitri

middle: D

last: Pervouchine

address: Bolshoy Bul'var, 30, str 1

department: Skoltech Center for Molecular and Cellular Biology

country: Russia

institute: Skolkovo Institute of Science and Technology

data_processing:
Reads were aligned to human genome (GRCh38) with STAR aligner (v2.7.8a) with --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMheaderHD @HD VN:1.4 SO:coordinate --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outSAMtype BAM SortedByCoordinate --sjdbScore 1 --outSAMstrandField intronMotif --chimSegmentMin 15 parameters and GENCODE v43 transcript annotation.
Split-read counts for junctions were extracted from alignments with pyIPSA software
Assembly: GRCh38
Supplementary files format and content: CSV file with split read support of splice junctions

source_name: Lung

growth_protocol: Human A549 lung adenocarcinoma cells were maintained in Dulbecco's modified Eagle's medium Nutrient Mixture F-12 with 10% v/v fetal bovine serum (FBS), 1% GlutaMAX (Thermo Fisher Scientific), 0.05 mg/ml streptomycin and 50 units/ml penicillin (all products from Thermo Fisher Scientific) at 37°C in 5% CO2. Cells were plated at a density of 150,000 cells per well in a 12-well plate.

extract_protocol:
Total RNA was isolated by a guanidinium thiocyanate-phenol-chloroform method using ExtractRNA Reagent (Evrogene) in accordance with the manufacturer's protocol. One microgram of total RNA was first subjected to RNase-free DNase I digestion (Thermo Fisher Scientific) at 37°C for 30 min to remove contaminating genomic DNA.
500 ng of total RNA was used for complementary DNA (cDNA) synthesis using Magnus First Strand cDNA Synthesis Kit for RT-qPCR (Evrogene) to a final volume of 20 μl

treatment_protocol: Cycloheximide was added to the cells 3 hours before harvest giving a final concentration of 300 mg/ml in the growth medium.

value: Lung

value: cancer

value: wild type

value: Cycloheximide


title: NC-1

value: OSCC cell line

value: NC


title: HPASMC, S3-miR637

value: HPASMC

value: Pulmonary artery smooth muscle cells

value: overexpressing miR637 overexpression

value: hypoxia (1% O2 and 5% CO2)


title: HPASMC, O1-miR661

value: overexpressing miR661 overexpression


title: H1, D, day 13, biol repl 2, run 1

description: 10x Genomics

value: brain organoid tissue

value: day 13

value: dorsal protocol (D)


title: HPASMC, N3-Negative Control3

value: WT


title: HPASMC, S2-miR637


title: A549, NT, rep1

value: Non-treated


title: DIPG33 G2, rep2 (RNA-seq)

city: Stanford

first: Anastasia

last: Hains

email: hainsa@uchicago.edu, hains@stanford.edu

state: CA

address: 269 Campus Drive

institute: Stanford University

data_processing:
QC was performed with FastQC
Reads were aligned to the hg38 genome with hisat2 and indexed with samtools
transcript assembly and fpkm value calculations were performed with Cufflinks
tests for differential expression were performed with Cuffdiff
Assembly: hg38
Supplementary files format and content: tab-delimited files include FPKM values for each sample

extract_protocol:
RNA was extracted after FACS with PureLink RNA Mini kit (Invitrogen, 12183025) instructions with DNAse treatment (Invitrogen, 12185010).
Libraries were prepped following the NEBNext Ultra II Directional RNA Library Prep Kit


title: NC-2


title: nmoD15b scRNA-seq

first: Cheng

address: Kaiyuan Ave 190

institute: Guangzhou Institute of Biomedicine and Health, Chinese Academy of Science

description: DNBelab C4

data_processing:
The barcoded processing, gene counting,  and aggregation were made using  the DNBelab_C_Series_HT_scRNA-analysis-software v1.0 (https://github.com/MGI-tech-bioinformatics/DNBelab_C_Series_HT_scRNA-analysis-software) The allele calling of amplicons was made using the Cassiopeia 2.0.0 software (https://github.com/YosefLab/Cassiopeia)
Assembly: mm10/GRCh38
Supplementary files format and content: normalized UMI counts (mtx), gene names (tsv), and cellIDs (tsv); molecular table containing filtered lineage tracer calls (csv).

extract_protocol:
Mouse neuromesodermal organoids were dissociated by Papain dissociation kit (Worthington). In brief, embryoid bodies were incubated in 1 ml Enzyme A along with 20 μl DnaseI at 37℃ for 20-25 min, following by gentle blowing every 5 minutes with wide-bore tips. After washing and filtering, a suitable volume of PBS with 0.04% BSA was added to resuspend the cells to achieve the cell concentration of 2x106 /ml.
Single-cell RNA libraries were prepared using DNBelab C4 kit (BGI-MGI) according to the user’s guide. The main steps of library preparation include droplet formation, demulsification, reverse transcription, second-strand synthesis, cDNA and oligo product amplification following size selection. Each obtained cDNA pool was divided into two parts. One part of cDNA was prepared by fragmentation, end repair, adaptor ligation and PCR to get a cDNA library for scRNA-seq. Another part of cDNA was used for amplicon sequencing. Corresponding oligo libraries were generated by PCR amplification from oligo products.In order to better capture information on target site, we divided the obtained  cDNA into two portions. One portion was used for normal transcriptome sequencing, while the other portion was used for amplicon sequencing.

value: in vitro organoid

value: organoid

value: nmpD0-D3+4-OHT, nmoD2-D8 +Dox


title: 178, V, day 120, biol repl 2, run 1

description: 10x Genomics

value: Human induced pluripotent stem cell (HipSci) line SCCF-178J clone#5 (178)

value: male

value: day 120

value: ventral protocol (V)


title: HPASMC, N2-Negative Control2

value: HPASMC


title: iWAT; CRE2; Lib160

city: Cincinnati

first: Joan

last: Sanchez-Gurmaches

address: 3333 Burnet Ave

institute: CIncinnati Children's Hospital Medical Center

data_processing:
Custom mm10 assembly was prepared by adding CRE and LoxP sequence as a separate chromosome to measure their expressions, and STAR genome index was prepared accordingly.
RNA-seq reads were aligned to to the custom index using STAR. Only uniquely aligned reads were used for downstream analysis. Raw read counts for each gene, CRE, and LoxP were measured using FeatureCounts in the subread package with an option, “-s 2 -O --fracOverlap 0.8”.
Assembly: Custom assembly: mm10 + Cre-LoxP
Supplementary files format and content: Excel file containing read counts per gene; columns names match the sample title.

source_name: Inguinal white adipose tissue

growth_protocol: Mice were breeded in house and maintained at room temperature fed standard chow.

extract_protocol:
Total RNA was extracted using Trizol and RNAeasy columns.
RNA libraries for RNA-seq were prepared using Illumina’s TruSeq® stranded mRNA library preparation kit.

treatment_protocol: Mice were sacrified at 6 weeks of age in the morning without further treatment.

value: Inguinal white adipose tissue


title: DIPG33 LS, rep2 (RNA-seq)


title: DIPG33 G2, rep1 (RNA-seq)


title: 178, V, day 80, biol repl 2, run 1

description: 10x Genomics

value: day 80


title: iWAT; CRE2; Lib159


title: HPASMC, N1-Negative Control1

value: Pulmonary artery smooth muscle cells

value: hypoxia (1% O2 and 5% CO2)


title: Triple_negative5 [SR_2244_020]

city: Gunma

first: Sasagu

last: Kurozumi

address: 3-39-22, Showa, Maebashi

department: General Surgical Science

institute: Gunma University

data_processing:
Illumina HiSeq2500 1.8 was used for processing.
Assembly: N/A
Supplementary files format and content: Raw dara: Fastq
Supplementary files format and content: Processed data: Excel

source_name: Breast

extract_protocol:
Total RNA was isolated from these frozen samples using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: All samples without pretreatment

value: invasive breast cancer

value: Triple negative


title: 178, V, day 40, biol repl 2, run 1

description: 10x Genomics

source_name: brain organoid tissue

value: brain organoid tissue

value: day 40


title: H1, D, day 25, biol repl 2, run 1

description: 10x Genomics

value: Human embryonic stem cell (hESCs) line WA01 (H1)

value: day 25

value: dorsal protocol (D)


title: iWAT; CRE1; Lib147


title: DIPG33 ES, rep2 (RNA-seq)


title: Triple_negative4 [SR_2244_019]


title: Triple_negative3 [SR_2244_018]


title: iWAT; CRE1; Lib146


title: DIPG33 ES, rep1 (RNA-seq)


title: NC2

city: Guangzhou

value: ACC brain tissue samples

value: Brain tissue cells

value: WT

value: Sham operation


title: 178, V, day 13, biol repl 2, run 1

description: 10x Genomics

value: Human induced pluripotent stem cell (HipSci) line SCCF-178J clone#5 (178)

value: male

value: day 13

value: ventral protocol (V)


title: NC1


title: iWAT; CRE0; Lib149

value: Inguinal white adipose tissue

value: Wildtype


title: 178, S, day 120, biol repl 2, run 1

description: 10x Genomics

value: day 120

value: striatum protocol (S)


title: Triple_negative2 [SR_2244_017]

value: invasive breast cancer

value: Triple negative


title: DIPG33, G1, rep2 (RNA-seq)


title: iBAT; CRE2; Lib138

source_name: Interscapular brown adipose tissue

value: Interscapular brown adipose tissue


title: Triple_negative1 [SR_2244_016]


title: DIPG33, G1, rep1 (RNA-seq)


title: HER2_positive5 [SR_2244_015]

value: HER positive


title: DIPG29 G2, rep2 (RNA-seq)


title: 178, pluripotent, day 0, biol repl 2, run 1

description: 10x Genomics

value: brain organoid tissue

value: day 0


title: iBAT; CRE2; Lib152


title: DIPG33 LS, rep1 (RNA-seq)


title: HER2_positive4 [SR_2244_014]


title: DIPG29 G2, rep1 (RNA-seq)


title: 178, M, day 120, biol repl 2, run 1

description: 10x Genomics

value: midbrain protocol (M)


title: HER2_positive3 [SR_2244_013]


title: 178, V, day 25, biol repl 2, run 1

description: 10x Genomics

value: day 25


title: DIPG29 LS, rep2 (RNA-seq)


title: 178, M, day 40, biol repl 2, run 1

description: 10x Genomics

value: day 40


title: 178, M, day 80, biol repl 2, run 1

description: 10x Genomics

value: Human induced pluripotent stem cell (HipSci) line SCCF-178J clone#5 (178)

value: day 80


title: iBAT; CRE0; Lib122


title: HER2_positive2 [SR_2244_012]


title: HER2_positive1 [SR_2244_011]


title: DIPG29 LS, rep1 (RNA-seq)


title: 178, M, day 16, biol repl 2, run 1

description: 10x Genomics

value: male

value: day 16


title: DIPG29 ES, rep2 (RNA-seq)


title: ER_positive_HER2_negative5 [SR_2244_010]

value: ER positive HER negative


title: 178, S, day 16, biol repl 2, run 1

description: 10x Genomics


title: iBAT; CRE0; Lib143

value: Wildtype


title: iWAT; CRE0; Lib150

value: Inguinal white adipose tissue


title: DIPG29 ES, rep1 (RNA-seq)


title: 178, D, day 120, biol repl 2, run 1

description: 10x Genomics

value: day 120

value: dorsal protocol (D)


title: iBAT; CRE1; Lib140


title: ER_positive_HER2_negative4 [SR_2244_009]

value: invasive breast cancer


title: 178, D, day 80, biol repl 2, run 1

description: 10x Genomics


title: DIPG29, G1, rep2 (RNA-seq)


title: ER_positive_HER2_negative3 [SR_2244_008]


title: macrophages (monocyte-derived), GM-CSF, CAR, rep2

city: Philadelphia

first: Michael

last: Klichinsky

state: Pennsylvania

address: 3675 Market Street Ste. 401

institute: Carisma Therapeutics

data_processing:
STAR mismatch=2
FeatureCounts default
Assembly: mm10
Supplementary files format and content: matrix of raw counts of Ensembl Genes from mm10, first coluimn is Ensemble gene IDs, and each subsequent column correponds to a sample

source_name: bone marrow derived macrophages

extract_protocol:
RNeasy Kit (74004, QIAGEN)
NEB Ultra II RNA lib prep kit used according instructions

value: bone marrow derived macrophages

tag: agent

value: GM-CSF

value: CAR


title: ER_positive_HER2_negative2 [SR_2244_007]

tag: tissue


title: DIPG29, G1, rep1 (RNA-seq)

tag: cell line


title: DIPG24 G2, rep2 (RNA-seq)


title: macrophages (monocyte-derived), GM-CSF, CAR, rep3


title: macrophages (monocyte-derived), GM-CSF, CAR, rep1


title: 178, D, day 40, biol repl 2, run 1

description: 10x Genomics

value: brain organoid tissue

tag: Sex


title: macrophages (monocyte-derived), M-CSF, CAR, rep3

value: M-CSF


title: iBAT; CRE1; Lib141

value: Interscapular brown adipose tissue


title: 178, D, day 25, biol repl 2, run 1

description: 10x Genomics

tag: time

value: day 25


title: 178, D, day 13, biol repl 2, run 1

description: 10x Genomics

value: Human induced pluripotent stem cell (HipSci) line SCCF-178J clone#5 (178)

value: day 13

tag: treatment


title: DIPG24 G2, rep1 (RNA-seq)


title: ER_positive_HER2_negative1 [SR_2244_006]


title: macrophages (monocyte-derived), M-CSF, CAR, rep2


title: 177, V, day 120, biol repl 2, run 1

description: 10x Genomics

value: Human induced pluripotent stem cell (HipSci) line SCCF-177J clone#8 (177)

value: female

value: ventral protocol (V)


title: DIPG24 LS, rep2 (RNA-seq)


title: Normal_Breast_tissue4 [SR_2244_004]

value: normal breast

value: Normal Breast tissue


title: Normal_Breast_tissue5 [SR_2244_005]


title: DIPG24 LS, rep1 (RNA-seq)


title: macrophages (monocyte-derived), M-CSF, CAR, rep1


title: Normal_Breast_tissue3 [SR_2244_003]


title: 177, V, day 80, biol repl 2, run 1

description: 10x Genomics

value: day 80


title: 177, V, day 40, biol repl 2, run 1

description: 10x Genomics

value: day 40


title: DIPG24 ES, rep2 (RNA-seq)


title: macrophages (HSC-derived), M-CSF, CAR, rep3


title: macrophages (HSC-derived), M-CSF, CAR, rep2


title: macrophages (HSC-derived), M-CSF, CAR, rep1


title: DIPG24 ES, rep1 (RNA-seq)


title: Normal_Breast_tissue2 [SR_2244_002]


title: 177, V, day 25, biol repl 2, run 1

description: 10x Genomics


title: Normal_Breast_tissue1 [SR_2244_001]


title: DIPG24, G1, rep2 (RNA-seq)


title: macrophages (monocyte-derived), GM-CSF, untransduced, rep3

value: untransduced


title: 177, S, day 120, biol repl 2, run 1

description: 10x Genomics

value: day 120

value: striatum protocol (S)


title: DIPG24, G1, rep1 (RNA-seq)


title: macrophages (monocyte-derived), GM-CSF, untransduced, rep2

value: bone marrow derived macrophages

value: GM-CSF


title: Donor19, SIC, scRNA-seq, T1

city: wuhan

first: Mingjie

last: Li

address: union hospital

institute: Huazhong University of Science and Technology

data_processing:
Raw reads were demultiplexed and mapped to the reference genome by 10x Genomics CellRanger pipeline (https://support.10xgenomics.com/single-cell-geneexpression/software/pipelines/latest/what-is-cell-ranger) using default parameters. For each gene and each cell barcode filtered by CellRanger, unique molecule identifiers (UMIs) were counted to construct digital expression matrices.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Primary locally advanced rectal cancer single-cell

extract_protocol:
Single-cell suspensions were generated using the Tumor Dissociation Kit (Miltenyi Biotec) according to the manufacturer’s protocol. A Dead Cell Removal Kit (Miltenyi Biotec) was applied to eliminate dead cells from the single-cell suspensions. CD45+ cells were sorted from processed LARC tumors.
Cell viability in single-cell suspensions was >90%. The concentration of single-cell suspension was adjusted to 700-1200 cells/uL. The cell suspension was loaded into Chromium microfluidic chips to establish single-cell gel beads in emulsion (GEMs) for the directed retrieval of approximately 5000 cells and barcoded with the Chromium Controller (10x Genomics). RNA from the barcoded cells was subsequently reverse transcribed, and sequencing libraries were constructed with reagents from a Chromium Single Cell 3’ Reagent Kit v3 (10x Genomics) according to the manufacturer’s instructions.

value: CD45+ cells

value: SCRT followed by immunochemotherapy


title: DIPG21 G2, rep2 (RNA-seq)


title: 177, S, day 40, biol repl 2, run 1

description: 10x Genomics

data_processing:
Sequencing was performed on Illumina NextSeq High Output 75 cycle lanes and Illumina Novaseq S1 100 cycle lanes and reads combined. Reads were preprocessed using umi2index (Lexogen) to add the UMI sequence to the read identifier, and trimmed using BBDuk v38.06 (ref=polyA.fa.gz,truseq.fa.gz k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20). Reads mapping to abundant sequences included in the iGenomes UCSC hg38 reference (human rDNA, human mitochondrial chromosome, phiX174 genome, adapter) were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCh38/hg38 assembly obtained from Homo sapiens Ensembl release 94. Reads were aligned to the genome using star v2.6.0c, alignments were processed using collapse_UMI_bam (Lexogen) and reads in genes were counted with featureCounts (subread v1.6.2) using strand-specific read counting (-s 1).
Assembly: GRCh38
Supplementary files format and content: sample-wise RDS files: raw counts (rows: genes)

value: brain organoid tissue


title: macrophages (monocyte-derived), GM-CSF, untransduced, rep1


title: Donor18, SIC, scRNA-seq, T3

value: Primary locally advanced rectal cancer single-cell


title: 177, S, day 16, biol repl 2, run 1

description: 10x Genomics

value: day 16


title: DIPG21 G2, rep1 (RNA-seq)


title: macrophages (monocyte-derived), M-CSF, untransduced, rep3

value: M-CSF


title: Donor18, SIC, scRNA-seq, T1


title: 177, pluripotent, day 0, biol repl 2, run 1

description: 10x Genomics

value: Human induced pluripotent stem cell (HipSci) line SCCF-177J clone#8 (177)

value: female

value: day 0


title: macrophages (monocyte-derived), M-CSF, untransduced, rep2


title: Donor17, SIC, scRNA-seq, T3


title: DIPG21 LS, rep1 (RNA-seq)


title: 177, V, day 13, biol repl 2, run 1

description: 10x Genomics

value: day 13

value: ventral protocol (V)


title: 177, M, day 120, biol repl 2, run 1

description: 10x Genomics

value: midbrain protocol (M)


title: DIPG21 ES, rep2 (RNA-seq)


title: Donor19, SIC, scRNA-seq, T3


title: 177, M, day 40, biol repl 2, run 1

description: 10x Genomics

value: day 40


title: Donor17, SIC, scRNA-seq, T1


title: 177, M, day 80, biol repl 2, run 1

description: 10x Genomics

value: day 80


title: macrophages (monocyte-derived), M-CSF, untransduced, rep1

value: untransduced


title: F4T_2

city: Higashihiroshima

first: Takafumi

last: Ogawa

state: Hiroshima

address: 1-3-1 Kagamiyama

institute: Hiroshima University

data_processing:
The annotated genes (Aligned.sortedByCoord.out.bam file from STAR outputs) were quantified using RSEM.
Assembly: Differential expression analysis of genes and transcripts was performed in R using the Bioconductor package DESeq2.
Supplementary files format and content: tab deliminated file includes raw counts.

source_name: human embryonic kidney

growth_protocol: Human embryonic kidney (HEK) 293E cells (provided by Brendan Manning) were grown in DMEM (high glucose, with L-glutamine), 10% FBS, and 1% penicillin/streptomycin supplement (all from Invitrogen).

extract_protocol:
Samples were snap-frozen in liquid nitrogen and stored at −80°C until needed. After five freeze-thaw steps in a 37°C water bath and liquid nitrogen, total RNA was extracted using TRIzol, then purified with the Direct-zol™ RNA Kit and treated with DNase I to remove possible DNA contamination.
FASTQ output files were aligned to C. elegans WBcel269 reference genomes using STAR with a 2-pass procedure.

treatment_protocol: Cells were starved by incubation in DMEM with 0.1 % FBS overnight. Re-feeding was achieved by treatment with regular growth media.

value: human embryonic kidney

value: HEK-293E cell

value: embryonic kidney cells

value: 4h feeding, Torin1


title: macrophages (HSC-derived), M-CSF, untransduced, rep3

value: bone marrow derived macrophages


title: F4T_3


title: DIPG21 G1, rep2 (RNA-seq)


title: 177, M, day 16, biol repl 2, run 1

description: 10x Genomics

value: brain organoid tissue


title: macrophages (HSC-derived), M-CSF, untransduced, rep2


title: DIPG21 ES, rep1 (RNA-seq)


title: monocytes, untreated, untransduced, rep3

source_name: monocytes

value: monocytes

value: untreated


title: F4T_1


title: F1T_3

value: 1h feeding, Torin1


title: DIPG21 G1, rep1 (RNA-seq)


title: 177, D, day 80, biol repl 2, run 1

description: 10x Genomics

value: Human induced pluripotent stem cell (HipSci) line SCCF-177J clone#8 (177)

value: female

value: dorsal protocol (D)


title: macrophages (HSC-derived), M-CSF, untransduced, rep1

value: M-CSF


title: 177, D, day 120, biol repl 2, run 1

description: 10x Genomics

value: day 120


title: monocytes, untreated, untransduced, rep2


title: DIPG21 LS, rep2 (RNA-seq)


title: F1T_2


title: DIPG19 G2, rep2 (RNA-seq)


title: DIPG19 G2, rep1 (RNA-seq)


title: 177, D, day 40, biol repl 2, run 1

description: 10x Genomics

value: day 40


title: monocytes, untreated, untransduced, rep1


title: F1T_1


title: 177, D, day 25, biol repl 2, run 1

description: 10x Genomics

value: day 25


title: DIPG19 LS, rep2 (RNA-seq)


title: HSCs, untreated, untransduced, rep3

source_name: hematopoietic stem cells

value: hematopoietic stem cells

value: untransduced


title: ST_3

value: human embryonic kidney

value: HEK-293E cell

value: starvation, Torin1


title: ST_2

value: embryonic kidney cells


title: HSCs, untreated, untransduced, rep2


title: 177, D, day 13, biol repl 2, run 1

description: 10x Genomics

value: brain organoid tissue

value: day 13


title: 176, V, day 120, biol repl 2, run 1

description: 10x Genomics

value: Human induced pluripotent stem cell (HipSci) line SCCF-176J clone#1 (176)

value: ventral protocol (V)


title: ST_1


title: HSCs, untreated, untransduced, rep1

value: untreated


title: DIPG19 ES, rep2 (RNA-seq)


title: PROSER1 KO+Rescue day2 in N2B27 RNA-seq biol rep 2

city: Dundee

first: Kasper

middle: Dindler

last: Rasmussen

address: Dow Street

department: Division of Molecular, Cellular, and Developmental Biology (MCDB)

country: United Kingdom

institute: School of Life Sciences, University of Dundee

data_processing:
Adapter sequences and low-quality nucleotides were trimmed using Trimmomatic
Genome mapping performed with RNA-STAR, parameters varied between analyses; see text
Gene expression measured from mapped reads using FeatureCounts for protein coding genes or TEtranscripts for transposable elements
Differential expression in protein coding genes analysed using DESeq2
Assembly: mm10
Supplementary files format and content: Normalised counts: Tabular file generated by DESeq2 normalisation

source_name: differentiated embryonic stem cells

growth_protocol: DMEM high-glucose plus GlutaMAX, 8.3% ES-qualified foetal bovine serum, 4.1% knock out serum replacement, 100UI/mL Pen/strep, 0.1mM β-mercaptoethanol, 1X non-essential amino acids, 1X sodium pyruvate, 3µM GSK3 inhibitor (CHIR99021), 1µM MEK inhibitor (PD0325901), 100ng/mL LIF-GST cleaved (DU1715). Plated at 0.02x10^6 cells/mL on gelatinised plates and incubated at 37°C, 5% CO2

extract_protocol:
RNA extracted by RNeasy (QIAGEN)
Prepared using NEBNext Ultra II Directional RNA Library Prep kit (NEB)

treatment_protocol: "day 2" samples subjected to 2 day monolayer differentiation in N2B27 medium: 1:1 mix of Advanced DMEM-F12 and Neurobasal, supplemented with 1x L-Glutamine, 1x NEAA, 0.5x N-2 supplement, 0.5x B-27 supplement, and 0.1 mM β-ME

value: differentiated embryonic stem cells

value: PROSER1 knockout +Rescue

value: 48 hr in N2B27


title: 176, V, day 80, biol repl 2, run 1

first: Julia

address: Dr. Bohr Gasse 9

department: Max Perutz Labs

institute: University of Vienna

description: 10x Genomics

extract_protocol:
RNA samples were extracted from organoids collected in Buffer RLT (Qiagen, cat. # 79216) using the RNA isolation kit provided by VBC core facilities. The kit uses carboxylate-modified Sear-Mag Speed beads and was applied using the Kingfisher instrument (Thermo).
Lexogen’s Quantseq kit was used, including the UMI extension (Lexogen, cat# 015.384, 081.96). All kits were used according to manufacturers’ instructions.

value: female

value: day 80


title: DIPG19 ES, rep1 (RNA-seq)


title: DIPG19, G1, rep2 (RNA-seq)


title: DIPG19, G1, rep1 (RNA-seq)


title: 176, V, day 25, biol repl 2, run 1

description: 10x Genomics

value: day 25


title: 176, V, day 40, biol repl 2, run 1

description: 10x Genomics

value: day 40


title: 176, V, day 13, biol repl 2, run 1

description: 10x Genomics


title: F4_1

value: 4h feeding


title: DIPG4 G2, rep2 (RNA-seq)


title: 176, S, day 120, biol repl 2, run 1

description: 10x Genomics

value: day 120

value: striatum protocol (S)


title: PROSER1 KO+Rescue mESC RNA-seq biol rep 2

source_name: embryonic stem cells

value: embryonic stem cells


title: PROSER1 KO+Rescue mESC RNA-seq biol rep 1


title: DIPG4 G2, rep1 (RNA-seq)


title: DIPG19 LS, rep1 (RNA-seq)


title: F1_3

value: human embryonic kidney

value: HEK-293E cell

value: embryonic kidney cells

value: 1h feeding


title: PROSER1 KO day2 in N2B27 RNA-seq biol rep 2

value: PROSER1 knockout


title: 176, S, day 80, biol repl 2, run 1

description: 10x Genomics

value: brain organoid tissue

value: Human induced pluripotent stem cell (HipSci) line SCCF-176J clone#1 (176)


title: F1_1


title: 176, S, day 40, biol repl 2, run 1

description: 10x Genomics


title: PROSER1 KO day2 in N2B27 RNA-seq biol rep 1

value: differentiated embryonic stem cells


title: F1_2


title: F4_3


title: PROSER1 KO mESC RNA-seq biol rep 2


title: S_3

value: starvation


title: PROSER1 KO mESC RNA-seq biol rep 1