title: SM-J39RW_S441_E1-50

description:
SMART-seq v2
Cell1

source_name: Pontine nucleus

extract_protocol:
Two 8-week-old Snap25-IRES2-Cre;Ai14 mice (one from each sex) were perfused with artificial cerebrospinal fluid comprised of CaCl2 (0.5 mM), glucose (25 mM), HCl (96 mM), HEPES (20 mM), MgSO4 (10 mM), NaH2PO4 (1.25 mM), myo-inositol (3 mM), N-acetylcysteine (12 mM), NMDG (96 mM), KCl (2.5 mM), NaHCO3 (25 mM), sodium L-ascorbate (5 mM), sodium pyruvate (3 mM), taurine (0.01 mM), and thiourea (2 mM), bubbled with carbogen (95% O2 and 5% CO2). The pontine nucleus was dissected and embedded in 2% agarose, sliced into 250-µm sections with a vibratome, then subjected to enzymatic digestion with pronase (1 mg/mL) for 70 min at room temperature and trituration using fire-polished Pasteur pipettes to generate single-cell suspensions. Live single Pn neurons were isolated into 8-well strips containing SSv4 lysis buffer based on DAPI-/tdTomato+ expression using fluorescence-activated cell sorting, then stored at -80°C.
To prepare single-cell transcriptome libraries, poly-adenylated RNAs were reverse-transcribed into full-length cDNA and subjected to 18 PCR amplification cycles according to the SSv4 protocol. Single-cell libraries were indexed and prepared for Illumina sequencing using the Nextera XT DNA Library Preparation Kit. Multiplexed libraries were sequenced on HiSeq2500 sequencers to generate 100-bp paired-end reads at a depth of 2.5 million reads per cell.
SMART-seq v2 (SSv4; TakaraBio)

value: Pontine nucleus

value: Neuron


title: Neuron,iPS,rep3

status: Public on Sep 12 2024

type: SRA

city: Jerusalem

first: Batia

last: Azria

state: Israel

address: Jerusalem

country: Israel

institute: Hebrew university of Jerusalem

library_source: genomic

data_processing:
RRBS data were trimmed and quality filtered by trim galore software (v.0.3.3) using default parameters for RRBS. Read alignment (genome build mm10) and extraction of single-base resolution methylation levels were carried out by BSMAP v.2.74. For RRBS segments, we first created a pseudo RRBS genome containing only the CpG sites found in all RRBS beta samples and segmented this RRBS genome into 446,860 blocks using all our RRBS samples as reference. For RRBS segments, we first created a pseudo RRBS genome containing only the CpG sites found in all RRBS beta samples and segmented this RRBS genome into 446,860 blocks using all our RRBS samples as reference
Assembly: mm10
Supplementary files format and content: Bed

molecule: genomic DNA

organism: Mus musculus

source_name: reprogramming cell

extract_protocol:
DNA was isolated from mouse hepatocytes or from snap-frozen mouse tissues and incubated in lysis buffer (25 mM Tris-HCl (pH 8), 2 mM ethylenediaminetetraacetic acid, 0.2% sodium dodecyl sulfate, 200 mM NaCl) supplemented with 300 μg/mL proteinase K (Roche) followed by phenol:chloroform extraction and ethanol precipitation
Bisulfite-seq reduced representation

tag: cell type

value: reprogramming cell


title: SM-J39RW_S450_E1-50

city: Chapel Hill

first: Jesse

last: Niehaus

state: NC

address: 116 Manning Drive, 7008B Mary Ellen Jones Building

department: Neuroscience Center

country: USA

institute: University of North Carolina at Chapel Hill

description:
SMART-seq v2
Cell4

library_source: transcriptomic single cell

data_processing:
Single-cell fastq files were aligned to the mm10 mouse genome (GRCm38) using STAR version 2.7.3a (STARsolo) under suggested parameters for unstranded Smartseq data. Uniquely aligned exonic reads were used for quantification.
Assembly: mm10
Supplementary files format and content: comma-separated values file

molecule: polyA RNA

tag: tissue

tag: genotype


title: #2 naive CD8+ T cells, blood, 4 hour stimulation

city: Saarbrücken

first: Fabian

last: Müller

address: Campus A 2.4

country: Germany

institute: Saarland University

data_processing:
Illumina RTA3 was used for basecalling.
Sequencing data was processed using the nf-core/methylseq pipeline (version 2.2.0), using default parameters, genome assembly GRCh38 and --accel=true (DOI:10.5281/zenodo.1343417, DOI:10.1038/s41587-020-0439-x). Briefly, the pipeline employs FASTQC (version 0.11.9), trimgalore (version 0.6.7) and bismark (version 0.24.0) (DOI:10.1093/bioinformatics/btr167) for read-level quality control, adapter trimming, bisulfite-aware alignment and cytosine-level DNA methylation quantification.
Assembly: GRCh38
Supplementary files format and content: *.bismark.cov.gz files contain CpG-level methylation calls in bismark covareage format

organism: Homo sapiens

source_name: peripheral blood

extract_protocol:
PBMCs were isolated from residual blood samples from disposable kits used during routine platelet apheresis via discontinuous gradient centrifugation. CD8+ T cells were pre enriched using human anti-CD8 MicroBeads and the automated magnetic activated cell sorting (autoMACS) system (Miltenyi Biotec) according to the manufacturer’s instructions. The cells were stimulated with CMVpp65 overlapping peptide pool (Miltenyi Biotec) at a concentration of 1 µg of each peptide/ml for 4 hours. Subsequently, IFN γ secreting cells were labelled using IFN γ Secretion Assay/Detection Kit (PE) (Miltenyi Biotec; manufacturer’s protocol) and antibodies for surface protein detection. Genomic DNA was prepared from flow cytometrically sorted naive CD8+ T cells, interferon-gamma negative memory CD8+ T cells and interferon-gamma positive CD8+ T cells by using DNeasy blood and tissue kit (Qiagen, manufacturer’s protocol). Genomic DNA was bisulfite converted using the EZ DNA Methylation Kit (Zymo Research,  manufacturer’s protocol) and subjected to library preparation.
The bisulfite converted DNA was fragmented by sonication and served as input for library preparation using the Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences, manufacturer’s protocol).

treatment_protocol: Pre-enriched human CD8+ Tcells were stimulated with CMVpp65 overlapping peptide pool (Miltenyi Biotec) at a concentration of 1 µg of each peptide/ml for 4 hours in TexMACS medium (Miltenyi Biotec).

tag: donor

tag: serotype

value: CMV positiv

value: peripheral blood

value: CD8 T cell

tag: marker

tag: treatment

value: 4 hour stimulation with CMVpp65 overlapping peptide pool


title: MSC5

city: Miaoli Conunty

first: Su-Fang

last: Lin

address: No 35, Keyan Road, Zhunan Town

department: NICR

country: Taiwan

institute: National Health Research Institutes, Taiwan

library_source: transcriptomic

data_processing:
CLC Genmomic Workbench (v10)  was used for basecalling, base trimming, filtering of quality <20 and adaptor removal.
Clean reads were aligned to the human reference genome (hg38) for gene count quantitation.
After controling for batch effect, abundance measurements (TPM) for each gene (rowSums>1) in each sample were used to construct the expression matrix (Lien_MBC_2019.txt)
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files comprising TPM values of 13490 genes for 8 samples

molecule: total RNA

source_name: metaplastic breast cancer cell line

extract_protocol:
Total RNA was extracted from indicated cell lines using TRIzol reagent (Thermo Fischer Scientific, Waltham, MA, USA according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using MGIEasy RNA Library kit (SE50) (BGI, Shenzhen, China)

value: human metaplastic breast cancer (MBC)

tag: histological subtype

value: squamous metaplasia

tag: batch

tag: library preparation kit

value: MGIEasy RNA Library kit (SE50)

tag: core lab

value: Tri-I Biotech Inc., Taipei, Taiwan


title: Rat, DI, rep3

city: Berlin

first: Hanyang

last: Liu

address: Augustenburger Platz 1

department: Department of Hepatology and Gastroenterology (CCM/CVK),

institute: Charité Universitätsmedizin Berlin

data_processing:
The FASTQ files were processed and aligned to rat reference genome using MobiVision software (version2.1) with unique molecular identifier (UMI) counts summarized for each barcode. The UMI count matrix was then analyzedusing Seurat(version 4.0.0) R package.
Assembly: Rno_6
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

organism: Rattus norvegicus

source_name: Liver

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

value: Liver

tag: cell line

value: Primary

value: Liver cells

tag: strain

value: SD

value: wild-type

value: Dietary intervention


title: Neuron,iPS,rep2


title: MSC1


title: HB6 hepatoblastoma tumoroid

city: Cincinnati

first: Peng

middle: Vijaykumar

last: Wu

state: OH

address: 3333 Burnet Ave., MLC7013

institute: Cincinnati Children's Hospital Medical Center

description: 10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2
Assembly: GRCh38 3.0.0
Supplementary files format and content: Tab-separated values files and matrix files

source_name: HB6 tumoroid

extract_protocol:
Fresh tumor specimens were obtained from patients and processed for primary tumoroid culture (Wu and Nusse, Methods Mol Biol 2022). Tumoroids grown in Matrigel were harvested at P1 or P2 for single cell RNA sequencing. Briefly, dispase was added for 30 minutes at 37C with intermittent mechanical disruption of Matrigel drops. Tumoroids released from Matrigel were spun down at 50g for 5 minutes and washed twice with liver perfusion media/5% FBS. Tryple Express was added for 10-15 minutes at 37C to digest tumoroids to single cells. Liver perfusion media/5% FBS was added at the end of the digestion and cells were collected by centrifugation at 300g x 5 minutes. Cells were resuspended in William's media/10% FBS, counted, and resuspended in the appropriate volume to target 5000 cells for 10x scRNA sequencing.
Libraries were constructed according to the manufacturer's specifications (10x Genomics 3' v2 for sample HB1 and v3 for all other samples)

value: HB6 tumoroid

value: hepatoblastoma


title: HB4 hepatoblastoma tumoroid

description: 10x Genomics

source_name: HB4 tumoroid

value: HB4 tumoroid


title: Rat, DI, rep2


title: Neuron,iPS,rep1

value: reprogramming cell


title: Neuron,invivo,rep4

source_name: Neuron

value: Neuron


title: ESC66


title: HB1 hepatoblastoma tumoroid

description: 10x Genomics

source_name: HB1 tumoroid

value: HB1 tumoroid


title: Rat, Sham, rep3

value: Sham surgery


title: Neuron,invivo,rep3


title: ESC60

value: human metaplastic breast cancer (MBC)


title: VisiumHuman_9_S9_L004

city: Irvine

first: Negin

last: Rahimzadeh

state: CA

address: 3224 Biological Sciences III

institute: UCI

description:
Human_visium_ADDS_seurat_processed.rds
visium_human_11-24-21_sample_meta.csv

data_processing:
snRNA-Seq:  Gene expression quantification was performed using splitpipe (version X) from Parse Biosciences. Ambient RNA signal was quantified and corrected using Cellbender1 remove-background (v 0.2.0). Heterotypic barcode collisions were inferred using Scrublet2 (v 0.2.3). The individual snRNA-seq experiments were merged into a single anndata (v 0.8.0) object, resulting in 611,999 barcodes and 29,889 genes before quality control (QC) filtering. Various QC filters were applied, including UMIs detected, Scrublet doublet score, and percentage of mitochondrial reads. Dataset-wide cutoffs were used to remove barcodes with specific criteria. Additionally, a more stringent filter was applied to one of the snRNA-seq experiments. After QC, a total of 431,534 barcodes were retained for downstream analysis  Visium data: Sequencing reads from the human and mouse Visium experiments were processed using the 10X Genomics Spaceranger (v 1.2.1) pipeline, with GRch38 and MM10 as the respective reference transcriptomes. Spaceranger count was used to align sequencing reads to the reference, quantify gene expression, and perform a preliminary clustering analysis for each sample. Unlike the snRNA-seq dataset, we did not filter out additional spots based on sequencing QC metrics. The UMI counts matrices and fluorescent images for the human and mouse samples were combined into merged Seurat3–5 objects for the respective species.
Assembly: GRCH38, MM10
Supplementary files format and content: snRNA-Seq and Visium data were saved as R data files (.rda), with corresponding metadata as comma-separated values (.csv) files.

source_name: Prefrontal Cortex

extract_protocol:
For snRNA-seq, single nucleus suspensions were isolated from about 50mg frozen human cortex following Parse biosciences recommendation. For spatial transcriptomics, fresh frozen mouse and human brain samples were embedded in OCT medium and cryosectioned at 10um thickness and mounted on visium slides.
snRNA-seq libraries were prepared using Parse biosciences Evercode WT kit (v1). For spatial transcriptomics, 10x genomics visium kit was used following manufacturer’s protocol.

tag: group

tag: diagnosis

value: Control

tag: Sex

value: M

value: Prefrontal Cortex

tag: age


title: HB

tag: cell type

value: squamous metaplasia

value: MGIEasy RNA Library kit (SE50)

value: Tri-I Biotech Inc., Taipei, Taiwan


title: Neuron,invivo,rep2


title: HM


title: VisiumHuman_8_S8_L004

value: F

tag: tissue


title: VisiumHuman_7_S7_L004

value: AD


title: Rat, Sham, rep1

value: Liver

value: Primary

value: Liver cells

value: SD

tag: genotype

value: wild-type


title: Neuron,invivo,rep1

value: Neuron


title: HE


title: gun1-102-G-3

city: Planegg

first: Tatjana

last: Kleine

address: Großhaderner Straße 2

department: Biologie I, Botanik

institute: Ludwig-Maximilians-Universität München

data_processing:
Galaxy platform
Adaptors were removed with Trimmomatic (Bolger et al., 2014)
Sequencing quality was accessed with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Reads were first mapped with the gapped-read mapper RNA STAR (Dobin et al., 2013) to generate the coverage plots in a subsequent step
Second, the reads were mapped to the Arabidopsis genome (AtRTD3; Zhang et al., Genome Biology 2022) with Salmon and further processed using 3D RNA-Seq
Assembly: AtRTD3, based on TAIR10
Supplementary files format and content: Text file includes gene TPM for all samples

organism: Arabidopsis thaliana

source_name: green cotyledon

growth_protocol: Surface-sterilized plant seeds were sowed on half-strength MS plates containing 1% sucrose. The plates were subsequently kept in the dark at 4°C for two days. Following stratification, the seedlings were grown under a photoperiod of 16 hours (light phase) and 8 hours (dark phase) at 22°C with a light intensity of 100 μmol photons m−2 sec−1 for four days.

extract_protocol:
Total RNA from plants was isolated using Trizol (Invitrogen, Carlsbad, USA) and purified using Direct-zol™ RNA MiniPrep Plus columns (Zymo Research, Irvine, USA) according to the manufacturer’s instructions. RNA integrity and quality was assessed by an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, USA).
RNA was depleted of ribosomal RNA with the RiboMinus Plant Kit for RNA-seq (Thermo Fisher Scientific), and rRNA-free RNA was cleaned by ethanol precipitation. The directional library was prepared at Novogene Biotech (Beijing, China) with the help of the NGS Stranded RNA Library Prep Set (Novogene Biotech, PT044).

tag: ecotype

value: green cotyledon

value: Long-day growth conditions

tag: time

value: Day 4


title: Rat, DI, rep1

value: Dietary intervention


title: Rat, Sham, rep2

value: Sham surgery


title: VisiumHuman_5_S5_L004

value: Control

value: Prefrontal Cortex


title: Direct reprogramming,rep1

source_name: Transdifferentiontion cell

value: Transdifferentiontion cell


title: WDA_WT_M3

city: Kansas City

first: Irina

last: Tikhanovich

state: Kansas

address: 3901 Rainbow blvd

institute: University of Kansas Medical Center

data_processing:
24 samples were sequenced using BGISEQ platform
HISAT was used to align the clean reads to the reference genome.
Bowtie2 was used to align the clean reads to the reference genes
Assembly: GRCm38.p6
Supplementary files format and content: log2 and Qvalues

source_name: liver

extract_protocol:
Livers were removed,  and RNA was harvested using Qiagen RNA miniprep kit.
RNA libraries were prepared for sequencing using standard BGI protocols

value: liver

value: male

value: Cebpb fl/fl

value: AAV-TBG-Control + WDA 16 weeks


title: gun1-102-G-1


title: gun1-102-G-2


title: Muscle, invitro,rep4

source_name: Muscle

value: Muscle


title: WDA_WT_M1


title: VisiumHuman_4_S4_L004

value: M


title: gun1-102-M-3

source_name: marble cotyledon

value: marble cotyledon


title: Muscle, invitro,rep3


title: VisiumHuman_3_S3_L004

value: AD

value: F


title: SM-J39RW_S550_E1-50

description:
SMART-seq v2
Cell19

value: Pontine nucleus

value: Neuron


title: gun1-102-M-2

value: Long-day growth conditions

value: Day 4


title: WDA_WT_F3

value: female


title: Direct reprogramming,rep2


title: Muscle, invitro,rep2


title: WDA_WT_F2


title: gun1-102-M-1


title: VisiumHuman_6_S6_L004

value: earlyAD


title: Muscle, invitro,rep1


title: gun1-102-W-3

source_name: white cotyledon

value: white cotyledon


title: VisiumHuman_16_S16_L004

value: Prefrontal Cortex


title: MEF,Invitro,rep4

source_name: MEF

value: MEF


title: WDA_KO_M3

value: liver

value: male

value: AAV-TBG-Cre + WDA 16 weeks


title: WDA_WT_F1

value: Cebpb fl/fl

value: AAV-TBG-Control + WDA 16 weeks


title: VisiumHuman_2_S2_L004


title: VisiumHuman_15_S15_L004

value: M


title: WDA_WT_M2


title: gun1-102-W-2


title: MEF,Invitro,rep2


title: SM-J39RW_S554_E1-50

description:
SMART-seq v2
Cell22

source_name: Pontine nucleus


title: MEF,Invitro,rep1


title: MEF,Invitro,rep3


title: WDA_KO_M2


title: Col-2

source_name: cotyledon

value: cotyledon


title: VisiumHuman_14_S14_L004


title: Col-3


title: VisiumHuman_13_S13_L004

value: Control

value: F


title: WDA_KO_M1


title: Direct reprogramming,DDC,rep4

value: Transdifferentiontion cell


title: VisiumHuman_12_S12_L004


title: Direct reprogramming,DDC,rep3


title: VisiumHuman_11_S11_L004

value: AD


title: gun1-102-W-1

value: Long-day growth conditions

value: Day 4


title: female_vehicle_340

first: Angelika

last: Kusch

address: Chariteplatz 1

department: Medizinische Klinik m. S. Nephrologie und internistische Intensivmedizin

institute: Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin

data_processing:
Sequencing reads mapped with STAR 2.5.0b
Reads counted using Bioconducotr package Rsubread, with gene models assembled with Bioconductor package GenomicRanges
Normalisation and differential expression carried out with Bioconductor package DESeq2 1.26.0
Assembly: mm10_GRCm38.p4
Supplementary files format and content: Tab-delimited files: ENSEMBL gene ID, gene symbol, raw counts

source_name: renal

growth_protocol: Gt(ROSA)26Sortm4(ACTB-tdTomato,-EGFP)Luo/J; NPHS2-cre (38 male and 38 female) from internal breeding were used at the aged of 12-18 weeks.

extract_protocol:
After infusion of magnetic beads via renal artery, kidney cortex was digested and podocytes were isolated utilizing magnetic bead separation. Separation of GFP positive podocytes from single cell fraction was carried out via fluorescence-activated cell sorting (FACS). Total RNA was harvested with Trizol protocol.
NEB Next Ultra II Directional RNA Library Prep Kit was used following manufactures instructions

treatment_protocol: Mice were treated with rapamycin or respective vehicle 3x per week for 21 days

value: renal

value: podocytes

value: yes


title: VisiumHuman_10_S10_L004

value: earlyAD

value: Prefrontal Cortex


title: female_vehicle_339


title: Direct reprogramming,DDC,rep1


title: VisiumHuman_1_S1_L004


title: Col-1


title: WDA_KO_F2

value: liver

value: female


title: Res_WT_M2

value: male

value: Cebpb fl/fl

value: WDA 16 weeks + AAV-TBG-Control + 4 weeks resolution


title: Direct reprogramming,DDC,rep2


title: WDA_KO_F3

value: AAV-TBG-Cre + WDA 16 weeks


title: vh_Undetermined_S0_L004


title: Res_WT_M3


title: female_vehicle_334


title: Cholangiocyte,DDC,Rep3

source_name: Cholangiocyte

value: Cholangiocyte


title: 7_S12_L003

description:
Human_visium_ADDS_seurat_processed.rds
visium_human_Oct_2021.csv

value: F


title: Res_WT_F2


title: WDA_KO_F1


title: male_vehicle_344


title: 8_S13_L003


title: Cholangiocyte,DDC,Rep4


title: SM-J39RW_S553_E1-50

description:
SMART-seq v2
Cell21

value: Pontine nucleus

value: Neuron


title: female_vehicle_324


title: female_vehicle_318


title: Cholangiocyte,DDC,Rep2


title: Res_WT_F1


title: 6_S11_L003

value: M


title: Res_WT_F3


title: Res_KO_M3

value: WDA 16 weeks + AAV-TBG-Cre + 4 weeks resolution


title: Leaves, Tre, 48h, repeat 1

city: Xinxiang

first: Ling

last: Wang

address: Eastern HuaLan Avenue, Xinxiang City , Henan Province , China

country: China

data_processing:
Use fastp (v0.20.0) to perform quality control on the raw data, with parameters set to - q 5 -n 5
Use HISAT2 (v2.1.0) to compare grape genome Vitis_vinifera.PN40024.v4 (http://ftp.ensemblgenomes.org/pub/plants/release-53/fasta/vitis_vinifera/), with parameters set to -- novelsplicesite-outfile XX.ss.. Compare the generated Sam files and use Samtools (version: 1.9) software to convert them to BAM format and sort them. Then use the rnaseq subroutine of qualimap (v2.2.1) software to calculate the comparison results and determine the comparison efficiency.
Use StringTie (stringtie-2.1.3b. Linux_x86_64) software to assemble transcripts based on the BAM file, with parameters set to - f 0.2 - a 30 - c 5 - j 5. Use StringTie to fuse all the reconstructed results of the samples to obtain the optimized transcript structure annotation file, and set the parameter -- merge.
Use StringTie to quantify gene expression based on the optimized annotation file of gene structure and the BAM file obtained from comparison, with parameters set to - e - p 4; Use Ballgown (R script) to organize the above results and obtain the readcount matrix of gene expression; Use your own script to obtain the FPKM matrix.
Assembly: Vitis_vinifera.PN40024.v4
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

organism: Vitis vinifera

source_name: leaf

growth_protocol: The self-rooted cuttings of ‘Thompson Seedless’ were grown in a greenhouse (Henan Institute of Science and Technology) at 25–30℃ and 60%–75% relative humidity.

extract_protocol:
RNA was harvested using Polysaccharide Polyphenols Plant Total RNA Extraction Kit (genepioneer, R411). 1 ug of total RNA was used for the construction ofsequencing lilbraries
RNA libraries for RNA-seg were prepared using Hieff NGS® Ultima Dual-mode RNA Library Prep Kit (Yeasen, 12308ES) following manufacturer's protocols

treatment_protocol: Collect grape leaves from the control group, trehalose, different stresses (low temperature (4 ℃), PEG6000, NaCl), and trehalose+different stress treatments for 48 hours, and perform RNA Seq analysis. The control group and the treatment group each contain three biological replicates. 8 samples examined:  CK, 4C, NaCl，PEG6000，Tre，Tre-4C，Tre-NaCl，Tre-PEG6000.

value: leaf

value: Tre, 48h


title: 5_S10_L003

value: Control


title: male_vehicle_317

value: renal

value: podocytes

value: yes


title: Hepatocyte,DDC,rep4

source_name: Hepatocyte

value: Hepatocyte


title: Res_WT_M1

value: liver

value: male


title: 4_S9_L003

value: Prefrontal Cortex


title: Hepatocyte,DDC,rep2


title: Res_KO_M1

value: Cebpb fl/fl


title: 2_S7_L003

value: earlyAD


title: Hepatocyte,DDC,rep1


title: Res_KO_M2


title: Hepatocyte,DDC,rep3


title: male_vehicle_313


title: male_vehicle_308


title: 3_S8_L003

value: AD

value: F


title: Cholangiocyte,DDC,Rep1

value: Cholangiocyte


title: 1_S6_L003


title: Cholangiocyte,WT,Rep4


title: Human8_S8_L003

description:
Human_visium_ADDS_seurat_processed.rds
visium_human_12-13-21_sample_meta.csv

value: M


title: Res_KO_F2

value: female

value: WDA 16 weeks + AAV-TBG-Cre + 4 weeks resolution


title: female_rapa_326


title: female_rapa_322


title: Cholangiocyte,WT,Rep3


title: Human7_S7_L003


title: female_rapa_315


title: Res_KO_F1


title: Glu_23_rep2

city: Tokyo

first: Kotaro

last: Chihara

address: 1-23-1 Toyama

department: Research Center for Drug and Vaccine Development

country: Japan

institute: National institute of infectious diseases

data_processing:
Sequencing quality was examined by FastQC v0.11.7 software
3' adapter was trimmed from raw reads by cutadapt ver 1.17
Trimmed reads were aligned to the cytoplasmic mature-tRNA sequences getting from GtRNAdb and the mitocondrial mature-tRNA sequences from mitotRNAdb using BWA (0.7.12-r1039) software (maximum mismatch was set to 2).
The tRNAs expression profiling was calculated based on uniquely mapped reads and including mapped reads, respectively. The differentially expressed tRNAs were screened based on the count value with R package edgeR (3.5.1)
Assembly: the cytoplasmic mature-tRNA sequences (GtRNAdb) and the mitocondrial mature-tRNA sequences (mitotRNAdb)
Supplementary files format and content: alignment results (BAM format); unique read count file (XLSX format)

organism: Escherichia coli

growth_protocol: An overnight culture of E. coli DH10B harboring plasmid with PtuAB was inoculated into 10 ml LB supplemented with chloramphenicol (20 μg/ml) until OD600 0.3.

extract_protocol:
Total RNA was extracted using miRNA isolation kit (QIAGEN, catalog number 217004), according to the manufacturer’s recommendation. Over 2g total RNA was resolved on Urea-PAGE and recovered within a size window of 60-100 nt for tRNA. Thereafter, purified tRNA was demethylated, alkaline-hydrolyzed by carbonate buffer, dephosphorylated by calf intestinal phosphatase (CIP), and re-phosphorylated by T4 polynucleotide kinase (T4 PNK).
Fragments of 19-35nt for partially hydrolyzed and re-phosphorylated tRNA were converted to small RNA sequencing libraries using NEBNext Multiplex Small RNA Library Prep Set for Illumina kit.
tRNA-seq

treatment_protocol: The bacteria were then induced with 0.2% arabinose (to induce PtuAB expression) or 0.2% glucose (to repress PtuAB expression) and cultured for 2h at 37°C with shaking at 200 rpm.  Following incubation, the culture was centrifuged at 6000 g for 5 minutes, and the pellet was washed twice with PBS buffer.

tag: condition

value: early stationary (OD600 = 1.0)

value: treated with 0.2% glucose


title: female_rapa_336

value: renal

tag: treatment


title: Cholangiocyte,WT,Rep2


title: Cholangiocyte,WT,Rep1


title: Human5_S5_L003

value: Control


title: Human4_S4_L003


title: male_rapa_347

value: podocytes

value: yes


title: Ara_23_rep2

value: treated with 0.2% arabinoese


title: Hepatocyte,WT,rep4

value: Hepatocyte


title: Human3_S3_L003

value: Prefrontal Cortex


title: Hepatocyte,WT,rep3


title: male_rapa_319


title: female_rapa_323


title: Ara_23_rep1


title: female_rapa_316


title: Hepatocyte,WT,rep1


title: Glu_PtuAB_rep 2


title: Human1_S1_L003


title: male_rapa_312


title: Res_KO_F3

value: liver

value: Cebpb fl/fl


title: Hepatocyte,WT,rep2


title: male_rapa_252


title: male_rapa_233


title: Glu_23_rep1


title: Human6_S6_L003

value: earlyAD


title: Human2_S2_L003


title: Ara_PtuAB_rep2


title: Glu_PtuAB_rep1


title: Math1-Cre; SmoM2, MB, P7 mice, rep1

city: Changsha

first: Siyi

last: Wanggou

state: Hunan

address: Xiangya Road, No.87

department: Departmeng of Neurosurgery

institute: Xiangya Hospital, Central South University

data_processing:
The Illumina sequencer’s base call files (BCls) were demultiplexed into FASTQ files using cellranger mkfastq.
The FASTQ files were aligned to GRCm38 (mm10) mouse genome reference to generate barcode-labeled sparse matrices individually by cellranger count.
Assembly: mm10

source_name: Medulloblastoma tissue

growth_protocol: Mice were maintained in specific pathogen-free conditions in the animal facility with 12:12 h light/dark cycles.

extract_protocol:
Math1-Cre; SmoM2 medulloblastoma from P7 mice were harvested followed by mechanical and enzymatic dissociation using the Papain Dissociation System (Worthington Biochemical Corporation). Single cell suspension was assessed by Trypan blue. Approximately 5,000 cells at a concentration of ~1,000 cells/μl were loaded onto the Chromium Controller.
Library generation for 10X Genomics v3 chemistry was performed using the Chromium Single Cell 3ʹ Reagents Kit. Quantifications of cDNA libraries were performed using the Kapa Library Quantification Illumina/ABI Prism Kit (KAPA Biosystems) and the high-sensitivity DNA chips. 10X libraries were sequenced using the Illumina 2500 sequencing platform to achieve ~25,000 reads per cell.
One library of Math1-Cre; SmoM2 medulloblastoma.

treatment_protocol: Math1-Cre; SmoM2 mice

value: Medulloblastoma tissue

value: Math1-Cre; SmoM2

value: post natal day 7

tag: disease state

value: medulloblastoma model


title: P7 Enu Nuc LG

city: Genève 4

first: Quentin

last: Lo Giudice

state: switzerland

address: 1 rue Michel Servet

department: Department of Basic Neurosciences

country: Switzerland

institute: University of Geneva

description: P7 timepoint LG nuclei Visual Deprivation condition

data_processing:
All single cell transcriptomics analyses were performed using R Statistical Software (v4.2.2), the Seurat V4 package and Bioconductor packages (Hao et al., 2021; Huber et al., 2015; R: The R Project for Statistical Computing). Graphs and visualization were generated with the ggplot2 package (Wickham).   For quality control, independent libraries were processed as Seurat objects. All cells with fewer than 200 detected genes and genes expressed in fewer than 3 cells were removed. PCA was performed on variable genes to reduce dimensionality of the dataset. UMAP was based on the reduced dimensional space of the 20 most significant dimensions of the PCA using the UMAP package Barnes-Hut version of Seurat with a perplexity set at 30. A UMAP-based clustering analysis was then performed by the shared nearest neighbor (SNN) modularity optimization algorithm (van der Maaten, 2014). The number of independent genes detected ranged between 2684 and 3994 with an average of 3148 by cluster. Differentially expressed genes between clusters were obtained by Seurat-implemented Wilcoxon rank sum tests with default parameters. The cluster identities in this UMAP-space were uncovered by feature plots of typical cell type marker genesThe first three embedded dimensions of the UMAP were output for further use to represent the pattern of various features during differentiation. The minimal distance parameter of the UMAP was set to 0.3 and the number of neighboring points used in local approximations was set to 30.
Assembly: Grc38/mm10
Supplementary files format and content: Comma separated values of mereged time points, "count" field of the seurat object.

source_name: Brain

extract_protocol:
Cell dissociation and FAC-sorting: Diencephalon of the embryos were collected in ice-cold Hank's Balanced Salt Solution (HBSS) and segments were microdissected under a stereomicroscope. Thalamic chunks were then incubated in 200 µl single-cell dissociation solution consisting of papain (1 mg/ml)-enriched HBSS at 37°C for 10 min with trituration every 2 min. Cells were further dissociated via gentle up-and-down pipetting and the reaction was stopped with the addition of 400 µl of 2 mg/ml ovalbumin-enriched cold FACS buffer (2mg/mL glucose, 0.1% BSA, 1:50 Citrate Phosphate Dextrose from Sigma (C7165), 10U/mL DNase I, and 1μM MgCl2) and the cell suspension was then passed through a 40-µm cell strainer to remove cellular aggregates. Cells were then centrifuged for 5 min at 500 g at 4°C. After removal of the liquid, the pellet was suspended in 250 µl of cold FACS buffer and the resulting solution was finally sorted on a MoFloAstrios device (Beckman) to reach a concentration of 410 cells/µl. Nuclei isolation: Diencephalon of the embryos were collected in ice-cold Hank's Balanced Salt Solution (HBSS) and segments were microdissected under a stereomicroscope. Thalamic chunks were frozen and stored at -80°C until further processing. Nuclei were isolated using EZ Nuclei isolation kit as previously described. In brief, the tissue was resuspended in 2 mL of ice-cold extraction buffer (Nuclei EZ prep, Sigma NUC101), gently dounce-homogenized (KIMBLE Dounce tissue grinder, Sigma D8938, 6 strokes with A and B pestle), and incubated for 5 minutes in a total of 4 ml EZ buffer. The extracted nuclei were collected by centrifugation (500 x g at 4°C, 5 minutes) and supernatant removal followed by resuspension and incubation in EZ buffer for 5 min. After centrifugation, nuclear pellet was washed in 4 ml washing buffer containing 1% BSA in PBS, with 50U/ml of SUPERase-In (Thermo Fisher, cat# AM2696) and 50U/ml of RNasin (Promega, cat# N2611), centrifuged and nuclei were resuspended in 1 ml of washing buffer, filtered through a 30 μm strainer, stained with Hoechst (Invitrogen H3570, 1:500) for 5-10 minutes and processed for fluorescence-activated nuclei sorting on Beckman Coulter MoFlo Astrios. 20k nuclei were sorted and 42 µl of nuclei suspension was used to load the 10x Genomics snRNA-seq preparation.
10X Single cell RNA sequencing: Cell suspensions were captured using 10X Genomics Chromium Single Cell 3’ v3 reagents following the manufacturer’s protocol. The quality control of the cDNA and libraries was performed using Agilent's 2100 Bioanalyzer. Subsequently, the libraries were sequenced using the HiSeq 4000 sequencer. The resulting FASTQ files obtained from the sequencing were processed and mapped with 10X Genomics Cell Ranger pipeline using the GRCm38 mouse genome as a reference. Default parameters for read mapping, counting and quality controls were used as described in the Cell Ranger V6.0.0 documentation. C1 Single cell RNA sequencing: Cells stained with FlashTag were captured using the C1-Fluidigm system. Following the previously mentioned dissociation protocol, 8 µL of cell suspension was sorted on a MoFloAstrios to enrich for the top 20% most FlashTag-positive cells. Each sample representing a different embryonic time points was mixed with C1 suspension reagents (2 µL; Fluidigm) for a total cell suspension volume of approximately 10 µL, containing ~500 cells per µL. This mixture was then loaded onto the C1 Single-Cell AutoPrep integrated fluidic circuit (HT-800, Fluidigm, 100-57-80). cDNA synthesis and preamplifications were conducted following the manufacturer's instructions for the C1 system (Fluidigm). Captured cells were imaged using the ImageXpress Micro Widefield High Content Screening System (Molecular Devices). Single-cell RNA-sequencing libraries of the cDNA were prepared using the Nextera XT DNA library prep kit (Illumina). Libraries were multiplexed and sequenced in accordance with the manufacturer's recommendations, employing paired-end reads on the HiSeq4000 platform (Illumina).

value: Brain

value: Thalamus

value: Neural cells

value: Visual Deprivation


title: OB_pat_LuC_123

city: Korolev

first: Daniil

middle: Vitalievich

last: Luppov

state: please choose

address: 1/9 Karla Libknehta Street, Upt 12

country: Russia

institute: Sechenov University

description: Sample collection timepoint: pretreatment; Tissue type: Primary solid tumor; Current site: Lung; Sex: male; Age of onset: 72

data_processing:
RNAseq FASTQ files were processed using the STAR aligner [PMID: 23104886] in "GeneCounts" mode.
Assembly: Build version GRCh38, transcript annotation GRCh38.89
Supplementary files format and content: Raw read counuts on genes. One table for all samples

source_name: lung cancer (adenocarcinoma)

extract_protocol:
To isolate RNA, 10 µM - thick paraffin slices were trimmed from each FFPE tissue block using a microtome. RNA was extracted from FFPE slices using QIAGEN RNeasy FFPE Kit following the manufacturer’s protocol. RNA 6000 Nano or Qubit RNA Assay kits were used to measure RNA concentration.
RNA was processed and  subjected to isolation of generation of sequencing libraries according to Suntsova et al., 2019 [PMID: 31015567].

value: lung cancer (adenocarcinoma)


title: BM_day10_3_Totals

city: Glasgow

first: Joseph

middle: Alexander

last: Waldron

address: Switchback road

country: United Kingdom

institute: Beatson Institute for Cancer Research

description: Cytoplasmic RNA (Paired to RPFs)

data_processing:
*library strategy: Ribosome-Profiling
Processing of all ribosome profiling data was carried out using the https://github.com/Bushell-lab/Ribo-seq GitHub package. All R scripts were carried out using R version 4.3.1.
For Ribosome Protected Fractments (RPFs): Cutadapt (version 1.18) was used to remove adaptors, trim 3’ bases with quality scores below 20 and discard reads less than 30 and more than 50 bases after trimming. Unique Molecular Indexes (UMIs)  (4nt at the start and end)  were extracted from the reads and appended to the read name using UMI tools (version 1.0.1). BBmap (version 38.18) was used to align reads to a FASTA file containing rRNA and then tRNA reads. All unaligned reads were then aligned to a filtered protein coding FASTA, containing the most abundant transcript per gene (calculated from cytoplasmic RNA samples). The resulting BAM files were sorted with samtools (version 1.9) and deduplicated using UMItools with the directional method. The number of reads in which the 5’ end is at each position of every transcript is then counted and the correct offset for each read length is calculated and applied, to collapse all reads into a single frame. Total counts across the entire CDS, excluding the first 20 and last 10 codons are then summed together.
For paired cytoplasmic RNA samples: Cutadapt (version 1.18) was used to remove adaptors, trim 3’ bases with quality scores below 20 and discard reads less than 30 bases after trimming. Unique Molecular Indexes (UMIs)  (12nt at the start)  were extracted from the reads and appended to the read name using UMI tools (version 1.0.1). Reads were aligned to the filtered protein coding transcriptome with bowtie2 (version 2.3.5.1), using the parameters recommended for use with RSEM, which are --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1. Both gene and isoform level quantification was carried out using RSEM (version 1.3.3).
Assembly: GENCODE vM27 Protein-coding transcript sequences, filtered to contain only transcripts that have both a 5’ and 3’ UTR, with a CDS equally divisible by 3 and an nUG start codon, a stop codon and that have been manually annotated by HAVANA. All PAR_Y transcripts were also removed.
Supplementary files format and content: pc_final_counts_all_frames.csv files contain the total RPF counts (not normalised) for every transcript, across the entire CDS, excluding the first 20 and last 10 codons
Supplementary files format and content: isoforms.results files are one of the output file from RSEM quantification. These were used to calculate the most abundant transcript per gene and also for input into DEseq2 for differential expression analysis. Although these files represent isoform level expression information, DESeq2 is able to collapse this down to the gene level. All DE analysis was performed at the gene level.

molecule: cytoplasmic RNA

source_name: Liver

growth_protocol: Mice were housed in conventional cages, in a pathogen-free facility between 19–23°C and 55 ± 10% humidity, subject to 12 hour day/night cycles and had access to standard diet and drinking water ad libitum. Experiments were performed on male mice, aged between 2-4 months and which were ≥20g.

extract_protocol:
Livers were dissected on surfaces cleaned and treated with RNase Zap to reduce RNAase exposure. Livers were rapidly dissected and snap frozen as 5x5x5mm fragments in liquid nitrogen. Livers were ground to powder using a mortar and pestle with the CryoGrinder system (OPS Diagnostics, Lebanon, NJ, USA) to ensure the samples were kept frozen. Roughly 200 mg tissue aliquots were stored in 1.5 ml tubes at -80 ºC until required.Ground liver tissue was poured directly from a 1.5 ml tube on dry ice into 900 µl ice cold lysis buffer (15 mM Tris-HCl (pH 7.5), 15 mM MgCl2, 150 mM NaCl, 1% Triton X100, 0.05% Tween 20, 2% n Dodecyl β Maltoside (Thermo Fisher 89903), 0.5 mM DDT, 100 µg/ml cycloheximide, 1X cOmplete, Mini, EDTA-free Protease Inhibitor Cocktail (Merck 11836170001),  1x Protease Inhibitor Cocktail (Sigma P9599-5ml), 5mM Sodium Fluoride, 500 U/ml RiboLock RNase Inhibitor (Thermo Fisher Scientific, EO0381), 25 U/ml Turbo DNase (Thermo Fisher Scientific, AM2239) on ice and immediately mixed together and placed on ice for 10 min, while being inverted every 2 minutes to maximise the dispersal and exposure of ground tissue to lysis buffer. Lysates were centrifuged at 4°C for 5 min at 16,000g and 800 µl supernatant pipetted into a fresh 1.5 ml tube on ice. For cytoplasmic RNA sample, RNA was extracted from 40 µl lysate with 1ml TRIzol, as per manufactures’ instructions. 600µl lysate was digested with 1µl Ambion RNase I cloned, 100 U/µL (Thermo Fisher Scientific, AM2295), 1µl MNase (1:20 diln; New England Biolabs # 0247S) with 3.6µl 0.25M CaCL2, at 22°C for 15 min at 650 rpm in a thermo mixer. The digestion was stopped with 5 µl SUPERaseIn RNase Inhibitor (20 U/μL) (Thermo Fisher Scientific, AM2696) and 26µl 0.5M EGTA (to stop RNase 1 and MNase respectively). The samples were loaded onto a 10-50% sucrose gradient, containing 15 mM Tris-HCl (pH 7.5), 15 mM MgCl2, 150 mM NaCl and 100 µg/ml cycloheximide, prepared with a BioComp gradient station and cooled to 4°C for at least 1 h. Samples were centrifuged in a Beckman XPN-90 Ultracentrifuge with an SW40ti rotor at 38,000 rpm for 2 h at 4°C. 1 ml fractions were collected with a Biocomp gradient station and Gilson FC 203B fraction collector. Fractions pertaining to the 80S peak were extracted with acid phenol chloroform, followed by two chloroform washes and RNA was precipitated with 2 µl glycogen (Roche 10901393001), 300 mM NaOac (pH 5.2) and an equal volume of isopropanol overnight at -20°C.
RNA was pelleted by centrifugation at 12,000 g for 45 min at 4 °C. The supernatant was removed with a pipette, and the pellet was washed twice with 70% ethanol and dissolved in 10 µl RNase-free water. RNA was diluted with 10 µl 2× TBE Urea sample buffer (Thermo Fisher Scientific, LC6876), heated at 80°C for 90 s, placed immediately on ice, and then loaded onto a pre-run 15% TBE-urea gel (Thermo Fisher Scientific, EC68852BOX) and ran at 200 V for 1 h alongside custom 28 nt (AGCGUGUACUCCGAAGAGGAUCCAACGU) and 34 nt (GCAUUAACGCGAACUCGGCCUACAAUAGUGACGU) RNA markers. The gel was stained with 1× SYBR gold (Thermo Fisher Scientific, S11494) and imaged on a Typhoon FLA 7000. An image was printed to size to allow bands, inclusive of 28 nt and exclusive of 34 nt markers, to be cut from the gel, placed into a 1.5 ml RNA low-binding microcentrifuge tube, and crushed with a RNase free disposable pestle. RNA was eluted from the crushed gel pieces in 500 µl extraction buffer (300 mM NaOAc pH 5.2, 1 mM EDTA, 0.25% SDS) overnight at 16°C at 600 rpm in a thermo-mixer. Gel pieces were filtered out with a Costar Spin-X centrifuge tube filter (0.45 µm; Scientific Laboratory Supplies Ltd, 8163) and RNA was precipitated with 2 µl glycogen and 500 µl isopropanol overnight at -20 °C. Precipitated RNA was again pelleted, washed, and dissolved in 13.5 µl RNase-free water, as above, and underwent rRNA depletion as follows. To the 13.5 µl RNA was added, 5 µl hybridisation buffer (10mM Tris-HCl pH7.5, 1mM EDTA, 2M NaCl), 1 µl RNasin Plus Ribonuclease Inhibitor (Promega N2615) and 0.5 µl biotinylated DNA oligo pool (100 uM total DNA with rRNA_depl_1 and rRNA_depl_2 at a 3:1 molar ratio compared to all other oligos), that had been denatured at 95 °C for 3min and then placed immediately on ice. This mix was incubated at 68 °C for 10 min at 1250 rpm in a thermo mixer and then allowed to cool slowly to room temp by turning off the thermomixer. rRNA was depleted with 160 µl Dynabeads MyOne Streptavidin C1 (Thermo Scientific, 65001) as per manufactures’ instructions and depleted RNA was precipitated with 2 µl glycogen and ethanol. Precipitated RNA was again pelleted and washed as above and then dissolved in 43 µl RNase-free water and heated at 80 °C for 90 s and immediately placed on ice. RNA then underwent 5′ phosphorylation and 3′ dephosphorylation with 1 µl T4 PNK (NEB, M0201S), 5 µl 10× PNK buffer, and 1 µl SUPERaseIn RNase Inhibitor (20 U/µl) at 37 °C for 35 min, with 5 µl 10 mM ATP added for the final 20 min. RNA was extracted with acid phenol:chloroform and isopropanol-precipitated as above. Purified RNA was quantified on a qubit with the high-sensitivity RNA kit (Q32852) and 5 ng was input into the Bioo Scientific Nextflex small RNA v3 kit (NOVA-5132-06), using the alternative step F bead clean-up, 14 PCR cycles, and gel-extraction option. Cytoplasmic RNA samples were run on an Agilent TapeStation to check RNA integrity. RNA concentration and sample purity were measured on a NanoDrop spectrophotometer. rRNA was depleted from 1 µg cytoplasmic RNA with the RiboCop v2, and sequencing libraries were prepared from the rRNA-depleted RNA with the Corall Total RNA-Seq Library Prep Kit v1 (Lexogen, 095.96) using 13 PCR cycles. Final cytoplasmic RNA and RPF libraries were quantified on an Agilent TapeStation, with a High Sensitivity D1000 ScreenTape (Agilent 5067-5584), and sequenced single-end on an Illumina NextSeq500 instrument with a 75 cycles high-output kit.

treatment_protocol: Genetic recombination was induced with an adeno-associated virus expressing Cre under the control of the TBG promoter (AAV8.TBG.Cre; AAV.TBG.PI.Cre.rBG was a gift from James M. Wilson (Addgene plasmid # 107787 ; http://n2t.net/addgene:107787 ; RRID:Addgene_107787)). To achieve temporal- and hepatocyte-specific Cre-mediated recombination of floxed alleles, AAV8.TBG.Cre was administered via intravenous (I.V.) tail-vein injections at 2×10^11 GC/ml. Samples were harvested either 4 or 10 days after viral-Cre administration.

value: Liver

value: Male

value: Ctnnb1ex3/+; R26-LSL-MYC

value: 10 days post-induction

value: mice were injected with 2 X 10^11 GC/mouse of AAV8.TBG.PI.Cre.rBG


title: Ara_PtuAB_rep1

value: early stationary (OD600 = 1.0)

value: treated with 0.2% arabinoese


title: Human8_S19_L003

description:
Human_visium_ADDS_seurat_processed.rds
visium_human_12-20-21_sample_meta.csv

source_name: Prefrontal Cortex

value: M

value: Prefrontal Cortex


title: HB4 hepatoblastoma

city: Stanford

address: 265 Campus Dr., Rm G2145

institute: Stanford University School of Medicine

description: FFPE Spatial transcriptomic sequencing

data_processing:
Data processing was performed using Space Ranger software (10x Genomics)
Assembly: GRCh38 3.0.0
Supplementary files format and content: Tab-separated values files, matrix files, jpg and png flies
Library strategy: Spatial Transcriptomics

source_name: Hepatoblastoma

extract_protocol:
RNA was extracted from FFPE sections according to the manufacturer's specifications (10x Visium)
Libraries were constructed according to the manufacturer's specifications (10x Visium)

value: Hepatoblastoma


title: P7 Control Nuc LP

description: P7 timepoint LP nuclei Control condition


title: Normal liver (paired to HB15)

description: FFPE Spatial transcriptomic sequencing


title: Human7_S19_L002

value: AD

value: F


title: P7 Control Nuc LG

description: P7 timepoint LG nuclei Control condition

value: Brain


title: OB_pat_LuC_122

description: Sample collection timepoint: pretreatment; Tissue type: Primary solid tumor; Current site: Lung; Sex: male; Age of onset: 59

source_name: lung cancer (squamous cell carcinoma)

value: lung cancer (squamous cell carcinoma)


title: Human7_S18_L003


title: P7 Enu Nuc LP

description: P7 timepoint LP nuclei Visual Deprivation condition

value: Thalamus

value: Neural cells


title: HB17 hepatoblastoma

description: FFPE Spatial transcriptomic sequencing

value: Female


title: BM_day10_1_Totals

description: Cytoplasmic RNA (Paired to RPFs)

value: Liver


title: P3 Control Nuc LP

description: P3 timepoint LP nuclei Control condition


title: OB_pat_LuC_128

description: Sample collection timepoint: pretreatment; Tissue type: Primary solid tumor; Current site: Lung; Sex: male; Age of onset: 68

value: lung cancer (adenocarcinoma)


title: Human4_S16_L003


title: Human8_S20_L002


title: Human5_S18_L002

value: Control


title: Myc_day10_3_Totals

description: Cytoplasmic RNA (Paired to RPFs)

value: Male

value: 10 days post-induction


title: OB_pat_LuC_136

description: Sample collection timepoint: pretreatment; Tissue type: Primary solid tumor; Current site: Lung; Sex: male; Age of onset: 66


title: OB_pat_LuC_130

description: Sample collection timepoint: pretreatment; Tissue type: Primary solid tumor; Current site: Lung; Sex: male; Age of onset: 45


title: BM_day10_2_Totals

description: Cytoplasmic RNA (Paired to RPFs)

value: Ctnnb1ex3/+; R26-LSL-MYC

value: mice were injected with 2 X 10^11 GC/mouse of AAV8.TBG.PI.Cre.rBG


title: OB_pat_LuC_126

description: Sample collection timepoint: pretreatment; Tissue type: Primary solid tumor; Current site: Lung; Sex: male; Age of onset: 64


title: Myc_day10_2_Totals

description: Cytoplasmic RNA (Paired to RPFs)


title: Human5_S17_L003

value: M


title: Human4_S17_L002

value: Prefrontal Cortex


title: Myc_day10_1_Totals

description: Cytoplasmic RNA (Paired to RPFs)


title: Human3_S15_L003


title: P3 Enu Nuc LG

description: P3 timepoint LG nuclei Visual Deprivation condition

value: Visual Deprivation


title: Human2_S14_L003

value: earlyAD


title: Bcat_day10_3_Totals

description: Cytoplasmic RNA (Paired to RPFs)


title: OB_pat_LuC_125

description: Sample collection timepoint: pretreatment; Tissue type: Primary solid tumor; Current site: Lung; Sex: male; Age of onset: 61


title: Human3_S16_L002

value: AD

value: F


title: OB_pat_LuC_129

value: lung cancer (squamous cell carcinoma)


title: P3 Control Nuc LG

description: P3 timepoint LG nuclei Control condition

value: Brain

value: Thalamus


title: OB_pat_LuC_134


title: WT_day10_3_Totals

description: Cytoplasmic RNA (Paired to RPFs)

value: Wild-type


title: E16 10X nuc

description: E16 timepoint

value: Neural cells


title: E11 C1

description: E11 timepoint


title: E18 10X nuc

description: E18 timepoint


title: OB_pat_LuC_131

description: Sample collection timepoint: pretreatment; Tissue type: Primary solid tumor; Current site: Lung; Sex: male; Age of onset: 67


title: Human2_S15_L002


title: Bcat_day10_2_Totals

description: Cytoplasmic RNA (Paired to RPFs)

value: Liver


title: OB_pat_LuC_111

description: Sample collection timepoint: pretreatment; Tissue type: Primary solid tumor; Current site: Lung; Sex: male; Age of onset: 65


title: OB_pat_LuC_135


title: E13 C1

description: E13 timepoint


title: Bcat_day10_1_Totals

description: Cytoplasmic RNA (Paired to RPFs)


title: OB_pat_LuC_108

description: Sample collection timepoint: posttreatment; Tissue type: Primary solid tumor; Current site: Lung; Sex: male; Age of onset: 66

value: lung cancer (adenocarcinoma)


title: E18 C1

description: E18 timepoint


title: Human1_S14_L002

value: Control


title: E14 C1

description: E14 timepoint


title: Human1_S13_L003


title: batch5_Sublibrary_8_S8_L004

description:
Human_snRNA-Seq_ADDS_integrated.rds
AD-DS_Cases.csv


title: OB_pat_LuC_121


title: WT_day10_2_Totals

description: Cytoplasmic RNA (Paired to RPFs)

value: Male

value: 10 days post-induction


title: batch5_Sublibrary_5_S5_L004


title: WT_day10_1_Totals

description: Cytoplasmic RNA (Paired to RPFs)

value: mice were injected with 2 X 10^11 GC/mouse of AAV8.TBG.PI.Cre.rBG


title: batch5_Sublibrary_7_S7_L004


title: OB_pat_LuC_105

description: Sample collection timepoint: pretreatment; Tissue type: Primary solid tumor; Current site: Lung; Sex: male; Age of onset: 70

source_name: lung cancer (mixed type: adenocarcinoma + squamous cell carcinoma)

value: lung cancer (mixed type:adenocarcinoma + squamous cell carcinoma)


title: E12 C1

description: E12 timepoint


title: OB_pat_LuC_104


title: BM_day4_1_Totals

description: Cytoplasmic RNA (Paired to RPFs)

value: Ctnnb1ex3/+; R26-LSL-MYC

value: 4 days post-induction


title: batch5_Sublibrary_3_S3_L004

value: Prefrontal Cortex


title: batch5_Sublibrary_6_S6_L004


title: OB_pat_LuC_100

description: Sample collection timepoint: pretreatment; Tissue type: Primary solid tumor; Current site: Lung; Sex: female; Age of onset: 47


title: BM_day4_3_Totals

description: Cytoplasmic RNA (Paired to RPFs)


title: OB_pat_LuC_107

description: Sample collection timepoint: pretreatment; Tissue type: Primary solid tumor; Current site: Lung; Sex: male; Age of onset: 60


title: E18 10X sc

description: E18 timepoint


title: batch5_Sublibrary_2_S2_L004


title: BM_day4_2_Totals

description: Cytoplasmic RNA (Paired to RPFs)


title: E14 10X sc

description: E14 timepoint


title: batch5_Sublibrary_4_S4_L004


title: E13 10X sc

description: E13 timepoint


title: OB_pat_LuC_99

description: Sample collection timepoint: pretreatment; Tissue type: Primary solid tumor; Current site: Lung; Sex: female; Age of onset: 73


title: Myc_day4_2_Totals

description: Cytoplasmic RNA (Paired to RPFs)


title: E12 10X sc

description: E12 timepoint


title: E8_control

city: New York

first: Hyein

middle: Sophia

last: Cho

state: NY

address: 430 E 67th St

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

library_source: other

data_processing:
Quantification by MAGeCK 0.5.9.4
Fold change calculation by GFP+ / GFP-
Gene lists defined by top and bottom 150 robust ranking algorithm (RRA) scores
Assembly: Brunello gRNA library
Supplementary files format and content: Excel table
Library strategy: CRISPR screen

molecule: other

source_name: H1 hESC

extract_protocol:
No extraction
Library construction protocol was followed per MSKCC's IGO core facility.

value: H1 hESC

value: WT


title: Myc_day4_3_Totals

description: Cytoplasmic RNA (Paired to RPFs)


title: Bcat_day4_3_Totals

description: Cytoplasmic RNA (Paired to RPFs)


title: E11 10X sc

description: E11 timepoint


title: OB_pat_LuC_95

description: Sample collection timepoint: pretreatment; Tissue type: Primary solid tumor; Current site: Lung; Sex: male; Age of onset: 75

value: lung cancer (squamous cell carcinoma)


title: OB_pat_LuC_92

source_name: Small cell lung cancer

value: Small cell lung cancer


title: Sublibrary_7_S7_L003


title: Myc_day4_1_Totals

description: Cytoplasmic RNA (Paired to RPFs)


title: IN8_treatment


title: OB_pat_LuC_98

description: Sample collection timepoint: pretreatment; Tissue type: Metastatic; Current site: Lung; Sex: female; Age of onset: 62

source_name: lung cancer (adenocarcinoma, paillary)

value: lung cancer (adenocarcinoma, paillary)


title: batch5_Sublibrary_1_S1_L004


title: Bcat_day4_1_Totals

description: Cytoplasmic RNA (Paired to RPFs)


title: Sublibrary_8_S8_L003


title: DE_GFP_low


title: WT_day4_3_Totals

description: Cytoplasmic RNA (Paired to RPFs)

value: Wild-type


title: DE_GFP_high


title: WT_day4_2_Totals

description: Cytoplasmic RNA (Paired to RPFs)


title: E6_survival


title: Sublibrary_4_S4_L003


title: P3 Enu Nuc LP

description: P3 timepoint LP nuclei Visual Deprivation condition

value: Brain

value: Thalamus

value: Neural cells

value: Visual Deprivation


title: Sublibrary_5_S5_L003


title: OB_pat_LuC_84

description: Sample collection timepoint: pretreatment; Tissue type: Primary solid tumor; Current site: Lung; Sex: male; Age of onset: 62


title: OB_pat_LuC_85

description: Sample collection timepoint: pretreatment; Tissue type: Primary solid tumor; Current site: Lung; Sex: female; Age of onset: 60


title: E8_T0


title: NE_GFP_low


title: Sublibrary_2_S2_L003


title: Bcat_day4_2_Totals

description: Cytoplasmic RNA (Paired to RPFs)

value: Liver

value: Male


title: WT_day4_1_Totals

description: Cytoplasmic RNA (Paired to RPFs)

value: mice were injected with 2 X 10^11 GC/mouse of AAV8.TBG.PI.Cre.rBG


title: BM_day10_3_RPFs

description: Ribosome protected fragments

value: 10 days post-induction


title: Sublibrary_6_S6_L003


title: OB_pat_LuC_91


title: Sublibrary_1_S1_L003


title: BM_day10_1_RPFs

description: Ribosome protected fragments

value: Ctnnb1ex3/+; R26-LSL-MYC


title: OB_pat_LuC_81

description: Sample collection timepoint: pretreatment; Tissue type: Primary solid tumor; Current site: Lung; Sex: male; Age of onset: 54


title: OB_pat_LuC_87

description: Sample collection timepoint: pretreatment; Tissue type: Primary solid tumor; Current site: Lung; Sex: female; Age of onset: 50

value: lung cancer (mixed type:adenocarcinoma + squamous cell carcinoma)


title: OB_pat_LuC_83

description: Sample collection timepoint: pretreatment; Tissue type: Metastatic; Current site: Brain; Sex: male; Age of onset: 63

value: lung cancer (adenocarcinoma)


title: Metastasis derived organoid harvested from mouse liver.  Origins from PDO23.

first: Yuan

address: 1275 York Avenue

data_processing:
Batch A: CutAdapt version cutadapt-1.6 was used to trim and filter reads. Adapters were trimmed with minimum overlap of 10 bases and reads of less than half original read length were filtered out.  STAR version STAR-STAR_2.5.0a was run using the 2-pass method. First pass was run with the following parameters: --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMattributes All --outSAMunmapped Within. Genome database was then generated using the minimum read length of half desired read length and second pass was run against the new genome file with the same parameters as pass 1.  Expression count matrix was computed using HTSeq version HTSeq-0.13.5. Parameters set were: -m intersection-strict -s no -t exon
Batch B: CutAdapt version cutadapt-1.6 was used to trim and filter reads. Adapters were trimmed with minimum overlap of 10 bases and reads of less than half original read length were filtered out.  STAR version STAR-STAR_2.5.0a was run using the 2-pass method. First pass was run with the following parameters: --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMattributes All --outSAMunmapped Within. Genome database was then generated using the minimum read length of half desired read length and second pass was run against the new genome file with the same parameters as pass 1.  Expression count matrix was computed using HTSeq version HTSeq-0.13.5. Parameters set were: -m intersection-strict -s reverse -t exon
Batch C: Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Indexes of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5). STAR used the method of Maximal Mappable Prefix(MMP) which can generate a precise mapping result for junction reads. Expression count matrix was computed using HTSeq version  HTSeq-0.13.5. Parameters set were: -m intersection-strict -s no -t exon
Assembly: GRC37/hg19
Supplementary files format and content: tab-delimited file containing raw counts

source_name: Metastasis-Liver

extract_protocol:
Total RNA was isolated using the RNeasy mini kit (74104, Qiagen), in accordance with the manufacturer’s protocol
Batch A: library preparation and RNA sequencing were performed by the Integrated Genomics Operation at MSK using Illumina HiSeq with 50 paired-end reads, and approximately 40 million reads were generated for each sample.
Batch B: library preparation and RNA sequencing were performed by the Integrated Genomics Operation at MSK using Illumina HiSeq with 100 paired-end reads, and approximately 20 million reads were for each sample.
Batch C: library preparation and RNA sequencing were performed by Novogene using Illumina Novaseq 6000 with 150 paired-end reads, and approximately 30 million reads were generated for each sample.

value: Metastasis-Liver

value: epithelial cells

value: MDO

tag: batch

value: b


title: Sublibrary_3_S3_L003

value: Prefrontal Cortex


title: Sublibrary_7_S7_L002


title: Myc_day10_3_RPFs

description: Ribosome protected fragments


title: Metastasis derived organoid harvested from mouse brain.  Origins from PDO23.

source_name: Metastasis-Brain

value: Metastasis-Brain


title: Metastasis derived organoid harvested from mouse gallbladder.  Origins from PDO23.

source_name: Metastasis-Gallbladder

value: Metastasis-Gallbladder


title: OB_pat_LuC_78

value: lung cancer (squamous cell carcinoma)


title: OB_pat_LuC_73

description: Sample collection timepoint: pretreatment; Tissue type: Primary solid tumor; Current site: Lung; Sex: female; Age of onset: 53


title: Patient derived organoid from sample 23 W. GL

source_name: Primary-Lung

value: Primary-Lung

value: PDO


title: Sublibrary_5_S5_L002


title: NE_GFP_high

value: H1 hESC

value: WT


title: Sublibrary_4_S4_L002


title: Sublibrary_6_S6_L002


title: Bcat_day10_2_RPFs

description: Ribosome protected fragments

value: Liver

value: Male

value: mice were injected with 2 X 10^11 GC/mouse of AAV8.TBG.PI.Cre.rBG


title: BM_day10_2_RPFs

description: Ribosome protected fragments

value: Ctnnb1ex3/+; R26-LSL-MYC

value: 10 days post-induction


title: OB_pat_LuC_71

value: lung cancer (mixed type:adenocarcinoma + squamous cell carcinoma)


title: Human tumor sample 23.

value: epithelial cells

value: Tumor

value: a


title: Sublibrary_2_S2_L002

value: Prefrontal Cortex


title: Sublibrary_8_S8_L002


title: Metastasis derived organoid harvested from mouse diaphram.  Origins from PDO23.

source_name: Metastasis-Diaphragm

value: Metastasis-Diaphragm

value: MDO

value: b


title: Bcat_day10_1_RPFs

description: Ribosome protected fragments


title: WT_day10_3_RPFs

description: Ribosome protected fragments

value: Wild-type


title: Myc_day10_2_RPFs

description: Ribosome protected fragments


title: OB_pat_LuC_80

description: Sample collection timepoint: pretreatment; Tissue type: Primary solid tumor; Current site: Lung; Sex: male; Age of onset: 63

value: lung cancer (adenocarcinoma)


title: Bcat_day10_3_RPFs

description: Ribosome protected fragments


title: OB_pat_LuC_69

description: Sample collection timepoint: pretreatment; Tissue type: Metastatic; Current site: Brain; Sex: male; Age of onset: 66


title: OB_pat_LuC_72

description: Sample collection timepoint: pretreatment; Tissue type: Metastatic; Current site: Lymph node; Sex: female; Age of onset: 57


title: Sublibrary_3_S3_L002

description:
Human_snRNA-Seq_ADDS_integrated.rds
AD-DS_Cases.csv


title: WT_day10_2_RPFs

description: Ribosome protected fragments


title: Patient derived organoid from sample 23 LATE PASSAGE

value: Primary-Lung

value: PDO


title: OB_pat_LuC_68

description: Sample collection timepoint: pretreatment; Tissue type: Primary solid tumor; Current site: Lung; Sex: male; Age of onset: 59


title: Patient derived organoid from sample 23 EARLY PASSAGE


title: Sublibrary_1_S1_L002


title: A549 con

city: Umeå

first: Yabing

last: Mu

address: Sjukhusområdet

country: Sweden

institute: Umeå University

data_processing:
The original raw data from Illumina are transformed to Sequenced Reads by base calling. Raw data are recorded in a FASTQ file, which contains sequence information (reads) and corresponding sequencing quality information. Base Quality and Phred score relationship with the Illumina CASAVA v1.8 software.
Raw reads are filtered (1) Discard reads with adaptor contamination.(2) Discard reads when uncertain nucleotides constitute more than 10 percents of either read (N > 10%).(3) Discard reads when low quality nucleotides (base quality less than 20) constitute more than 50 percents of the read.
Assembly: TopHat2 is chosen for the characteristics of the reference genome, and only filtered reads are used to analyze the mapping status of RNA-seq data to the reference genome.
Supplementary files format and content: tab_delimited text file inludes raw counts for each sample
Supplementary files format and content: tab_delimited text file inludes RPKM for each sample

growth_protocol: PC3U and A549  cells were grown in RPMI-1640 (Sigma, Cat. R0883) with L-glutamine (Sigma, Cat. G7513), supplemented with 10% fetal bovine serum (FBS) (Sigma, Cat. F7524).

extract_protocol:
RNA was extracted from PC3U cells or A549 cells treated with or without TGFβ1 using the AllPrep DNA/RNA/Protein Mini Kit (QIAGEN, Cat. 80004)
After the QC procedures, mRNA is enriched using oligo(dT) beads. The mRNA is then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamersand reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) is added with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation. The final cDNA library is ready after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR enrichment.

treatment_protocol: The cells were starved for 12–18 h in the medium supplemented with 1% FBS before stimulation with TGFβ1 (Prospec, Ness-Ziona, Israel) at 10 ng/mL.  TGFβ receptor I kinase inhibitor LY2157299 was used 1 hour before TGFβ1 stimulation.

value: WT

value: control


title: OB_pat_LuC_70

value: lung cancer (squamous cell carcinoma)


title: Sublibrary_8_S8_L004


title: A549 TGFb 6h

value: TGF b 6h


title: Sublibrary_7_S7_L004


title: WT_day10_1_RPFs

description: Ribosome protected fragments

value: Liver

value: Male

value: 10 days post-induction

value: mice were injected with 2 X 10^11 GC/mouse of AAV8.TBG.PI.Cre.rBG


title: BM_day4_3_RPFs

description: Ribosome protected fragments

value: Ctnnb1ex3/+; R26-LSL-MYC

value: 4 days post-induction


title: OB_pat_LuC_66

description: Sample collection timepoint: pretreatment; Tissue type: Primary solid tumor; Current site: Lung; Sex: female; Age of onset: 79


title: OB_pat_LuC_67

description: Sample collection timepoint: posttreatment; Tissue type: Metastatic; Current site: Liver; Sex: female; Age of onset: 51


title: Sublibrary_6_S6_L004

value: Prefrontal Cortex


title: BM_day4_2_RPFs

description: Ribosome protected fragments


title: PC3U TGFb 6h


title: OB_pat_LuC_65

description: Sample collection timepoint: pretreatment; Tissue type: Primary solid tumor; Current site: Lung; Sex: male; Age of onset: 74


title: PC3U LY 2157299


title: OB_pat_LuC_64

description: Sample collection timepoint: pretreatment; Tissue type: Primary solid tumor; Current site: Lung; Sex: female; Age of onset: 64


title: Sublibrary_5_S5_L004


title: Sublibrary_4_S4_L004


title: OB_pat_LuC_63

description: Sample collection timepoint: pretreatment; Tissue type: Primary solid tumor; Current site: Lung; Sex: male; Age of onset: 56


title: PC3U LY2157299 +TGFb 6h


title: Myc_day4_3_RPFs

description: Ribosome protected fragments


title: Sublibrary_3_S3_L004


title: N88S_4

city: Porto

first: Vitor

last: Teixeira

state: Porto

address: Rua Alfredo Allen 208

department: YSN

country: Portugal

data_processing:
Sequencing was performed on a DNBSEQ platform with PE150 (read length). The sequencing data was filtered with SOAPnuke by (1) removing reads containing sequencing adapter; (2) removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
Saccharomyces_cerevisiae_S288C_559292.NCBI.GCF_000146045.2_R64.v2201 was used a reference from NCBI. The clean reads were mapped to the reference genome using HISAT2. After that, Ericscript (v0.5.5) and rMATS (V3.2.5) were used to detect fusion genes and differential splicing genes (DSGs), respectively.
Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Expression level of gene was calculated by RSEM (v1.3.1). Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) (or DEGseq or PoissonDis) with Q value ≤ 0.05 (or FDR ≤ 0.001).
Assembly: Saccharomyces_cerevisiae_S288C_559292.NCBI.GCF_000146045.2_R64.v2201 was used a reference from NCBI. The clean reads were mapped to the reference genome using HISAT2. After that, Ericscript (v0.5.5) and rMATS (V3.2.5) were used to detect fusion genes and differential splicing genes (DSGs), respectively.
Supplementary files format and content: GroupPlan.xls contains the plan for comparison of DGEs (G2 vs G1)
Supplementary files format and content: gene_diff file contains gene_id, gene_symbol, diffexp_log2fc_G1-vs-G2, diffexp_deseq2_qvalue_G1-vs-G2, diffexp_deseq2 pvalue_G1-vs-G2

organism: Saccharomyces cerevisiae

source_name: W303 alpha

growth_protocol: WT and N88S seipin-expressing cells were grown in SC-glucose medium to exponential phase and then iron chelator bathophenanthrolinedisulfonate (BPS) was added to a final concentration of 100 micromolar. Cells were incubated in the presence of BPS for an additional 4 hour period.

extract_protocol:
Cells were homogenized by mechanical disruption in 1.5 mL TRIzol lysis buffer. Samples were centrifuged at 12,000g for 5 min in 4ºC. The supernatant was transferred to new centrifuge tubes containing a chloroform/isoamyl alcohol (24:1) mix. After each shaking step, the samples were centrifuged at 12,000g for 8 minutes at 4ºC. Then, the supernatant was transferred to a new centrifuge tube containing isopropyl alcohol (2/3 vol/vol), gently shaken and cooled at -20ºC. Samples were then centrifuged for 25 minutes at 17,500 g (4ºC) and the supernatant was transferred to new microcentrifuge tubes, and combined twice with 75% (vol/vol) ethanol and mixed by pipetting. After centrifugation at 17,500 g for 3 minutes (4ºC), the supernantant was discarded, and the pellet was resuspended in 20-200 μL DEPC-H2O or RNase-free water.
mRNA enrichment was performed on total RNA using oligo(dT)-attached magnetic beads. The enriched mRNA with poly(A) tails was fragmented using a fragmentation buffer, followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double-stranded DNA was then end-repaired and 5'-phosphorylated, with a protruding 'A' at the 3' end forming a blunt end, followed by ligation of a bubble-shaped adapter with a protruding 'T' at the 3'end. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands, and then single-stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality-checked and sequenced after passing the quality control.

value: W303 alpha

value: yeast cells

value: W303 alpha ldb16D::natNT2 fld1D::hphmx4 pRS306-GPDpr-N88ShBSCL2-VN-CYC1t pRS413-GPDpr-N88ShBSCL2-VC-CYC1t

value: BPS, 4 hour


title: N88S_3


title: OB_pat_LuC_62

description: Sample collection timepoint: pretreatment; Tissue type: Metastatic; Current site: Pleura; Sex: female; Age of onset: 52

value: lung cancer (adenocarcinoma)


title: N88S_2


title: Sublibrary_1_S1_L004


title: Myc_day4_1_RPFs

description: Ribosome protected fragments


title: PC3U con


title: OB_pat_LuC_59

description: Sample collection timepoint: pretreatment; Tissue type: Primary solid tumor; Current site: Lung; Sex: male; Age of onset: 71

source_name: lung cancer (Large cell neuroendocrine carcinoma)


title: Bcat_day4_3_RPFs

description: Ribosome protected fragments


title: OB_pat_LuC_61

description: Sample collection timepoint: posttreatment; Tissue type: Metastatic; Current site: lymph node; Sex: female; Age of onset:

source_name: lung cancer

value: lung cancer


title: Undetermined_S0_L004


title: Bcat_day4_2_RPFs

description: Ribosome protected fragments


title: BM_day4_1_RPFs

description: Ribosome protected fragments


title: N88S_1


title: Sublibrary8_S8_L004


title: Bcat_day4_1_RPFs

description: Ribosome protected fragments


title: OB_pat_LuC_57

description: Sample collection timepoint: pretreatment; Tissue type: Metastatic; Current site: lymph node; Sex: male; Age of onset: 43

source_name: lung cancer (adenocarcinoma)


title: WT_4

value: W303 alpha ldb16D::natNT2 fld1D::hphmx4 pRS306-GPDpr-WThBSCL2-VN-CYC1t pRS413-GPDpr-WThBSCL2-VC-CYC1t


title: Sublibrary7_S7_L004


title: WT_day4_3_RPFs

description: Ribosome protected fragments

source_name: Liver

value: Wild-type


title: Myc_day4_2_RPFs

description: Ribosome protected fragments


title: WT_3


title: OB_pat_LuC_56

description: Sample collection timepoint: pretreatment; Tissue type: Metastatic; Current site: lymph node; Sex: female; Age of onset:


title: Sublibrary6_S6_L004

source_name: Prefrontal Cortex


title: WT_day4_2_RPFs

description: Ribosome protected fragments


title: WT_2


title: WT_1


title: Sublibrary_2_S2_L004


title: Sublibrary5_S5_L004


title: OB_pat_LuC_55

description: Sample collection timepoint: pretreatment; Tissue type: Primary solid tumor; Current site: Lung; Sex: male; Age of onset: 62

value: lung cancer (mixed type:adenocarcinoma + squamous cell carcinoma)


title: Sublibrary4_S4_L004


title: WT_day4_1_RPFs

description: Ribosome protected fragments


title: cbp-seed.experiment_1.RNAseq.replicate2

city: Uppsala

first: Juan

middle: C

last: Santos-González

state: Uppsala

address: Almas Allé 5

department: Department of Plant Biology and Forest Genetics

institute: SLU

description:
Capsella bursa-pastoris seed 6DAP
final_RNAseq.experiment_1.RPKM.txt.gz
cbp_x_cbp.rep2

data_processing:
small-RNA: Adapters were removed from the 150-bp long on the first read of the read pair of the library using cutadapt and the resulting 18–25 bp long reads were selected. Reads belonging to chloroplast, mitochondria and to structural noncoding RNAs (tRNAs, snRNAs, rRNAs, or snoRNAs) were removed using bowtie (-v 1). Surviving reads were mapped to the Capsella rubella v1.0 genome using ShorStack (--align_only –mismatches 0 –mmap f) mismatches (command: bowtie -f -t -v0) , and sequences that did not map were discarded.
Bisulfite-seq:The 150-bp-long pair-end reads were quality trimmed by removing the first five bases from the 5’ end and the last 15 bases from the 3’ end. Reads were mapped to the Capsella rubella v1.0 reference genome in paired-end mode (–score_min L, 0, 0.6) using Bismark v0.16.3. Mapped reads were deduplicated and cytosine methylation values calculated using the Bismark Methylation Extractor.
RNA-seq: Reads were quality trimmed using Trimmomatic (--three_prime_clip_R1 15 --three_prime_clip_R2 15 --clip_R1 10 --clip_R2 10) and mapped to the C. rubella v1.0 genome in pair-end mode using HISAT2. Transcript counts and RPKM values were calculated using featureCounts.
Assembly: Capsella rubella v1.0  (also listed as 183) http://www.phytozome.org/dataUsagePolicy.php?org=Org_Crubella
Assembly: Capsella grandiflora (GEnBank JAVXYZ000000000)
Supplementary files format and content: small-RNA: Unique small RNAs (between 18-25 nts) and their accumulation number (raw reads) are represented in a two column format file: <unique_smallRNA> <number_of_raw_reads>.<length_nts>
Supplementary files format and content: Bisulfite-seq: Three genome-wide cytosine methylation reports (for CG, CHG, CHH) per sample were created. These reports have the  following format: <chromosome> <position> <strand> <count methylated> <count unmethylated> <C-context> <trinucleotide context>
Supplementary files format and content: RNA-seq: expression levels (RPKM) are shown for genes in the chromosome-like first eight scaffolds of the Capsella rubella genome for each condition and replicate.

organism: Capsella bursa-pastoris

source_name: Cbp 6DAP Seed wt

growth_protocol: Seeds were surface sterilized with 30% bleach and 70% ethanol, rinsed with distilled water and sown on agar plates containing ½ Murashige and Skoog (MS) medium and 1% sucrose. They were then stratified for 2 days in the darkness at 4 °C and moved into a growth chamber with long-day photoperiod (16 h and 22 °C light, 8 h and 19 °C darkness) with a light intensity of 110 µE. 7 days olds seedlings were transferred to pots filled with sterile soli and plants were grown in a growth chamber with 60% humidity and daily cycles of 16 h light at 21 °C and 8 h darkness at 18 °C with light intensity of 150 µE.

extract_protocol:
Seeds of manually pollinated crossing were taken out of siliques 6 DAP and put into 20 µl of RNA later solution (Sigma-Aldrich). Each sample consisted of 10-15 siliques. RNA was extracted with RNeasy Plant Mini Kit (Qiagen) according to manufacturer’s instruction.
500 ng of RNA was used for RNA Seq library preparation with NEBNext Poly(A)mRNA Magnetic Isolation Module (NEB E7490) and NEBNext Ultra RNA LibraryPrep Kit for Illumina (E7530). For each analyzed genotype there were three biological replicates. Libraries were sequenced on HiSeqX in a 150 bp paired-end mode.

treatment_protocol: Material was generated by manually crossing of indicated genotypes

value: seed


title: Direct reprogramming,rep2

city: Jerusalem

first: Batia

last: Azria

address: Jerusalem

institute: Hebrew university of Jerusalem

data_processing:
Low quality bases and sequencing adaptors of raw fastq files RNA-seq containing single-end 61bp-long reads were trimmed using Trim Galore (V 0.6.0, https://github.com/FelixKrueger/TrimGalore) and then mapped to the mm10 reference genome using HISAT2 (V 2.1.0) with default parameters. Read counting was performed using featureCounts (V 1.6.2) with mm10 gtf annotation. Differential gene expression analysis was performed using DESeq2 R package (V 1.26.0).
Assembly: mm10
Supplementary files format and content: Row Counts, Csv

source_name: Transdifferentiontion cell

extract_protocol:
Total RNA was isolated using the Qiagen RNeasy kit
mRNA libraries were prepared using the SENSE mRNA-seq library prep kit V2 (Lexogen), and pooled libraries were sequenced on an Illumina NextSeq 500 platform to generate 75-bp single-end reads.

value: Transdifferentiontion cell


title: OB_pat_LuC_54

description: Sample collection timepoint: pretreatment; Tissue type: Primary solid tumor; Current site: Lung; Sex: female; Age of onset: 74

source_name: lung cancer (mixed type: adenocarcinoma + squamous cell carcinoma)


title: cbp-seed.experiment_1.RNAseq.replicate3

description:
Capsella bursa-pastoris seed 6DAP
final_RNAseq.experiment_1.RPKM.txt.gz
cbp_x_cbp.rep3


title: Sublibrary3_S3_L004

address: 3224 Biological Sciences III

data_processing:
snRNA-Seq:  Gene expression quantification was performed using splitpipe (version X) from Parse Biosciences. Ambient RNA signal was quantified and corrected using Cellbender1 remove-background (v 0.2.0). Heterotypic barcode collisions were inferred using Scrublet2 (v 0.2.3). The individual snRNA-seq experiments were merged into a single anndata (v 0.8.0) object, resulting in 611,999 barcodes and 29,889 genes before quality control (QC) filtering. Various QC filters were applied, including UMIs detected, Scrublet doublet score, and percentage of mitochondrial reads. Dataset-wide cutoffs were used to remove barcodes with specific criteria. Additionally, a more stringent filter was applied to one of the snRNA-seq experiments. After QC, a total of 431,534 barcodes were retained for downstream analysis  Visium data: Sequencing reads from the human and mouse Visium experiments were processed using the 10X Genomics Spaceranger (v 1.2.1) pipeline, with GRch38 and MM10 as the respective reference transcriptomes. Spaceranger count was used to align sequencing reads to the reference, quantify gene expression, and perform a preliminary clustering analysis for each sample. Unlike the snRNA-seq dataset, we did not filter out additional spots based on sequencing QC metrics. The UMI counts matrices and fluorescent images for the human and mouse samples were combined into merged Seurat3–5 objects for the respective species.
Assembly: GRCH38, MM10
Supplementary files format and content: snRNA-Seq and Visium data were saved as R data files (.rda), with corresponding metadata as comma-separated values (.csv) files.

extract_protocol:
For snRNA-seq, single nucleus suspensions were isolated from about 50mg frozen human cortex following Parse biosciences recommendation. For spatial transcriptomics, fresh frozen mouse and human brain samples were embedded in OCT medium and cryosectioned at 10um thickness and mounted on visium slides.
snRNA-seq libraries were prepared using Parse biosciences Evercode WT kit (v1). For spatial transcriptomics, 10x genomics visium kit was used following manufacturer’s protocol.


title: cbp-seed.experiment_1.RNAseq.replicate1

description:
Capsella bursa-pastoris seed 6DAP
final_RNAseq.experiment_1.RPKM.txt.gz
cbp_x_cbp.rep1


title: cr4x_x_cg-endosperm.BSseq.replicate2

description: Capsella rubella 4x crossed with Capsella grandiflora 6DAP endosperm

organism: Capsella rubella x Capsella grandiflora

source_name: Cr4x x Cg  6DAP Endosperm wt

extract_protocol:
Seeds of manually pollinated crossing were taken out of siliques 6 DAP and the endosperm were manually dissected and absorbed by the small part of tissue paper. Samples were stored at -20 °C and then used for isolation of genomic DNA with DNeasy Plant Mini Kit (Qiagen).
Bisulfite libraries were prepared with the Accel-NGS Methyl-Seq DNA Library Kit from Illumina (Cat No. 30096, Swift), and the sequencing was performed at Novogene (Hongkong, China) on a NovaSeq 6000 platform in 150-bp paired-end mode

value: endosperm


title: OB_pat_LuC_51

description: Sample collection timepoint: pretreatment; Tissue type: Primary solid tumor; Current site: Lung; Sex: female; Age of onset: 51


title: Direct reprogramming,rep1


title: OB_pat_LuC_50

description: Sample collection timepoint: pretreatment; Tissue type: Primary solid tumor; Current site: Lung; Sex: male; Age of onset: 60

source_name: lung cancer  (squamous cell carcinoma)

value: lung cancer  (squamous cell carcinoma)


title: Muscle,rep2

source_name: Muscle

value: Muscle


title: Sublibrary2_S2_L004

description:
Human_snRNA-Seq_ADDS_integrated.rds
AD-DS_Cases.csv


title: Sublibrary1_S1_L004


title: Muscle,rep1


title: MECP2 mutant cerebral organoid GEX replicate 2

city: Cambridge

first: Danielle

last: Tomasello

state: Massachusetts

address: 455 Main St

institute: Whitehead Institute

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the the 10X Genomics Cell Ranger ARC software v2.0.1. We used “cellranger-arc mkfastq” to make the fastq files, and “cellranger-arc count” to align the reads, assign them to cells, remove duplicates and count.
Assembly: hg38
Supplementary files format and content: filtered_gene_bc_matrices tab separated text files  (barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz),  and atac_fragments tab separated text files generated by Cell Ranger ARC software.

extract_protocol:
At Day 100, organoids were flash frozen and stored in -80 °C. We followed the 10X Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression (1000285) protocol. Nuclei isolation was followed according to protocol (CG000375 Rev B).  Organoids were homogenized with pestle (VWR 47747-358) with 50 strokes and incubated on ice for 5 min. After checking that cells were completely lysed, nuclei were counted with EVE automated cell counter (NanoEnTek). Nuclei were not sorted to maintain integrity. Equal number of nuclei were loaded (4500) according to protocol CG000338 Rev A.
According to 10X Genomics protocol PN-1000190
multiomics snRNA-seq plus snATAC-seq, SingleCell-10X-3P-Multiom, SingleCell-10X-ATAC-Multi

value: hESC

value: MECP2 Mutant


title: OB_pat_LuC_45

description: Sample collection timepoint: pretreatment; Tissue type: Metastatic; Current site: lymph node; Sex: female; Age of onset: 61


title: OB_pat_LuC_53

description: Sample collection timepoint: pretreatment; Tissue type: Primary solid tumor; Current site: Lung; Sex: male; Age of onset: 41


title: cr4x_x_cg-endosperm.BSseq.replicate1


title: MECP2 mutant cerebral organoid GEX replicate 1


title: MEF,rep1

source_name: MEF

value: MEF


title: OB_pat_LuC_43

description: Sample collection timepoint: pretreatment; Tissue type: Metastatic; Current site: lymph node; Sex: male; Age of onset: 64

source_name: lung cancer (squamous cell carcinoma)

value: lung cancer (squamous cell carcinoma)


title: MEF,rep2


title: cr4x_x_cg-endosperm.sRNA.WT.replicate2

description: Capsella rubella 4x x Capsella grandiflora endosperm 6DAP

source_name: Cr4x x Cg 6DAP Endosperm wt

extract_protocol:
For each cross around 600 seeds at 6 DAP were opoened and the endopserm was manually dissected. sRNAs were extracted using the mirVana miRNA isolation kit (Ambion/Life Technologies) following the enrichment procedure for small RNAs resulting in a small RNA fraction ≤200nt.
Libraries were prepared with NEBNext® Multiplex Small RNA Library Prep Set for Illumina® using 50 -100 ng of input for each sample. Size selection was performed with 6% polyacrylamide gel; bands corresponding to about 150 bp were cut and purified from the gel for further analysis. Sequencing was performed at Novogene (Hongkong, China) on a NovaSeq 6000 platform in 150-bp paired-end mode.


title: OB_pat_LuC_27

description: Sample collection timepoint: pretreatment; Tissue type: Primary solid tumor; Current site: Lung; Sex: male; Age of onset: 66


title: Control cerebral organoid GEX replicate 2

value: Control


title: cr4x_x_cg-endosperm.sRNA.WT.replicate1


title: MECP2 mutant cerebral organoid ATAC replicate 2


title: OB_pat_LuC_52

description: Sample collection timepoint: pretreatment; Tissue type: Primary solid tumor; Current site: Lung; Sex: male; Age of onset: 58


title: cr_x_cg.experiment_1.RNAseq.replicate2

description:
Capsella rubella wt4x crossed with Capsella grandiflora seeds 6DAP
final_RNAseq.experiment_1.RPKM.txt.gz
cr_x_cg.rep2

source_name: Cr x Cg 6DAP Seed wt


title: The Chromatin Immunoprecipitation of RNA polymerase II - Rep1

city: Freiburg

first: Senthilkumar

last: Ramamoorthy

address: Stübeweg 51

department: Cellular & Molecular Immunology

institute: Max Planck Institute of Immunobiology and Epigenetics

description:
The Chromatin Immunoprecipitation of RNA polymerase II - Replicate 1
POL2_WT.ucsc.bedGraph.gz

data_processing:
The base calling was performed by using BCL2Fastq pipeline (version: 0.3.1) and bcl2fastq (version 2.20.0.422).
RNA-seq:The 151bp paired-end reads were mapped to the mouse reference genome (mm10) using the STAR aligner (2.5.3a). Total read counts for the Gencode (vM23) reference genes were calculated using featureCounts (v2.0.0). The log-transformed total count per million (CPM) was calculated for each gene and genes with values below 0 were excluded. Differential gene expression was calculated by a linear modelling approach with the use of functions available in the R package limma. For differential expression analysis, the functions lmfit, eBayes and contrast.fit available in limma were applied to the voom-transformed expression values.  A set of significant differentially expressed genes was selected with an adjusted p-value cut-off of 0.05 after the Benjamini-Hochberg correction for multiple testing was applied.
ChIP-seq:The sequencing reads of two replicates each from MSL2, YY1 and RNA polymerase II ChIP was trimmed using trim_galore and mapped to mouse reference genome (mm10) using bowtie2 (2.2.3) with the default settings. The read duplicates and reads mapping to blacklisted regions were removed using programs available in picard, samtools  and bedtools. The properly mapped reads from both the replicates of MSL2 or YY1 ChIP and their corresponding input controls were used for identifying peaks by MACS2 (v2.1.0) with a q-value cut-off 0.05.
Assembly: mouse (mm10)
Supplementary files format and content: ChIP-seq: The CPM nomalized bigWig files (bw) generated using deep tools and bedGraph files generated by makeUCSCfile tool.
Supplementary files format and content: RNA-seq: The raw read count extracted by featureCounts.

source_name: preB cells

growth_protocol: Cells from bone marrow of SLP65KO were subcloned to a single cell and cultured as a single clone. The cells were electroporated with Msl2KO gRNA under the condition 0.27kV 0.925 CAP to generate Msl2KO cell line.  SLP65KO cell lines were grown in IMDM medium with 10%FCS, 5.46 ng/µl IL7 and 2mM L‐Glutamine with penicillin and streptomycin at 37°C 5%CO2 in an incubator.

extract_protocol:
ChIP: The cells were crosslinked with EGS and formaldehyde, lysed and DNA was fragmented into pieces of average 300-500bp by sonication. Chromatin was precipitated with a specific antibody and protein A-coupled sepharose beads. After elution from the beads, chromatin was decrosslinked and purified via QIAquick PCR Purification Kit according to the manufacturer's manual.  RNA: RNA were extracted by Nucleospin®RNAII isolation kit (Macherey‐Nagel).
ChIP:Library preparation for ChIP analysis was performed with the NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (Catalog #E7370) according to the manufacturer’s protocol. No size selection was used and amplification was performed using 10 PCR cycles. RNA-seq: rRNA depleted total RNA was prepared using Ribozero magnetic beads for library preparation.

treatment_protocol: No treatment

tag: antibody

value: RNA polymerase II

value: preB cells


title: cr_x_cg.experiment_1.RNAseq.replicate3

description:
Capsella rubella wt4x crossed with Capsella grandiflora seeds 6DAP
final_RNAseq.experiment_1.RPKM.txt.gz
cr_x_cg.rep3


title: OB_pat_LuC_17

description: Sample collection timepoint: pretreatment; Tissue type: Metastatic; Current site: skin; Sex: female; Age of onset: 52

value: lung cancer (adenocarcinoma)


title: cr_x_cg-endosperm.sRNA.WT.replicate2

description: Capsella rubella crossed with Capsella grandifllora 6DAP endosperm

source_name: Cr x Cg 6DAP Endosperm wt

extract_protocol:
For each cross around 600 seeds at 6 DAP were opened and the endopserm was manually dissected. sRNAs were extracted using the mirVana miRNA isolation kit (Ambion/Life Technologies) following the enrichment procedure for small RNAs resulting in a small RNA fraction ≤200nt.
Libraries were prepared with NEBNext® Multiplex Small RNA Library Prep Set for Illumina® using 50 -100 ng of input for each sample. Size selection was performed with 6% polyacrylamide gel; bands corresponding to about 150 bp were cut and purified from the gel for further analysis. Sequencing was performed at Novogene (Hongkong, China) on a NovaSeq 6000 platform in 150-bp paired-end mode.


title: OB_pat_LuC_3


title: The Chromatin Immunoprecipitation of YY1 - Input


title: The Chromatin Immunoprecipitation of YY1 - Rep2

description:
The Chromatin Immunoprecipitation of YY1 - Replicate 2
YY1_WT.ucsc.bedGraph.gz


title: The Chromatin Immunoprecipitation of YY1 - Rep1

description:
The Chromatin Immunoprecipitation of YY1 - Replicate 1
YY1_WT.ucsc.bedGraph.gz


title: OB_pat_LuC_16

description: Sample collection timepoint: pretreatment; Tissue type: Primary solid tumor; Current site: Lung; Sex: male; Age of onset: 75


title: OB_pat_LuC_1

description: Sample collection timepoint: pretreatment; Tissue type: Primary solid tumor; Current site: Lung; Sex: male; Age of onset: 69


title: Control cerebral organoid ATAC replicate 2


title: Control cerebral organoid ATAC replicate 1


title: MECP2 mutant cerebral organoid ATAC replicate 1


title: cr_x_cg.experiment_1.RNAseq.replicate1

description:
Capsella rubella wt4x crossed with Capsella grandiflora seeds 6DAP
final_RNAseq.experiment_1.RPKM.txt.gz
cr_x_cg.rep1


title: OB_pat_LuC_2

description: Sample collection timepoint: pretreatment; Tissue type: Primary solid tumor; Current site: Lung; Sex: female; Age of onset: 77


title: Control cerebral organoid GEX replicate 1


title: Cerebellar Barhl1 Knock Down(KD)_1 stage 41 sample 4

status: Public on Sep 11 2024

city: Paris

first: Mohamed

last: Doulazmi

state: Paris

address: 9 quai St Bernard

department: Neurocsiences

country: France

institute: Sorbonne Unversity

data_processing:
feature Counts V2.0.1
Assembly: X. laevis v10.1
Supplementary files format and content: tab-delimated text file includes raw counts for each sample

organism: Xenopus laevis

source_name: Hindbrain Rh_1 dissected

growth_protocol: Xenopus tadpole grown in 0.3X MMR

extract_protocol:
Trizol (ambion) RNA extraction
Stranded mRNA prep Ligation-Illumina

treatment_protocol: Dissected rhombomere 1 stage 41

value: Hindbrain Rh_1 dissected

value: stage 41

value: cerebellar primordium

value: Inj MOBarHl1_1


title: Cerebellar Barhl1 Knock Down(KD)_1 stage 41 sample 1


title: Cerebellar Control stage 41 sample 3

value: Injected Morpholino (MO) Control (Ct)


title: Cerebellar Barhl1 Knock Down(KD)_2 stage 41 sample 2

value: Inj MOBarHl1_2


title: Cerebellar Barhl1 Knock Down(KD)_1 stage 41 sample 3


title: Cerebellar Barhl1 Knock Down(KD)_2 stage 41 sample 4


title: The Chromatin Immunoprecipitation of RNA polymerase II - Rep2

description:
The Chromatin Immunoprecipitation of RNA polymerase II - Replicate 2
POL2_WT.ucsc.bedGraph.gz


title: Cerebellar Barhl1 Knock Down(KD)_2 stage 41 sample 1


title: Cerebellar Control stage 41 sample 4


title: cr_x_cg-endosperm.sRNA.WT.replicate1

value: endosperm


title: Cerebellar Barhl1 Knock Down(KD)_2 stage 41 sample 3


title: NSUN2-2

city: Guangzhou

first: Xiaoyun

state: Guangdong

address: 190 Kaiyuan Avenue, Huangpu

department: Infection and Immunity

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

description: The cells were collected after transfecting the plasmids for 48h

data_processing:
Raw reads were subjected to base calling using Guppy basecaller (version 6.3.8+d9e0f64) from fast5 raw files. The base calling process included setting a minimum quality score threshold of 7, utilizing the rna_r9.4.1_70bps_hac.cfg configuration file, and employing the --fast5_out parameter.
The "pass" reads were further aligned to a reference genome sequence (mm39) using Minimap2 (version 2.17-r941) with the following parameters: "-ax splice -uf -k14."
Samtools was utilized for bam file conversion and sorting.
Fast5 files were aligned to their corresponding fastq files using "Nanopolish index". The "Nanopolish eventalign" command was then applied to partition the signal values from fast5 files onto individual 5-mer sequences.
Using the m6Anet, m5Cnet and Nanopsu to detect and quantify the modified sites. Using NanoCount to quantify transcripts.
Assembly: mm39, hg38
Supplementary files format and content: tsv

extract_protocol:
Total RNA was extracted using Trizol reagent (#AG21102, Accurate Bioeng. Co., Ltd., Hunan, China) and the mRNA was purified using the Dynabeads® mRNA Purification Kit Dynabeads Oligo(dT)25 (#61002, Invitrogen). mRNA was treated by DNaseⅠ buffer (AM8170G, Thermo Fisher Scientific) and Turbo DNase (Thermo Fisher Scientific, AM2238) at 37 ℃ for 10 min and purified by ethanol precipitation to remove genomic DNA.
Nanopore direct RNA sequencing libraries were prepared using about 1000ng mRNA following the SQK-RNA002 kit protocol (version: DRS_9080_v2_revK_14Aug2019). DRS library was added to the flow cell for sequencing on the Mk1C and GridION platform.

value: Overexpression NSUN2 plasmids


title: Myc_day10_1_RPFs

description: Ribosome protected fragments

value: Liver

value: Male

value: 10 days post-induction

value: mice were injected with 2 X 10^11 GC/mouse of AAV8.TBG.PI.Cre.rBG


title: Cerebellar Barhl1 Knock Down(KD)_1 stage 41 sample 2


title: pcDNA3-2

value: Empty pcDNA3 plasmids


title: REM_day7_2

city: New Orleans

first: Jovanny

last: Zabaleta

state: LA

address: 1700 Tulane Ave

department: Interdisciplinary Oncology

institute: LSUHSC

data_processing:
BaseCall performed with CASAVA v1.8.2
Reads were aligned to the mm10 version of the mouse genome as reference using STAR v2.7.8a after removal of contaminants  (rDNA, tRNA, mtrDNA) using Bowtie2 (version 2.2.5)
Reads aligned to STAR were quantified to the mm10-RefSeq Transcripts 96 and normalized by TMM (+0.0001 / TMM / log2 transformation)
Normalized counts were used to determine differential gene expression between tumor and non-tumor (control) with limma-trend
All analyses were done at p < 0.05 and fold change 2
Assembly: mm10
Supplementary files format and content: RawCounts
Supplementary files format and content: TMM_Normalized_counts

source_name: lung

growth_protocol: The virus was propagated from Stanley Perlman’s MA30 stock virus in TMPRSS2 expressing Vero cells. The TMPRSS2 Vero cells were grown in Dulbecco’s modified Eagle’s medium DMEM, supplemented with 10% FBS

extract_protocol:
Total RNA was extracted from FFPE tissue samples using the AllPrep DNA/RNA FFPE kit (Qiagen) following the manufacturer's protocol
Paired-end libraries (2 x 76) were prepared (600ng per sample) using the TruSeq RNA exome library preparation kit

treatment_protocol: Mice were intraperitoneally injected with 10 mg/kg compound prior to infection and the treatment was continued daily for the duration of the experiment.

value: REM

tag: time point

value: lung


title: REM_day7_1


title: REM_day7_4


title: REM_day4_3


title: REM_day4_4


title: REM_day7_3


title: REM_day4_2


title: REM_day4_1


title: Vehicle_day7_3

value: vehicle


title: Cerebellar Control stage 41 sample 2

tag: cell line


title: Cerebellar Control stage 41 sample 1

source_name: Hindbrain Rhombomere(Rh)_1 dissected

value: Hindbrain Rhombomere(Rh)_1 dissected


title: Vehicle_day7_2


title: Vehicle_day4_3


title: Vehicle_day4_2


title: Vehicle_day4_1


title: Vehicle_day7_1