title: FLUC Control, sgRNAS 1 and 2, replicate 1, 6h harringtonine

city: Seattle

first: Arvind

last: Subramaniam

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences Division

institute: Fred Hutchinson Cancer Center

data_processing:
FASTQ reads aligned to GRCh38 with Ensembl v108 transcript annotations using STAR v2.7.11a with parameters `--runMode alignReads         --alignSJoverhangMin 300         --alignSJDBoverhangMin 6         --outSAMmultNmax 1         --quantMode GeneCounts`.
Full analysis pipeline in https://github.com/rasilab/nugent_2024/blob/main/analysis/rnaseq/scripts/run_analysis.smk
Assembly: GRCh38
Supplementary files format and content: ReadsPerGene.out.tab in tab-delimted text format as output by STAR

growth_protocol: HEK293T were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C. Doxycycline was added to a final concentration of 2μg/ml to induce Cas9 for 4 days (group 1) or for 7 days (group 2)

extract_protocol:
Total RNA was isolated using the Direct-zol RNA Miniprep kit (Zymo) following manufacturer’s instructions. polyA RNA was selected using oligo dT25 magnetic beads (NEB) following manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: Harringtonine was added to a concentration of 1mM for samples labeled as ‘6h’. All other samples were harvested without treatment.

value: fluc control sgrnas 1 and 2

value: 6h harringtonine

tag: batch

value: Replicate 1


title: H1, pluripotent, day 0, biol repl 3, 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 embryonic stem cell (hESCs) line WA01 (H1)

tag: Sex

value: male

tag: time

value: day 0

tag: treatment


title: H1, M, day 120, biol repl 3, run 2

description: 10x Genomics

value: day 120

value: midbrain protocol (M)


title: GCN1 KO, sgRNAs 3 and 4, replicate 1, 6h harringtonine

middle: R

country: USA

molecule: polyA RNA

tag: genotype

value: gcn1 ko sgrnas 3 and 4


title: GCN1 KO, sgRNAs 3 and 4, replicate 2, 6h harringtonine

value: Replicate 2


title: H1, M, day 80, biol repl 3, run 2

description: 10x Genomics

value: day 80


title: GCN1 KO, sgRNAs 1 and 2, replicate 2, 6h harringtonine

value: gcn1 ko sgrnas 1 and 2


title: C_358_S26,Control vehicle

city: Pamplona

first: Daniel

last: Ajona

state: Navarra

address: Adva Pio XII 55

country: Spain

institute: Cima-University of Navarra

data_processing:
The quality of the samples was verified using FastQC v0.11.8 software.
FASTQ files were mapped to GRCm39 human assembly using STAR v2.7.9a with default parameters.
featureCounts v1.6.0 software and Gencode vM31 release were used to obtain read counts at gene level considering only those genes aligned to exonic regions
Obtained gene counts were normalized using edgeR and voom function of limma (Processed data.xlsx)
Assembly: mm38
Supplementary files format and content: Processed data.xlsx

organism: Mus musculus

source_name: Tumor

growth_protocol: RPMI-1640 with Glutamax (Gibco), 10% Fetalclone (Thermo Fisher Scientific), 100 U/mL penicillin and 100 µg/mL streptomycin (Invitrogen). Cells were routinely tested for Mycoplasma.

extract_protocol:
RNA was then extracted with the NucleoSpin RNA isolation kit (Macherey-Nagel), according to manufacturer's instructions.
Library preparation was performed using the Illumina Stranded mRNA Prep Ligation kit (Illumina) following the manufacturer’s protocol.

treatment_protocol: Mice were then treated with vehicle, 1 mg/kg PMX53 (s.c.; daily starting on day 6), 100 μg anti-PD-1 (i.p.; days 7, 10 and 14) and/or 50 μg poly I:C (i.t.; days 11 and 15).

value: Tumor

value: Lewis Lung Cancer

tag: cell type

value: Lung adenocarcinoma

value: WT

value: Vehicle


title: H1, M, day 16, biol repl 3, run 2

description: 10x Genomics

value: day 16


title: GCN1 KO, sgRNAs 1 and 2, replicate 1, 6h harringtonine

value: 6h harringtonine

value: Replicate 1


title: FLUC Control, sgRNAS 1 and 2, replicate 2, no harringtonine

value: fluc control sgrnas 1 and 2


title: H1, D, day 80, biol repl 3, run 2

description: 10x Genomics

value: brain organoid tissue

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

value: male

value: dorsal protocol (D)


title: H1, D, day 120, biol repl 3, run 2

description: 10x Genomics

value: day 120


title: FLUC Control, sgRNAS 1 and 2, replicate 1, no harringtonine


title: GCN1 KO, sgRNAs 3 and 4, replicate 1, no harringtonine

value: gcn1 ko sgrnas 3 and 4


title: H1, D, day 25, biol repl 3, run 2

description: 10x Genomics

value: day 25


title: H1, D, day 13, biol repl 3, run 2

description: 10x Genomics

value: day 13


title: GCN1 KO, sgRNAs 3 and 4, replicate 2, no harringtonine

value: Replicate 2


title: H1, D, day 40, biol repl 3, run 2

description: 10x Genomics

value: day 40


title: GCN1 KO, sgRNAs 1 and 2, replicate 2, no harringtonine

value: gcn1 ko sgrnas 1 and 2


title: GCN1 KO, sgRNAs 1 and 2, replicate 1, no harringtonine


title: SF3B6 depletion after 4 days of Cas9 induction

value: sf3b6 ko


title: 178, V, day 120, biol repl 3, run 2

description: 10x Genomics

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

value: ventral protocol (V)


title: FLUC Control, sgRNAS 1 and 2, replicate 2, 6h harringtonine

value: 6h harringtonine


title: 178, V, day 40, biol repl 3, run 2

description: 10x Genomics


title: 178, V, day 25, biol repl 3, run 2

description: 10x Genomics


title: AQR depletion after 4 days of Cas9 induction

value: aqr ko


title: H1, M, day 40, biol repl 3, run 2

description: 10x Genomics

value: midbrain protocol (M)


title: 178, V, day 13, biol repl 3, run 2

description: 10x Genomics

value: brain organoid tissue


title: 178, S, day 16, biol repl 3, run 2

description: 10x Genomics

value: day 16

value: striatum protocol (S)


title: respiratory organoids_WT_3

city: Kyoto

first: Kazuo

last: Takayama

state: Kyoto

address: Shogoin Kawaharacho 53, Sakyo-ku

department: Center for iPS Cell Research and Application

country: Japan

institute: Kyoto University

data_processing:
Sequencing was performed on an Illumina NextSeq 2000 platform with the paired-end mode.
Illumina RTA version 4.12.2 and  bcl2fastq version 2.20 were used for basecalling and fastq generation, respectively.
Adapter sequences and low-quality bases were trimmed from the raw reads by cutadapt v4.6. The trimmed reads were mapped to the human reference genome sequences (hg38) using STAR v2.7.11a with the GENCODE (release 32, GRCh38.p13) gtf file.
The uniquely mapped reads were used for further analysis. Raw read counts were calculated using htseq-count v2.0.5 with the GENCODE gtf file. Gene expression levels were determined as transcripts per million (TPM).
Assembly: hg38
Supplementary files format and content: Matrix table with TPM for every gene and every sample

source_name: respiratory tract

growth_protocol: To start the differentiation, human iPS cell colonies were treated with TrypLE Select Enzyme (Cat# 12563029, Thermo Fisher Scientific) for 10 min at 37°C. After centrifugation, cells were seeded onto Matrigel Growth Factor Reduced Basement Membrane (Cat# 354230, Corning)-coated cell culture plates (2.0×105 cells/4 cm2) and cultured for 2 days. The differentiation of the respiratory organoids was performed in serum-free differentiation (SFD) medium, composed of DMEM/F12 (3:1) (Cat# 044-29765, FUJIFILM Wako Pure Chemical and Cat# 11320033, Thermo Fisher Scientific) supplemented with N2 (Cat# 141-08941, FUJIFILM Wako Pure Chemical), B-27 Supplement Minus Vitamin A (Cat# 12587001, Thermo Fisher Scientific), ascorbic acid (50 μg/mL, Cat# ST-72132, STEMCELL Technologies), 1× GlutaMAX (Cat# 35050-061, Thermo Fisher Scientific), 1% monothioglycerol (Cat# 195-15791, FUJIFILM Wako Pure Chemical), 0.05% bovine serum albumin (Cat# 820024, Sigma-Aldrich), and 1× penicillin/streptomycin). During days 0-1 of differentiation, cells were cultured with SFD medium supplemented with 10 μM Y-27632 (Cat# 034-24024, FUJIFILM Wako Pure Chemical), and 100 ng/mL recombinant Activin A (Cat# 338-AC-01M, R&D Systems). During days 1–3 of differentiation, cells were cultured with SFD medium supplemented with 10 μM Y-27632 (Cat# 034-24024, FUJIFILM Wako Pure Chemical), 100 ng/mL recombinant Activin A (Cat# 338-AC-01M, R&D Systems) and 1% FBS. Between days 3–5 of differentiation, cells were cultured in SFD medium supplemented with 1.5 μM Dorsomorphin dihydrochloride (Cat# 047-33763, FUJIFILM Wako Pure Chemical) and 10 μM SB431542 (Cat# 037-24293, FUJIFILM Wako Pure Chemical) for 24 h, and then SFD medium supplemented with 10 μM SB431542 and 1 μM IWP2 (Cat# 04-0034, Stemolecule) for another 24 h. During days 5–12 of differentiation, cells were cultured with SFD medium supplemented with 3 μM CHIR99021 (Cat# 034-23103, FUJIFILM Wako Pure Chemical), 10 ng/mL human FGF10 (Cat# AF-100-26, PeproTech), 10 ng/mL human FGF7 (Cat# AF-100-19, PeproTech), 10 ng/mL human BMP4 (Cat# 120-05ET, PeproTech), 20 ng/mL human EGF (Cat# AF-100-15, PeproTech), and all-trans retinoic acid (Cat# R2625 ATRA, Sigma-Aldrich). On day 12 of differentiation, cells were dissociated and embedded in the Matrigel Growth Factor Reduced Basement Membrane to generate organoids. During days 12–20 of the differentiation, organoids were cultured in SFD medium containing 3 μM CHIR99021, 10 ng/mL human FGF10, 10 ng/mL human FGF7, 10 ng/mL human BMP4, and 50 nM ATRA. On day 20 of differentiation, organoids were recovered from the Matrigel, and the resulting suspension of organoids (small free-floating clumps) was seeded onto Matrigel-coated cell culture plates. During days 20–30 of differentiation, organoids were cultured in SFD medium containing 50 nM dexamethasone (Cat# S1322, Selleck Chemicals), 0.1 mM 8-bromo-cAMP (Cat# 1140/50, Tocris Bioscience), and 0.1 mM IBMX (3-isobutyl-1-methylxanthine) (Cat# 095-03413, FUJIFILM Wako Pure Chemical).

extract_protocol:
Total RNA was isolated from human respiratory organoids using ISOGENE (Cat# 319-90211, NIPPON GENE).
Library preparation was performed using an Illumina Stranded mRNA Prep Kit (Cat# 20040532, Illumina) according to the manufacturer’s instructions.

treatment_protocol: TMPRSS2 gene was deleted by homologous recombination using the CRISPR-Cas9 system.

value: respiratory tract

value: human iPS cells

value: iPS cell-derived respiratory organoids

value: wild type


title: respiratory organoids_WT_2


title: respiratory organoids_WT_1


title: 178, pluripotent, day 0, biol repl 3, run 2

description: 10x Genomics

value: male

value: day 0


title: 178, M, day 80, biol repl 3, run 2

description: 10x Genomics

value: day 80


title: 178, M, day 120, biol repl 3, run 2

description: 10x Genomics

value: day 120


title: respiratory organoids_TMPRSS2 KO_2

value: TMPRSS2 knockout


title: 178, M, day 40, biol repl 3, run 2

description: 10x Genomics

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

value: day 40


title: 178, M, day 16, biol repl 3, run 2

description: 10x Genomics


title: FLUC depletion after 4 days of Cas9 induction

value: fluc control


title: HEK293T (SLAM-Seq), STM2457, 180mins, rep3

city: Würzburg

first: Julian

last: Konig

address: Am Hubland

country: Germany

institute: Würzburg University

data_processing:
Quality control: FastQC (v0.11.9)
Mapping: STAR (v2.7.8a) --runThreadN 16 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 1 --outSAMattributes All --readFilesCommand zcat --alignEndsType EndToEnd
SLAMseq data process: GRAND-SLAM (v2.0.5f) -e Slam -allGenes -progress -plot -D -minEstimateReads 1000
Using grandR (v0.2.5) to calculate the half lives.
Assembly: GRCh38.p12
Supplementary files format and content: txt half lives data (per gene)

growth_protocol: HEK293T cells were grown and cultured in DMEM supplemented with 10% fetal bovine serum, 1% L-glutamine, and 1% penicillin/streptomycin and were incubated at 37 °C with 5% CO2.

extract_protocol:
After incubation, cells were directly lysed in TRIzol (Thermo Fisher Scientific, #15596026) reagent in reducing conditions. RNA was resuspended in the elution buffer provided in the Lexogen anabolic kit. Exactly 5 µg of RNA was subjected to iodoacetamide treatment.
NGS library prep was performed with Lexogen`s QuantSeq 3´mRNA-Seq V2 Library Prep Kit FWD with Unique Dual Indices (12nt) following Lexogen`s standard protocol (0191UG444V0111). Libraries were prepared with a starting amount of 200ng (except sample 7 with 59ng) and amplified in 15 PCR cycles. Libraries were profiled in a High Sensitivity DNA on a 2100 Bioanalyzer (Agilent technologies) and quantified using the Qubit 1x dsDNA HS Assay Kit, in a Qubit 4.0 Fluorometer (Life technologies).  All 24 samples were pooled in equimolar ratio and sequenced on 1 NextSeq2000 P3 (100cycles) FC,SR for 1x 114 cycles plus 2x 12 cycles for the dual index read.
SLAM-seq with Lexogen`s QuantSeq 3´mRNA-Seq V2 Library Prep Kit FWD

treatment_protocol: HEK293T cells were seeded in 24 h well plate. At 80% confluency, cells were treated with STM2457 inhibitor or DMSO. After 3h, the metabolic labeling was performed by addition of 100 µM s4U.

value: Human embryonic kidney 293T cell line

value: WT


title: 178, V, day 80, biol repl 3, run 2

description: 10x Genomics

value: brain organoid tissue

value: ventral protocol (V)


title: HEK293T (SLAM-Seq), STM2457, 180mins, rep1


title: 178, D, day 120, biol repl 3, run 2

description: 10x Genomics

value: dorsal protocol (D)


title: HEK293T (SLAM-Seq), STM2457, 180mins, rep2


title: HEK293T (SLAM-Seq), DMSO, 180mins, rep3

value: DMSO


title: 178, D, day 80, biol repl 3, run 2

description: 10x Genomics


title: HEK293T (SLAM-Seq), DMSO, 180mins, rep2


title: 178, D, day 40, biol repl 3, run 2

description: 10x Genomics


title: SF3B5 depletion after 4 days of Cas9 induction

value: sf3b5 ko


title: 178, D, day 25, biol repl 3, run 2

description: 10x Genomics

value: day 25


title: HEK293T (SLAM-Seq), DMSO, 180mins, rep1


title: 177, V, day 120, biol repl 3, run 2

description: 10x Genomics

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

value: female


title: 178, D, day 13, biol repl 3, run 2

description: 10x Genomics

value: male

value: day 13


title: HEK293T (SLAM-Seq), STM2457, 90mins, rep3


title: 177, V, day 80, biol repl 3, run 2

description: 10x Genomics

value: day 80


title: 177, V, day 40, biol repl 3, run 2

description: 10x Genomics


title: 177, V, day 25, biol repl 3, run 2

description: 10x Genomics


title: HEK293T (SLAM-Seq), STM2457, 90mins, rep1


title: HEK293T (SLAM-Seq), DMSO, 90mins, rep3


title: HEK293T (SLAM-Seq), DMSO, 90mins, rep2


title: respiratory organoids_TMPRSS2 KO_1

value: respiratory tract

value: human iPS cells

value: iPS cell-derived respiratory organoids

value: TMPRSS2 knockout


title: HEK293T (SLAM-Seq), STM2457, 90mins, rep2

value: Human embryonic kidney 293T cell line


title: HEK293T (SLAM-Seq), DMSO, 90mins, rep1

value: WT


title: 177, V, day 13, biol repl 3, run 2

description: 10x Genomics

value: brain organoid tissue


title: respiratory organoids_TMPRSS2 KO_3


title: 177, S, day 16, biol repl 3, run 2

description: 10x Genomics

value: day 16

value: striatum protocol (S)


title: 177, S, day 120, biol repl 3, run 2

description: 10x Genomics

value: day 120


title: HEK293T (SLAM-Seq), STM2457, no4SU, rep3


title: 177, pluripotent, day 0, biol repl 3, run 2

description: 10x Genomics

value: day 0


title: HEK293T (SLAM-Seq), STM2457, no4SU, rep2


title: 177, M, day 80, biol repl 3, run 2

description: 10x Genomics

value: midbrain protocol (M)


title: HEK293T (SLAM-Seq), STM2457, no4SU, rep1


title: 177, M, day 120, biol repl 3, run 2

description: 10x Genomics

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


title: HEK293T (SLAM-Seq), DMSO, no4SU, rep2

value: DMSO


title: HEK293T (SLAM-Seq), DMSO, no4SU, rep1


title: 177, D, day 120, biol repl 3, run 2

description: 10x Genomics

value: female

value: dorsal protocol (D)


title: 177, M, day 16, biol repl 3, run 2

description: 10x Genomics


title: HEK293T (RNA-Seq), STM2457 6h, Emetine 2h, rep3

data_processing:
Quality control: FastQC (v0.11.8 [HEK293T 9h treatment], v0.11.9 [HEK293T 6h treatment, HEK293T YTHDF2 KD, HEK293T 2h DMSO/Emetine treatment])
Trimming [HEK293T 9h treatment]: Cutadapt (v1.18) with parameters: cutadapt -a file:NexteraPE-PE.fa --overlap=3 --minimum-length 50 --error-rate 0.1 (NexteraPE-PE.fa was used as provided here: https://github.com/timflutre/trimmomatic/blob/master/adapters/NexteraPE-PE.fa)
Trimming [HEK293T 2h DMSO/Emetine treatment]: Cutadapt (v4.0) with parameters: cutadapt --adapter Nextera=ACTGTCTCTTATACACATCT --overlap=5 --minimum-length 30 --nextseq-trim=20 --error-rate 0.1
Mapping [HEK293T 9h treatment]: STAR (v2.7.3a) with parameters: STAR --runMode alignReads --outFilterMismatchNoverLmax 0.04 --outFilterMismatchNmax 999 --outSAMattributes NH HI AS nM MD --outSJfilterReads Unique --outSAMunmapped Within --outStd SAM --readFilesCommand zcat --sjdbOverhang 78 --genomeDir Gencode_release-31_GRCh38.p12.starindex --sjdbGTFfile gencode.v31.primary_assembly.annotation.gtf --runThreadN 4
Mapping [HEK293T 6h treatment, HEK293T YTHDF2 KD]: STAR (v2.7.3a) with parameters: STAR --runMode alignReads --outFilterMismatchNoverReadLmax 0.04 --outFilterMismatchNmax 999 --outSAMattributes NH HI AS nM MD --outSJfilterReads Unique --outSAMunmapped Within --outStd SAM --readFilesCommand zcat --sjdbOverhang 78 --genomeDir Gencode_release-31_GRCh38.p12_ERCC.starindex --sjdbGTFfile gencode.v31.primary_assembly.annotation_ERCC.gtf --runThreadN 1 --outMultimapperOrder Random
Mapping [HEK293T 2h DMSO/Emetine treatment]: STAR (v2.7.3a) with parameters: STAR --runMode alignReads --outFilterMismatchNoverReadLmax 0.04 --outFilterMismatchNmax 999 --outSAMattributes NH HI AS nM MD --outSJfilterReads Unique --outSAMunmapped Within --outStd SAM --readFilesCommand zcat --sjdbOverhang 115 --genomeDir Gencode_release-31_GRCh38.p12_ERCC.starindex --sjdbGTFfile gencode.v31.primary_assembly.annotation_ERCC.gtf --runThreadN 1 --outMultimapperOrder Random
Filter/remove secondary hits: Samtools (v1.9 [HEK293T 9h treatment], v1.10 [HEK293T 6h treatment, HEK293T YTHDF2 KD, HEK293T 2h DMSO/Emetine treatment]) with parameters: samtools view -F 256
Counts per gene: Subread (v2.0.0) with non-default parameters: featureCounts --donotsort -s 2 -T 4 (defaults used for -t exon -g gene_id)
Assembly: GRCh38.p12
Supplementary files format and content: tsv count tables (read count per gene)

extract_protocol:
RNA was purified using Rneasy PLUS Mini Kit (Qiagen)
RNA libraries for RNA-seq were prepared using TruSeq Strand-Specific mRNA Library Prep with PolyA-Selection

treatment_protocol:
m6A depletion was performed by adding medium supplemented with 20 µM STM2457 in DMSO 0.2% (v/v) or with DMSO 0.2% (v/v) alone as control for 6-24 h.
Small interfering RNAs targeting YTHDF2 or a non-targeting control siRNA were transfected into the cells 24 h after seeding using RNAiMAX following the manufacturer's instructions at a final concentration of 20 nM. Cells were harvested 48 h after transfection for further analysis.
To combine the siRNA knockdown with m6A depletion, 42 h after transfection, cells were treated with 20 µM STM2457 or DMSO for additional 6 h.
Inhibition of translational elongation in HEK293T cells was performed using 1.8 μM emetine dihydrochloride (Sigma-Aldrich, E2375) in DMSO for 2 h.
For the combination of m6A depletion and translational inhibition, 1.8μM emetine was added for the last 2 h of a 6 h incubation period with 20 μM STM2457 or DMSO.

value: Emetine 2h and STM2457 6h


title: 177, D, day 80, biol repl 3, run 2

description: 10x Genomics

value: day 80


title: 177, D, day 40, biol repl 3, run 2

description: 10x Genomics

value: day 40


title: HEK293T (RNA-Seq), STM2457 6h, Emetine 2h, rep1


title: HEK293T (RNA-Seq), STM2457 6h, Emetine 2h, rep2


title: HEK293T (RNA-Seq), DMSO 6h, Emetine 2h, rep3

value: Emetine 2h


title: 176, V, day 120, biol repl 3, run 2

description: 10x Genomics

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

value: ventral protocol (V)


title: HEK293T (RNA-Seq), DMSO 6h, Emetine 2h, rep2

value: Human embryonic kidney 293T cell line


title: 177, D, day 13, biol repl 3, run 2

description: 10x Genomics

value: brain organoid tissue

value: day 13


title: HEK293T (RNA-Seq), DMSO 6h, Emetine 2h, rep1


title: 176, V, day 80, biol repl 3, run 2

description: 10x Genomics


title: HEK293T (RNA-Seq), STM2457 6h, DMSO 2h, rep3


title: 176, V, day 40, biol repl 3, run 2

description: 10x Genomics


title: HEK293T (RNA-Seq), STM2457 6h, DMSO 2h, rep2


title: 176, V, day 25, biol repl 3, run 2

description: 10x Genomics

value: day 25


title: 177, M, day 40, biol repl 3, run 2

description: 10x Genomics


title: 176, V, day 13, biol repl 3, run 2

description: 10x Genomics


title: 176, S, day 120, biol repl 3, run 2

description: 10x Genomics

value: day 120

value: striatum protocol (S)


title: HEK293T (RNA-Seq), STM2457 6h, DMSO 2h, rep1


title: 176, S, day 16, biol repl 3, run 2

description: 10x Genomics

value: day 16


title: 176, S, day 40, biol repl 3, run 2

description: 10x Genomics


title: HEK293T (RNA-Seq), DMSO 6h, DMSO 2h, rep3

value: DMSO 6h


title: PBMCs, D3

city: Jinan

first: yuwei

last: Zhang

state: Shandong

address: No.16992 Jingshi Road

department: Pathogenobiology

country: China

institute: SDCDC

data_processing:
RNA-seq data were processed quality control (QC), trimming and mapping to the human reference genome hg38 using CLC Genomics Workbench. Gene expression level was measured based on the transcripts per million (TPM).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

source_name: PBMC

extract_protocol:
Total RNA was extracted from PBMCs by using the RNeasy Mini Kit.
A total amount of 100ng total RNA per sample was used to prepare for the rRNA-depleted cDNA library by Stranded Total RNA Prep Ligation with Ribo-Zero Plus Kit (Illumina, USA)

value: PBMC

tag: disease state

value: SFTS

tag: disease severity

value: fatal


title: HEK293T (RNA-Seq), DMSO 6h, DMSO 2h, rep1


title: HEK293T (SLAM-Seq), DMSO, no4SU, rep3

value: WT

value: DMSO


title: PBMCs, D2


title: 176, pluripotent, day 0, biol repl 3, run 2

description: 10x Genomics

value: female

value: day 0


title: 176, M, day 120, biol repl 3, run 2

description: 10x Genomics

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

value: midbrain protocol (M)


title: 176, M, day 40, biol repl 3, run 2

description: 10x Genomics

value: day 40


title: 176, M, day 80, biol repl 3, run 2

description: 10x Genomics

value: brain organoid tissue

value: day 80


title: PBMCs, C6

value: severe


title: PBMCs, C5


title: 177, D, day 25, biol repl 3, run 2

description: 10x Genomics

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

value: day 25

value: dorsal protocol (D)


title: PBMCs, C4


title: 176, D, day 80, biol repl 3, run 2

description: 10x Genomics


title: PBMCs, C1


title: 176, D, day 40, biol repl 3, run 2

description: 10x Genomics


title: HEK293T (RNA-Seq), DMSO 6h, DMSO 2h, rep2

value: Human embryonic kidney 293T cell line

value: DMSO 6h


title: PBMCs, B4

value: PBMC

value: SFTS

value: moderate


title: PBMCs, B5


title: PBMCs, B1


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

description: 10x Genomics

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

value: ventral protocol (V)


title: 176, D, day 25, biol repl 3, run 2

description: 10x Genomics

value: female


title: 176, D, day 13, biol repl 3, run 2

description: 10x Genomics

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

value: day 13


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

description: 10x Genomics

value: day 120


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

description: 10x Genomics

value: brain organoid tissue


title: PBMCs, B3


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

description: 10x Genomics

value: day 40


title: PBMCs, D1

value: fatal


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

description: 10x Genomics


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

description: 10x Genomics

value: striatum protocol (S)


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

description: 10x Genomics

value: day 80


title: PBMCs, A3

value: healthy


title: PBMCs, A4


title: PBMCs, A6


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

description: 10x Genomics


title: 176, D, day 120, biol repl 3, run 2

description: 10x Genomics

value: dorsal protocol (D)


title: PBMCs, A5


title: PBMCs, A2


title: PBMCs, C2

value: severe


title: 176, M, day 16, biol repl 3, run 2

description: 10x Genomics

value: day 16

value: midbrain protocol (M)


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

description: 10x Genomics


title: PBMCs, C3

value: PBMC

value: SFTS


title: PBMCs, A1


title: lactotroph PitNET scRNAseq H-171

city: Münster

first: Carolin

last: Walter

address: Domagkstraße 9

department: Medical Faculty of the WWU Münster

library_source: transcriptomic single cell

data_processing:
All samples were demultiplexed and then processed with the 10x Genomics CellRanger v6.0.2 pipeline.
For all samples, the raw 10X scRNA-seq data was converted to fastq format with CellRanger's mkfastq function.
CellRanger's count algorithm was then used to align the data against the human reference transcriptome GRCh38.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PitNET (PIT1-Tumor)

extract_protocol:
Cell dissociation and erylysis were performed with Papain (CellSystems) and ACK Lysing Buffer (ThermoFisher Scientific) according to manufacturer's protocol.
Libraries were generated with Chromium Single Cell 3’ v3.1 technology (10x Genomics) and sequenced using a NextSeq 2000 sequencing instrument.

value: PitNET (PIT1-Tumor)


title: lactotroph PitNET scRNAseq H-129


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

description: 10x Genomics

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

value: female


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

description: 10x Genomics


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

description: 10x Genomics


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

description: 10x Genomics


title: lactotroph PitNET scRNAseq H-036


title: PBMCs, B2

value: moderate


title: gonadotroph PitNET scRNAseq H-130

source_name: PitNET (SF1-Tumor)

value: PitNET (SF1-Tumor)


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

description: 10x Genomics

value: brain organoid tissue

value: day 120


title: gonadotroph PitNET scRNAseq H-111


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

description: 10x Genomics

value: day 40


title: gonadotroph PitNET scRNAseq H-082


title: gonadotroph PitNET scRNAseq H-099


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

description: 10x Genomics

value: day 13


title: gonadotroph PitNET scRNAseq H-034


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

description: 10x Genomics

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

value: ventral protocol (V)


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

description: 10x Genomics

value: day 25

value: dorsal protocol (D)


title: gonadotroph PitNET scRNAseq H-014


title: gonadotroph PitNET scRNAseq H-018


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

description: 10x Genomics

value: day 80


title: B WT CD46 Only KO

city: Durham

first: Jana

last: Cable

state: NC

address: 213 Research Dr.

department: Molecular Genetics and Microbiology

institute: Duke University

data_processing:
Reads were aligned to hg38 with concatentated EBV Type 1 genome (NC007605)
Sam files were converted to bam files
bam files were used to generate count matrix with Rsubread
Normalized z scores were calculated with DESeq2
Assembly: hg38 with concatentated EBV Type 1 genome (NC007605)
Supplementary files format and content: csv file contains raw counts for each sample

source_name: B cells

extract_protocol:
RNA was extracted using Rneasy mini (Qiagen)
Librarys were constructed with NEBNext Ultra II RNA Library Prep Kit

value: B cells

value: CD46 KO

value: WT Infected

tag: replicate


title: B LPKO SP140L KO

value: SP140L KO

value: LPKO Infected


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

description: 10x Genomics

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

value: female

value: day 0


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

description: 10x Genomics

value: brain organoid tissue


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

description: 10x Genomics


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

description: 10x Genomics

value: day 120

value: striatum protocol (S)


title: A LPKO SP140L KO


title: B LPKO SP100 KO

value: SP100 KO


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

description: 10x Genomics

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


title: B LPKO CD46 Only KO


title: A WT CD46 Only KO


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

description: 10x Genomics

value: day 40


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

description: 10x Genomics

value: day 16


title: A LPKO CD46 Only KO


title: A LPKO SP100 KO


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

description: 10x Genomics


title: B WT infected B cells, 8 days post-infection

data_processing:
Reads were aligned to hg38
Sam files were converted to bam files
bam files were used to generate count matrix with Rsubread
Normalized z scores were calculated with DESeq2
Assembly: hg38
Supplementary files format and content: csv file contains raw counts for each sample


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

description: 10x Genomics

value: midbrain protocol (M)


title: A WT infected B cells, 8 days post-infection


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

description: 10x Genomics


title: B LPKO infected B cells, 8 days post-infection


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

description: 10x Genomics

value: dorsal protocol (D)


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

description: 10x Genomics


title: SAMN36705973_GL, scRNA-seq

city: Tallahassee

first: Li

last: Guo

address: Thrasher Medical Researcher Building, Suite 2300-D

department: College of Medicine

institute: Florida State University

description: 10X Genomics

data_processing:
FASTQ files were aligned to the GRCH38 using Cell Ranger v7.1.0. The raw gene expression matrices were input to Soup X 1.6.2 for ambient RNA removal using autoEstCont and adjustCounts to estimate and remove the contamination fraction.
Data quality control, filtering, dimensionality reduction, clustering, and differential expression analysis were conducted using Seurat v5.0.1 with ambient RNA removed data. Briefly, cells were filtered based on nFeature_RNA > 200, percent.mt < 10, and nCount_RNA < 10,000. Data normalization and batch effect correction were performed using IntegrateLayers function with CCAIntegration method. Dimensionality reduction and cell clustering were carried out sequentially with RunPCA, RunUMAP, FindNeighbors, and FindClusters. Cell types were classified based on the expression of canonical pancreatic markers within each cluster, supplemented by Azimuth reference mapping to refine the cell type identification.
Assembly: GRCH38
Supplementary files format and content: seurat objects containing gene expression matrix post ambient RNA removal, cell clustering, and other metadata

source_name: pancreas

extract_protocol:
Cultured islets were dissociated with TrypLE at 37oC for 9 minutes with manual trituration every 2 minutes.
scRNA-seq libraries were prepared with the Chromium Next GEM Single Cell 3′ Reagent Kits v 3.1 (PN-1000128, 10x Genomics) according to the user guide (CG000204, 10x Genomics).
scRNA-seq, Sequencing was carried out as paired-end (PE28x88) using a combination of Illumina NovaSeq 6000 and NovaSeq X Plus.

treatment_protocol: Human islets were cultured for 48 hours under either 5.1mM glucose (control) or 25mM glucose + 0.5mM palmitic acid (glucolipotoxicity condition).

value: pancreas

value: islet cells

value: GL


title: SAMN36705973_Ctrl, scRNA-seq

description: 10X Genomics

value: control


title: HP23166_GL, scRNA-seq

description: 10X Genomics


title: A LPKO infected B cells, 8 days post-infection

value: B cells

value: LPKO Infected


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

description: 10x Genomics

value: female

value: ventral protocol (V)


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

description: 10x Genomics

value: brain organoid tissue

value: day 80


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

description: 10x Genomics


title: HP23166_Ctrl, scRNA-seq

description: 10X Genomics


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

description: 10x Genomics

value: day 25


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

description: 10x Genomics

value: day 13


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

description: 10x Genomics

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

value: day 120


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

description: 10x Genomics


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

description: 10x Genomics


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

description: 10x Genomics

value: day 40


title: Donor16_TumorCoculture_12hrs

city: Memphis

first: Liqing

last: Tian

state: TN

address: 262 Danny Thomas Pl

institute: St. Jude Children's Research Hospital

data_processing:
C.TNC CAR and Zip18R sequences were added to human reference transcriptome (refdata-gex-GRCh38-2020-A) for reads mapping. The Cell Ranger v.7.1.0 Single-Cell software suite (10X Genomics) was used to process scRNA-seq FASTQ files. The ‘cellranger multi’ and ‘cellranger bamtofastq’ commands were performed for sample demultiplexing and extracting sample fastq files. The ‘cellranger count’ command was performed to align FASTQ files to reference genome and summarize the data into matrices describing gene read counts (UMI) per cell.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: CAR-T cells

extract_protocol:
C.TNC-CAR.Zip18R T cells were generated by double retroviral transduction for two biological donors. C.TNC-CAR.Zip18R T cells were collected at baseline or after 12-, 24-, and 48-hours stimulation with LM7.GFP.ffLuc in the presence of IL-15 (Peprotech; 5 ng/mL). Samples were sorted for viability and hashed for multiplexing with TotalSeq-C anti-human Hashtag Antibodies (Biolegend 394661, 394663, 394665). To add hashing antibodies, up to 5e6 cells were collected and incubated with Human TruStain FcX block (Biolegend), followed by a hashing antibody in a volume of 100 uL.
Equal cell numbers from each hashed sample were pooled before loading onto a Chromium Controller to generate 10,000 single-cell gel beads in emulsion for single cell RNA sequencing (scRNA-seq). Libraries were prepared using Chromium Next GEM Single Cell 5’ v.2 (Dual index) and Gel Bead Kit (10X Genomics). Complementary DNA was amplified (13 cycles), after which it was used for preparation of gene expression and cell surface protein libraries. The cDNA content of each sample and library was quality checked using a high-sensitivity DNA chip with a 2100 Bioanalyzer (Agilent Technologies).

value: CAR-T cells

value: T cells


title: Donor16_TumorCoculture_48hrs


title: Donor14_TumorCoculture_48hrs


title: Donor14_TumorCoculture_24hrs


title: Donor16_TumorCoculture_24hrs


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

description: 10x Genomics


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

description: 10x Genomics

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

value: midbrain protocol (M)


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

description: 10x Genomics

value: striatum protocol (S)


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

description: 10x Genomics


title: Tg_lactobacillus_murinus_RNAseq_bio_rep_3

city: SAN DIEGO

first: Xinyi

state: California

address: 9500 Gilman Dr, La Jolla

department: Pathology

institute: University of California, San Diego

description: RNAseq of single lactobacillus murinus species isolated from 41-week-age Tg 5XFAD Alzheimer's mice feces

data_processing:
Raw reads generated by RNA-seq experiments were quality controled first.
QC steps: Remove adapter sequences from the reads; Trim and remove bases at the 5’ end that are not A, G, C, or T; Trim the ends of reads with low sequencing quality (sequencing quality value less than Q20); Remove reads where the proportion of bases containing N reaches 10%; Discard small fragments less than 25bp in length after adapter removal and quality trimming.
Then, we mapped the reads to rfam to determine rRNA contamination.
Next, we mapped reads to the reference genome of the species generated in this study.
Genes were further annotated with functional database like NR, Swiss-Prot, Pfam, COG, GO, KEGG
Assembly: lactobacillus murinus
Supplementary files format and content: prokaryotic_WT_Tg_Lm_RNA_seq_processed_expression_matrix.csv. This csv file containing the log10(TPM+1) RNA expression values of each sample and the functional annotation results of each identified expressed genes.

organism: Ligilactobacillus murinus

growth_protocol: Lactobacillus murinus strains from either WT or Tg were cultured under anaerobic condition in the MRS culture medium. After passaging for three generations to reach log-phase growth, collect bacteria pellets and subjected to RNA extraction.

extract_protocol:
Total RNA Extraction Total RNA was extracted from tissue samples, and its concentration and purity were measured using Nanodrop2000
Removal of rRNA, fragmentation of mRNA, reverse Transcription of cDNA, adaptor Ligation. Then, digestion of the Second cDNA Strand with UNG Enzyme Before PCR amplification, the second cDNA strand is digested with UNG enzyme, so that the library contains only the first strand of cDNA.

value: bacteria

value: Tg


title: Donor14_TumorCoculture_12hrs


title: Donor16


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

description: 10x Genomics

value: day 0


title: Tg_lactobacillus_murinus_RNAseq_bio_rep_2


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

description: 10x Genomics

value: female


title: WT_lactobacillus_murinus_RNAseq_bio_rep_3

description: RNAseq of single lactobacillus murinus species isolated from 41-week-age WT mice feces

value: WT


title: WT_lactobacillus_murinus_RNAseq_bio_rep_2


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

description: 10x Genomics

value: brain organoid tissue


title: WT_lactobacillus_murinus_RNAseq_bio_rep_1


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

description: 10x Genomics

value: day 80


title: x6

city: taian

first: zb

last: Ji

address: Daizong street NO.61,

institute: shandong agricultural university

data_processing:
The original data format of the off-line data sequenced by Nanopore is fast5 format, which contains all the original sequencing signals. After Base Calling analysis by GUPPY (version: 5.0.16) software, the data in fast5 format is converted into fastq.gz format.
The quality of ONT original sequencing data is controlled. According to the quality value of sequencing data (the threshold value is 7 by default), those above the threshold value are pass and those below the threshold value are fail.
The original sequencing data is filtered to get clean reads, which are still stored in fastq.gz format.
Use NanoFilt (version: 2.8.0; Parameter: -q 7 -l 50)(De Coster et al., 2018) filters the original fastq.gz data to obtain valid data for subsequent analysis, and uses SeqKit (version: 0.12.0; Parameter: default)(Shen et al., 2016) statistics.
Identification of full-length sequences in valid sequencing data by Pychopper software
Assembly: According to minimap2 (version: 2.17-r941；; Parameters: -ax splice -uf -k14)(Li, 2018) The filtered full-length sequence was compared with the reference gene.
Supplementary files format and content: README
Library strategy: ONT-seq

organism: Ovis aries

source_name: hypothalamus

extract_protocol:
Experimental steps of RNA extraction：（1）Weighing 15mg-30mg of sample, grinding with liquid nitrogen, adding TRK Lysis Buffer or adding TRK Lysis Buffer to homogenize with homogenizer, transferring the lysate to a homogenizing column, putting the homogenizing column into a 2mL centrifuge tube, centrifuging at room temperature of 14,000xg for 2min to remove insoluble impurities, and collecting filtrate;(2) adding 70% ethanol with the same volume into the filtrate, and vortex mixing;(3) Put the RNA binding column into a collection tube, transfer the mixed solution obtained in the second step (the mixed solution transferred each time is less than or equal to 700 L), centrifuge at room temperature of 10000xg for 1min, and discard the filtrate;(4) repeat step 3 until all the mixed solution is bound to the RNA binding column;(5) Put the RNA binding column into the collection tube, add 500µl RNA Wash Buffer I into the binding column, centrifuge at 10000xg for 30s, and discard the filtrate;(6) Put the RNA binding column back into the collection tube, add 500µl RNA Wash Buffer II into the binding column, centrifuge at 10000xg for 1min, and discard the filtrate;(7) repeat step 6;(8) Put the RNA binding column back into the collection tube, and centrifuge at 10000xg for 2 min;(9) Put the RNA binding column into a new 1.5mL centrifuge tube, add 30-70L Nuclease-Free Water into the binding column, and centrifuge at 10000xg for 2min to elute RNA;(10)Nanodrop, Qbuit and electrophoretic quality inspection.
Steps for building a full-length transcription library (using ONT's kit: SQK-PCS109+SQK-PBK004): (1) Take 500 ng of Total RNA samples qualified in quality inspection, and adjust the volume to 9 ul by using Nuclease Free Water; (2) connecting a reverse transcription primer; (3). Reverse transcription reaction; (4) amplification reaction; (5) purifying with AMPure beads magnetic beads; (6) sequencing linker connection; (7) configuring a computer library; (8) On the computer: the library was Loading into the R9.4 sequencing chip, and the Prometheon Sequencer (Oxford Nano Pore Technologies, Oxford, UK) was used for sequencing for 48-72 hours.

value: hypothalamus

tag: group

value: LP group


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

description: 10x Genomics

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


title: x5


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

description: 10x Genomics

value: day 16


title: x4


title: Donor14


title: x3

value: HP group


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

description: 10x Genomics

value: dorsal protocol (D)


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

description: 10x Genomics

value: day 40


title: x2


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

description: 10x Genomics

value: day 13


title: metVali1_OCC_lib2

city: Worcester

first: Xuhang

last: Li

state: Massachusetts

address: 55 N Lake Ave

department: Department of Systems Biology

institute: University of Massachusetts Medical School

description: Multiplexed RNA-seq library generated by Worm Perturb-seq (WPS) technology. Contains 63 samples for biological triplicate of a series of RNAi knockdowns and metabolite supplementation treatments. To analyze the data, refer to our publication and supplementary files for the metadata (barcode) table and WPS data processing pipeline.

data_processing:
As part of the WPS data processing pipeline, raw reads were processed using an in-house dolphinNext pipeline to generate a gene-by-sample read count matrix.
Raw reads were demultiplexed by a homemade python script that extracts the barcode information from read 1 and combines that with read 2.
The processed reads were passed to Trimmomatic (v0.32) to remove polyA and adaptor sequences.
Next, reads were aligned to the C. elegans genome (WormBase WS279) by STAR (parameter: --runThreadN 4 --alignIntronMax 25000 --outFilterIntronMotifs RemoveNoncanonicalUnannotated).
Finally, the output bam file was processed by ESAT to obtain the read counts of genes. In ESAT, we used an extension window of 1000 bp and the ‘proper’ method of multiple mappings. Unique Molecular Identifier (UMI) features were not used by setting umiMin = 1. Read counts, rather than UMI counts, were used as the gene expression quantity. We did not observe significant PCR duplicates during the development of our method (i.e., read counts highly correlate with UMI counts, data not shown), which is consistent with the low number of PCR cycles for library construction. Therefore, we directly used the read counts regardless of the presence of UMI in our library.
Assembly: WormBase WS279
Supplementary files format and content: a comma-separated values (CSV) file for the gene-by-sample read count matrix
Supplementary files format and content: a comma-separated values (CSV) file detailed annotation of sample barcode and sample information for all libraries included here

organism: Caenorhabditis elegans

source_name: WPS multiplexed RNA-seq library - gene knockdowns related to one carbon cycle metabolism w/ and w/o B12 or choline supplementation - lib2

growth_protocol: The N2 strain was used as the wild-type strain. Animals were maintained at 20°C on nematode growth media (NGM) and fed with E. coli HT115 containing the empty RNAi vector L4440. In RNAi experiments, animals were fed with the RNAi bacteria from first larval (L1) stage, followed by incubation at 20°C for approximately 63 hours to collect gravid adults. To prepare PFA-killed HT115 diet, we followed established protocols as described previously (Safa Beydoun,Communications Biology, 2021). The animals fed on PFA-killed HT115 developed slightly slower, therefore were harvested at 65 hours post L1.

extract_protocol:
Animals were transferred to 96-well plates for high-throughput RNA extraction following protocol described in the WPS method paper. Importantly, this method only extracts total RNA from adult animal tissues and leaves any eggs intact.
Extracted total RNA was barcoded during reverse transcription to enable early pooling of samples. Multiplexed RNA-seq libraries each containing ~50 samples were constructed following a protocol adapted from the CEL-seq2 single-cell RNA-seq library construction method (Hashimshony, Genome Biology, 2016). For detailed protocols, refer to our WPS method paper. This library construction method produces a multiplexed RNA-seq library comprising ~50 samples.

treatment_protocol: RNAi treatments were performed by feeding HT115 bacteria expressing corresponding dsRNA, as stated in "growth protocol". Double knockdowns were performed using newly constructed RNAi clones that expressed a dsRNA covering both targeted genes, each with ~500bp fragment aligned to the targeted gene's protein coding region. Feeding C. elegans with bacteria expressing double RNAi in one plasmid was shown to have higher knockdown efficiency than feeding a mixture of bacteria that each expressed a single dsRNA species (Kyoengwoo Min, Biotechniques, 2010). Metabolite supplementation was achieved through supplementing metabolites in the NGM plate with final concentrations labeled in corresponding metadata information column.

value: Whole animal (excluding eggs)

tag: strain

tag: developmental stage

value: Gravid adult (63-66 hours post L1 seeding)

value: Hermaphrodite

value: Including vector control (L4440) RNAi and RNAi knockdowns of genes related to Met/SAM cycle (pmt-1, metr-1, mthf-1, cbs-1,  metr-1/cbs-1 double knockdown) with and without the supplementation of vitamin B12 or choline


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

description: 10x Genomics

value: day 25


title: Tg_lactobacillus_murinus_RNAseq_bio_rep_1

value: bacteria

value: Tg


title: x1


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

description: 10x Genomics

value: brain organoid tissue

value: female

value: striatum protocol (S)


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

description: 10x Genomics

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

value: male

value: day 120

value: ventral protocol (V)


title: PFA_killed_HT115_rep3

description: Column name in processed data matrix is "PFA_rep3".Note: the provided raw data are demultiplexed single-end reads from a multiplexed RNA-seq library constructed by WPS method

source_name: C. elegans fed PFA-killed HT115 bacteria, replicate 3

value: Animals were fed on paraformaldehyde-killed HT115 bacteria with empty vector control (L4440), without induction of dsRNA expression


title: PFA_killed_HT115_rep2

description: Column name in processed data matrix is "PFA_rep2".Note: the provided raw data are demultiplexed single-end reads from a multiplexed RNA-seq library constructed by WPS method

source_name: C. elegans fed PFA-killed HT115 bacteria, replicate 2


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

description: 10x Genomics

value: day 40


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

description: 10x Genomics

value: day 80


title: PFA_killed_HT115_rep1

description: Column name in processed data matrix is "PFA_rep1". Note: the provided raw data are demultiplexed single-end reads from a multiplexed RNA-seq library constructed by WPS method

source_name: C. elegans fed PFA-killed HT115 bacteria, replicate 1

value: Whole animal (excluding eggs)


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

description: 10x Genomics

value: day 13


title: live_HT115_rep2

description: Column name in processed data matrix is "live_rep2". Note: the provided raw data are demultiplexed single-end reads from a multiplexed RNA-seq library constructed by WPS method

source_name: C. elegans fed live HT115 bacteria, replicate 2

value: Gravid adult (63-66 hours post L1 seeding)

value: Hermaphrodite

value: Animals were fed on HT115 bacteria with empty vector control (L4440), without induction of dsRNA expression


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

description: 10x Genomics


title: live_HT115_rep3

description: Column name in processed data matrix is "live_rep3". Note: the provided raw data are demultiplexed single-end reads from a multiplexed RNA-seq library constructed by WPS method

source_name: C. elegans fed live HT115 bacteria, replicate 3


title: live_HT115_rep1

description: Column name in processed data matrix is "live_rep1". Note: the provided raw data are demultiplexed single-end reads from a multiplexed RNA-seq library constructed by WPS method

source_name: C. elegans fed live HT115 bacteria, replicate 1


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

description: 10x Genomics

source_name: brain organoid tissue


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

description: 10x Genomics

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

value: dorsal protocol (D)


title: 1-week post traumatic injury, rep4

city: Fukuoka

first: Keitaro

last: Yamagami

address: 3-1-1, Maidashi, Higashi-ku

institute: Kyushu University

data_processing:
RNA quality was assessed by Bioanalyzer (Agilent) to ensure that RIN (RNA integrity number) is over 7.0 and A260/280 and 260/230 ratios were over 1.7. First-strand cDNAs were transcribed to the 5’ end of capped RNAs, attached to CAGE “barcode” tags, with sequenced CAGE tags mapped to the mouse mm9 genome using BWA software (version 0.5.9) after discarding ribosomal or non-A/C/G/T base-containing RNA sequences. For tag clustering, CAGE-tag 5’ coordinates were input for RECLU clustering, with the maximum irreproducible discovery rate (IDR) and minimum count per million (CPM) value both set to 0.1.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include CPM values for each sample.

source_name: brain

growth_protocol: All mice had access ad libitum to standard mouse food and water and were housed under a 12-h light/dark cycle for the duration of the study.

extract_protocol:
Extraction of total RNA was performed using RNeasy MiNi kit (QIAGEN) following manufacturer's protocol.
CAGE libraries were sequenced using single end reads of 75nt on a NextSeq 500 instrument (Illumina).

treatment_protocol: For gene expression, 11-week-old male mice (C57BL/6NCrSlc) were anesthetized, and small midline skin incisions were made. Craniotomy (2×2 mm) over the motor cortex was performed using an electric drill (Minitor Co., Ltd., Tokyo, Japan) and a small cavity (0.5 to 2.5 mm rostral to the bregma, 0.5 to 2.5 mm lateral to the midline, and 1 mm in depth from the cortical surface) was made by aspirating the cortical tissue. After induction of euthanasia by cervical dislocation, whole brains were extracted immediately (n=4) or one week after the lesion (n=4). Whole brains were then transected using a brain slicer (Muromachi Kikai Co., Ltd., Tokyo, Japan), and brain tissues adjacent to the cavity with a 1.0 mm margin were collected.

value: brain

value: traumatic injury


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

description: 10x Genomics

value: brain organoid tissue

value: day 16

value: striatum protocol (S)


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

description: 10x Genomics

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

value: male


title: metVali1_OCC_lib1

source_name: WPS multiplexed RNA-seq library - gene knockdowns related to one carbon cycle metabolism w/ and w/o B12 or choline supplementation - lib1

value: Including vector control (L4440) RNAi and RNAi knockdowns of genes related to Met/SAM cycle (sams-1, ahcy-1, gcst-1, mel-32,  gcst-1/mel-32 double knockdown) with and without the supplementation of vitamin B12 or choline


title: 1-week post traumatic injury, rep3


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

description: 10x Genomics

value: day 0


title: 1-week post traumatic injury, rep2


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

description: 10x Genomics

value: day 80

value: midbrain protocol (M)


title: 1-week post traumatic injury, rep1


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

description: 10x Genomics

value: day 40


title: No-delay, rep4


title: No-delay, rep3


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

description: 10x Genomics


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

description: 10x Genomics

value: day 25

value: ventral protocol (V)


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

description: 10x Genomics

value: day 120


title: No-delay, rep2


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

description: 10x Genomics


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

description: 10x Genomics


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

description: 10x Genomics


title: No-delay, rep1


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

description: 10x Genomics

value: day 13


title: S18_MutK

city: Berlin

first: Achim

last: Leutz

address: Robert-Rössle-Straße 10

institute: Max Delbrück Center

data_processing:
Raw sequencing reads were aligned to the mm10 reference genome using STAR version 2.7.9a.
Htseq-count version 0.1 was applied for gene expression quantification.
Normalization and differential gene expression were performed with DESeq2
Assembly: mm10
Supplementary files format and content: xlsx file includes DESeq2 normalized counts for each Sample

source_name: v-Abl transformed pre-B cell line

growth_protocol: Cells were cultivated in complete DMEM (10% fetal bovine serum (FBS), 10 mM HEPES and penicillin/streptomycin) supplemented with 50 mM β-mercaptoethanol.

extract_protocol:
After GFP-sorting, cell pellets were resuspended in RNA lysis buffer (RNeasy Kit, Qiagen) and stored at -80°C before being processed using RNAeasy Kit (Qiagen) according to manufacturer's protocol.
For RNA-seq, 1 ug of total RNA was used. Preparation of barcoded mRNA-seq library and sequencing using NextSeq500 platform (Illumina) with paired-end reading at 75 bps read-length were performed at the EMBL Genomics Core Facility (Heidelberg, Germany)

treatment_protocol: Retroviral supernatant containing various C/EBP constructs was added to dKO-B cells together with 8 ug/mL polybrene (Sigma). Cells were infected by spinoculation at 2000 rpm at 37°C for 1 hour, following by overnight incubation. Cells were then washed and resuspended in fresh medium. After virus infection, EGFP+ cells were sorted at day 4 p.i. and subjected to bulk RNA-sequencing

value: MutK

value: v-Abl transformed pre-B cell line

value: retrovirally infected, EGFP+ sorted day 4 p.i.


title: S19_MutK


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

description: 10x Genomics

value: brain organoid tissue

value: dorsal protocol (D)


title: S17_MutK


title: S16_MutL

value: MutL


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

description: 10x Genomics

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


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

description: 10x Genomics

value: male


title: S15_MutL


title: S14_MutL


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

description: 10x Genomics


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

description: 10x Genomics


title: S12_MutA

value: MutA


title: S20_MutK


title: S13_MutL


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

description: 10x Genomics

value: striatum protocol (S)


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

description: 10x Genomics

value: day 16


title: S11_MutA


title: S10_MutA


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

description: 10x Genomics

value: midbrain protocol (M)


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

description: 10x Genomics

value: day 0


title: S9_MutA


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

description: 10x Genomics

value: day 80


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

description: 10x Genomics


title: S7_WT

value: WT


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

description: 10x Genomics

value: day 120


title: S5_WT


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

description: 10x Genomics

value: day 40


title: S2_MiEG

value: MiEG


title: S4_MiEG

value: v-Abl transformed pre-B cell line


title: Sample ns7 technical replicate d

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

country: France

institute: IBENS

description:
2017_544d
Blood vessels of sciatic nerves, sample ns7, technical replicate d

data_processing:
Illumina bcl2fastq 2.18.0.12 software used for basecalling.
The analyses were performed using the Eoulsan pipeline version 2.4. Before mapping, poly N read tails were trimmed, reads ≤40 bases were removed, and reads with quality mean ≤30 were discarded. Reads were then aligned against the Rattus norvegicus genome (GRCm38 from Ensembl version 88) using the STAR mapper (version 2.7.2d, with –outSAMunmapped Within parameter). Alignments from reads matching more than once on the reference genome were removed. To compute gene expression, Mus musculus GTF genome annotation version 88 from Ensembl database was used. All overlapping regions between alignments and referenced exons were counted and aggregated by genes using HTSeq-count 0.5.3.
Assembly: GRCm38 from Ensembl 88
Supplementary files format and content: tab-delimited text files include transcripts counting for each Sample

source_name: Blood vessels of sciatic nerves

extract_protocol:
Total mRNAs were extracted and purified using the NucleoSpin RNA XS kit
Messenger (polyA+) RNAs were purified from 300 ng of total RNA using oligo(dT). Libraries were prepared using the strand specific RNA-Seq library preparation TruSeq Stranded mRNA kit (Illumina).

value: Blood vessels of sciatic nerves


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

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

value: day 13


title: Sample ns7 technical replicate c

description:
2017_544c
Blood vessels of sciatic nerves, sample ns7, technical replicate c


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

description: 10x Genomics

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

value: female

value: ventral protocol (V)


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

description: 10x Genomics


title: Sample ns7 technical replicate b

description:
2017_544b
Blood vessels of sciatic nerves, sample ns7, technical replicate b


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

description: 10x Genomics

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

value: male

value: dorsal protocol (D)


title: Sample ns7 technical replicate a

description:
2017_544a
Blood vessels of sciatic nerves, sample ns7, technical replicate a


title: S8_WT

value: retrovirally infected, EGFP+ sorted day 4 p.i.


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

description: 10x Genomics

value: day 25


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

description: 10x Genomics

value: striatum protocol (S)


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

description: 10x Genomics


title: Sample ns6 technical replicate c

description:
2017_543c
Blood vessels of sciatic nerves, sample ns6, technical replicate c


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

description: 10x Genomics

value: midbrain protocol (M)


title: Sample ns6 technical replicate d

description:
2017_543d
Blood vessels of sciatic nerves, sample ns6, technical replicate d


title: S6_WT

value: WT


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

description: 10x Genomics

value: day 40


title: Sample ns6 technical replicate b

description:
2017_543b
Blood vessels of sciatic nerves, sample ns6, technical replicate b


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

description: 10x Genomics


title: Sample ns4 technical replicate d

description:
2017_541d
Blood vessels of sciatic nerves, sample ns4, technical replicate d


title: S3_MiEG

value: MiEG


title: Sample ns4 technical replicate c

description:
2017_541c
Blood vessels of sciatic nerves, sample ns4, technical replicate c


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

description: 10x Genomics


title: Sample ns6 technical replicate a

description:
2017_543a
Blood vessels of sciatic nerves, sample ns6, technical replicate a


title: S1_MiEG

value: v-Abl transformed pre-B cell line


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

description: 10x Genomics

value: day 16


title: Sample ns4 technical replicate b

description:
2017_541b
Blood vessels of sciatic nerves, sample ns4, technical replicate b

value: Blood vessels of sciatic nerves


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

description: 10x Genomics

value: brain organoid tissue

value: day 80


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

description: 10x Genomics

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

value: female


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

description: 10x Genomics

value: day 120


title: Sample br7 technical replicate c

description:
2017_540c
Brain blood vessels, sample br7, technical replicate c

source_name: Brain blood vessels

value: Brain blood vessels


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

description: 10x Genomics


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

description: 10x Genomics

value: dorsal protocol (D)


title: Sample ns4 technical replicate a

description:
2017_541a
Blood vessels of sciatic nerves, sample ns4, technical replicate a


title: Sample br7 technical replicate b

description:
2017_540b
Brain blood vessels, sample br7, technical replicate b


title: Sample br7 technical replicate a

description:
2017_540a
Brain blood vessels, sample br7, technical replicate a


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

description: 10x Genomics


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

description: 10x Genomics


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

description: 10x Genomics

value: day 13


title: Sample br6 technical replicate c

description:
2017_539c
Brain blood vessels, sample br6, technical replicate c


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

description: 10x Genomics

value: day 25


title: Sample br6 technical replicate d

description:
2017_539d
Brain blood vessels, sample br6, technical replicate d


title: Sample br6 technical replicate b

description:
2017_539b
Brain blood vessels, sample br6, technical replicate b


title: Sample br6 technical replicate a

description:
2017_539a
Brain blood vessels, sample br6, technical replicate a


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

description: 10x Genomics

value: day 0


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

description: 10x Genomics

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

value: ventral protocol (V)


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

description: 10x Genomics


title: Sample br4 technical replicate c

description:
2017_537c
Brain blood vessels, sample br4, technical replicate c


title: Sample br4 technical replicate b

description:
2017_537b
Brain blood vessels, sample br4, technical replicate b


title: Sample br4 technical replicate a

description:
2017_537a
Brain blood vessels, sample br4, technical replicate a


title: Sample br4 technical replicate d

description:
2017_537d
Brain blood vessels, sample br4, technical replicate d


title: SH-SY5Y cells/ etoposide#3

city: Chengdu City

first: xiangyu

last: jin

address: No. 24, South Section 1, First Ring Road

institute: sichuan university

data_processing:
StringTie version 2.1.4
aligning the RNA sequencing reads to the reference genome using alignment tool HISAT2 to get DMSO and etoposide bam file
Calling StringTie version 2.1.4 for transcriptome assembly
Assembly: hg18
Supplementary files format and content: The transcriptomes of each sample

growth_protocol: SH-SY5Y cells were cultivated in DMEM with 10 % FBS and maintained at 37 °C in a 5 % CO2 environment.

extract_protocol:
Cell lysis was carried out using TRIzol reagent, followed by total RNA extraction.
RNA lilbraries for RNA-seq were prepared using SMARTER mRNA-Seg Library Prep Kit following manufacturer's protocols

treatment_protocol: SH-SY5Y was treated with etoposide at a concentration of 2 µm for 12 h, and cells were harvested for RNA extraction

value: WT


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

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: striatum protocol (S)


title: Sample br7 technical replicate d

description:
2017_540d
Brain blood vessels, sample br7, technical replicate d


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

description: 10x Genomics


title: SH-SY5Y cells/ etoposide#2

value: etoposide at a concentration of 2 µm for 12 h


title: SH-SY5Y cells/ etoposide#1


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

description: 10x Genomics

value: day 40


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

description: 10x Genomics

value: day 16


title: SH-SY5Y cells/ DMSO#2

value: DMSO


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

description: 10x Genomics

value: brain organoid tissue


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

description: 10x Genomics


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

description: 10x Genomics

value: midbrain protocol (M)


title: SH-SY5Y cells/ DMSO#1


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

description: 10x Genomics

value: female


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

description: 10x Genomics

value: day 80


title: NKX_IP

city: Guang Zhou

first: Qun

last: Miao

address: Huangpu avenue

institute: Jinan University

library_source: genomic

data_processing: none provided

molecule: genomic DNA

source_name: Human colorectal cancer

extract_protocol: none provided

value: Human colorectal cancer

value: TPCs

value: stromal cell

value: NKX2-3 overexpression

value: Transfection of overexpressing lentivirus


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

city: Vienna

first: Julia

address: Dr. Bohr Gasse 9

description: 10x Genomics

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

value: day 13


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

description: 10x Genomics

value: ventral protocol (V)


title: NKX_Input


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

description: 10x Genomics

value: day 120

value: dorsal protocol (D)


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

description: 10x Genomics


title: BMDM-BEVpH8_3

city: Cincinnati

first: Guo-Chang

last: Fan

state: ohio

address: 231 Albert Sabin Way

department: Pharmacology & Systems Physiology

institute: University of Cincinnati

description: BMDM-Ctrl_vs_BMDM-BEVpH8.genes.deseq.res.csv

data_processing:
Isas (3.19.5.13)
SAMtools (0.1.20)
STAR (Aligner, STAR_2.6.1a)
Salmon Quantificartion (0.11.2)
Illumina Annotation Engine (2.0.10.0)
Assembly: Mus musculus (mm10)
Supplementary files format and content: *.genes.deseq.res.csv

source_name: Bone marrow derived macrophages

growth_protocol: Mouse bone marrow monocytes were isolated and cultured/differentiated into bone marrow-derived macrophages (BMDMs). The BMDMs were cultured in complete culture medium (DMEM supplemented with 15% of L929 cell culture supernatant, 10% FBS, 1% penicillin/streptomycin solution), and cultured in a humidified atmosphere of 5% CO2 at 37◦C.

extract_protocol:
RNA was extracted using the RNeasy kit (Qiagen, Cat. 217004). 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The BMDMs were treated with BEVpH5, BEVpH6.5, BEVpH8, or PBS as a control for 12 h, followed by isolating total RNAs for RNA-seq

value: Wild type

tag: age

value: 6-8 weeks


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

last: Naas

institute: University of Vienna

description: 10x Genomics


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

description: 10x Genomics

value: day 40


title: BMDM-BEVpH8_1


title: BMDM-BEVpH6.5_3

description: BMDM-BEVpH6.5_vs_BMDM-BEVpH8.genes.deseq.res.csv


title: BMDM-BEVpH6.5_2


title: BMDM-BEVpH8_2


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

description: 10x Genomics

value: brain organoid tissue

value: day 25


title: BMDM-BEVpH6.5_1


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

description: 10x Genomics

value: female


title: SH-SY5Y cells/ DMSO#3

value: WT

value: DMSO


title: BMDM-BEVpH5_3

description: BMDM-BEVpH5_vs_BMDM-BEVpH8.genes.deseq.res.csv


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

description: 10x Genomics

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


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

description: 10x Genomics

value: day 80


title: BMDM-BEVpH5_2


title: BMDM-BEVpH5_1


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

description: 10x Genomics


title: BMDM-Ctrl_3

value: PBS


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

description: 10x Genomics


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

description: 10x Genomics


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

description: 10x Genomics

value: striatum protocol (S)


title: BMDM-Ctrl_1


title: BMDM-Ctrl_2


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

description: 10x Genomics


title: RADICL_H3K27me3_IP_1FA_5

city: Yokohama

first: XUFENG

last: SHU

state: Kanagawa

address: 1 Chome-7-22 Suehirocho, Tsurumi Ward

department: IMS

institute: RIKEN

description:
total RNA and genomic DNA
RADICL_K27me3_IP_RNA_DNA_siginificant_interactions.tsv.gz

library_source: other

data_processing:
Basecalls performed using CASAVA version 1.8.2
RNA and DNA tags at both ends of the adapter were extracted from raw sequencing reads using TagDust2 (ver. 2.31).
PCR duplicates were removed from paired RNA-DNA tags using FastUniq.
Ribosomal RNAs were identified and removed from the extracted RNA tags using RNAdust (ver. 1.0.6) with a ribosomal DNA repeating unit (GenBank: BK000964.2).
RNA and DNA tags were aligned to the mouse genome using STAR (ver. 2.5.0a) and BWA (ver. 0.7.15-r1140).
Assembly: mm10
Supplementary files format and content: Two tab-delimited text files including RADICL_H3K27me3_input and RADICL_H3K27me3_IP statistically significant RNA-DNA interaction pairs.
Library strategy: RADICL-seq

molecule: other

growth_protocol: mESCs  were cultured in DMEM supplemented with 15% fetal bovine serum, 0.1 mM 2-mercaptoethanol, 1000 U/mL Leukemia Inhibitory Factor, and 1× NEAA.

extract_protocol:
Around 20 million mouse cells were crosslinked with 1% formaldehyde. Nuclei were isolated, washed, and genomic DNA was sheared by controlled DNase I digestion. Genomic DNA was end-repaired and dA-tailed. During dA-tailing, RNA is treated with RNase H. After washes, nuclei were mixed with RADICL-seq adapter and T4 RNA Ligase 2-truncated KQ for ssRNA ligation. Subsequently, nuclei were resuspended in T4 DNA ligase solution for ligation of RADICL-seq adapter to genomic DNA. The nuclear membrane was disrupted by sonication and immunoprecipitation was performed by using anti-H3K27me3 antibody with RNA-adaptor double-strand-DNA chimeric molecules. In parallel, we kept ten percentage of RNA-adaptor double-strand-DNA chimeric molecules and prepared libraries without antibody selection as the Input sample. RNA- and DNA-ligated adapter molecules were first reverse-crosslinked by Proteinase K digestion at 65°C, then precipitated and used for library preparation.
The RNA ligated to the RADICL-seq adapter was first reverse transcribed with SuperScript IV and then converted into double stranded DNA by second strand synthesis. Newly formed dsDNA molecules containing RADICL-seq adapter were first digested with EcoP15I for generate paired-end tags, ligated with sequencing linkers and then affinity-purified by Streptavidin-conjugated beads. Recovered dsDNA was PCR amplified to generate libraries for Illumina sequencing and size-selected using a 6% native polyacrylamide gel.

tag: fraction

value: IP

value: embryonic stem cells

tag: antibody


title: RADICL_H3K27me3_IP_1FA_8


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

description: 10x Genomics

value: midbrain protocol (M)


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

description: 10x Genomics

value: day 16


title: RADICL_H3K27me3_IP_1FA_3


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

description: 10x Genomics

value: day 0


title: RADICL_H3K27me3_IP_1FA_4


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

description: 10x Genomics

value: day 120


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

description: 10x Genomics


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

description: 10x Genomics


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

description: 10x Genomics


title: RADICL_H3K27me3_IP_1FA_2


title: RADICL_H3K27me3_IP_1FA_1


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

description: 10x Genomics

value: dorsal protocol (D)


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

description: 10x Genomics

value: day 40


title: RADICL_H3K27me3_input_1FA_7

description:
total RNA and genomic DNA
RADICL_K27me3_input_RNA_DNA_siginificant_interactions.tsv.gz

value: input


title: RADICL_H3K27me3_input_1FA_6


title: RADICL_H3K27me3_input_1FA_8


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

description: 10x Genomics

value: brain organoid tissue

value: day 13


title: RADICL_H3K27me3_IP_1FA_6


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

description: 10x Genomics

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

value: female

value: ventral protocol (V)


title: RADICL_H3K27me3_IP_1FA_7


title: RADICL_H3K27me3_input_1FA_4


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

description: 10x Genomics

value: day 80


title: RADICL_H3K27me3_input_1FA_2


title: RADICL_H3K27me3_input_1FA_3


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

description: 10x Genomics


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

description: 10x Genomics

value: day 25


title: RADICL_H3K27me3_input_1FA_1


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

description: 10x Genomics

value: striatum protocol (S)


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

description: 10x Genomics


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

description: 10x Genomics


title: 7166.MR.144_5

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street

department: Neuroscience

institute: Medical University of South Carolina

data_processing:
Bulk RNA-seq reads were aligned with STAR 2.7.1a to the reference sequence (mm10 from UCSC). Mouse reference was used for gene annotation and counting (gencode M27). Uniquely mapped reads were quantified using featureCounts using protein coding genes by gene.
Assembly: Mouse mm10
Supplementary files format and content: tab-delimited text files raw counts for each sample

source_name: Spleen

growth_protocol: T cells were stimulated with gp100 antigen (1ug/mL) and cultured in IMDM media supplemented with 10% FBS + 100 IU IL2/mL

extract_protocol:
mRNA was extracted using TRIzol reagent, per the manufacturer's protocol
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep following manufacturer's protocols.Libraries and sequencing were performed at the Translational Sequencing Core at MUSC. RNA was harvested using RNeasy Mini Kit (Qiagen). 500 ug of total RNA was used for the construction of sequencing libraries.

treatment_protocol: T cells were treated with either vehicle control or 0.5 mM GYY4137 (H2S donor)

value: Spleen

value: CD8+ T lymphocytes

value: WT

value: H2S treatment


title: 7166.MR.144_4


title: 7166.MR.144_3

value: vehicle control


title: 7166.MR.144_2


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

description: 10x Genomics

value: midbrain protocol (M)


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

description: 10x Genomics

value: day 16


title: RADICL_H3K27me3_input_1FA_5

value: embryonic stem cells


title: 7166.MR.144_6


title: tol_DC_rMDK_3

city: Madrid

first: Xavier

last: Catena

state: Madrid

address: Melchor Fernandez Almagro 3

department: Molecular Oncology

institute: CNIO

data_processing:
RNA-seq processing:
Eightyfive-base-pair single-end sequenced reads followed adapter and polyA tail removal as indicated by Lexogen. The resulting reads were analysed with the nextpresso pipeline as follows: sequencing quality was checked with FastQC v0.11.0. Reads were aligned to the mouse genome (GRCm38/mm10) with TopHat-2.0.10 using Bowtie 1.0.0 and Samtools 0.1.19, allowing 3 mismatches and 20 multihits. The Gencode vM20 gene annotation for GRCm38 was used. Read counts were obtained with HTSeq. Differential expression and normalization was performed with DESeq2, filtering out those genes where the normalized count value was lower than 2 in more than 50% of the samples.
Assembly: GRCm38/mm10
Supplementary files format and content: Normalized counts obtained with DESeq2

source_name: Bone marrow

growth_protocol: Bone marrow cells were cultured at 1.5x106 cells/ml in RPMI-1640 Glutamax supplemented with 10% heat-inactivated FBS, 1% non-essential amino acids, 10 mM HEPES, 1mM Sodium Pyruvate, 50 nM β-mercaptoethanol, and 50ng/ml gentamicin, with Fms Related Receptor Tyrosine Kinase 3 Ligand (FLT3LG) (50 ng/ml) for 7 days. Media supplmented with FLT3LG was renewed on day 7th.

extract_protocol:
~500ng of total RNA samples were used. Average sample RNA Integrity Number was 8 (range 5-10) when assayed on an Agilent 2100 Bioanalyzer. Sequencing libraries were prepared with the "QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina" (Lexogen, Cat.No. 015) by following manufacturer instructions.
Illumina HiSeq 2500, v4 Chemistry

treatment_protocol: Bone marrow cells were treated with or without human recombinant MIDKINE (10ng/ml) during the last 2 days of culture.

value: Bone marrow

value: bone marrow derived dendritic cells

value: MIDKINE


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

description: 10x Genomics

value: brain organoid tissue

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

value: dorsal protocol (D)


title: tol_DC_rMDK_1


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

description: 10x Genomics

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

value: female

value: day 40


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

description: 10x Genomics

value: ventral protocol (V)


title: tol_DC_Control_3

value: Control


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

description: 10x Genomics

value: day 120


title: tol_DC_Control_2

value: WT


title: tol_DC_Control_1


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

description: 10x Genomics

value: day 80


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

description: 10x Genomics


title: Dev_DC_rMDK_5

growth_protocol: Bone marrow cells were cultured at 1.5x106 cells/ml in RPMI-1640 Glutamax supplemented with 10% heat-inactivated FBS, 1% non-essential amino acids, 10 mM HEPES, 1mM Sodium Pyruvate, 50 nM β-mercaptoethanol, and 50ng/ml gentamicin, with Fms Related Receptor Tyrosine Kinase 3 Ligand (FLT3LG) (50 ng/ml) for 3 days.

treatment_protocol: Bone marrow cells were treated with or without human recombinant MIDKINE (10ng/ml) during the 3 days with FLT3LG culture.

value: bone marrow cells


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

description: 10x Genomics

value: day 16

value: midbrain protocol (M)


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

description: 10x Genomics

value: day 13


title: 7166.MR.144_1

value: Spleen

value: CD8+ T lymphocytes

value: vehicle control


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

description: 10x Genomics

value: brain organoid tissue

value: day 0


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

description: 10x Genomics

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


title: Dev_DC_control_4

value: Bone marrow


title: Dev_DC_rMDK_3

value: MIDKINE


title: Dev_DC_control_2


title: tol_DC_rMDK_2

value: bone marrow derived dendritic cells


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

description: 10x Genomics

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

value: female

value: day 25

value: dorsal protocol (D)


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

description: 10x Genomics

value: day 40

value: ventral protocol (V)


title: XUJA_2, V, day 120, biol repl 3, run 1

description: 10x Genomics

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

value: day 120


title: Dev_DC_control_1

value: bone marrow cells

value: WT

value: Control


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

description: 10x Genomics

value: brain organoid tissue

value: midbrain protocol (M)


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

description: 10x Genomics

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

value: day 80


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

description: 10x Genomics


title: XUJA_2, V, day 80, biol repl 3, run 1

description: 10x Genomics


title: XUJA_2, V, day 40, biol repl 3, run 1

description: 10x Genomics


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

description: 10x Genomics

value: day 13


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

description: 10x Genomics

value: striatum protocol (S)


title: XUJA_2, V, day 25, biol repl 3, run 1

description: 10x Genomics


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

description: 10x Genomics


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

description: 10x Genomics

value: day 16


title: XUJA_2, S, day 120, biol repl 3, run 1

description: 10x Genomics

value: female


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

description: 10x Genomics


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

description: 10x Genomics

value: day 0


title: Dev_DC_rMDK_4

value: Bone marrow

value: MIDKINE


title: XUJA_2, S, day 40, biol repl 3, run 1

description: 10x Genomics

value: day 40


title: XUJA_2, S, day 80, biol repl 3, run 1

description: 10x Genomics

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


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

description: 10x Genomics


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

description: 10x Genomics

value: day 120


title: XUJA_2, S, day 16, biol repl 3, run 1

description: 10x Genomics


title: XUJA_2, M, day 80, biol repl 3, run 1

description: 10x Genomics


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

description: 10x Genomics

value: dorsal protocol (D)


title: XUJA_2, pluripotent, day 0, biol repl 3, run 1

description: 10x Genomics


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

description: 10x Genomics


title: XUJA_2, M, day 120, biol repl 3, run 1

description: 10x Genomics


title: XUJA_2, D, day 120, biol repl 3, run 1

description: 10x Genomics


title: XUJA_2, M, day 40, biol repl 3, run 1

description: 10x Genomics


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

description: 10x Genomics


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

description: 10x Genomics

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

value: male

value: ventral protocol (V)


title: XUJA_2, M, day 16, biol repl 3, run 1

description: 10x Genomics

value: brain organoid tissue

value: midbrain protocol (M)


title: XUJA_2, D, day 40, biol repl 3, run 1

description: 10x Genomics


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

description: 10x Genomics

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

value: day 80


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

description: 10x Genomics

value: day 25


title: XUJA_2, V, day 13, biol repl 3, run 1

description: 10x Genomics

value: day 13


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

description: 10x Genomics

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


title: XUJA_2, D, day 25, biol repl 3, run 1

description: 10x Genomics

value: female


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

description: 10x Genomics


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

description: 10x Genomics


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

description: 10x Genomics


title: XUJA_2, D, day 13, biol repl 3, run 1

description: 10x Genomics


title: ROZH_5, V, day 80, biol repl 3, run 1

description: 10x Genomics

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


title: ROZH_5, V, day 120, biol repl 3, run 1

description: 10x Genomics


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

description: 10x Genomics


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

description: 10x Genomics

value: day 16


title: ROZH_5, V, day 40, biol repl 3, run 1

description: 10x Genomics

value: day 40


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

description: 10x Genomics

value: striatum protocol (S)


title: ROZH_5, V, day 25, biol repl 3, run 1

description: 10x Genomics


title: ROZH_5, V, day 13, biol repl 3, run 1

description: 10x Genomics


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

description: 10x Genomics


title: ROZH_5, S, day 120, biol repl 3, run 1

description: 10x Genomics

value: day 120


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

description: 10x Genomics


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

description: 10x Genomics


title: ROZH_5, S, day 80, biol repl 3, run 1

description: 10x Genomics


title: ROZH_5, S, day 40, biol repl 3, run 1

description: 10x Genomics


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

description: 10x Genomics


title: ROZH_5, S, day 16, biol repl 3, run 1

description: 10x Genomics


title: ROZH_5, pluripotent, day 0, biol repl 3, run 1

description: 10x Genomics

value: day 0


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

description: 10x Genomics


title: ROZH_5, M, day 120, biol repl 3, run 1

description: 10x Genomics


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

description: 10x Genomics


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

description: 10x Genomics


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

description: 10x Genomics


title: ROZH_5, M, day 16, biol repl 3, run 1

description: 10x Genomics


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

description: 10x Genomics


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

description: 10x Genomics

value: dorsal protocol (D)


title: ROZH_5, M, day 40, biol repl 3, run 1

description: 10x Genomics


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

description: 10x Genomics

value: male


title: ROZH_5, D, day 120, biol repl 3, run 1

description: 10x Genomics


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

description: 10x Genomics


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

description: 10x Genomics


title: ROZH_5, M, day 80, biol repl 3, run 1

description: 10x Genomics


title: ROZH_5, D, day 25, biol repl 3, run 1

description: 10x Genomics


title: ROZH_5, D, day 40, biol repl 3, run 1

description: 10x Genomics


title: ROZH_5, D, day 13, biol repl 3, run 1

description: 10x Genomics


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

description: 10x Genomics

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

value: ventral protocol (V)


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

description: 10x Genomics

value: brain organoid tissue


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

description: 10x Genomics


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

description: 10x Genomics


title: H9, V, day 40, biol repl 3, run 1

description: 10x Genomics

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


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

description: 10x Genomics


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

description: 10x Genomics


title: H9, V, day 120, biol repl 3, run 1

description: 10x Genomics


title: H9, V, day 13, biol repl 3, run 1

description: 10x Genomics


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

description: 10x Genomics


title: H9, V, day 25, biol repl 3, run 1

description: 10x Genomics


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

description: 10x Genomics

value: day 80

value: midbrain protocol (M)


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

description: 10x Genomics


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

description: 10x Genomics


title: H9, S, day 16, biol repl 3, run 1

description: 10x Genomics


title: H9, pluripotent, day 0, biol repl 3, run 1

description: 10x Genomics


title: H9, S, day 80, biol repl 3, run 1

description: 10x Genomics


title: H9, M, day 120, biol repl 3, run 1

description: 10x Genomics


title: H9, S, day 40, biol repl 3, run 1

description: 10x Genomics


title: ROZH_5, D, day 80, biol repl 3, run 1

description: 10x Genomics


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

description: 10x Genomics


title: H9, M, day 40, biol repl 3, run 1

description: 10x Genomics


title: H9, V, day 80, biol repl 3, run 1

description: 10x Genomics


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

description: 10x Genomics


title: H9, M, day 80, biol repl 3, run 1

description: 10x Genomics


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

description: 10x Genomics


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

description: 10x Genomics


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

description: 10x Genomics

value: day 25


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

description: 10x Genomics

value: day 13


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

description: 10x Genomics


title: H9, D, day 120, biol repl 3, run 1

description: 10x Genomics

value: female


title: H9, M, day 16, biol repl 3, run 1

description: 10x Genomics


title: H9, S, day 120, biol repl 3, run 1

description: 10x Genomics


title: H9, D, day 80, biol repl 3, run 1

description: 10x Genomics


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

description: 10x Genomics

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


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

description: 10x Genomics


title: H9, D, day 13, biol repl 3, run 1

description: 10x Genomics


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

description: 10x Genomics

value: day 16


title: H9, D, day 40, biol repl 3, run 1

description: 10x Genomics

value: day 40


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

description: 10x Genomics

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


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

description: 10x Genomics


title: H1, V, day 25, biol repl 3, run 1

description: 10x Genomics


title: H1, V, day 40, biol repl 3, run 1

description: 10x Genomics


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

description: 10x Genomics


title: H1, V, day 80, biol repl 3, run 1

description: 10x Genomics


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

description: 10x Genomics

value: day 120

value: striatum protocol (S)


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

description: 10x Genomics


title: H1, S, day 120, biol repl 3, run 1

description: 10x Genomics


title: H1, S, day 40, biol repl 3, run 1

description: 10x Genomics


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

description: 10x Genomics


title: H1, S, day 16, biol repl 3, run 1

description: 10x Genomics


title: H1, pluripotent, day 0, biol repl 3, run 1

description: 10x Genomics

value: day 0


title: H1, M, day 120, biol repl 3, run 1

description: 10x Genomics

value: male


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

description: 10x Genomics


title: H1, M, day 80, biol repl 3, run 1

description: 10x Genomics


title: H1, M, day 40, biol repl 3, run 1

description: 10x Genomics


title: H1, M, day 16, biol repl 3, run 1

description: 10x Genomics


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

description: 10x Genomics


title: H1, S, day 80, biol repl 3, run 1

description: 10x Genomics


title: H9, D, day 25, biol repl 3, run 1

description: 10x Genomics

value: dorsal protocol (D)


title: H1, D, day 120, biol repl 3, run 1

description: 10x Genomics


title: H1, D, day 40, biol repl 3, run 1

description: 10x Genomics


title: dcm-/dam- lambda phage DNA, M.SssI + Tet [LMD_cadC]

city: Munich

first: Raheleh

last: Salehi

state: Bavaria

address: Würmtalstraße 201

department: Chemisty

institute: LMU

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

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


title: dcm-/dam- lambda phage DNA, M.SssI [LMD_mdC]


title: H1, D, day 80, biol repl 3, run 1

description: 10x Genomics

value: brain organoid tissue


title: H1, V, day 120, biol repl 3, run 1

description: 10x Genomics

value: ventral protocol (V)


title: H1, D, day 25, biol repl 3, run 1

description: 10x Genomics